scverse-doc 0.0.1__tar.gz

scverse_doc-0.0.1/.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

scverse_doc-0.0.1/.cruft.json

@@ -0,0 +1,44 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "9345e6250d37a482c0bed3ecfd2ffb082f123bc3",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "scverse-doc",
+      "package_name": "scverse_doc",
+      "project_description": "Scverse documentation theme and utilities.",
+      "author_full_name": "Lukas Heumos",
+      "author_email": "lukas.heumos@scverse.org",
+      "github_user": "scverse",
+      "github_repo": "scverse-doc",
+      "license": "Mozilla Public License Version 2.0",
+      "ide_integration": true,
+      "issue_categorization": "issue types",
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "9345e6250d37a482c0bed3ecfd2ffb082f123bc3"
+    }
+  },
+  "directory": null
+}

scverse_doc-0.0.1/.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

scverse_doc-0.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,93 @@
+name: Bug report
+description: Report something that is broken or incorrect
+type: Bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

scverse_doc-0.0.1/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

scverse_doc-0.0.1/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for scverse-doc
+type: Enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

scverse_doc-0.0.1/.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: pre-commit
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns: ["*"]
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"

scverse_doc-0.0.1/.github/workflows/autofix.yaml

@@ -0,0 +1,29 @@
+# The workflow name is mandated by autofix.ci.
+# It needs to be a dedicated workflow, as autofix.ci times out on long runs.
+name: autofix.ci
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+          filter: blob:none
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          enable-cache: true
+      - run: uv tool install hatch
+      - name: Run pre-commit hooks
+        run: uvx prek run --all-files --show-diff-on-failure --color=always
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
+        if: '!cancelled()'

scverse_doc-0.0.1/.github/workflows/build.yaml

@@ -0,0 +1,30 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

scverse_doc-0.0.1/.github/workflows/release.yaml

@@ -0,0 +1,33 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scverse_doc
+    permissions:
+      contents: read
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          enable-cache: false
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

scverse_doc-0.0.1/.github/workflows/sync.yaml

@@ -0,0 +1,30 @@
+name: Sync data
+
+on:
+  schedule:
+    - cron: "0 5 * * *"
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - src/scverse_doc/theme/scverse/static/_tokens.css
+      - src/scverse_doc/theme/scverse/static/scverse-fa.svg
+      - scripts/**
+
+permissions:
+  contents: read
+
+jobs:
+  regenerate:
+    name: Generated files match upstream
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          repository: scverse/scverse.github.io
+          path: .upstream/website
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - run: uv run scripts/sync_brand_tokens.py --website .upstream/website --check

scverse_doc-0.0.1/.github/workflows/test.yaml

@@ -0,0 +1,109 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-slim
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - &clone
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - &setup-uv
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+    permissions:
+       id-token: write  # for codecov OIDC
+       contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
+    env:
+      UV_PYTHON: ${{ matrix.env.python }}
+
+    steps:
+      - *clone
+      - *setup-uv
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: generate coverage report
+        run: |
+          # See https://coverage.readthedocs.io/page/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+      - name: Upload coverage
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
+        with:
+          # Codecov answers "Repository not found" until scverse/scverse-doc is added there.
+          # Flip back to true once it is.
+          fail_ci_if_error: false
+          use_oidc: true
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
+          with:
+            jobs: ${{ toJSON(needs) }}

scverse_doc-0.0.1/.gitignore

@@ -0,0 +1,29 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+uv.lock
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# Local development
+.venv/
+docs/generated/
+docs/jupyter_execute/
+*.lock
+tests/roots/*/generated/

scverse_doc-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,63 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.5.15
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+        groups: [format]
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.30.0
+    hooks:
+      - id: pyproject-fmt
+        groups: [format]
+  - repo: https://github.com/djlint/djLint
+    rev: v1.46.4
+    hooks:
+      - id: djlint-reformat
+      - id: djlint
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.10
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        groups: [format]
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: hatch check types
+        language: system
+        types: [python]
+        files: ^(src|tests)/
+        require_serial: true
+        pass_filenames: false
+        groups: [typecheck]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        groups: [format]
+      - id: mixed-line-ending
+        args: [--fix=lf]
+        groups: [format]
+      - id: trailing-whitespace
+        groups: [format]
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.30.1
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]

scverse_doc-0.0.1/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/page/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.14"
+    nodejs: latest
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uvx hatch run docs:build -T
+        - mv docs/_build $READTHEDOCS_OUTPUT

scverse_doc-0.0.1/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}

scverse_doc-0.0.1/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

scverse_doc-0.0.1/.vscode/settings.json

@@ -0,0 +1,19 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll.ruff": "always",
+            "source.organizeImports.ruff": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+    "python-envs.defaultEnvManager": "pypa.hatch:hatch",
+    "python-envs.defaultPackageManager": "pypa.hatch:hatch",
+}

scverse_doc-0.0.1/CHANGELOG.md

@@ -0,0 +1,21 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/
+[semantic versioning]: https://semver.org/
+
+## [0.1.0]
+
+### Added
+
+- `scverse` Sphinx theme: branding, dark mode, shared sidebar, footer, and announcement banner
+- Package registry, fetched at runtime: “scverse packages” dropdown and intersphinx cross-links
+- Source links: “edit this page” and repository icon
+- Read the Docs integration: version selector and search, both with dark mode
+- Autodoc, prose, and confval rendering extensions (from scverse-misc)
+
+[0.1.0]: https://github.com/scverse/scverse-doc/releases/tag/v0.1.0