diff --git a/.autohooks/update_citations.py b/.autohooks/update_citations.py new file mode 100644 index 0000000..543a6f4 --- /dev/null +++ b/.autohooks/update_citations.py @@ -0,0 +1,131 @@ +from contextlib import contextmanager +from pathlib import Path +from rich.progress import Progress +import os +import re +from autohooks.api import ReportProgress +from autohooks.api.git import ( + get_staged_status, + stage_files, + stash_unstaged_changes, + exec_git, +) +from rich.prompt import Confirm + +from packaging.version import Version +import sys +import yaml +import tomllib as toml + +pyproject_path = Path("pyproject.toml") + + +has_stdin = False +if os.path.exists("/dev/tty"): + sys.stdin = open("/dev/tty", "r") + has_stdin = True + + +# https://github.com/Textualize/rich/issues/1535#issuecomment-1745297594 +@contextmanager +def hide(progress: Progress): + transient = progress.live.transient # save the old value + progress.live.transient = True + progress.stop() + progress.live.transient = transient # restore the old value + try: + yield + finally: + # make space for the progress to use so it doesn't overwrite any previous lines + print("\n" * (len(progress.tasks) - 2)) + progress.start() + + +def precommit(report_progress: ReportProgress, config=None, **kwargs): + pyproject_changed = False + for f in get_staged_status(): + if f.path == pyproject_path: + pyproject_changed = True + break + if not pyproject_changed: + return 0 + + with stash_unstaged_changes(): + with pyproject_path.open("rb") as f: + project_info = toml.load(f) + with Path("CITATION.cff").open() as f: + citations = yaml.load(f, Loader=yaml.Loader) + + changed_citations = False + project_version = Version(project_info["project"]["version"]) + if Version(citations["version"]) != project_info: + citations["version"] = str(project_version) + changed_citations = True + + tags = exec_git("tag", "-l", "v*", "--sort", "v:refname").split() + last_tag = tags[-1] + authors_since_last_tag = exec_git( + "shortlog", "--summary", "--email", f"{last_tag}..HEAD" + ).splitlines() + + def find_cited_author(name=None, email=None): + for i, a in enumerate(citations["authors"]): + if name in [ + f"{a.get('given-names', '')} {a.get('family-names', '')}", + f"{a.get('family-names', '')} {a.get('given-names', '')}", + ]: + return i + elif email == a.get("email", ""): + return i + return None + + with hide(report_progress._progress): + # git hooks can be passed arguments via stdin, which messes up the prompt here, + # so we flush the input + author_regex = re.compile("(.*) <(.*)>") + for author in authors_since_last_tag: + add_author = False + author = author.split("\t")[1] + match = author_regex.search(author) + if match: + name = match.group(1) + email = match.group(2) + + author_index = find_cited_author(name=name) + + if author_index is not None: + if citations["authors"][author_index]["email"] != email: + # Names match, but emails don’t + add_author = Confirm.ask( + f"Add {name} <{email}> to CITATION.cff? There already is another author with the same name.", + default=False, + ) + else: + author_index = find_cited_author(email=email) + if author_index is not None: + # emails match, but names don’t + add_author = Confirm.ask( + f"Add {name} <{email}> to CITATION.cff? There already is another author with the same email.", + default=False, + ) + else: + # completely unknown author + add_author = Confirm.ask( + f"Add {name} <{email}> to CITATION.cff?", + default=False, + ) + + if add_author: + citations["authors"].append( + { + "given-names": name.split()[0], + "family-names": " ".join(name.split()[1:]), + "email": email, + } + ) + changed_citations = True + + if changed_citations: + with Path("CITATION.cff").open("w") as f: + yaml.dump(citations, f) + stage_files([Path("CITATION.cff")]) diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index 0596105..87ce563 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -13,25 +13,23 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v7 with: fetch-depth: 0 # Fetch all history and tags - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1 with: - python-version: '3.12' - + # Install a specific version of uv. + version: "0.12.10" + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install build twine - pip install . - pip install -e .[dev] + uv sync --all-groups - name: Run tests run: | - pytest --cov=pycoupler --cov-report=xml + uv run pytest --cov --cov-report=xml - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v5 @@ -40,23 +38,10 @@ jobs: - name: Check code formatting with Black run: | - black --check . + uv run black --check . - name: Lint code with Flake8 run: | - flake8 . - - - name: Build package - run: | - python -m build - - - name: Check package - run: | - twine check dist/* - - - name: Test package installation - run: | - pip install dist/*.whl - python -c "import pycoupler; print(f'pycoupler version: {pycoupler.