diff --git a/.github/workflows/python_deploy_dev.yml b/.github/workflows/python_deploy_dev.yml index 96c85b8..74d9100 100644 --- a/.github/workflows/python_deploy_dev.yml +++ b/.github/workflows/python_deploy_dev.yml @@ -12,7 +12,7 @@ jobs: with: package-name: 'peak-finder-app' 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: 'peak-finder-app' 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 713f1b8..b93bdee 100644 --- a/.github/workflows/python_deploy_prod.yml +++ b/.github/workflows/python_deploy_prod.yml @@ -2,28 +2,28 @@ 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: 'peak-finder-app' 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 }} call-workflow-pypi-publish: - name: Publish development pypi package on JFrog Artifactory + 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: 'peak-finder-app' version-tag: ${{ github.ref_name }} python-version: '3.10' - virtual-repo-name: 'public-pypi-dev' + virtual-repo-names: '["public-pypi-prod"]' secrets: JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }} JFROG_ARTIFACTORY_TOKEN: ${{ secrets.JFROG_ARTIFACTORY_TOKEN }} diff --git a/.gitignore b/.gitignore index 86b7480..052dc93 100644 --- a/.gitignore +++ b/.gitignore @@ -144,4 +144,3 @@ dmypy.json # tempory generated files pyproject-sha.toml -/.jfrog/projects/poetry.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 34845f8..ca2230e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -74,6 +74,7 @@ repos: exclude_types: [jupyter] - id: check-toml - id: check-yaml + exclude: ^meta.yaml$ # - id: check-added-large-files # crashing on some configuration. To be investigated - id: check-case-conflict - id: check-merge-conflict diff --git a/meta.yaml b/meta.yaml index 58eecf5..3c66ca2 100644 --- a/meta.yaml +++ b/meta.yaml @@ -6,8 +6,6 @@ package: version: {{ version }} source: - # url: https://github.com/MiraGeoscience/{{ name }}/archive/v{{ version }}.tar.gz - # sha256: 926956a113b9af644a6a599bfad166ba228683dff98b86abbce6282765ceac5d path: ../{{ name }} build: diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 196e5c0..0000000 --- a/poetry.lock +++ /dev/null @@ -1,2654 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - -[[package]] -name = "alabaster" -version = "0.7.16" -description = "A light, configurable Sphinx theme" -optional = false -python-versions = ">=3.9" -files = [ - {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, - {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 = "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.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" -description = "An abstract syntax tree for Python with inference support." -optional = false -python-versions = ">=3.9.0" -files = [ - {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 = "2.16.0" -description = "Internationalization utilities" -optional = false -python-versions = ">=3.8" -files = [ - {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 = "blinker" -version = "1.8.2" -description = "Fast, simple object-to-object and broadcast signaling" -optional = true -python-versions = ">=3.8" -files = [ - {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, - {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, -] - -[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" -description = "Python package for providing Mozilla's CA Bundle." -optional = false -python-versions = ">=3.6" -files = [ - {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" -description = "The Real First Universal Charset Detector. 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-[extras] -dash = ["dash", "dash-daq", "flask", "pyqt5-qt5", "pyqtwebengine", "pyqtwebengine-qt5", "pyside2"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.10, <3.11" -content-hash = "60f5027bb473271007f7afdc244c0b72ad99d206a9902657a791a5bbadae2817" diff --git a/pyproject.toml b/pyproject.toml index e5c43a4..6b33302 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,166 +1,193 @@ -[build-system] -build-backend = 'poetry.core.masonry.api' -requires = ['poetry-core>=1.0.0', 'setuptools'] - -[tool] -[tool.conda-lock] -channels = ['conda-forge'] -platforms = ['win-64', 'linux-64'] - -[tool.conda-lock.dependencies] -h5py = '>=3.2.1, <4.0.0' -pillow = '>=10.3.0, <10.4.0' -pydantic = '>=2.5.2, <3.0.0' -scikit-image = '>=0.20.0, <0.21.0' - -[tool.conda-lock.dependencies.pyside2] -optional = true -version = '5.15.