From 0f03a557b518e9e5330d6f80e71fa75f80610ba2 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 2 Apr 2025 18:26:34 +0000
Subject: [PATCH 1/2] Automated template update to v0.5.0
---
.bumpversion.cfg | 8 -
.codecov.yaml | 22 +-
.cruft.json | 62 ++--
.editorconfig | 3 +
.github/ISSUE_TEMPLATE/bug_report.yml | 169 +++++-----
.github/ISSUE_TEMPLATE/config.yml | 6 +-
.github/ISSUE_TEMPLATE/feature_request.yml | 16 +-
.github/workflows/build.yaml | 48 +--
.github/workflows/release.yaml | 34 ++
.github/workflows/test.yaml | 94 +++---
.gitignore | 12 +-
.pre-commit-config.yaml | 87 +++--
.readthedocs.yaml | 22 +-
.vscode/extensions.json | 18 +
.vscode/launch.json | 33 ++
.vscode/settings.json | 18 +
biome.jsonc | 16 +
docs/_static/css/custom.css | 4 +
docs/_templates/autosummary/class.rst | 8 +-
docs/conf.py | 33 +-
docs/contributing.md | 250 +++++++-------
docs/extensions/typed_returns.py | 2 +-
docs/make.bat | 35 --
docs/template_usage.md | 364 ---------------------
pyproject.toml | 212 ++++++------
25 files changed, 664 insertions(+), 912 deletions(-)
delete mode 100644 .bumpversion.cfg
create mode 100644 .github/workflows/release.yaml
create mode 100644 .vscode/extensions.json
create mode 100644 .vscode/launch.json
create mode 100644 .vscode/settings.json
create mode 100644 biome.jsonc
create mode 100644 docs/_static/css/custom.css
delete mode 100644 docs/make.bat
delete mode 100644 docs/template_usage.md
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
deleted file mode 100644
index fdba9e4..0000000
--- a/.bumpversion.cfg
+++ /dev/null
@@ -1,8 +0,0 @@
-[bumpversion]
-current_version = 0.0.1
-tag = True
-commit = True
-
-[bumpversion:file:./pyproject.toml]
-search = version = "{current_version}"
-replace = version = "{new_version}"
diff --git a/.codecov.yaml b/.codecov.yaml
index 829e56c..d0c0e29 100644
--- a/.codecov.yaml
+++ b/.codecov.yaml
@@ -1,17 +1,17 @@
# Based on pydata/xarray
codecov:
- require_ci_to_pass: no
+ require_ci_to_pass: no
coverage:
- status:
- project:
- default:
- # Require 1% coverage, i.e., always succeed
- target: 1
- patch: false
- changes: false
+ 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
+ layout: diff, flags, files
+ behavior: once
+ require_base: no
diff --git a/.cruft.json b/.cruft.json
index cd4163a..d50c971 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,23 +1,43 @@
{
- "template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "5f091ed0952e4adac0c95bda4006bec0b4532995",
- "checkout": null,
- "context": {
- "cookiecutter": {
- "project_name": "genomic-annotations",
- "package_name": "genomic_annotations",
- "project_description": "Genomic annotations using BioConductor resources in Python.",
- "author_full_name": "Isaac Virshup",
- "author_email": "ivirshup@gmail.com",
- "github_user": "ivirshup",
- "project_repo": "https://github.com/ivirshup/genomic-annotations",
- "license": "BSD 3-Clause License",
- "_copy_without_render": [
- ".github/workflows/**.yaml",
- "docs/_templates/autosummary/**.rst"
- ],
- "_template": "https://github.com/scverse/cookiecutter-scverse"
- }
- },
- "directory": null
+ "template": "https://github.com/scverse/cookiecutter-scverse",
+ "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+ "checkout": "v0.5.0",
+ "context": {
+ "cookiecutter": {
+ "project_name": "genomic-features",
+ "package_name": "genomic_features",
+ "project_description": "Genomic annotations using BioConductor resources in Python.",
+ "author_full_name": "Isaac Virshup",
+ "author_email": "ivirshup@gmail.com",
+ "github_user": "ivirshup",
+ "github_repo": "genomic-features",
+ "license": "BSD 3-Clause License",
+ "ide_integration": true,
+ "_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": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+ }
+ },
+ "directory": null
}
diff --git a/.editorconfig b/.editorconfig
index 2fe0ce0..66678e3 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,5 +8,8 @@ charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
[Makefile]
indent_style = tab
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 8d3ddaa..3ca1ccb 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,88 +2,93 @@ name: Bug report
description: Report something that is broken or incorrect
labels: 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.
- * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
- available datasets or to share a subset of your data.
+ - 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.
+ * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+ available datasets or to share a subset of your data.
- - type: textarea
- id: report
- attributes:
- label: Report
- description: A clear and concise description of what the bug is.
- validations:
- required: true
+ - 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: Version information
- description: |
- Please paste below the output of
+ - type: textarea
+ id: versions
+ attributes:
+ label: Versions
+ description: |
+ Which version of packages.
- ```python
- import session_info
- session_info.show(html=False, dependencies=True)
- ```
- placeholder: |
- -----
- anndata 0.8.0rc2.dev27+ge524389
- session_info 1.0.0
- -----
- asttokens NA
- awkward 1.8.0
- backcall 0.2.0
- cython_runtime NA
- dateutil 2.8.2
- debugpy 1.6.0
- decorator 5.1.1
- entrypoints 0.4
- executing 0.8.3
- h5py 3.7.0
- ipykernel 6.15.0
- jedi 0.18.1
- mpl_toolkits NA
- natsort 8.1.0
- numpy 1.22.4
- packaging 21.3
- pandas 1.4.2
- parso 0.8.3
- pexpect 4.8.0
- pickleshare 0.7.5
- pkg_resources NA
- prompt_toolkit 3.0.29
- psutil 5.9.1
- ptyprocess 0.7.0
- pure_eval 0.2.2
- pydev_ipython NA
- pydevconsole NA
- pydevd 2.8.0
- pydevd_file_utils NA
- pydevd_plugins NA
- pydevd_tracing NA
- pygments 2.12.0
- pytz 2022.1
- scipy 1.8.1
- setuptools 62.5.0
- setuptools_scm NA
- six 1.16.0
- stack_data 0.3.0
- tornado 6.1
- traitlets 5.3.0
- wcwidth 0.2.5
- zmq 23.1.0
- -----
- IPython 8.4.0
- jupyter_client 7.3.4
- jupyter_core 4.10.0
- -----
- Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
- Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
- -----
- Session information updated at 2022-07-07 17:55
+ 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
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
index 5cad625..5b62547 100644
--- a/.github/ISSUE_TEMPLATE/config.yml
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +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.