__version__}')" + uv run flake8 # Publishing is handled by the separate release.yml workflow \ No newline at end of file diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 4df58bf..5432db7 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -2,115 +2,36 @@ name: release on: push: - branches: [main, master] + tags: + # Publish on version tags, e.g. v0.1.0 + - "v[0-9]+.[0-9]+.[0-9]+" + - "v[0-9]+.[0-9]+.[0-9]+dev[0-9]+" jobs: - release: + # See https://docs.astral.sh/uv/guides/integration/github/#publishing-to-pypi + check_and_build: runs-on: ubuntu-latest permissions: - contents: write - + contents: read + id-token: write # for Trusted Publishing + attest-action + steps: - name: Checkout code - uses: actions/checkout@v4 - with: - fetch-depth: 0 # Fetch all history and tags - fetch-tags: true # Ensure all tags are fetched for version resolution - token: ${{ secrets.GITHUB_TOKEN }} - - - name: Detect version and tag - id: version - run: | - echo "πŸ” Checking for version tags in this push to main/master..." - - # Debug: Show recent commits - echo "Recent commits:" - git log --oneline -5 - - # Debug: Show all tags - echo "All tags:" - git tag -l | tail -10 - - # Check if this push contains a commit with "Version" in the message - # This indicates a release was created locally and pushed - if git log --oneline -1 --grep="Version" | grep -q "Version"; then - # Get the commit hash of the "Version" commit - VERSION_COMMIT=$(git log --oneline -1 --grep="Version" --format="%H") - echo "Found version commit: $VERSION_COMMIT" - - # Find tags that point to this specific commit - TAGS_ON_COMMIT=$(git tag --points-at $VERSION_COMMIT | grep "^v" | head -1) - - if [ -n "$TAGS_ON_COMMIT" ]; then - VERSION=${TAGS_ON_COMMIT#v} - echo "version=$VERSION" >> $GITHUB_OUTPUT - echo "tag_name=$TAGS_ON_COMMIT" >> $GITHUB_OUTPUT - echo "βœ… Version tag found for this commit: $TAGS_ON_COMMIT" - - # Additional verification: check if this is the most recent tag - LATEST_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "") - if [ "$LATEST_TAG" = "$TAGS_ON_COMMIT" ]; then - echo "βœ… Confirmed: $TAGS_ON_COMMIT is the latest tag" - else - echo "⚠️ Warning: $TAGS_ON_COMMIT is not the latest tag (latest: $LATEST_TAG)" - echo "This might indicate multiple tags in the same push" - fi - else - echo "⚠️ Version commit found but no tag points to it" - echo "Available tags:" - git tag -l | tail -5 - echo "should_release=false" >> $GITHUB_OUTPUT - exit 0 - fi - else - echo "⚠️ No version commit found in this push" - echo "Looking for any commit with 'Version' in the message..." - git log --oneline --grep="Version" -10 - - # Fallback: Check if there's a recent tag that might be from this push - echo "Checking for recent tags as fallback..." - LATEST_TAG=$(git describe --tags --abbrev=0 2>/dev/null || echo "") - if [ -n "$LATEST_TAG" ]; then - echo "Found latest tag: $LATEST_TAG" - # Check if this tag was created recently (within last 5 commits) - if git log --oneline -5 | grep -q "$LATEST_TAG"; then - VERSION=${LATEST_TAG#v} - echo "version=$VERSION" >> $GITHUB_OUTPUT - echo "tag_name=$LATEST_TAG" >> $GITHUB_OUTPUT - echo "βœ… Using latest tag as fallback: $LATEST_TAG" - else - echo "Latest tag is not recent enough" - echo "should_release=false" >> $GITHUB_OUTPUT - exit 0 - fi - else - echo "No tags found at all" - echo "should_release=false" >> $GITHUB_OUTPUT - exit 0 - fi - fi - - - name: Check if release should proceed - if: steps.version.outputs.should_release == 'false' - run: | - echo "Skipping release - no version tag found" - exit 0 + uses: actions/checkout@v7 - - name: Set up Python - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1 with: - python-version: '3.12' - + # Install a specific version of uv. + version: "0.12.10" + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install build twine - pip install . - pip install -e .