fair-ca-visualization 0.4.1__tar.gz

fair_ca_visualization-0.4.1/.bumpversion.toml

@@ -0,0 +1,45 @@
+[tool.bumpversion]
+current_version = "0.4.1"
+commit = true
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+# no tag: the bump is merged into develop through a pull request, which
+# rewrites the commit, so the tag is created on develop afterwards
+tag = false
+sign_tags = false
+tag_name = "{new_version}"
+tag_message = "Bump version: {current_version} to {new_version}"
+allow_dirty = false
+message = "Bump version: {current_version} to {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "./pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "./uv.lock"
+search = """
+name = "fair-ca-visualization"
+version = "{current_version}"
+"""
+replace = """
+name = "fair-ca-visualization"
+version = "{new_version}"
+"""
+
+[[tool.bumpversion.files]]
+filename = "./src/fairvis/__init__.py"
+
+[[tool.bumpversion.files]]
+filename = "./CITATION.cff"
+search = 'version: "{current_version}"'
+replace = 'version: "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "./tests/test_package.py"

fair_ca_visualization-0.4.1/.editorconfig

@@ -0,0 +1,20 @@
+# Editor Configuration (http://editorconfig.org)
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 4
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 88
+
+[*.{json,yml}]
+indent_size = 2
+
+[*.{md,rst}]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab

fair_ca_visualization-0.4.1/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# the maintainer is requested for review on every pull request
+* @matthiaskoenig

fair_ca_visualization-0.4.1/.github/ISSUE_TEMPLATE/01-bug-report.md

@@ -0,0 +1,21 @@
+---
+name: Bug report
+about: Something in the app or the package does not work as expected
+labels: bug
+---
+
+**What happened**
+
+<!-- what you did and what you saw, e.g., the error message -->
+
+**What you expected**
+
+**How to reproduce**
+
+<!-- the steps, and the assessment file if an upload is involved -->
+
+**Environment**
+
+- app at faircombine.streamlit.app or local installation:
+- version of fair-ca-visualization (`pip show fair-ca-visualization`):
+- operating system and browser:

fair_ca_visualization-0.4.1/.github/ISSUE_TEMPLATE/02-question.md

@@ -0,0 +1,9 @@
+---
+name: Question
+about: A question about the app, the indicators or the package
+labels: question
+---
+
+**Question**
+
+<!-- what would you like to know -->

fair_ca_visualization-0.4.1/.github/ISSUE_TEMPLATE/03-feature-request.md

@@ -0,0 +1,11 @@
+---
+name: Feature request
+about: An idea for the app or the package
+labels: enhancement
+---
+
+**What problem would it solve**
+
+**What you propose**
+
+**Alternatives you considered**

fair_ca_visualization-0.4.1/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: FAIR COMBINE Archive Indicators
+    url: https://github.com/FAIR-CA-indicators/FAIR-CA-indicators.github.io
+    about: Questions about the indicators themselves

fair_ca_visualization-0.4.1/.github/dependabot.yml

@@ -0,0 +1,47 @@
+# Keep the GitHub Actions, the locked python dependencies and the pre-commit hooks up to date.
+# See https://docs.github.com/code-security/dependabot/dependabot-version-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "develop"
+    schedule:
+      interval: "monthly"
+    # a single pull request for all action updates instead of one per action
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "ci"
+
+  # the locked python dependencies (uv.lock), which Streamlit Community Cloud installs
+  - package-ecosystem: "uv"
+    directory: "/"
+    target-branch: "develop"
+    # only uv.lock is updated, the lower bounds in pyproject.toml are changed by hand
+    versioning-strategy: lockfile-only
+    schedule:
+      interval: "monthly"
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "build"
+
+  # the hook revisions in .pre-commit-config.yaml (ruff and ty are also locked in uv.lock, see the ruff workflow)
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    target-branch: "develop"
+    schedule:
+      interval: "monthly"
+    groups:
+      pre-commit-hooks:
+        patterns:
+          - "*"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "ci"

fair_ca_visualization-0.4.1/.github/pull_request_template.md

@@ -0,0 +1,12 @@
+## Summary
+
+<!-- what does this change and why -->
+
+## Checklist
+
+- [ ] the pull request targets `develop`
+- [ ] tests were added or updated for the change
+- [ ] `uv run pytest -n auto` and `uv run ty check` pass locally
+- [ ] `ruff check` and `ruff format` are clean, e.g., via `uv run pre-commit run --all-files`
+- [ ] public functions and classes have type annotations and a docstring
+- [ ] user visible changes are in `release-notes/` and, if needed, in `docs/`

