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 605c522..cdd876d 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,23 +1,29 @@
{
- "template": "https://github.com/scverse/cookiecutter-scverse",
- "commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
- "checkout": null,
- "context": {
- "cookiecutter": {
- "project_name": "cell2module",
- "package_name": "cell2module",
- "project_description": "cell2module: gene module discovery from scRNA and scATAC using count-based Bayesian NMF",
- "author_full_name": "Vitalii Kleshchevnikov",
- "author_email": "vitalii.kleshchevnikov@sanger.ac.uk",
- "github_user": "vitkl",
- "project_repo": "https://github.com/vitkl/cell2module",
- "license": "Apache License Version 2.0",
- "_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": "87a407a65408d75a949c0b54b19fd287475a56f8",
+ "checkout": "v0.4.0",
+ "context": {
+ "cookiecutter": {
+ "project_name": "cell2module",
+ "package_name": "cell2module",
+ "project_description": "cell2module: gene module discovery from scRNA and scATAC using count-based Bayesian NMF",
+ "author_full_name": "Vitalii Kleshchevnikov",
+ "author_email": "vitalii.kleshchevnikov@sanger.ac.uk",
+ "github_user": "vitkl",
+ "project_repo": "https://github.com/vitkl/cell2module",
+ "license": "Apache License Version 2.0",
+ "_copy_without_render": [
+ ".github/workflows/build.yaml",
+ ".github/workflows/test.yaml",
+ "docs/_templates/autosummary/**.rst"
+ ],
+ "_render_devdocs": false,
+ "_jinja2_env_vars": {
+ "lstrip_blocks": true,
+ "trim_blocks": true
+ },
+ "_template": "https://github.com/scverse/cookiecutter-scverse"
+ }
+ },
+ "directory": null
}
diff --git a/.editorconfig b/.editorconfig
index 2fe0ce0..050f911 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,5 +8,11 @@ charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true
+[*.{yml,yaml}]
+indent_size = 2
+
+[.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 9dfd4ac..a5a20e6 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,88 +2,88 @@ 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 procecure.
- * 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: Version information
+ description: |
+ Please paste below the output of
- ```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
+ ```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
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 f9fd4b4..b75a25a 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -2,10 +2,10 @@ name: Feature request
description: Propose a new feature for cell2module
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 0242943..265a95e 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -1,23 +1,29 @@
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
jobs:
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - 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@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
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..a3cc1b6
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,29 @@
+name: Release
+
+on:
+ release:
+ types: [published]
+
+# 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/cell2module
+ permissions:
+ id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - uses: actions/setup-python@v4
+ with:
+ python-version: "3.x"
+ cache: "pip"
+ - run: pip install build
+ - run: python -m build
+ - name: Publish package distributions to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/sync.yaml b/.github/workflows/sync.yaml
deleted file mode 100644
index 5219499..0000000
--- a/.github/workflows/sync.yaml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: Sync Template
-
-on:
- workflow_dispatch:
- schedule:
- - cron: "0 2 * * *" # every night at 2:00 UTC
-
-jobs:
- sync:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v4
- with:
- python-version: "3.10"
- - name: Install dependencies
- # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
- run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
- - name: Find Latest Tag
- uses: oprypin/find-latest-tag@v1.1.0
- id: get-latest-tag
- with:
- repository: scverse/cookiecutter-scverse
- releases-only: false
- sort-tags: true
- regex: '^v\d+\.\d+\.\d+$' # vX.X.X
- - name: Sync
- run: |
- cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
- - name: Create Pull Request
- uses: peter-evans/create-pull-request@v4
- with:
- commit-message: Automated template update from cookiecutter-scverse
- branch: template-update
- title: Automated template update from cookiecutter-scverse
- body: |
- A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
- got released. This PR adds all new changes to your repository and helps to to stay in sync with
- the latest best-practice template maintained by the scverse team.