[dev] + uv sync --all-groups - name: Run tests run: | - pytest --cov=pycoupler --cov-report=xml + uv run pytest --cov --cov-report=xml - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v5 @@ -119,67 +40,60 @@ jobs: - name: Check code formatting with Black run: | - black --check . + uv run black --check . - name: Lint code with Flake8 run: | - flake8 . - + uv run flake8 + - name: Build package run: | - python -m build + uv build - - name: Check package with twine - run: | - twine check dist/* - - - name: Test package installation - run: | - pip install dist/*.whl + - name: Smoke test (wheel) + run: uv run --isolated --no-project --with dist/*.whl "import pycoupler; print(pycoupler.read_config)" + - name: Smoke test (source distribution) + run: uv run --isolated --no-project --with dist/*.tar.gz "import pycoupler; print(pycoupler.read_config)" - - name: Display release info - run: | - echo "πŸš€ Releasing version: ${{ steps.version.outputs.version }}" - echo "πŸ“¦ Tag name: ${{ steps.version.outputs.tag_name }}" - echo "🏷️ Is tag push: ${{ steps.version.outputs.is_tag_push }}" - - - name: Verify tag exists - run: | - echo "πŸ” Verifying tag ${{ steps.version.outputs.tag_name }} exists..." - if git tag -l | grep -q "^${{ steps.version.outputs.tag_name }}$"; then - echo "βœ… Tag ${{ steps.version.outputs.tag_name }} found locally" - else - echo "❌ Tag ${{ steps.version.outputs.tag_name }} not found locally" - echo "Available tags:" - git tag -l | head -10 - exit 1 - fi - - # Show tag details - echo "Tag details:" - git show ${{ steps.version.outputs.tag_name }} --no-patch --format="%H %s" - - - name: Publish to PyPI - env: - TWINE_USERNAME: __token__ - TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} - run: twine upload dist/* + - name: Upload distributions as artifacts + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1 + with: + name: dist + path: dist/ - - name: Ensure tag is pushed to remote - run: | - echo "🏷️ Ensuring tag ${{ steps.version.outputs.tag_name }} is available for GitHub release..." - # The tag should already be available from the merge, but let's make sure - git fetch origin --tags - echo "βœ… Tags fetched from remote" + publish: + runs-on: ubuntu-latest + needs: + - check_and_build + environment: + name: pypi + permissions: + contents: write - - name: Create Release - uses: softprops/action-gh-release@v1 - with: - tag_name: ${{ steps.version.outputs.tag_name }} - name: Release of version ${{ steps.version.outputs.version }} - body: | - Changes in this Release - - Automated release notes - draft: false - prerelease: false - files: dist/* + steps: + - name: Install uv + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 + with: + # Install a specific version of uv. + version: "0.12.10" + + - name: Download distributions artifact + uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1 + with: + name: dist + path: dist/ + + - name: Generate PEP 740 attestations + uses: astral-sh/attest-action@f589a42a7efb6fe400b4f400de60b4bc90390027 # v0.0.6 + + - name: Publish + run: uv publish + + - name: Create Release + uses: softprops/action-gh-release@v3 + with: + name: "${{ github.ref_name }}: Automated release" + generate_release_notes: true + draft: false + prerelease: false + files: dist/* \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/CITATION.cff b/CITATION.cff index baa6a3b..291c516 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,32 +1,30 @@ -cff-version: 1.2.0 -message: If you use this software, please cite it using the metadata from this file. -type: software -title: 'pycoupler: dynamic model coupling of LPJmL' -version: 1.7.0 -date-released: '2025-09-22' -abstract: An LPJmL-Python interface for operating LPJmL in a Python environment - and coupling it with Python models, programmes or simple programming scripts. - pycoupler was written with the aim of establishing the coupling of copan:CORE - with LPJmL. Coupling with LPJmL is possible on an annual basis, i.e. for each - year in which LPJmL is in coupling mode, the desired inputs must be passed via - pycoupler. LPJmL simulates the corresponding year and returns the desired - outputs at the end of the year. The coupled programme can use the output data - to generate new inputs for the next year. +abstract: An LPJmL-Python interface for operating LPJmL in a Python environment and + coupling it with Python models, programmes or simple programming scripts. pycoupler + was written with the aim of establishing the coupling of copan:CORE with LPJmL. + Coupling with LPJmL is possible on an annual basis, i.e. for each year in which + LPJmL is in coupling mode, the desired inputs must be passed via pycoupler. LPJmL + simulates the corresponding year and returns the desired outputs at the end of the + year. The coupled programme can use the output data to generate new inputs for the + next year. authors: -- family-names: Breier +- email: jannesbr@pik-potsdam.de + family-names: Breier given-names: Jannes - email: jannesbr@pik-potsdam.de orcid: 0000-0002-9055-6904 -- family-names: von Bloh +- email: bloh@pik-potsdam.de + family-names: von Bloh given-names: Werner - email: bloh@pik-potsdam.de orcid: 0000-0002-7399-2704 -- family-names: Sieben +- email: sieben@gea.mpg.de + family-names: Sieben given-names: Lorenz - email: sieben@gea.mpg.de orcid: 0009-0006-5307-9391 - +cff-version: 1.2.0 +date-released: '2025-09-22' +doi: 10.5281/zenodo.11576705 license: AGPL-3.0 +message: If you use this software, please cite it using the metadata from this file. repository-code: https://github.com/PIK-LPJmL/pycoupler -doi: 10.5281/zenodo.11576705 - +title: 'pycoupler: dynamic model coupling of LPJmL' +type: software +version: 1.7.1 diff --git a/hooks/pre-tag b/hooks/pre-tag deleted file mode 100755 index 33f3c27..0000000 --- a/hooks/pre-tag +++ /dev/null @@ -1,35 +0,0 @@ -#!/bin/bash -# Pre-tag hook to update CITATION.cff before creating a tag - -echo "Pre-tag hook: Updating CITATION.cff..." - -# Get the tag name from command line arguments -TAG_NAME="$1" -if [ -n "$TAG_NAME" ]; then - # Remove 'v' prefix if present - VERSION=${TAG_NAME#v} - echo "Using tag version: $VERSION" - - # Update CITATION.cff with the specific version - python3 -c "from pycoupler.release import update_citation_file; update_citation_file('$VERSION')" -else - echo "No tag name provided, using current version detection" - # Fallback to current version detection - python3 -c "from pycoupler.release import update_citation_file; import pycoupler; update_citation_file(pycoupler.__version__)" -fi - -# Check if CITATION.cff was updated -if ! git diff --quiet CITATION.cff; then - echo "CITATION.cff updated, committing changes..." - - # Add and commit the changes - git add CITATION.cff - git commit -m "Update CITATION.cff to current version" - - echo "CITATION.cff changes committed successfully" -else - echo "No changes to CITATION.cff needed" -fi - -# Allow the tag to proceed -exit 0 diff --git a/pycoupler/__init__.py b/pycoupler/__init__.py index 37185fb..8f64352 100644 --- a/pycoupler/__init__.py +++ b/pycoupler/__init__.py @@ -1,9 +1,3 @@ -try: - from ._version import __version__ -except ModuleNotFoundError: # pragma: no cover - # package is not installed - __version__ = "1.5.0" - from .config import ( LpjmlConfig, CoupledConfig, @@ -59,5 +53,3 @@ "read_json", "detect_io_type", ] - -__all__ += ["__version__"] diff --git a/pyproject.toml b/pyproject.toml index 7ebe5a2..0dac9ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,18 +1,12 @@ -[build-system] -requires = [ - "hatchling>=1.8.0", - "hatch-vcs" -] -build-backend = "hatchling.build" - [project] name = "pycoupler" -dynamic = ["version"] +version = "1.7.1" description = "dynamic model coupling of LPJmL" readme = "README.md" license = {file = "LICENSE.md"} authors = [ { name = "Jannes Breier", email = "jannes.breier@pik-potsdam.de" }, + { name = "Lorenz Sieben", email = "sieben@gea.mpg.de" }, ] requires-python = ">=3.9" keywords = ["DGVM", "ABM", "model coupling", "LPJmL", "copan:CORE"] @@ -40,25 +34,36 @@ dependencies = [ "Levenshtein>=0.12.2" ] -[project.optional-dependencies] +[dependency-groups] dev = [ "pytest", "pytest-cov", "pytest-subprocess", "sphinx", "black", - "flake8" + "flake8", + "autohooks>=26.2.0", + "autohooks-plugin-flake8>=23.10.0", + "autohooks-plugin-black>=23.10.0", + "pyyaml>=6.0.3", ] [project.urls] -Homepage = "https://github.com/PIK-LPJmL/pycoupler" -Issues = "https://github.com/PIK-LPJmL/pycoupler/issues" -Documentation = "https://github.com/PIK-LPJmL/pycoupler/wiki" -Repository = "https://github.com/PIK-LPJmL/pycoupler" +homepage = "https://github.com/PIK-LPJmL/pycoupler" +issues = "https://github.com/PIK-LPJmL/pycoupler/issues" +documentation = "https://github.com/PIK-LPJmL/pycoupler/wiki" +repository = "https://github.com/PIK-LPJmL/pycoupler" + +[build-system] +requires = ["uv_build>=0.12.10,<0.13"] +build-backend = "uv_build" + +[tool.uv.build-backend] +module-name="pycoupler" +module-root="" -[tool.aliases] -test = "pytest" -docs = "sphinx-build -b html ./docs ./docs/_build" +[tool.uv.dependency-groups] +dev = {requires-python = ">=3.11"} [tool.pytest.ini_options] minversion = "6.0" @@ -69,20 +74,6 @@ line-length = 88 target-version = ['py37', 'py38', 'py39', 'py310'] extend-exclude = "pycoupler/_version.py" - -# [project.scripts] -# pycoupler-cli = "pycoupler.cli:main" - -[tool.hatch.version] -source = "vcs" -fallback_version = "1.5.6" - -[tool.hatch.version.raw-options] -local_scheme = "no-local-version" - -[tool.hatch.metadata] -allow-direct-references = true - -[tool.hatch.build.hooks.vcs] -version-file = "pycoupler/_version.py" -template = "__version__ = '{version}'" +[tool.autohooks] +mode = "uv" +pre-commit = 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