From 99a692c26b5f2de2ca31cb014f1219305a177e95 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Fri, 5 Jul 2024 01:34:26 -0400 Subject: [PATCH 001/107] user newer version of geoh5py --- .github/workflows/pytest-unix-os.yml | 2 +- .github/workflows/pytest-windows.yml | 2 +- poetry.lock | 374 ++++++++++++++------------- pyproject.toml | 12 +- 4 files changed, 203 insertions(+), 187 deletions(-) diff --git a/.github/workflows/pytest-unix-os.yml b/.github/workflows/pytest-unix-os.yml index bc621948..c3bee95e 100644 --- a/.github/workflows/pytest-unix-os.yml +++ b/.github/workflows/pytest-unix-os.yml @@ -24,7 +24,7 @@ jobs: strategy: fail-fast: false matrix: - python_ver: ['3.9', '3.10'] + python_ver: ['3.9', '3.10', '3.11', '3.12'] os: [ubuntu-latest] runs-on: ${{ matrix.os }} defaults: diff --git a/.github/workflows/pytest-windows.yml b/.github/workflows/pytest-windows.yml index cc6c1a6f..a416656e 100644 --- a/.github/workflows/pytest-windows.yml +++ b/.github/workflows/pytest-windows.yml @@ 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+version = "2.0.5" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "sphinxcontrib-htmlhelp-2.0.1.tar.gz", hash = "sha256:0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff"}, - {file = "sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl", hash = "sha256:c38cb46dccf316c79de6e5515e1770414b797162b23cd3d06e67020e1d2a6903"}, + {file = "sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl", hash = "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"}, + {file = "sphinxcontrib_htmlhelp-2.0.5.tar.gz", hash = "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015"}, ] [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] +standalone = ["Sphinx (>=5)"] test = ["html5lib", "pytest"] [[package]] @@ -893,32 +907,34 @@ test = ["flake8", "mypy", "pytest"] [[package]] name = "sphinxcontrib-qthelp" -version = "1.0.3" -description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." +version = "1.0.7" +description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" files = [ - {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"}, - {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"}, + {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"}, + {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"}, ] [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] +standalone = ["Sphinx (>=5)"] test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.5" -description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." +version = "1.1.10" +description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" files = [ - {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"}, - {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"}, + {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"}, + {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"}, ] [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] +standalone = ["Sphinx (>=5)"] test = ["pytest"] [[package]] @@ -934,35 +950,35 @@ files = [ [[package]] name = "tomlkit" -version = "0.12.4" +version = "0.12.5" description = "Style preserving TOML library" optional = false python-versions = ">=3.7" files = [ - {file = "tomlkit-0.12.4-py3-none-any.whl", hash = "sha256:5cd82d48a3dd89dee1f9d64420aa20ae65cfbd00668d6f094d7578a78efbb77b"}, - {file = "tomlkit-0.12.4.tar.gz", hash = "sha256:7ca1cfc12232806517a8515047ba66a19369e71edf2439d0f5824f91032b6cc3"}, + {file = "tomlkit-0.12.5-py3-none-any.whl", hash = "sha256:af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f"}, + {file = "tomlkit-0.12.5.tar.gz", hash = "sha256:eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c"}, ] [[package]] name = "typing-extensions" -version = "4.11.0" +version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, - {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] [[package]] name = "urllib3" -version = "2.2.1" +version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"}, - {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"}, + {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, + {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, ] [package.extras] @@ -986,20 +1002,20 @@ numpy = ">=1.7" [[package]] name = "zipp" -version = "3.18.1" +version = "3.19.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, + {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, + {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = "^3.9,<3.11" -content-hash = "952d75dfc5109f72ce2339b75e42bbfb3dfe5f874b9a2ea294f674bb59f7bfad" +python-versions = "^3.9" +content-hash = "dd7cf6d48c026e9be0554e815c8add94689c594b5e11d9d4ce2e4f7336da0cdd" diff --git a/pyproject.toml b/pyproject.toml index 1bb1f884..7adccd18 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,9 +45,9 @@ geoh5_to_omf = 'omf.scripts.geoh5_to_omf:main' omf_to_geoh5 = 'omf.scripts.omf_to_geoh5:main' [tool.poetry.dependencies] -python = "^3.9,<3.11" +python = "^3.9" -numpy = "~1.23.5" # also in geoh5py +numpy = "~1.26.0" # also in geoh5py properties = "~0.6.0" pypng = "^0.20220715" six = "^1.16" @@ -55,10 +55,10 @@ vectormath = "~0.2.0" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = "~0.9.0", allow-prereleases = true} -#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", branch = "release/0.9.0"} -#geoh5py = {url = "https://github.com/MiraGeoscience/geoh5py/archive/refs/heads/release/0.9.0.zip#sha256="} -#geoh5py = {url = "http://localhost:8888/geoh5py.tar.gz#sha256="} +geoh5py = {version = ">=0.9.1, <0.11", allow-prereleases = true} +#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} +#geoh5py = {url = "http://localhost:8888/geoh5py.tar.gz"} +#geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] Pygments = "*" From 5b69d67bf0bcea6c144be6df49ad748e348f7800 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Fri, 5 Jul 2024 01:48:46 -0400 Subject: [PATCH 002/107] GEOPY-1630: static analysis on Python 3.9 --- .github/workflows/static-analysis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml index f0760207..a3958af7 100644 --- a/.github/workflows/static-analysis.yml +++ b/.github/workflows/static-analysis.yml @@ -36,7 +36,7 @@ jobs: - name: Set up Python version uses: actions/setup-python@v4 with: - python-version: '3.10' + python-version: '3.9' - name: Get full Python version id: full-python-version shell: bash From 4e1defc0ad29aed27a592c462b8e080c6a3fcb20 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 18 Jul 2024 16:00:30 -0400 Subject: [PATCH 003/107] [GEOPY-1233] Use reusable github workflows --- .github/workflows/issue_to_jira.yml | 34 ++-------- .github/workflows/pr_add_jira_summary.yml | 60 +----------------- .github/workflows/pytest-unix-os.yml | 64 ------------------- .github/workflows/pytest-windows.yml | 70 --------------------- .github/workflows/python_analysis.yml | 45 ++++++++++++++ .github/workflows/static-analysis.yml | 75 ----------------------- 6 files changed, 53 insertions(+), 295 deletions(-) delete mode 100644 .github/workflows/pytest-unix-os.yml delete mode 100644 .github/workflows/pytest-windows.yml create mode 100644 .github/workflows/python_analysis.yml delete mode 100644 .github/workflows/static-analysis.yml diff --git a/.github/workflows/issue_to_jira.yml b/.github/workflows/issue_to_jira.yml index e3a5c066..2818e29e 100644 --- a/.github/workflows/issue_to_jira.yml +++ b/.github/workflows/issue_to_jira.yml @@ -1,5 +1,3 @@ -# This workflow will create a JIRA issue upon creation of a GitHub issue - name: Create JIRA issue on: @@ -7,30 +5,8 @@ on: types: [opened] jobs: - new_jira_issue: - runs-on: ubuntu-latest - - steps: - - name: JIRA Login - uses: atlassian/gajira-login@v3.0.1 - env: - JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }} - JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }} - JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }} - - name: Jira Create issue - id: create_jira_issue - uses: atlassian/gajira-create@v3.0.1 - with: - project: GEOPY - issuetype: Story - summary: ${{ github.event.issue.title }} - description: "_from [GitHub issue #${{ github.event.issue.number }}|${{ github.event.issue.html_url }}]_" - # Additional fields in JSON format - fields: '{"components": [{"name": "OMF"}]}' - - name: Post JIRA link - uses: peter-evans/create-or-update-comment@v3 - with: - # The number of the issue or pull request in which to create a comment. - issue-number: ${{ github.event.issue.number }} - # The comment body. - body: "JIRA issue [${{ steps.create_jira_issue.outputs.issue }}] was created." + call-workflow-create-jira-issue: + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@main + secrets: inherit + with: + project_key: 'GEOPY' diff --git a/.github/workflows/pr_add_jira_summary.yml b/.github/workflows/pr_add_jira_summary.yml index f0c8a8dd..794bf3f0 100644 --- a/.github/workflows/pr_add_jira_summary.yml +++ b/.github/workflows/pr_add_jira_summary.yml @@ -1,6 +1,3 @@ -# This workflow will comment the PR with the JIRA issue summary -# if a JIRA issue number is detected in the branch name or title - name: Add JIRA issue summary on: @@ -8,57 +5,6 @@ on: types: [opened] jobs: - add_jira_summary: - runs-on: ubuntu-latest - - steps: - - name: Find JIRA issue key - id: find_jira_key - env: - HEAD_REF: ${{ github.head_ref}} - PR_TITLE: ${{ github.event.pull_request.title }} - run: > - echo $HEAD_REF $PR_TITLE - | echo "issue_key=$( - grep -osi "\b\(GA\|GEOPY\|DEVOPS\)[ #-]*[0-9]\+" - | head -n1 - | sed -E "s/([A-Z]+)[-# ]*([0-9]+)/\1-\2/i" - | tr [:lower:] [:upper:] - )" - >> $GITHUB_OUTPUT - - name: Get JIRA summary - id: get_jira_summary - if: ${{ steps.find_jira_key.outputs.issue_key }} - env: - JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }} - JIRA_BASIC_AUTH: ${{ secrets.JIRA_BASIC_AUTH }} - run: > - curl -sS -X GET - -H "Authorization: Basic $JIRA_BASIC_AUTH" - -H "Content-Type: application/json" - "$JIRA_BASE_URL/rest/api/2/issue/${{ steps.find_jira_key.outputs.issue_key }}" - | echo "summary=$(jq -r '.fields.summary // empty')" >> $GITHUB_OUTPUT - - name: Extract PR title - id: get_pr_title - env: - PR_TITLE: ${{ github.event.pull_request.title }} - run: | - echo "text=$(echo $PR_TITLE | sed -E "s/^\s*[?[A-Z]+[-# ]*[0-9]+]?[-: ]*(.*)/\1/i")" >> $GITHUB_OUTPUT - - name: Add comment - if: ${{ steps.find_jira_key.outputs.issue_key }} - env: - ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }} - TITLE_TEXT: ${{ steps.get_pr_title.outputs.text }} - PR_BODY: ${{ github.event.pull_request.body }} - run: > - jq - --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}" - --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)" - --arg TITLE_TEXT "$(cat <<< ${TITLE_TEXT:-$ISSUE_SUMMARY})" - --arg PR_BODY "$(cat <<< $PR_BODY)" - -c '{"title": ($ISSUE_ID + ": " + $TITLE_TEXT), "body": ("**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY)}' <<< {} - | curl -sS -X POST -d @- - -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" - -H "Content-Type: application/json" - "$GITHUB_API_URL/repos/$GITHUB_REPOSITORY/pulls/${{ github.event.pull_request.number }}" - > /dev/null + call-workflow-add-jira-issue-summary: + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-pr_add_jira_summary.yml@main + secrets: inherit diff --git a/.github/workflows/pytest-unix-os.yml b/.github/workflows/pytest-unix-os.yml deleted file mode 100644 index c3bee95e..00000000 --- a/.github/workflows/pytest-unix-os.yml +++ /dev/null @@ -1,64 +0,0 @@ -name: pytest on Unix OS - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -jobs: - pytest: - name: pytest (Unix) - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - strategy: - fail-fast: false - matrix: - python_ver: ['3.9', '3.10', '3.11', '3.12'] - os: [ubuntu-latest] - runs-on: ${{ matrix.os }} - defaults: - run: - shell: bash - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python_ver }} - - name: Get full Python version - id: full-python-version - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: pytest - run: poetry run pytest --cov --cov-report=xml diff --git a/.github/workflows/pytest-windows.yml b/.github/workflows/pytest-windows.yml deleted file mode 100644 index a416656e..00000000 --- a/.github/workflows/pytest-windows.yml +++ /dev/null @@ -1,70 +0,0 @@ -name: pytest on Windows - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -jobs: - pytest: - name: pytest (Windows) - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - strategy: - fail-fast: false - matrix: - python_ver: ['3.9', '3.10', '3.11', '3.12'] - defaults: - run: - shell: bash - runs-on: windows-latest - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python_ver }} - - name: Get full Python version - id: full-python-version - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: pytest - run: poetry run pytest --cov --cov-report=xml - - name: Codecov - if: ${{ success() && matrix.python_ver == '3.10' }} - uses: codecov/codecov-action@v4 - with: - name: GitHub - fail_ci_if_error: true - token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml new file mode 100644 index 00000000..6ea1fc07 --- /dev/null +++ b/.github/workflows/python_analysis.yml @@ -0,0 +1,45 @@ +name: Python analysis + +on: + pull_request: + types: [opened, synchronize, reopened, ready_for_review] + branches: + - develop + - main + - release/** + - feature/** + - hotfix/** + push: + branches: + - develop + - main + - release/** + - feature/** + - hotfix/** + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + +jobs: + call-workflow-static-analysis: + name: Static analysis + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main + with: + app_name: 'omf' + python_vers: '3.9' + call-workflow-pytest-on-windows: + name: Pytest on Windows + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_windows.yml@main + with: + python_ver: '["3.9", "3.10", "3.11", "3.12"]' + cache_number: 1 + codecov_reference_python_ver: '3.10' + secrets: inherit + call-workflow-pytest-on-unix-os: + name: Pytest on Unix OS + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@main + with: + python_ver: '["3.9", "3.10", "3.11", "3.12"]' + os: '["ubuntu-latest"]' + cache_number: 1 diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml deleted file mode 100644 index a3958af7..00000000 --- a/.github/workflows/static-analysis.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: static analysis - -on: - pull_request: - types: [opened, synchronize, reopened, ready_for_review] - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - push: - branches: - - develop - - main - - release/** - - feature/** - - hotfix/** - -env: - source_dir: omf - -jobs: - pylint: - name: pylint - if: github.event_name != 'pull_request' || github.event.pull_request.draft == false - runs-on: ubuntu-latest - defaults: - run: - shell: bash - env: - POETRY_VIRTUALENVS_CREATE: true - POETRY_VIRTUALENVS_IN_PROJECT: true - steps: - - uses: actions/checkout@v3 - - name: Set up Python version - uses: actions/setup-python@v4 - with: - python-version: '3.9' - - name: Get full Python version - id: full-python-version - shell: bash - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python - --version 1.3.2 - echo "$HOME/.poetry/bin" >> $GITHUB_PATH - - name: Set up cache - uses: actions/cache@v3 - id: cache - env: - # Increase this value to reset cache if poetry.lock has not changed - CACHE_NUMBER: 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}-{{ env.CACHE_NUMBER }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - shell: bash - run: timeout 10s poetry run pip --version || rm -rf .venv - - name: Install dependencies - run: poetry install -vvv - - name: capture modified files - if: github.event_name == 'pull_request' - run: >- - git fetch --deepen=500 origin ${{github.base_ref}} - && echo "FILES_PARAM=$( - git diff --diff-filter=AM --name-only refs/remotes/origin/${{github.base_ref}}... -- | grep -E "^(${source_dir}|tests)/.*\.py$" | xargs - )" >> $GITHUB_ENV - - name: Run pylint on modified files - if: github.event_name == 'pull_request' && env.FILES_PARAM - run: poetry run pylint $FILES_PARAM - - name: Run pylint on all files - if: github.event_name == 'push' - run: poetry run pylint $source_dir/fileio/geoh5* tests From 85a94d8cd4e62da4809924074324c5def43a91aa Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 18 Jul 2024 16:04:07 -0400 Subject: [PATCH 004/107] [GEOPY-1233] Use mirageoscience.pre-commit-hooks package + Update mirrors-mypy + codespell + rstcheck --- .pre-commit-config.yaml | 28 ++++++++-------------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ab017d9a..59a7365e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -41,7 +41,7 @@ repos: - id: pyupgrade args: [--py39-plus] - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.0 + rev: v1.10.1 hooks: - id: mypy files: ^(omf/fileio/geoh5|tests/) @@ -58,6 +58,11 @@ repos: - id: relint args: [-W] # to fail on warnings files: ^omf/fileio/geoh5/ +- repo: http://github.com/MiraGeoscience/pre-commit-hooks + rev: v1.0.0 + hooks: + - id: prepare-commit-msg + - id: check-commit-msg - repo: local hooks: - id: pylint @@ -67,25 +72,8 @@ repos: require_serial: true # pylint does its own parallelism types: [python] files: ^(omf/fileio/geoh5|tests/) -# - id: check-copyright # TODO: add missing copyright statements in source files -# name: Check copyright -# entry: python devtools/check-copyright.py -# language: python -# types: [text] -# exclude: (^\.|^docs/) -# files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ - - id: prepare-commit-msg - stages: [prepare-commit-msg] - name: Prepare commit message - entry: python devtools/git_message_hook.py --prepare - language: python - - id: check-commit-msg - stages: [commit-msg] - name: Check commit message - entry: python devtools/git_message_hook.py --check - language: python - repo: https://github.com/codespell-project/codespell - rev: v2.2.6 + rev: v2.3.0 hooks: - id: codespell exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$ @@ -119,7 +107,7 @@ repos: exclude_types: [jupyter] exclude: ^docs/(.*/)?images/ - repo: https://github.com/rstcheck/rstcheck - rev: v6.2.0 + rev: v6.2.4 hooks: - id: rstcheck exclude: ^THIRD_PARTY_SOFTWARE.rst$ From 5ced5d68429639c9cabcdf8d1de81d332d6e5745 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 24 Jul 2024 12:28:47 -0400 Subject: [PATCH 005/107] [DEVOPS-452] Add ruff hooks and update .pre-commit-config.yaml --- .pre-commit-config.yaml | 28 +++++++++------------------- 1 file changed, 9 insertions(+), 19 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 59a7365e..49a7aade 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -21,27 +21,17 @@ repos: hooks: - id: pycln args: [--config=pyproject.toml] -- repo: https://github.com/PyCQA/isort - rev: 5.13.2 +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.5.1 hooks: - - id: isort - additional_dependencies: [tomli] # to read config from pyproject.toml -- repo: https://github.com/psf/black - rev: 24.4.2 - hooks: - - id: black -- repo: https://github.com/PyCQA/flake8 - rev: 7.0.0 - hooks: - - id: flake8 - files: ^(omf/fileio/geoh5|tests/) -- repo: https://github.com/asottile/pyupgrade - rev: v3.15.2 - hooks: - - id: pyupgrade - args: [--py39-plus] + - id: ruff + args: + - --fix + - --exit-non-zero-on-fix +# - --unsafe-fixes + - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.10.1 + rev: v1.11.0 hooks: - id: mypy files: ^(omf/fileio/geoh5|tests/) From 7509761d14ec67562d0fad28dabfb8472c8b8d02 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 24 Jul 2024 12:29:05 -0400 Subject: [PATCH 006/107] [DEVOPS-452] Ruff fixes --- omf/base.py | 7 ++----- omf/data.py | 8 ++------ omf/fileio/geoh5.py | 15 +++++++++++---- omf/serializers.py | 1 - 4 files changed, 15 insertions(+), 16 deletions(-) diff --git a/omf/base.py b/omf/base.py index c0c3ee48..983da60c 100644 --- a/omf/base.py +++ b/omf/base.py @@ -68,9 +68,7 @@ def serialize( return str(self.uid) @classmethod - def deserialize( - cls, uid, trusted=True, registry=None, **kwargs - ): # pylint: disable=arguments-differ + def deserialize(cls, uid, trusted=True, registry=None, **kwargs): # pylint: disable=arguments-differ """Deserialize nested UidModels from flat pointer dictionary""" if registry is None: raise ValueError("no registry provided") @@ -161,8 +159,7 @@ def _validate_data(self): assert self.geometry is not None, "ProjectElement must have a mesh" for i, dat in enumerate(self.data): if ( - dat.location - not in self.geometry._valid_locations # pylint: disable=protected-access + dat.location not in self.geometry._valid_locations # pylint: disable=protected-access ): raise ValueError( f"Invalid location {dat.location} - valid values: " diff --git a/omf/data.py b/omf/data.py index eba5ffdd..1fc453da 100644 --- a/omf/data.py +++ b/omf/data.py @@ -249,9 +249,7 @@ def indices(self, value): def value_dict(self, i): """Return a dictionary of legend entries based on index""" entry = { - legend.name: legend.values[ - self.indices[i] - ] # pylint: disable=unsubscriptable-object + legend.name: legend.values[self.indices[i]] # pylint: disable=unsubscriptable-object for legend in self.legends } # pylint: disable=not-an-iterable return entry @@ -270,9 +268,7 @@ def _validate_indices(self): if np.min(self.indices.array) < -1: # pylint: disable=no-member raise ValueError(f"Indices of DataMap {self.name} must be >= -1") for legend in self.legends: # pylint: disable=not-an-iterable - if np.max(self.indices.array) >= len( - legend.values - ): # pylint: disable=no-member + if np.max(self.indices.array) >= len(legend.values): # pylint: disable=no-member raise ValueError( "Indices of DataMap {dm} exceed number of available " "entries in Legend {leg}".format(dm=self.name, leg=legend.name) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 5ab5dad0..39077061 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -425,7 +425,10 @@ def from_geoh5(self, entity: ObjectBase, **kwargs) -> UidModel: # type: ignore element._backend.update({"uid": uid}) # pylint: disable=W0212 element.data = self.process_dependents( - entity, element, workspace, self.compression # type: ignore + entity, + element, + workspace, + self.compression, # type: ignore ) return element @@ -480,7 +483,10 @@ def from_geoh5(self, entity: RootGroup, **kwargs) -> Project: # type: ignore project = self.omf_type(**kwargs) getattr(project, "_backend").update({"uid": uid}) # pylint: disable=W0212 project.elements = self.process_dependents( - entity, project, workspace, self.compression # type: ignore + entity, + project, + workspace, + self.compression, # type: ignore ) return project @@ -976,8 +982,9 @@ def collect_h5_attributes( with fetch_h5_handle(workspace): geometry = {} for key, alias in cls._attribute_map.items(): - cell_size, count = getattr(entity, f"{alias}_cell_size"), getattr( - entity, f"{alias}_count" + cell_size, count = ( + getattr(entity, f"{alias}_cell_size"), + getattr(entity, f"{alias}_count"), ) tensor = np.ones(count) * np.abs(cell_size) geometry.update({f"tensor_{key}": tensor}) diff --git a/omf/serializers.py b/omf/serializers.py index a7fab580..99c9998d 100644 --- a/omf/serializers.py +++ b/omf/serializers.py @@ -4,7 +4,6 @@ from io import BytesIO import numpy as np -from six import PY2 def array_serializer(arr, open_file, **kwargs): # pylint: disable=unused-argument From 995fb462e7f1ccd79e54bd4871c123dc52402850 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 30 Jul 2024 10:17:45 -0400 Subject: [PATCH 007/107] [DEVOPS-452] Update with new github workflows + pre-commit-hooks --- .github/workflows/python_analysis.yml | 3 +++ .pre-commit-config.yaml | 6 ++--- pyproject.toml | 37 ++++++++++++++++++++++++--- 3 files changed, 39 insertions(+), 7 deletions(-) diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index 6ea1fc07..395da608 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -26,12 +26,14 @@ jobs: name: Static analysis uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main with: + package_manager: 'poetry' app_name: 'omf' python_vers: '3.9' call-workflow-pytest-on-windows: name: Pytest on Windows uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_windows.yml@main with: + package_manager: 'poetry' python_ver: '["3.9", "3.10", "3.11", "3.12"]' cache_number: 1 codecov_reference_python_ver: '3.10' @@ -40,6 +42,7 @@ jobs: name: Pytest on Unix OS uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@main with: + package_manager: 'poetry' python_ver: '["3.9", "3.10", "3.11", "3.12"]' os: '["ubuntu-latest"]' cache_number: 1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 49a7aade..8d7f012e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,7 +22,7 @@ repos: - id: pycln args: [--config=pyproject.toml] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.1 + rev: v0.5.5 hooks: - id: ruff args: @@ -48,8 +48,8 @@ repos: - id: relint args: [-W] # to fail on warnings files: ^omf/fileio/geoh5/ -- repo: http://github.com/MiraGeoscience/pre-commit-hooks - rev: v1.0.0 +- repo: https://github.com/MiraGeoscience/pre-commit-hooks + rev: v1.0.1 hooks: - id: prepare-commit-msg - id: check-commit-msg diff --git a/pyproject.toml b/pyproject.toml index 7adccd18..5fa5ae9d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,11 +68,40 @@ pytest-cov = "*" sphinx = "^5.3" tomli = "*" # for tests only -[tool.isort] -profile = "black" +[tool.ruff] +target-version = "py310" + +[tool.ruff.lint] +ignore = [ + "B028", # no-explicit-stacklevel for warnings.warn() + "E501", # line-too-long - code is reformatted (do not care about comments and docstring) + "F401", # unsused-import - covered by pycln +] +select = [ + "A", # flake8-builtins + "B", # flake8-bugbear + "B006", # Do not use mutable data structures for argument defaults + "B9", # flake8-bugbear opiniated warnings + "BLE", # flake8-blind-except + "C4", # flake8-comprehensions + "C9", # mccabe + "E", # pycodestyle errors + "F", # pyflakes + "I", # isort + "RUF", # ruff rules + "TID", # flake8-tidy-imports + "UP", # pyupgrade + "W", # pycodestyle warnings +] + +[tool.ruff.lint.mccabe] +max-complexity = 18 + +[tool.ruff.lint.isort] +lines-after-imports = 2 -[tool.black] -# defaults are just fine +[tool.ruff.format] +# default formatting is just fine [tool.mypy] warn_unused_configs = true From a36d8653d038f21efe7b79c6fc2b1c736530d422 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 14:19:31 +0000 Subject: [PATCH 008/107] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- devtools/check-copyright.py | 1 + omf/__init__.py | 1 + omf/data.py | 4 ++-- omf/fileio/fileio.py | 1 + omf/fileio/geoh5.py | 3 ++- omf/fileio/utils.py | 2 +- omf/scripts/geoh5_to_omf.py | 1 + omf/scripts/omf_to_geoh5.py | 1 + omf/surface.py | 4 ++-- tests/script_geoh5_to_omf_test.py | 1 + 10 files changed, 13 insertions(+), 6 deletions(-) diff --git a/devtools/check-copyright.py b/devtools/check-copyright.py index d53a61ed..b1029aad 100644 --- a/devtools/check-copyright.py +++ b/devtools/check-copyright.py @@ -15,6 +15,7 @@ import sys from datetime import date + if __name__ == "__main__": current_year = date.today().year copyright_re = re.compile( diff --git a/omf/__init__.py b/omf/__init__.py index 96c6ed10..88ea8ebf 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -29,6 +29,7 @@ from .texture import ImageTexture from .volume import VolumeElement, VolumeGridGeometry + __version__ = "3.2.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" diff --git a/omf/data.py b/omf/data.py index 1fc453da..5d41a45f 100644 --- a/omf/data.py +++ b/omf/data.py @@ -270,7 +270,7 @@ def _validate_indices(self): for legend in self.legends: # pylint: disable=not-an-iterable if np.max(self.indices.array) >= len(legend.values): # pylint: disable=no-member raise ValueError( - "Indices of DataMap {dm} exceed number of available " - "entries in Legend {leg}".format(dm=self.name, leg=legend.name) + f"Indices of DataMap {self.name} exceed number of available " + f"entries in Legend {legend.name}" ) return True diff --git a/omf/fileio/fileio.py b/omf/fileio/fileio.py index d07293a9..0ad7dd13 100644 --- a/omf/fileio/fileio.py +++ b/omf/fileio/fileio.py @@ -9,6 +9,7 @@ from omf.base import UidModel from omf.fileio.geoh5 import GeoH5Writer + __version__ = b"OMF-v0.9.0" diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 39077061..7430e8d7 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -34,6 +34,7 @@ from omf.surface import SurfaceElement, SurfaceGeometry, SurfaceGridGeometry from omf.volume import VolumeElement, VolumeGridGeometry + _logger = logging.getLogger(__package__) @@ -481,7 +482,7 @@ def from_geoh5(self, entity: RootGroup, **kwargs) -> Project: # type: ignore kwargs = self.collect_attributes(entity, workspace, **kwargs) uid = kwargs.pop("uid") project = self.omf_type(**kwargs) - getattr(project, "_backend").update({"uid": uid}) # pylint: disable=W0212 + project._backend.update({"uid": uid}) # pylint: disable=W0212 project.elements = self.process_dependents( entity, project, diff --git a/omf/fileio/utils.py b/omf/fileio/utils.py index 743c31c8..54f76d1e 100644 --- a/omf/fileio/utils.py +++ b/omf/fileio/utils.py @@ -7,7 +7,7 @@ def compare_elements(elem_a, elem_b): assert elem_a.name == elem_b.name if hasattr(elem_a, "geometry"): - for attr in getattr(elem_a.geometry, "_valid_locations"): + for attr in elem_a.geometry._valid_locations: if getattr(elem_a.geometry, attr, None) is not None: testing.assert_allclose( getattr(elem_a.geometry, attr).array, diff --git a/omf/scripts/geoh5_to_omf.py b/omf/scripts/geoh5_to_omf.py index b2b6a9df..c58bcb67 100644 --- a/omf/scripts/geoh5_to_omf.py +++ b/omf/scripts/geoh5_to_omf.py @@ -6,6 +6,7 @@ from omf.fileio import OMFWriter from omf.fileio.geoh5 import GeoH5Reader + _logger = logging.getLogger(__package__ + "." + Path(__file__).stem) diff --git a/omf/scripts/omf_to_geoh5.py b/omf/scripts/omf_to_geoh5.py index 1ffffad4..f710ed5b 100644 --- a/omf/scripts/omf_to_geoh5.py +++ b/omf/scripts/omf_to_geoh5.py @@ -6,6 +6,7 @@ from omf.fileio import OMFReader from omf.fileio.geoh5 import GeoH5Writer + _logger = logging.getLogger(__package__ + "." + Path(__file__).stem) diff --git a/omf/surface.py b/omf/surface.py index fa8b0a3c..7f3e0aac 100644 --- a/omf/surface.py +++ b/omf/surface.py @@ -87,8 +87,8 @@ def _validate_mesh(self): return True if len(self.offset_w) != self.num_nodes: raise ValueError( - "Length of offset_w, {zlen}, must equal number of nodes, " - "{nnode}".format(zlen=len(self.offset_w), nnode=self.num_nodes) + f"Length of offset_w, {len(self.offset_w)}, must equal number of nodes, " + f"{self.num_nodes}" ) return True diff --git a/tests/script_geoh5_to_omf_test.py b/tests/script_geoh5_to_omf_test.py index df98f2ea..e21705fb 100644 --- a/tests/script_geoh5_to_omf_test.py +++ b/tests/script_geoh5_to_omf_test.py @@ -7,6 +7,7 @@ import omf from omf.scripts import geoh5_to_omf + # pylint: disable=duplicate-code From ffeefed5cee47767f82745fbc729d97068af4e21 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 30 Jul 2024 10:58:33 -0400 Subject: [PATCH 009/107] [DEVOPS-452] Delete useless scripts --- devtools/check-copyright.py | 53 --------- devtools/git_message_hook.py | 224 ----------------------------------- 2 files changed, 277 deletions(-) delete mode 100644 devtools/check-copyright.py delete mode 100644 devtools/git_message_hook.py diff --git a/devtools/check-copyright.py b/devtools/check-copyright.py deleted file mode 100644 index d53a61ed..00000000 --- a/devtools/check-copyright.py +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env python3 - -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2024 Mira Geoscience Ltd. ' -# ' -# This file is part of mira-omf package. ' -# ' -# mira-omf is distributed under the terms and conditions of the MIT License ' -# (see LICENSE file at the root of this source code package). ' -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' - -from __future__ import annotations - -import re -import sys -from datetime import date - -if __name__ == "__main__": - current_year = date.today().year - copyright_re = re.compile( - rf"\bcopyright \(c\) (:?\d{{4}}-|)\b{current_year}\b", re.IGNORECASE - ) - files = sys.argv[1:] - max_lines = 10 - report_files = [] - for f in files: - with open(f, encoding="utf-8") as file: - count = 0 - has_dated_copyright = False - for line in file: - count += 1 - if count >= max_lines and not ( - f.endswith("README.rst") or f.endswith("README-dev.rst") - ): - break - if re.search(copyright_re, line): - has_dated_copyright = True - break - - if not has_dated_copyright: - report_files.append(f) - - if len(report_files) > 0: - for f in report_files: - sys.stderr.write(f"{f}: No copyright or invalid year\n") - sys.exit(1) - -# readonly CURRENT_YEAR=$(date +"%Y") - -# if ! grep -e "Copyright (c) .*$CURRENT_YEAR" $(head -10 $f) 2>&1 1>/dev/null; then -# echo "File '$f' has no copyright or an invalid year" -# exit 1 -# fi diff --git a/devtools/git_message_hook.py b/devtools/git_message_hook.py deleted file mode 100644 index 1633ee58..00000000 --- a/devtools/git_message_hook.py +++ /dev/null @@ -1,224 +0,0 @@ -#!/usr/bin/env python3 - -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2024 Mira Geoscience Ltd. ' -# ' -# This file is part of mira-omf package. ' -# ' -# mira-omf is distributed under the terms and conditions of the MIT License ' -# (see LICENSE file at the root of this source code package). ' -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' - -"""Some Git pre-commit hooks implementations.""" - -from __future__ import annotations - -import argparse -import re -import shlex -import subprocess -import sys - - -def get_jira_id(text) -> str: - """Detect a JIRA issue ID at the begging of the given text. - - :return: the JIRA issue ID if found, else empty string - """ - - class JiraPattern: - """Internal class that encapsulates the regular expression for the JIRA pattern, - making sure it gets compiled only once.""" - - __pattern = re.compile( - r"(?:GEOPY|DEVOPS|QA|GI|GA|GMS|VPem1D|VPem3D|VPmg|UBCGIF|LICMGR)-\d+" - ) - - @staticmethod - def get(): - """:return: the compiled regular expression for the JIRA pattern""" - return JiraPattern.__pattern - - # use re.match() rather than re.search() to enforce the JIRA reference to be at the beginning - match = re.match(JiraPattern.get(), text.strip()) - return match.group(0) if match else "" - - -def get_branch_name() -> str | None: - """:return: the name of the current branch""" - - git_proc = subprocess.run( - shlex.split("git branch --list"), stdout=subprocess.PIPE, text=True, check=False - ) - - # cannot use HEAD during rebase - # git_proc = subprocess.run( - # shlex.split('git symbolic-ref --short HEAD'), stdout=subprocess.PIPE, universal_newlines=True - # ) - # Note: version above suggested by Atlassian. Could also use: git rev-parse --abbrev-ref HEAD - - if git_proc.returncode != 0: - return None - - current_branch = None - # current branch is prefixed by '*' - for line in git_proc.stdout.splitlines(): - stripped = line.strip() - if stripped and stripped[0] == "*": - current_branch = stripped[1:] - break - assert current_branch is not None - - class RebasingPattern: - """Internal class that encapsulates the regular expression for the rebasing - message pattern, making sure it gets compiled only once.""" - - __pattern = re.compile(r"\(.*\s(\S+)\s*\)") - - @staticmethod - def get(): - """:return: the compiled regular expression for the Rebasing pattern""" - return RebasingPattern.__pattern - - match = re.match(RebasingPattern.get(), current_branch.strip()) - if match: - return match.group(1) - - return current_branch - - -def check_commit_message(filepath: str) -> tuple[bool, str]: - """Check if the branch name or the commit message starts with a reference to JIRA, - and if the message meets the minimum required length for the summary line. - - The JIRA reference has to be at the beginning of the branch name, or of the commit - message. - :return: a tuple telling whether the commit message is valid or not, and an error - message (empty in case the message is valid). - """ - - branch_jira_id = "" - branch_name = get_branch_name() - if branch_name: - branch_jira_id = get_jira_id(branch_name) - - message_jira_id = "" - first_line = None - with open(filepath) as message_file: - for line in message_file: - if not line.startswith("#") and len(line.strip()) > 0: - # test only the first non-comment line that is not empty - # (should we reject messages with empty first line?) - first_line = line - message_jira_id = get_jira_id(first_line) - break - assert first_line is not None - - if not branch_jira_id and not ( - message_jira_id or first_line.strip().lower().startswith("merge") - ): - return ( - False, - "Either the branch name or the commit message must start with a JIRA ID.", - ) - - if branch_jira_id and message_jira_id and branch_jira_id != message_jira_id: - return ( - False, - "Different JIRA ID in commit message %s and in branch name %s." - % (message_jira_id, branch_jira_id), - ) - - stripped_message_line = "" - if first_line: - stripped_message_line = first_line.strip() - if message_jira_id: - stripped_message_line = stripped_message_line[ - len(message_jira_id) + 1 : - ].strip() - - min_required_length = 10 - if len(stripped_message_line) < min_required_length: - return ( - False, - "First line of commit message must be at least %s characters long, " - "beyond the JIRA ID." % min_required_length, - ) - - return True, "" - - -def check_commit_msg(filepath: str) -> None: - """To be used a the Git commit-msg hook. - - Exit with non-0 status if the commit message is deemed invalid. - """ - - (is_valid, error_message) = check_commit_message(filepath) - if not is_valid: - print( - """commit-msg hook: **ERROR** %s - Message has been saved to %s.""" - % (error_message, filepath) - ) - sys.exit(1) - - -def prepare_commit_msg(filepath: str, source: str | None = None) -> None: - """To be used a the Git prepare-commit-msg hook. - - Will add the JIRA ID found in the branch name in case it is missing from the commit - message. - """ - - branch_jira_id = "" - branch_name = get_branch_name() - if branch_name: - branch_jira_id = get_jira_id(branch_name) - - if not branch_jira_id: - return - - if source not in [None, "message", "template"]: - return - - with open(filepath, "r+", encoding="utf-8") as message_file: - message_has_jira_id = False - message_lines = message_file.readlines() - for line_index, line_content in enumerate(message_lines): - if not line_content.startswith("#"): - # test only the first non-comment line - message_jira_id = get_jira_id(line_content) - if not message_jira_id: - message_lines[line_index] = branch_jira_id + ": " + line_content - message_has_jira_id = True - break - - if not message_has_jira_id: - # message is empty or all lines are comments: insert JIRA ID at the very beginning - message_lines.insert(0, branch_jira_id + ": ") - - message_file.seek(0, 0) - message_file.write("".join(message_lines)) - - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument("msg_file", help="the message file") - group = parser.add_mutually_exclusive_group(required=True) - group.add_argument( - "-p", "--prepare", action="store_true", help="prepare the commit message" - ) - group.add_argument( - "-c", - "--check", - action="store_true", - help="check if the commit message is valid", - ) - parser.add_argument("args", nargs=argparse.REMAINDER) - - args = parser.parse_args() - if args.prepare: - prepare_commit_msg(args.msg_file, *args.args) - elif args.check: - check_commit_msg(args.msg_file) From 846510e357e326ff1f3498bd257b13c54f1835b0 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 31 Jul 2024 15:45:21 -0400 Subject: [PATCH 010/107] [DEVOPS-452] Update python_analysis with the new CI-tool relase + Disable some Ruff rules --- .github/workflows/python_analysis.yml | 3 ++- pyproject.toml | 4 ++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index 395da608..ee7f8ccb 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -37,7 +37,8 @@ jobs: python_ver: '["3.9", "3.10", "3.11", "3.12"]' cache_number: 1 codecov_reference_python_ver: '3.10' - secrets: inherit + secrets: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} call-workflow-pytest-on-unix-os: name: Pytest on Unix OS uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@main diff --git a/pyproject.toml b/pyproject.toml index 5fa5ae9d..5e74456d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -76,6 +76,10 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln + "RUF005", # TO DO + "RUF012", # TO DO + "UP038", # TO DO + "C408", # TO DO ] select = [ "A", # flake8-builtins From 788fbfd15145aaf1ffccd746635c16021bdc3dd8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Wed, 31 Jul 2024 17:57:05 -0400 Subject: [PATCH 011/107] TODO to add check-copyright --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8d7f012e..a2e5599f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -52,7 +52,7 @@ repos: rev: v1.0.1 hooks: - id: prepare-commit-msg - - id: check-commit-msg +# - id: check-copyright # TODO: add missing copyright statements in source files - repo: local hooks: - id: pylint From 564b60eb5bfada51f840402b44efeab7f9ac1005 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 10:53:59 -0400 Subject: [PATCH 012/107] [DEVOPS-452] Restrict ruff check to devtools|omf/fileio/geoh5|tests --- .pre-commit-config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8d7f012e..7862e5fc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,7 +29,9 @@ repos: - --fix - --exit-non-zero-on-fix # - --unsafe-fixes + files: ^(omf/fileio/geoh5|tests/) - id: ruff-format + files: ^(omf/fileio/geoh5|tests/) - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.11.0 hooks: @@ -51,6 +53,8 @@ repos: - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.1 hooks: + - id: check-copyright + files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ - id: prepare-commit-msg - id: check-commit-msg - repo: local From faac269e85fd79615ba393f6370eefa9ecda3902 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 10:56:47 -0400 Subject: [PATCH 013/107] [DEVOPS-452] Fix .pre-commit-config syntax --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 53958a1d..7fb74f0f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -53,8 +53,8 @@ repos: - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.1 hooks: - - id: check-copyright - files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ + - id: check-copyright + files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ - id: prepare-commit-msg # - id: check-copyright # TODO: add missing copyright statements in source files - repo: local From 25baea9819a8b8f66e7c364a40c506d4bd1b5e01 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 10:59:58 -0400 Subject: [PATCH 014/107] [DEVOPS-452] Restrict which files are gonna be check by MiraGeoscience/pre-commit-hook --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7fb74f0f..602ca6ed 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -54,7 +54,7 @@ repos: rev: v1.0.1 hooks: - id: check-copyright - files: ^(LICENSE|README(-dev)?.rst|((devtools|omf/fileio/geoh5|tests)/.*\.pyi?))$ + files: ^((devtools|omf/fileio/geoh5|tests)/.*\.pyi?)$ - id: prepare-commit-msg # - id: check-copyright # TODO: add missing copyright statements in source files - repo: local From 75c6bc19bcb4a79e3f208690fe7ae8bf5fe65df8 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 11:13:14 -0400 Subject: [PATCH 015/107] [DEVOPS-452] Enable some ruff rules --- .pre-commit-config.yaml | 1 - pyproject.toml | 4 ---- 2 files changed, 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 602ca6ed..9824ec8c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -56,7 +56,6 @@ repos: - id: check-copyright files: ^((devtools|omf/fileio/geoh5|tests)/.*\.pyi?)