From eeb1bf56d286f8b02281c32e9eec4916f2f051d3 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Thu, 12 Mar 2026 12:00:43 +0100 Subject: [PATCH 1/3] Add type checking (#31) * Add basic utils module for testing * Apply new templates * Add utils docs and utility functions * Add pydoclint for docstring/type checks * Clarify pydoclint; reorder hooks; bump template * Add type hints * Update test lint ignores: asserts, types, docs * Update pixi lock * Apply new templates * Update SPDX header checks to license headers * Apply new templates * Apply new templates * Apply new templates * Apply new templates * Apply new templates * Apply new templates * Apply new templates * Enable A rule * Apply new templates --- .copier-answers.yml | 10 +- .github/actions/setup-pixi/action.yml | 2 +- .github/configs/pages-deployment.json | 6 + .github/configs/rulesets-develop.json | 37 + .github/configs/rulesets-gh-pages.json | 19 + .github/configs/rulesets-master.json | 30 + .github/scripts/backmerge-conflict-issue.js | 69 ++ .github/workflows/backmerge.yml | 101 ++- .github/workflows/dashboard.yml | 3 + .github/workflows/docs.yml | 10 +- .github/workflows/issues-labels.yml | 42 + .github/workflows/lint-format.yml | 132 +++ .../workflows/{labels.yml => pr-labels.yml} | 18 +- .github/workflows/pypi-test.yml | 3 + .github/workflows/quality.yml | 119 --- .github/workflows/release-pr.yml | 6 +- .github/workflows/security.yml | 103 ++- .github/workflows/test-trigger.yml | 3 + .github/workflows/test.yml | 3 +- .github/workflows/tutorial-tests-trigger.yml | 3 + .github/workflows/tutorial-tests.yml | 5 +- .gitignore | 14 +- .pre-commit-config.yaml | 32 +- CONTRIBUTING.md | 445 ++++++++++ README.md | 18 +- docs/docs/api-reference/utils.md | 1 + docs/docs/assets/javascripts/extra.js | 14 +- docs/docs/assets/javascripts/mathjax.js | 33 + docs/docs/installation-and-setup/index.md | 15 +- docs/docs/introduction/index.md | 24 +- docs/mkdocs.yml | 11 +- pixi.lock | 840 +++++------------- pixi.toml | 54 +- pyproject.toml | 201 ++++- src/easypeasy/__init__.py | 2 +- src/easypeasy/utils/__init__.py | 3 + src/easypeasy/utils/utils.py | 29 + tests/integration/fitting/test_dummy.py | 2 +- .../integration/scipp-analysis/test_dummy.py | 2 +- tests/unit/{easypeasy => }/test_dummy.py | 2 +- tools/add_license_headers.py | 151 ++++ tools/check_license_headers.py | 45 + tools/remove_license_headers.py | 41 + tools/test_scripts.py | 2 + tools/update_github_labels.py | 14 +- tools/update_spdx.py | 106 --- 46 files changed, 1773 insertions(+), 1052 deletions(-) create mode 100644 .github/configs/pages-deployment.json create mode 100644 .github/configs/rulesets-develop.json create mode 100644 .github/configs/rulesets-gh-pages.json create mode 100644 .github/configs/rulesets-master.json create mode 100644 .github/scripts/backmerge-conflict-issue.js create mode 100644 .github/workflows/issues-labels.yml create mode 100644 .github/workflows/lint-format.yml rename .github/workflows/{labels.yml => pr-labels.yml} (71%) delete mode 100644 .github/workflows/quality.yml create mode 100644 CONTRIBUTING.md create mode 100644 docs/docs/api-reference/utils.md create mode 100644 docs/docs/assets/javascripts/mathjax.js create mode 100644 src/easypeasy/utils/__init__.py create mode 100644 src/easypeasy/utils/utils.py rename tests/unit/{easypeasy => }/test_dummy.py (60%) create mode 100644 tools/add_license_headers.py create mode 100644 tools/check_license_headers.py create mode 100644 tools/remove_license_headers.py delete mode 100644 tools/update_spdx.py diff --git a/.copier-answers.yml b/.copier-answers.yml index 1cdef6e..12859ad 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,14 +1,16 @@ # WARNING: Do not edit this file manually. # Any changes will be overwritten by Copier. -_commit: v0.4.8 +_commit: v0.10.1-22-g084280c _src_path: gh:easyscience/templates app_docs_url: https://easyscience.github.io/peasy-app -app_doi: 10.5281/zenodo.18163581 +app_doi: 10.5281/zenodo.18700888 app_package_name: easypeasy_app app_python: '3.13' app_repo_name: peasy-app +home_page_url: https://easyscience.github.io/peasy +home_repo_name: peasy lib_docs_url: https://easyscience.github.io/peasy-lib -lib_doi: 10.5281/zenodo.18163581 +lib_doi: 10.5281/zenodo.18700888 lib_package_name: easypeasy lib_python_max: '3.13' lib_python_min: '3.11' @@ -17,9 +19,7 @@ project_contact_email: support@easyscience.org project_copyright_years: 2025-2026 project_extended_description: A software for performing imaginary calculations based on a imaginary model and refining its parameters against imaginary data -project_homepage_url: https://easyscience.github.io/peasy project_name: EasyPeasy -project_repo_name: peasy project_short_description: Imaginary data analysis project_shortcut: EP project_type: both diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml index eb891e1..167ee62 100644 --- a/.github/actions/setup-pixi/action.yml +++ b/.github/actions/setup-pixi/action.yml @@ -33,7 +33,7 @@ inputs: runs: using: 'composite' steps: - - uses: prefix-dev/setup-pixi@v0.9.3 + - uses: prefix-dev/setup-pixi@v0.9.4 with: environments: ${{ inputs.environments }} activate-environment: ${{ inputs.activate-environment }} diff --git a/.github/configs/pages-deployment.json b/.github/configs/pages-deployment.json new file mode 100644 index 0000000..c0d3fbe --- /dev/null +++ b/.github/configs/pages-deployment.json @@ -0,0 +1,6 @@ +{ + "source": { + "branch": "gh-pages", + "path": "/" + } +} diff --git a/.github/configs/rulesets-develop.json b/.github/configs/rulesets-develop.json new file mode 100644 index 0000000..04489e5 --- /dev/null +++ b/.github/configs/rulesets-develop.json @@ -0,0 +1,37 @@ +{ + "name": "develop branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/develop"], + "exclude": [] + } + }, + "bypass_actors": [ + { + "actor_id": 2476259, + "actor_type": "Integration", + "bypass_mode": "always" + } + ], + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["squash"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/configs/rulesets-gh-pages.json b/.github/configs/rulesets-gh-pages.json new file mode 100644 index 0000000..ebf3892 --- /dev/null +++ b/.github/configs/rulesets-gh-pages.json @@ -0,0 +1,19 @@ +{ + "name": "gh-pages branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["refs/heads/gh-pages"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + } + ] +} diff --git a/.github/configs/rulesets-master.json b/.github/configs/rulesets-master.json new file mode 100644 index 0000000..f658a5c --- /dev/null +++ b/.github/configs/rulesets-master.json @@ -0,0 +1,30 @@ +{ + "name": "master branch", + "target": "branch", + "enforcement": "active", + "conditions": { + "ref_name": { + "include": ["~DEFAULT_BRANCH"], + "exclude": [] + } + }, + "rules": [ + { + "type": "non_fast_forward" + }, + { + "type": "deletion" + }, + { + "type": "pull_request", + "parameters": { + "allowed_merge_methods": ["merge"], + "dismiss_stale_reviews_on_push": false, + "require_code_owner_review": false, + "require_last_push_approval": false, + "required_approving_review_count": 0, + "required_review_thread_resolution": false + } + } + ] +} diff --git a/.github/scripts/backmerge-conflict-issue.js b/.github/scripts/backmerge-conflict-issue.js new file mode 100644 index 0000000..f6bd98b --- /dev/null +++ b/.github/scripts/backmerge-conflict-issue.js @@ -0,0 +1,69 @@ +module.exports = async ({ github, context, core }) => { + // Repo context + const owner = context.repo.owner + const repo = context.repo.repo + + // Link to the exact workflow run that detected the conflict + const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}` + + // We use a *stable title* so we can find/reuse the same "conflict tracker" issue + // instead of creating a new issue on every failed run. + const title = 'Backmerge conflict: master โ†’ develop' + + // Comment/issue body includes the run URL so maintainers can jump straight to logs. + const body = [ + 'Automatic backmerge failed due to merge conflicts.', + '', + `Workflow run: ${runUrl}`, + '', + 'Manual resolution required.', + ].join('\n') + + // Label applied to the tracker issue (assumed to already exist in the repo). + const label = '[bot] backmerge' + + // Search issues by title across *open and closed* issues. + // Why: if the conflict was resolved previously and the issue was closed, + // we prefer to reopen it and append a new comment instead of creating duplicates. + const q = `repo:${owner}/${repo} is:issue in:title "${title}"` + const search = await github.rest.search.issuesAndPullRequests({ + q, + per_page: 10, + }) + + // Pick the first exact-title match (search can return partial matches). + const existing = search.data.items.find((i) => i.title === title) + + if (existing) { + // If a tracker issue exists, reuse it: + // - reopen it if needed + // - add a comment with the new run URL + if (existing.state === 'closed') { + await github.rest.issues.update({ + owner, + repo, + issue_number: existing.number, + state: 'open', + }) + } + + await github.rest.issues.createComment({ + owner, + repo, + issue_number: existing.number, + body, + }) + + core.notice(`Conflict issue updated: #${existing.number}`) + return + } + + // No tracker issue exists yet -> create the first one. + await github.rest.issues.create({ + owner, + repo, + title, + body, + labels: [label], + }) +} diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml index abe0ef0..47b3384 100644 --- a/.github/workflows/backmerge.yml +++ b/.github/workflows/backmerge.yml @@ -1,34 +1,29 @@ # This workflow automatically merges `master` into `develop` whenever a -# new version tag is pushed (v*). -# -# Key points: -# - Directly merges master into develop without creating a PR. -# - Skips CI on the merge commit using [skip ci] in the commit message. -# - The code being merged has already been tested as part of the release process. -# - This ensures develop stays up-to-date with release changes (version bumps, etc.). -# -# Required organization config: -# https://github.com/organizations/easyscience/settings/secrets/actions -# https://github.com/organizations/easyscience/settings/variables/actions -# - Actions secret: EASYSCIENCE_APP_KEY (GitHub App private key PEM) -# - Actions variable: EASYSCIENCE_APP_ID (GitHub App ID) -# -# IMPORTANT: -# The GitHub App must be added to the develop branch ruleset bypass list. - -name: Backmerge (master -> develop) +# new version release with a tag is published. It can also be triggered +# manually via workflow_dispatch for cases where an automatic backmerge +# is needed outside of the standard release process. +# If a merge conflict occurs, the workflow creates an issue to notify +# maintainers for manual resolution. + +name: Backmerge (master โ†’ develop) on: - push: - tags: ['v*'] + release: + types: [published, prereleased] workflow_dispatch: permissions: contents: write + issues: write + +concurrency: + group: backmerge-master-into-develop + cancel-in-progress: false jobs: backmerge: runs-on: ubuntu-latest + timeout-minutes: 10 steps: - name: Checkout repository (for local actions) @@ -53,34 +48,62 @@ jobs: git config user.name "easyscience[bot]" git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com" - - name: Merge master into develop + - name: Set merge message run: | - set -euo pipefail + if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then + MESSAGE="Backmerge: master into develop (manual) [skip ci]" + else + TAG="${{ github.event.release.tag_name }}" + MESSAGE="Backmerge: master (${TAG}) into develop [skip ci]" + fi - echo "Fetching develop branch" - git fetch origin develop:develop + echo "MESSAGE=$MESSAGE" >> "$GITHUB_ENV" + echo "message=$MESSAGE" >> "$GITHUB_OUTPUT" + echo "๐Ÿ“ Merge message: $MESSAGE" | tee -a "$GITHUB_STEP_SUMMARY" - echo "Switching to develop branch" - git checkout develop + - name: Prepare branches + run: | + git fetch origin master develop + git checkout -B develop origin/develop - echo "Checking if already up-to-date" + - name: Check if develop is already up-to-date + id: up_to_date + run: | if git merge-base --is-ancestor origin/master develop; then - echo "โ„น๏ธ Develop is already up-to-date with master" - exit 0 + echo "value=true" >> "$GITHUB_OUTPUT" + echo "โ„น๏ธ Develop is already up-to-date with master" | tee -a "$GITHUB_STEP_SUMMARY" + else + echo "value=false" >> "$GITHUB_OUTPUT" fi - echo "Preparing merge message" - if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then - MESSAGE="Backmerge: master into develop (manual) [skip ci]" - else - TAG="${{ github.ref_name }}" - MESSAGE="Backmerge: ${TAG} from master into develop [skip ci]" + - name: Try merge master into develop + id: merge + if: steps.up_to_date.outputs.value == 'false' + continue-on-error: true + run: | + if ! git merge origin/master --no-ff -m "${MESSAGE}"; then + echo "conflict=true" >> "$GITHUB_OUTPUT" + echo "โŒ Backmerge conflict detected." | tee -a "$GITHUB_STEP_SUMMARY" + git status --porcelain || true + exit 0 fi - echo "Merging master into develop" - git merge origin/master --no-ff -m "${MESSAGE}" + echo "conflict=false" >> "$GITHUB_OUTPUT" + echo "โœ… Merge commit created." | tee -a "$GITHUB_STEP_SUMMARY" - echo "Pushing to develop" + - name: Push to develop (if merge succeeded) + if: + steps.up_to_date.outputs.value == 'false' && steps.merge.outputs.conflict == + 'false' + run: | git push origin develop + echo "๐Ÿš€ Backmerge successful: master โ†’ develop" | tee -a "$GITHUB_STEP_SUMMARY" - echo "โœ… Successfully merged master into develop" + - name: Create issue (if merge failed with conflicts) + if: steps.merge.outputs.conflict == 'true' + uses: ./.github/actions/github-script + with: + github-token: ${{ steps.bot.outputs.token }} + script: | + const run = require('./.github/scripts/backmerge-conflict-issue.js') + await run({ github, context, core }) diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml index e1e232b..5159f71 100644 --- a/.github/workflows/dashboard.yml +++ b/.github/workflows/dashboard.yml @@ -4,6 +4,9 @@ on: workflow_dispatch: workflow_call: +permissions: + contents: read + # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f5e9cb5..46bcee2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -14,16 +14,16 @@ name: Docs build and deployment on: - # Trigger the workflow on pull request - pull_request: - # Selected branches - branches: [master, main, develop] # Trigger the workflow on push push: # Selected branches - branches: [master, main, develop] + branches: [develop] # master and main are already verified in PR # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3' tags: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Selected branches + branches: [master, main, develop] # Allows you to run this workflow manually from the Actions tab workflow_dispatch: diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml new file mode 100644 index 0000000..3a60cdd --- /dev/null +++ b/.github/workflows/issues-labels.yml @@ -0,0 +1,42 @@ +# Verifies if an issue has at least one of the `[scope]` and one of the +# `[priority]` labels. If not, the bot adds labels with a warning emoji +# to indicate that those labels need to be added. + +name: Issue labels check + +on: + issues: + types: [opened, labeled, unlabeled] + +permissions: + issues: write + +jobs: + check-labels: + runs-on: ubuntu-latest + + steps: + - name: Setup easyscience[bot] + id: bot + uses: ./.github/actions/setup-easyscience-bot + with: + app-id: ${{ vars.EASYSCIENCE_APP_ID }} + private-key: ${{ secrets.EASYSCIENCE_APP_KEY }} + + - name: Check for required [scope] label + uses: trstringer/require-label-prefix@v1 + with: + secret: ${{ steps.bot.outputs.token }} + prefix: '[scope]' + labelSeparator: ' ' + addLabel: true + defaultLabel: '[scope] โš ๏ธ label needed' + + - name: Check for required [priority] label + uses: trstringer/require-label-prefix@v1 + with: + secret: ${{ steps.bot.outputs.token }} + prefix: '[priority]' + labelSeparator: ' ' + addLabel: true + defaultLabel: '[priority] โš ๏ธ label needed' diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml new file mode 100644 index 0000000..457d67f --- /dev/null +++ b/.github/workflows/lint-format.yml @@ -0,0 +1,132 @@ +# The workflow checks +# - the validity of pyproject.toml, +# - the presence and correctness of SPDX license headers, +# - linting and formatting of Python code, +# - linting and formatting of docstrings in Python code, +# - formatting of non-Python files (like markdown and toml). +# - linting of Python code in Jupyter notebooks (for library template). +# +# A summary of the checks is added to the GitHub Actions summary. + +name: Lint and format checks + +on: + # Trigger the workflow on push + push: + branches-ignore: [master, main] # Already verified in PR + # Do not run this workflow on creating a new tag starting with + # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) + tags-ignore: ['v*'] + # Trigger the workflow on pull request + pull_request: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Allow only one concurrent workflow, skipping runs queued between the run +# in-progress and latest queued. And cancel in-progress runs. +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +permissions: + contents: read + +# Set the environment variables to be used in all jobs defined in this workflow +env: + CI_BRANCH: ${{ github.head_ref || github.ref_name }} + +jobs: + lint-format: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v5 + + - name: Set up pixi + uses: ./.github/actions/setup-pixi + + - name: Run post-install developer steps + run: pixi run post-install + + - name: Check validity of pyproject.toml + id: pyproject + continue-on-error: true + shell: bash + run: pixi run pyproject-check + + - name: Check SPDX license headers + id: license_headers + continue-on-error: true + shell: bash + run: pixi run license-check + + - name: Check linting of Python code + id: py_lint + continue-on-error: true + shell: bash + run: pixi run py-lint-check + + - name: Check formatting of Python code + id: py_format + continue-on-error: true + shell: bash + run: pixi run py-format-check + + - name: Check linting of docstrings in Python code + id: docstring_lint + continue-on-error: true + shell: bash + run: pixi run docstring-lint-check + + - name: Check formatting of docstrings in Python code + id: docstring_format + continue-on-error: true + shell: bash + run: pixi run docstring-format-check + + - name: Check formatting of non-Python files (md, toml, etc.) + id: nonpy_format + continue-on-error: true + shell: bash + run: pixi run nonpy-format-check + + - name: Check linting of Python code in Jupyter notebooks (ipynb) + id: notebook_lint + continue-on-error: true + shell: bash + run: pixi run notebook-lint-check + + # Add summary + - name: Add quality checks summary + if: always() + shell: bash + run: | + { + echo "## ๐Ÿงช Checks Summary" + echo "" + echo "| Check | Status |" + echo "|-------|--------|" + echo "| pyproject.toml | ${{ steps.pyproject.