+ - name: Scverse Community Forum
+ url: https://discourse.scverse.org/
+ about: If you have questions about “How to do X”, please ask them here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 4921254..35f0493 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,11 +1,11 @@
name: Feature request
-description: Propose a new feature for genomic-annotations
+description: Propose a new feature for genomic-features
labels: 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
+ - 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
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index d6bc33f..83e01a1 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -1,29 +1,33 @@
name: Check Build
on:
- push:
- branches: [main]
- pull_request:
- branches: [main]
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
- cancel-in-progress: true
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
jobs:
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v3
- - name: Set up Python 3.10
- uses: actions/setup-python@v4
- with:
- python-version: "3.10"
- cache: "pip"
- cache-dependency-path: "**/pyproject.toml"
- - name: Install build dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ with:
+ cache-dependency-glob: pyproject.toml
+ - name: Build package
+ run: uv build
+ - name: Check package
+ run: uvx twine check --strict dist/*.whl
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..f3d4541
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,34 @@
+name: Release
+
+on:
+ release:
+ types: [published]
+
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+ release:
+ name: Upload release to PyPI
+ runs-on: ubuntu-latest
+ environment:
+ name: pypi
+ url: https://pypi.org/p/genomic_features
+ permissions:
+ id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ with:
+ cache-dependency-glob: pyproject.toml
+ - name: Build package
+ run: uv build
+ - name: Publish package distributions to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 13267d1..d5cfb2a 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -1,53 +1,59 @@
name: Test
on:
- push:
- branches: [main]
- pull_request:
- branches: [main]
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+ schedule:
+ - cron: "0 5 1,15 * *"
concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
- cancel-in-progress: true
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
+defaults:
+ run:
+ # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+ shell: bash -euo pipefail {0}
jobs:
- test:
- runs-on: ${{ matrix.os }}
- defaults:
- run:
- shell: bash -e {0} # -e to fail on error
-
- strategy:
- fail-fast: false
- matrix:
- python: ["3.8", "3.10"]
- os: [ubuntu-latest]
+ test:
+ runs-on: ${{ matrix.os }}
+
+ strategy:
+ fail-fast: false
+ matrix:
+ include:
+ - os: ubuntu-latest
+ python: "3.10"
+ - os: ubuntu-latest
+ python: "3.12"
+ - os: ubuntu-latest
+ python: "3.12"
+ pip-flags: "--pre"
+ name: PRE-RELEASE DEPENDENCIES
+
+ name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+ env:
+ OS: ${{ matrix.os }}
+ PYTHON: ${{ matrix.python }}
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ with:
+ cache-dependency-glob: pyproject.toml
+ - name: run tests using hatch
env:
- OS: ${{ matrix.os }}
- PYTHON: ${{ matrix.python }}
-
- steps:
- - uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python }}
- cache: "pip"
- cache-dependency-path: "**/pyproject.toml"
-
- - name: Install test dependencies
- run: |
- python -m pip install --upgrade pip wheel
- - name: Install dependencies
- run: |
- pip install ".[dev,test]"
- - name: Test
- env:
- MPLBACKEND: agg
- PLATFORM: ${{ matrix.os }}
- DISPLAY: :42
- run: |
- pytest -v --cov --color=yes
- - name: Upload coverage
- uses: codecov/codecov-action@v3
+ MPLBACKEND: agg
+ PLATFORM: ${{ matrix.os }}
+ DISPLAY: :42
+ run: uvx hatch test --cover --python ${{ matrix.python }}
+ - name: Upload coverage
+ uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index dcdc618..31e10b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,23 +6,15 @@ buck-out/
# Compiled files
.venv/
__pycache__/
-.mypy_cache/
-.ruff_cache/
+.*cache/
# Distribution / packaging
-/build/
/dist/
-/*.egg-info/
# Tests and coverage
-/.pytest_cache/
-/.cache/
/data/
+/node_modules/
# docs
/docs/generated/
/docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3aafe67..0fcce11 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,50 +1,47 @@
fail_fast: false
default_language_version:
- python: python3
+ python: python3
default_stages:
- - commit
- - push
+ - pre-commit
+ - pre-push
minimum_pre_commit_version: 2.16.0
repos:
- - repo: https://github.com/psf/black
- rev: "23.3.0"
- hooks:
- - id: black
- - repo: https://github.com/asottile/blacken-docs
- rev: 1.13.0
- hooks:
- - id: blacken-docs
- - repo: https://github.com/pre-commit/mirrors-prettier
- rev: v3.0.0-alpha.9-for-vscode
- hooks:
- - id: prettier
- # Newer versions of node don't work on systems that have an older version of GLIBC
- # (in particular Ubuntu 18.04 and Centos 7)
- # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
- # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
- # https://github.com/jupyterlab/jupyterlab/issues/12675
- language_version: "17.9.1"
- - repo: https://github.com/charliermarsh/ruff-pre-commit
- rev: v0.0.262
- hooks:
- - id: ruff
- args: [--fix, --exit-non-zero-on-fix]
- - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.4.0
- hooks:
- - id: detect-private-key
- - id: check-ast
- - id: end-of-file-fixer
- - id: mixed-line-ending
- args: [--fix=lf]
- - id: trailing-whitespace
- - id: check-case-conflict
- - repo: local
- hooks:
- - id: forbid-to-commit
- name: Don't commit rej files
- entry: |
- Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
- Fix the merge conflicts manually and remove the .rej files.
- language: fail
- files: '.*\.rej$'
+ - repo: https://github.com/biomejs/pre-commit
+ rev: v1.9.4
+ hooks:
+ - id: biome-format
+ exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+ - repo: https://github.com/tox-dev/pyproject-fmt
+ rev: v2.5.1
+ hooks:
+ - id: pyproject-fmt
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.11.2
+ hooks:
+ - id: ruff
+ types_or: [python, pyi, jupyter]
+ args: [--fix, --exit-non-zero-on-fix]
+ - id: ruff-format
+ types_or: [python, pyi, jupyter]
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v5.0.0
+ hooks:
+ - id: detect-private-key
+ - id: check-ast
+ - id: end-of-file-fixer
+ - id: mixed-line-ending
+ args: [--fix=lf]
+ - id: trailing-whitespace
+ - 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: local
+ hooks:
+ - id: forbid-to-commit
+ name: Don't commit rej files
+ entry: |
+ Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+ Fix the merge conflicts manually and remove the .rej files.
+ language: fail
+ files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 9e5d5fa..69897c3 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,16 @@
# https://docs.readthedocs.io/en/stable/config-file/v2.html
version: 2
build:
- os: ubuntu-20.04
- tools:
- python: "3.10"
+ os: ubuntu-20.04
+ tools:
+ python: "3.10"
sphinx:
- configuration: docs/conf.py
- # disable this for more lenient docs builds
- fail_on_warning: true
+ configuration: docs/conf.py
+ # disable this for more lenient docs builds
+ fail_on_warning: true
python:
- install:
- - method: pip
- path: .
- extra_requirements:
- - doc
+ install:
+ - method: pip
+ path: .
+ extra_requirements:
+ - doc
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..caaeb4f
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+ "recommendations": [
+ // GitHub integration
+ "github.vscode-github-actions",
+ "github.vscode-pull-request-github",
+ // Language support
+ "ms-python.python",
+ "ms-python.vscode-pylance",
+ "ms-toolsai.jupyter",
+ "tamasfe.even-better-toml",
+ // Dependency management
+ "ninoseki.vscode-mogami",
+ // Linting and formatting
+ "editorconfig.editorconfig",
+ "charliermarsh.ruff",
+ "biomejs.biome",
+ ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000..36d1874
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,33 @@
+{
+ // Use IntelliSense to learn about possible attributes.
+ // Hover to view descriptions of existing attributes.
+ // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+ "version": "0.2.0",
+ "configurations": [
+ {
+ "name": "Python: Build Documentation",
+ "type": "debugpy",
+ "request": "launch",
+ "module": "sphinx",
+ "args": ["-M", "html", ".", "_build"],
+ "cwd": "${workspaceFolder}/docs",
+ "console": "internalConsole",
+ "justMyCode": false,
+ },
+ {
+ "name": "Python: Debug Test",
+ "type": "debugpy",
+ "request": "launch",
+ "program": "${file}",
+ "purpose": ["debug-test"],
+ "console": "internalConsole",
+ "justMyCode": false,
+ "env": {
+ "PYTEST_ADDOPTS": "--color=yes",
+ },
+ "presentation": {
+ "hidden": true,
+ },
+ },
+ ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..e034b91
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,18 @@
+{
+ "[python][json][jsonc]": {
+ "editor.formatOnSave": true,
+ },
+ "[python]": {
+ "editor.defaultFormatter": "charliermarsh.ruff",
+ "editor.codeActionsOnSave": {
+ "source.fixAll": "always",
+ "source.organizeImports": "always",
+ },
+ },
+ "[json][jsonc]": {
+ "editor.defaultFormatter": "biomejs.biome",
+ },
+ "python.analysis.typeCheckingMode": "basic",
+ "python.testing.pytestEnabled": true,
+ "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 0000000..2175c16
--- /dev/null
+++ b/biome.jsonc
@@ -0,0 +1,16 @@
+{
+ "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+ "formatter": { "useEditorconfig": true },
+ "overrides": [
+ {
+ "include": ["./.vscode/*.json", "**/*.jsonc"],
+ "json": {
+ "formatter": { "trailingCommas": "all" },
+ "parser": {
+ "allowComments": true,
+ "allowTrailingCommas": true,
+ },
+ },
+ },
+ ],
+}
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 0000000..b8c8d47
--- /dev/null
+++ b/docs/_static/css/custom.css
@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+ font-size: 0.8em;
+}
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
index e4665df..7b4a0cf 100644
--- a/docs/_templates/autosummary/class.rst
+++ b/docs/_templates/autosummary/class.rst
@@ -9,11 +9,11 @@
{% block attributes %}
{% if attributes %}
Attributes table
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
.. autosummary::
{% for item in attributes %}
- ~{{ fullname }}.{{ item }}
+ ~{{ name }}.{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
@@ -26,7 +26,7 @@ Methods table
.. autosummary::
{% for item in methods %}
{%- if item != '__init__' %}
- ~{{ fullname }}.{{ item }}
+ ~{{ name }}.{{ item }}
{%- endif -%}
{%- endfor %}
{% endif %}
@@ -35,7 +35,7 @@ Methods table
{% block attributes_documentation %}
{% if attributes %}
Attributes
-~~~~~~~~~~~
+~~~~~~~~~~
{% for item in attributes %}
diff --git a/docs/conf.py b/docs/conf.py
index db7ff96..03e0605 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,5 @@
# Configuration file for the Sphinx documentation builder.
-#
+
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -18,7 +18,7 @@
# NOTE: If you installed your project in editable mode, this might be stale.
# If this is the case, reinstall it to refresh the metadata
-info = metadata("genomic-annotations")
+info = metadata("genomic-features")
project_name = info["Name"]
author = info["Author"]
copyright = f"{datetime.now():%Y}, {author}."
@@ -36,10 +36,10 @@
html_context = {
"display_github": True, # Integrate GitHub
- "github_user": "ivirshup", # Username
- "github_repo": project_name, # Repo name
- "github_version": "main", # Version
- "conf_py_path": "/docs/", # Path in the checkout to the docs root
+ "github_user": "ivirshup",
+ "github_repo": project_name,
+ "github_version": "main",
+ "conf_py_path": "/docs/",
}
# -- General configuration ---------------------------------------------------
@@ -55,8 +55,10 @@
"sphinx.ext.napoleon",
"sphinxcontrib.bibtex",
"sphinx_autodoc_typehints",
+ "sphinx_tabs.tabs",
"sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
+ "sphinxext.opengraph",
*[p.stem for p in (HERE / "extensions").glob("*.py")],
]
@@ -92,6 +94,7 @@
intersphinx_mapping = {
"python": ("https://docs.python.org/3", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+ "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
}
@@ -108,12 +111,15 @@
#
html_theme = "sphinx_book_theme"
html_static_path = ["_static"]
+html_css_files = ["css/custom.css"]
+
html_title = project_name
html_theme_options = {
"repository_url": repository_url,
"use_repository_button": True,
"path_to_docs": "docs/",
+ "navigation_with_keys": False,
}
pygments_style = "default"
@@ -123,18 +129,3 @@
# you can add an exception to this list.
# ("py:class", "igraph.Graph"),
]
-
-
-def setup(app):
- """App setup hook."""
- app.add_config_value(
- "recommonmark_config",
- {
- "auto_toc_tree_section": "Contents",
- "enable_auto_toc_tree": True,
- "enable_math": True,
- "enable_inline_math": False,
- "enable_eval_rst": True,
- },
- True,
- )
diff --git a/docs/contributing.md b/docs/contributing.md
index 8f10bd8..19ce004 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,27 +1,49 @@
# Contributing guide
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too.
-This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
-information to get you started on contributing.
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
-We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
-to the [scanpy developer guide][].
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
## Installing dev dependencies
-In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
-the documentation_. It's easy to install them using `pip`:
+In addition to the packages needed to _use_ this package,
+you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+
+:::::{tabs}
+::::{group-tab} Hatch
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build # defined in the table [tool.hatch.envs.docs]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
```bash
-cd genomic-annotations
+cd genomic-features
+python3 -m venv .venv
+source .venv/bin/activate
pip install -e ".[dev,test,doc]"
```
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
## Code-style
-This template uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either
-automatically fix issues with the code, or raise an error message. See [pre-commit checks](template_usage.md#pre-commit-checks) for
-a full list of checks enabled for this repository.
+This package uses [pre-commit][] to enforce consistent code-styles.
+On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
To enable pre-commit locally, simply run
@@ -29,10 +51,11 @@ To enable pre-commit locally, simply run
pre-commit install
```
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+in the root of the repository.
+Pre-commit will automatically download all dependencies when it is run for the first time.
-Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub. If you didn't run `pre-commit` before
-pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
+If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
@@ -43,156 +66,149 @@ git pull --rebase
to integrate the changes into yours.
While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
-Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [black][black-editors]
-and [prettier][prettier-editors].
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
-[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
-[prettier-editors]: https://prettier.io/docs/en/editors.html
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
+[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
-## Writing tests
+(writing-tests)=
-```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
-```
+## Writing tests
-This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
-to the package.
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
-Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the
-command line by executing
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
```bash
-pytest
+hatch env create hatch-test # create test environments for all supported versions
+hatch env find hatch-test # list all possible test environment paths
```
-in the root of the repository. Continuous integration will automatically run the tests on all pull requests.
-
-[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+Alternatively, you can run all tests from the command line by executing
-## Publishing a release
-
-### Updating the version number
-
-Before making a release, you need to update the version number. Please adhere to [Semantic Versioning][semver], in brief
-
-> Given a version number MAJOR.MINOR.PATCH, increment the:
->
-> 1. MAJOR version when you make incompatible API changes,
-> 2. MINOR version when you add functionality in a backwards compatible manner, and
-> 3. PATCH version when you make backwards compatible bug fixes.