$ - id: prepare-commit-msg -# - id: check-copyright # TODO: add missing copyright statements in source files - repo: local hooks: - id: pylint diff --git a/pyproject.toml b/pyproject.toml index 5e74456d..5fa5ae9d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -76,10 +76,6 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln - "RUF005", # TO DO - "RUF012", # TO DO - "UP038", # TO DO - "C408", # TO DO ] select = [ "A", # flake8-builtins From d71f15cc5752ccd8b2bb200caa8eb68dd0342885 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 11:15:12 -0400 Subject: [PATCH 016/107] [DEVOPS-452] Disable RUF012 and UP038 rules --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 5fa5ae9d..40fdc401 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -92,6 +92,8 @@ select = [ "TID", # flake8-tidy-imports "UP", # pyupgrade "W", # pycodestyle warnings + "RUF012", # TODO + "UP038", # TODO ] [tool.ruff.lint.mccabe] From 59e79a762c27e3eaa8374439f2d9a1d033589fd5 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 1 Aug 2024 11:22:08 -0400 Subject: [PATCH 017/107] [DEVOPS-452] Disable RUF012 and UP038 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 40fdc401..501e312c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -76,6 +76,8 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln + "RUF012", # TODO + "UP038", # TODO ] select = [ "A", # flake8-builtins @@ -92,8 +94,6 @@ select = [ "TID", # flake8-tidy-imports "UP", # pyupgrade "W", # pycodestyle warnings - "RUF012", # TODO - "UP038", # TODO ] [tool.ruff.lint.mccabe] From edfee231749faf67bc99dfa20923e7ebee448c42 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Fri, 2 Aug 2024 17:54:42 -0400 Subject: [PATCH 018/107] pyproject: remove commented out git URL not using URLs anymore to refer to packages --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7adccd18..ea390f99 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,6 @@ vectormath = "~0.2.0" #------------------------------------ geoh5py = {version = ">=0.9.1, <0.11", allow-prereleases = true} #geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} -#geoh5py = {url = "http://localhost:8888/geoh5py.tar.gz"} #geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] From e970864544875c55dc2a6f0ab595b6c4238ffd66 Mon Sep 17 00:00:00 2001 From: SophieCurinier <90750457+SophieCurinier@users.noreply.github.com> Date: Mon, 5 Aug 2024 07:55:43 -0400 Subject: [PATCH 019/107] [DEVOPS-452] Change python target version used by ruff MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Sébastien Hensgen --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 501e312c..0ddb4997 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -69,7 +69,7 @@ sphinx = "^5.3" tomli = "*" # for tests only [tool.ruff] -target-version = "py310" +target-version = "py39" [tool.ruff.lint] ignore = [ From aeebf850d9603a63d33b45191b7e1b3c6de8276f Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 5 Aug 2024 10:25:45 -0400 Subject: [PATCH 020/107] [DEVOPS-452] Update mypy ignore path --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 501e312c..123e4e6c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -117,6 +117,9 @@ plugins = [ # "numpy.typing.mypy_plugin" ] +[tool.pylint.MASTER] +ignore-paths = '^(?!.*(omf/fileio/|omf/scripts/|tests/)).*$' + [tool.pytest.ini_options] [tool.coverage.run] From 09210800756b288e9f22878655dd2a8cbb40b972 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 10:31:01 -0400 Subject: [PATCH 021/107] [DEVOPS-452] also run pre-commit on omf/scripts --- .pre-commit-config.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9824ec8c..4f276ce4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,14 +29,14 @@ repos: - --fix - --exit-non-zero-on-fix # - --unsafe-fixes - files: ^(omf/fileio/geoh5|tests/) + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - id: ruff-format - files: ^(omf/fileio/geoh5|tests/) + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.11.0 hooks: - id: mypy - files: ^(omf/fileio/geoh5|tests/) + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ additional_dependencies: [ # numpy==1.26.*, # TODO: fix mypy errors related to numpy tomli, # to read config from pyproject.toml @@ -49,12 +49,12 @@ repos: hooks: - id: relint args: [-W] # to fail on warnings - files: ^omf/fileio/geoh5/ + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.1 hooks: - id: check-copyright - files: ^((devtools|omf/fileio/geoh5|tests)/.*\.pyi?)$ + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - id: prepare-commit-msg - repo: local hooks: @@ -64,7 +64,7 @@ repos: language: system require_serial: true # pylint does its own parallelism types: [python] - files: ^(omf/fileio/geoh5|tests/) + files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - repo: https://github.com/codespell-project/codespell rev: v2.3.0 hooks: From 3dfe15c3cdc7f49e02a42b9f1a8bd5cb876373ce Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 10:34:27 -0400 Subject: [PATCH 022/107] [DEVOPS-452] do not check for copyrights just differ to upstream repo license and copyrights --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4f276ce4..5a46656b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -53,8 +53,8 @@ repos: - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.1 hooks: - - id: check-copyright - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ +# - id: check-copyright # no copyright nor license notice: differ to upstream repo +# files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - id: prepare-commit-msg - repo: local hooks: From 85a3df286aa57efce4c6066f80848ca172cc4af5 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 10:35:00 -0400 Subject: [PATCH 023/107] [DEVOPS-452] re-enable check-added-large-files --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5a46656b..64937cf9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -80,7 +80,7 @@ repos: exclude_types: [jupyter] - id: check-toml - id: check-yaml -# - id: check-added-large-files # crashing on some configuration. To be investigated + - id: check-added-large-files - id: check-case-conflict - id: check-merge-conflict - id: debug-statements From 467cf8a43811eeb54ad8b2bbb0f6080232af0ad5 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 5 Aug 2024 11:16:26 -0400 Subject: [PATCH 024/107] [DEVOPS-452] Update ignore-paths in pylintrc --- pylintrc | 2 +- pyproject.toml | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/pylintrc b/pylintrc index 7ec2fca1..f1742cac 100644 --- a/pylintrc +++ b/pylintrc @@ -46,7 +46,7 @@ ignore=CVS # Add files or directories matching the regex patterns to the ignore-list. The # regex matches against paths and can be in Posix or Windows format. -ignore-paths= +ignore-paths=^omf/(?!(scripts|fileio)).* # Files or directories matching the regex patterns are skipped. The regex # matches against base names, not paths. The default value ignores Emacs file diff --git a/pyproject.toml b/pyproject.toml index 064a605f..0ddb4997 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -117,9 +117,6 @@ plugins = [ # "numpy.typing.mypy_plugin" ] -[tool.pylint.MASTER] -ignore-paths = '^(?!.*(omf/fileio/|omf/scripts/|tests/)).*$' - [tool.pytest.ini_options] [tool.coverage.run] From da5623538bec415c89f892a1aed167b14a8b8eba Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 11:26:10 -0400 Subject: [PATCH 025/107] pylint ignore: skip source files from upstream repo --- .pre-commit-config.yaml | 2 +- pylintrc | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 64937cf9..f916ccdf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -64,7 +64,7 @@ repos: language: system require_serial: true # pylint does its own parallelism types: [python] - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ + exclude: ^docs/ - repo: https://github.com/codespell-project/codespell rev: v2.3.0 hooks: diff --git a/pylintrc b/pylintrc index f1742cac..0b78e3e0 100644 --- a/pylintrc +++ b/pylintrc @@ -46,7 +46,9 @@ ignore=CVS # Add files or directories matching the regex patterns to the ignore-list. The # regex matches against paths and can be in Posix or Windows format. -ignore-paths=^omf/(?!(scripts|fileio)).* +ignore-paths=^omf/fileio/fileio\.py$, # skip source files from upstream repo + ^omf/fileio/utils\.py$, + ^omf/[^/]+$ # Files or directories matching the regex patterns are skipped. The regex # matches against base names, not paths. The default value ignores Emacs file From 7a21edf5ef71a4745120c426e288a1b406ff802c Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 5 Aug 2024 11:31:57 -0400 Subject: [PATCH 026/107] [DEVOPS-452] Correct pylint ignore-paths --- pylintrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pylintrc b/pylintrc index f1742cac..633d3135 100644 --- a/pylintrc +++ b/pylintrc @@ -46,7 +46,7 @@ ignore=CVS # Add files or directories matching the regex patterns to the ignore-list. The # regex matches against paths and can be in Posix or Windows format. -ignore-paths=^omf/(?!(scripts|fileio)).* +ignore-paths=^omf/(?!(scripts|fileio/geoh5)).* # Files or directories matching the regex patterns are skipped. The regex # matches against base names, not paths. The default value ignores Emacs file From 60cdb4e6cb4acea3882fa5a794f7102d7b9f1509 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 11:52:12 -0400 Subject: [PATCH 027/107] explicit list of files exclusion for pylint so that newly added files will be parsed --- pylintrc | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pylintrc b/pylintrc index 0b78e3e0..2470ecc6 100644 --- a/pylintrc +++ b/pylintrc @@ -46,9 +46,8 @@ ignore=CVS # Add files or directories matching the regex patterns to the ignore-list. The # regex matches against paths and can be in Posix or Windows format. -ignore-paths=^omf/fileio/fileio\.py$, # skip source files from upstream repo - ^omf/fileio/utils\.py$, - ^omf/[^/]+$ +ignore-paths=^omf/fileio/(fileio|utils)[.]py$, # skip source files from upstream repo + ^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$ # Files or directories matching the regex patterns are skipped. The regex # matches against base names, not paths. The default value ignores Emacs file From 4e80149fab26fc6008b6b5bc4d638ba385d4216a Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 12:15:05 -0400 Subject: [PATCH 028/107] move ruff exclusion from pre-commit to config --- .pre-commit-config.yaml | 2 -- pyproject.toml | 13 +++++++++++++ 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f916ccdf..113ca722 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,9 +29,7 @@ repos: - --fix - --exit-non-zero-on-fix # - --unsafe-fixes - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - id: ruff-format - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.11.0 hooks: diff --git a/pyproject.toml b/pyproject.toml index d9a819a6..f88ad1af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,6 +71,12 @@ tomli = "*" # for tests only target-version = "py39" [tool.ruff.lint] +exclude = [ + "^docs/", + # skip source files from upstream repo + "^omf/fileio/(fileio|utils)[.]py$", + "^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$", +] ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) @@ -102,6 +108,13 @@ max-complexity = 18 lines-after-imports = 2 [tool.ruff.format] +exclude = [ + "^docs/", + # skip source files from upstream repo + "^omf/fileio/(fileio|utils)[.]py$", + "^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$", +] + # default formatting is just fine [tool.mypy] From f370027a4b25c861ad424490ffa09ef9b432916d Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 12:15:17 -0400 Subject: [PATCH 029/107] fix precommit file inclusions --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 113ca722..8bba81c3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -34,25 +34,25 @@ repos: rev: v1.11.0 hooks: - id: mypy - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ additional_dependencies: [ # numpy==1.26.*, # TODO: fix mypy errors related to numpy tomli, # to read config from pyproject.toml types-six, types-toml, ] + files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) exclude: ^docs/ - repo: https://github.com/codingjoe/relint rev: 3.1.1 hooks: - id: relint args: [-W] # to fail on warnings - files: ^(omf/fileio/geoh5|omf/scripts|tests)/ + files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.1 hooks: # - id: check-copyright # no copyright nor license notice: differ to upstream repo -# files: ^(omf/fileio/geoh5|omf/scripts|tests)/ +# files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) - id: prepare-commit-msg - repo: local hooks: From cec2114b0ab3783a6849e67c749eef6913c23694 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 12:34:01 -0400 Subject: [PATCH 030/107] use libpath instead of os.path --- tests/conftest.py | 0 tests/doc_example_test.py | 269 +++++++++++++++++++------------------- 2 files changed, 131 insertions(+), 138 deletions(-) create mode 100644 tests/conftest.py diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/doc_example_test.py b/tests/doc_example_test.py index 3b5f31a4..6037c73c 100644 --- a/tests/doc_example_test.py +++ b/tests/doc_example_test.py @@ -1,165 +1,158 @@ # pylint: disable=duplicate-code -import os -import unittest +from pathlib import Path import numpy as np +import pytest import omf -class TestDocEx(unittest.TestCase): - @staticmethod - def make_random_project(): - dirname, _ = os.path.split(os.path.abspath(__file__)) - pngfile = os.path.sep.join( - dirname.split(os.path.sep)[:-1] + ["docs", "images", "PointSetGeometry.png"] - ) - proj = omf.Project( - name="Test project", description="Just some assorted elements" - ) - - pts = omf.PointSetElement( - name="Random Points", - description="Just random points", - geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), - data=[ - omf.ScalarData( - name="rand data", array=np.random.rand(100), location="vertices" - ), - omf.ScalarData( - name="More rand data", - array=np.random.rand(100), - location="vertices", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 1, 0], - ), - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 0, 1], - ), - ], - color="green", - ) - - lin = omf.LineSetElement( - name="Random Line", - geometry=omf.LineSetGeometry( - vertices=np.random.rand(100, 3), - segments=np.floor(np.random.rand(50, 2) * 100).astype(int), +@pytest.fixture +def random_project() -> omf.Project: + tests_dir = Path(__file__).resolve().parent + png_file_path = tests_dir.parent / "docs" / "images" / "PointSetGeometry.png" + proj = omf.Project(name="Test project", description="Just some assorted elements") + + pts = omf.PointSetElement( + name="Random Points", + description="Just random points", + geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), + data=[ + omf.ScalarData( + name="rand data", array=np.random.rand(100), location="vertices" + ), + omf.ScalarData( + name="More rand data", + array=np.random.rand(100), + location="vertices", ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand segment data", - array=np.random.rand(50), - location="segments", - ), - ], - color="#0000FF", - ) - - surf = omf.SurfaceElement( - name="trisurf", - geometry=omf.SurfaceGeometry( - vertices=np.random.rand(100, 3), - triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 1, 0], ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand face data", array=np.random.rand(50), location="faces" - ), - ], - color=[100, 200, 200], - ) - - grid = omf.SurfaceElement( - name="gridsurf", - geometry=omf.SurfaceGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - origin=[50.0, 50.0, 50.0], - axis_u=[1.0, 0, 0], - axis_v=[0, 0, 1.0], - offset_w=np.random.rand(11, 16).flatten(), + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 0, 1], + ), + ], + color="green", + ) + + lin = omf.LineSetElement( + name="Random Line", + geometry=omf.LineSetGeometry( + vertices=np.random.rand(100, 3), + segments=np.floor(np.random.rand(50, 2) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(11, 16).flatten(), - location="vertices", - ), - omf.ScalarData( - name="rand face data", - array=np.random.rand(10, 15).flatten(order="f"), - location="faces", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=pngfile, - origin=[2.0, 2.0, 2.0], - axis_u=[5.0, 0, 0], - axis_v=[0, 2.0, 5.0], - ) - ], - ) - - vol = omf.VolumeElement( - name="vol", - geometry=omf.VolumeGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - tensor_w=np.ones(20).astype(float), - origin=[10.0, 10.0, -10], + omf.ScalarData( + name="rand segment data", + array=np.random.rand(50), + location="segments", ), - data=[ - omf.ScalarData( - name="Random Data", - location="cells", - array=np.random.rand(10, 15, 20).flatten(), - ) - ], - ) + ], + color="#0000FF", + ) - proj.elements = [pts, lin, surf, grid, vol] + surf = omf.SurfaceElement( + name="trisurf", + geometry=omf.SurfaceGeometry( + vertices=np.random.rand(100, 3), + triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", + ), + omf.ScalarData( + name="rand face data", array=np.random.rand(50), location="faces" + ), + ], + color=[100, 200, 200], + ) + + grid = omf.SurfaceElement( + name="gridsurf", + geometry=omf.SurfaceGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + origin=[50.0, 50.0, 50.0], + axis_u=[1.0, 0, 0], + axis_v=[0, 0, 1.0], + offset_w=np.random.rand(11, 16).flatten(), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(11, 16).flatten(), + location="vertices", + ), + omf.ScalarData( + name="rand face data", + array=np.random.rand(10, 15).flatten(order="f"), + location="faces", + ), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[2.0, 2.0, 2.0], + axis_u=[5.0, 0, 0], + axis_v=[0, 2.0, 5.0], + ) + ], + ) + + vol = omf.VolumeElement( + name="vol", + geometry=omf.VolumeGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + tensor_w=np.ones(20).astype(float), + origin=[10.0, 10.0, -10], + ), + data=[ + omf.ScalarData( + name="Random Data", + location="cells", + array=np.random.rand(10, 15, 20).flatten(), + ) + ], + ) - return proj + proj.elements = [pts, lin, surf, grid, vol] + return proj -def test_doc_ex(tmp_path): - proj = TestDocEx.make_random_project() - assert proj.validate() +def test_doc_ex(tmp_path: Path, random_project): + assert random_project.validate() serial_file = str(tmp_path / "out.omf") - omf.OMFWriter(proj, serial_file) + omf.OMFWriter(random_project, serial_file) reader = omf.OMFReader(serial_file) new_proj = reader.get_project() assert new_proj.validate() assert str(new_proj.elements[3].textures[0].uid) == str( - proj.elements[3].textures[0].uid + random_project.elements[3].textures[0].uid ) proj_overview = reader.get_project_overview() From bf3a5c23debf2a6bbac23dae26e2bdb210e6dee6 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 12:34:24 -0400 Subject: [PATCH 031/107] use shared test fixture for random project --- tests/conftest.py | 143 +++++++++++++++++++++++++++++++++ tests/convert_curve_test.py | 4 +- tests/convert_grid2d_test.py | 3 +- tests/convert_pointset_test.py | 4 +- tests/convert_project_test.py | 23 +++--- tests/convert_surface_test.py | 4 +- tests/convert_volume_test.py | 4 +- tests/doc_example_test.py | 139 -------------------------------- 8 files changed, 166 insertions(+), 158 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index e69de29b..088d863b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -0,0 +1,143 @@ +from pathlib import Path + +import numpy as np +import pytest + +import omf + + +# pylint: disable=duplicate-code + + +@pytest.fixture +def random_project() -> omf.Project: + tests_dir = Path(__file__).resolve().parent + png_file_path = tests_dir.parent / "docs" / "images" / "PointSetGeometry.png" + proj = omf.Project(name="Test project", description="Just some assorted elements") + + pts = omf.PointSetElement( + name="Random Points", + description="Just random points", + geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), + data=[ + omf.ScalarData( + name="rand data", array=np.random.rand(100), location="vertices" + ), + omf.ScalarData( + name="More rand data", + array=np.random.rand(100), + location="vertices", + ), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 1, 0], + ), + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[0, 0, 0], + axis_u=[1, 0, 0], + axis_v=[0, 0, 1], + ), + ], + color="green", + ) + + lin = omf.LineSetElement( + name="Random Line", + geometry=omf.LineSetGeometry( + vertices=np.random.rand(100, 3), + segments=np.floor(np.random.rand(50, 2) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", + ), + omf.ScalarData( + name="rand segment data", + array=np.random.rand(50), + location="segments", + ), + ], + color="#0000FF", + ) + + surf = omf.SurfaceElement( + name="trisurf", + geometry=omf.SurfaceGeometry( + vertices=np.random.rand(100, 3), + triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(100), + location="vertices", + ), + omf.ScalarData( + name="rand face data", array=np.random.rand(50), location="faces" + ), + ], + color=[100, 200, 200], + ) + + grid = omf.SurfaceElement( + name="gridsurf", + geometry=omf.SurfaceGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + origin=[50.0, 50.0, 50.0], + axis_u=[1.0, 0, 0], + axis_v=[0, 0, 1.0], + offset_w=np.random.rand(11, 16).flatten(), + ), + data=[ + omf.ScalarData( + name="rand vert data", + array=np.random.rand(11, 16).flatten(), + location="vertices", + ), + omf.ScalarData( + name="rand face data", + array=np.random.rand(10, 15).flatten(order="f"), + location="faces", + ), + ], + textures=[ + omf.ImageTexture( + name="test image", + image=str(png_file_path), + origin=[2.0, 2.0, 2.0], + axis_u=[5.0, 0, 0], + axis_v=[0, 2.0, 5.0], + ) + ], + ) + + vol = omf.VolumeElement( + name="vol", + geometry=omf.VolumeGridGeometry( + tensor_u=np.ones(10).astype(float), + tensor_v=np.ones(15).astype(float), + tensor_w=np.ones(20).astype(float), + origin=[10.0, 10.0, -10], + ), + data=[ + omf.ScalarData( + name="Random Data", + location="cells", + array=np.random.rand(10, 15, 20).flatten(), + ) + ], + ) + + proj.elements = [pts, lin, surf, grid, vol] + + return proj diff --git a/tests/convert_curve_test.py b/tests/convert_curve_test.py index df0f3866..bba8f5a3 100644 --- a/tests/convert_curve_test.py +++ b/tests/convert_curve_test.py @@ -1,12 +1,14 @@ """Tests for PointSet validation""" +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_lineset_to_geoh5(tmp_path): +def test_lineset_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" line = omf.LineSetElement( name="Random Line", diff --git a/tests/convert_grid2d_test.py b/tests/convert_grid2d_test.py index 37418de8..0975ba14 100644 --- a/tests/convert_grid2d_test.py +++ b/tests/convert_grid2d_test.py @@ -1,6 +1,7 @@ """Tests for PointSet validation""" import logging +from pathlib import Path import numpy as np from geoh5py.workspace import Workspace @@ -8,7 +9,7 @@ import omf -def test_grid2d_to_geoh5(tmp_path, caplog): +def test_grid2d_to_geoh5(tmp_path: Path, caplog): """Test pointset geometry validation""" dip = np.random.uniform(low=0.0, high=90, size=1) diff --git a/tests/convert_pointset_test.py b/tests/convert_pointset_test.py index 1513afa4..bbc259bc 100644 --- a/tests/convert_pointset_test.py +++ b/tests/convert_pointset_test.py @@ -1,12 +1,14 @@ """Tests for PointSet validation""" +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_pointset_to_geoh5(tmp_path): +def test_pointset_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" colormap = omf.ColorArray( array=[ diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index 