fair_ca_visualization-0.4.1/.github/rulesets/apply.sh

@@ -0,0 +1,76 @@
+#!/usr/bin/env bash
+#
+# Apply the repository policies of fair-ca-visualization: the settings of the
+# repository, the deployment branches of its environments and the rulesets in
+# this directory. The script is idempotent, i.e., a ruleset which already
+# exists is updated instead of added a second time, so it can be run again
+# after every change of the json files.
+#
+# The file name of a ruleset has to match the "name" in the json. A ruleset which
+# is removed from this directory stays on the repository, delete it with
+# `gh api -X DELETE repos/<owner>/<repo>/rulesets/<id>`.
+#
+# Requires the github cli (https://cli.github.com) authenticated as a user with
+# admin permission on the repository:
+#
+#   gh auth login
+#   .github/rulesets/apply.sh [owner/repo]
+#
+set -euo pipefail
+
+REPO="${1:-matthiaskoenig/fair-ca-visualization}"
+DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+echo "repository settings of ${REPO}"
+gh api -X PATCH "repos/${REPO}" \
+  -f default_branch=develop \
+  -F allow_auto_merge=true \
+  -F delete_branch_on_merge=true \
+  -F allow_update_branch=true \
+  -F allow_squash_merge=true \
+  -F allow_rebase_merge=true \
+  -F allow_merge_commit=false \
+  --silent
+
+# add a deployment branch or tag policy to an environment unless it exists
+ensure_policy() {
+  local environment="$1" name="$2" type="$3"
+  gh api -X PUT "repos/${REPO}/environments/${environment}" --silent --input - <<'JSON'
+{"deployment_branch_policy": {"protected_branches": false, "custom_branch_policies": true}}
+JSON
+  local policies
+  policies="$(gh api "repos/${REPO}/environments/${environment}/deployment-branch-policies" \
+    --jq ".branch_policies[] | select(.type == \"${type}\") | .name")"
+  if grep -qxF "${name}" <<<"${policies}"; then
+    echo "environment ${environment}: ${type} ${name} may deploy"
+  else
+    gh api -X POST "repos/${REPO}/environments/${environment}/deployment-branch-policies" \
+      -f name="${name}" -f type="${type}" --silent
+    echo "environment ${environment}: ${type} ${name} may deploy (added)"
+  fi
+}
+
+# GitHub Pages is built by the documentation workflow, not from a branch
+if gh api "repos/${REPO}/pages" --silent 2>/dev/null; then
+  gh api -X PUT "repos/${REPO}/pages" -f build_type=workflow --silent
+else
+  gh api -X POST "repos/${REPO}/pages" -f build_type=workflow --silent
+fi
+echo "GitHub Pages built by GitHub Actions"
+
+# the documentation workflow deploys from develop
+ensure_policy github-pages develop branch
+# the release workflow publishes to PyPI from a tag
+ensure_policy pypi '*' tag
+
+for path in "${DIR}"/*.json; do
+  name="$(basename "${path}" .json)"
+  id="$(gh api "repos/${REPO}/rulesets" --jq "map(select(.name == \"${name}\")) | .[0].id // empty")"
+  if [[ -n "${id}" ]]; then
+    gh api -X PUT "repos/${REPO}/rulesets/${id}" --input "${path}" --silent
+    echo "ruleset ${name} updated (${id})"
+  else
+    id="$(gh api -X POST "repos/${REPO}/rulesets" --input "${path}" --jq .id)"
+    echo "ruleset ${name} created (${id})"
+  fi
+done

fair_ca_visualization-0.4.1/.github/rulesets/develop.json

@@ -0,0 +1,42 @@
+{
+  "name": "develop",
+  "target": "branch",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/develop"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "deletion"},
+    {"type": "non_fast_forward"},
+    {"type": "required_linear_history"},
+    {
+      "type": "pull_request",
+      "parameters": {
+        "required_approving_review_count": 0,
+        "dismiss_stale_reviews_on_push": true,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_review_thread_resolution": true,
+        "allowed_merge_methods": ["squash", "rebase"],
+        "require_extra_approval_for_unattributed_changes": false
+      }
+    },
+    {
+      "type": "required_status_checks",
+      "parameters": {
+        "strict_required_status_checks_policy": false,
+        "do_not_enforce_on_create": false,
+        "required_status_checks": [
+          {"context": "tests"},
+          {"context": "ruff"},
+          {"context": "ty"},
+          {"context": "docs"}
+        ]
+      }
+    }
+  ]
+}