-
- **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
- manually merge these changes.**
-
- For more information about the template sync, please refer to the
- [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej
new file mode 100644
index 0000000..f125858
--- /dev/null
+++ b/.github/workflows/test.yaml.rej
@@ -0,0 +1,124 @@
+diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks)
+@@ -1,62 +1,67 @@
+ 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
+
+ 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 }}
++ defaults:
++ run:
++ shell: bash -e {0} # -e to fail on error
++
++ 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@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 ${{ matrix.pip-flags }} ".[dev,test]"
++ - name: Test
+ env:
+- OS: ${{ matrix.os }}
+- PYTHON: ${{ matrix.python }}
+-
+- steps:
+- - uses: actions/checkout@v2
+- - name: Set up Python ${{ matrix.python }}
+- uses: actions/setup-python@v2
+- with:
+- python-version: ${{ matrix.python }}
+-
+- - name: Get pip cache dir
+- id: pip-cache-dir
+- run: |
+- echo "::set-output name=dir::$(pip cache dir)"
+- - name: Restore pip cache
+- uses: actions/cache@v2
+- with:
+- path: ${{ steps.pip-cache-dir.outputs.dir }}
+- key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+- restore-keys: |
+- pip-${{ runner.os }}-${{ env.pythonLocation }}-
+- - name: Install test dependencies
+- run: |
+- python -m pip install --upgrade pip wheel
+- pip install codecov
+- - 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
+- env:
+- CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+- run: |
+- codecov --required --flags=unittests
++ MPLBACKEND: agg
++ PLATFORM: ${{ matrix.os }}
++ DISPLAY: :42
++ run: |
++ coverage run -m pytest -v --color=yes
++ - name: Report coverage
++ run: |
++ coverage report
++ - name: Upload coverage
++ uses: codecov/codecov-action@v3
diff --git a/.gitignore b/.gitignore
index 7bb0bd5..eeec7e2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,13 @@
# Temp files
.DS_Store
*~
+buck-out/
# Compiled files
+.venv/
__pycache__/
+.mypy_cache/
+.ruff_cache/
# Distribution / packaging
/build/
@@ -14,6 +18,7 @@ __pycache__/
/.pytest_cache/
/.cache/
/data/
+/node_modules/
# docs
/docs/generated/
diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej
new file mode 100644
index 0000000..7c76634
--- /dev/null
+++ b/.pre-commit-config.yaml.rej
@@ -0,0 +1,118 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks)
+@@ -1,79 +1,42 @@
+ fail_fast: false
+ default_language_version:
+- python: python3
++ python: python3
+ default_stages:
+- - commit
+- - push
++ - commit
++ - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+- - repo: https://github.com/psf/black
+- rev: 24.4.2
+- hooks:
+- - id: black
+- - repo: https://github.com/pre-commit/mirrors-prettier
+- rev: v4.0.0-alpha.8
+- hooks:
+- - id: prettier
+- - repo: https://github.com/asottile/blacken-docs
+- rev: 1.16.0
+- hooks:
+- - id: blacken-docs
+- - repo: https://github.com/PyCQA/isort
+- rev: 5.13.2
+- hooks:
+- - id: isort
+- - repo: https://github.com/asottile/yesqa
+- rev: v1.5.0
+- hooks:
+- - id: yesqa
+- additional_dependencies:
+- - flake8-tidy-imports
+- - flake8-docstrings
+- - flake8-rst-docstrings
+- - flake8-comprehensions
+- - flake8-bugbear
+- - flake8-blind-except
+- - repo: https://github.com/pre-commit/pre-commit-hooks
+- rev: v4.6.0
+- 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: https://github.com/myint/autoflake
+- rev: v2.3.1
+- hooks:
+- - id: autoflake
+- args:
+- - --in-place
+- - --remove-all-unused-imports
+- - --remove-unused-variable
+- - --ignore-init-module-imports
+- - repo: https://github.com/PyCQA/flake8
+- rev: 7.0.0
+- hooks:
+- - id: flake8
+- additional_dependencies:
+- - flake8-tidy-imports
+- - flake8-docstrings
+- - flake8-rst-docstrings
+- - flake8-comprehensions
+- - flake8-bugbear
+- - flake8-blind-except
+- - repo: https://github.com/asottile/pyupgrade
+- rev: v3.15.2
+- hooks:
+- - id: pyupgrade
+- args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+- - 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/pre-commit/mirrors-prettier
++ rev: v4.0.0-alpha.8
++ hooks:
++ - id: prettier