5d1dc712..586d12f7 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -2,43 +2,38 @@ import logging import os +from pathlib import Path from geoh5py.workspace import Workspace import omf -from .doc_example_test import TestDocEx - -def test_project_to_geoh5(tmp_path, caplog): +def test_project_to_geoh5(random_project: omf.Project, tmp_path: Path, caplog): """Test pointset geometry validation""" - proj = TestDocEx.make_random_project() - file = str(tmp_path / "project.geoh5") - omf.OMFWriter(proj, file) + omf.OMFWriter(random_project, file) warning_records = [r for r in caplog.records if r.levelno == logging.WARNING] assert len(warning_records) == 1 with Workspace(file) as workspace: - assert len(workspace.objects) == len(proj.elements) + assert len(workspace.objects) == len(random_project.elements) project = omf.fileio.geoh5.GeoH5Reader(file).project - assert len(project.elements) == len(proj.elements) + assert len(project.elements) == len(random_project.elements) -def test_project_compression(tmp_path): +def test_project_compression(random_project: omf.Project, tmp_path: Path): """Test pointset geometry validation""" - proj = TestDocEx.make_random_project() - file_low_comp = str(tmp_path / "project_low_comp.geoh5") file_med_comp = str(tmp_path / "project_med_comp.geoh5") file_high_comp = str(tmp_path / "project_high_comp.geoh5") - omf.OMFWriter(proj, file_low_comp, compression=1) - omf.OMFWriter(proj, file_med_comp, compression=5) - omf.OMFWriter(proj, file_high_comp, compression=9) + omf.OMFWriter(random_project, file_low_comp, compression=1) + omf.OMFWriter(random_project, file_med_comp, compression=5) + omf.OMFWriter(random_project, file_high_comp, compression=9) size_low_comp = os.stat(file_low_comp).st_size size_med_comp = os.stat(file_med_comp).st_size diff --git a/tests/convert_surface_test.py b/tests/convert_surface_test.py index 795a459a..0b33e6eb 100644 --- a/tests/convert_surface_test.py +++ b/tests/convert_surface_test.py @@ -1,12 +1,14 @@ """Tests for PointSet validation""" +from pathlib import Path + import numpy as np from geoh5py.workspace import Workspace import omf -def test_surface_to_geoh5(tmp_path): +def test_surface_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" surf = omf.SurfaceElement( name="trisurf", diff --git a/tests/convert_volume_test.py b/tests/convert_volume_test.py index 61dcc754..db292c2e 100644 --- a/tests/convert_volume_test.py +++ b/tests/convert_volume_test.py @@ -1,5 +1,7 @@ """Tests for PointSet validation""" +from pathlib import Path + import numpy as np from geoh5py.objects import BlockModel from geoh5py.workspace import Workspace @@ -8,7 +10,7 @@ from omf.fileio.geoh5 import block_model_reordering -def test_volume_to_geoh5(tmp_path): +def test_volume_to_geoh5(tmp_path: Path): """Test pointset geometry validation""" dims = [10, 15, 20] vol = omf.VolumeElement( diff --git a/tests/doc_example_test.py b/tests/doc_example_test.py index 6037c73c..4374b72f 100644 --- a/tests/doc_example_test.py +++ b/tests/doc_example_test.py @@ -1,147 +1,8 @@ -# pylint: disable=duplicate-code - from pathlib import Path -import numpy as np -import pytest - import omf -@pytest.fixture -def random_project() -> omf.Project: - tests_dir = Path(__file__).resolve().parent - png_file_path = tests_dir.parent / "docs" / "images" / "PointSetGeometry.png" - proj = omf.Project(name="Test project", description="Just some assorted elements") - - pts = omf.PointSetElement( - name="Random Points", - description="Just random points", - geometry=omf.PointSetGeometry(vertices=np.random.rand(100, 3)), - data=[ - omf.ScalarData( - name="rand data", array=np.random.rand(100), location="vertices" - ), - omf.ScalarData( - name="More rand data", - array=np.random.rand(100), - location="vertices", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=str(png_file_path), - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 1, 0], - ), - omf.ImageTexture( - name="test image", - image=str(png_file_path), - origin=[0, 0, 0], - axis_u=[1, 0, 0], - axis_v=[0, 0, 1], - ), - ], - color="green", - ) - - lin = omf.LineSetElement( - name="Random Line", - geometry=omf.LineSetGeometry( - vertices=np.random.rand(100, 3), - segments=np.floor(np.random.rand(50, 2) * 100).astype(int), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand segment data", - array=np.random.rand(50), - location="segments", - ), - ], - color="#0000FF", - ) - - surf = omf.SurfaceElement( - name="trisurf", - geometry=omf.SurfaceGeometry( - vertices=np.random.rand(100, 3), - triangles=np.floor(np.random.rand(50, 3) * 100).astype(int), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(100), - location="vertices", - ), - omf.ScalarData( - name="rand face data", array=np.random.rand(50), location="faces" - ), - ], - color=[100, 200, 200], - ) - - grid = omf.SurfaceElement( - name="gridsurf", - geometry=omf.SurfaceGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - origin=[50.0, 50.0, 50.0], - axis_u=[1.0, 0, 0], - axis_v=[0, 0, 1.0], - offset_w=np.random.rand(11, 16).flatten(), - ), - data=[ - omf.ScalarData( - name="rand vert data", - array=np.random.rand(11, 16).flatten(), - location="vertices", - ), - omf.ScalarData( - name="rand face data", - array=np.random.rand(10, 15).flatten(order="f"), - location="faces", - ), - ], - textures=[ - omf.ImageTexture( - name="test image", - image=str(png_file_path), - origin=[2.0, 2.0, 2.0], - axis_u=[5.0, 0, 0], - axis_v=[0, 2.0, 5.0], - ) - ], - ) - - vol = omf.VolumeElement( - name="vol", - geometry=omf.VolumeGridGeometry( - tensor_u=np.ones(10).astype(float), - tensor_v=np.ones(15).astype(float), - tensor_w=np.ones(20).astype(float), - origin=[10.0, 10.0, -10], - ), - data=[ - omf.ScalarData( - name="Random Data", - location="cells", - array=np.random.rand(10, 15, 20).flatten(), - ) - ], - ) - - proj.elements = [pts, lin, surf, grid, vol] - - return proj - - def test_doc_ex(tmp_path: Path, random_project): assert random_project.validate() From cf8a1d04240e41940f2c05cc0e4d66ad97541293 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 14:24:25 -0400 Subject: [PATCH 032/107] exclude ^docs through pre-commit config for ruff --- .pre-commit-config.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8bba81c3..6a0eb29d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,7 +29,9 @@ repos: - --fix - --exit-non-zero-on-fix # - --unsafe-fixes + exclude: ^docs/ - id: ruff-format + exclude: ^docs/ - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.11.0 hooks: From 5becb3bea0a5e313093ea11bc6ed9926b61cc3d2 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 16:58:33 -0400 Subject: [PATCH 033/107] ruff uses glob for exclude patterns --- .pre-commit-config.yaml | 2 -- pyproject.toml | 24 +++++++++++++----------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6a0eb29d..8bba81c3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -29,9 +29,7 @@ repos: - --fix - --exit-non-zero-on-fix # - --unsafe-fixes - exclude: ^docs/ - id: ruff-format - exclude: ^docs/ - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.11.0 hooks: diff --git a/pyproject.toml b/pyproject.toml index f88ad1af..f86798dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,13 +70,22 @@ tomli = "*" # for tests only [tool.ruff] target-version = "py39" -[tool.ruff.lint] exclude = [ - "^docs/", + "docs/*", # skip source files from upstream repo - "^omf/fileio/(fileio|utils)[.]py$", - "^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$", + "omf/fileio/fileio.py", + "omf/fileio/utils.py", + "omf/base.py", + "omf/data.py", + "omf/lineset.py", + "omf/pointset.py", + "omf/serializers.py", + "omf/surface.py", + "omf/texture.py", + "omf/volume.py", ] + +[tool.ruff.lint] ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) @@ -108,13 +117,6 @@ max-complexity = 18 lines-after-imports = 2 [tool.ruff.format] -exclude = [ - "^docs/", - # skip source files from upstream repo - "^omf/fileio/(fileio|utils)[.]py$", - "^omf/(base|data|lineset|pointset|serializers|surface|texture|volume)[.]py$", -] - # default formatting is just fine [tool.mypy] From 802b27bbc523a8341910ecb97048f4ceaef39bd0 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 17:47:31 -0400 Subject: [PATCH 034/107] remove unused class member --- omf/fileio/geoh5.py | 1 - 1 file changed, 1 deletion(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 7430e8d7..dc855ff8 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -157,7 +157,6 @@ class BaseConversion(ABC): } _geoh5 = None _parent = None - _mapping = None def __init__( self, From 47753325c5975e5a7cda7b57a79aa21ae2cf1e78 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 17:48:38 -0400 Subject: [PATCH 035/107] remove wrong class members which are instance members --- omf/fileio/geoh5.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index dc855ff8..8038249f 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -155,8 +155,6 @@ class BaseConversion(ABC): "uid": "uid", "name": "name", } - _geoh5 = None - _parent = None def __init__( self, @@ -168,7 +166,9 @@ def __init__( if element is None: raise ValueError("Input 'element' cannot be None.") + self._geoh5 = None self.geoh5 = geoh5 + self.compression = compression self._parent = parent From 2dbcc02b8ef38b75649a1d3a495ee516e9cc7c00 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 17:51:04 -0400 Subject: [PATCH 036/107] disable RUF012 where appropriate proper fix would require introducing a classmethod with memoization --- omf/fileio/geoh5.py | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 8038249f..46418c88 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -151,7 +151,7 @@ class BaseConversion(ABC): geoh5_type: type[Entity] omf_type: type[UidModel] - _attribute_map: dict = { + _attribute_map: dict = { # noqa: RUF012 "uid": "uid", "name": "name", } @@ -290,7 +290,7 @@ class DataConversion(BaseConversion): :obj:`geoh5py.data.Data` """ - _attribute_map: dict[str, Any] = { + _attribute_map: dict[str, Any] = { # noqa: RUF012 "uid": "uid", "name": "name", } @@ -368,7 +368,7 @@ class ElementConversion(BaseConversion): :param compression: Compression level for data. """ - _attribute_map: dict[str, Any] = { + _attribute_map: dict[str, Any] = { # noqa: RUF012 "name": "name", "uid": "uid", } @@ -441,7 +441,7 @@ class ProjectConversion(BaseConversion): omf_type = Project geoh5_type = RootGroup - _attribute_map: dict = { + _attribute_map: dict = { # noqa: RUF012 "uid": "uid", "name": "name", "units": "distance_unit", @@ -499,7 +499,7 @@ class ArrayConversion(BaseConversion): omf_type = ScalarArray geoh5_type = Data - _attribute_map: dict = {"array": "values"} + _attribute_map: dict = {"array": "values"} # noqa: RUF012 def from_omf(self, element: UidModel, **kwargs) -> dict: """ @@ -617,7 +617,7 @@ class StringArrayConversion(ArrayConversion): """ omf_type = StringArray - geoh5_type = list # type: ignore + geoh5_type = list class ReferenceMapConversion(ArrayConversion): @@ -626,7 +626,7 @@ class ReferenceMapConversion(ArrayConversion): of :obj:`geoh5py.data.referenced_data`. """ - geoh5_type = ReferencedData # type: ignore + geoh5_type = ReferencedData def collect_attributes( # type: ignore self, @@ -732,7 +732,7 @@ class ColormapConversion(ArrayConversion): omf_type = ScalarColormap geoh5_type = Data - _attribute_map: dict = {"colormap": "color_map"} + _attribute_map: dict = {"colormap": "color_map"} # noqa: RUF012 def collect_attributes( self, element: UidModel | Entity, workspace: str | Workspace | Path, **kwargs @@ -871,7 +871,7 @@ class PointSetGeometryConversion(BaseGeometryConversion): omf_type = PointSetGeometry geoh5_type = Points - _attribute_map: dict = {"vertices": "vertices"} + _attribute_map: dict = {"vertices": "vertices"} # noqa: RUF012 class LineSetGeometryConversion(BaseGeometryConversion): @@ -882,7 +882,7 @@ class LineSetGeometryConversion(BaseGeometryConversion): omf_type = LineSetGeometry geoh5_type = Curve - _attribute_map: dict = {"vertices": "vertices", "segments": "cells"} + _attribute_map: dict = {"vertices": "vertices", "segments": "cells"} # noqa: RUF012 class SurfaceGeometryConversion(BaseGeometryConversion): @@ -893,7 +893,7 @@ class SurfaceGeometryConversion(BaseGeometryConversion): omf_type = SurfaceGeometry geoh5_type = Surface - _attribute_map: dict = {"vertices": "vertices", "triangles": "cells"} + _attribute_map: dict = {"vertices": "vertices", "triangles": "cells"} # noqa: RUF012 class SurfaceGridGeometryConversion(BaseGeometryConversion): @@ -904,7 +904,7 @@ class SurfaceGridGeometryConversion(BaseGeometryConversion): omf_type = SurfaceGridGeometry geoh5_type = Grid2D - _attribute_map: dict = { + _attribute_map: dict = { # noqa: RUF012 "u": "u", "v": "v", } @@ -1021,7 +1021,7 @@ class VolumeGridGeometryConversion(BaseGeometryConversion): omf_type = VolumeGridGeometry geoh5_type = BlockModel - _attribute_map: dict = {"u": "u", "v": "v", "w": "z"} + _attribute_map: dict = {"u": "u", "v": "v", "w": "z"} # noqa: RUF012 def __init__( self, From 90617ece4f714464f13edabc102e005a0f71ef9c Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 17:52:20 -0400 Subject: [PATCH 037/107] Ruff report addressed --- pyproject.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f86798dd..5c77186c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -90,8 +90,6 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln - "RUF012", # TODO - "UP038", # TODO ] select = [ "A", # flake8-builtins From a46430c8b62c9fe61d81298dbf163bef66ab985d Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 5 Aug 2024 22:05:59 -0400 Subject: [PATCH 038/107] do not disable RUF012 should still be address properly. Leave as TODO --- omf/fileio/geoh5.py | 26 +++++++++++++------------- pyproject.toml | 1 + 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 46418c88..8038249f 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -151,7 +151,7 @@ class BaseConversion(ABC): geoh5_type: type[Entity] omf_type: type[UidModel] - _attribute_map: dict = { # noqa: RUF012 + _attribute_map: dict = { "uid": "uid", "name": "name", } @@ -290,7 +290,7 @@ class DataConversion(BaseConversion): :obj:`geoh5py.data.Data` """ - _attribute_map: dict[str, Any] = { # noqa: RUF012 + _attribute_map: dict[str, Any] = { "uid": "uid", "name": "name", } @@ -368,7 +368,7 @@ class ElementConversion(BaseConversion): :param compression: Compression level for data. """ - _attribute_map: dict[str, Any] = { # noqa: RUF012 + _attribute_map: dict[str, Any] = { "name": "name", "uid": "uid", } @@ -441,7 +441,7 @@ class ProjectConversion(BaseConversion): omf_type = Project geoh5_type = RootGroup - _attribute_map: dict = { # noqa: RUF012 + _attribute_map: dict = { "uid": "uid", "name": "name", "units": "distance_unit", @@ -499,7 +499,7 @@ class ArrayConversion(BaseConversion): omf_type = ScalarArray geoh5_type = Data - _attribute_map: dict = {"array": "values"} # noqa: RUF012 + _attribute_map: dict = {"array": "values"} def from_omf(self, element: UidModel, **kwargs) -> dict: """ @@ -617,7 +617,7 @@ class StringArrayConversion(ArrayConversion): """ omf_type = StringArray - geoh5_type = list + geoh5_type = list # type: ignore class ReferenceMapConversion(ArrayConversion): @@ -626,7 +626,7 @@ class ReferenceMapConversion(ArrayConversion): of :obj:`geoh5py.data.referenced_data`. """ - geoh5_type = ReferencedData + geoh5_type = ReferencedData # type: ignore def collect_attributes( # type: ignore self, @@ -732,7 +732,7 @@ class ColormapConversion(ArrayConversion): omf_type = ScalarColormap geoh5_type = Data - _attribute_map: dict = {"colormap": "color_map"} # noqa: RUF012 + _attribute_map: dict = {"colormap": "color_map"} def collect_attributes( self, element: UidModel | Entity, workspace: str | Workspace | Path, **kwargs @@ -871,7 +871,7 @@ class PointSetGeometryConversion(BaseGeometryConversion): omf_type = PointSetGeometry geoh5_type = Points - _attribute_map: dict = {"vertices": "vertices"} # noqa: RUF012 + _attribute_map: dict = {"vertices": "vertices"} class LineSetGeometryConversion(BaseGeometryConversion): @@ -882,7 +882,7 @@ class LineSetGeometryConversion(BaseGeometryConversion): omf_type = LineSetGeometry geoh5_type = Curve - _attribute_map: dict = {"vertices": "vertices", "segments": "cells"} # noqa: RUF012 + _attribute_map: dict = {"vertices": "vertices", "segments": "cells"} class SurfaceGeometryConversion(BaseGeometryConversion): @@ -893,7 +893,7 @@ class SurfaceGeometryConversion(BaseGeometryConversion): omf_type = SurfaceGeometry geoh5_type = Surface - _attribute_map: dict = {"vertices": "vertices", "triangles": "cells"} # noqa: RUF012 + _attribute_map: dict = {"vertices": "vertices", "triangles": "cells"} class SurfaceGridGeometryConversion(BaseGeometryConversion): @@ -904,7 +904,7 @@ class SurfaceGridGeometryConversion(BaseGeometryConversion): omf_type = SurfaceGridGeometry geoh5_type = Grid2D - _attribute_map: dict = { # noqa: RUF012 + _attribute_map: dict = { "u": "u", "v": "v", } @@ -1021,7 +1021,7 @@ class VolumeGridGeometryConversion(BaseGeometryConversion): omf_type = VolumeGridGeometry geoh5_type = BlockModel - _attribute_map: dict = {"u": "u", "v": "v", "w": "z"} # noqa: RUF012 + _attribute_map: dict = {"u": "u", "v": "v", "w": "z"} def __init__( self, diff --git a/pyproject.toml b/pyproject.toml index 5c77186c..342addc0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -90,6 +90,7 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln + "RUF012", # TODO ] select = [ "A", # flake8-builtins From b65b073bbc33fdd9345309f8e0cfaf78ec3b1857 Mon Sep 17 00:00:00 2001 From: dominiquef Date: Mon, 17 Jun 2024 14:25:42 -0700 Subject: [PATCH 039/107] Bump version --- omf/__init__.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/omf/__init__.py b/omf/__init__.py index 88ea8ebf..b884741e 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -29,8 +29,7 @@ from .texture import ImageTexture from .volume import VolumeElement, VolumeGridGeometry - -__version__ = "3.2.1" +__version__ = "3.3.0-alpha.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" From 0abbfbb3d238500fe3f8159607417deb976bc679 Mon Sep 17 00:00:00 2001 From: dominiquef Date: Mon, 17 Jun 2024 14:29:16 -0700 Subject: [PATCH 040/107] Bump version in toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f86798dd..d403c265 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.2.1" +version = "3.3.0-alpha.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 3d5fc796a186052904da11afd278aa7cf1d407ab Mon Sep 17 00:00:00 2001 From: dominiquef Date: Mon, 17 Jun 2024 14:46:02 -0700 Subject: [PATCH 041/107] more versions --- README.rst | 2 +- docs/conf.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index eb323f86..f401df27 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.2.1 +Version: 3.3.0-alpha.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index a7428b53..f9fc9eef 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -62,9 +62,9 @@ # built documents. # # The short X.Y version. -version = u'3.2.1' +version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.2.1' +release = u'3.3.0-alpha.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From f7a081a9a6e62f51193b8a2cf42895614455951c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 6 Aug 2024 03:06:55 +0000 Subject: [PATCH 042/107] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- omf/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/omf/__init__.py b/omf/__init__.py index b884741e..d72f491a 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -29,6 +29,7 @@ from .texture import ImageTexture from .volume import VolumeElement, VolumeGridGeometry + __version__ = "3.3.0-alpha.