diff --git a/.cruft.json b/.cruft.json index 45f63f0..e431a4d 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "3dcfe1fd2bdfc3c1cc9cc4c2108fba1e973b9dcb", - "checkout": null, + "commit": "586b1652162ff7994b0070a034023d64289ae416", + "checkout": "v0.3.1", "context": { "cookiecutter": { "project_name": "FlowSOM", @@ -13,9 +13,15 @@ "project_repo": "https://github.com/artuurC/FlowSOM", "license": "GNU General Public License Version 3", "_copy_without_render": [ - ".github/workflows/**.yaml", + ".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" } }, diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 9352d04..bd1b09e 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -1,30 +1,29 @@ name: Release on: - push: - tags: - - "*.*.*" + release: + types: [published] +# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/ jobs: release: - name: Release + name: Upload release to PyPI runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/FlowSOM + permissions: + id-token: write # IMPORTANT: this permission is mandatory for trusted publishing steps: - - name: Checkout code - uses: actions/checkout@v3 - - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 with: - python-version: "3.10" - - - name: Install hatch - run: pip install hatch - - - name: Build project for distribution - run: hatch build - - - name: Publish a Python distribution to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + filter: blob:none + fetch-depth: 0 + - uses: actions/setup-python@v4 with: - password: ${{ secrets.PYPI_API_TOKEN }} + 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/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6d0aa48..185ddd5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,6 +39,9 @@ repos: 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 diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej new file mode 100644 index 0000000..831fbdc --- /dev/null +++ b/.pre-commit-config.yaml.rej @@ -0,0 +1,34 @@ +diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks) +@@ -6,29 +6,18 @@ default_stages: + - push + minimum_pre_commit_version: 2.16.0 + repos: +- - repo: https://github.com/psf/black +- rev: "24.2.0" +- 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: v4.0.0-alpha.8 + 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: v0.2.2 + 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: v4.5.0 + hooks: diff --git a/LICENSE.rej b/LICENSE.rej new file mode 100644 index 0000000..a814344 --- /dev/null +++ b/LICENSE.rej @@ -0,0 +1,677 @@ +diff a/LICENSE b/LICENSE (rejected hunks) +@@ -1 +1,675 @@ + ++ GNU GENERAL PUBLIC LICENSE ++ Version 3, 29 June 2007 ++ ++ Copyright (C) 2007 Free Software Foundation, Inc. ++ Everyone is permitted to copy and distribute verbatim copies ++ of this license document, but changing it is not allowed. ++ ++ Preamble ++ ++ The GNU General Public License is a free, copyleft license for ++software and other kinds of works. ++ ++ The licenses for most software and other practical works are designed ++to take away your freedom to share and change the works. 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Use with the GNU Affero General Public License. ++ ++ Notwithstanding any other provision of this License, you have ++permission to link or combine any covered work with a work licensed ++under version 3 of the GNU Affero General Public License into a single ++combined work, and to convey the resulting work. The terms of this ++License will continue to apply to the part which is the covered work, ++but the special requirements of the GNU Affero General Public License, ++section 13, concerning interaction through a network will apply to the ++combination as such. ++ ++ 14. Revised Versions of this License. ++ ++ The Free Software Foundation may publish revised and/or new versions of ++the GNU General Public License from time to time. Such new versions will ++be similar in spirit to the present version, but may differ in detail to ++address new problems or concerns. ++ ++ Each version is given a distinguishing version number. If the ++Program specifies that a certain numbered version of the GNU General ++Public License "or any later version" applies to it, you have the ++option of following the terms and conditions either of that numbered ++version or of any later version published by the Free Software ++Foundation. If the Program does not specify a version number of the ++GNU General Public License, you may choose any version ever published ++by the Free Software Foundation. ++ ++ If the Program specifies that a proxy can decide which future ++versions of the GNU General Public License can be used, that proxy's ++public statement of acceptance of a version permanently authorizes you ++to choose that version for the Program. ++ ++ Later license versions may give you additional or different ++permissions. However, no additional obligations are imposed on any ++author or copyright holder as a result of your choosing to follow a ++later version. ++ ++ 15. Disclaimer of Warranty. ++ ++ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY ++APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT ++HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY ++OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ++THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR ++PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM ++IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ++ALL NECESSARY SERVICING, REPAIR OR CORRECTION. ++ ++ 16. Limitation of Liability. ++ ++ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING ++WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS ++THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY ++GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE ++USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF ++DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD ++PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), ++EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF ++SUCH DAMAGES. ++ ++ 17. Interpretation of Sections 15 and 16. ++ ++ If the disclaimer of warranty and limitation of liability provided ++above cannot be given local legal effect according to their terms, ++reviewing courts shall apply local law that most closely approximates ++an absolute waiver of all civil liability in connection with the ++Program, unless a warranty or assumption of liability accompanies a ++copy of the Program in return for a fee. ++ ++ END OF TERMS AND CONDITIONS ++ ++ How to Apply These Terms to Your New Programs ++ ++ If you develop a new program, and you want it to be of the greatest ++possible use to the public, the best way to achieve this is to make it ++free software which everyone can redistribute and change under these terms. ++ ++ To do so, attach the following notices to the program. It is safest ++to attach them to the start of each source file to most effectively ++state the exclusion of warranty; and each file should have at least ++the "copyright" line and a pointer to where the full notice is found. ++ ++ ++ Copyright (C) ++ ++ This program is free software: you can redistribute it and/or modify ++ it under the terms of the GNU General Public License as published by ++ the Free Software Foundation, either version 3 of the License, or ++ (at your option) any later version. ++ ++ This program is distributed in the hope that it will be useful, ++ but WITHOUT ANY WARRANTY; without even the implied warranty of ++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++ GNU General Public License for more details. ++ ++ You should have received a copy of the GNU General Public License ++ along with this program. If not, see . ++ ++Also add information on how to contact you by electronic and paper mail. ++ ++ If the program does terminal interaction, make it output a short ++notice like this when it starts in an interactive mode: ++ ++ FlowSOM Copyright (C) 2024, Artuur Couckuyt ++ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. ++ This is free software, and you are welcome to redistribute it ++ under certain conditions; type `show c' for details. ++ ++The hypothetical commands `show w' and `show c' should show the appropriate ++parts of the General Public License. Of course, your program's commands ++might be different; for a GUI interface, you would use an "about box". ++ ++ You should also get your employer (if you work as a programmer) or school, ++if any, to sign a "copyright disclaimer" for the program, if necessary. ++For more information on this, and how to apply and follow the GNU GPL, see ++. ++ ++ The GNU General Public License does not permit incorporating your program ++into proprietary programs. If your program is a subroutine library, you ++may consider it more useful to permit linking proprietary applications with ++the library. If this is what you want to do, use the GNU Lesser General ++Public License instead of this License. But first, please read ++. 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 b/docs/conf.py index 946930b..1ca2901 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -107,6 +107,8 @@ # html_theme = "sphinx_book_theme" html_static_path = ["_static"] +html_css_files = ["css/custom.css"] + html_title = project_name html_theme_options = { @@ -123,18 +125,3 @@ # 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 d100320..f0c945f 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 @@ -43,10 +42,10 @@ 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 @@ -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 @@ -83,55 +92,8 @@ Before making a release, you need to update the version number in the `pyproject > > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format. -Once you are done, run - -``` -git push --tags -``` - -to publish the created tag on GitHub. Alternatively, it is possible to create a tag through the Github web interface. For more information, see [managing Github releases][]. This will automatically trigger a Github workflow that creates a release on PyPI. - -### The release Github workflow - -#### Behind the scenes - -This section explains how releases can be created manually purely for educational purposes. Experienced developers may skip this section. -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][]. - -#### Configuring the Github workflow - -Tags adhering to `"*.*.