++ - repo: https://github.com/astral-sh/ruff-pre-commit
++ rev: v0.4.4
++ 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: v4.6.0
++ 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/LICENSE b/LICENSE
index bc98b11..b0694df 100644
--- a/LICENSE
+++ b/LICENSE
@@ -199,3 +199,4 @@ distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
+
diff --git a/README.md b/README.md
index afcfade..0bd4d32 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
## Installation
-You need to have Python 3.8 or newer installed on your system. If you don't have
+You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install cell2module:
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 17dc123..e4665df 100644
--- a/docs/_templates/autosummary/class.rst
+++ b/docs/_templates/autosummary/class.rst
@@ -39,9 +39,6 @@ Attributes
{% for item in attributes %}
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
.. autoattribute:: {{ [objname, item] | join(".") }}
{%- endfor %}
@@ -56,9 +53,6 @@ Methods
{% for item in methods %}
{%- if item != '__init__' %}
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
.. automethod:: {{ [objname, item] | join(".") }}
{%- endif -%}
{%- endfor %}
diff --git a/docs/conf.py b/docs/conf.py
index 346af4f..828a06f 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
@@ -16,12 +16,15 @@
# -- Project information -----------------------------------------------------
+# 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("cell2module")
project_name = info["Name"]
author = info["Author"]
copyright = f"{datetime.now():%Y}, {author}."
version = info["Version"]
-repository_url = f"https://github.com/vitkl/{project_name}"
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
# The full version, including alpha/beta/rc tags
release = info["Version"]
@@ -33,10 +36,10 @@
html_context = {
"display_github": True, # Integrate GitHub
- "github_user": "vitkl", # 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": "vitkl",
+ "github_repo": "https://github.com/vitkl/cell2module",
+ "github_version": "main",
+ "conf_py_path": "/docs/",
}
# -- General configuration ---------------------------------------------------
@@ -54,6 +57,7 @@
"sphinx_autodoc_typehints",
"sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
+ "sphinxext.opengraph",
*[p.stem for p in (HERE / "extensions").glob("*.py")],
]
@@ -65,7 +69,7 @@
napoleon_include_init_with_doc = False
napoleon_use_rtype = True # having a separate entry generally helps readability
napoleon_use_param = True
-myst_heading_anchors = 3 # create anchors for h1-h3
+myst_heading_anchors = 6 # create anchors for h1-h6
myst_enable_extensions = [
"amsmath",
"colon_fence",
@@ -87,6 +91,7 @@
}
intersphinx_mapping = {
+ "python": ("https://docs.python.org/3", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
}
@@ -104,11 +109,15 @@
#
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"
@@ -118,18 +127,3 @@
# 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 cf82252..839d352 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,6 +1,6 @@
# Contributing guide
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too.
+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.
@@ -19,9 +19,8 @@ pip install -e ".[dev,test,doc]"
## 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
@@ -43,16 +42,16 @@ 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]
+Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [ruff][ruff-editors]
and [prettier][prettier-editors].
-[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
[prettier-editors]: https://prettier.io/docs/en/editors.html
## Writing tests
```{note}
-Remember to first install the package with `pip install '-e[dev,test]'`
+Remember to first install the package with `pip install -e '.[dev,test]'`
```
This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
@@ -65,7 +64,17 @@ command line by executing
pytest
```
-in the root of the repository. Continuous integration will automatically run the tests on all pull requests.
+in the root of the repository.
+
+### Continuous integration
+
+Continuous integration 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). 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.