fair_ca_visualization-0.4.1/.github/rulesets/main.json

@@ -0,0 +1,17 @@
+{
+  "name": "main",
+  "target": "branch",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/main"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "deletion"},
+    {"type": "non_fast_forward"},
+    {"type": "required_linear_history"}
+  ]
+}

fair_ca_visualization-0.4.1/.github/rulesets/tag-creation.json

@@ -0,0 +1,17 @@
+{
+  "name": "tag-creation",
+  "target": "tag",
+  "enforcement": "active",
+  "bypass_actors": [
+    {"actor_id": 5, "actor_type": "RepositoryRole", "bypass_mode": "always"}
+  ],
+  "conditions": {
+    "ref_name": {
+      "include": ["~ALL"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "creation"}
+  ]
+}

fair_ca_visualization-0.4.1/.github/rulesets/tags.json

@@ -0,0 +1,16 @@
+{
+  "name": "tags",
+  "target": "tag",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": ["~ALL"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "deletion"},
+    {"type": "non_fast_forward"}
+  ]
+}

fair_ca_visualization-0.4.1/.github/workflows/ci-cd.yml

@@ -0,0 +1,193 @@
+name: CI-CD
+
+on:
+  push:
+    # feature branches are tested through their pull request, tags release
+    branches: [develop, main]
+    tags: ['*']
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+# least privilege by default, the release and sync jobs raise what they need
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  # superseded branch runs are cancelled, release runs are never cancelled
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+env:
+  # the tools run with uvx are pinned, dependabot does not update them
+  TWINE_VERSION: "7.0.0"
+  # the standalone interpreters uv manages, not the ones of the runner image
+  UV_PYTHON_PREFERENCE: only-managed
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        # the app runs on the one python version of .python-version; the
+        # platforms are those of the users who install the package locally
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.14"]
+
+    steps:
+    - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+      with:
+        persist-credentials: false
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884  # v10.3.0
+      with:
+        version: "0.12.21"
+        python-version: ${{ matrix.python-version }}
+        # a release run restores no cache, which zizmor cannot tell from the
+        # expression; the distributions are built without one, see `package`
+        enable-cache: ${{ !startsWith(github.ref, 'refs/tags/') }}  # zizmor: ignore[cache-poisoning]
+    - name: Install the locked dependencies (fails if uv.lock is out of date with pyproject.toml, run `uv lock`)
+      # the environment Streamlit Community Cloud installs, from the same uv.lock
+      run: uv sync --locked
+    - name: Test
+      # the tests run on every core, the slowest are listed so they stay visible
+      run: uv run pytest -n auto --durations=15
+
+  package:
+    # builds the distributions and runs the app from the installed wheel; on a
+    # tag the distributions are the ones published, see `publish`
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+      with:
+        # the history of develop, a release tag has to be on it
+        fetch-depth: 0
+        persist-credentials: false
+    - name: Install uv
+      uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884  # v10.3.0
+      with:
+        version: "0.12.21"
+        python-version: "3.14"
+        # a release is built from a clean state, never from a restored cache
+        enable-cache: false
+    - name: Check the release
+      # the tagged commit is on develop, otherwise `sync-main` would move main
+      # off develop; the tag, the version of the package and the citation agree,
+      # and the release notes exist; checked before anything is published
+      if: startsWith(github.ref, 'refs/tags/')
+      env:
+        TAG: ${{ github.ref_name }}
+      run: |
+        git merge-base --is-ancestor "${GITHUB_SHA}" origin/develop
+        grep -qx "__version__ = \"${TAG}\"" src/fairvis/__init__.py
+        grep -qx "version: \"${TAG}\"" CITATION.cff
+        test -f "release-notes/${TAG}.md"
+    - name: Build the package
+      # --no-sources: built the way a user builds it, without uv specific sources
+      run: uv build --no-sources
+    - name: Check the package
+      run: uvx "twine@${TWINE_VERSION}" check --strict dist/*
+    - name: Run the app from the installed wheel
+      run: scripts/smoke_test.sh dist/*.whl
+    - name: Upload the distributions
+      uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9  # v7.0.2
+      with:
+        name: dist
+        path: dist/
+        if-no-files-found: error
+
+  tests:
+    # the one check the branch protection requires; the names of the matrix
+    # jobs change with the matrix, this name does not
+    name: tests
+    needs: [test, package]
+    if: always()
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+    - name: Check the results of the tests and the package
+      env:
+        TEST: ${{ needs.test.result }}
+        PACKAGE: ${{ needs.package.result }}
+      run: |
+        echo "test matrix: $TEST, package: $PACKAGE"
+        test "$TEST" = "success"
+        test "$PACKAGE" = "success"
+
+  publish:
+    # the only job which can publish to PyPI, by trusted publishing through the
+    # `pypi` environment; nothing is checked out and nothing is built here
+    needs: tests
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fair-ca-visualization
+    permissions:
+      id-token: write  # trusted publishing to PyPI
+    steps:
+    - name: Download the distributions
+      uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333  # v8.0.2
+      with:
+        name: dist
+        path: dist/
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33  # v1.14.2
+      with:
+        packages-dir: dist/
+        # PEP 740 attestations, signed with the identity of this workflow
+        attestations: true
+
+  github-release:
+    # created once the package is on PyPI; Zenodo archives the release
+    needs: publish
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      contents: write  # create the GitHub release
+    steps:
+    - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+      with:
+        persist-credentials: false
+    - name: Download the distributions
+      uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333  # v8.0.2
+      with:
+        name: dist
+        path: dist/
+    - name: Create GitHub release
+      # the GitHub cli of the runner, no third party action gets write access
+      env:
+        GH_TOKEN: ${{ github.token }}
+        TAG: ${{ github.ref_name }}
+      run: >-
+        gh release create "$TAG"
+        --repo "$GITHUB_REPOSITORY"
+        --verify-tag
+        --title "fair-ca-visualization $TAG"
+        --notes-file "release-notes/${TAG}.md"
+        dist/*
+
+  sync-main:
+    # main tracks the latest release, Streamlit Community Cloud deploys from it,
+    # see docs/development.md
+    needs: [publish, github-release]
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      contents: write  # fast-forward main to the released commit
+    steps:
+    - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+      with:
+        # a shallow clone cannot be pushed to another branch
+        fetch-depth: 0
+        # the push below needs the credentials, nothing else runs in this job
+        persist-credentials: true
+    - name: Fast-forward main to the release
+      # no --force: the push fails loudly if it would not be a fast-forward
+      run: git push origin HEAD:main