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| license headers | ${{ steps.license_headers.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| py lint | ${{ steps.py_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| py format | ${{ steps.py_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| docstring lint | ${{ steps.docstring_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| docstring format | ${{ steps.docstring_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| nonpy format | ${{ steps.nonpy_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + echo "| notebooks lint | ${{ steps.notebook_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" + } >> "$GITHUB_STEP_SUMMARY" + + # Fail job if any check failed + - name: Fail job if any check failed + if: | + steps.pyproject.outcome == 'failure' + || steps.license_headers.outcome == 'failure' + || steps.py_lint.outcome == 'failure' + || steps.py_format.outcome == 'failure' + || steps.docstring_lint.outcome == 'failure' + || steps.docstring_format.outcome == 'failure' + || steps.nonpy_format.outcome == 'failure' + || steps.notebook_lint.outcome == 'failure' + shell: bash + run: exit 1 diff --git a/.github/workflows/labels.yml b/.github/workflows/pr-labels.yml similarity index 71% rename from .github/workflows/labels.yml rename to .github/workflows/pr-labels.yml index 4ea4e2f..642cd31 100644 --- a/.github/workflows/labels.yml +++ b/.github/workflows/pr-labels.yml @@ -1,7 +1,16 @@ # Verifies if a pull request has at least one label from a set of valid # labels before it can be merged. +# +# NOTE: +# This workflow may be triggered twice in quick succession when a PR is +# created: +# 1) `opened` โ€” when the pull request is initially created +# 2) `labeled` โ€” if labels are added immediately after creation +# (e.g. by manual labeling, another workflow, or GitHub App). +# +# These are separate GitHub events, so two workflow runs can be started. -name: PR label checks +name: PR labels check on: pull_request_target: @@ -11,16 +20,17 @@ permissions: pull-requests: read jobs: - require-label: + check-labels: runs-on: ubuntu-latest + steps: - - name: Validate required labels + - name: Check for valid labels run: | PR_LABELS=$(echo '${{ toJson(github.event.pull_request.labels.*.name) }}' | jq -r '.[]') echo "Current PR labels: $PR_LABELS" VALID_LABELS=( - "[bot] pull request" + "[bot] release" "[scope] bug" "[scope] documentation" "[scope] enhancement" diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index f1bafb7..b330135 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -13,6 +13,9 @@ concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true +permissions: + contents: read + # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml deleted file mode 100644 index b11f909..0000000 --- a/.github/workflows/quality.yml +++ /dev/null @@ -1,119 +0,0 @@ -# The workflow is divided into several steps to ensure code quality: -# - Check the validity of pyproject.toml -# - Check code linting -# - Check code formatting -# - Check formatting of docstrings in the code -# - Check formatting of Markdown, YAML, TOML, etc. files - -name: Code quality checks - -on: - # Trigger the workflow on push - push: - # Every branch - branches: ['**'] - # Do not run this workflow on creating a new tag starting with - # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) - tags-ignore: ['v*'] - # Trigger the workflow on pull request - pull_request: - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -# Allow only one concurrent workflow, skipping runs queued between the run -# in-progress and latest queued. And cancel in-progress runs. -concurrency: - group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true - -# Set the environment variables to be used in all jobs defined in this workflow -env: - CI_BRANCH: ${{ github.head_ref || github.ref_name }} - -jobs: - code-quality: - runs-on: ubuntu-latest - - steps: - - name: Checkout repository - uses: actions/checkout@v5 - - - name: Set up pixi - uses: ./.github/actions/setup-pixi - - - name: Run post-install developer steps - run: pixi run post-install - - # Check the validity of pyproject.toml - - name: Check validity of pyproject.toml - id: check_pyproject - continue-on-error: true - shell: bash - run: pixi run pyproject-check - - # Check code linting with Ruff in the project root - - name: Check code linting - id: check_code_linting - continue-on-error: true - shell: bash - run: pixi run py-lint-check - - # Check code formatting with Ruff in the project root - - name: Check code formatting - id: check_code_formatting - continue-on-error: true - shell: bash - run: pixi run py-format-check - - # Check formatting of docstrings in the code with docformatter - - name: Check formatting of docstrings in the code - id: check_docs_formatting - continue-on-error: true - shell: bash - run: pixi run docs-format-check - - # Check formatting of MD, YAML, TOML, etc. files with Prettier in - # the project root - - name: Check formatting of MD, YAML, TOML, etc. files - id: check_others_formatting - continue-on-error: true - shell: bash - run: pixi run nonpy-format-check - # Check formatting of Jupyter Notebooks in the tutorials folder - - name: Prepare notebooks and check formatting - id: check_notebooks_formatting - continue-on-error: true - shell: bash - run: | - pixi run notebook-prepare - pixi run notebook-format-check - - # Add summary - - name: Add quality checks summary - if: always() - shell: bash - run: | - { - echo "## ๐Ÿงช Code Quality Checks Summary" - echo "" - echo "| Check | Status |" - echo "|-------|--------|" - echo "| pyproject.toml | ${{ steps.check_pyproject.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| py lint | ${{ steps.check_code_linting.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| py format | ${{ steps.check_code_formatting.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| docstring format | ${{ steps.check_docs_formatting.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| nonpy format | ${{ steps.check_others_formatting.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| notebooks format | ${{ steps.check_notebooks_formatting.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - } >> "$GITHUB_STEP_SUMMARY" - - # Fail job if any check failed - - name: Fail job if any check failed - if: | - steps.check_pyproject.outcome == 'failure' - || steps.check_code_linting.outcome == 'failure' - || steps.check_code_formatting.outcome == 'failure' - || steps.check_docs_formatting.outcome == 'failure' - || steps.check_others_formatting.outcome == 'failure' - || steps.check_notebooks_formatting.outcome == 'failure' - shell: bash - run: exit 1 diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml index 3192f59..7e6fda4 100644 --- a/.github/workflows/release-pr.yml +++ b/.github/workflows/release-pr.yml @@ -3,7 +3,7 @@ # Usage: # - Triggered manually via workflow_dispatch. # - Creates a PR titled "Release: merge into ". -# - Adds the label "[bot] pull request" so it is excluded from changelogs. +# - Adds the label "[bot] release" so it is excluded from changelogs. # - The PR body makes clear that this is automation only (no review needed). name: 'Release PR (develop โ†’ master)' @@ -49,7 +49,7 @@ jobs: --base ${{ env.DEFAULT_BRANCH }} \ --head ${{ env.SOURCE_BRANCH }} \ --title "Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \ - --label "[bot] pull request" \ + --label "[bot] release" \ --body "This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from \`${{ env.SOURCE_BRANCH }}\` into \`${{ env.DEFAULT_BRANCH }}\`. - โš ๏ธ It is labeled \`[bot] pull request\` and is excluded from release notes and version bump logic." + โš ๏ธ It is labeled \`[bot] release\` and is excluded from release notes and version bump logic." diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml index 4bbb91f..9b34ccc 100644 --- a/.github/workflows/security.yml +++ b/.github/workflows/security.yml @@ -1,40 +1,93 @@ -# Integrates a collection of open source static analysis tools with -# GitHub code scanning. -# https://github.com/github/ossar-action +# Code scanning (CodeQL) for vulnerabilities and insecure coding patterns. +# +# What this workflow does +# - Runs GitHub CodeQL analysis and uploads results to your repository's Security tab. +# - Triggers on PRs (so findings appear as PR checks) and on pushes to `develop`. +# - Runs on a weekly schedule. +# +# Where to find results on GitHub +# - Repository โ†’ Security โ†’ Code scanning alerts +# (You can filter by tool = CodeQL and by branch.) +# +# Where to configure on GitHub +# - Repository โ†’ Settings โ†’ Advanced Security +# Enable "GitHub Advanced Security" (if available) and configure CodeQL there. +# - Repository โ†’ Security โ†’ Code scanning alerts +# This page shows findings produced by this workflow. +# +# Notes about the scheduled run +# - Scheduled workflows are triggered from the repository's *default branch*. +# If your default branch is `master` but you want the scheduled scan to analyze +# `develop`, this workflow checks out `develop` explicitly for scheduled runs. +# +# References +# - CodeQL Action: https://github.com/github/codeql-action +# - Advanced setup docs: https://docs.github.com/en/code-security/code-scanning -name: Security scans +name: Security scans with CodeQL on: - # Trigger the workflow on pull request + # Run on pull requests so results show up as PR checks and code + # scanning alerts. pull_request: + branches: [master, main, develop] - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: + # Run on pushes (e.g., after merging PRs). + push: + branches: [master, main, develop] + + # Run weekly. (Cron is in UTC.) + schedule: + - cron: '0 3 * * 1' + +permissions: + contents: read + security-events: write jobs: - scan-security-ossar: - # OSSAR runs on windows-latest. - # ubuntu-latest and macos-latest support coming soon - runs-on: windows-latest + codeql: + name: Code scanning + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + # Keep this list tight to avoid noise and speed up runs. + language: [python, actions] steps: + # Scheduled workflows run from the default branch. + # We explicitly analyze `develop` on the schedule to keep the scan + # focused on the active dev branch. + - name: Checkout repository (scheduled โ†’ develop) + if: ${{ github.event_name == 'schedule' }} + uses: actions/checkout@v5 + with: + ref: develop + - name: Checkout repository + if: ${{ github.event_name != 'schedule' }} uses: actions/checkout@v5 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v4 with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 + languages: ${{ matrix.language }} - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v4 - - name: Run open source static analysis tools - uses: github/ossar-action@main - id: ossar + print-link: + name: Print results link + runs-on: ubuntu-latest - - name: Upload results to Security tab - uses: github/codeql-action/upload-sarif@v3 - with: - sarif_file: ${{ steps.ossar.outputs.sarifFile }} + needs: codeql + permissions: {} # no special perms needed just to print links + + steps: + - name: Add Code Scanning link to job summary + run: | + echo "## ๐Ÿ”Ž CodeQL Results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "View Code Scanning alerts here:" >> $GITHUB_STEP_SUMMARY + echo "${{ github.server_url }}/${{ github.repository }}/security/code-scanning" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml index a68e1fa..ecf6b40 100644 --- a/.github/workflows/test-trigger.yml +++ b/.github/workflows/test-trigger.yml @@ -7,6 +7,9 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: +permissions: + contents: read + jobs: code-tests-trigger: runs-on: ubuntu-latest diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5993078..be01657 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,8 +20,7 @@ name: Code and package tests on: # Trigger the workflow on push push: - # Every branch - branches: ['**'] + branches-ignore: [master, main] # Already verified in PR # But do not run this workflow on creating a new tag starting with # 'v', e.g. 'v1.0.3' (see publish-pypi.yml) tags-ignore: ['v*'] diff --git a/.github/workflows/tutorial-tests-trigger.yml b/.github/workflows/tutorial-tests-trigger.yml index 4cbb8bb..1bc27f4 100644 --- a/.github/workflows/tutorial-tests-trigger.yml +++ b/.github/workflows/tutorial-tests-trigger.yml @@ -7,6 +7,9 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: +permissions: + contents: read + jobs: tutorial-tests-trigger: runs-on: ubuntu-latest diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml index 5599884..4c9244d 100644 --- a/.github/workflows/tutorial-tests.yml +++ b/.github/workflows/tutorial-tests.yml @@ -4,7 +4,7 @@ on: # Trigger the workflow on push push: # Selected branches - branches: [master, main, develop] + branches: [develop] # master and main are already verified in PR # Trigger the workflow on pull request pull_request: branches: ['**'] @@ -15,6 +15,9 @@ on: # Allows you to run this workflow manually from the Actions tab workflow_dispatch: +permissions: + contents: read + # Allow only one concurrent workflow, skipping runs queued between the run # in-progress and latest queued. And cancel in-progress runs. concurrency: diff --git a/.gitignore b/.gitignore index f7ce4ac..0500ede 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,10 @@ __pycache__/ .venv/ .coverage +.pyc + +# Pixi +.pixi/ # PyInstaller dist/ @@ -19,16 +23,10 @@ node_modules/ # QtCreator *.autosave - -# QtCreator Qml *.qmlproject.user *.qmlproject.user.* - -# QtCreator Python *.pyproject.user *.pyproject.user.