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" From e6f1be147aa8aa69ab5996e993d48246a39d925e Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 29 Aug 2024 15:39:34 -0400 Subject: [PATCH 043/107] [DEVOPS-440] Use regular double quote in README.rst --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index f401df27..e7ff1da3 100644 --- a/README.rst +++ b/README.rst @@ -112,7 +112,7 @@ SOFTWARE. Third Party Software ^^^^^^^^^^^^^^^^^^^^ -The mira-omf Software may provide links to third party libraries or code (collectively “Third Party Software”) +The mira-omf Software may provide links to third party libraries or code (collectively "Third Party Software") to implement various functions. Third Party Software does not comprise part of the Software. The use of Third Party Software is governed by the terms of such software license(s). Third Party Software notices and/or additional terms and conditions are located in the From 0106345f05a8f175b336dc913a53e597d0e605eb Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 16 Sep 2024 15:37:31 -0400 Subject: [PATCH 044/107] [DEVOPS-466] Update input variable in shared workflows --- .github/workflows/issue_to_jira.yml | 4 ++-- .github/workflows/python_analysis.yml | 26 +++++++++++++------------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/issue_to_jira.yml b/.github/workflows/issue_to_jira.yml index 2818e29e..db42f497 100644 --- a/.github/workflows/issue_to_jira.yml +++ b/.github/workflows/issue_to_jira.yml @@ -6,7 +6,7 @@ on: jobs: call-workflow-create-jira-issue: - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@main + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@DEVOPS-466 secrets: inherit with: - project_key: 'GEOPY' + project-key: 'GEOPY' diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index ee7f8ccb..af5c3b97 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -24,26 +24,26 @@ concurrency: jobs: call-workflow-static-analysis: name: Static analysis - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@DEVOPS-466 with: - package_manager: 'poetry' - app_name: 'omf' - python_vers: '3.9' + package-manager: 'poetry' + app-name: 'omf' + python-version: '3.9' call-workflow-pytest-on-windows: name: Pytest on Windows - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_windows.yml@main + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_windows.yml@DEVOPS-466 with: - package_manager: 'poetry' - python_ver: '["3.9", "3.10", "3.11", "3.12"]' - cache_number: 1 - codecov_reference_python_ver: '3.10' + package-manager: 'poetry' + python-versions: '["3.9", "3.10", "3.11", "3.12"]' + cache-number: 1 + codecov-reference-python-version: '3.10' secrets: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} call-workflow-pytest-on-unix-os: name: Pytest on Unix OS - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@main + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@DEVOPS-466 with: - package_manager: 'poetry' - python_ver: '["3.9", "3.10", "3.11", "3.12"]' + package-manager: 'poetry' + python-versions: '["3.9", "3.10", "3.11", "3.12"]' os: '["ubuntu-latest"]' - cache_number: 1 + cache-number: 1 From f60b42a309dab0bc0d58341c797315fcb076752f Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Sep 2024 08:45:47 -0400 Subject: [PATCH 045/107] [DEVOPS-466] Relaunch worklfows From df0be6e16642712d65ce8f9b7cfc615482584dc0 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Sep 2024 08:48:27 -0400 Subject: [PATCH 046/107] [DEVOPS-466] Relaunch worklfows From c45a8db2adf95edc6eaf7fc53aefc17eed461452 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 18 Sep 2024 15:50:10 -0400 Subject: [PATCH 047/107] [GEOPY-1712] Exclude RUFF005 --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index f2a91927..97d9c3ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -90,6 +90,7 @@ ignore = [ "B028", # no-explicit-stacklevel for warnings.warn() "E501", # line-too-long - code is reformatted (do not care about comments and docstring) "F401", # unsused-import - covered by pycln + "RUF005", # collection-literal-concatenation - wrong suggestion with numpy arrays "RUF012", # TODO ] select = [ From a01c6491d6cdb6f6d4dbd2916b7e8383bf420090 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 25 Sep 2024 09:46:01 -0400 Subject: [PATCH 048/107] [DEVOPS-466] Update python_analysis --- .github/workflows/python_analysis.yml | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index af5c3b97..7f5fce4c 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -29,21 +29,15 @@ jobs: package-manager: 'poetry' app-name: 'omf' python-version: '3.9' - call-workflow-pytest-on-windows: - name: Pytest on Windows - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_windows.yml@DEVOPS-466 + call-workflow-pytest: + name: Pytest + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@DEVOPS-466 with: package-manager: 'poetry' python-versions: '["3.9", "3.10", "3.11", "3.12"]' + os: '["ubuntu-latest", "windows-latest"]' cache-number: 1 codecov-reference-python-version: '3.10' + codecov-reference-os: '["windows-latest", "ubuntu-latest"]' secrets: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - call-workflow-pytest-on-unix-os: - name: Pytest on Unix OS - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest_unix_os.yml@DEVOPS-466 - with: - package-manager: 'poetry' - python-versions: '["3.9", "3.10", "3.11", "3.12"]' - os: '["ubuntu-latest"]' - cache-number: 1 From 78f99edd2312156c9649c451c9af5400afd5c84e Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Fri, 27 Sep 2024 16:26:50 -0400 Subject: [PATCH 049/107] [DEVOPS-466] Update before merging --- .github/workflows/issue_to_jira.yml | 2 +- .github/workflows/python_analysis.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/issue_to_jira.yml b/.github/workflows/issue_to_jira.yml index db42f497..057d0782 100644 --- a/.github/workflows/issue_to_jira.yml +++ b/.github/workflows/issue_to_jira.yml @@ -6,7 +6,7 @@ on: jobs: call-workflow-create-jira-issue: - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@DEVOPS-466 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-issue_to_jira.yml@main secrets: inherit with: project-key: 'GEOPY' diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index 7f5fce4c..a04d5328 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -24,14 +24,14 @@ concurrency: jobs: call-workflow-static-analysis: name: Static analysis - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@DEVOPS-466 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-static_analysis.yml@main with: package-manager: 'poetry' app-name: 'omf' python-version: '3.9' call-workflow-pytest: name: Pytest - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@DEVOPS-466 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@main with: package-manager: 'poetry' python-versions: '["3.9", "3.10", "3.11", "3.12"]' From 171af42787f4f1354b5df9fc66b81d10ce3f715c Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 7 Oct 2024 08:40:17 -0400 Subject: [PATCH 050/107] [DEVOPS-504] Add conda's recipe and deploy workflows --- .github/workflows/python_deploy_dev.yml | 18 +++++++++ .github/workflows/python_deploy_prod.yml | 17 +++++++++ meta.yaml | 47 ++++++++++++++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 .github/workflows/python_deploy_dev.yml create mode 100644 .github/workflows/python_deploy_prod.yml create mode 100644 meta.yaml diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml new file mode 100644 index 00000000..049d3a83 --- /dev/null +++ b/.github/workflows/python_deploy_dev.yml @@ -0,0 +1,18 @@ +name: Deploy python package in development + +on: + push: + tags: + - 'v*' # Push events to every tag not containing + +jobs: + call-workflow-conda-publish: + name: Publish development conda package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@DEVOPS-504 + with: + package-name: 'mira-omf' + python-version: '3.10' + virtual-repo-name: 'public-conda-dev' + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml new file mode 100644 index 00000000..118be828 --- /dev/null +++ b/.github/workflows/python_deploy_prod.yml @@ -0,0 +1,17 @@ +name: Deploy python package in production + +on: + release: + types: [published] # Trigger for draft release + +jobs: + call-workflow-conda-publish: + name: Publish development conda package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@DEVOPS-504 + with: + package-name: 'mira-omf' + python-version: '3.10' + virtual-repo-name: 'public-conda-prod' + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/meta.yaml b/meta.yaml new file mode 100644 index 00000000..0f4ec6c0 --- /dev/null +++ b/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "mira-omf" %} +{% set version = "3.3.0a1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + path: ../{{ name}} + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.10.0,<3.11 + - poetry-core >=1.0.0 + - setuptools + - pip + run: + - python >=3.9.0,<3.11 + - numpy >=1.26.0,<1.27.0 + - properties >=0.6.0,<0.7.0 + - pypng 20220715.* + - six >=1.16.0,<1.17.0 + - vectormath >=0.2.0,<0.3.0 + - geoh5py >=0.9.1a0.dev0,<0.11.0 + +test: + imports: + - omf + commands: + - pip check + requires: + - pip + +about: + license: MIT + license_file: + - LICENSE + +extra: + recipe-maintainers: + - SophieCurinier + - sebhmg From e859b8c7183948ae87438e0f53cb093459ac1ac8 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 7 Oct 2024 08:47:11 -0400 Subject: [PATCH 051/107] [DEVOPS-504] Modify pypng version in conda's recipe --- meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/meta.yaml b/meta.yaml index 0f4ec6c0..3f60ab11 100644 --- a/meta.yaml +++ b/meta.yaml @@ -23,7 +23,7 @@ requirements: - python >=3.9.0,<3.11 - numpy >=1.26.0,<1.27.0 - properties >=0.6.0,<0.7.0 - - pypng 20220715.* + - pypng 0.20220715.* - six >=1.16.0,<1.17.0 - vectormath >=0.2.0,<0.3.0 - geoh5py >=0.9.1a0.dev0,<0.11.0 From bfb1a78fdc3309ab575d87f158e054ce2f985bde Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Mon, 7 Oct 2024 19:22:46 -0400 Subject: [PATCH 052/107] [DEVOPS-504] Update conda's recipe --- meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/meta.yaml b/meta.yaml index 3f60ab11..16020d89 100644 --- a/meta.yaml +++ b/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} source: - path: ../{{ name}} + path: ../omf build: noarch: python From 785bdbcae9a39cfca99037780e3112299b43b6fc Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 7 Oct 2024 21:27:44 -0400 Subject: [PATCH 053/107] DEVOPS-515: prepare release v3.2.2 --- README.rst | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index e7ff1da3..61464e22 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-alpha.1 +Version: 3.2.2-beta.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/pyproject.toml b/pyproject.toml index 97d9c3ea..9ab8c379 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-alpha.1" +version = "3.2.2-beta.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 695dfa6c5cde20e9caea21b134d8a615e4582755 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 7 Oct 2024 22:14:45 -0400 Subject: [PATCH 054/107] [DEVOPS-515] set version in code: 3.2.2-beta.1 to match the one in pyproject.toml --- docs/conf.py | 4 ++-- omf/__init__.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index f9fc9eef..433c3102 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -62,9 +62,9 @@ # built documents. # # The short X.Y version. -version = u'3.3.0' +version = u'3.2.2' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-alpha.1' +release = u'3.2.2-beta.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/omf/__init__.py b/omf/__init__.py index d72f491a..6ee6fafa 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-alpha.1" +__version__ = "3.2.2-beta.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" From 206c879ee39bdae6bb35f37952a9b6e3f57e3bfd Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 7 Oct 2024 21:32:59 -0400 Subject: [PATCH 055/107] [DEVOPS-515] change dependency to geoh5py@release/0.1.0 --- poetry.lock | 639 +++++++++++++++++++++++++++++-------------------- pyproject.toml | 6 +- 2 files changed, 389 insertions(+), 256 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7106a9d5..3b819aaa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,15 +11,26 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + [[package]] name = "astroid" -version = "3.2.2" +version = "3.3.5" description = "An abstract syntax tree for Python with inference support." optional = false -python-versions = ">=3.8.0" +python-versions = ">=3.9.0" files = [ - {file = "astroid-3.2.2-py3-none-any.whl", hash = "sha256:e8a0083b4bb28fcffb6207a3bfc9e5d0a68be951dd7e336d5dcf639c682388c0"}, - {file = "astroid-3.2.2.tar.gz", hash = "sha256:8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94"}, + {file = "astroid-3.3.5-py3-none-any.whl", hash = "sha256:a9d1c946ada25098d790e079ba2a1b112157278f3fb7e718ae6a9252f5835dc8"}, + {file = "astroid-3.3.5.tar.gz", hash = "sha256:5cfc40ae9f68311075d27ef68a4841bdc5cc7f6cf86671b49f00607d30188e2d"}, ] [package.dependencies] @@ -27,13 +38,13 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = 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"dd7cf6d48c026e9be0554e815c8add94689c594b5e11d9d4ce2e4f7336da0cdd" +python-versions = "^3.10" +content-hash = "db0bffcbfd23367a6e8a0fb2a84e95f5081d27c0d4ea712e938c29e8980b8e5f" diff --git a/pyproject.toml b/pyproject.toml index 9ab8c379..e0207346 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ geoh5_to_omf = 'omf.scripts.geoh5_to_omf:main' omf_to_geoh5 = 'omf.scripts.omf_to_geoh5:main' [tool.poetry.dependencies] -python = "^3.9" +python = "^3.10" numpy = "~1.26.0" # also in geoh5py properties = "~0.6.0" @@ -55,8 +55,8 @@ vectormath = "~0.2.0" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = ">=0.9.1, <0.11", allow-prereleases = true} -#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} +#geoh5py = {version = ">=0.9.1, <0.11", allow-prereleases = true} +geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} #geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] From b571fb7e58930110c193b9b7c5c46b54dfdf3682 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 7 Oct 2024 22:10:36 -0400 Subject: [PATCH 056/107] [DEVOPS-515] stop testing py39, pyupgrade to py310 --- .github/workflows/python_analysis.yml | 4 ++-- omf/fileio/geoh5.py | 2 +- pyproject.toml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index a04d5328..d0124554 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -28,13 +28,13 @@ jobs: with: package-manager: 'poetry' app-name: 'omf' - python-version: '3.9' + python-version: '3.10' call-workflow-pytest: name: Pytest uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@main with: package-manager: 'poetry' - python-versions: '["3.9", "3.10", "3.11", "3.12"]' + python-versions: '["3.10", "3.11", "3.12"]' os: '["ubuntu-latest", "windows-latest"]' cache-number: 1 codecov-reference-python-version: '3.10' diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 8038249f..c4f9ad2c 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -68,7 +68,7 @@ def __init__( file_name: str | Path, compression: int = 5, ): - if not isinstance(file_name, (str, Path)): + if not isinstance(file_name, str | Path): raise TypeError("Input 'file' must be of str or Path.") self.file = file_name diff --git a/pyproject.toml b/pyproject.toml index e0207346..1d70dfd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ sphinx = "^5.3" tomli = "*" # for tests only [tool.ruff] -target-version = "py39" +target-version = "py310" exclude = [ "docs/*", From 3830466cb4a7d7001665dd477992e7197131aec6 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Mon, 7 Oct 2024 22:36:12 -0400 Subject: [PATCH 057/107] bump minor version and set to alpha status => 3.3.0-alpha As coming release is not compatible with geoh5py 0.9, and thus will forces other modules depending on geoh5py to update as well --- README.rst | 2 +- docs/conf.py | 4 ++-- omf/__init__.py | 2 +- pyproject.toml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 61464e22..e7ff1da3 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.2.2-beta.1 +Version: 3.3.0-alpha.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index 433c3102..f9fc9eef 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -62,9 +62,9 @@ # built documents. # # The short X.Y version. -version = u'3.2.2' +version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.2.2-beta.1' +release = u'3.3.0-alpha.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/omf/__init__.py b/omf/__init__.py index 6ee6fafa..d72f491a 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.2.2-beta.1" +__version__ = "3.3.0-alpha.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index 9ab8c379..97d9c3ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.2.2-beta.1" +version = "3.3.0-alpha.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 8a33ec3566bf47bb9d05b5a6a98a183f8d0ff6ac Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 8 Oct 2024 12:57:06 -0400 Subject: [PATCH 058/107] [DEVOPS-504] Update deployment workflows --- .github/workflows/python_deploy_dev.yml | 12 + .github/workflows/python_deploy_prod.yml | 16 +- .gitignore | 1 + poetry.lock | 706 ++++++++++++++++------- pyproject.toml | 8 + 5 files changed, 524 insertions(+), 219 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 049d3a83..39061781 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -16,3 +16,15 @@ jobs: secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + call-workflow-pypi-publish: + name: Publish development pypi package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@DEVOPS-504 + with: + package-manager: 'poetry' + package-name: 'mira-omf' + version-tag: ${{ github.ref_name }} + python-version: '3.10' + virtual-repo-name: 'public-pypi-dev' + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 118be828..e60d05fc 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -2,11 +2,11 @@ name: Deploy python package in production on: release: - types: [published] # Trigger for draft release + types: [published] jobs: call-workflow-conda-publish: - name: Publish development conda package on JFrog Artifactory + name: Publish production conda package on JFrog Artifactory uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@DEVOPS-504 with: package-name: 'mira-omf' @@ -15,3 +15,15 @@ jobs: secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + call-workflow-pypi-publish: + name: Publish production pypi package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@DEVOPS-504 + with: + package-manager: 'poetry' + package-name: 'mira-omf' + version-tag: ${{ github.ref_name }} + python-version: '3.10' + virtual-repo-name: 'public-pypi-prod' + secrets: + JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} + JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.gitignore b/.gitignore index aabfdb04..c88128e6 100644 --- a/.gitignore +++ b/.gitignore @@ -141,3 +141,4 @@ dmypy.json # geoh5 locks *.geoh5.lock +/.jfrog/projects/poetry.yaml diff --git a/poetry.lock b/poetry.lock index 7106a9d5..24597daa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,45 +11,65 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "astroid" -version = "3.2.2" +version = "3.3.5" description = "An abstract syntax tree for Python with inference support." optional = false -python-versions = ">=3.8.0" +python-versions = ">=3.9.0" files = [ - {file = "astroid-3.2.2-py3-none-any.whl", hash = "sha256:e8a0083b4bb28fcffb6207a3bfc9e5d0a68be951dd7e336d5dcf639c682388c0"}, - {file = "astroid-3.2.2.tar.gz", hash = "sha256:8ead48e31b92b2e217b6c9733a21afafe479d52d6e164dd25fb1a770c7c3cf94"}, + {file = "astroid-3.3.5-py3-none-any.whl", hash = "sha256:a9d1c946ada25098d790e079ba2a1b112157278f3fb7e718ae6a9252f5835dc8"}, + {file = "astroid-3.3.5.tar.gz", hash = "sha256:5cfc40ae9f68311075d27ef68a4841bdc5cc7f6cf86671b49f00607d30188e2d"}, ] [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "certifi" -version = "2024.7.4" +version = "2024.8.30" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, - {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, + {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, + {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, ] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "charset-normalizer" version = "3.3.2" @@ -149,6 +169,11 @@ files = [ {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"}, ] +[package.source] +type = 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[[package]] name = "sphinxcontrib-applehelp" -version = "1.0.8" +version = "2.0.0" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" optional = false python-versions = ">=3.9" files = [ - {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"}, - {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"}, + {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"}, + {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"}, ] [package.extras] -lint = ["docutils-stubs", "flake8", "mypy"] +lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "sphinxcontrib-devhelp" -version = "1.0.6" +version = "2.0.0" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" optional = false python-versions = ">=3.9" files = [ - {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"}, - {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"}, + {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"}, + {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"}, ] [package.extras] -lint = ["docutils-stubs", "flake8", "mypy"] +lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "sphinxcontrib-htmlhelp" -version = "2.0.5" +version = "2.1.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" optional = false python-versions = ">=3.9" files = [ - {file = "sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl", hash = "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"}, - {file = "sphinxcontrib_htmlhelp-2.0.5.tar.gz", hash = "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015"}, + {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"}, + {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"}, ] [package.extras] -lint = ["docutils-stubs", "flake8", "mypy"] +lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["html5lib", "pytest"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "sphinxcontrib-jsmath" version = "1.0.1" @@ -905,60 +1128,85 @@ files = [ [package.extras] test = ["flake8", "mypy", "pytest"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "sphinxcontrib-qthelp" -version = "1.0.7" +version = "2.0.0" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" optional = false python-versions = ">=3.9" files = [ - {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"}, - {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"}, + {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"}, + {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"}, ] [package.extras] -lint = ["docutils-stubs", "flake8", "mypy"] +lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] -test = ["pytest"] +test = ["defusedxml (>=0.7.1)", "pytest"] + +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.10" +version = "2.0.0" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" optional = false python-versions = ">=3.9" files = [ - {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"}, - {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"}, + {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"}, + {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"}, ] [package.extras] -lint = ["docutils-stubs", "flake8", "mypy"] +lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "tomli" -version = "2.0.1" +version = "2.0.2" description = "A lil' TOML parser" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"}, - {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, + {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"}, + {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"}, ] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "tomlkit" -version = "0.12.5" +version = "0.13.2" description = "Style preserving TOML library" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "tomlkit-0.12.5-py3-none-any.whl", hash = "sha256:af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f"}, - {file = "tomlkit-0.12.5.tar.gz", hash = "sha256:eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c"}, + {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"}, + {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"}, ] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "typing-extensions" version = "4.12.2" @@ -970,15 +1218,20 @@ files = [ {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "urllib3" -version = "2.2.2" +version = "2.2.3" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, - {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, + {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"}, + {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"}, ] [package.extras] @@ -987,6 +1240,11 @@ h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "vectormath" version = "0.2.2" @@ -1000,22 +1258,36 @@ files = [ [package.dependencies] numpy = ">=1.7" +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" + [[package]] name = "zipp" -version = "3.19.2" +version = "3.20.