*' - -[tool.coverage] -[tool.coverage.html] -skip_covered = true -skip_empty = true - -[tool.coverage.report] -exclude_lines = ['raise NotImplementedError', 'pass', 'if TYPE_CHECKING', 'pragma: no cover'] -fail_under = 75 - -[tool.coverage.run] -branch = true -source = ['peak_finder'] - -[tool.mypy] -check_untyped_defs = true -ignore_missing_imports = true -plugins = [] -scripts_are_modules = true -show_column_numbers = true -show_error_context = true -warn_unused_configs = true - [tool.poetry] -authors = ['Mira Geoscience '] -classifiers = ['Development Status :: 3 - Alpha', 'Intended Audience :: Science/Research', 'Programming Language :: Python', 'Topic :: Scientific/Engineering', 'Topic :: Scientific/Engineering :: Mathematics', 'Topic :: Scientific/Engineering :: Physics', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Operating System :: Unix', 'Natural Language :: English'] -description = 'Peak Finder App' -documentation = 'https://mirageoscience-peak-finder-app.readthedocs-hosted.com/' -homepage = 'https://www.mirageoscience.com/mining-industry-software/python-integration/' -license = 'MIT' -maintainers = ['Dominique Fournier '] -name = 'peak-finder-app' -readme = 'README.rst' -repository = 'https://github.com/MiraGeoscience/peak-finder-app' -version = '0.2.0-alpha.1' +name = "peak-finder-app" +version = "0.2.0-alpha.1" +license = "MIT" +description = "Peak Finder App" +authors = ["Mira Geoscience "] +maintainers = ["Dominique Fournier "] +repository = "https://github.com/MiraGeoscience/peak-finder-app" +documentation = "https://mirageoscience-peak-finder-app.readthedocs-hosted.com/" +homepage = "https://www.mirageoscience.com/mining-industry-software/python-integration/" + +readme = "README.rst" +packages = [ + { include = "peak_finder" }, + { include = "peak_finder-assets" }, +] + +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"] }, +] + +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "Programming Language :: Python", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Mathematics", + "Topic :: Scientific/Engineering :: Physics", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX", + "Operating System :: Unix", + "Natural Language :: English", +] [tool.poetry.dependencies] -distributed = '2024.6.*' -numpy = '~1.26.0' -plotly = '~5.19.0' -python = '^3.10, <3.11' -scipy = '~1.14.0' -tqdm = '^4.66.1' - -[tool.poetry.dependencies.curve-apps] -allow-prereleases = true -version = '>=0.2.0-alpha0.dev0, <=0.3.0' - -[tool.poetry.dependencies.dash] -optional = true -version = '^2.12' - -[tool.poetry.dependencies.dash-daq] -optional = true -version = '~0.5.0' - -[tool.poetry.dependencies.dask] -extras = ['distributed'] -version = '2024.6.*' - -[tool.poetry.dependencies.flask] -optional = true -version = '^3.0.3' - -[tool.poetry.dependencies.geoapps-utils] -allow-prereleases = true -version = '>=0.4.0-alpha0.dev0, <0.5.0' - -[tool.poetry.dependencies.geoh5py] -allow-prereleases = true -version = '>=0.10.0-alpha0.dev0, <0.11.0' +python = "^3.10, <3.11" # limited to 3.10 because of geoapps-utils (due to PySide2) + +dash = {version="^2.12", optional = true} +dash-daq = {version="~0.5.0", optional = true} +dask = {version = "2024.6.*", extras = ["distributed"]} +distributed = "2024.6.*" # because conda-lock doesn't take dask extras into account +flask = {version="^3.0.3", optional = true} +numpy = "~1.26.0" # also in geoapps-utils, geoh5py +plotly = "~5.19.0" +pyqtwebengine = {version = "~5.15.2, <5.15.7", optional = true} +pyside2 = {version = "~5.15.2.1", optional = true} +scipy = "~1.14.0" +tqdm = "^4.66.1" + +## Pip dependencies from Git repositories +#---------------------------------------- +geoh5py = {version = "~0.10.0-alpha.1", allow-prereleases = true} # also in geoapps-utils +#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "develop"} + +geoapps-utils = {version = "~0.4.0-alpha.1", allow-prereleases = true} +#geoapps-utils = {git = "https://github.com/MiraGeoscience/geoapps-utils.git", rev = "develop"} + +curve-apps = {version = "~0.2.0-alpha.1", allow-prereleases = true} +#curve-apps = {git = "https://github.com/MiraGeoscience/curve-apps.git", rev = "develop"} + +## force some versions to resolve incompatible resolution between PyPI and Conda +#------------------------------------------------------------------------------- +# these two *-qt5 dependencies are not relevant for Conda and will be discarded, +# but conda-lock still look for them in PyPI during its dependency resolution +pyqt5-qt5 = {version="5.15.2", source = "pypi", optional=true} # to avoid conda-lock resolving to a dependency version not available on PyPI +pyqtwebengine-qt5 = {version="5.15.2", source = "pypi", optional=true} # to avoid conda-lock resolving to a dependency version not available on PyPI + +## about pip dependencies +# to be specified to work with conda-lock +# - from PyPI: my_package = { version = "1.2.3", source = "pypi" } +# - from URL: !!! no actual lock, as tag or branch can move and installation will fetch current !!! +# - for a tag: my_package = { url = "https://github.com/ORGANISATION/REPO/archive/refs/tags/TAG.tar.gz" } +# - for a branch: my_package = { url = "https://github.com/ORGANISATION/REPO/archive/refs/heads/BRANCH.tar.gz" } +# - to actually lock on a revision: my_package = { git = "https://github.com/ORGANISATION/REPO.git", rev = "GIT_REV" } +# (where rev value is a tag, a branch name or a commit hash). Can also use ``branch`` or ``tag`` instead of ``rev`` -[tool.poetry.dependencies.pyqt5-qt5] -optional = true -version = '5.15.2' - -[tool.poetry.dependencies.pyqtwebengine] -optional = true -version = '~5.15.2, <5.15.7' +[tool.conda-lock.dependencies] +pyside2 = {version = "5.15.