* - -# QtCreator CMake CMakeLists.txt.user* # PyCharm @@ -41,3 +39,7 @@ CMakeLists.txt.user* .DS_Store *.app *.dmg + +# Misc +*.log +*.zip diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 007d238..5fa0c2c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,6 +11,13 @@ repos: pass_filenames: false stages: [manual] + - id: license-headers-check + name: pixi run license-check + entry: pixi run license-check + language: system + pass_filenames: false + stages: [manual] + - id: pixi-py-lint-check name: pixi run py-lint-check entry: pixi run py-lint-check @@ -25,23 +32,30 @@ repos: pass_filenames: false stages: [manual] - - id: pixi-nonpy-format-check - name: pixi run nonpy-format-check - entry: pixi run nonpy-format-check + - id: pixi-docstring-lint-check + name: pixi run docstring-lint-check + entry: pixi run docstring-lint-check language: system pass_filenames: false stages: [manual] - - id: pixi-docs-format-check - name: pixi run docs-format-check - entry: pixi run docs-format-check + - id: pixi-docstring-format-check + name: pixi run docstring-format-check + entry: pixi run docstring-format-check + language: system + pass_filenames: false + stages: [manual] + + - id: pixi-nonpy-format-check + name: pixi run nonpy-format-check + entry: pixi run nonpy-format-check language: system pass_filenames: false stages: [manual] - - id: pixi-notebook-format-check - name: pixi run notebook-format-check - entry: pixi run notebook-format-check + - id: pixi-notebook-lint-check + name: pixi run notebook-lint-check + entry: pixi run notebook-lint-check language: system pass_filenames: false stages: [manual] diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..c82b095 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,445 @@ +# Contributing to EasyPeasy + +Thank you for your interest in contributing to **EasyPeasy**! + +This guide explains how you can: + +- Report issues +- Contribute code +- Improve documentation +- Suggest enhancements +- Interact with the EasyScience community + +Whether you are an experienced developer or contributing for the first +time, this document walks you through the entire process step by step. + +Please make sure you follow the EasyScience organization-wide +[Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md). + +--- + +## Table of Contents + +- [How to Interact With This Project](#how-to-interact-with-this-project) +- [1. Understanding the Development Model](#1-understanding-the-development-model) +- [2. Getting the Code](#2-getting-the-code) +- [3. Setting Up the Development Environment](#3-setting-up-the-development-environment) +- [4. Creating a Branch](#4-creating-a-branch) +- [5. Implementing Your Changes](#5-implementing-your-changes) +- [6. Code Quality Checks](#6-code-quality-checks) +- [7. Opening a Pull Request](#7-opening-a-pull-request) +- [8. Continuous Integration (CI)](#8-continuous-integration-ci) +- [9. Code Review](#9-code-review) +- [10. Documentation Contributions](#10-documentation-contributions) +- [11. Reporting Issues](#11-reporting-issues) +- [12. Security Issues](#12-security-issues) +- [13. Releases](#13-releases) + +--- + +## How to Interact With This Project + +If you are not planning to contribute code, you may want to: + +- ๐Ÿž Report a bug โ€” see [Reporting Issues](#11-reporting-issues) +- ๐Ÿ›ก Report a security issue โ€” see + [Security Issues](#12-security-issues) +- ๐Ÿ’ฌ Ask a question or start a discussion at + [Project Discussions](https://github.com/easyscience/peasy-lib/discussions) + +If you plan to contribute code or documentation, continue below. + +--- + +## 1. Understanding the Development Model + +Before you start coding, it is important to understand how development +works in this project. + +### Branching Strategy + +We use the following branches: + +- `master` โ€” stable releases only +- `develop` โ€” active development branch +- Short-lived branches โ€” feature or fix branches created for a single + contribution and deleted after merge + +> [!IMPORTANT] +> +> All normal contributions must target the `develop` branch. +> +> - Do **not** open Pull Requests against `master` +> - Always create your branch from `develop` +> - Always target `develop` when opening a Pull Request + +See ADR easyscience/.github#12 for more details on the branching +strategy. + +--- + +## 2. Getting the Code + +### 2.1. If You Are an External Contributor + +If you are not a core maintainer of this repository, follow these steps. + +1. Open the repository page: `https://github.com/easyscience/peasy-lib` + +2. Click the **Fork** button (top-right corner). This creates your own + copy of the repository. + +3. Clone your fork locally: + + ```bash + git clone https://github.com//peasy-lib.git + cd peasy-lib + ``` + +4. Add the original repository as `upstream`: + + ```bash + git remote add upstream https://github.com/easyscience/peasy-lib.git + ``` + +5. Switch to the `develop` branch and update it: + + ```bash + git fetch upstream + git checkout develop + git pull upstream develop + ``` + +If you have contributed before, make sure your local `develop` branch is +up to date before starting new work. You can update it with: + +```bash +git fetch upstream +git pull upstream develop +``` + +This ensures you are working on the latest version of the project. + +### 2.2. If You Are a Core Team Member + +Core team members can create branches directly in this repository and +therefore do not need to fork it, but the rest of the workflow remains +the same. + +--- + +## 3. Setting Up the Development Environment + +You need: + +- Git +- Pixi + +EasyScience projects use **Pixi** to manage the development environment. + +To install Pixi, follow the official instructions: +https://pixi.prefix.dev/latest/installation/ + +You do **not** need to manually install Python. Pixi automatically: + +- Creates the correct Python environment +- Installs all required dependencies +- Installs development tools (linters, formatters, test tools) + +Set up the environment: + +```bash +pixi install +pixi run post-install # Install additional tooling +``` + +After this step, your development environment is ready. + +See ADR easyscience/.github#63 for more details about using Pixi for +development. + +--- + +## 4. Creating a Branch + +Never work directly on `develop`. + +Create a new branch: + +```bash +git checkout -b my-change develop +``` + +> [!IMPORTANT] +> +> Use a clear and descriptive name, for example: +> +> - `improve-solver-speed` +> - `fix-boundary-condition` +> - `add-tutorial-example` + +Clear branch names make reviews and history easier to understand. + +--- + +## 5. Implementing Your Changes + +While developing, make small, logical commits with clear messages. + +Example: + +```bash +git add . +git commit -m "Improve performance of time integrator for large systems" +``` + +--- + +## 6. Code Quality Checks + +> [!IMPORTANT] +> +> When adding new functionality or making changes, make sure to add or +> update the following as needed: +> +> - ๐Ÿ“˜ docstrings +> - ๐Ÿงช unit tests + +Before opening a Pull Request, always run: + +```bash +pixi run check +``` + +This command: + +- Validates the pyproject.toml file +- Checks for licence headers in code files +- Identifies linting and formatting issues in Python code +- Checks docstring linting and formatting issues in Python code +- Detects formatting issues in non-Python files (MD, YAML, TOML etc.) +- Checks linting issues in Jupyter notebooks (if applicable) +- Runs unit tests + +A successful run should look like this: + +```bash +pixi run pyproject-check.......................Passed +pixi run license-check.........................Passed +pixi run py-lint-check.........................Passed +pixi run py-format-check.......................Passed +pixi run docstring-lint-check..................Passed +pixi run docstring-format-check................Passed +pixi run nonpy-format-check....................Passed +pixi run notebook-lint-check...................Passed +pixi run unit-tests............................Passed +``` + +If something fails, read the error message carefully and fix the issue. + +You can run individual checks, for example, to run only unit tests: + +```bash +pixi run unit-tests +``` + +or to run only Python linting checks: + +```bash +pixi run py-lint-check +``` + +Some formatting issues can be fixed automatically: + +```bash +pixi run fix +``` + +If everything is correctly formatted, you will see: + +```text +โœ… All auto-formatting steps completed successfully! +``` + +This indicates that the auto-formatting pipeline completed successfully. +If you do not see this message and no error messages appear, try running +the command again. + +If errors are reported, resolve them and re-run: + +```bash +pixi run check +``` + +> [!IMPORTANT] +> +> All checks must pass before your Pull Request can be merged. + +If you are unsure how to fix an issue, ask for help in your Pull Request +discussion. + +--- + +## 7. Opening a Pull Request + +Push your branch: + +```bash +git push origin my-change +``` + +On GitHub: + +- Click **Compare & Pull Request** +- Ensure the base branch is `develop` +- Write a clear and concise title +- Add a description explaining what changed and why +- Add the required `[scope]` label + +### Pull Request Title + +> [!IMPORTANT] +> +> The PR title appears in release notes and changelogs. It should be +> concise and informative. + +Good examples: + +- Improve performance of time integrator for large systems +- Fix incorrect boundary condition handling in solver +- Add adaptive step-size control to ODE solver +- Add tutorial for custom model configuration +- Refactor solver API for improved readability + +### Required `[scope]` Label + +> [!IMPORTANT] +> +> Each Pull Request must include a `[scope]` label, which is used for +> automatically suggesting version bumps when preparing a new release. + +The available scopes are: + +| Label | Description | +| ----------------------- | ----------------------------------------------------------------------- | +| `[scope] bug` | Bug report or fix (major.minor.**PATCH**) | +| `[scope] documentation` | Documentation-only changes (major.minor.patch.**POST**) | +| `[scope] enhancement` | Adds or improves features (major.**MINOR**.patch) | +| `[scope] maintenance` | Code/tooling cleanup without feature or bug fix (major.minor.**PATCH**) | +| `[scope] significant` | Breaking or major changes (**MAJOR**.minor.patch) | + +See ADR easyscience/.github#33 for more details on the standardized +labeling scheme. + +--- + +## 8. Continuous Integration (CI) + +After opening a Pull Request: + +- Automated checks run automatically +- You will see green checkmarks or red crosses + +If checks fail: + +1. Open the failing check +2. Read the logs +3. Fix the issue locally +4. Run `pixi run check` +5. Push your changes + +The Pull Request updates automatically. + +--- + +## 9. Code Review + +All Pull Requests are reviewed by at least one core team member. + +Code review is collaborative and aims to improve quality. + +Do not take comments personally โ€” they are meant to help. + +To update your PR: + +```bash +git add . +git commit -m "Address review comments" +git push +``` + +--- + +## 10. Documentation Contributions + +> [!IMPORTANT] +> +> If your change affects user-facing functionality, update the project +> documentation accordingly โ€” specifically the `nav:` (navigation) +> structure in `mkdocs.yml` and the relevant documentation Markdown +> files in `docs/docs/`. +> +> ```text +> ๐Ÿ“ docs +> โ”œโ”€โ”€ ๐Ÿ“ docs - Markdown files for documentation +> โ”‚ โ””โ”€โ”€ ... +> โ””โ”€โ”€ ๐Ÿ“„ mkdocs.yml - Configuration file (navigation, theme, etc.) +> ``` + +This may include: + +- API documentation +- Examples +- Tutorials +- Jupyter notebooks + +Preview documentation locally: + +```bash +pixi run docs-serve +``` + +Open the URL shown in the terminal to review your changes. + +--- + +## 11. Reporting Issues + +If you find a bug but cannot work on a fix, please consider opening an +issue. + +When reporting an issue, it helps to: + +- Search existing issues first. +- Provide clear reproduction steps. +- Include logs, screenshots, and environment details. + +Clear and detailed reports help maintainers investigate and resolve +issues more effectively. + +--- + +## 12. Security Issues + +> [!IMPORTANT] +> +> Please do **not** report security vulnerabilities publicly. + +If you discover a potential vulnerability, please contact the +maintainers privately so the issue can be investigated and addressed +responsibly. + +--- + +## 13. Releases + +Once your contribution is merged into `develop`, it will eventually be +included in the next stable release. + +When enough changes have accumulated in `develop`, core team members +merge `develop` into `master` to prepare a new release. The release is +then tagged and published on GitHub and PyPI. + +--- + +Thank you for contributing to EasyPeasy and the EasyScience ecosystem! diff --git a/README.md b/README.md index 1d25ba6..cfec989 100644 --- a/README.md +++ b/README.md @@ -21,8 +21,13 @@ Here, we focus on the Python library. For the graphical user interface (GUI), please see the corresponding [GUI resources](https://github.com/easyscience/peasy-app). +License: +[BSD 3-Clause](https://github.com/easyscience/peasy-lib/blob/master/LICENSE) + ## Useful Links +### For Users + - ๐Ÿ“– [Documentation](https://easyscience.github.io/peasy-lib/latest) - ๐Ÿš€ [Getting Started](https://easyscience.github.io/peasy-lib/latest/introduction) @@ -32,10 +37,13 @@ Here, we focus on the Python library. For the graphical user interface [Get in Touch](https://easyscience.github.io/peasy-lib/latest/introduction/#get-in-touch) - ๐Ÿงพ [Citation](https://easyscience.github.io/peasy-lib/latest/introduction/#citation) -- ๐Ÿค - [Contributing](https://easyscience.github.io/peasy-lib/latest/introduction/#contributing) + +### For Contributors + +- ๐Ÿง‘โ€๐Ÿ’ป [Source Code](https://github.com/easyscience/peasy-lib) - ๐Ÿž [Issue Tracker](https://github.com/easyscience/peasy-lib/issues) - ๐Ÿ’ก [Discussions](https://github.com/easyscience/peasy-lib/discussions) -- ๐Ÿง‘โ€๐Ÿ’ป [Source Code](https://github.com/easyscience/peasy-lib) -- โš–๏ธ - [License](https://raw.githubusercontent.com/easyscience/peasy-lib/refs/heads/master/LICENSE) +- ๐Ÿค + [Contributing Guide](https://github.com/easyscience/peasy-lib/blob/master/CONTRIBUTING.md) +- ๐Ÿ›ก + [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md) diff --git a/docs/docs/api-reference/utils.md b/docs/docs/api-reference/utils.md new file mode 100644 index 0000000..4c66ed3 --- /dev/null +++ b/docs/docs/api-reference/utils.md @@ -0,0 +1 @@ +::: easypeasy.utils diff --git a/docs/docs/assets/javascripts/extra.js b/docs/docs/assets/javascripts/extra.js index dd3fc35..9596ee0 100644 --- a/docs/docs/assets/javascripts/extra.js +++ b/docs/docs/assets/javascripts/extra.js @@ -1,6 +1,5 @@ -(function() { - - "use strict" +;(function () { + 'use strict' // Variables const header = document.getElementsByTagName('header')[0] @@ -10,20 +9,19 @@ // Hide-show header shadow function toggleHeaderShadow() { if (window.pageYOffset <= 0) { - header.classList.remove("md-header--shadow") + header.classList.remove('md-header--shadow') } else { - header.classList.add("md-header--shadow") + header.classList.add('md-header--shadow') } } // Onload - window.onload = function() { + window.onload = function () { toggleHeaderShadow() } // Onscroll - window.onscroll = function() { + window.onscroll = function () { toggleHeaderShadow() } - })() diff --git a/docs/docs/assets/javascripts/mathjax.js b/docs/docs/assets/javascripts/mathjax.js new file mode 100644 index 0000000..333524e --- /dev/null +++ b/docs/docs/assets/javascripts/mathjax.js @@ -0,0 +1,33 @@ +window.MathJax = { + tex: { + //inlineMath: [['\\(', '\\)']], + //displayMath: [['\\[', '\\]']], + // Add support for $...$ and \(...\) delimiters + inlineMath: [ + ['$', '$'], + ['\\(', '\\)'], + ], + // Add support for $$...$$ and \[...]\ delimiters + displayMath: [ + ['$$', '$$'], + ['\\[', '\\]'], + ], + processEscapes: true, + processEnvironments: true, + }, + options: { + //ignoreHtmlClass: ".