diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml deleted file mode 100644 index 9065b5e..0000000 --- a/.github/workflows/black.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: Lint - -on: [push, pull_request] - -jobs: - lint: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: psf/black@stable diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..f875e45 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,92 @@ +name: CI + +on: + workflow_dispatch: + + push: + paths-ignore: + - "docs/**" + - "*.md" + + pull_request: + paths-ignore: + - "docs/**" + - "*.md" + +jobs: + test: + # We want to run on external PRs, but not on our own internal PRs as they'll be run + # by the push to the branch. Without this if check, checks are duplicated since + # internal PRs match both the push and pull_request events. + if: + github.event_name == 'push' || github.event.pull_request.head.repo.full_name != + github.repository + + name: Python ${{ matrix.python-version }} tests + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12"] + + steps: + - uses: actions/checkout@v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + fetch-depth: 0 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + id: setup-python + with: + python-version: ${{ matrix.python-version }} + + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + + - name: Load cached venv + uses: actions/cache@v2 + id: cached-poetry-dependencies + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }} + + - name: Install dependencies + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: | + poetry lock --no-update + poetry install + python -m pip install pytest-github-actions-annotate-failures + + - name: Run tests + id: tests + run: | + poetry run pytest -vvv + + lint: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Check format with black + uses: psf/black@stable + with: + options: "--diff --check --color --verbose" + + commit-lint: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Lint commit messages + uses: wagoid/commitlint-github-action@v6 + with: + token: ${{ secrets.GITHUB_TOKEN }} + failOnWarnings: 'false' + commitDepth: 1 diff --git a/.github/workflows/commit-message-lint.yml b/.github/workflows/commit-message-lint.yml deleted file mode 100644 index 1057e0c..0000000 --- a/.github/workflows/commit-message-lint.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: "Lint Commit Messages" - -on: [push, pull_request] - -jobs: - commitlint: - runs-on: ubuntu-latest - steps: - - name: Check out code - uses: actions/checkout@v2 - with: - fetch-depth: 0 # Fetches the entire history which is necessary for commitlint to work correctly - - - name: Lint Commit Messages - uses: wagoid/commitlint-github-action@v4 - with: - configFile: './commitlint.config.js' - token: ${{ secrets.GITHUB_TOKEN }} - failOnWarnings: 'false' # Set to true if you want warnings to cause the action to fail - # Add this line to check only the latest commit - firstParent: true diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..97e3894 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,129 @@ +name: Test & Release + +on: + workflow_dispatch: + + push: + branches: + - main + +permissions: + contents: read + +jobs: + test: + name: Python ${{ matrix.python-version }} tests + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12"] + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + id: setup-python + with: + python-version: ${{ matrix.python-version }} + + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + + - name: Load cached venv + uses: actions/cache@v2 + id: cached-poetry-dependencies + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }} + + - name: Install dependencies + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: | + poetry lock --no-update + poetry install + python -m pip install pytest-github-actions-annotate-failures + + - name: Run tests + id: tests + run: | + poetry run pytest -vvv + + lint: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Check format with black + uses: psf/black@stable + with: + options: "--diff --check --color --verbose" + + commit-lint: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Lint commit messages + uses: wagoid/commitlint-github-action@v6 + with: + token: ${{ secrets.GITHUB_TOKEN }} + failOnWarnings: 'false' + commitDepth: 1 + + release: + name: