From 34b8e169ab79f46cdc8ad5edf42e7cb8f766a62c Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 24 Aug 2026 23:14:40 -0700 Subject: [PATCH 1/5] migrate to hatch + uv --- .coveragerc | 21 +- .github/dependabot.yml | 15 ++ .github/workflows/pre-commit.yml | 16 ++ .github/workflows/publish-pypi.yml | 11 +- .github/workflows/run-tests.yml | 9 +- .gitignore | 56 +++++ .pre-commit-config.yaml | 8 +- .readthedocs.yml | 23 -- CONTRIBUTING.md | 377 +---------------------------- docs/conf.py | 67 +++-- docs/requirements.txt | 4 +- docs/tutorial.md | 14 +- pyproject.toml | 69 +++++- setup.cfg | 132 ---------- setup.py | 20 -- src/biocframe/py.typed | 0 tox.ini | 76 ++---- 17 files changed, 249 insertions(+), 669 deletions(-) create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/pre-commit.yml delete mode 100644 .readthedocs.yml delete mode 100644 setup.cfg delete mode 100644 setup.py create mode 100644 src/biocframe/py.typed diff --git a/.coveragerc b/.coveragerc index 760cc92..a920d99 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,28 +1,13 @@ -# .coveragerc to control coverage.py [run] -branch = True -source = biocframe -# omit = bad_file.py - -[paths] -source = - src/ - */site-packages/ +source = src +omit = tests/* [report] -# Regexes for lines to exclude from consideration exclude_lines = - # Have to re-enable the standard pragma pragma: no cover - - # Don't complain about missing debug-only code: def __repr__ - if self\.debug - - # Don't complain if tests don't hit defensive assertion code: + if self.debug: raise AssertionError raise NotImplementedError - - # Don't complain if non-runnable code isn't run: if 0: if __name__ == .__main__.: diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..12eea0d --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,15 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" + labels: + - "dependencies" + + - package-ecosystem: "pip" + directory: "/" + schedule: + interval: "weekly" + labels: + - "dependencies" diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..d638c47 --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,16 @@ +name: pre-commit + +on: + pull_request: + push: + branches: [main] + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: '3.12' + - uses: pre-commit/action@v3.0.1 diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 405fee0..81ef189 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -24,15 +24,16 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install tox + pip install uv tox + uv sync - - name: Test with tox + - name: Test run: | - tox + tox -e default - - name: Build Project and Publish + - name: Build Project run: | - python -m tox -e clean,build + tox -e build # This uses the trusted publisher workflow so no token is required. - name: Publish to PyPI diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 3d3bc95..0093104 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -46,13 +46,12 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install tox coverage + pip install uv tox + uv sync - name: Run tests - run: >- - pipx run --python '${{ steps.setup-python.outputs.python-path }}' - tox - -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml # pytest args + run: | + tox -e default -- --cov --cov-branch --cov-report=xml - name: Check for codecov token availability id: codecov-check diff --git a/.gitignore b/.gitignore index e9e1e9b..99af268 100644 --- a/.gitignore +++ b/.gitignore @@ -52,3 +52,59 @@ MANIFEST .venv*/ .conda*/ .python-version + +# Byte-compiled / optimized / DLL files +__pycache__/ +*$py.class +# C extensions +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +# PyInstaller +*.manifest +*.spec +# Installer logs +pip-log.txt +pip-delete-this-directory.txt +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.cache +nosetests.xml +*.cover +*.py,cover +.hypothesis/ +cover/ +# Sphinx documentation +docs/_build/ +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ +# mypy, ruff, etc +.mypy_cache/ +.ruff_cache/ +.pyre/ +# Editors +.vscode/ +.idea/ +*.swp +*.swo diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3f91485..863ce2d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,10 +33,12 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.15.6 + rev: v0.16.2 hooks: - - id: ruff - args: [--fix, --exit-non-zero-on-fix] + # Run the linter. + - id: ruff-check + args: [--fix, --exit-zero] + # Run the formatter. - id: ruff-format ## If like to embrace black styles even in the docs: diff --git a/.readthedocs.yml b/.readthedocs.yml deleted file mode 100644 index 21b0814..0000000 --- a/.readthedocs.yml +++ /dev/null @@ -1,23 +0,0 @@ -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -# Required -version: 2 - -# Build documentation in the docs/ directory with Sphinx -sphinx: - configuration: docs/conf.py - -# Build documentation with MkDocs -#mkdocs: -# configuration: mkdocs.yml - -# Optionally build your docs in additional formats such as PDF -formats: - - pdf - -python: - version: 3.8 - install: - - requirements: docs/requirements.txt - - {path: ., method: pip} diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index cc9c819..02b4546 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,371 +1,20 @@ -```{todo} THIS IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS! - - The document assumes you are using a source repository service that promotes a - contribution model similar to [GitHub's fork