*|", + //processHtmlClass: "arithmatex" + // Skip code blocks only + skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'], + // Only ignore explicit opt-out + ignoreHtmlClass: 'no-mathjax|tex2jax_ignore', + }, +} + +document$.subscribe(() => { + MathJax.startup.output.clearCache() + MathJax.typesetClear() + MathJax.texReset() + MathJax.typesetPromise() +}) diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md index f6885c2..929cd7c 100644 --- a/docs/docs/installation-and-setup/index.md +++ b/docs/docs/installation-and-setup/index.md @@ -94,19 +94,8 @@ This section describes the simplest way to set up EasyPeasy using ## Classical Installation This section describes how to install EasyPeasy using the traditional -method with **pip**. This approach is more flexible and suitable for -users familiar with Python package management and virtual environments. - -!!! warning - - Currently, classical installation doesn't allow installing the - GNU Scientific Library (GSL) dependency automatically. As a result, - the calculation engine **pdffit2** will not be available. To make it - work, ensure that GSL is installed on your system. - - Alternatively, consider using the **Pixi installation method** described - in the [Installing with Pixi](#installing-with-pixi) section, which - handles GSL installation automatically. +method with **pip**. It is assumed that you are familiar with Python +package management and virtual environments. ### Environment Setup optional { #environment-setup data-toc-label="Environment Setup" } diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md index 6a4bb91..3a06030 100644 --- a/docs/docs/introduction/index.md +++ b/docs/docs/introduction/index.md @@ -45,26 +45,28 @@ Zenodo, each with a version-specific Digital Object Identifier (DOI). Citation details in various styles (e.g., APA, MLA) and formats (e.g., BibTeX, JSON) are available on the -[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581). +[Zenodo archive page](https://doi.org/10.5281/zenodo.18700888). ## Contributing -We welcome contributions from the community! **EasyPeasy** is intended -to be a community-driven, open-source project supported by a diverse -group of contributors. +We welcome contributions of any kind! + +**EasyPeasy** is intended to be a community-driven, open-source project +supported by a diverse group of contributors. The project is maintained by the [European Spallation Source (ESS)](https://ess.eu). -To contribute, see our +If you would like to report a bug or request a new feature, please use +the +[GitHub Issue Tracker](https://github.com/easyscience/peasy-lib/issues) +(A free GitHub account is required.) + +To contribute code, documentation, or tests, please see our [:material-account-plus: Contributing Guidelines](https://github.com/easyscience/peasy-lib/blob/master/CONTRIBUTING.md) -on GitHub. +for detailed development instructions. ## Get in Touch -For general questions or feedback, contact us at +For general questions or feedback, please contact us at [support@easyscience.org](mailto:support@easyscience.org). - -To report bugs or request features, please use the -[GitHub Issue Tracker](https://github.com/easyscience/peasy-lib/issues) -(free registration required). diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 068621a..a1154b8 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -21,7 +21,7 @@ theme: - 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md5: 0f9817ffbe25f9e69ceba5ea70c52606 - depends: - - libhwloc >=2.12.2,<2.12.3.0a0 - - ucrt >=10.0.20348.0 - - vc >=14.3,<15 - - vc14_runtime >=14.44.35208 - license: Apache-2.0 - license_family: APACHE - purls: [] - size: 155869 - timestamp: 1767886839029 - pypi: https://files.pythonhosted.org/packages/6a/9e/2064975477fdc887e47ad42157e214526dcad8f317a948dee17e1659a62f/terminado-0.18.1-py3-none-any.whl name: terminado version: 0.18.1 diff --git a/pixi.toml b/pixi.toml index 8256133..998caba 100644 --- a/pixi.toml +++ b/pixi.toml @@ -42,10 +42,10 @@ channels = ['conda-forge'] [dependencies] nodejs = '*' # Required for Prettier (non-Python formatting) -gsl = '*' # GNU Scientific Library; required for pdffit2. +#gsl = '*' # GNU Scientific Library; required for pdffit2 [pypi-dependencies] # == [feature.default.pypi-dependencies] -pip = '*' # Native package installer +#pip = '*' # Native package installer easypeasy = { path = ".", editable = true, extras = ['dev'] } # Specific features: Set specific Python versions @@ -92,8 +92,9 @@ test = { depends-on = ['unit-tests'] } ########### pyproject-check = 'python -m validate_pyproject pyproject.toml' -docs-format-check = 'docformatter --check src/ docs/docs/tutorials/' -notebook-format-check = 'nbqa ruff docs/docs/tutorials/' +docstring-lint-check = 'pydoclint --quiet src/' +docstring-format-check = 'docformatter --check src/' +notebook-lint-check = 'nbqa ruff docs/docs/tutorials/' py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/' py-format-check = "ruff format --check src/ tests/ docs/docs/tutorials/" nonpy-format-check = "npx prettier --list-different --config=prettierrc.toml --ignore-unknown ." @@ -106,19 +107,19 @@ check = 'pre-commit run --hook-stage manual --all-files' ########## docs-format-fix = 'docformatter --in-place src/ docs/docs/tutorials/' -notebook-format-fix = 'nbqa ruff --fix docs/docs/tutorials/' +notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/' py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/' py-format-fix = "ruff format src/ tests/ docs/docs/tutorials/" nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .' nonpy-format-fix-modified = "python tools/nonpy_prettier_modified.py --write" -success-message-fix = 'echo "โœ… All code auto-formatting steps have been applied."' +success-message-fix = 'echo "โœ… All auto-formatting steps completed successfully!"' fix = { depends-on = [ 'py-format-fix', 'docs-format-fix', 'py-lint-fix', 'nonpy-format-fix', - 'notebook-format-fix', + 'notebook-lint-fix', 'success-message-fix', ] } @@ -199,12 +200,46 @@ pre-commit-setup = { depends-on = [ 'pre-commit-install', ] } +################# +# ๐Ÿ™๏ธ GitHub Tasks +################# + +repo-wiki = 'gh api -X PATCH repos/easyscience/peasy-lib -f has_wiki=false' +repo-discussions = 'gh api -X PATCH repos/easyscience/peasy-lib -f has_discussions=true' +repo-description = "gh api -X PATCH repos/easyscience/peasy-lib -f description='Imaginary data analysis'" +repo-homepage = "gh api -X PATCH repos/easyscience/peasy-lib -f homepage='https://easyscience.github.io/peasy-lib'" +repo-config = { depends-on = [ + 'repo-wiki', + 'repo-discussions', + 'repo-description', + 'repo-homepage', +] } + +master-protection = 'gh api -X POST repos/easyscience/peasy-lib/rulesets --input .github/configs/rulesets-master.json' +develop-protection = 'gh api -X POST repos/easyscience/peasy-lib/rulesets --input .github/configs/rulesets-develop.json' +gh-pages-protection = 'gh api -X POST repos/easyscience/peasy-lib/rulesets --input .github/configs/rulesets-gh-pages.json' +branch-protection = { depends-on = [ + 'master-protection', + 'develop-protection', + 'gh-pages-protection', +] } + +pages-deployment = 'gh api -X POST repos/easyscience/peasy-lib/pages --input .github/configs/pages-deployment.json' + +github-labels = 'python tools/update_github_labels.py' + +######################### +# โš–๏ธ SPDX License Headers +######################### + +license-remove = 'python tools/remove_license_headers.py src/ tests/' +license-add = 'python tools/add_license_headers.py src/ tests/' +license-check = 'python tools/check_license_headers.py src/ tests/' + #################################### # ๐Ÿš€ Other Development & Build Tasks #################################### -github-labels = 'python tools/update_github_labels.py' - default-build = 'python -m build' dist-build = 'python -m build --wheel --outdir dist' @@ -212,7 +247,6 @@ npm-config = 'npm config set registry https://registry.npmjs.org/' prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml' clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +" -spdx-update = 'python tools/update_spdx.py' post-install = { depends-on = [ 'npm-config', diff --git a/pyproject.toml b/pyproject.toml index b75b245..4edcc89 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,9 +6,10 @@ name = 'easypeasy' dynamic = ['version'] # Use versioningit to manage the version description = 'Imaginary data analysis' -authors = [{ name = 'EasyPeasy contributors' }] +authors = [{ name = 'EasyScience contributors' }] readme = 'README.md' -license = { file = 'LICENSE' } +license = 'BSD-3-Clause' +license-files = ['LICENSE'] classifiers = [ 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering', @@ -34,6 +35,7 @@ dependencies = [ [project.optional-dependencies] dev = [ + 'GitPython', # Interact with Git repositories 'build', # Building the package 'pre-commit', # Pre-commit hooks 'jinja2', # Templating @@ -49,8 +51,9 @@ dev = [ 'versioningit', # Automatic versioning from git tags 'jupytext', # Jupyter notebook text format support 'jupyterquiz', # Quizzes in Jupyter notebooks - 'docformatter', # Code formatter for docstrings - 'interrogate', # Check for missing docstrings + 'pydoclint', # Docstring linter + 'docformatter', # Docstring formatter + 'interrogate', # Docstring coverage checker 'copier', # Template management 'mike', # MkDocs: Versioned documentation support 'mkdocs', # Static site generator @@ -61,24 +64,20 @@ dev = [ 'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables 'mkdocstrings-python', # MkDocs: Python docstring support 'pyyaml', # YAML parser + 'spdx-headers', # SPDX license header validation ] [project.urls] -homepage = 'https://easyscience.github.io/peasy' -documentation = 'https://easyscience.github.io/peasy-lib' -source = 'https://github.com/easyscience/peasy-lib' -tracker = 'https://github.com/easyscience/peasy-lib/issues' +Homepage = 'https://easyscience.github.io/peasy' +Documentation = 'https://easyscience.github.io/peasy-lib' +'Release Notes' = 'https://github.com/easyscience/peasy-lib/releases' +'Source Code' = 'https://github.com/easyscience/peasy-lib' +'Issue Tracker' = 'https://github.com/easyscience/peasy-lib/issues' ############################ # Build system configuration ############################ -# Build system 'hatch' -- Python project manager -# https://hatch.pypa.io/ - -# Versioning system 'versioningit' -- Versioning from git tags -# https://versioningit.readthedocs.io/ - [build-system] build-backend = 'hatchling.build' requires = ['hatchling', 'versioningit'] @@ -87,6 +86,9 @@ requires = ['hatchling', 'versioningit'] # Configuration for hatchling ############################# +# 'hatch' -- Build system for Python +# https://hatch.pypa.io/ + [tool.hatch.build.targets.wheel] packages = ['src/easypeasy'] @@ -100,6 +102,9 @@ source = 'versioningit' # Use versioningit to manage the version # Configuration for versioningit ################################ +# 'versioningit' -- Versioning from git tags +# https://versioningit.readthedocs.io/ + # Versioningit generates versions from git tags, so we don't need to # either specify them statically in pyproject.toml or save them in the # source code. Do not use {distance} in the version format, as it @@ -119,24 +124,11 @@ method = 'git' match = ['v*'] default-tag = 'v999.0.0' -################################ -# Configuration for docformatter -################################ - -# 'docformatter' -- Code formatter for docstrings -# https://docformatter.readthedocs.io/en/latest/ - -[tool.docformatter] -recursive = true -wrap-summaries = 72 -wrap-descriptions = 72 -close-quotes-on-newline = true - ################################ # Configuration for interrogate ################################ -# 'interrogate' -- Check for missing docstrings +# 'interrogate' -- Docstring coverage checker # https://interrogate.readthedocs.io/en/latest/ [tool.interrogate] @@ -148,6 +140,9 @@ verbose = 1 # Configuration for coverage/pytest-cov ####################################### +# 'coverage' -- Code coverage measurement tool +# https://coverage.readthedocs.io/en/latest/ + [tool.coverage.run] branch = true # Measure branch coverage as well source = ['src'] # Limit coverage to the source code directory @@ -161,6 +156,9 @@ fail_under = 0 # Minimum coverage percentage to pass # Configuration for pytest ########################## +# 'pytest' -- Testing framework +# https://docs.pytest.org/en/stable/ + [tool.pytest.ini_options] addopts = '--import-mode=importlib' markers = ['fast: mark test as fast (should be run on every push)'] @@ -179,6 +177,8 @@ indent-width = 4 line-length = 99 preview = true # Enable new rules that are not yet stable, like DOC +# Formatting options for Ruff + [tool.ruff.format] docstring-code-format = true # Whether to format code snippets in docstrings docstring-code-line-length = 72 # Line length for code snippets in docstrings @@ -186,35 +186,148 @@ indent-style = 'space' # PEP 8 recommends using spaces over tabs line-ending = 'lf' # Line endings will be converted to \n quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) -# https://docs.astral.sh/ruff/rules/ +# Linting rules to use with Ruff + [tool.ruff.lint] select = [ - # 'E', # General PEP 8 style errors - # 'E9', # Runtime errors (e.g., syntax errors, undefined names) - # 'F', # Pyflakes-specific checks (e.g., unused variables, imports) - # 'F63', # Issues related to invalid escape sequences in strings - # 'F7', # Type-related errors (e.g., mismatched argument types, unsupported operations) - # 'F82', # Import-related errors (e.g., unresolved imports, reimported modules) - # 'I', # Import sorting issues (e.g., unsorted imports) - # 'S', # Security-related issues (e.g., use of insecure functions or libraries) - # 'W', # General PEP 8 warnings (e.g., lines too long, trailing whitespace) + # Various rules + 'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90 + 'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f + 'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly + 'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb + 'I', # https://docs.astral.sh/ruff/rules/#isort-i + 'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n + 'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy + 'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh + 'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf + 'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf + 'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try + 'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up + # pycodestyle (E, W) rules + 'E', # https://docs.astral.sh/ruff/rules/#error-e + 'W', # https://docs.astral.sh/ruff/rules/#warning-w + # Pylint (PL) rules + 'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc + 'PLE', # https://docs.astral.sh/ruff/rules/#error-ple + 'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr + 'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw + # flake8 rules + 'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + 'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async + 'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + 'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble + 'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + 'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com + 'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + 'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + 'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa + 'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt + 'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix + 'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + 'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn + 'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp + 'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc + 'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log + 'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + 'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + 'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + 'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi + 'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret + 'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + 'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + 'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf + 'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot + 'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20 + 'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc + 'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td + 'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid +] + +# Exceptions to the linting rules + +# Ignore specific rules globally +ignore = [ + 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ + # The following covered by [tool.pydoclint] section below + 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc ] +# Ignore specific rules in certain files or directories [tool.ruff.lint.per-file-ignores] -'tests/**/*.py' = ['S101'] # Allow assert statements in tests +'tests/**' = [ + 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'S101', # https://docs.astral.sh/ruff/rules/assert/ +] +'docs/**' = [ + 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ + 'T201', # https://docs.astral.sh/ruff/rules/print/ +] + +# Specific options for certain rules [tool.ruff.lint.flake8-tidy-imports] +# Disallow all relative imports ban-relative-imports = 'all' [tool.ruff.lint.isort] +# Forces all from imports to appear on their own line force-single-line = true [tool.ruff.lint.mccabe] -max-complexity = 10 # default is 10 +# Cyclomatic complexity threshold (default is 10) +max-complexity = 10 [tool.ruff.lint.pycodestyle] -max-line-length = 99 # https://peps.python.org/pep-0008/#maximum-line-length -max-doc-length = 72 # https://peps.python.org/pep-0008/#maximum-line-length +# PEP 8 line length guidance: +# https://peps.python.org/pep-0008/#maximum-line-length +# Use 99 characters as the project-wide maximum for regular code lines. +max-line-length = 99 +# allow longer lines so that parameter declarations such as +# `name (Type | Type | None):` remain on a single line. Splitting these +# lines can prevent tools such as MkDocs and IDEs from correctly +# parsing and rendering parameter documentation. +# The descriptive text itself is wrapped more strictly by +# `docformatter` (see the configuration in [tool.docformatter] below) +# whenever it is treated as normal paragraph text. +# The line length for code snippets in docstrings is also more strict, +# as defined in the [tool.ruff.format] section above. +max-doc-length = 99 + +############################# +# Configuration for pydoclint +############################# + +# 'pydoclint' -- Docstring linter, a faster alternative to +# 'darglint' or 'darglint2'. +# https://pypi.org/project/pydoclint/ + +# This is a more advanced docstring linter compared to Ruff's built-in +# docstring check rules D or DOC. For example, among many other things, +# it can check that arguments in the docstring, which are used by MkDocs +# and IDEs to render parameter documentation, remain synchronized with +# the parameter declarations in the code (in function's signature). + +[tool.pydoclint] +style = "google" +check-style-mismatch = true +check-arg-defaults = true +allow-init-docstring = true -[tool.ruff.lint.pydocstyle] -convention = 'google' +################################ +# Configuration for docformatter +################################ + +# 'docformatter' -- Code formatter for docstrings +# https://docformatter.readthedocs.io/en/latest/ + +[tool.docformatter] +recursive = true +wrap-summaries = 72 +wrap-descriptions = 72 +close-quotes-on-newline = true diff --git a/src/easypeasy/__init__.py b/src/easypeasy/__init__.py index 26479d1..f808f0e 100644 --- a/src/easypeasy/__init__.py +++ b/src/easypeasy/__init__.py @@ -1,3 +1,3 @@ -# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors +# SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause """EasyPeasy library.""" diff --git a/src/easypeasy/utils/__init__.py b/src/easypeasy/utils/__init__.py new file mode 100644 index 0000000..f808f0e --- /dev/null +++ b/src/easypeasy/utils/__init__.py @@ -0,0 +1,3 @@ +# SPDX-FileCopyrightText: 2025 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""EasyPeasy library.""" diff --git a/src/easypeasy/utils/utils.py b/src/easypeasy/utils/utils.py new file mode 100644 index 0000000..15248b2 --- /dev/null +++ b/src/easypeasy/utils/utils.py @@ -0,0 +1,29 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Utility functions for EasyPeasy.""" + +from __future__ import annotations + +import logging + +logger = logging.getLogger(__name__) + + +def dummy_method( + left: str, + right: str, +) -> str: + """Dummy method for testing. It concatenates the left and right + strings. + + Args: + left (str): Left side of the new string. + right (str): Right side of the new string. + + Returns: + str: The output string. + """ + + logger.debug('Calling dummy method') + + return left + right diff --git a/tests/integration/fitting/test_dummy.py b/tests/integration/fitting/test_dummy.py index 61ba32d..2256189 100644 --- a/tests/integration/fitting/test_dummy.py +++ b/tests/integration/fitting/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause import pytest diff --git a/tests/integration/scipp-analysis/test_dummy.py b/tests/integration/scipp-analysis/test_dummy.py index 61ba32d..2256189 100644 --- a/tests/integration/scipp-analysis/test_dummy.py +++ b/tests/integration/scipp-analysis/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause import pytest diff --git a/tests/unit/easypeasy/test_dummy.py b/tests/unit/test_dummy.py similarity index 60% rename from tests/unit/easypeasy/test_dummy.py rename to tests/unit/test_dummy.py index 2e02771..3c4448b0 100644 --- a/tests/unit/easypeasy/test_dummy.py +++ b/tests/unit/test_dummy.py @@ -1,4 +1,4 @@ -# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors +# SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause diff --git a/tools/add_license_headers.py b/tools/add_license_headers.py new file mode 100644 index 0000000..28febde --- /dev/null +++ b/tools/add_license_headers.py @@ -0,0 +1,151 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Add SPDX headers to Python files. + +- SPDX-FileCopyrightText with the license holder name and organization + URL from ``pyproject.toml`` as well as the file's creation year. +- SPDX-License-Identifier is taken from the project license value in + ``pyproject.toml``. +""" + +from __future__ import annotations + +import argparse +import tomllib +from datetime import datetime +from pathlib import Path +from typing import Optional +from typing import Union + +from git import Repo +from spdx_headers.core import find_repository_root +from spdx_headers.core import get_copyright_info +from spdx_headers.data import load_license_data +from spdx_headers.operations import add_header_to_single_file + +LICENSE_DATABASE = load_license_data() + + +def load_pyproject(repo_path: Union[str, Path]) -> dict: + """Load and return parsed ``pyproject.toml`` data for the + repository. + """ + repo_root = find_repository_root(repo_path) + pyproject_path = repo_root / 'pyproject.toml' + + with open(pyproject_path, 'rb') as file_handle: + return tomllib.load(file_handle) + + +def get_file_creation_year(file_path: Union[str, Path]) -> str: + """Return the year the file was first added to Git history. + + If the year cannot be determined, fall back to the current year. + """ + file_path = Path(file_path) + + repo = Repo(file_path, search_parent_directories=True) + root = Path(repo.working_tree_dir).resolve() + rel_path = file_path.resolve().relative_to(root) + + rel_path_git = rel_path.as_posix() # IMPORTANT for git pathspec + + # Get the year when the file was first added to Git history. + # NOTE: Do not combine `--reverse` with `--max-count=1` here, as it can + # yield an empty result with some Git versions. Instead, get the full + # filtered output and take the first line. + log_output = repo.git.log( + '--follow', + '--diff-filter=A', + '--reverse', + '--format=%ad', + '--date=format:%Y', + '--', + rel_path_git, + ).strip() + + year = log_output.splitlines()[0].strip() if log_output else '' + + return year or str(datetime.now().year) + + +def get_org_url(repo_path: Union[str, Path]) -> str: + """Return the organization URL derived from the repository source + URL. + """ + pyproject_data = load_pyproject(repo_path) + repo_url = pyproject_data['project']['urls']['Source Code'] + return repo_url.rsplit('/', 1)[0] + + +def get_project_license(repo_path: Union[str, Path]) -> str: + """Return the project license value from ``pyproject.toml``.""" + pyproject_data = load_pyproject(repo_path) + return pyproject_data['project']['license'] + + +def get_copyright_holder(repo_path: Union[str, Path]) -> str: + """Return the repository copyright holder name.""" + _, name, _ = get_copyright_info(repo_path) + return name + + +def add_spdx_header( + target_file: Union[str, Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> None: + """Add SPDX headers.""" + year = get_file_creation_year(target_file) + + add_header_to_single_file( + filepath=target_file, + license_key=license_key, + license_data=LICENSE_DATABASE, + year=year, + name=copyright_holder, + email=org_url, + ) + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description='Add SPDX headers to Python files under the given paths.', + ) + parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + parser = build_parser() + args = parser.parse_args(argv) + + repo_path = Path('.').resolve() + license_key = get_project_license(repo_path) + copyright_holder = get_copyright_holder(repo_path) + org_url = get_org_url(repo_path) + + for base_dir in args.paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + for py_file in base_path.rglob('*.py'): + add_spdx_header( + py_file, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + + return 0 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/check_license_headers.py b/tools/check_license_headers.py new file mode 100644 index 0000000..c8a4df2 --- /dev/null +++ b/tools/check_license_headers.py @@ -0,0 +1,45 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Check SPDX headers in Python files.""" + +from __future__ import annotations + +import argparse +from pathlib import Path +from typing import Optional + +from spdx_headers.operations import check_headers + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description='Check SPDX headers in Python files under the given paths.', + ) + parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + parser = build_parser() + args = parser.parse_args(argv) + + exit_codes = [] + + for base_dir in args.paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + print('=' * 50) + print(f'Checking SPDX headers in: {base_dir}') + exit_codes.append(check_headers(base_dir)) + + return 0 if all(code == 0 for code in exit_codes) else 1 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/remove_license_headers.py b/tools/remove_license_headers.py new file mode 100644 index 0000000..f5d09da --- /dev/null +++ b/tools/remove_license_headers.py @@ -0,0 +1,41 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Remove SPDX headers from Python files.""" + +from __future__ import annotations + +import argparse +from pathlib import Path +from typing import Optional + +from spdx_headers.operations import remove_header_from_py_files + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + description='Remove SPDX headers from Python files under the given paths.', + ) + parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + parser = build_parser() + args = parser.parse_args(argv) + + for base_dir in args.paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + remove_header_from_py_files(base_dir) + + return 0 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/test_scripts.py b/tools/test_scripts.py index 2d34757..e24b28e 100644 --- a/tools/test_scripts.py +++ b/tools/test_scripts.py @@ -1,3 +1,5 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause """Test runner for tutorial scripts in the 'tutorials' directory. This test discovers and executes all Python scripts located under the diff --git a/tools/update_github_labels.py b/tools/update_github_labels.py index 615da8e..84de575 100644 --- a/tools/update_github_labels.py +++ b/tools/update_github_labels.py @@ -1,3 +1,5 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause """Set/update GitHub labels for current or specified easyscience repository. @@ -17,7 +19,7 @@ import argparse import json import shlex -import subprocess +import subprocess # noqa: S404 import sys from dataclasses import dataclass @@ -54,6 +56,7 @@ class Colors: LABEL_RENAMES = [ + # Default GitHub labels to rename (if they exist) LabelRename('bug', '[scope] bug'), LabelRename('documentation', '[scope] documentation'), LabelRename('duplicate', '[maintainer] duplicate'), @@ -63,6 +66,8 @@ class Colors: LabelRename('invalid', '[maintainer] invalid'), LabelRename('question', '[maintainer] question'), LabelRename('wontfix', '[maintainer] wontfix'), + # Custom label renames (if they exist) + LabelRename('[bot] pull request', '[bot] release'), ] LABELS = [ @@ -161,10 +166,15 @@ class Colors: ), # Bot label Label( - '[bot] pull request', + '[bot] release', Colors.BOT, 'Automated release PR. Excluded from changelog/versioning', ), + Label( + '[bot] backmerge', + Colors.BOT, + 'Automated backmerge master โ†’ develop failed due to conflicts', + ), ] diff --git a/tools/update_spdx.py b/tools/update_spdx.py deleted file mode 100644 index 5e75e70..0000000 --- a/tools/update_spdx.py +++ /dev/null @@ -1,106 +0,0 @@ -"""Update or insert SPDX headers in Python files. - -- Ensures SPDX-FileCopyrightText has the current year. -- Ensures SPDX-License-Identifier is set to BSD-3-Clause. -""" - -import fnmatch -import re -from pathlib import Path - -COPYRIGHT_TEXT = ( - '# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors ' -) -LICENSE_TEXT = '# SPDX-License-Identifier: BSD-3-Clause' - -# Patterns to exclude from SPDX header updates (vendored code) -EXCLUDE_PATTERNS = [ - '*/_vendored/jupyter_dark_detect/*', -] - - -def should_exclude(file_path: Path) -> bool: - """Check if a file should be excluded from SPDX header updates.""" - path_str = str(file_path) - return any(fnmatch.fnmatch(path_str, pattern) for pattern in EXCLUDE_PATTERNS) - - -def update_spdx_header(file_path: Path): - # Use Path.open to satisfy lint rule PTH123. - with file_path.open('r', encoding='utf-8') as f: - original_lines = f.readlines() - - # Regexes for SPDX lines - copy_re = re.compile(r'^#\s*SPDX-FileCopyrightText:.*$') - lic_re = re.compile(r'^#\s*SPDX-License-Identifier:.*$') - - # 1) Preserve any leading shebang / coding cookie lines - prefix = [] - body_start = 0 - if original_lines: - # Shebang line like "#!/usr/bin/env python3" - if original_lines[0].startswith('#!'): - prefix.append(original_lines[0]) - body_start = 1 - # PEP 263 coding cookie on first or second line - # e.g. "# -*- coding: utf-8 -*-" or "# coding: utf-8" - for _ in range(2): # at most one more line to inspect - if body_start < len(original_lines): - line = original_lines[body_start] - if re.match(r'^#.*coding[:=]\s*[-\w.]+', line): - prefix.append(line) - body_start += 1 - else: - break - - # 2) Work on the remaining body - body = original_lines[body_start:] - - # Remove any existing SPDX lines anywhere in the body - body = [ln for ln in body if not (copy_re.match(ln) or lic_re.match(ln))] - - # Strip leading blank lines in the body so header is tight - while body and not body[0].strip(): - body.pop(0) - - # 3) Build canonical SPDX block: two lines + exactly one blank - spdx_block = [ - COPYRIGHT_TEXT + '\n', - LICENSE_TEXT + '\n', - '\n', - ] - - # 4) New content: prefix + SPDX + body - new_lines = prefix + spdx_block + body - - # 5) Normalize: collapse any extra blank lines immediately after - # LICENSE to exactly one. This keeps the script idempotent. - # Find the index of LICENSE we just inserted (prefix may be 0, 1, - # or 2 lines) - lic_idx = len(prefix) + 1 # spdx_block[1] is the license line - # Ensure exactly one blank line after LICENSE - # Remove all blank lines after lic_idx, then insert a single blank. - j = lic_idx + 1 - # Remove any number of blank lines following - while j < len(new_lines) and not new_lines[j].strip(): - new_lines.pop(j) - # Insert exactly one blank line at this position - new_lines.insert(j, '\n') - - with file_path.open('w', encoding='utf-8') as f: - f.writelines(new_lines) - - -def main(): - """Recursively update or insert SPDX headers in all Python files - under the 'src' and 'tests' directories. - """ - for base_dir in ('src', 'tests'): - for py_file in Path(base_dir).rglob('*.py'): - if should_exclude(py_file): - continue - update_spdx_header(py_file) - - -if __name__ == '__main__': - main() From 6333bd79385a4405bdeec448a06eddc6e29701b5 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Tue, 5 May 2026 20:13:50 +0200 Subject: [PATCH 2/3] Apply latest templates (#33) --- .copier-answers.yml | 2 +- .github/actions/download-artifact/action.yml | 4 +- .github/actions/github-script/action.yml | 2 +- .../actions/setup-easyscience-bot/action.yml | 4 +- .github/actions/setup-pixi/action.yml | 2 +- .github/actions/upload-artifact/action.yml | 4 +- .github/actions/upload-codecov/action.yml | 4 +- .github/scripts/publish-dashboard.sh | 77 + .github/workflows/backmerge.yml | 4 +- .github/workflows/cleanup.yml | 4 +- .github/workflows/coverage.yml | 16 +- .github/workflows/dashboard.yml | 35 +- .github/workflows/docs.yml | 2 +- .github/workflows/issues-labels.yml | 9 + .github/workflows/lint-format.yml | 10 +- .github/workflows/pypi-publish.yml | 2 +- .github/workflows/pypi-test.yml | 22 +- .github/workflows/release-notes.yml | 4 +- .github/workflows/release-pr.yml | 2 +- .github/workflows/security.yml | 4 +- .github/workflows/test-trigger.yml | 2 +- .github/workflows/test.yml | 53 +- .github/workflows/tutorial-tests-trigger.yml | 2 +- .github/workflows/tutorial-tests.yml | 6 +- .gitignore | 1 + .pre-commit-config.yaml | 7 - .prettierignore | 17 +- CONTRIBUTING.md | 1 - docs/mkdocs.yml | 2 +- pixi.lock | 8902 ++++++++--------- pixi.toml | 81 +- pyproject.toml | 70 +- tests/functional/test_dummy.py | 8 + tests/unit/test_dummy.py | 2 +- tools/add_license_headers.py | 151 - tools/check_license_headers.py | 45 - tools/license_headers.py | 321 + tools/remove_license_headers.py | 41 - 38 files changed, 4830 insertions(+), 5095 deletions(-) create mode 100644 .github/scripts/publish-dashboard.sh create mode 100644 tests/functional/test_dummy.py delete mode 100644 tools/add_license_headers.py delete mode 100644 tools/check_license_headers.py create mode 100644 tools/license_headers.py delete mode 100644 tools/remove_license_headers.py diff --git a/.copier-answers.yml b/.copier-answers.yml index 12859ad..57fbadb 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,6 +1,6 @@ # WARNING: Do not edit this file manually. # Any changes will be overwritten by Copier. -_commit: v0.10.1-22-g084280c +_commit: v0.11.0-9-g7085ef7 _src_path: gh:easyscience/templates app_docs_url: https://easyscience.github.io/peasy-app app_doi: 10.5281/zenodo.18700888 diff --git a/.github/actions/download-artifact/action.yml b/.github/actions/download-artifact/action.yml index e4fd62f..d1fff1a 100644 --- a/.github/actions/download-artifact/action.yml +++ b/.github/actions/download-artifact/action.yml @@ -1,5 +1,5 @@ name: 'Download artifact' -description: 'Generic wrapper for actions/download-artifact' +description: 'Wrapper for actions/download-artifact' inputs: name: description: 'Name of the artifact to download' @@ -39,7 +39,7 @@ runs: using: 'composite' steps: - name: Download artifact - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: ${{ inputs.name }} path: ${{ inputs.path }} diff --git a/.github/actions/github-script/action.yml b/.github/actions/github-script/action.yml index ab32da5..50de89b 100644 --- a/.github/actions/github-script/action.yml +++ b/.github/actions/github-script/action.yml @@ -13,7 +13,7 @@ inputs: runs: using: 'composite' steps: - - uses: actions/github-script@v8 + - uses: actions/github-script@v9 with: script: ${{ inputs.script }} github-token: ${{ inputs.github-token }} diff --git a/.github/actions/setup-easyscience-bot/action.yml b/.github/actions/setup-easyscience-bot/action.yml index 4b28eaf..e51eb01 100644 --- a/.github/actions/setup-easyscience-bot/action.yml +++ b/.github/actions/setup-easyscience-bot/action.yml @@ -22,9 +22,9 @@ runs: steps: - name: Create GitHub App installation token id: app-token - uses: actions/create-github-app-token@v2 + uses: actions/create-github-app-token@v3 with: - app-id: ${{ inputs.app-id }} + client-id: ${{ inputs.app-id }} private-key: ${{ inputs.private-key }} repositories: ${{ inputs.repositories }} diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml index 167ee62..ec7d7ba 100644 --- a/.github/actions/setup-pixi/action.yml +++ b/.github/actions/setup-pixi/action.yml @@ -1,5 +1,5 @@ name: 'Setup Pixi Environment' -description: 'Sets up pixi with common configuration' +description: 'Wrapper for prefix-dev/setup-pixi' inputs: environments: description: 'Pixi environments to setup' diff --git a/.github/actions/upload-artifact/action.yml b/.github/actions/upload-artifact/action.yml index 825ac39..fe8e468 100644 --- a/.github/actions/upload-artifact/action.yml +++ b/.github/actions/upload-artifact/action.yml @@ -1,5 +1,5 @@ name: 'Upload artifact' -description: 'Generic wrapper for actions/upload-artifact' +description: 'Wrapper for actions/upload-artifact' inputs: name: description: 'Artifact name' @@ -38,7 +38,7 @@ runs: using: 'composite' steps: - name: Upload artifact - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: ${{ inputs.name }} path: ${{ inputs.path }} diff --git a/.github/actions/upload-codecov/action.yml b/.github/actions/upload-codecov/action.yml index 37d6298..0cb15d1 100644 --- a/.github/actions/upload-codecov/action.yml +++ b/.github/actions/upload-codecov/action.yml @@ -1,5 +1,5 @@ name: 'Upload coverage to Codecov' -description: 'Generic wrapper for codecov/codecov-action@v5' +description: 'Wrapper for codecov/codecov-action' inputs: name: @@ -32,7 +32,7 @@ inputs: runs: using: composite steps: - - uses: codecov/codecov-action@v5 + - uses: codecov/codecov-action@v6 with: name: ${{ inputs.name }} flags: ${{ inputs.flags }} diff --git a/.github/scripts/publish-dashboard.sh b/.github/scripts/publish-dashboard.sh new file mode 100644 index 0000000..dcbd0b3 --- /dev/null +++ b/.github/scripts/publish-dashboard.sh @@ -0,0 +1,77 @@ +#!