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, - {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, ] [package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[package.source] +type = "legacy" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +reference = "jfrog-server" [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "dd7cf6d48c026e9be0554e815c8add94689c594b5e11d9d4ce2e4f7336da0cdd" +content-hash = "1053d3ec9f6b00b29d423f97e7d533b087e8a3527b9a9d6e94a9b2bd4aa2dbc4" diff --git a/pyproject.toml b/pyproject.toml index 97d9c3ea..23e99ffd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,6 +67,14 @@ pytest-cov = "*" sphinx = "^5.3" tomli = "*" # for tests only +## about jfrog repository +# change url to have access to other repo (e.g. public-pypi-prod, public-pypi-dev) + +[[tool.poetry.source]] +name = "jfrog-server" +url = 'https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple' +priority = "primary" + [tool.ruff] target-version = "py39" From 64e5e0019a36b0a6f59131c2f9857890aac54ee0 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 9 Oct 2024 13:26:56 -0400 Subject: [PATCH 059/107] [DEVOPS-504] Cleaning for PR --- .github/workflows/python_deploy_dev.yml | 4 +- .github/workflows/python_deploy_prod.yml | 4 +- .pre-commit-config.yaml | 1 + meta.yaml | 4 +- poetry.lock | 698 ++++++++--------------- pyproject.toml | 12 +- 6 files changed, 243 insertions(+), 480 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 39061781..7f219e91 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -12,7 +12,7 @@ jobs: with: package-name: 'mira-omf' python-version: '3.10' - virtual-repo-name: 'public-conda-dev' + virtual-repo-names: '["public-conda-dev"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} @@ -24,7 +24,7 @@ jobs: package-name: 'mira-omf' version-tag: ${{ github.ref_name }} python-version: '3.10' - virtual-repo-name: 'public-pypi-dev' + virtual-repo-names: '["public-pypi-dev"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index e60d05fc..0663a9ac 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -11,7 +11,7 @@ jobs: with: package-name: 'mira-omf' python-version: '3.10' - virtual-repo-name: 'public-conda-prod' + virtual-repo-names: '["public-conda-prod"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} @@ -23,7 +23,7 @@ jobs: package-name: 'mira-omf' version-tag: ${{ github.ref_name }} python-version: '3.10' - virtual-repo-name: 'public-pypi-prod' + virtual-repo-names: '["public-pypi-prod"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8bba81c3..71107e8f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -78,6 +78,7 @@ repos: exclude_types: [jupyter] - id: check-toml - id: check-yaml + exclude: ^meta.yaml$ - id: check-added-large-files - id: check-case-conflict - id: check-merge-conflict diff --git a/meta.yaml b/meta.yaml index 16020d89..a0984f08 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0a1" %} +{% set version = "3.4.0a1" %} package: name: {{ name|lower }} @@ -24,7 +24,7 @@ requirements: - numpy >=1.26.0,<1.27.0 - properties >=0.6.0,<0.7.0 - pypng 0.20220715.* - - six >=1.16.0,<1.17.0 + - six >=1.16.0,<2.0.0 - vectormath >=0.2.0,<0.3.0 - geoh5py >=0.9.1a0.dev0,<0.11.0 diff --git a/poetry.lock b/poetry.lock index 24597daa..5f39dc9d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,11 +11,6 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "astroid" version = "3.3.5" @@ -30,11 +25,6 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "babel" version = "2.16.0" @@ -49,11 +39,6 @@ files = [ [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "certifi" version = "2024.8.30" @@ -65,115 +50,120 @@ files = [ {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "charset-normalizer" -version = 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+763,6 @@ files = [ {file = "pypng-0.20220715.0.tar.gz", hash = "sha256:739c433ba96f078315de54c0db975aee537cbc3e1d0ae4ed9aab0ca1e427e2c1"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "pytest" version = "8.3.3" @@ -925,11 +785,6 @@ tomli = {version = ">=1", markers = "python_version < \"3.11\""} [package.extras] dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "pytest-cov" version = "5.0.0" @@ -948,11 +803,6 @@ pytest = ">=4.6" [package.extras] testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "requests" version = "2.32.3" @@ -974,11 +824,6 @@ urllib3 = ">=1.21.1,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "six" version = "1.16.0" @@ -990,11 +835,6 @@ files = [ {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "snowballstemmer" version = "2.2.0" @@ -1006,11 +846,6 @@ files = [ {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinx" version = "5.3.0" @@ -1046,11 +881,6 @@ docs = ["sphinxcontrib-websupport"] lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.981)", "sphinx-lint", "types-requests", "types-typed-ast"] test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-applehelp" version = "2.0.0" @@ -1067,11 +897,6 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-devhelp" version = "2.0.0" @@ -1088,11 +913,6 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-htmlhelp" version = "2.1.0" @@ -1109,11 +929,6 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["html5lib", "pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-jsmath" version = "1.0.1" @@ -1128,11 +943,6 @@ files = [ [package.extras] test = ["flake8", "mypy", "pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-qthelp" version = "2.0.0" @@ -1149,11 +959,6 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["defusedxml (>=0.7.1)", "pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "sphinxcontrib-serializinghtml" version = "2.0.0" @@ -1170,11 +975,6 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"] standalone = ["Sphinx (>=5)"] test = ["pytest"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "tomli" version = "2.0.2" @@ -1186,11 +986,6 @@ files = [ {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "tomlkit" version = "0.13.2" @@ -1202,11 +997,6 @@ files = [ {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "typing-extensions" version = "4.12.2" @@ -1218,11 +1008,6 @@ files = [ {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "urllib3" version = "2.2.3" @@ -1240,11 +1025,6 @@ h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "vectormath" version = "0.2.2" @@ -1258,11 +1038,6 @@ files = [ [package.dependencies] numpy = ">=1.7" -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [[package]] name = "zipp" version = "3.20.2" @@ -1282,12 +1057,7 @@ enabler = ["pytest-enabler (>=2.2)"] test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] -[package.source] -type = "legacy" -url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -reference = "jfrog-server" - [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "1053d3ec9f6b00b29d423f97e7d533b087e8a3527b9a9d6e94a9b2bd4aa2dbc4" +content-hash = "3ea1112ac33b5317906d2a43c4d2b76a6f3d820ab353ed4c65561cf942bf5389" diff --git a/pyproject.toml b/pyproject.toml index 23e99ffd..2464b104 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-alpha.1" +version = "3.4.0-alpha.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ @@ -67,14 +67,6 @@ pytest-cov = "*" sphinx = "^5.3" tomli = "*" # for tests only -## about jfrog repository -# change url to have access to other repo (e.g. public-pypi-prod, public-pypi-dev) - -[[tool.poetry.source]] -name = "jfrog-server" -url = 'https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple' -priority = "primary" - [tool.ruff] target-version = "py39" @@ -161,4 +153,4 @@ skip_covered = true [build-system] requires = ["poetry-core>=1.0.0", "setuptools"] -build-backend = "poetry.core.masonry.api" +build-backend = "poetry.core.masonry.api" \ No newline at end of file From 5de866713ab8674144aafaf0a62c7beb088ae2e1 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 9 Oct 2024 13:27:42 -0400 Subject: [PATCH 060/107] [DEVOPS-504] Delete useless line in .gitignore --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index c88128e6..aabfdb04 100644 --- a/.gitignore +++ b/.gitignore @@ -141,4 +141,3 @@ dmypy.json # geoh5 locks *.geoh5.lock -/.jfrog/projects/poetry.yaml From 565b9e2d9ddeca0b1b5e8cbdd94fbe2456c4a853 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 9 Oct 2024 17:28:43 +0000 Subject: [PATCH 061/107] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2464b104..f9ace8a4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -153,4 +153,4 @@ skip_covered = true [build-system] requires = ["poetry-core>=1.0.0", "setuptools"] -build-backend = "poetry.core.masonry.api" \ No newline at end of file +build-backend = "poetry.core.masonry.api" From 373a65e2b870e0affded493619f3f7c86bfa0134 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 10 Oct 2024 11:09:22 -0400 Subject: [PATCH 062/107] [DEVOPS-504] Add source to pyproject --- pyproject.toml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 2464b104..384269a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,6 +67,12 @@ pytest-cov = "*" sphinx = "^5.3" tomli = "*" # for tests only + +[[tool.poetry.source]] +name = "public" +url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" +priority = "supplemental" + [tool.ruff] target-version = "py39" From b4e620b876c743b7c720063db0721cd1574638ac Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 10 Oct 2024 15:09:03 -0400 Subject: [PATCH 063/107] [DEVOPS-504] Update conda's recipe dependencies --- meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/meta.yaml b/meta.yaml index a0984f08..06bad86f 100644 --- a/meta.yaml +++ b/meta.yaml @@ -22,11 +22,11 @@ requirements: run: - python >=3.9.0,<3.11 - numpy >=1.26.0,<1.27.0 - - properties >=0.6.0,<0.7.0 + - properties >=0.6 - pypng 0.20220715.* - - six >=1.16.0,<2.0.0 - - vectormath >=0.2.0,<0.3.0 - - geoh5py >=0.9.1a0.dev0,<0.11.0 + - six >=1.16.0 + - vectormath >=0.2.0 + - geoh5py >=0.9.1a0.dev0,<0.11.0a0.dev0 test: imports: From 2e1ac2740e1d0f981bfdc7dd25ab3b70f736906b Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 10 Oct 2024 15:10:33 -0400 Subject: [PATCH 064/107] [DEVOPS-504] Update github refs --- .github/workflows/python_deploy_dev.yml | 4 ++-- .github/workflows/python_deploy_prod.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 7f219e91..4ba0496d 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -8,7 +8,7 @@ on: jobs: call-workflow-conda-publish: name: Publish development conda package on JFrog Artifactory - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@DEVOPS-504 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@main with: package-name: 'mira-omf' python-version: '3.10' @@ -18,7 +18,7 @@ jobs: JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-publish: name: Publish development pypi package on JFrog Artifactory - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@DEVOPS-504 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main with: package-manager: 'poetry' package-name: 'mira-omf' diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 0663a9ac..8b7da53a 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -7,7 +7,7 @@ on: jobs: call-workflow-conda-publish: name: Publish production conda package on JFrog Artifactory - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@DEVOPS-504 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@main with: package-name: 'mira-omf' python-version: '3.10' @@ -17,7 +17,7 @@ jobs: JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-publish: name: Publish production pypi package on JFrog Artifactory - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@DEVOPS-504 + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main with: package-manager: 'poetry' package-name: 'mira-omf' From 2bba99dec42067626c7180f8460f239540a6fcb0 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 10 Oct 2024 15:18:38 -0400 Subject: [PATCH 065/107] [DEVOPS-504] Disable test part in conda's recipe --- meta.yaml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/meta.yaml b/meta.yaml index 06bad86f..4941be5c 100644 --- a/meta.yaml +++ b/meta.yaml @@ -28,14 +28,6 @@ requirements: - vectormath >=0.2.0 - geoh5py >=0.9.1a0.dev0,<0.11.0a0.dev0 -test: - imports: - - omf - commands: - - pip check - requires: - - pip - about: license: MIT license_file: From 618dcbb5236df9e8c1c6259da84d4fdc9ee8eb19 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 15 Oct 2024 09:13:53 -0400 Subject: [PATCH 066/107] [DEVOPS-504] Generate poetry.lock --- poetry.lock | 128 ++++++++++++++++++++++++------------------------- pyproject.toml | 6 --- 2 files changed, 64 insertions(+), 70 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5f39dc9d..956863c5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -177,73 +177,73 @@ files = [ [[package]] name = "coverage" 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-url = "https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple" -priority = "supplemental" - [tool.ruff] target-version = "py39" From 798012ca58b243c988804ab2a3ba0cf91853dd41 Mon Sep 17 00:00:00 2001 From: dominiquef Date: Tue, 15 Oct 2024 10:56:07 -0700 Subject: [PATCH 067/107] Fix reference to value_map.map --- .pre-commit-config.yaml | 2 +- omf/fileio/geoh5.py | 5 ++++- tests/convert_volume_test.py | 4 ++-- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8bba81c3..0ef3deeb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ default_language_version: python: python3 exclude: ^docs/(conf.py|_ext/) -default_stages: [commit,push] +default_stages: [pre-commit,pre-push] fail_fast: false ci: diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index c4f9ad2c..54d3bcc1 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -685,7 +685,10 @@ def collect_h5_attributes( element: ReferencedData, workspace: str | Workspace | Path, **kwargs ) -> dict: with fetch_h5_handle(workspace): - labels = list(element.value_map.map.values()) + if element.value_map is None: + return kwargs + + labels = list(element.value_map().values()) ind = 0 if "Unknown" in labels: ind = 1 diff --git a/tests/convert_volume_test.py b/tests/convert_volume_test.py index db292c2e..913e9323 100644 --- a/tests/convert_volume_test.py +++ b/tests/convert_volume_test.py @@ -91,8 +91,8 @@ def test_volume_to_geoh5(tmp_path: Path): ref_b = block_model.get_entity("Reference Data 2")[0] assert all( - key in ref_a.value_map.map and value == ref_a.value_map.map[key] - for key, value in ref_b.value_map.map.items() + key in ref_a.value_map() and value == ref_a.value_map()[key] + for key, value in ref_b.value_map().items() ) omf.fileio.utils.compare_elements(converted_omf, vol) From fdd3640c34da31ad331e1457037df42ee55fc1f4 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Wed, 16 Oct 2024 10:57:24 -0400 Subject: [PATCH 068/107] [DEVOPS-504] Update comment in python_deploy_dev --- .github/workflows/python_deploy_dev.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 4ba0496d..1308f14e 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -3,7 +3,7 @@ name: Deploy python package in development on: push: tags: - - 'v*' # Push events to every tag not containing + - 'v*' # Push events to every version tag (eg. v1.0.0) jobs: call-workflow-conda-publish: From 5807b7c790b1ce6a79aaa53d0a5f1156ea7fe4a6 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Wed, 16 Oct 2024 15:34:45 -0400 Subject: [PATCH 069/107] [DEVOPS-515] enough to publish to codecov from one OS --- .github/workflows/python_analysis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_analysis.yml b/.github/workflows/python_analysis.yml index d0124554..9db19bde 100644 --- a/.github/workflows/python_analysis.yml +++ b/.github/workflows/python_analysis.yml @@ -38,6 +38,6 @@ jobs: os: '["ubuntu-latest", "windows-latest"]' cache-number: 1 codecov-reference-python-version: '3.10' - codecov-reference-os: '["windows-latest", "ubuntu-latest"]' + codecov-reference-os: '["windows-latest"]' secrets: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} From 93c83aa7ef7c28643e5ed6300134224a32af4378 Mon Sep 17 00:00:00 2001 From: sebhmg Date: Wed, 16 Oct 2024 15:36:52 -0400 Subject: [PATCH 070/107] [DEVOPS-515] apply pre-commit autoupdate --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0ef3deeb..b4576732 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,7 +22,7 @@ repos: - id: pycln args: [--config=pyproject.toml] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.5 + rev: v0.6.9 hooks: - id: ruff args: @@ -31,7 +31,7 @@ repos: # - --unsafe-fixes - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.11.0 + rev: v1.12.0 hooks: - id: mypy additional_dependencies: [ @@ -43,7 +43,7 @@ repos: files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) exclude: ^docs/ - repo: https://github.com/codingjoe/relint - rev: 3.1.1 + rev: 3.2.0 hooks: - id: relint args: [-W] # to fail on warnings @@ -70,7 +70,7 @@ repos: exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$ entry: codespell -I .codespellignore - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: trailing-whitespace exclude: \.mdj$ From 1c7881d1781dd0a0aea89501a85b1632052b3125 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 17 Oct 2024 08:46:35 -0400 Subject: [PATCH 071/107] [DEVOPS-504] Update omf version --- omf/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/omf/__init__.py b/omf/__init__.py index d72f491a..804cfadf 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-alpha.1" +__version__ = "3.4.0-alpha.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" From da1632eb26f3fa3e49063c6ad4f6df9c335f506d Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Thu, 17 Oct 2024 08:57:06 -0400 Subject: [PATCH 072/107] [DEVOPS-504] Update version in README.rst --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index e7ff1da3..2c746f5b 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-alpha.1 +Version: 3.4.0-alpha.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. From 8221ad0e48fcb37bf76ad04080f8bea36a6fbbaa Mon Sep 17 00:00:00 2001 From: sebhmg Date: Thu, 17 Oct 2024 17:35:14 -0400 Subject: [PATCH 073/107] [DEVOPS-515] restore 3.3.0 alpha version (moved by mistake) --- README.rst | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index 2c746f5b..e7ff1da3 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.4.0-alpha.1 +Version: 3.3.0-alpha.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/meta.yaml b/meta.yaml index 4941be5c..a3da72c5 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.4.0a1" %} +{% set version = "3.3.0a1" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index 804cfadf..d72f491a 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.4.0-alpha.1" +__version__ = "3.3.0-alpha.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index 8d945b4e..bbd39823 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.4.0-alpha.1" +version = "3.3.0-alpha.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From b14395efc343e0d14a3050e9579069c14fa70f9f Mon Sep 17 00:00:00 2001 From: sebhmg Date: Thu, 17 Oct 2024 17:39:38 -0400 Subject: [PATCH 074/107] [DEVOPS-515] apply pre-commit autoupdate --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d2164594..32c89854 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,7 +22,7 @@ repos: - id: pycln args: [--config=pyproject.toml] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.7.0 hooks: - id: ruff args: From 773b1cb85795be90c9b0430f6cd26635c4788d02 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Sun, 20 Oct 2024 19:01:23 -0400 Subject: [PATCH 075/107] [DEVOPS-511] Update deploy workflows to release pip package on pypi (cherry picked from commit 552d0a3abc449e43c8b17863b7c66ab2b5b13260) --- .github/workflows/python_deploy_dev.yml | 3 ++- .github/workflows/python_deploy_prod.yml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 1308f14e..d4dc46ae 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -24,7 +24,8 @@ jobs: package-name: 'mira-omf' version-tag: ${{ github.ref_name }} python-version: '3.10' - virtual-repo-names: '["public-pypi-dev"]' + virtual-repo-names: '["public-pypi-dev", "test-pypi"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + PYPI_TOKEN: ${{ secrets.TEST_PYPI_TOKEN }} diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 8b7da53a..7bd15dab 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -23,7 +23,8 @@ jobs: package-name: 'mira-omf' version-tag: ${{ github.ref_name }} python-version: '3.10' - virtual-repo-names: '["public-pypi-prod"]' + virtual-repo-names: '["public-pypi-prod", "pypi"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} From ae362f00e483ff55bc8b6a7a1cf7419a4068f6f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Wed, 30 Oct 2024 17:57:06 -0400 Subject: [PATCH 076/107] lock on published geoh5py 0.10.0b1 --- poetry.lock | 330 +++++++++++++++++++++---------------------------- pyproject.toml | 4 +- 2 files changed, 144 insertions(+), 190 deletions(-) diff --git a/poetry.lock b/poetry.lock index 02aed1ad..dd29d4a3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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#------------------------------------ -#geoh5py = {version = ">=0.9.1, <0.11", allow-prereleases = true} -geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} +geoh5py = {version = "~0.10.0-alpha.1", allow-prereleases = true} +#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} #geoh5py = {path = "../geoh5py", develop = true} [tool.poetry.group.dev.dependencies] From 273baf9d7226309e20f303090006f93942b2d1d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Wed, 30 Oct 2024 18:19:31 -0400 Subject: [PATCH 077/107] bump version to 3.3.0 alpha.2 --- README.rst | 2 +- docs/conf.py | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index e7ff1da3..098e602d 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-alpha.1 +Version: 3.3.0-alpha.2 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index f9fc9eef..a6b4231a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,7 @@ # The short X.Y version. version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-alpha.1' +release = u'3.3.0-alpha.