->
-> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
-
-We use [bump2version][] to automatically update the version number in all places and automatically create a git tag.
-Run one of the following commands in the root of the repository
+:::::{tabs}
+::::{group-tab} Hatch
```bash
-bump2version patch
-bump2version minor
-bump2version major
+hatch test # test with the highest supported Python version
+# or
+hatch test --all # test with all supported Python versions
```
-Once you are done, run
-
-```
-git push --tags
-```
+::::
-to publish the created tag on GitHub.
+::::{group-tab} Pip
-[bump2version]: https://github.com/c4urself/bump2version
+```bash
+source .venv/bin/activate
+pytest
+```
-### Building and publishing the package on PyPI
+::::
+:::::
-Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run
+in the root of the repository.
-```bash
-python -m build
-```
+[pytest]: https://docs.pytest.org/
-This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.
+### Continuous integration
-Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
+Continuous integration will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
-```bash
-twine check dist/*
-```
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
-and finally publishing it with:
+## Publishing a release
-```bash
-twine upload dist/*
-```
+### Updating the version number
-Provide your username and password when requested and then go check out your package on [PyPI][]!
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
-For more information, follow the [Python packaging tutorial][].
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
-It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
-in the cookiecutter-scverse template.
+Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
-[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
-[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
## Writing documentation
-Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
-- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
-- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
-- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
-- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
-- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
-See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
-on how to write documentation.
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
### Tutorials with myst-nb and jupyter notebooks
The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
-It is your reponsibility to update and re-run the notebook whenever necessary.
+It is your responsibility to update and re-run the notebook whenever necessary.
-If you are interested in automatically running notebooks as part of the continuous integration, please check
-out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
-repository.
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Hints
-- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
- if you do so can sphinx automatically create a link to the external documentation.
-- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
- the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+ Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+ you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
#### Building the docs locally
+:::::{tabs}
+::::{group-tab} Hatch
+
```bash
+hatch run docs:build
+hatch run docs:open
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
cd docs
make html
-open _build/html/index.html
+(xdg-)open _build/html/index.html
```
-
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
-[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
-[pypi]: https://pypi.org/
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 1135204..0fbffef 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -12,7 +12,7 @@
def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
for line in lines:
if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line):
- yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+ yield f"-{m['param']} (:class:`~{m['type']}`)"
else:
yield line
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index 954237b..0000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
- echo.
- echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
- echo.installed, then set the SPHINXBUILD environment variable to point
- echo.to the full path of the 'sphinx-build' executable. Alternatively you
- echo.may add the Sphinx directory to PATH.
- echo.
- echo.If you don't have Sphinx installed, grab it from
- echo.https://www.sphinx-doc.org/
- exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/docs/template_usage.md b/docs/template_usage.md
deleted file mode 100644
index 0022c98..0000000
--- a/docs/template_usage.md
+++ /dev/null
@@ -1,364 +0,0 @@
-# Using this template
-
-Welcome to the developer guidelines! This document is split into two parts:
-
-1. The [repository setup](#setting-up-the-repository). This section is relevant primarily for the repository maintainer and shows how to connect
- continuous integration services and documents initial set-up of the repository.
-2. The [contributor guide](contributing.md#contributing-guide). It contains information relevant to all developers who want to make a contribution.
-
-## Setting up the repository
-
-### First commit
-
-If you are reading this, you should have just completed the repository creation with :
-
-```bash
-cruft create https://github.com/scverse/cookiecutter-scverse
-```
-
-and you should have
-
-```
-cd genomic-annotations
-```
-
-into the new project directory. Now that you have created a new repository locally, the first step is to push it to github. To do this, you'd have to create a **new repository** on github.
-You can follow the instructions directly on [github quickstart guide][].
-Since `cruft` already populated the local repository of your project with all the necessary files, we suggest to _NOT_ initialize the repository with a `README.md` file or `.gitignore`, because you might encounter git conflicts on your first push.
-If you are familiar with git and knows how to handle git conflicts, you can go ahead with your preferred choice.
-
-:::{note}
-If you are looking at this document in the [cookiecutter-scverse-instance][] repository documentation, throughout this document the name of the project is `cookiecutter-scverse-instance`. Otherwise it should be replaced by your new project name: `genomic-annotations`.
-:::
-
-Now that your new project repository has been created on github at `https://github.com/ivirshup/genomic-annotations` you can push your first commit to github.
-To do this, simply follow the instructions on your github repository page or a more verbose walkthrough here:
-
-Assuming you are in `/your/path/to/genomic-annotations`. Add all files and commit.
-
-```bash
-# stage all files of your new repo
-git add --all
-# commit
-git commit -m "first commit"
-```
-
-You'll notice that the command `git commit` installed a bunch of packages and triggered their execution: those are pre-commit! To read more about what they are and what they do, you can go to the related section [Pre-commit checks](#pre-commit-checks) in this document.
-
-:::{note}
-There is a chance that `git commit -m "first commit"` fails due to the `prettier` pre-commit formatting the file `.cruft.json`. No problem, you have just experienced what pre-commit checks do in action. Just go ahead and re-add the modified file and try to commit again:
-
-```bash
- git add -u # update all tracked file
- git commit -m "first commit"
-```
-
-:::
-
-Now that all the files of the newly created project have been committed, go ahead with the remaining steps:
-
-```bash
-# update the `origin` of your local repo with the remote github link
-git remote add origin https://github.com/ivirshup/genomic-annotations.git
-# rename the default branch to main
-git branch -M main
-# push all your files to remote
-git push -u origin main
-```
-
-Your project should be now available at `https://github.com/ivirshup/genomic-annotations`. While the repository at this point can be directly used, there are few remaining steps that needs to be done in order to achieve full functionality.
-
-### Coverage tests with _Codecov_
-
-Coverage tells what fraction of the code is "covered" by unit tests, thereby encouraging contributors to
-[write tests](contributing.md#writing-tests).
-To enable coverage checks, head over to [codecov][] and sign in with your GitHub account.
-You'll find more information in "getting started" section of the [codecov docs][].
-
-In the `Actions` tab of your projects' github repository, you can see that the workflows are failing due to the **Upload coverage** step. The error message in the workflow should display something like:
-
-```
-...
- Retrying 5/5 in 2s..
- {'detail': ErrorDetail(string='Could not find a repository, try using repo upload token', code='not_found')}
-Error: 404 Client Error: Not Found for url:
-...
-```
-
-While [codecov docs][] has a very extensive documentation on how to get started, _if_ you are using the default settings of this template we can assume that you are using [codecov][] in a github action workflow and hence you can make use of the [codecov bot][].
-
-To set it up, simply go to the [codecov app][] page and follow the instructions to activate it for your repository.
-Once the activation is completed, go back to the `Actions` tab and re-run the failing workflows.
-
-The workflows should now succeed and you will be able to find the code coverage at this link: `https://app.codecov.io/gh/ivirshup/genomic-annotations`. You might have to wait couple of minutes and the coverage of this repository should be ~60%.
-
-If your repository is private, you will have to specify an additional token in the repository secrets. In brief, you need to:
-
-1. Generate a Codecov Token by clicking _setup repo_ in the codecov dashboard.