Semantic Release + runs-on: ubuntu-latest + concurrency: push + needs: [test, lint, commit-lint] + if: github.repository == 'xability/py_maidr' + environment: + name: pypi + url: https://pypi.org/project/maidr/ + permissions: + # https://docs.github.com/en/rest/overview/permissions-required-for-github-apps?apiVersion=2022-11-28#metadata + id-token: write + contents: write + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: ${{ github.ref_name }} + + - name: Python Semantic Release + id: release + uses: python-semantic-release/python-semantic-release@master + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + root_options: "-vv" + + # see https://docs.pypi.org/trusted-publishers/ + - name: Publish package distributions to PyPI + id: pypi-publish + # NOTE: DO NOT wrap the conditional in ${{ }} as it will always evaluate to true. + # See https://github.com/actions/runner/issues/1173 + if: steps.release.outputs.released == 'true' + uses: pypa/gh-action-pypi-publish@release/v1 + with: + verbose: true + + - name: Publish package distributions to GitHub Releases + id: github-release + # NOTE: DO NOT wrap the conditional in ${{ }} as it will always evaluate to true. + # See https://github.com/actions/runner/issues/1173 + if: steps.release.outputs.released == 'true' + uses: python-semantic-release/upload-to-gh-release@main + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + tag: ${{ steps.release.outputs.tag }} + root_options: "-vv" diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml deleted file mode 100644 index adef105..0000000 --- a/.github/workflows/tox.yml +++ /dev/null @@ -1,35 +0,0 @@ -name: Run Tox - -on: [push, pull_request] - -jobs: - build: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [ '3.8', '3.9', '3.10', '3.11' ] - fail-fast: false - steps: - - name: Check out - uses: actions/checkout@v4 - - - name: Set up python - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - - - name: Install Poetry - uses: snok/install-poetry@v1 - - - name: Load cached venv - uses: actions/cache@v4 - with: - path: .tox - key: venv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('poetry.lock') }} - - - name: Install tox - run: | - python -m pip install --upgrade pip - python -m pip install tox tox-gh-actions - - name: Test with tox - run: tox diff --git a/docs/_get_started.qmd b/docs/_get_started.qmd new file mode 100644 index 0000000..e69de29 diff --git a/docs/_index.qmd b/docs/_index.qmd new file mode 100644 index 0000000..e69de29 diff --git a/docs/_quarto.yml b/docs/_quarto.yml new file mode 100644 index 0000000..cf7ca38 --- /dev/null +++ b/docs/_quarto.yml @@ -0,0 +1,70 @@ +project: + type: website + output-dir: _site + +website: + title: "PyMAIDR" + + site-url: https://xability.github.io/py_maidr/ + repo-url: https://github.com/xability/py_maidr + issue-url: https://github.com/xability/py_maidr/issues/new/choose + repo-actions: [issue] + + page-navigation: true + bread-crumbs: true + + navbar: + background: light + # logo: quarto.png + logo-alt: "Maidr logo." + logo-href: https://xability.github.io/py_maidr/ + title: PyMAIDR + collapse-below: lg + left: + - text: "Overview" + href: _index.qmd + - text: "Get Started" + href: _get_started.qmd + - text: "API Reference" + href: api/core/index.qmd + right: + - icon: github + href: https://github.com/xability/maidr + aria-label: GitHub + +format: + html: + theme: cosmo + css: styles.css + toc: true + +quartodoc: + package: maidr + dir: api/core + sidebar: _sidebar.yml + style: pkgdown + title: "PyMAIDR" + renderer: + style: markdown + sections: + - title: Plot API + desc: "" + contents: + - bar + - box + - count + - heat + - hist + - line + - scatter + + - title: Maidr API + desc: "" + package: maidr.core + contents: + - Maidr.render + - Maidr.show + - Maidr.save_html + + + diff --git a/docs/styles.css b/docs/styles.css new file mode 100644 index 0000000..2ddf50c --- /dev/null +++ b/docs/styles.css @@ -0,0 +1 @@ +/* css styles */ diff --git a/maidr/__init__.py b/maidr/__init__.py index 7fabbb6..ceef213 100644 --- a/maidr/__init__.py +++ b/maidr/__init__.py @@ -1,5 +1,4 @@ -# __version__ will be automatically updated by python-semantic-release -__version__ = "0.0.1" +__version__ = "0.1.2" from .core import Maidr from .core.enum import PlotType diff --git a/maidr/core/figure_manager.py