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml index a3da72c5..e3b61965 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0a1" %} +{% set version = "3.3.0a2" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index d72f491a..9fb21c5d 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-alpha.1" +__version__ = "3.3.0-alpha.2" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index 8ce93088..2a1989c6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-alpha.1" +version = "3.3.0-alpha.2" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 201f8c150d852e4f46d7113014c46e25c1392f3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 31 Oct 2024 12:22:24 -0400 Subject: [PATCH 078/107] change labels of publish tasks --- .github/workflows/python_deploy_dev.yml | 2 +- .github/workflows/python_deploy_prod.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index d4dc46ae..6e5e151d 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -17,7 +17,7 @@ jobs: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-publish: - name: Publish development pypi package on JFrog Artifactory + name: Publish development pypi package (JFrog Artifactory and TestPyPI) uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main with: package-manager: 'poetry' diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 7bd15dab..87bf8d4c 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -16,7 +16,7 @@ jobs: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-publish: - name: Publish production pypi package on JFrog Artifactory + name: Publish production pypi package on (JFrog Artifactory and PyPI) uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main with: package-manager: 'poetry' From 59be20aa9530c401e5df2bc25f195f717bb95ab8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 1 Nov 2024 10:23:59 -0400 Subject: [PATCH 079/107] add concurrency conditions to github publish workflows --- .github/workflows/python_deploy_dev.yml | 4 ++++ .github/workflows/python_deploy_prod.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 6e5e151d..89bcf8d3 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -5,6 +5,10 @@ on: tags: - 'v*' # Push events to every version tag (eg. v1.0.0) +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + jobs: call-workflow-conda-publish: name: Publish development conda package on JFrog Artifactory diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 87bf8d4c..4de7d57a 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -4,6 +4,10 @@ on: release: types: [published] +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + cancel-in-progress: true + jobs: call-workflow-conda-publish: name: Publish production conda package on JFrog Artifactory From a63e3a94775a15d402c7e4971eedbb1aa506857f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 15 Nov 2024 21:58:31 -0500 Subject: [PATCH 080/107] use new publish workflows --- .github/workflows/python_deploy_dev.yml | 2 +- .github/workflows/python_deploy_prod.yml | 36 ++++++++++++++++-------- 2 files changed, 25 insertions(+), 13 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 89bcf8d3..ee32a166 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -6,7 +6,7 @@ on: - 'v*' # Push events to every version tag (eg. v1.0.0) concurrency: - group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + group: ${{ github.workflow }}-${{ github.ref || github.run_id }} cancel-in-progress: true jobs: diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 4de7d57a..27c73b97 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -3,31 +3,43 @@ name: Deploy python package in production on: release: types: [published] + workflow_dispatch: + inputs: + release-tag: + description: 'Tag for the existing (draft) release to publish assets from' + required: true + publish-conda: + description: 'Publish Conda package' + required: false + default: true + publish-pypi: + description: 'Publish PyPI package' + required: false + default: true concurrency: - group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} + group: ${{ github.workflow }}-${{ github.event.release.tag_name || github.event.inputs.release-tag || github.run_id }} cancel-in-progress: true jobs: - call-workflow-conda-publish: - name: Publish production conda package on JFrog Artifactory - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_conda_package.yml@main + call-workflow-conda-release: + name: Publish production Conda package on JFrog Artifactory + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_conda_assets.yml@main + if: ${{ github.event_name == 'release' || github.event.inputs.publish-conda == 'true' }} with: - package-name: 'mira-omf' - python-version: '3.10' virtual-repo-names: '["public-conda-prod"]' + release-tag: ${{ github.event.release.tag_name || github.event.inputs.release-tag }} secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} - call-workflow-pypi-publish: - name: Publish production pypi package on (JFrog Artifactory and PyPI) - uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main + call-workflow-pypi-release: + name: Publish production PyPI package (JFrog Artifactory and PyPI) + if: ${{ github.event_name == 'release' || github.event.inputs.publish-pypi == 'true' }} + uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_pypi_assets.yml@main with: - package-manager: 'poetry' package-name: 'mira-omf' - version-tag: ${{ github.ref_name }} - python-version: '3.10' virtual-repo-names: '["public-pypi-prod", "pypi"]' + release-tag: ${{ github.event.release.tag_name || github.event.inputs.release-tag }} secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} From 50935df48569d1057b3f7bb81d1031f7b598f70a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 15 Nov 2024 22:01:24 -0500 Subject: [PATCH 081/107] relocked on newer published geoh5py --- poetry.lock | 146 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 74 insertions(+), 74 deletions(-) diff --git a/poetry.lock b/poetry.lock index dd29d4a3..3eb20291 100644 --- 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-content-hash = "5935c653adb0aebe58d54c374b9833f4df1f3541ab1b97a568b4d7804303babd" +content-hash = "72cc48eec2e6149606d9df66c2a72bedcfe198896d38e079333cd6ca7144b191" diff --git a/pyproject.toml b/pyproject.toml index 2a1989c6..0fa6186e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ vectormath = "~0.2.0" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = "~0.10.0-alpha.1", allow-prereleases = true} +geoh5py = {version = "~0.10.0-beta.1", allow-prereleases = true} #geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} #geoh5py = {path = "../geoh5py", develop = true} From a8d0ff0dbbfa3dae2e23968853591fff35fc0553 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 15 Nov 2024 22:04:42 -0500 Subject: [PATCH 082/107] bump version to beta.1 --- README.rst | 2 +- docs/conf.py | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 098e602d..66e90972 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-alpha.2 +Version: 3.3.0-beta.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index a6b4231a..1475b540 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,7 @@ # The short X.Y version. version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-alpha.2' +release = u'3.3.0-beta.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml index e3b61965..368e3849 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0a2" %} +{% set version = "3.3.0b1" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index 9fb21c5d..97f1cdeb 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-alpha.2" +__version__ = "3.3.0-beta.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index 0fa6186e..e69e8548 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-alpha.2" +version = "3.3.0-beta.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 950af1636709ce300268e8432272fcebbd0bb9ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 15 Nov 2024 23:34:56 -0500 Subject: [PATCH 083/107] change version specs to >=0.x instead of ~0.x meaning is somewhat unclear, and greyskull rejects it --- meta.yaml | 2 +- poetry.lock | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/meta.yaml b/meta.yaml index 368e3849..61850da8 100644 --- a/meta.yaml +++ b/meta.yaml @@ -26,7 +26,7 @@ requirements: - pypng 0.20220715.* - six >=1.16.0 - vectormath >=0.2.0 - - geoh5py >=0.9.1a0.dev0,<0.11.0a0.dev0 + - geoh5py >=0.9.1a.dev,<0.11.0a.dev about: license: MIT diff --git a/poetry.lock b/poetry.lock index 3eb20291..af29bb3f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1152,4 +1152,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "72cc48eec2e6149606d9df66c2a72bedcfe198896d38e079333cd6ca7144b191" +content-hash = "11a833bc762bbc266e2496a74268ed324e63a541fe70a665b86fe22e160b01d7" diff --git a/pyproject.toml b/pyproject.toml index e69e8548..1f86d3bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ vectormath = "~0.2.0" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = "~0.10.0-beta.1", allow-prereleases = true} +geoh5py = {version = ">=0.10.0-beta.1, <0.11.0a.dev", allow-prereleases = true} #geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} #geoh5py = {path = "../geoh5py", develop = true} From 5144bafa6c72686cb4957ade36ab11cdc67fe28b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 15 Nov 2024 23:37:53 -0500 Subject: [PATCH 084/107] align version spec in conda meta and pyproject.toml --- meta.yaml | 2 +- poetry.lock | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/meta.yaml b/meta.yaml index 61850da8..7a77fa4d 100644 --- a/meta.yaml +++ b/meta.yaml @@ -26,7 +26,7 @@ requirements: - pypng 0.20220715.* - six >=1.16.0 - vectormath >=0.2.0 - - geoh5py >=0.9.1a.dev,<0.11.0a.dev + - geoh5py >=0.10.0b1,<0.11.0a.dev about: license: MIT diff --git a/poetry.lock b/poetry.lock index af29bb3f..0a4f63bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1152,4 +1152,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "11a833bc762bbc266e2496a74268ed324e63a541fe70a665b86fe22e160b01d7" +content-hash = "3a08f336abb650823de5aef811422f66e733d12e662675b340df37307179cab4" diff --git a/pyproject.toml b/pyproject.toml index 1f86d3bf..c135b46b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ vectormath = "~0.2.0" ## dependencies from Git repositories #------------------------------------ -geoh5py = {version = ">=0.10.0-beta.1, <0.11.0a.dev", allow-prereleases = true} +geoh5py = {version = ">=0.10.0b1, <0.11.0a.dev", allow-prereleases = true} #geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"} #geoh5py = {path = "../geoh5py", develop = true} From 6fba672c55525b0b25fb237dcde581cfd52bb851 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Sun, 17 Nov 2024 21:34:08 -0500 Subject: [PATCH 085/107] minor github workflow job renaming --- .github/workflows/python_deploy_dev.yml | 2 +- .github/workflows/python_deploy_prod.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index ee32a166..5c681284 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -21,7 +21,7 @@ jobs: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-publish: - name: Publish development pypi package (JFrog Artifactory and TestPyPI) + name: Publish development pypi package (JFrog Artifactory, TestPyPI) uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-publish_pypi_package.yml@main with: package-manager: 'poetry' diff --git a/.github/workflows/python_deploy_prod.yml b/.github/workflows/python_deploy_prod.yml index 27c73b97..7813ef40 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -33,7 +33,7 @@ jobs: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} call-workflow-pypi-release: - name: Publish production PyPI package (JFrog Artifactory and PyPI) + name: Publish production PyPI package (JFrog Artifactory, PyPI) if: ${{ github.event_name == 'release' || github.event.inputs.publish-pypi == 'true' }} uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-release_pypi_assets.yml@main with: From 32c9a8779bd60f1c3fca0019c99516a662ae03d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Sun, 17 Nov 2024 22:42:10 -0500 Subject: [PATCH 086/107] bump version to beta.2 --- README.rst | 2 +- docs/conf.py | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 66e90972..0b07f53b 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-beta.1 +Version: 3.3.0-beta.2 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index 1475b540..a2ca2f53 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,7 @@ # The short X.Y version. version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-beta.1' +release = u'3.3.0-beta.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml index 7a77fa4d..b56a2170 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0b1" %} +{% set version = "3.3.0b2" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index 97f1cdeb..ab041f45 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-beta.1" +__version__ = "3.3.0-beta.2" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index c135b46b..9c2880b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-beta.1" +version = "3.3.0-beta.2" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 5c4198a41c040796bbbc29cf1ef8d3328576fee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Tue, 19 Nov 2024 12:39:16 -0500 Subject: [PATCH 087/107] do not use ~0.x in version constraints that semantic is ambiguous and not supported by greyskull --- poetry.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0a4f63bc..a5da352d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1152,4 +1152,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "3a08f336abb650823de5aef811422f66e733d12e662675b340df37307179cab4" +content-hash = "220bd5a8f23bd8b20867fb89ca2bc5af2447b06a110bdde45047db9dcc7542a6" diff --git a/pyproject.toml b/pyproject.toml index 9c2880b5..c0ff68f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,10 +48,10 @@ omf_to_geoh5 = 'omf.scripts.omf_to_geoh5:main' python = "^3.10" numpy = "~1.26.0" # also in geoh5py -properties = "~0.6.0" +properties = "0.6.*" pypng = "^0.20220715" six = "^1.16" -vectormath = "~0.2.0" +vectormath = "0.2.*" ## dependencies from Git repositories #------------------------------------ From 398a7d54094a86e872da00288c89dd8ec0e9e792 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Wed, 20 Nov 2024 01:01:12 -0500 Subject: [PATCH 088/107] [GEOPY-1860] do not include top level files in wheels According to Poetry doc: When a wheel is installed, its includes are unpacked straight into the site-packages directory. Pay attention to include top level files and directories with common names like CHANGELOG.md, LICENSE, tests or docs only in sdists and not in wheels. --- pyproject.toml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c0ff68f4..0b7f64b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,12 +32,12 @@ packages = [ ] include = [ - { path = "COPYING", format = ["sdist", "wheel"] }, - { path = "COPYING.LESSER", format = ["sdist", "wheel"] }, - { path = "LICENSE", format = ["sdist", "wheel"] }, - { path = "README.rst", format = ["sdist", "wheel"] }, - { path = "THIRD_PARTY_SOFTWARE.rst", format = ["sdist", "wheel"] }, - { path = "docs/**/THIRD_PARTY_SOFTWARE.rst", format = ["sdist", "wheel"] }, + { path = "COPYING" }, + { path = "COPYING.LESSER" }, + { path = "LICENSE" }, + { path = "README.rst" }, + { path = "THIRD_PARTY_SOFTWARE.rst" }, + { path = "docs/**/THIRD_PARTY_SOFTWARE.rst" }, ] [tool.poetry.scripts] From 023ccfb85af49bc444cb75e3e433adaafe651947 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 28 Nov 2024 22:17:03 -0500 Subject: [PATCH 089/107] fix URL to readthedocs --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 0b07f53b..672e7de0 100644 --- a/README.rst +++ b/README.rst @@ -63,7 +63,7 @@ This library makes use of the `properties `_. -Connection to the geoh5 format makes use of `geoh5py `_ +Connection to the geoh5 format makes use of `geoh5py `_ publicly supported by `Mira Geoscience `_ Installation From 7a628b51cc167db829cf726cf23353ad33387395 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 28 Nov 2024 22:17:23 -0500 Subject: [PATCH 090/107] in conda recipe, allow for Python 3.* --- meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/meta.yaml b/meta.yaml index b56a2170..d32bc215 100644 --- a/meta.yaml +++ b/meta.yaml @@ -15,7 +15,7 @@ build: requirements: host: - - python >=3.10.0,<3.11 + - python >=3.10.0,<4.0.0 - poetry-core >=1.0.0 - setuptools - pip From d9d111bb2144181590245951430df922f1cac7af Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Dec 2024 09:31:26 -0500 Subject: [PATCH 091/107] [DEVOPS-540] Add a version consistency test --- tests/version_test.py | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/tests/version_test.py b/tests/version_test.py index fef69d24..6f7c3725 100644 --- a/tests/version_test.py +++ b/tests/version_test.py @@ -6,11 +6,14 @@ from pathlib import Path import tomli as toml +import yaml +from jinja2 import Template +from packaging.version import Version import omf -def get_version(): +def get_pyproject_version(): path = Path(__file__).resolve().parents[1] / "pyproject.toml" with open(str(path), encoding="utf-8") as file: @@ -19,6 +22,20 @@ def get_version(): return pyproject["tool"]["poetry"]["version"] +def get_conda_recipe_version(): + path = Path(__file__).resolve().parents[1] / "meta.yaml" + + with open(str(path), encoding="utf-8") as file: + content = file.read() + + template = Template(content) + rendered_yaml = template.render() + + recipe = yaml.safe_load(rendered_yaml) + + return recipe["package"]["version"] + + def get_version_in_readme() -> str | None: path = Path(__file__).resolve().parents[1] / "README.rst" @@ -32,7 +49,10 @@ def get_version_in_readme() -> str | None: def test_version_is_consistent(): - assert omf.__version__ == get_version() + assert omf.__version__ == get_pyproject_version() + normalized_conda_version = Version(get_conda_recipe_version()) + normalized_version = Version(omf.__version__) + assert normalized_conda_version == normalized_version def version_base_and_pre() -> tuple[str, str]: From 57c78569806ba88ddc4a1a76e1a2c3112f10748e Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Dec 2024 10:14:17 -0500 Subject: [PATCH 092/107] [DEVOPS-540] Add test dependencies --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 0b7f64b0..eb7bd8f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,6 +65,9 @@ pylint = "*" pytest = "*" pytest-cov = "*" sphinx = "^5.3" +pyyaml = '*' +jinja2 = '*' +packaging = '*' tomli = "*" # for tests only [tool.ruff] From 789c3f2b7dd1cf61ae8b610362c846a0b583f7c5 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Dec 2024 10:17:01 -0500 Subject: [PATCH 093/107] [DEVOPS-540] Lock poetry --- poetry.lock | 470 +++++++++++++++++++++++++++++++--------------------- 1 file changed, 285 insertions(+), 185 deletions(-) diff --git a/poetry.lock b/poetry.lock index a5da352d..6cc93ff2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -24,13 +24,13 @@ files = [ [[package]] name = "astroid" -version = "3.3.5" +version = "3.3.6" description = "An abstract syntax tree for Python with inference support." optional = false python-versions = ">=3.9.0" files = [ 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"sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"}, ] [[package]] @@ -1152,4 +1252,4 @@ numpy = ">=1.7" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "220bd5a8f23bd8b20867fb89ca2bc5af2447b06a110bdde45047db9dcc7542a6" +content-hash = "79edfb3e198b9e9159d3cb8ada4e9722b5d43949b7f0a67884d18f0f4fc36361" From e01eefa18b07d38e5456b20e891c48246689b5d3 Mon Sep 17 00:00:00 2001 From: SophieCurinier Date: Tue, 17 Dec 2024 13:39:01 -0500 Subject: [PATCH 094/107] [DEVOPS-540] Correct mypy config --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 32c89854..930fc1ef 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,6 +39,7 @@ repos: tomli, # to read config from pyproject.toml types-six, types-toml, + types-PyYAML ] files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) exclude: ^docs/ From 8dc0108f020fdfab279f47c30fa9dd0c27fb9ddc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 9 Jan 2025 19:21:36 -0500 Subject: [PATCH 095/107] [GEOPY-1933] update copyright year --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 672e7de0..dac50313 100644 --- a/README.rst +++ b/README.rst @@ -89,7 +89,7 @@ License ^^^^^^^ MIT License -Copyright (c) 2024 Mira Geoscience +Copyright (c) 2025 Mira Geoscience Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 5bd2be706897be4e176c1f864850789f5b4c1581 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 9 Jan 2025 19:14:14 -0500 Subject: [PATCH 096/107] [GEOPY-1935] bump version to rc.1 --- README.rst | 2 +- docs/conf.py | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index dac50313..95c7b8c0 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,7 @@ omf :alt: pytest -Version: 3.3.0-beta.2 +Version: 3.3.0-rc.1 API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/docs/conf.py b/docs/conf.py index a2ca2f53..a720c1e6 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,7 @@ # The short X.Y version. version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-beta.2' +release = u'3.3.0-rc.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml index d32bc215..f9f0702a 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0b2" %} +{% set version = "3.3.0rc1" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index ab041f45..cc5c7b13 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -30,7 +30,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-beta.2" +__version__ = "3.3.0-rc.1" __author__ = "Global Mining Standards and Guidelines Group" __license__ = "MIT License" __copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" diff --git a/pyproject.toml b/pyproject.toml index eb7bd8f4..d32c0416 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-beta.2" +version = "3.3.0-rc.1" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 81ae0d9bc7898ca13abf13860137010b2b221998 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 9 Jan 2025 19:17:35 -0500 Subject: [PATCH 097/107] [GEOPY-1935] relock on newer geoh5py --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6cc93ff2..aa71f3a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. [[package]] name = "alabaster" @@ -305,13 +305,13 @@ test = ["pytest (>=6)"] [[package]] name = "geoh5py" -version = "0.10.0b4" +version = "0.10.0rc1" description = "Python API for geoh5, an open file format for geoscientific data" optional = false python-versions = "<4.0,>=3.10" files = [ - {file = "geoh5py-0.10.0b4-py3-none-any.whl", hash = "sha256:debf979f0e5ef2ac3dee51a50fc44eb3a5eb9ef5ff18d1de7b2fd6b5e76734f6"}, - {file = "geoh5py-0.10.0b4.tar.gz", hash = "sha256:8695cc1b75cb5194729354e9dcd6c67487fc6ecc5aeb12df6c717b20d4fef67f"}, + {file = "geoh5py-0.10.0rc1-py3-none-any.whl", hash = "sha256:50a6b8f52a0dafd9cff1706155c50262d66d193a063822f32837e0e424ead9f2"}, + {file = "geoh5py-0.10.0rc1.tar.gz", hash = "sha256:19d5a89f4d340e937ae6741af086df8ac3048905457dc405dcc60472a24aa1c0"}, ] [package.dependencies] From 71d9d4c36c720d12ece8b0bf97ef7b102dbe38e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 9 Jan 2025 19:25:53 -0500 Subject: [PATCH 098/107] [GEOPY-1935] pecommit autoupdate --- .pre-commit-config.