- - If you have already set up codecov in the repository by following the previous steps, you can directly go to the codecov repo webpage.
-2. Go to _Settings_ and copy **only** the token `_______-____-...`.
-3. Go to _Settings_ of your newly created repository on GitHub.
-4. Go to _Security > Secrets > Actions_.
-5. Create new repository secret with name `CODECOV_TOKEN` and paste the token generated by codecov.
-6. Past these additional lines in `/.github/workflows.test.yaml` under the **Upload coverage** step:
- ```bash
- - name: Upload coverage
- uses: codecov/codecov-action@v3
- with:
- token: ${{ secrets.CODECOV_TOKEN }}
- ```
-7. Go back to github `Actions` page an re-run previously failed jobs.
-
-### Documentation on _readthedocs_
-
-We recommend using [readthedocs.org][] (RTD) to build and host the documentation for your project.
-To enable readthedocs, head over to [their website][readthedocs.org] and sign in with your GitHub account.
-On the RTD dashboard choose "Import a Project" and follow the instructions to add your repository.
-
-- Make sure to choose the correct name of the default branch. On GitHub, the name of the default branch should be `main` (it has
- recently changed from `master` to `main`).
-- We recommend to enable documentation builds for pull requests (PRs). This ensures that a PR doesn't introduce changes
- that break the documentation. To do so, got to `Admin -> Advanced Settings`, check the
- `Build pull requests for this projects` option, and click `Save`. For more information, please refer to
- the [official RTD documentation](https://docs.readthedocs.io/en/stable/pull-requests.html).
-- If you find the RTD builds are failing, you can disable the `fail_on_warning` option in `.readthedocs.yaml`.
-
-If your project is private, there are ways to enable docs rendering on [readthedocs.org][] but it is more cumbersome and requires a different subscription for read the docs. See a guide [here](https://docs.readthedocs.io/en/stable/guides/importing-private-repositories.html).
-
-### Pre-commit checks
-
-[Pre-commit][] checks are fast programs that
-check code for errors, inconsistencies and code styles, before the code
-is committed.
-
-This template uses a number of pre-commit checks. In this section we'll detail what is used, where they're defined, and how to modify these checks.
-
-#### Pre-commit CI
-
-We recommend setting up [pre-commit.ci][] to enforce consistency checks on every commit
-and pull-request.
-
-To do so, head over to [pre-commit.ci][] and click "Sign In With GitHub". Follow
-the instructions to enable pre-commit.ci for your account or your organization. You
-may choose to enable the service for an entire organization or on a per-repository basis.
-
-Once authorized, pre-commit.ci should automatically be activated.
-
-#### Overview of pre-commit hooks used by the template
-
-The following pre-commit hooks are for code style and format:
-
-- [black](https://black.readthedocs.io/en/stable/):
- standard code formatter in Python.
-- [blacken-docs](https://github.com/asottile/blacken-docs):
- black on Python code in docs.
-- [prettier](https://prettier.io/docs/en/index.html):
- standard code formatter for non-Python files (e.g. YAML).
-- [ruff][] based checks:
- - [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
- sort module imports into sections and types.
- - [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
- pydocstyle extension of flake8.
- - [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
- tidy module imports.
- - [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
- write better list/set/dict comprehensions.
- - [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
- upgrade syntax for newer versions of the language.
-
-The following pre-commit hooks are for errors and inconsistencies:
-
-- [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks for text files.
- - **detect-private-key**: checks for the existence of private keys.
- - **check-ast**: check whether files parse as valid python.
- - **end-of-file-fixer**: check files end in a newline and only a newline.
- - **mixed-line-ending**: checks mixed line ending.
- - **trailing-whitespace**: trims trailing whitespace.
- - **check-case-conflict**: check files that would conflict with case-insensitive file systems.
- - **forbid-to-commit**: Make sure that `*.rej` files cannot be commited.
- These files are created by the [automated template sync](#automated-template-sync)
- if there's a merge conflict and need to be addressed manually.
-- [ruff][] based checks:
- - [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
- various checks for errors.
- - [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
- various checks for errors.
- - [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
- find possible bugs and design issues in program.
- - [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
- checks for blind, catch-all `except` statements.
- - [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
- - `RUF100`: remove unneccesary `# noqa` comments ()
-
-#### How to add or remove pre-commit checks
-
-The [pre-commit checks](#pre-commit-checks) check for both correctness and stylistic errors.
-In some cases it might overshoot and you may have good reasons to ignore certain warnings.
-This section shows you where these checks are defined, and how to enable/ disable them.
-
-##### pre-commit
-
-You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file under the repository root.
-Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` (for `ruff` and `black`) or tool-specific
-config files, such as `.prettierrc.yml` for **prettier**.
-
-##### Ruff
-
-This template configures `ruff` through the `[tool.ruff]` entry in the `pyproject.toml`.
-For further information `ruff` configuration, see [the docs](https://beta.ruff.rs/docs/configuration/).
-
-Ruff assigns code to the rules it checks (e.g. `E401`) and groups them under a rule category (e.g. `E`).
-Rule categories are selectively enabled by including them under the `select` key:
-
-```toml
-[tool.ruff]
-...
-
-select = [
- "F", # Errors detected by Pyflakes
- "E", # Error detected by Pycodestyle
- "W", # Warning detected by Pycodestyle
- "I", # isort
- ...
-]
-```
-
-The `ignore` entry is used to disable specific rules for the entire project.
-Add the rule code(s) you want to ignore and don't forget to add a comment explaining why.
-You can find a long list of checks that this template disables by default sitting there already.
-
-```toml
-ignore = [
- ...
- # __magic__ methods are are often self-explanatory, allow missing docstrings
- "D105",
- ...
-]
-```
-
-Checks can be ignored per-file (or glob pattern) with `[tool.ruff.per-file-ignores]`.
-
-```toml
-[tool.ruff.per-file-ignores]
-"docs/*" = ["I"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
-```
-
-To ignore a specific rule on a per-case basis, you can add a `# noqa: [, , …]` comment to the offending line.
-Specify the rule code(s) to ignore, with e.g. `# noqa: E731`. Check the [Ruff guide][] for reference.
-
-```{note}
-The `RUF100` check will remove rule codes that are no longer necessary from `noqa` comments.
-If you want to add a code that comes from a tool other than Ruff,
-add it to Ruff’s [`external = [...]`](https://beta.ruff.rs/docs/settings/#external) setting to prevent `RUF100` from removing it.
-```
-
-[ruff]: https://beta.ruff.rs/docs/
-[ruff guide]: https://beta.ruff.rs/docs/configuration/#suppressing-errors
-
-### API design
-
-Scverse ecosystem packages should operate on [AnnData][] and/or [MuData][] data structures and typically use an API
-as originally [introduced by scanpy][scanpy-api] with the following submodules:
-
-- `pp` for preprocessing
-- `tl` for tools (that, compared to `pp` generate interpretable output, often associated with a corresponding plotting
- function)
-- `pl` for plotting functions
-
-You may add additional submodules as appropriate. While we encourage to follow a scanpy-like API for ecosystem packages,
-there may also be good reasons to choose a different approach, e.g. using an object-oriented API.