/usr/bin/env bash + +set -euo pipefail + +remote_repository="${DASHBOARD_REMOTE_REPOSITORY:?}" +publish_branch="${DASHBOARD_PUBLISH_BRANCH:-master}" +source_dir="${DASHBOARD_SOURCE_DIR:?}" +token="${DASHBOARD_TOKEN:?}" +git_user_name="${DASHBOARD_GIT_USER_NAME:-easyscience[bot]}" +git_user_email="${DASHBOARD_GIT_USER_EMAIL:?}" +commit_message="${DASHBOARD_COMMIT_MESSAGE:?}" +max_attempts="${DASHBOARD_PUSH_ATTEMPTS:-3}" +delay_seconds="${DASHBOARD_PUSH_DELAY_SECONDS:-15}" + +workspace_dir="$(mktemp -d)" +repo_dir="${workspace_dir}/dashboard" +remote_url="https://x-access-token:${token}@github.com/${remote_repository}.git" + +cleanup() { + rm -rf "${workspace_dir}" +} + +prepare_worktree() { + if [[ ! -d "${repo_dir}/.git" ]]; then + git clone --branch "${publish_branch}" --depth 1 "${remote_url}" "${repo_dir}" + else + git -C "${repo_dir}" fetch origin "${publish_branch}" + git -C "${repo_dir}" checkout "${publish_branch}" + git -C "${repo_dir}" reset --hard "origin/${publish_branch}" + git -C "${repo_dir}" clean -fd + fi + + git -C "${repo_dir}" config user.name "${git_user_name}" + git -C "${repo_dir}" config user.email "${git_user_email}" +} + +sync_publish_dir() { + cp -R "${source_dir}/." "${repo_dir}/" + git -C "${repo_dir}" add . + + if git -C "${repo_dir}" diff --cached --quiet; then + return 1 + fi + + git -C "${repo_dir}" commit -m "${commit_message}" +} + +trap cleanup EXIT + +prepare_worktree + +if ! sync_publish_dir; then + echo "No dashboard changes to publish." + exit 0 +fi + +for ((attempt = 1; attempt <= max_attempts; attempt += 1)); do + if git -C "${repo_dir}" push origin "HEAD:${publish_branch}"; then + echo "Dashboard published on attempt ${attempt}." + exit 0 + fi + + if ((attempt == max_attempts)); then + echo "Dashboard publish failed after ${max_attempts} attempts." >&2 + exit 1 + fi + + echo "Dashboard push attempt ${attempt} failed. Retrying in ${delay_seconds}s." >&2 + sleep "${delay_seconds}" + + prepare_worktree + + if ! sync_publish_dir; then + echo "Dashboard changes already exist in the target repository." + exit 0 + fi +done \ No newline at end of file diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml index 47b3384..36ce6f5 100644 --- a/.github/workflows/backmerge.yml +++ b/.github/workflows/backmerge.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Checkout repository (for local actions) - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Setup easyscience[bot] id: bot @@ -38,7 +38,7 @@ jobs: repositories: ${{ github.event.repository.name }} - name: Checkout repository (with bot token) - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: fetch-depth: 0 token: ${{ steps.bot.outputs.token }} diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml index 7305679..21c72b3 100644 --- a/.github/workflows/cleanup.yml +++ b/.github/workflows/cleanup.yml @@ -15,11 +15,11 @@ on: days: description: 'Number of days.' required: true - default: 30 + default: '30' minimum_runs: description: 'The minimum runs to keep for each workflow.' required: true - default: 6 + default: '6' delete_workflow_pattern: description: 'The name or filename of the workflow. if not set then it will target all diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index cd9ff1e..95c190c 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -1,8 +1,10 @@ name: Coverage checks on: - # Trigger the workflow on push + # Trigger the workflow on push to develop push: + branches: + - develop # Do not run on version tags (those are handled by other workflows) tags-ignore: ['v*'] # Trigger the workflow on pull request @@ -15,11 +17,11 @@ permissions: actions: write contents: read -# Allow only one concurrent workflow, skipping runs queued between the run -# in-progress and latest queued. And cancel in-progress runs. +# Allow only one concurrent workflow per PR or branch ref. +# Cancel in-progress runs only for pull requests, but let branch push runs finish. concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - cancel-in-progress: true + cancel-in-progress: ${{ github.event_name == 'pull_request' }} # Set the environment variables to be used in all jobs defined in this workflow env: @@ -32,7 +34,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -46,7 +48,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -69,7 +71,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml index 5159f71..9d1f2b0 100644 --- a/.github/workflows/dashboard.yml +++ b/.github/workflows/dashboard.yml @@ -7,6 +7,10 @@ on: permissions: contents: read +concurrency: + group: dashboard-publish-${{ github.repository }} + cancel-in-progress: false + # Set the environment variables to be used in all jobs defined in this workflow env: CI_BRANCH: ${{ github.head_ref || github.ref_name }} @@ -21,7 +25,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: fetch-depth: 0 @@ -81,22 +85,25 @@ jobs: ${{ github.event.repository.name }} dashboard - # Publish to external dashboard repository with retry logic. + # Push to external dashboard repository with retry logic. # Retry is needed to handle transient GitHub API/authentication issues # that occasionally cause 403 errors when multiple workflows push concurrently. # Uses personal_token (not github_token) as GITHUB_TOKEN cannot access external repos. - - name: Publish to main branch of ${{ github.repository }} - uses: Wandalen/wretry.action@v3.8.0 - with: - attempt_limit: 3 - attempt_delay: 15000 # 15 seconds between retries - action: peaceiris/actions-gh-pages@v4 - with: | - publish_dir: ./_dashboard_publish - keep_files: true - external_repository: ${{ env.REPO_OWNER }}/dashboard - publish_branch: master - personal_token: ${{ steps.bot.outputs.token }} + - name: + Push to ${{ env.REPO_OWNER }}/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH + }} + shell: bash + env: + DASHBOARD_COMMIT_MESSAGE: ${{ env.CI_BRANCH }} + DASHBOARD_GIT_USER_EMAIL: + ${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com + DASHBOARD_PUSH_ATTEMPTS: '3' + DASHBOARD_PUSH_DELAY_SECONDS: '15' + DASHBOARD_PUBLISH_BRANCH: master + DASHBOARD_REMOTE_REPOSITORY: ${{ env.REPO_OWNER }}/dashboard + DASHBOARD_SOURCE_DIR: ./_dashboard_publish + DASHBOARD_TOKEN: ${{ steps.bot.outputs.token }} + run: bash ./.github/scripts/publish-dashboard.sh - name: Add dashboard link to summary run: | diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 46bcee2..b854401 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -83,7 +83,7 @@ jobs: # Check out the repository source code. # Note: The gh-pages branch is fetched separately later for mike deployment. - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 # Activate dark mode to create documentation with Plotly charts in dark mode # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml index 3a60cdd..31a69ad 100644 --- a/.github/workflows/issues-labels.yml +++ b/.github/workflows/issues-labels.yml @@ -13,9 +13,18 @@ permissions: jobs: check-labels: + if: github.actor != 'easyscience[bot]' + runs-on: ubuntu-latest + concurrency: + group: issue-labels-${{ github.event.issue.number }} + cancel-in-progress: true + steps: + - name: Checkout repository + uses: actions/checkout@v6 + - name: Setup easyscience[bot] id: bot uses: ./.github/actions/setup-easyscience-bot diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml index 457d67f..16dd95c 100644 --- a/.github/workflows/lint-format.yml +++ b/.github/workflows/lint-format.yml @@ -41,7 +41,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -79,12 +79,6 @@ jobs: shell: bash run: pixi run docstring-lint-check - - name: Check formatting of docstrings in Python code - id: docstring_format - continue-on-error: true - shell: bash - run: pixi run docstring-format-check - - name: Check formatting of non-Python files (md, toml, etc.) id: nonpy_format continue-on-error: true @@ -112,7 +106,6 @@ jobs: echo "| py lint | ${{ steps.py_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" echo "| py format | ${{ steps.py_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" echo "| docstring lint | ${{ steps.docstring_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" - echo "| docstring format | ${{ steps.docstring_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" echo "| nonpy format | ${{ steps.nonpy_format.outcome == 'success' && 'โœ…' || 'โŒ' }} |" echo "| notebooks lint | ${{ steps.notebook_lint.outcome == 'success' && 'โœ…' || 'โŒ' }} |" } >> "$GITHUB_STEP_SUMMARY" @@ -125,7 +118,6 @@ jobs: || steps.py_lint.outcome == 'failure' || steps.py_format.outcome == 'failure' || steps.docstring_lint.outcome == 'failure' - || steps.docstring_format.outcome == 'failure' || steps.nonpy_format.outcome == 'failure' || steps.notebook_lint.outcome == 'failure' shell: bash diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index 88834ed..5699235 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -20,7 +20,7 @@ jobs: steps: - name: Check-out repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: fetch-depth: 0 # full history with tags to get the version number by versioningit diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index b330135..f0b686b 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -32,7 +32,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -45,6 +45,10 @@ jobs: - name: Init pixi project run: pixi init easypeasy + - name: Set the minimum system requirements + working-directory: easypeasy + run: pixi project system-requirements add macos 14.0 + - name: Add Python 3.13 from Conda working-directory: easypeasy run: pixi add "python=3.13" @@ -53,22 +57,18 @@ jobs: working-directory: easypeasy run: pixi add gsl - - name: Add easypeasy from PyPI - working-directory: easypeasy - run: pixi add --pypi "easypeasy" - - - name: Add dev dependencies from PyPI + - name: Add easypeasy (with dev dependencies) from PyPI working-directory: easypeasy - run: pixi add --pypi pytest pytest-xdist - - - name: Add Pixi task as a shortcut - working-directory: easypeasy - run: pixi task add easypeasy "python -m easypeasy" + run: pixi add --pypi "easypeasy[dev]" - name: Run unit tests to verify the installation working-directory: easypeasy run: pixi run python -m pytest ../tests/unit/ --color=yes -v + - name: Run functional tests to verify the installation + working-directory: easypeasy + run: pixi run python -m pytest ../tests/functional/ --color=yes -v + - name: Run integration tests to verify the installation working-directory: easypeasy run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml index 3a3e39e..3dcd665 100644 --- a/.github/workflows/release-notes.yml +++ b/.github/workflows/release-notes.yml @@ -20,7 +20,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: fetch-depth: 0 # full history with tags to get the version number @@ -61,7 +61,7 @@ jobs: GITHUB_TOKEN: ${{ steps.bot.outputs.token }} - name: Create GitHub draft release - uses: softprops/action-gh-release@v2 + uses: softprops/action-gh-release@v3 with: draft: true tag_name: ${{ steps.draft.outputs.tag_name }} diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml index 7e6fda4..0e716c2 100644 --- a/.github/workflows/release-pr.yml +++ b/.github/workflows/release-pr.yml @@ -30,7 +30,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout ${{ env.SOURCE_BRANCH }} branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: ${{ env.SOURCE_BRANCH }} diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml index 9b34ccc..0f43db3 100644 --- a/.github/workflows/security.yml +++ b/.github/workflows/security.yml @@ -61,13 +61,13 @@ jobs: # focused on the active dev branch. - name: Checkout repository (scheduled โ†’ develop) if: ${{ github.event_name == 'schedule' }} - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: develop - name: Checkout repository if: ${{ github.event_name != 'schedule' }} - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Initialize CodeQL uses: github/codeql-action/init@v4 diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml index ecf6b40..440bae3 100644 --- a/.github/workflows/test-trigger.yml +++ b/.github/workflows/test-trigger.yml @@ -16,7 +16,7 @@ jobs: steps: - name: Checkout develop branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: develop diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index be01657..6d76d2d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -74,13 +74,13 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-24.04, macos-14, windows-2022] + os: [ubuntu-24.04, macos-15, windows-2022] runs-on: ${{ matrix.os }} steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi @@ -96,12 +96,27 @@ jobs: echo echo "๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น Python: $py_ver ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น" - env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env echo "Running tests in environment: $env" pixi run --environment $env unit-tests done + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น Python: $py_ver ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น" + + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env + + echo "Running tests in environment: $env" + pixi run --environment $env functional-tests + done + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} shell: bash run: | @@ -111,7 +126,7 @@ jobs: echo echo "๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น Python: $py_ver ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น" - env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env + env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env echo "Running tests in environment: $env" pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }} @@ -163,13 +178,13 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-24.04, macos-14, windows-2022] + os: [ubuntu-24.04, macos-15, windows-2022] runs-on: ${{ matrix.os }} steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Download package (incl. extras) from previous job uses: ./.github/actions/download-artifact @@ -202,11 +217,8 @@ jobs: echo "Adding Python $py_ver" pixi add "python=$py_ver" - echo "Adding Conda dependencies" - pixi add gsl - - #echo "Adding PyPI dependencies" - #pixi add --pypi pytest pytest-xdist + echo "Setting macOS 14.0 as minimum required" + pixi project system-requirements add macos 14.0 echo "Looking for wheel in ../dist/py$py_ver/" ls -l "../dist/py$py_ver/" @@ -245,6 +257,25 @@ jobs: cd .. done + - name: Run functional tests + shell: bash + run: | + set -euo pipefail + + for py_ver in $PY_VERSIONS; do + echo + echo "๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น Python: $py_ver ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น๐Ÿ”ธ๐Ÿ”น" + + echo "Entering pixi project directory easypeasy_py$py_ver" + cd easypeasy_py$py_ver + + echo "Running tests" + pixi run python -m pytest ../tests/functional/ --color=yes -v + + echo "Exiting pixi project directory" + cd .. + done + - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }} shell: bash run: | diff --git a/.github/workflows/tutorial-tests-trigger.yml b/.github/workflows/tutorial-tests-trigger.yml index 1bc27f4..4b160d8 100644 --- a/.github/workflows/tutorial-tests-trigger.yml +++ b/.github/workflows/tutorial-tests-trigger.yml @@ -16,7 +16,7 @@ jobs: steps: - name: Checkout develop branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 with: ref: develop diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml index 4c9244d..a4fc940 100644 --- a/.github/workflows/tutorial-tests.yml +++ b/.github/workflows/tutorial-tests.yml @@ -40,15 +40,11 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up pixi uses: ./.github/actions/setup-pixi - - name: Test tutorials as python scripts - shell: bash - run: pixi run script-tests - - name: Prepare notebooks shell: bash run: pixi run notebook-prepare diff --git a/.gitignore b/.gitignore index 0500ede..6dc595c 100644 --- a/.gitignore +++ b/.gitignore @@ -41,5 +41,6 @@ CMakeLists.txt.user* *.dmg # Misc +.cache/ *.log *.zip diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5fa0c2c..9a3855f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,13 +39,6 @@ repos: pass_filenames: false stages: [manual] - - id: pixi-docstring-format-check - name: pixi run docstring-format-check - entry: pixi run docstring-format-check - language: system - pass_filenames: false - stages: [manual] - - id: pixi-nonpy-format-check name: pixi run nonpy-format-check entry: pixi run nonpy-format-check diff --git a/.prettierignore b/.prettierignore index 788ec8f..a08c3c4 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,3 +1,6 @@ +# Git +.git/ + # Copier .copier-answers*.yml @@ -14,4 +17,16 @@ docs/docs/assets/ .pytest_cache/ # MyPy -.mypy_cache +.mypy_cache/ + +# Ruff +.ruff_cache/ + +# Node +node_modules + +# Misc +.benchmarks +.cache +deps/ +tmp/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c82b095..2a3e08c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -229,7 +229,6 @@ pixi run license-check.........................Passed pixi run py-lint-check.........................Passed pixi run py-format-check.......................Passed pixi run docstring-lint-check..................Passed -pixi run docstring-format-check................Passed pixi run nonpy-format-check....................Passed pixi run notebook-lint-check...................Passed pixi run unit-tests............................Passed diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index a1154b8..48fc71c 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -148,7 +148,7 @@ plugins: python: paths: ['src'] # Change 'src' to your actual sources directory options: - docstring_style: google + docstring_style: numpy group_by_category: false heading_level: 1 show_root_heading: true diff --git a/pixi.lock b/pixi.lock index e6090c0..0155acf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,15 +11,74 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py313h07c4f96_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda + - 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vc >=14.3,<15 + - vc14_runtime >=14.44.35208 + - ucrt >=10.0.20348.0 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 388453 + timestamp: 1764777142545 diff --git a/pixi.toml b/pixi.toml index 998caba..ad7b03c 100644 --- a/pixi.toml +++ b/pixi.toml @@ -5,7 +5,7 @@ # Platform-independent [activation.env] -PYTHONIOENCODING = "utf-8" +PYTHONIOENCODING = 'utf-8' # Platform-specific @@ -29,11 +29,23 @@ PYTHONPATH = "${PIXI_PROJECT_ROOT}/src;%PYTHONPATH%" [workspace] # Supported platforms for the lock file (pixi.lock) -platforms = ['win-64', 'linux-64', 'osx-64', 'osx-arm64'] +platforms = ['win-64', 'linux-64', 'osx-arm64'] # Channels for fetching packages channels = ['conda-forge'] +##################### +# SYSTEM REQUIREMENTS +##################### + +[system-requirements] + +# Set minimum supported version for macOS to be 14.0 to ensure packages +# like `skipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64) +# are used instead of building from source. This is a workaround for +# Pixi, see https://github.com/prefix-dev/pixi/issues/5667 +macos = '14.0' + ########## # FEATURES ########## @@ -41,12 +53,13 @@ channels = ['conda-forge'] # Default feature configuration [dependencies] -nodejs = '*' # Required for Prettier (non-Python formatting) -#gsl = '*' # GNU Scientific Library; required for pdffit2 +nodejs = '*' # Required for Prettier (non-Python formatting) +jupyterlab = '*' # Jupyter notebooks +pixi-kernel = '*' # Pixi Jupyter kernel [pypi-dependencies] # == [feature.default.pypi-dependencies] #pip = '*' # Native package installer -easypeasy = { path = ".", editable = true, extras = ['dev'] } +easypeasy = { path = '.', editable = true, extras = ['dev'] } # Specific features: Set specific Python versions @@ -63,12 +76,12 @@ python = '3.13.*' # The `default` feature is always included in all environments. # Additional features can be specified per environment. -py-311-env = { features = ['default', 'py-min'] } -py-313-env = { features = ['default', 'py-max'] } +py-311-env = { features = ['py-min'] } +py-313-env = { features = ['py-max'] } # The `default` environment is always created and includes the `default` feature. # It does not need to be specified explicitly unless non-default features are included. -default = { features = ['default', 'py-max'] } +default = { features = ['py-max'] } ####### # TASKS @@ -81,9 +94,9 @@ default = { features = ['default', 'py-max'] } ################## unit-tests = 'python -m pytest tests/unit/ --color=yes -v' +functional-tests = 'python -m pytest tests/functional/ --color=yes -v' integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v' -notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --color=yes -n auto -v' -script-tests = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v' +notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v' test = { depends-on = ['unit-tests'] } @@ -93,12 +106,11 @@ test = { depends-on = ['unit-tests'] } pyproject-check = 'python -m validate_pyproject pyproject.toml' docstring-lint-check = 'pydoclint --quiet src/' -docstring-format-check = 'docformatter --check src/' notebook-lint-check = 'nbqa ruff docs/docs/tutorials/' py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/' -py-format-check = "ruff format --check src/ tests/ docs/docs/tutorials/" -nonpy-format-check = "npx prettier --list-different --config=prettierrc.toml --ignore-unknown ." -nonpy-format-check-modified = "python tools/nonpy_prettier_modified.py" +py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/' +nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .' +nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py' check = 'pre-commit run --hook-stage manual --all-files' @@ -106,21 +118,23 @@ check = 'pre-commit run --hook-stage manual --all-files' # ๐Ÿ› ๏ธ Fixes ########## -docs-format-fix = 'docformatter --in-place src/ docs/docs/tutorials/' +docstring-transform = 'pixi run docstripy src/ -s=numpy -w' +docstring-format-fix = 'format-docstring src/' notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/' py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/' -py-format-fix = "ruff format src/ tests/ docs/docs/tutorials/" +py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/' +py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/' nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .' -nonpy-format-fix-modified = "python tools/nonpy_prettier_modified.py --write" -success-message-fix = 'echo "โœ… All auto-formatting steps completed successfully!"' +nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write' +success-message = 'echo "โœ… All auto-formatting steps completed successfully!"' fix = { depends-on = [ + 'docstring-format-fix', 'py-format-fix', - 'docs-format-fix', 'py-lint-fix', 'nonpy-format-fix', 'notebook-lint-fix', - 'success-message-fix', + 'success-message', ] } #################### @@ -139,6 +153,7 @@ raw-metrics-json = 'radon raw -s -j src/' ############# unit-tests-coverage = 'pixi run unit-tests --cov=src/easypeasy --cov-report=term-missing' +functional-tests-coverage = 'pixi run functional-tests --cov=src/easypeasy --cov-report=term-missing' integration-tests-coverage = 'pixi run integration-tests --cov=src/easypeasy --cov-report=term-missing' docstring-coverage = 'interrogate -c pyproject.toml src/easypeasy' @@ -154,8 +169,8 @@ cov = { depends-on = [ notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb' notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb' -notebook-tweak = 'python tools/tweak_notebooks.py tutorials/' -notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v' +notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/' +notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v' notebook-prepare = { depends-on = [ #'notebook-convert', @@ -168,11 +183,11 @@ notebook-prepare = { depends-on = [ ######################## docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'" -docs-pre = "pixi run docs-vars python -m mkdocs" -docs-serve = "pixi run docs-pre serve -f docs/mkdocs.yml" -docs-serve-dirty = "pixi run docs-serve --dirty" -docs-build = "pixi run docs-pre build -f docs/mkdocs.yml" -docs-build-local = "pixi run docs-build --no-directory-urls" +docs-pre = 'pixi run docs-vars python -m mkdocs' +docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml' +docs-serve-dirty = 'pixi run docs-serve --dirty' +docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml' +docs-build-local = 'pixi run docs-build --no-directory-urls' docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect' docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages' @@ -183,9 +198,9 @@ docs-update-assets = 'python tools/update_docs_assets.py' # ๐Ÿ“ฆ Template Management Tasks ############################## -copier-copy = "copier copy gh:easyscience/templates . --data-file ../peasy/.copier-answers.yml --data template_type=lib" -copier-recopy = "copier recopy --data-file ../peasy/.copier-answers.yml --data template_type=lib" -copier-update = "copier update --data-file ../peasy/.copier-answers.yml --data template_type=lib" +copier-copy = 'copier copy gh:easyscience/templates . --data-file ../peasy/.copier-answers.yml --data template_type=lib' +copier-recopy = 'copier recopy --data-file ../peasy/.copier-answers.yml --data template_type=lib' +copier-update = 'copier update --data-file ../peasy/.copier-answers.yml --data template_type=lib' ##################### # ๐Ÿช Pre-commit Hooks @@ -232,9 +247,9 @@ github-labels = 'python tools/update_github_labels.py' # โš–๏ธ SPDX License Headers ######################### -license-remove = 'python tools/remove_license_headers.py src/ tests/' -license-add = 'python tools/add_license_headers.py src/ tests/' -license-check = 'python tools/check_license_headers.py src/ tests/' +license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' +license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude' #################################### # ๐Ÿš€ Other Development & Build Tasks diff --git a/pyproject.toml b/pyproject.toml index 4edcc89..1df8f22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,13 +24,7 @@ classifiers = [ requires-python = '>=3.11' dependencies = [ #'easyscience', # The base library of the EasyScience framework - 'pooch', # Data downloader - 'darkdetect', # Detecting dark mode (system-level) - 'pandas', # Displaying tables in Jupyter notebooks - 'plotly', # Interactive plots - 'py3Dmol', # Visualisation of crystal structures - 'jupyterlab', # Jupyter notebooks - 'pixi-kernel', # Pixi Jupyter kernel + 'pooch', # Data downloader ] [project.optional-dependencies] @@ -52,7 +46,8 @@ dev = [ 'jupytext', # Jupyter notebook text format support 'jupyterquiz', # Quizzes in Jupyter notebooks 'pydoclint', # Docstring linter - 'docformatter', # Docstring formatter + 'format-docstring', # Docstring formatter + 'docstripy', # Convert docstrings to other formats 'interrogate', # Docstring coverage checker 'copier', # Template management 'mike', # MkDocs: Versioned documentation support @@ -174,7 +169,7 @@ testpaths = ['tests'] [tool.ruff] exclude = ['tmp'] indent-width = 4 -line-length = 99 +line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle] preview = true # Enable new rules that are not yet stable, like DOC # Formatting options for Ruff @@ -183,7 +178,6 @@ preview = true # Enable new rules that are not yet stable, like DOC docstring-code-format = true # Whether to format code snippets in docstrings docstring-code-line-length = 72 # Line length for code snippets in docstrings indent-style = 'space' # PEP 8 recommends using spaces over tabs -line-ending = 'lf' # Line endings will be converted to \n quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257) # Linting rules to use with Ruff @@ -251,15 +245,20 @@ select = [ # Ignore specific rules globally ignore = [ 'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/ - # The following covered by [tool.pydoclint] section below - 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d + # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc + # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout + 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/ ] # Ignore specific rules in certain files or directories [tool.ruff.lint.per-file-ignores] +'*/__init__.py' = [ + 'F401', # re-exports are intentional in __init__.py +] 'tests/**' = [ 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann + 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc 'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/ 'S101', # https://docs.astral.sh/ruff/rules/assert/ @@ -287,17 +286,18 @@ max-complexity = 10 # PEP 8 line length guidance: # https://peps.python.org/pep-0008/#maximum-line-length # Use 99 characters as the project-wide maximum for regular code lines. -max-line-length = 99 -# allow longer lines so that parameter declarations such as -# `name (Type | Type | None):` remain on a single line. Splitting these -# lines can prevent tools such as MkDocs and IDEs from correctly -# parsing and rendering parameter documentation. -# The descriptive text itself is wrapped more strictly by -# `docformatter` (see the configuration in [tool.docformatter] below) -# whenever it is treated as normal paragraph text. -# The line length for code snippets in docstrings is also more strict, -# as defined in the [tool.ruff.format] section above. -max-doc-length = 99 +# Use 72 characters for docstrings. +max-line-length = 99 # See also `line-length` in [tool.ruff] +max-doc-length = 72 + +[tool.ruff.lint.pydocstyle] +convention = 'numpy' + +[tool.ruff.lint.pylint] +# Ruff counts `self`/`cls` in max-args; traditional pylint does not. +# Setting 6 here matches pylint's default of 5 (excluding self). +max-args = 6 +max-positional-args = 6 ############################# # Configuration for pydoclint @@ -314,20 +314,22 @@ max-doc-length = 99 # the parameter declarations in the code (in function's signature). [tool.pydoclint] -style = "google" +exclude = '\.' # Temporarily disable pydoclint until we are ready +style = 'numpy' check-style-mismatch = true check-arg-defaults = true allow-init-docstring = true -################################ -# Configuration for docformatter -################################ +#################################### +# Configuration for format-docstring +#################################### -# 'docformatter' -- Code formatter for docstrings -# https://docformatter.readthedocs.io/en/latest/ +# 'format-docstring' -- Code formatter for docstrings +# https://github.com/jsh9/format-docstring -[tool.docformatter] -recursive = true -wrap-summaries = 72 -wrap-descriptions = 72 -close-quotes-on-newline = true +[tool.format_docstring] +exclude = '\.' # Temporarily disable format-docstring until we are ready +docstring_style = 'numpy' +line_length = 72 +fix_rst_backticks = true +verbose = 'default' diff --git a/tests/functional/test_dummy.py b/tests/functional/test_dummy.py new file mode 100644 index 0000000..a47f64d --- /dev/null +++ b/tests/functional/test_dummy.py @@ -0,0 +1,8 @@ +# SPDX-FileCopyrightText: 2025-2026 EasyPeasy contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_dummy(): + calculated = 2 + 2 + expected = 4 + assert calculated == expected diff --git a/tests/unit/test_dummy.py b/tests/unit/test_dummy.py index 3c4448b0..6927fe8 100644 --- a/tests/unit/test_dummy.py +++ b/tests/unit/test_dummy.py @@ -2,7 +2,7 @@ # SPDX-License-Identifier: BSD-3-Clause -def test_dummy_fast(): +def test_dummy(): calculated = 2 + 2 expected = 4 assert calculated == expected diff --git a/tools/add_license_headers.py b/tools/add_license_headers.py deleted file mode 100644 index 28febde..0000000 --- a/tools/add_license_headers.py +++ /dev/null @@ -1,151 +0,0 @@ -# SPDX-FileCopyrightText: 2026 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause -"""Add SPDX headers to Python files. - -- SPDX-FileCopyrightText with the license holder name and organization - URL