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 930fc1ef..18510fba 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,12 +17,12 @@ repos: - id: poetry-check args: [--lock] - repo: https://github.com/hadialqattan/pycln - rev: v2.4.0 + rev: v2.5.0 hooks: - id: pycln args: [--config=pyproject.toml] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.0 + rev: v0.9.0 hooks: - id: ruff args: @@ -31,7 +31,7 @@ repos: # - --unsafe-fixes - id: ruff-format - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.12.0 + rev: v1.14.1 hooks: - id: mypy additional_dependencies: [ @@ -44,13 +44,13 @@ repos: files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) exclude: ^docs/ - repo: https://github.com/codingjoe/relint - rev: 3.2.0 + rev: 3.3.1 hooks: - id: relint args: [-W] # to fail on warnings files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) - repo: https://github.com/MiraGeoscience/pre-commit-hooks - rev: v1.0.1 + rev: v1.0.2 hooks: # - id: check-copyright # no copyright nor license notice: differ to upstream repo # files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) From 6eac7b4c139fcfe6db094ebffdacd105812dcca9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Thu, 9 Jan 2025 19:41:38 -0500 Subject: [PATCH 099/107] [GEOPY-1935] fix expected error text in test for Python 3.12 --- tests/script_omf_to_geoh5_test.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/script_omf_to_geoh5_test.py b/tests/script_omf_to_geoh5_test.py index 8ea40236..65d4bb79 100644 --- a/tests/script_omf_to_geoh5_test.py +++ b/tests/script_omf_to_geoh5_test.py @@ -1,3 +1,4 @@ +import re from pathlib import Path from unittest.mock import patch @@ -144,7 +145,4 @@ def test_omf_to_geoh5_with_gzip_level_too_high(capsys, tmp_path: Path): assert not output_path.exists() assert captured_exception.value.code == 2 captured_err = capsys.readouterr().err - assert any( - "error: argument --gzip: invalid choice: 10" in line - for line in captured_err.splitlines() - ) + assert re.search(r"error: argument --gzip: invalid choice:", captured_err) From 9e7c58eb1b34a69924a30f4a19dbe78d626f5792 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 10 Jan 2025 00:01:01 -0500 Subject: [PATCH 100/107] [GEOPY-1933] configure and add copyrights statements --- .idea/copyright/GMG.xml | 8 ++++++++ .idea/copyright/MiraGeoscience.xml | 8 ++++++++ .idea/copyright/profiles_settings.xml | 21 +++++++++++++++++++++ .idea/scopes/sources.xml | 4 ++-- .pre-commit-config.yaml | 25 +++++++++++++++++++++++-- LICENSE | 1 + README.rst | 3 ++- omf/__init__.py | 10 ++++++++++ omf/base.py | 10 ++++++++++ omf/data.py | 10 ++++++++++ omf/fileio/__init__.py | 10 ++++++++++ omf/fileio/fileio.py | 10 ++++++++++ omf/fileio/geoh5.py | 10 ++++++++++ omf/fileio/utils.py | 10 ++++++++++ omf/lineset.py | 10 ++++++++++ omf/pointset.py | 10 ++++++++++ omf/scripts/__init__.py | 9 +++++++++ omf/scripts/geoh5_to_omf.py | 10 ++++++++++ omf/scripts/omf_to_geoh5.py | 10 ++++++++++ omf/serializers.py | 10 ++++++++++ omf/surface.py | 10 ++++++++++ omf/texture.py | 10 ++++++++++ omf/volume.py | 10 ++++++++++ tests/__init__.py | 9 +++++++++ tests/conftest.py | 10 ++++++++++ tests/convert_curve_test.py | 10 ++++++++++ tests/convert_grid2d_test.py | 10 ++++++++++ tests/convert_pointset_test.py | 10 ++++++++++ tests/convert_project_test.py | 10 ++++++++++ tests/convert_surface_test.py | 10 ++++++++++ tests/convert_volume_test.py | 10 ++++++++++ tests/doc_example_test.py | 10 ++++++++++ tests/script_geoh5_to_omf_test.py | 10 ++++++++++ tests/script_omf_to_geoh5_test.py | 10 ++++++++++ tests/version_test.py | 10 ++++++++++ 35 files changed, 343 insertions(+), 5 deletions(-) create mode 100644 .idea/copyright/GMG.xml create mode 100644 .idea/copyright/MiraGeoscience.xml create mode 100644 .idea/copyright/profiles_settings.xml diff --git a/.idea/copyright/GMG.xml b/.idea/copyright/GMG.xml new file mode 100644 index 00000000..f32445b3 --- /dev/null +++ b/.idea/copyright/GMG.xml @@ -0,0 +1,8 @@ + + + + \ No newline at end of file diff --git a/.idea/copyright/MiraGeoscience.xml b/.idea/copyright/MiraGeoscience.xml new file mode 100644 index 00000000..2d6a4985 --- /dev/null +++ b/.idea/copyright/MiraGeoscience.xml @@ -0,0 +1,8 @@ + + + + \ No newline at end of file diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml new file mode 100644 index 00000000..d2e98418 --- /dev/null +++ b/.idea/copyright/profiles_settings.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/scopes/sources.xml b/.idea/scopes/sources.xml index ac2cbbb6..f4755295 100644 --- a/.idea/scopes/sources.xml +++ b/.idea/scopes/sources.xml @@ -1,3 +1,3 @@ - - + + \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 18510fba..01c4a45b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -52,9 +52,30 @@ repos: - repo: https://github.com/MiraGeoscience/pre-commit-hooks rev: v1.0.2 hooks: -# - id: check-copyright # no copyright nor license notice: differ to upstream repo -# files: ^(omf/fileio/geoh5\.py$|omf/scripts/|tests/) + - id: check-copyright + files: (^package\.rst|^LICENSE|^README(|-dev)\.rst|\.py|\.pyi)$ + # do not check sources from the original omf package + exclude: | + (?x)( + ^\.| + ^docs/| + omf/( + fileio/__init__| + fileio/fileio| + fileio/utils| + __init__| + base| + data| + lineset| + pointset| + serializers| + surface| + texture| + volume).py| + tests/doc_example_test.py + )$ - id: prepare-commit-msg + - id: check-commit-msg - repo: local hooks: - id: pylint diff --git a/LICENSE b/LICENSE index 79729d2b..3833ab50 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,7 @@ MIT License Copyright (c) 2017 Global Mining Standards and Guidelines Group +Copyright (c) 2022-2025 Mira Geoscience Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.rst b/README.rst index 95c7b8c0..7d7187c8 100644 --- a/README.rst +++ b/README.rst @@ -89,7 +89,8 @@ License ^^^^^^^ MIT License -Copyright (c) 2025 Mira Geoscience +Copyright (c) 2017 Global Mining Standards and Guidelines Group +Copyright (c) 2022-2025 Mira Geoscience Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/omf/__init__.py b/omf/__init__.py index cc5c7b13..0ce739b5 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -1,5 +1,15 @@ """omf: API library for Open Mining Format file interchange format""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import logging import sys diff --git a/omf/base.py b/omf/base.py index 983da60c..b1a76611 100644 --- a/omf/base.py +++ b/omf/base.py @@ -1,5 +1,15 @@ """base.py: OMF Project and base classes for its components""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from __future__ import annotations import datetime diff --git a/omf/data.py b/omf/data.py index 5d41a45f..3cd34a28 100644 --- a/omf/data.py +++ b/omf/data.py @@ -1,5 +1,15 @@ """data.py: different ProjectElementData classes""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import numpy as np import properties diff --git a/omf/fileio/__init__.py b/omf/fileio/__init__.py index ac53c272..0e87312f 100644 --- a/omf/fileio/__init__.py +++ b/omf/fileio/__init__.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from .fileio import OMFReader, OMFWriter from .geoh5 import GeoH5Writer from .utils import compare_elements diff --git a/omf/fileio/fileio.py b/omf/fileio/fileio.py index 0ad7dd13..bd214e95 100644 --- a/omf/fileio/fileio.py +++ b/omf/fileio/fileio.py @@ -1,5 +1,15 @@ """fileio.py: OMF Writer and Reader for serializing to and from .omf files""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from __future__ import annotations import json diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 54d3bcc1..3e40652d 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + # pylint: disable=too-many-lines from __future__ import annotations diff --git a/omf/fileio/utils.py b/omf/fileio/utils.py index 54f76d1e..c1128530 100644 --- a/omf/fileio/utils.py +++ b/omf/fileio/utils.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from numpy import testing diff --git a/omf/lineset.py b/omf/lineset.py index d40c81d9..eb90d340 100644 --- a/omf/lineset.py +++ b/omf/lineset.py @@ -1,5 +1,15 @@ """lineset.py: LineSet element and geometry""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import numpy as np import properties diff --git a/omf/pointset.py b/omf/pointset.py index 64f4c140..e957a5ee 100644 --- a/omf/pointset.py +++ b/omf/pointset.py @@ -1,5 +1,15 @@ """pointset.py: PointSet element and geometry""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import properties from .base import ProjectElement, ProjectElementGeometry diff --git a/omf/scripts/__init__.py b/omf/scripts/__init__.py index e69de29b..d8b6fd73 100644 --- a/omf/scripts/__init__.py +++ b/omf/scripts/__init__.py @@ -0,0 +1,9 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' diff --git a/omf/scripts/geoh5_to_omf.py b/omf/scripts/geoh5_to_omf.py index c58bcb67..a9412926 100644 --- a/omf/scripts/geoh5_to_omf.py +++ b/omf/scripts/geoh5_to_omf.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import argparse import logging import sys diff --git a/omf/scripts/omf_to_geoh5.py b/omf/scripts/omf_to_geoh5.py index f710ed5b..a0e285df 100644 --- a/omf/scripts/omf_to_geoh5.py +++ b/omf/scripts/omf_to_geoh5.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import argparse import logging import sys diff --git a/omf/serializers.py b/omf/serializers.py index 99c9998d..3715d52d 100644 --- a/omf/serializers.py +++ b/omf/serializers.py @@ -1,5 +1,15 @@ """serializers.py: array and image serializers/deserializers for OMF file IO""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import zlib from io import BytesIO diff --git a/omf/surface.py b/omf/surface.py index 7f3e0aac..cea30fac 100644 --- a/omf/surface.py +++ b/omf/surface.py @@ -1,5 +1,15 @@ """surface.py: Surface element and geometry""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import numpy as np import properties diff --git a/omf/texture.py b/omf/texture.py index 631406c7..8f00c902 100644 --- a/omf/texture.py +++ b/omf/texture.py @@ -1,5 +1,15 @@ """texture.py: contains ImageTexture definition""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import properties from .base import ContentModel diff --git a/omf/volume.py b/omf/volume.py index d399e47e..8982fb14 100644 --- a/omf/volume.py +++ b/omf/volume.py @@ -1,5 +1,15 @@ """volume.py: Volume element and geometry""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import numpy as np import properties diff --git a/tests/__init__.py b/tests/__init__.py index e69de29b..d8b6fd73 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,9 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' diff --git a/tests/conftest.py b/tests/conftest.py index 088d863b..4d71bdda 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import numpy as np diff --git a/tests/convert_curve_test.py b/tests/convert_curve_test.py index bba8f5a3..4094a1c3 100644 --- a/tests/convert_curve_test.py +++ b/tests/convert_curve_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import numpy as np diff --git a/tests/convert_grid2d_test.py b/tests/convert_grid2d_test.py index 0975ba14..219eff30 100644 --- a/tests/convert_grid2d_test.py +++ b/tests/convert_grid2d_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import logging from pathlib import Path diff --git a/tests/convert_pointset_test.py b/tests/convert_pointset_test.py index bbc259bc..3ca2cb98 100644 --- a/tests/convert_pointset_test.py +++ b/tests/convert_pointset_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import numpy as np diff --git a/tests/convert_project_test.py b/tests/convert_project_test.py index 586d12f7..2feca2fc 100644 --- a/tests/convert_project_test.py +++ b/tests/convert_project_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import logging import os from pathlib import Path diff --git a/tests/convert_surface_test.py b/tests/convert_surface_test.py index 0b33e6eb..407df7c9 100644 --- a/tests/convert_surface_test.py +++ b/tests/convert_surface_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import numpy as np diff --git a/tests/convert_volume_test.py b/tests/convert_volume_test.py index 913e9323..b0a887d4 100644 --- a/tests/convert_volume_test.py +++ b/tests/convert_volume_test.py @@ -1,5 +1,15 @@ """Tests for PointSet validation""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import numpy as np diff --git a/tests/doc_example_test.py b/tests/doc_example_test.py index 4374b72f..6131451f 100644 --- a/tests/doc_example_test.py +++ b/tests/doc_example_test.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path import omf diff --git a/tests/script_geoh5_to_omf_test.py b/tests/script_geoh5_to_omf_test.py index e21705fb..8c6c200f 100644 --- a/tests/script_geoh5_to_omf_test.py +++ b/tests/script_geoh5_to_omf_test.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from pathlib import Path from unittest.mock import patch diff --git a/tests/script_omf_to_geoh5_test.py b/tests/script_omf_to_geoh5_test.py index 65d4bb79..159607cf 100644 --- a/tests/script_omf_to_geoh5_test.py +++ b/tests/script_omf_to_geoh5_test.py @@ -1,3 +1,13 @@ +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import re from pathlib import Path from unittest.mock import patch diff --git a/tests/version_test.py b/tests/version_test.py index 6f7c3725..571408d8 100644 --- a/tests/version_test.py +++ b/tests/version_test.py @@ -1,5 +1,15 @@ """Test the version follows SemVer and is consistent across files.""" +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2025 Mira Geoscience Ltd. ' +# ' +# This file is part of mira-omf package. ' +# ' +# mira-omf is distributed under the terms and conditions of the MIT License ' +# (see LICENSE file at the root of this source code package). ' +# ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + from __future__ import annotations import re From 2e5a1b86b4e21aa4a7b7f75f8f985cc4b23ba709 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 10 Jan 2025 00:08:32 -0500 Subject: [PATCH 101/107] [GEOPY-1933] dual copyright in __init__.py --- .pre-commit-config.yaml | 1 - omf/__init__.py | 10 ++++++++-- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 01c4a45b..97e94612 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -63,7 +63,6 @@ repos: fileio/__init__| fileio/fileio| fileio/utils| - __init__| base| data| lineset| diff --git a/omf/__init__.py b/omf/__init__.py index 0ce739b5..c9ead514 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -2,6 +2,9 @@ # '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' # Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2022-2025 Mira Geoscience Ltd. ' # ' # This file is part of mira-omf package. ' # ' @@ -41,9 +44,12 @@ __version__ = "3.3.0-rc.1" -__author__ = "Global Mining Standards and Guidelines Group" +__author__ = "Global Mining Standards and Guidelines Group, Mira Geoscience Ltd." __license__ = "MIT License" -__copyright__ = "Copyright 2017 Global Mining Standards and Guidelines Group" +__copyright__ = ( + "Copyright 2017 Global Mining Standards and Guidelines Group, " + "Copyright 2022-2025 Mira Geoscience Ltd." +) def _create_logger(): From ddb77e4a342a75e3397fbc5c24533d999cf73cc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 10 Jan 2025 00:31:53 -0500 Subject: [PATCH 102/107] [GEOPY-1933] dual copyright in __init__.py --- .idea/copyright/profiles_settings.xml | 2 +- omf/__init__.py | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml index d2e98418..0313fd03 100644 --- a/.idea/copyright/profiles_settings.xml +++ b/.idea/copyright/profiles_settings.xml @@ -1,5 +1,5 @@ - + diff --git a/omf/__init__.py b/omf/__init__.py index c9ead514..b17ec295 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -1,8 +1,5 @@ """omf: API library for Open Mining Format file interchange format""" -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' -# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' # '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' # Copyright (c) 2022-2025 Mira Geoscience Ltd. ' # ' @@ -13,6 +10,10 @@ # ' # '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' +# Copyright (c) 2017 Global Mining Standards and Guidelines Group ' +# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + import logging import sys From 1c8e039ef678b75eef98aeb54ae8aedc189e6238 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 10 Jan 2025 00:32:28 -0500 Subject: [PATCH 103/107] [GEOPY-1933] copyright date range: since 2022 --- omf/fileio/geoh5.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/omf/fileio/geoh5.py b/omf/fileio/geoh5.py index 3e40652d..143525fa 100644 --- a/omf/fileio/geoh5.py +++ b/omf/fileio/geoh5.py @@ -1,5 +1,5 @@ # '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -# Copyright (c) 2025 Mira Geoscience Ltd. ' +# Copyright (c) 2022-2025 Mira Geoscience Ltd. ' # ' # This file is part of mira-omf package. ' # ' From 8c2dd42388cbd3f3cfc2f387e0bad16d1d951970 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 10 Jan 2025 01:00:24 -0500 Subject: [PATCH 104/107] [GEOPY-1933] fix file exclusion for copyright check --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 97e94612..4dc9ef07 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -57,8 +57,8 @@ repos: # do not check sources from the original omf package exclude: | (?x)( - ^\.| - ^docs/| + ^\..*| + ^docs/.*| omf/( fileio/__init__| fileio/fileio| @@ -70,8 +70,8 @@ repos: serializers| surface| texture| - volume).py| - tests/doc_example_test.py + volume)\.py| + tests/doc_example_test\.py )$ - id: prepare-commit-msg - id: check-commit-msg From 9f050f0666d22d58ffda5df392a6f857c8035992 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 7 Feb 2025 22:53:33 -0500 Subject: [PATCH 105/107] official 3.3.0 version --- docs/conf.py | 2 +- meta.yaml | 2 +- omf/__init__.py | 2 +- pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index a720c1e6..e8621612 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,7 +64,7 @@ # The short X.Y version. version = u'3.3.0' # The full version, including alpha/beta/rc tags. -release = u'3.3.0-rc.1' +release = u'3.3.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/meta.yaml b/meta.yaml index f9f0702a..b834419f 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-omf" %} -{% set version = "3.3.0rc1" %} +{% set version = "3.3.0" %} package: name: {{ name|lower }} diff --git a/omf/__init__.py b/omf/__init__.py index b17ec295..f7328d6b 100644 --- a/omf/__init__.py +++ b/omf/__init__.py @@ -44,7 +44,7 @@ from .volume import VolumeElement, VolumeGridGeometry -__version__ = "3.3.0-rc.1" +__version__ = "3.3.0" __author__ = "Global Mining Standards and Guidelines Group, Mira Geoscience Ltd." __license__ = "MIT License" __copyright__ = ( diff --git a/pyproject.toml b/pyproject.toml index d32c0416..04693982 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "mira-omf" -version = "3.3.0-rc.1" +version = "3.3.0" description = "API Library for Open Mining Format" license = "MIT" authors = [ From 6cb3a4ebd8c8e72e3a5cf4f8a07b7deef1158c44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 7 Feb 2025 22:55:00 -0500 Subject: [PATCH 106/107] relock on newer geoh5py --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index aa71f3a4..ba4dc764 100644 --- a/poetry.lock +++ b/poetry.lock @@ -305,13 +305,13 @@ test = ["pytest (>=6)"] [[package]] name = "geoh5py" -version = "0.10.0rc1" +version = "0.10.1rc1" description = "Python API for geoh5, an open file format for geoscientific data" optional = false python-versions = "<4.0,>=3.10" files = [ - {file = "geoh5py-0.10.0rc1-py3-none-any.whl", hash = "sha256:50a6b8f52a0dafd9cff1706155c50262d66d193a063822f32837e0e424ead9f2"}, - {file = "geoh5py-0.10.0rc1.tar.gz", hash = "sha256:19d5a89f4d340e937ae6741af086df8ac3048905457dc405dcc60472a24aa1c0"}, + {file = "geoh5py-0.10.1rc1-py3-none-any.whl", hash = "sha256:17a94dabab81e686d3f8638c9f56573ae6d86dc699cf137a9b4b9d89f873ee25"}, + {file = "geoh5py-0.10.1rc1.tar.gz", hash = "sha256:f45d85b03acc5456fc78fa63dac423f92a82d9a8dce6fd5c1935da59d99d0993"}, ] [package.dependencies] From 8215583217fb5c5e93e5514d9912c8c67d2bec5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Hensgen?= Date: Fri, 7 Feb 2025 23:02:06 -0500 Subject: [PATCH 107/107] remove version from README one less place to update when version changes And whether Readme is looked at from github or from pip, the version information is already exposed. --- README.rst | 2 -- tests/version_test.py | 22 ---------------------- 2 files changed, 24 deletions(-) diff --git a/README.rst b/README.rst index 7d7187c8..415632cb 100644 --- a/README.rst +++ b/README.rst @@ -18,8 +18,6 @@ omf :alt: pytest -Version: 3.3.0-rc.1 - API library for Open Mining Format, a new standard for mining data backed by the `Global Mining Standards & Guidelines Group `_. diff --git a/tests/version_test.py b/tests/version_test.py index 571408d8..84f1f176 100644 --- a/tests/version_test.py +++ b/tests/version_test.py @@ -46,18 +46,6 @@ def get_conda_recipe_version(): return recipe["package"]["version"] -def get_version_in_readme() -> str | None: - path = Path(__file__).resolve().parents[1] / "README.rst" - - version_re = r"^\s*Version:\s*(\S*)\s*$" - with open(str(path), encoding="utf-8") as file: - for line in file: - match = re.match(version_re, line) - if match: - return match[1] - return None - - def test_version_is_consistent(): assert omf.__version__ == get_pyproject_version() normalized_conda_version = Version(get_conda_recipe_version()) @@ -76,16 +64,6 @@ def version_base_and_pre() -> tuple[str, str]: return match[1], match[2] -def test_version_in_readme(): - version_base, prerelease = version_base_and_pre() - version_readme = get_version_in_readme() - assert version_readme is not None - if prerelease is not None and prerelease.startswith("-rc."): - assert version_readme in [omf.__version__, version_base] - else: - assert version_readme == omf.__version__ - - def test_version_is_semver(): semver_re = ( r"^(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)"