-
-[scanpy-api]: https://scanpy.readthedocs.io/en/stable/usage-principles.html
-
-### Using VCS-based versioning
-
-By default, the template uses hard-coded version numbers that are set in `pyproject.toml` and [managed with
-bump2version](contributing.md#publishing-a-release). If you prefer to have your project automatically infer version numbers from git
-tags, it is straightforward to switch to vcs-based versioning using [hatch-vcs][].
-
-In `pyproject.toml` add the following changes, and you are good to go!
-
-```diff
---- a/pyproject.toml
-+++ b/pyproject.toml
-@@ -1,11 +1,11 @@
- [build-system]
- build-backend = "hatchling.build"
--requires = ["hatchling"]
-+requires = ["hatchling", "hatch-vcs"]
-
-
- [project]
- name = "genomic-annotations"
--version = "0.3.1dev"
-+dynamic = ["version"]
-
-@@ -60,6 +60,9 @@
-+[tool.hatch.version]
-+source = "vcs"
-+
- [tool.coverage.run]
- source = ["genomic-annotations"]
- omit = [
-```
-
-Don't forget to update the [Making a release section](contributing.md#publishing-a-release) in this document accordingly, after you are done!
-
-[hatch-vcs]: https://pypi.org/project/hatch-vcs/
-
-### Automated template sync
-
-Automated template sync is enabled by default. This means that every night, a GitHub action runs [cruft][] to check
-if a new version of the `scverse-cookiecutter` template got released. If there are any new changes, a pull request
-proposing these changes is created automatically. This helps keeping the repository up-to-date with the latest
-coding standards.
-
-It may happen that a template sync results in a merge conflict. If this is the case a `*.ref` file with the
-diff is created. You need to manually address these changes and remove the `.rej` file when you are done.
-The pull request can only be merged after all `*.rej` files have been removed.
-
-:::{tip}
-The following hints may be useful to work with the template sync:
-
-- GitHub automatically disables scheduled actions if there has been not activity to the repository for 60 days.
- You can re-enable or manually trigger the sync by navigating to `Actions` -> `Sync Template` in your GitHub repository.
-- If you want to ignore certain files from the template update, you can add them to the `[tool.cruft]` section in the
- `pyproject.toml` file in the root of your repository. More details are described in the
- [cruft documentation][cruft-update-project].
-- To disable the sync entirely, simply remove the file `.github/workflows/sync.yaml`.
-
-:::
-
-[cruft]: https://cruft.github.io/cruft/
-[cruft-update-project]: https://cruft.github.io/cruft/#updating-a-project
-
-## Moving forward
-
-You have reached the end of this document. Congratulations! You have successfully set up your project and are ready to start.
-For everything else related to documentation, code style, testing and publishing your project ot pypi, please refer to the [contributing docs](contributing.md#contributing-guide).
-
-
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
-[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
-[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
diff --git a/pyproject.toml b/pyproject.toml
index 180bb94..f76df20 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,133 +1,135 @@
[build-system]
build-backend = "hatchling.build"
-requires = ["hatchling"]
+requires = [ "hatchling" ]
[project]
-name = "genomic-annotations"
+name = "genomic-features"
version = "0.0.1"
description = "Genomic annotations using BioConductor resources in Python."
readme = "README.md"
-requires-python = ">=3.9"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
+maintainers = [
+ { name = "Isaac Virshup", email = "ivirshup@gmail.com" },
+]
authors = [
- {name = "Isaac Virshup"},
+ { name = "Isaac Virshup" },
]
-maintainers = [
- {name = "Isaac Virshup", email = "ivirshup@gmail.com"},
+requires-python = ">=3.10"
+classifiers = [
+ "Programming Language :: Python :: 3 :: Only",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.13",
]
-urls.Documentation = "https://genomic-annotations.readthedocs.io/"
-urls.Source = "https://github.com/ivirshup/genomic-annotations"
-urls.Home-page = "https://github.com/ivirshup/genomic-annotations"
dependencies = [
- "anndata",
- # for debug logging (referenced from the issue template)
- "session-info"
+ "anndata",
+ # for debug logging (referenced from the issue template)
+ "session-info2",
]
-
-[project.optional-dependencies]
-dev = [
- # CLI for bumping the version number
- "bump2version",
- "pre-commit",
- "twine>=4.0.2"
+optional-dependencies.dev = [
+ "pre-commit",
+ "twine>=4.0.2",
]
-doc = [
- "sphinx>=4",
- "sphinx-book-theme>=1.0.0",
- "myst-nb",
- "sphinxcontrib-bibtex>=1.0.0",
- "sphinx-autodoc-typehints",
- # For notebooks
- "ipykernel",
- "ipython",
- "sphinx-copybutton",
+optional-dependencies.doc = [
+ "docutils>=0.8,!=0.18.*,!=0.19.*",
+ "ipykernel",
+ "ipython",
+ "myst-nb>=1.1",
+ "pandas",
+ # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+ "setuptools",
+ "sphinx>=4",
+ "sphinx-autodoc-typehints",
+ "sphinx-book-theme>=1",
+ "sphinx-copybutton",
+ "sphinx-tabs",
+ "sphinxcontrib-bibtex>=1",
+ "sphinxext-opengraph",
]
-test = [
- "pytest",
- "pytest-cov",
+optional-dependencies.test = [
+ "coverage",
+ "pytest",
]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://genomic-features.readthedocs.io/"
+urls.Homepage = "https://github.com/ivirshup/genomic-features"
+urls.Source = "https://github.com/ivirshup/genomic-features"
-[tool.coverage.run]
-source = ["genomic_annotations"]
-omit = [
- "**/test_*.py",
-]
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-xfail_strict = true
-addopts = [
- "--import-mode=importlib", # allow using test files with same name
-]
+[tool.hatch.envs.docs]
+features = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+scripts.clean = "git clean -fdX -- {args:docs}"
-[tool.black]
-line-length = 88
-target-version = ["py39"]
+[tool.hatch.envs.hatch-test]
+features = [ "test" ]
[tool.ruff]
-src = ["src"]
-line-length = 88
-target-version = "py39"
-select = [
- "F", # Errors detected by Pyflakes
- "E", # Error detected by Pycodestyle
- "W", # Warning detected by Pycodestyle
- "I", # isort
- "D", # pydocstyle
- "B", # flake8-bugbear
- "TID", # flake8-tidy-imports
- "C4", # flake8-comprehensions
- "BLE", # flake8-blind-except
- "UP", # pyupgrade
- "RUF100", # Report unused noqa directives
+line-length = 120
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+
+format.docstring-code-format = true
+
+lint.select = [
+ "B", # flake8-bugbear
+ "BLE", # flake8-blind-except
+ "C4", # flake8-comprehensions
+ "D", # pydocstyle
+ "E", # Error detected by Pycodestyle
+ "F", # Errors detected by Pyflakes
+ "I", # isort
+ "RUF100", # Report unused noqa directives
+ "TID", # flake8-tidy-imports
+ "UP", # pyupgrade
+ "W", # Warning detected by Pycodestyle
]
-ignore = [
- # line too long -> we accept long comment lines; black gets rid of long code lines
- "E501",
- # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
- "E731",
- # allow I, O, l as variable names -> I is the identity matrix
- "E741",
- # Missing docstring in public package
- "D104",
- # Missing docstring in public module
- "D100",
- # Missing docstring in __init__
- "D107",
- # Errors from function calls in argument defaults. These are fine when the result is immutable.