*", optional = true} # allow Conda to resolve to a higher existing version than in PyPI -[tool.poetry.dependencies.pyqtwebengine-qt5] -optional = true -version = '5.15.2' +## indirect dependencies, forcing them here for installation through Conda not pip +#--------------------------------------------------------------------------------- +h5py = ">=3.2.1, <4.0.0" # from geoh5py +Pillow = ">=10.3.0, <10.4.0" # from geoh5py +pydantic = ">=2.5.2, <3.0.0" # from geoh5py, curve-apps, geoapps-utils +scikit-image = ">=0.20.0, <0.21.0" # from curve-apps, also used by geo-unsup-mapper -[tool.poetry.dependencies.pyside2] -optional = true -version = '~5.15.2.1' +[tool.poetry.group.dev.dependencies] +Pygments = "*" +pylint = "*" +pytest = "*" +pytest-cov = "*" +pyyaml = '*' +jinja2 = '*' +packaging = '*' +readthedocs-sphinx-ext = "*" +sphinx = "^5.0" +tomli = "*" # for tests only [tool.poetry.extras] -dash = ['dash', 'dash-daq', 'flask', 'pyqt5-qt5', 'pyqtwebengine', 'pyqtwebengine-qt5', 'pyside2'] +dash = [ + "dash", + "dash-daq", + "flask", + "pyqt5-qt5", + "pyqtwebengine", + "pyqtwebengine-qt5", + "pyside2", +] -[tool.poetry.group] -[tool.poetry.group.dev] -[tool.poetry.group.dev.dependencies] -pygments = '*' -pylint = '*' -pytest = '*' -pytest-cov = '*' -readthedocs-sphinx-ext = '*' -sphinx = '^5.0' -tomli = '*' +[tool.conda-lock] +platforms = ['win-64', 'linux-64'] +channels = ['conda-forge'] -[[tool.poetry.include]] -format = ['sdist', 'wheel'] -path = 'COPYING' +[tool.ruff] +target-version = "py310" -[[tool.poetry.include]] -format = ['sdist', 'wheel'] -path = 'COPYING.LESSER' +[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 + "RUF015", # TO DO + "RUF005", # collection-literal-concatenation - wrong suggestion with numpy arrays + "B007", # TO DO + "A001" # TO DO +] +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.poetry.include]] -format = ['sdist', 'wheel'] -path = 'LICENSE' +[tool.ruff.lint.mccabe] +max-complexity = 18 -[[tool.poetry.include]] -format = ['sdist', 'wheel'] -path = 'README.rst' +[tool.ruff.lint.isort] +lines-after-imports = 2 -[[tool.poetry.include]] -format = ['sdist', 'wheel'] -path = 'THIRD_PARTY_SOFTWARE.rst' +[tool.ruff.format] +# default formatting is just fine -[[tool.poetry.include]] -format = ['sdist', 'wheel'] -path = 'docs/**/THIRD_PARTY_SOFTWARE.rst' +[tool.mypy] +warn_unused_configs = true +ignore_missing_imports = true +scripts_are_modules = true +show_error_context = true +show_column_numbers = true +check_untyped_defs = true -[[tool.poetry.packages]] -include = 'peak_finder' +plugins = [ +# "numpy.typing.mypy_plugin" +] -[[tool.poetry.packages]] -include = 'peak_finder-assets' +[tool.pytest.ini_options] +#addopts = -[[tool.poetry.source]] -name = 'jfrog-server' -url = 'https://mirageoscienceltd.jfrog.io/artifactory/api/pypi/public-pypi-dev/simple' +[tool.coverage.run] +branch = true +source = ["peak_finder"] -[tool.ruff] -target-version = 'py310' +[tool.coverage.report] +exclude_lines = [ + "raise NotImplementedError", + "pass", + "if TYPE_CHECKING", + "pragma: no cover" +] -[tool.ruff.lint] -ignore = ['B028', 'E501', 'F401', 'RUF015', 'RUF005', 'B007', 'A001'] -select = ['A', 'B', 'B006', 'B9', 'BLE', 'C4', 'C9', 'E', 'F', 'I', 'RUF', 'TID', 'UP', 'W'] +fail_under = 75 -[tool.ruff.lint.isort] -lines-after-imports = 2 +[tool.coverage.html] +skip_empty = true +skip_covered = true -[tool.ruff.lint.mccabe] -max-complexity = 18 +[build-system] +requires = ["poetry-core>=1.0.0", "setuptools"] +build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/tests/version_test.py b/tests/version_test.py index ed1d9b1..a126de4 100644 --- a/tests/version_test.py +++ b/tests/version_test.py @@ -7,14 +7,39 @@ from __future__ import annotations import re +from pathlib import Path + +import tomli as toml +import yaml +from jinja2 import Template +from packaging.version import Version import peak_finder +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 test_version_is_consistent(pyproject: dict): assert peak_finder.__version__ == pyproject["tool"]["poetry"]["version"] +def test_conda_version_is_pep440(): + version = Version(get_conda_recipe_version()) + assert version is not None + + def test_version_is_semver(): semver_re = ( r"^(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)"