fair_ca_visualization-0.4.1/.github/workflows/docs.yml

@@ -0,0 +1,72 @@
+name: documentation
+
+on:
+  push:
+    # feature branches are built through their pull request
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  # a superseded pull request build is cancelled; a push is never cancelled,
+  # the deployment it starts would be left half published
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+jobs:
+  docs:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: docs
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    env:
+      UV_PYTHON_PREFERENCE: only-managed
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+      - name: Configure GitHub Pages
+        # a pull request builds the site but never deploys it
+        if: github.event_name != 'pull_request'
+        uses: actions/configure-pages@45bfe0192ca1faeb007ade9deae92b16b8254a0d  # v6.0.0
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884  # v10.3.0
+        with:
+          version: "0.12.21"
+          python-version: "3.14"
+          enable-cache: true
+      - name: Install the locked dependencies (fails if uv.lock is out of date with pyproject.toml, run `uv lock`)
+        run: uv sync --locked
+      - name: Build the documentation
+        # the API reference is rendered from the docstrings by mkdocstrings,
+        # so the package has to be importable
+        run: uv run zensical build --clean --strict
+      - name: Generate the agent facing files
+        # llms.txt, llms-full.txt and the markdown of every page
+        run: uv run python scripts/llms_txt.py
+      - name: Upload the site
+        if: github.event_name != 'pull_request'
+        uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9  # v5.0.0
+        with:
+          path: site
+
+  deploy:
+    needs: docs
+    # only the default branch publishes to https://matthiaskoenig.github.io/fair-ca-visualization
+    if: github.ref == 'refs/heads/develop'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      pages: write     # deploy to GitHub Pages
+      id-token: write  # verify the deployment originates from this workflow
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@368f82528645a54fb793d4d04e342629a3f51346  # v5.0.1

fair_ca_visualization-0.4.1/.github/workflows/ruff.yml

@@ -0,0 +1,39 @@
+name: ruff
+
+on:
+  push:
+    # feature branches are checked through their pull request
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ruff:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: ruff
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+      # the ruff version is read from the lock (the same file `uv run ruff` uses locally), not from the
+      # `ruff>=` bound in pyproject.toml, which would resolve to the latest release
+      - name: Lint
+        uses: astral-sh/ruff-action@278981a28ce3188b1e39527901f38254bf3aac89  # v4.1.0
+        with:
+          version-file: uv.lock
+          args: check --output-format=github
+      - name: Format
+        uses: astral-sh/ruff-action@278981a28ce3188b1e39527901f38254bf3aac89  # v4.1.0
+        with:
+          version-file: uv.lock
+          args: format --check --diff