[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
@@ -73,7 +82,7 @@ in the root of the repository. Continuous integration will automatically run the
### Updating the version number
-Before making a release, you need to update the version number. Please adhere to [Semantic Versioning][semver], in brief
+Before making a release, you need to update the version number in the `pyproject.toml` file. Please adhere to [Semantic Versioning][semver], in brief
> Given a version number MAJOR.MINOR.PATCH, increment the:
>
@@ -83,56 +92,8 @@ Before making a release, you need to update the version number. Please adhere to
>
> 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
-
-```bash
-bump2version patch
-bump2version minor
-bump2version major
-```
-
-Once you are done, run
-
-```
-git push --tags
-```
-
-to publish the created tag on GitHub.
-
-[bump2version]: https://github.com/c4urself/bump2version
-
-### 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
-
-```bash
-python -m build
-```
-
-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.
-
-Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
-
-```bash
-twine check dist/*
-```
-
-and finally publishing it with:
-
-```bash
-twine upload dist/*
-```
-
-Provide your username and password when requested and then go check out your package on [PyPI][]!
-
-For more information, follow the [Python packaging tutorial][].
-
-It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
-in the cookiecutter-scverse template.
-
-[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
+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.
## Writing documentation
@@ -142,6 +103,7 @@ Please write documentation for new or changed features and use-cases. This proje
- [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.
@@ -150,7 +112,7 @@ on how to write documentation.
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`
@@ -195,3 +157,4 @@ open _build/html/index.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/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 9447813..1135204 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -1,24 +1,27 @@
# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
# with some minor adjustment
+from __future__ import annotations
+
import re
+from collections.abc import Generator, Iterable
from sphinx.application import Sphinx
from sphinx.ext.napoleon import NumpyDocstring
-def _process_return(lines):
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
for line in lines:
- m = re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line)
- if m:
- # Once this is in scanpydoc, we can use the fancy hover stuff
+ if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line):
yield f'-{m["param"]} (:class:`~{m["type"]}`)'
else:
yield line
-def _parse_returns_section(self, section):
- lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
- lines = self._format_block(":returns: ", lines_raw)
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+ lines_raw = self._dedent(self._consume_to_next_section())
+ if lines_raw[0] == ":":
+ del lines_raw[0]
+ lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
if lines and lines[-1]:
lines.append("")
return lines
diff --git a/docs/index.md b/docs/index.md
index 04d594a..8b5f298 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -8,7 +8,6 @@
api.md
changelog.md
-template_usage.md
contributing.md
references.md
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 8ca5bfd..0000000
--- a/docs/template_usage.md
+++ /dev/null
@@ -1,322 +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 cell2module
-```
-
-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: `cell2module`.
-:::
-
-Now that your new project repository has been created on github at `https://github.com/vitkl/cell2module` 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/cell2module`. 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/vitkl/cell2module.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/vitkl/cell2module`. 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/vitkl/cell2module`. 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.
-
-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 checks are for code style and format:
-
-- [black](https://black.readthedocs.io/en/stable/): standard code
- formatter in Python.
-- [isort](https://pycqa.github.io/isort/): sort module imports into
- sections and types.
-- [prettier](https://prettier.io/docs/en/index.html): standard code
- formatter for non-Python files (e.g. YAML).
-- [blacken-docs](https://github.com/asottile/blacken-docs): black on
- python code in docs.
-
-The following pre-commit checks are for errors and inconsistencies:
-
-- [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files.
- - [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports):
- tidy module imports.
- - [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings):
- pydocstyle extension of flake8.
- - [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings):
- extension of `flake8-docstrings` for `rst` docs.
- - [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions):
- write better list/set/dict comprehensions.
- - [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear):
- find possible bugs and design issues in program.
- - [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except):
- checks for blind, catch-all `except` statements.
-- [yesqa](https://github.com/asottile/yesqa):
- remove unneccesary `# noqa` comments, follows additional dependencies listed above.
-- [autoflake](https://github.com/PyCQA/autoflake):
- remove unused imports and variables.
-- [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks.
- - **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.
-- [pyupgrade](https://github.com/asottile/pyupgrade):
- upgrade syntax for newer versions of the language.
-- **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.
-
-### How to disable or add pre-commit checks
-
-- To ignore lint warnigs from **flake8**, see [Ignore certain lint warnings](#how-to-ignore-certain-lint-warnings).