b/maidr/core/figure_manager.py index 112af68..565862f 100644 --- a/maidr/core/figure_manager.py +++ b/maidr/core/figure_manager.py @@ -63,7 +63,7 @@ def _get_maidr(cls, fig: Figure) -> Maidr: def get_axes( artist: Artist | Axes | BarContainer | dict | list | None, ) -> Any: - """Recursively extracts Axes objects from the input artist or container.""" + """Recursively extract Axes objects from the input artist or container.""" if artist is None: return None elif isinstance(artist, Axes): diff --git a/maidr/core/maidr.py b/maidr/core/maidr.py index 1281b51..892fafd 100644 --- a/maidr/core/maidr.py +++ b/maidr/core/maidr.py @@ -108,7 +108,7 @@ def _create_html_doc(self) -> HTMLDocument: return HTMLDocument(self._create_html_tag(), lang="en") def _flatten_maidr(self) -> dict | list[dict]: - """Returns a single plot schema or a list of schemas from the Maidr instance.""" + """Return a single plot schema or a list of schemas from the Maidr instance.""" maidr = [plot.schema for plot in self._plots] return maidr if len(maidr) != 1 else maidr[0] diff --git a/poetry.lock b/poetry.lock index b880b82..1798fd3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,7 @@ +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + [tool.poetry] name = "maidr" description = "Multimodal Access and Interactive Data Representations" @@ -16,10 +20,10 @@ classifiers = [ "Intended Audience :: Healthcare Industry", "Intended Audience :: Developers", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "Programming Language :: Python", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "Programming Language :: Python :: Implementation :: PyPy", "Topic :: Internet :: WWW/HTTP :: Dynamic Content", "Topic :: Software Development :: Libraries :: Python Modules", @@ -30,17 +34,15 @@ classifiers = [ [project.urls] homepage = "https://github.com/xability/py_maidr" - [tool.poetry.dependencies] -python = ">=3.8" -matplotlib = ">=3.7" -numpy = ">=1.24" +python = ">=3.9" +matplotlib = ">=3.8" +numpy = ">=1.26" seaborn = ">=0.12" lxml = ">=5.1.0" htmltools = ">=0.5" jupyter = "^1.0.0" - [tool.poetry.group.dev.dependencies] black = "23.3.0" sphinx = "^7.0.1" @@ -49,16 +51,62 @@ pytest = "^7.3.2" python-semantic-release = "^8.7.0" pytest-mock = "^3.12.0" tox = "^4.13.0" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +quartodoc = "^0.7.2" [tool.black] line-length = 88 [tool.semantic_release] -branch = "main" -version_variable = "maidr/__init__.py:__version__" -upload_to_pypi = "true" -upload_to_release = "true" +build_command = "pip install poetry && poetry build" +commit_message = "{version}\n\nAutomatically generated by python-semantic-release" +commit_parser = "angular" +logging_use_named_masks = false +major_on_zero = false +tag_format = "v{version}" +version_variables = ["maidr/__init__.py:__version__"] +version_toml = ["pyproject.toml:tool.poetry.version"] + +[tool.semantic_release.branches.main] +match = "(main|master)" +prerelease_token = "rc" +prerelease = false + +[tool.semantic_release.changelog] +template_dir = "templates" +changelog_file = "CHANGELOG.md" +exclude_commit_patterns = [] + +[tool.semantic_release.changelog.environment] +block_start_string = "{%" +block_end_string = "%}" +variable_start_string = "{{" +variable_end_string = "}}" +comment_start_string = "{#" +comment_end_string = "#}" +trim_blocks = false +lstrip_blocks = false +newline_sequence = "\n" +keep_trailing_newline = false +extensions = [] +autoescape = true + +[tool.semantic_release.commit_author] +env = "GIT_COMMIT_AUTHOR" +default = "semantic-release " + +[tool.semantic_release.commit_parser_options] +allowed_tags = ["build", "chore", "ci", "docs", "feat", "fix", "perf", "style", "refactor", "test"] +minor_tags = ["feat"] +patch_tags = ["fix", "perf"] + +[tool.semantic_release.remote] +name = "origin" +type = "github" +ignore_token_for_push = false + +[tool.semantic_release.remote.token] +env = "GH_TOKEN" + +[tool.semantic_release.publish] +dist_glob_patterns = ["dist/*"] +upload_to_vcs_release = true diff --git a/tox.ini b/tox.ini index b330ddf..cd0df86 100644 --- a/tox.ini +++ b/tox.ini @@ -1,13 +1,13 @@ [tox] skipsdist = true -envlist = py38, py39, py310, py311 +envlist = py39, py310, py311, py312 [gh-actions] python = - 3.8: py38 3.9: py39 3.10: py310 3.11: py311 + 3.12: py312 [testenv] passenv = PYTHON_VERSION