from ``pyproject.toml`` as well as the file's creation year. -- SPDX-License-Identifier is taken from the project license value in - ``pyproject.toml``. -""" - -from __future__ import annotations - -import argparse -import tomllib -from datetime import datetime -from pathlib import Path -from typing import Optional -from typing import Union - -from git import Repo -from spdx_headers.core import find_repository_root -from spdx_headers.core import get_copyright_info -from spdx_headers.data import load_license_data -from spdx_headers.operations import add_header_to_single_file - -LICENSE_DATABASE = load_license_data() - - -def load_pyproject(repo_path: Union[str, Path]) -> dict: - """Load and return parsed ``pyproject.toml`` data for the - repository. - """ - repo_root = find_repository_root(repo_path) - pyproject_path = repo_root / 'pyproject.toml' - - with open(pyproject_path, 'rb') as file_handle: - return tomllib.load(file_handle) - - -def get_file_creation_year(file_path: Union[str, Path]) -> str: - """Return the year the file was first added to Git history. - - If the year cannot be determined, fall back to the current year. - """ - file_path = Path(file_path) - - repo = Repo(file_path, search_parent_directories=True) - root = Path(repo.working_tree_dir).resolve() - rel_path = file_path.resolve().relative_to(root) - - rel_path_git = rel_path.as_posix() # IMPORTANT for git pathspec - - # Get the year when the file was first added to Git history. - # NOTE: Do not combine `--reverse` with `--max-count=1` here, as it can - # yield an empty result with some Git versions. Instead, get the full - # filtered output and take the first line. - log_output = repo.git.log( - '--follow', - '--diff-filter=A', - '--reverse', - '--format=%ad', - '--date=format:%Y', - '--', - rel_path_git, - ).strip() - - year = log_output.splitlines()[0].strip() if log_output else '' - - return year or str(datetime.now().year) - - -def get_org_url(repo_path: Union[str, Path]) -> str: - """Return the organization URL derived from the repository source - URL. - """ - pyproject_data = load_pyproject(repo_path) - repo_url = pyproject_data['project']['urls']['Source Code'] - return repo_url.rsplit('/', 1)[0] - - -def get_project_license(repo_path: Union[str, Path]) -> str: - """Return the project license value from ``pyproject.toml``.""" - pyproject_data = load_pyproject(repo_path) - return pyproject_data['project']['license'] - - -def get_copyright_holder(repo_path: Union[str, Path]) -> str: - """Return the repository copyright holder name.""" - _, name, _ = get_copyright_info(repo_path) - return name - - -def add_spdx_header( - target_file: Union[str, Path], - *, - license_key: str, - copyright_holder: str, - org_url: str, -) -> None: - """Add SPDX headers.""" - year = get_file_creation_year(target_file) - - add_header_to_single_file( - filepath=target_file, - license_key=license_key, - license_data=LICENSE_DATABASE, - year=year, - name=copyright_holder, - email=org_url, - ) - - -def build_parser() -> argparse.ArgumentParser: - parser = argparse.ArgumentParser( - description='Add SPDX headers to Python files under the given paths.', - ) - parser.add_argument( - 'paths', - nargs='+', - help='Relative paths to scan (e.g. src tests)', - ) - return parser - - -def main(argv: Optional[list[str]] = None) -> int: - parser = build_parser() - args = parser.parse_args(argv) - - repo_path = Path('.').resolve() - license_key = get_project_license(repo_path) - copyright_holder = get_copyright_holder(repo_path) - org_url = get_org_url(repo_path) - - for base_dir in args.paths: - base_path = Path(base_dir) - if not base_path.exists(): - parser.error(f'Path does not exist: {base_dir}') - - for py_file in base_path.rglob('*.py'): - add_spdx_header( - py_file, - license_key=license_key, - copyright_holder=copyright_holder, - org_url=org_url, - ) - - return 0 - - -if __name__ == '__main__': - raise SystemExit(main()) diff --git a/tools/check_license_headers.py b/tools/check_license_headers.py deleted file mode 100644 index c8a4df2..0000000 --- a/tools/check_license_headers.py +++ /dev/null @@ -1,45 +0,0 @@ -# SPDX-FileCopyrightText: 2026 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause -"""Check SPDX headers in Python files.""" - -from __future__ import annotations - -import argparse -from pathlib import Path -from typing import Optional - -from spdx_headers.operations import check_headers - - -def build_parser() -> argparse.ArgumentParser: - parser = argparse.ArgumentParser( - description='Check SPDX headers in Python files under the given paths.', - ) - parser.add_argument( - 'paths', - nargs='+', - help='Relative paths to scan (e.g. src tests)', - ) - return parser - - -def main(argv: Optional[list[str]] = None) -> int: - parser = build_parser() - args = parser.parse_args(argv) - - exit_codes = [] - - for base_dir in args.paths: - base_path = Path(base_dir) - if not base_path.exists(): - parser.error(f'Path does not exist: {base_dir}') - - print('=' * 50) - print(f'Checking SPDX headers in: {base_dir}') - exit_codes.append(check_headers(base_dir)) - - return 0 if all(code == 0 for code in exit_codes) else 1 - - -if __name__ == '__main__': - raise SystemExit(main()) diff --git a/tools/license_headers.py b/tools/license_headers.py new file mode 100644 index 0000000..f276ca1 --- /dev/null +++ b/tools/license_headers.py @@ -0,0 +1,321 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Add, remove, or check SPDX headers in Python files.""" + +from __future__ import annotations + +import argparse +import fnmatch +import tomllib +from datetime import datetime +from pathlib import Path +from typing import Any +from typing import Optional +from typing import Union + +from git import Repo +from spdx_headers.core import find_repository_root +from spdx_headers.core import get_copyright_info +from spdx_headers.core import has_spdx_header +from spdx_headers.data import load_license_data +from spdx_headers.operations import add_header_to_single_file +from spdx_headers.operations import remove_header_from_single_file + +LICENSE_DATABASE = load_license_data() + + +def load_pyproject(repo_path: Union[str, Path]) -> dict[str, Any]: + """ + Load and return parsed ``pyproject.toml`` data for the repository. + """ + repo_root = find_repository_root(repo_path) + pyproject_path = repo_root / 'pyproject.toml' + + with pyproject_path.open('rb') as file_handle: + return tomllib.load(file_handle) + + +def get_pyproject_value(pyproject_data: dict[str, Any], dotted_key: str) -> Any: + """Return a nested ``pyproject.toml`` value from a dotted key.""" + value: Any = pyproject_data + for part in dotted_key.split('.'): + if not isinstance(value, dict) or part not in value: + raise KeyError(dotted_key) + value = value[part] + return value + + +def normalize_pattern(pattern: str) -> str: + """Normalize an exclude pattern to a POSIX-style relative path.""" + normalized = Path(pattern).as_posix() + if normalized.startswith('./'): + normalized = normalized[2:] + return normalized.rstrip('/') + + +def get_exclude_patterns( + repo_path: Union[str, Path], + exclude_values: list[str], + exclude_from_pyproject_toml: Optional[str], +) -> list[str]: + """ + Return normalized exclude patterns from CLI and ``pyproject.toml``. + """ + pyproject_data = load_pyproject(repo_path) + patterns: list[str] = [] + + if exclude_from_pyproject_toml: + value = get_pyproject_value(pyproject_data, exclude_from_pyproject_toml) + if not isinstance(value, list) or not all(isinstance(item, str) for item in value): + raise ValueError( + f'{exclude_from_pyproject_toml} in pyproject.toml must be a list of strings.', + ) + patterns.extend(value) + + for item in exclude_values: + try: + value = get_pyproject_value(pyproject_data, item) + except KeyError: + patterns.append(item) + continue + + if not isinstance(value, list) or not all(isinstance(entry, str) for entry in value): + raise ValueError(f'{item} in pyproject.toml must be a list of strings.') + patterns.extend(value) + + normalized_patterns: list[str] = [] + seen: set[str] = set() + for pattern in patterns: + normalized = normalize_pattern(pattern) + if normalized and normalized not in seen: + normalized_patterns.append(normalized) + seen.add(normalized) + + return normalized_patterns + + +def get_file_creation_year(file_path: Union[str, Path]) -> str: + """Return the year the file was first added to Git history. + + If the year cannot be determined, fall back to the current year. + """ + file_path = Path(file_path) + + repo = Repo(file_path, search_parent_directories=True) + root = Path(repo.working_tree_dir).resolve() + rel_path = file_path.resolve().relative_to(root) + + rel_path_git = rel_path.as_posix() + + log_output = repo.git.log( + '--follow', + '--diff-filter=A', + '--reverse', + '--format=%ad', + '--date=format:%Y', + '--', + rel_path_git, + ).strip() + + year = log_output.splitlines()[0].strip() if log_output else '' + + return year or str(datetime.now().year) + + +def get_org_url(repo_path: Union[str, Path]) -> str: + """ + Return the organization URL derived from the repository source URL. + """ + pyproject_data = load_pyproject(repo_path) + repo_url = pyproject_data['project']['urls']['Source Code'] + return repo_url.rsplit('/', 1)[0] + + +def get_project_license(repo_path: Union[str, Path]) -> str: + """Return the project license value from ``pyproject.toml``.""" + pyproject_data = load_pyproject(repo_path) + return pyproject_data['project']['license'] + + +def get_copyright_holder(repo_path: Union[str, Path]) -> str: + """Return the repository copyright holder name.""" + _, name, _ = get_copyright_info(repo_path) + return name + + +def add_spdx_header( + target_file: Union[str, Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> None: + """Add SPDX headers to one file.""" + year = get_file_creation_year(target_file) + + add_header_to_single_file( + filepath=target_file, + license_key=license_key, + license_data=LICENSE_DATABASE, + year=year, + name=copyright_holder, + email=org_url, + ) + + +def is_excluded(relative_path: str, exclude_patterns: list[str]) -> bool: + """Return whether a relative path should be excluded.""" + for pattern in exclude_patterns: + if fnmatch.fnmatch(relative_path, pattern): + return True + if relative_path == pattern: + return True + if relative_path.startswith(f'{pattern}/'): + return True + return False + + +def iter_python_files( + paths: list[str], + *, + repo_root: Path, + exclude_patterns: list[str], + parser: argparse.ArgumentParser, +) -> list[Path]: + """Collect Python files under the given paths after exclusions.""" + files: list[Path] = [] + seen: set[Path] = set() + + for base_dir in paths: + base_path = Path(base_dir) + if not base_path.exists(): + parser.error(f'Path does not exist: {base_dir}') + + if base_path.is_file(): + candidates = [base_path] if base_path.suffix == '.py' else [] + else: + candidates = sorted(base_path.rglob('*.py')) + + for py_file in candidates: + resolved = py_file.resolve() + try: + relative_path = resolved.relative_to(repo_root).as_posix() + except ValueError: + relative_path = py_file.as_posix() + + if is_excluded(relative_path, exclude_patterns): + continue + + if resolved not in seen: + files.append(py_file) + seen.add(resolved) + + return files + + +def run_add( + files: list[Path], + *, + license_key: str, + copyright_holder: str, + org_url: str, +) -> int: + """Add SPDX headers to all selected files.""" + for py_file in files: + add_spdx_header( + py_file, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + return 0 + + +def run_remove(files: list[Path]) -> int: + """Remove SPDX headers from all selected files.""" + for py_file in files: + remove_header_from_single_file(py_file) + return 0 + + +def run_check(files: list[Path]) -> int: + """Check SPDX headers in all selected files.""" + missing_files = [py_file for py_file in files if not has_spdx_header(py_file)] + + if not missing_files: + print('โœ“ All Python files have valid SPDX headers.') + return 0 + + print('โœ— The following files are missing SPDX headers:') + for py_file in missing_files: + print(f' - {py_file.as_posix()}') + print(f'\nFound {len(missing_files)} files without SPDX headers.') + return 1 + + +def build_parser() -> argparse.ArgumentParser: + """Build the CLI argument parser.""" + parser = argparse.ArgumentParser( + description='Add, remove, or check SPDX headers in Python files.', + ) + subparsers = parser.add_subparsers(dest='command', required=True) + + for command_name in ('check', 'remove', 'add'): + command_parser = subparsers.add_parser(command_name) + command_parser.add_argument( + 'paths', + nargs='+', + help='Relative paths to scan (e.g. src tests)', + ) + command_parser.add_argument( + '--exclude', + nargs='*', + default=[], + help='Exclude paths, glob patterns, or pyproject dotted keys.', + ) + command_parser.add_argument( + '--exclude-from-pyproject-toml', + help='Read exclude patterns from a dotted key in pyproject.toml.', + ) + + return parser + + +def main(argv: Optional[list[str]] = None) -> int: + """Run the SPDX header CLI.""" + parser = build_parser() + args = parser.parse_args(argv) + + repo_path = Path('.').resolve() + repo_root = find_repository_root(repo_path).resolve() + exclude_patterns = get_exclude_patterns( + repo_path, + args.exclude, + args.exclude_from_pyproject_toml, + ) + files = iter_python_files( + args.paths, + repo_root=repo_root, + exclude_patterns=exclude_patterns, + parser=parser, + ) + + if args.command == 'check': + return run_check(files) + + if args.command == 'remove': + return run_remove(files) + + license_key = get_project_license(repo_path) + copyright_holder = get_copyright_holder(repo_path) + org_url = get_org_url(repo_path) + return run_add( + files, + license_key=license_key, + copyright_holder=copyright_holder, + org_url=org_url, + ) + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/tools/remove_license_headers.py b/tools/remove_license_headers.py deleted file mode 100644 index f5d09da..0000000 --- a/tools/remove_license_headers.py +++ /dev/null @@ -1,41 +0,0 @@ -# SPDX-FileCopyrightText: 2026 EasyScience contributors -# SPDX-License-Identifier: BSD-3-Clause -"""Remove SPDX headers from Python files.""" - -from __future__ import annotations - -import argparse -from pathlib import Path -from typing import Optional - -from spdx_headers.operations import remove_header_from_py_files - - -def build_parser() -> argparse.ArgumentParser: - parser = argparse.ArgumentParser( - description='Remove SPDX headers from Python files under the given paths.', - ) - parser.add_argument( - 'paths', - nargs='+', - help='Relative paths to scan (e.g. src tests)', - ) - return parser - - -def main(argv: Optional[list[str]] = None) -> int: - parser = build_parser() - args = parser.parse_args(argv) - - for base_dir in args.paths: - base_path = Path(base_dir) - if not base_path.exists(): - parser.error(f'Path does not exist: {base_dir}') - - remove_header_from_py_files(base_dir) - - return 0 - - -if __name__ == '__main__': - raise SystemExit(main()) From 0bfa0f43f7b79f5721fdfd4883dbae01d19482b9 Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Tue, 5 May 2026 20:51:20 +0200 Subject: [PATCH 3/3] Fix documentation build (#34) * Enable pydoclint and format-docstring * Bump dependencies --- pixi.lock | 2112 +++++++++++++++---------------- pyproject.toml | 4 +- 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[tool.pydoclint] -exclude = '\.' # Temporarily disable pydoclint until we are ready +#exclude = '\.' # Temporarily disable pydoclint until we are ready style = 'numpy' check-style-mismatch = true check-arg-defaults = true @@ -328,7 +328,7 @@ allow-init-docstring = true # https://github.com/jsh9/format-docstring [tool.format_docstring] -exclude = '\.' # Temporarily disable format-docstring until we are ready +#exclude = '\.' # Temporarily disable format-docstring until we are ready docstring_style = 'numpy' line_length = 72 fix_rst_backticks = true diff --git a/src/easypeasy/utils/__init__.py b/src/easypeasy/utils/__init__.py index f808f0e..70d1abb 100644 --- a/src/easypeasy/utils/__init__.py +++ b/src/easypeasy/utils/__init__.py @@ -1,3 +1,4 @@ # SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -"""EasyPeasy library.""" + +"""Utilities for EasyPeasy.""" diff --git a/src/easypeasy/utils/utils.py b/src/easypeasy/utils/utils.py index 15248b2..1b4393a 100644 --- a/src/easypeasy/utils/utils.py +++ b/src/easypeasy/utils/utils.py @@ -13,15 +13,22 @@ def dummy_method( left: str, right: str, ) -> str: - """Dummy method for testing. It concatenates the left and right - strings. + """ + Dummy method for testing. + + It concatenates the left and right strings. - Args: - left (str): Left side of the new string. - right (str): Right side of the new string. + Parameters + ---------- + left : str + Left side of the new string. + right : str + Right side of the new string. - Returns: - str: The output string. + Returns + ------- + str + The output string. """ logger.debug('Calling dummy method')