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 bed9587..b1a3305 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "03ef73af73ea4a927decc396232d9c2c5e958ee1", - "checkout": "v0.2.11", + "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48", + "checkout": "v0.3.0", "context": { "cookiecutter": { "project_name": "biolord", @@ -16,6 +16,11 @@ ".github/workflows/**.yaml", "docs/_templates/autosummary/**.rst" ], + "_render_devdocs": false, + "_jinja2_env_vars": { + "lstrip_blocks": true, + "trim_blocks": true + }, "_template": "https://github.com/scverse/cookiecutter-scverse" } }, 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 8d3ddaa..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 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: 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 96e3622..85c8b2b 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 biolord 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..265a95e 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -1,29 +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 + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true 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@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..bd82eb5 --- /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/{{ cookiecutter.package_name }} + 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/test.yaml.rej b/.github/workflows/test.yaml.rej new file mode 100644 index 0000000..95161f8 --- /dev/null +++ b/.github/workflows/test.yaml.rej @@ -0,0 +1,113 @@ +diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks) +@@ -1,53 +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 ++ 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: "3.9" ++ - os: ubuntu-latest ++ python: "3.11" ++ - os: ubuntu-latest ++ python: "3.11" ++ 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@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: | ++ coverage run -m pytest -v --color=yes ++ - name: Report coverage ++ run: | ++ coverage report ++ - name: Upload coverage ++ uses: codecov/codecov-action@v3 diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej new file mode 100644 index 0000000..c0a8e7c --- /dev/null +++ b/.pre-commit-config.yaml.rej @@ -0,0 +1,100 @@ +diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks) +@@ -1,50 +1,53 @@ + 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: "23.11.0" +- hooks: +- - id: black +- - repo: https://github.com/asottile/blacken-docs +- rev: 1.16.0 +- hooks: +- - id: blacken-docs +- - repo: https://github.com/pre-commit/mirrors-prettier +- rev: v3.1.0 +- 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: v0.1.6 +- hooks: +- - id: ruff +- args: [--fix, --exit-non-zero-on-fix] +- - repo: https://github.com/pre-commit/pre-commit-hooks +- rev: v4.5.0 +- 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/psf/black ++ rev: "23.11.0" ++ hooks: ++ - id: black ++ - repo: https://github.com/asottile/blacken-docs ++ rev: 1.16.0 ++ hooks: ++ - id: blacken-docs ++ - repo: https://github.com/pre-commit/mirrors-prettier ++ rev: v3.1.0 ++ 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/astral-sh/ruff-pre-commit ++ rev: v0.1.6 ++ hooks: ++ - id: ruff ++ args: [--fix, --exit-non-zero-on-fix] ++ - repo: https://github.com/pre-commit/pre-commit-hooks ++ rev: v4.5.0 ++ 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.rej b/.readthedocs.yaml.rej new file mode 100644 index 0000000..6e4581a --- /dev/null +++ b/.readthedocs.yaml.rej @@ -0,0 +1,29 @@ +diff a/.readthedocs.yaml b/.readthedocs.yaml (rejected hunks) +@@ -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/README.md.rej b/README.md.rej new file mode 100644 index 0000000..e4af59f --- /dev/null +++ b/README.md.rej @@ -0,0 +1,19 @@ +diff a/README.md b/README.md (rejected hunks) +@@ -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 3.9 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 biolord: +@@ -33,7 +33,7 @@ pip install biolord + 1. Install the latest development version: + + ```bash +-pip install git+https://github.com/zoepiran/biolord.git@main ++pip install git+https://github.com/nitzanlab/biolord.git@main + ``` + + ## Release notes 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/conf.py.rej b/docs/conf.py.rej index d8e0c36..97caeb8 100644 --- a/docs/conf.py.rej +++ b/docs/conf.py.rej @@ -1,18 +1,44 @@ diff a/docs/conf.py b/docs/conf.py (rejected hunks) -@@ -16,12 +16,15 @@ sys.path.insert(0, str(HERE / "extensions")) +@@ -57,6 +57,7 @@ extensions = [ + "sphinx_autodoc_typehints", + "sphinx.ext.mathjax", + "IPython.sphinxext.ipython_console_highlighting", ++ "sphinxext.opengraph", + *[p.stem for p in (HERE / "extensions").glob("*.py")], + ] - # -- Project information ----------------------------------------------------- +@@ -108,12 +109,15 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] + # + html_theme = "sphinx_book_theme" + html_static_path = ["_static"] ++html_css_files = ["css/custom.css"] ++ + html_title = project_name -+# 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("biolord") - project_name = info["Name"] - author = info["Author"] - copyright = f"{datetime.now():%Y}, {author}." - version = info["Version"] --repository_url = f"https://github.com/zoepiran/{project_name}" -+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL")) -+repository_url = urls["Source"] + html_theme_options = { + "repository_url": repository_url, + "use_repository_button": True, + "path_to_docs": "docs/", ++ "navigation_with_keys": False, + } - # The full version, including alpha/beta/rc tags - release = info["Version"] + pygments_style = "default" +@@ -123,18 +127,3 @@ nitpick_ignore = [ + # 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/index.md.rej b/docs/index.md.rej new file mode 100644 index 0000000..14a8d31 --- /dev/null +++ b/docs/index.md.rej @@ -0,0 +1,9 @@ +diff a/docs/index.md b/docs/index.md (rejected hunks) +@@ -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/pyproject.toml b/pyproject.toml index 9b58a12..133c354 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,12 +65,10 @@ addopts = [ [tool.black] line-length = 120 -target-version = ["py38"] [tool.ruff] src = ["src"] line-length = 120 -target-version = "py38" select = [ "F", # Errors detected by Pyflakes "E", # Error detected by Pycodestyle @@ -119,9 +117,6 @@ ignore = [ "tests/*" = ["D"] "*/__init__.py" = ["F401"] -[tool.jupytext] -formats = "ipynb,md" - [tool.cruft] skip = [ "tests", diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 0000000..41a4b5a --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,40 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ name = "biolord" + version = "0.0.1" + description = "A deep generative framework for disentangling known and unknown attributes in single-cell data." + readme = "README.md" +-requires-python = ">=3.8" ++requires-python = ">=3.9" + license = {file = "LICENSE"} + authors = [ + {name = "Zoe Piran"}, +@@ -26,25 +26,26 @@ dependencies = [ + + [project.optional-dependencies] + dev = [ +- # CLI for bumping the version number +- "bump2version", + "pre-commit", + "twine>=4.0.2" + ] + doc = [ ++ "docutils>=0.8,!=0.18.*,!=0.19.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", + "myst-nb", + "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]