- "B008",
- # __magic__ methods are are often self-explanatory, allow missing docstrings
- "D105",
- # first line should end with a period [Bug: doesn't work with single-line docstrings]
- "D400",
- # First line should be in imperative mood; try rephrasing
- "D401",
- ## Disable one in each pair of mutually incompatible rules
- # We don’t want a blank line before a class docstring
- "D203",
- # We want docstrings to start immediately after the opening triple quote
- "D213",
+lint.ignore = [
+ "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+ "D100", # Missing docstring in public module
+ "D104", # Missing docstring in public package
+ "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+ "D107", # Missing docstring in __init__
+ # Disable one in each pair of mutually incompatible rules
+ "D203", # We don’t want a blank line before a class docstring
+ "D213", # <> We want docstrings to start immediately after the opening triple quote
+ "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+ "D401", # First line should be in imperative mood; try rephrasing
+ "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+ "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+ "E741", # allow I, O, l as variable names -> I is the identity matrix
]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
-[tool.ruff.pydocstyle]
-convention = "numpy"
-
-[tool.ruff.per-file-ignores]
-"docs/*" = ["I"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+ "--import-mode=importlib", # allow using test files with same name
+]
-[tool.jupytext]
-formats = "ipynb,md"
+[tool.coverage.run]
+source = [ "genomic_features" ]
+omit = [
+ "**/test_*.py",
+]
[tool.cruft]
skip = [
- "tests",
- "src/**/__init__.py",
- "src/**/basic.py",
- "docs/api.md",
- "docs/changelog.md",
- "docs/references.bib",
- "docs/references.md",
- "docs/notebooks/example.ipynb"
+ "tests",
+ "src/**/__init__.py",
+ "src/**/basic.py",
+ "docs/api.md",
+ "docs/changelog.md",
+ "docs/references.bib",
+ "docs/references.md",
+ "docs/notebooks/example.ipynb",
]
From f60699128f0490edcc235459a6bb690270153285 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Tue, 30 Sep 2025 06:33:11 +0000
Subject: [PATCH 2/2] Automated template update to v0.6.0
---
.cruft.json | 6 +-
.github/workflows/test.yaml | 80 +++++++++++++++-----
.gitignore | 1 +
.pre-commit-config.yaml | 19 ++---
.readthedocs.yaml | 23 +++---
biome.jsonc | 5 +-
docs/Makefile | 20 -----
docs/contributing.md | 144 ++++++++++++++++++++++++++++++++----
pyproject.toml | 27 ++++++-
9 files changed, 238 insertions(+), 87 deletions(-)
delete mode 100644 docs/Makefile
diff --git a/.cruft.json b/.cruft.json
index d50c971..0c9c182 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
{
"template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
- "checkout": "v0.5.0",
+ "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+ "checkout": "v0.6.0",
"context": {
"cookiecutter": {
"project_name": "genomic-features",
@@ -36,7 +36,7 @@
"trim_blocks": true
},
"_template": "https://github.com/scverse/cookiecutter-scverse",
- "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+ "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
}
},
"directory": null
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index d5cfb2a..0bd76e8 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -18,27 +18,48 @@ defaults:
shell: bash -euo pipefail {0}
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-latest
+ outputs:
+ envs: ${{ steps.get-envs.outputs.envs }}
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - name: Install uv
+ uses: astral-sh/setup-uv@v5
+ - name: Get test environments
+ id: get-envs
+ run: |
+ ENVS_JSON=$(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:
- runs-on: ${{ matrix.os }}
+ needs: get-environments
strategy:
fail-fast: false
matrix:
- include:
- - os: ubuntu-latest
- python: "3.10"
- - os: ubuntu-latest
- python: "3.12"
- - os: ubuntu-latest
- python: "3.12"
- pip-flags: "--pre"
- name: PRE-RELEASE DEPENDENCIES
-
- name: ${{ matrix.name }} Python ${{ matrix.python }}
-
- env:
- OS: ${{ matrix.os }}
- PYTHON: ${{ matrix.python }}
+ os: [ubuntu-latest]
+ env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+ name: ${{ matrix.env.label }}
+ runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
@@ -48,12 +69,35 @@ jobs:
- name: Install uv
uses: astral-sh/setup-uv@v5
with:
+ python-version: ${{ matrix.env.python }}
cache-dependency-glob: pyproject.toml
+ - name: create hatch environment
+ run: uvx hatch env create ${{ matrix.env.name }}
- name: run tests using hatch
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
- run: uvx hatch test --cover --python ${{ matrix.python }}
+ run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+ - name: generate coverage report
+ run: |
+ # See https://coverage.readthedocs.io/en/latest/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@v4
+ uses: codecov/codecov-action@v5
+
+ # 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@release/v1
+ with:
+ jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
index 31e10b3..bd24e4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ __pycache__/
# Tests and coverage
/data/
/node_modules/
+/.coverage*
# docs
/docs/generated/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0fcce11..b9de3fe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,24 +7,24 @@ default_stages:
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/biomejs/pre-commit
- rev: v1.9.4
+ rev: v2.2.4
hooks:
- id: biome-format
exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
- repo: https://github.com/tox-dev/pyproject-fmt
- rev: v2.5.1
+ rev: v2.6.0
hooks:
- id: pyproject-fmt
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.11.2
+ rev: v0.13.2
hooks:
- - id: ruff
+ - id: ruff-check
types_or: [python, pyi, jupyter]
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v5.0.0
+ rev: v6.0.0
hooks:
- id: detect-private-key
- id: check-ast
@@ -36,12 +36,3 @@ repos:
# Check that there are no merge conflicts (could be generated by template sync)
- id: check-merge-conflict
args: [--assume-in-merge]
- - repo: local
- hooks:
- - id: forbid-to-commit
- name: Don't commit rej files
- entry: |
- Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
- Fix the merge conflicts manually and remove the .rej files.
- language: fail
- files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 69897c3..c3f3f96 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,15 @@
# https://docs.readthedocs.io/en/stable/config-file/v2.html
version: 2
build:
- os: ubuntu-20.04
+ os: ubuntu-24.04
tools:
- python: "3.10"
-sphinx:
- configuration: docs/conf.py
- # disable this for more lenient docs builds
- fail_on_warning: true
-python:
- install:
- - method: pip
- path: .
- extra_requirements:
- - doc
+ python: "3.12"
+ jobs:
+ create_environment:
+ - asdf plugin add uv
+ - asdf install uv latest
+ - asdf global uv latest
+ build:
+ html:
+ - uvx hatch run docs:build
+ - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/biome.jsonc b/biome.jsonc
index 2175c16..9f8f220 100644
--- a/biome.jsonc
+++ b/biome.jsonc
@@ -1,9 +1,10 @@
{
- "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+ "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+ "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
"formatter": { "useEditorconfig": true },
"overrides": [
{
- "include": ["./.vscode/*.json", "**/*.jsonc"],
+ "includes": ["./.vscode/*.json", "**/*.jsonc"],
"json": {
"formatter": { "trailingCommas": "all" },
"parser": {
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index d4bb2cb..0000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS ?=
-SPHINXBUILD ?= sphinx-build
-SOURCEDIR = .