*"` that are pushed to the `main` branch will trigger the release Github workflow that automatically builds and uploads the Python package to [PyPI][]. -For this to work, the `PYPI_API_TOKEN` Github secret needs to be set to the value of the [PyPI][] token. -See [Creating PyPI tokens][] for instructions on how to create a [PyPI][] token. -Finally, set your `PYPI_API_TOKEN` Github secret equal to the value of the just created [PyPI][] token by following [creating Github secrets][]. - -[creating github secrets]: https://docs.github.com/en/actions/security-guides/encrypted-secrets -[creating pypi tokens]: https://pypi.org/help/#apitoken -[managing github releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository -[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 @@ -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/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/template_usage.md b/docs/template_usage.md deleted file mode 100644 index 42c2b93..0000000 --- a/docs/template_usage.md +++ /dev/null @@ -1,400 +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 FlowSOM -``` - -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: `FlowSOM`. -::: - -Now that your new project repository has been created on github at `https://github.com/artuurC/FlowSOM` 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/FlowSOM`. 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/artuurC/FlowSOM.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/artuurC/FlowSOM`. 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. - -### The pyproject.toml file - -Modern Python package management uses a `pyproject.toml` that was first introduced in [PEP 518](https://peps.python.org/pep-0518/). -This file contains build system requirements and information, which are used by pip to build the package. -For more details please have a look at [pip's description of the pyproject.toml file](https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/). - -#### Important metadata fields - -The `[project]` section in the `pyproject.toml` file defines several important metadata fields that might require editing. -For example, the `name`, `description`, `authors` fields could need updates as the project evolves. -Especially, the `version` field needs to be adapted if newer versions of the package are to be released. -See {ref}`vcs-based-versioning` for more details. - -#### Dependency management - -Package dependencies can be added to the `dependencies` of the `[project]` section. -You can constrain versions using `>=` and other less useful operators (`>`, `<`, `<=`, `==`, `!=`, and `~=`). -A common example would be `twine>=4.0.2` which requires `twine` to be installed with at least version `4.0.2` or greater. -As another example, if there is a known buggy version, you could exclude it like `numpy >=3.0, !=3.0.5`. - -Further optional dependencies are defined in the `[project.optional-dependencies]` section such as dependencies only for tests (`test`). -All dependencies listed in such optional dependency groups can then be installed by specifying them like: `pip install [test]`. - -#### Tool configurations - -The `pyproject.toml` file also serves as single configuration file for many tools such as many {ref}`pre-commit`. -For example, the line length of [black](https://github.com/psf/black) can be configured as follows: - -```toml -[tool.black] -line-length = 120 -``` - -### 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/artuurC/FlowSOM`. 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)= - -### 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 - -(vcs-based-versioning)= - -### Using VCS-based versioning - -By default, the template uses hard-coded version numbers that are set in `pyproject.toml`. 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 = "FlowSOM" --version = "0.3.1dev" -+dynamic = ["version"] - -@@ -60,6 +60,9 @@ -+[tool.hatch.version] -+source = "vcs" -+ - [tool.coverage.run] - source = ["FlowSOM"] - 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 70214c8..1fd78b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,10 +42,11 @@ doc = [ "ipykernel", "ipython", "sphinx-copybutton", + "pandas", ] test = [ "pytest", - "pytest-cov", + "coverage", ] [tool.hatch.build.targets.wheel] @@ -64,12 +65,15 @@ addopts = [ "--import-mode=importlib", # allow using test files with same name ] -[tool.black] -line-length = 120 - [tool.ruff] -src = ["src"] line-length = 120 +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 @@ -84,7 +88,7 @@ select = [ "RUF100", # Report unused noqa directives ] ignore = [ - # line too long -> we accept long comment lines; black gets rid of long code lines + # 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", @@ -111,10 +115,10 @@ ignore = [ "D213", ] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "numpy" -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "docs/*" = ["I"] "tests/*" = ["D"] "*/__init__.py" = ["F401"] @@ -128,5 +132,5 @@ 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..e3a858d --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,17 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -21,13 +21,13 @@ urls.Home-page = "https://github.com/artuurC/FlowSOM" + dependencies = [ + "anndata", + # for debug logging (referenced from the issue template) +- "session-info" ++ "session-info", + ] + + [project.optional-dependencies] + dev = [ + "pre-commit", +- "twine>=4.0.2" ++ "twine>=4.0.2", + ] + doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*",