-- You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file.
- Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or tool-specific
- config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**.
-
-### How to ignore certain lint warnings
-
-The [pre-commit checks](#pre-commit-checks) include [flake8](https://flake8.pycqa.org/en/latest/) which checks
-for errors in Python files, including stylistic errors.
-
-In some cases it might overshoot and you may have good reasons to ignore certain warnings.
-
-To ignore an specific error on a per-case basis, you can add a comment `# noqa` to the offending line. You can also
-specify the error ID to ignore, with e.g. `# noqa: E731`. Check the [flake8 guide][] for reference.
-
-Alternatively, you can disable certain error messages for the entire project. To do so, edit the `.flake8`
-file in the root of the repository. Add one line per linting code you wish to ignore and don't forget to add a comment.
-
-```toml
-...
-# line break before a binary operator -> black does not adhere to PEP8
-W503
-# line break occured after a binary operator -> black does not adhere to PEP8
-W504
-...
-```
-
-[flake8 guide]: https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html
-
-### 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 = "cell2module"
--version = "0.3.1dev"
-+dynamic = ["version"]
-
-@@ -60,6 +60,9 @@
-+[tool.hatch.version]
-+source = "vcs"
-+
- [tool.coverage.run]
- source = ["cell2module"]
- 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 0772e05..6ca9b50 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,13 +2,12 @@
build-backend = "hatchling.build"
requires = ["hatchling"]
-
[project]
name = "cell2module"
version = "0.0.1"
description = "cell2module: gene module discovery from scRNA and scATAC using count-based Bayesian NMF"
readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
{name = "Vitalii Kleshchevnikov"},
@@ -62,35 +61,63 @@ addopts = [
"--import-mode=importlib", # allow using test files with same name
]
-[tool.isort]
-include_trailing_comma = true
-multi_line_output = 3
-profile = "black"
-skip_glob = ["docs/*"]
-
-[tool.black]
+[tool.ruff]
line-length = 120
-target-version = ['py38']
-include = '\.pyi?$'
-exclude = '''
-(
- /(
- \.eggs
- | \.git
- | \.hg
- | \.mypy_cache
- | \.tox
- | \.venv
- | _build
- | buck-out
- | build
- | dist
- )/
-)
-'''
+src = ["src"]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+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
+]
+ignore = [
+ # line too long -> we accept long comment lines; formatter 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 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",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
-[tool.jupytext]
-formats = "ipynb,md"
+[tool.ruff.lint.per-file-ignores]
+"docs/*" = ["I"]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
[tool.cruft]
skip = [
@@ -101,5 +128,5 @@ skip = [
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
- "docs/notebooks/example.ipynb"
+ "docs/notebooks/example.ipynb",
]
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..abd041d
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,40 @@
+diff a/pyproject.toml b/pyproject.toml (rejected hunks)
+@@ -22,30 +21,31 @@ urls.Home-page = "https://github.com/vitkl/cell2module"
+ dependencies = [
+ "anndata",
+ # for debug logging (referenced from the issue template)
+- "session-info"
++ "session-info",
+ ]
+
+ [project.optional-dependencies]
+ dev = [
+- # CLI for bumping the version number
+- "bump2version",
+ "pre-commit",
+- "twine>=4.0.2"
++ "twine>=4.0.2",
+ ]
+ doc = [
++ "docutils>=0.8,!=0.18.*,!=0.19.*",
+ "sphinx>=4",
+- "sphinx-book-theme>=0.3.3",
+- "myst-nb",
++ "sphinx-book-theme>=1.0.0",
++ "myst-nb>=1.1.0",
+ "sphinxcontrib-bibtex>=1.0.0",
+ "sphinx-autodoc-typehints",
++ "sphinxext-opengraph",
+ # For notebooks
+ "ipykernel",
+ "ipython",
+ "sphinx-copybutton",
++ "pandas",
+ ]
+ test = [
+ "pytest",
+- "pytest-cov",
++ "coverage",
+ ]
+
+ [tool.coverage.run]