-BUILDDIR = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/contributing.md b/docs/contributing.md
index 19ce004..699d942 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,14 +1,33 @@
# Contributing guide
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
-This document will not reproduce the entire content from there.
-Instead, it aims at summarizing the most important information to get you started on contributing.
-
+This document aims at summarizing the most important information for getting you started on contributing to this project.
We assume that you are already familiar with git and with making pull requests on GitHub.
-If not, please refer to the [scanpy developer guide][].
+For more extensive tutorials, that also cover the absolute basics,
+please refer to other resources such as the [pyopensci tutorials][],
+the [scientific Python tutorials][], or the [scanpy developer guide][].
+
+[pyopensci tutorials]: https://www.pyopensci.org/learn.html
+[scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+:::{tip} The *hatch* project manager
+
+We highly recommend to familiarize yourself with [`hatch`][hatch].
+Hatch is a Python project manager that
+
+- manages virtual environments, separately for development, testing and building the documentation.
+ Separating the environments is useful to avoid dependency conflicts.
+- allows to run tests locally in different environments (e.g. different python versions)
+- allows to run tasks defined in `pyproject.toml`, e.g. to build documentation.
+
+While the project is setup with `hatch` in mind,
+it is still possible to use different tools to manage dependencies, such as `uv` or `pip`.
+
+:::
+
+[hatch]: https://hatch.pypa.io/latest/
+
## Installing dev dependencies
In addition to the packages needed to _use_ this package,
@@ -16,29 +35,103 @@ you need additional python packages to [run tests](#writing-tests) and [build th
:::::{tabs}
::::{group-tab} Hatch
-The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+On the command line, you typically interact with hatch through its command line interface (CLI).
+Running one of the following commands will automatically resolve the environments for testing and
+building the documentation in the background:
```bash
hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
hatch run docs:build # defined in the table [tool.hatch.envs.docs]
```
+When using an IDE such as VS Code,
+you’ll have to point the editor at the paths to the virtual environments manually.
+The environment you typically want to use as your main development environment is the `hatch-test`
+environment with the latest Python version.
+
+To get a list of all environments for your projects, run
+
+```bash
+hatch env show -i
+```
+
+This will list “Standalone” environments and a table of “Matrix” environments like the following:
+
+```
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| Name | Type | Envs | Features | Dependencies | Scripts |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| hatch-test | virtual | hatch-test.py3.10-stable | dev | coverage-enable-subprocess==1.0 | cov-combine |
+| | | hatch-test.py3.13-stable | test | coverage[toml]~=7.4 | cov-report |
+| | | hatch-test.py3.13-pre | | pytest-mock~=3.12 | run |
+| | | | | pytest-randomly~=3.15 | run-cov |
+| | | | | pytest-rerunfailures~=14.0 | |
+| | | | | pytest-xdist[psutil]~=3.5 | |
+| | | | | pytest~=8.1 | |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+```
+
+From the `Envs` column, select the environment name you want to use for development.
+In this example, it would be `hatch-test.py3.13-stable`.
+
+Next, create the environment with
+
+```bash
+hatch env create hatch-test.py3.13-stable
+```
+
+Then, obtain the path to the environment using
+
+```bash
+hatch env find hatch-test.py3.13-stable
+```
+
+In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
+Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+
+In this future, this may become easier through a hatch vscode extension.
+
+::::
+
+::::{group-tab} uv
+
+A popular choice for managing virtual environments is [uv][].
+The main disadvantage compared to hatch is that it supports only a single environment per project at a time,
+which requires you to mix the dependencies for running tests and building docs.
+This can have undesired side-effects,
+such as requiring to install a lower version of a library your project depends on,
+only because an outdated sphinx plugin pins an older version.
+
+To initalize a virtual environment in the `.venv` directory of your project, simply run
+
+```bash
+uv sync --all-extras
+```
+
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
::::
::::{group-tab} Pip
-If you prefer managing environments manually, you can use `pip`:
+
+Pip is nowadays mostly superseded by environment manager such as [hatch][].
+However, for the sake of completeness, and since it’s ubiquitously available,
+we describe how you can manage environments manually using `pip`:
```bash
-cd genomic-features
python3 -m venv .venv
source .venv/bin/activate
pip install -e ".[dev,test,doc]"
```
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
::::
:::::
[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[uv]: https://docs.astral.sh/uv/
## Code-style
@@ -55,7 +148,7 @@ in the root of the repository.
Pre-commit will automatically download all dependencies when it is run for the first time.
Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
@@ -102,6 +195,14 @@ hatch test --all # test with all supported Python versions
::::
+::::{group-tab} uv
+
+```bash
+uv run pytest
+```
+
+::::
+
::::{group-tab} Pip
```bash
@@ -118,12 +219,17 @@ in the root of the repository.
### Continuous integration
-Continuous integration will automatically run the tests on all pull requests and test
+Continuous integration via GitHub actions will automatically run the tests on all pull requests and test
against the minimum and maximum supported Python version.
-Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+Additionally, there’s a CI job that tests against pre-releases of all dependencies (if there are any).
The purpose of this check is to detect incompatibilities of new package versions early on and
-gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+gives you time to fix the issue or reach out to the developers of the dependency before the package
+is released to a wider audience.
+
+The CI job is defined in `.github/workflows/test.yaml`,
+however the single point of truth for CI jobs is the Hatch test matrix defined in `pyproject.toml`.
+This means that local testing via hatch and remote testing on CI tests against the same python versions and uses the same environments.
## Publishing a release
@@ -189,7 +295,7 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
(docs-building)=
-#### Building the docs locally
+### Building the docs locally
:::::{tabs}
::::{group-tab} Hatch
@@ -201,12 +307,22 @@ hatch run docs:open
::::
+::::{group-tab} uv
+
+```bash
+cd docs
+uv run sphinx-build -M html . _build -W
+(xdg-)open _build/html/index.html
+```
+
+::::
+
::::{group-tab} Pip
```bash
source .venv/bin/activate
cd docs
-make html
+sphinx-build -M html . _build -W
(xdg-)open _build/html/index.html
```
diff --git a/pyproject.toml b/pyproject.toml
index f76df20..ec4b159 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ optional-dependencies.doc = [
"pandas",
# Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"setuptools",
- "sphinx>=4",
+ "sphinx>=8.1",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
@@ -48,8 +48,9 @@ optional-dependencies.doc = [
"sphinxext-opengraph",
]
optional-dependencies.test = [
- "coverage",
+ "coverage>=7.10",
"pytest",
+ "pytest-cov", # For VS Code’s coverage functionality
]
# https://docs.pypi.org/project_metadata/#project-urls
urls.Documentation = "https://genomic-features.readthedocs.io/"
@@ -62,12 +63,29 @@ features = [ "dev" ]
[tool.hatch.envs.docs]
features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"
+# Test the lowest and highest supported Python versions with normal deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "stable" ]
+python = [ "3.10", "3.13" ]
+
+# Test the newest supported Python version also with pre-release deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
[tool.hatch.envs.hatch-test]
-features = [ "test" ]
+features = [ "dev", "test" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+matrix.deps.env-vars = [
+ { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
[tool.ruff]
line-length = 120
@@ -118,6 +136,7 @@ addopts = [
[tool.coverage.run]
source = [ "genomic_features" ]
+patch = [ "subprocess" ]
omit = [
"**/test_*.py",
]