Merge pull request #31 from MiraGeoscience/release/3.0.0

Release/3.0.0

.bumpversion.cfg

@@ -1,4 +1,3 @@
 [bumpversion]
-current_version = 0.9.0
-files = omf/__init__.py setup.py README.rst
-
+current_version = 0.9.3
+files = omf/__init__.py setup.py README.rst docs/conf.py

.codespellignore

@@ -0,0 +1,2 @@
+ba
+nd

.coveragerc

@@ -0,0 +1 @@
+[run]

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503
+max-line-length = 80
+max-complexity = 16
+select = B,C,E,F,W,T4,B9

.gitattributes

@@ -0,0 +1,8 @@
+# can only push Git LFS objects to public forks if the repository network already has Git LFS objects
+# or you have write access to the root of the repository network.
+# (from https://docs.github.com/en/repositories/working-with-files/managing-large-files/collaboration-with-git-large-file-storage)
+#
+#*.pt filter=lfs diff=lfs merge=lfs -text
+#*.geoh5 filter=lfs diff=lfs merge=lfs -text
+#/assets/** filter=lfs diff=lfs merge=lfs -text
+#*.h5 filter=lfs diff=lfs merge=lfs -text

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/issue_to_jira.yml

@@ -0,0 +1,36 @@
+# This workflow will create a JIRA issue upon creation of a GitHub issue
+
+name: Create JIRA issue
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  new_jira_issue:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: JIRA Login
+      uses: atlassian/[email protected]
+      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/[email protected]
+      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@v2
+      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."

.github/workflows/pr_add_jira_summary.yml

@@ -0,0 +1,50 @@
+# 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:
+  pull_request_target:
+    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 -os "\b\(GA\|GEOPY\)-[0-9]\+" | head -n1)" >> $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')" >> $GITHUB_OUTPUT
+    - name: Add comment
+      if: ${{ steps.find_jira_key.outputs.issue_key }}
+      env:
+        ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }}
+        PR_BODY: ${{ github.event.pull_request.body }}
+      run: >
+        jq
+        --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}"
+        --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)"
+        --arg PR_BODY "$(cat <<< $PR_BODY)"
+        -c '."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

.github/workflows/pytest-unix-os.yml

@@ -0,0 +1,65 @@
+name: pytest on Unix OS
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+  push:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+
+env:
+  source_dir: omf
+
+jobs:
+  pytest:
+    name: pytest (Unix)
+    strategy:
+      fail-fast: false
+      matrix:
+        python_ver: ['3.8', '3.9', '3.10']
+        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-report=xml --cov=${source_dir} --cov-branch --cov-fail-under=79

.github/workflows/pytest-windows.yml

@@ -0,0 +1,69 @@
+name: pytest on Windows
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+  push:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+
+env:
+  source_dir: omf
+
+jobs:
+  pytest:
+    name: pytest (Windows)
+    strategy:
+      fail-fast: false
+      matrix:
+        python_ver: ['3.8', '3.9', '3.10']
+    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-report=xml --cov=${source_dir} --cov-branch --cov-fail-under=79
+      - name: Codecov
+        if: ${{ success() && matrix.python_ver == '3.10' }}
+        uses: codecov/codecov-action@v3
+        with:
+          name: GitHub

.github/workflows/static-analysis.yml

@@ -0,0 +1,73 @@
+name: static analysis
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+  push:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+
+env:
+  source_dir: omf
+
+jobs:
+  pylint:
+    name: pylint
+    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: '3.10'
+      - 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