and pull request workflow]. - While this is true for the majority of services (like GitHub, GitLab, - BitBucket), it might not be the case for private repositories (e.g., when - using Gerrit). - - Also notice that the code examples might refer to GitHub URLs or the text - might use GitHub specific terminology (e.g., *Pull Request* instead of *Merge - Request*). - - Please make sure to check the document having these assumptions in mind - and update things accordingly. -``` - -```{todo} Provide the correct links/replacements at the bottom of the document. -``` - -```{todo} You might want to have a look on [PyScaffold's contributor's guide], - - especially if your project is open source. The text should be very similar to - this template, but there are a few extra contents that you might decide to - also include, like mentioning labels of your issue tracker or automated - releases. -``` - # Contributing -Welcome to `BiocFrame` contributor's guide. - -This document focuses on getting any potential contributor familiarized with -the development processes, but [other kinds of contributions] are also appreciated. - -If you are new to using [git] or have never collaborated in a project previously, -please have a look at [contribution-guide.org]. Other resources are also -listed in the excellent [guide created by FreeCodeCamp] [^contrib1]. - -Please notice, all users and contributors are expected to be **open, -considerate, reasonable, and respectful**. When in doubt, -[Python Software Foundation's Code of Conduct] is a good reference in terms of -behavior guidelines. - -## Issue Reports - -If you experience bugs or general issues with `BiocFrame`, please have a look -on the [issue tracker]. -If you don't see anything useful there, please feel free to fire an issue report. - -:::{tip} -Please don't forget to include the closed issues in your search. -Sometimes a solution was already reported, and the problem is considered -**solved**. -::: - -New issue reports should include information about your programming environment -(e.g., operating system, Python version) and steps to reproduce the problem. -Please try also to simplify the reproduction steps to a very minimal example -that still illustrates the problem you are facing. By removing other factors, -you help us to identify the root cause of the issue. - -## Documentation Improvements - -You can help improve `BiocFrame` docs by making them more readable and coherent, or -by adding missing information and correcting mistakes. - -`BiocFrame` documentation uses [Sphinx] as its main documentation compiler. -This means that the docs are kept in the same repository as the project code, and -that any documentation update is done in the same way was a code contribution. - -```{todo} Don't forget to mention which markup language you are using. - - e.g., [reStructuredText] or [CommonMark] with [MyST] extensions. -``` - -```{todo} If your project is hosted on GitHub, you can also mention the following tip: - - :::{tip} - Please notice that the [GitHub web interface] provides a quick way of - propose changes in `BiocFrame`'s files. While this mechanism can - be tricky for normal code contributions, it works perfectly fine for - contributing to the docs, and can be quite handy. - - If you are interested in trying this method out, please navigate to - the `docs` folder in the source [repository], find which file you - would like to propose changes and click in the little pencil icon at the - top, to open [GitHub's code editor]. Once you finish editing the file, - please write a message in the form at the bottom of the page describing - which changes have you made and what are the motivations behind them and - submit your proposal. - ::: -``` - -When working on documentation changes in your local machine, you can -compile them using [tox] : - -``` -tox -e docs -``` - -and use Python's built-in web server for a preview in your web browser -(`http://localhost:8000`): - -``` -python3 -m http.server --directory 'docs/_build/html' -``` - -## Code Contributions - -```{todo} Please include a reference or explanation about the internals of the project. - - An architecture description, design principles or at least a summary of the - main concepts will make it easy for potential contributors to get started - quickly. -``` - -### Submit an issue - -Before you work on any non-trivial code contribution it's best to first create -a report in the [issue tracker] to start a discussion on the subject. -This often provides additional considerations and avoids unnecessary work. - -### Create an environment - -Before you start coding, we recommend creating an isolated [virtual environment] -to avoid any problems with your installed Python packages. -This can easily be done via either [virtualenv]: - -``` -virtualenv -source /bin/activate -``` - -or [Miniconda]: - -``` -conda create -n BiocFrame python=3 six virtualenv pytest pytest-cov -conda activate BiocFrame -``` - -### Clone the repository - -1. Create an user account on GitHub if you do not already have one. - -2. Fork the project [repository]: click on the *Fork* button near the top of the - page. This creates a copy of the code under your account on GitHub. - -3. Clone this copy to your local disk: - - ``` - git clone git@github.com:YourLogin/BiocFrame.git - cd BiocFrame - ``` - -4. You should run: - - ``` - pip install -U pip setuptools -e . - ``` - - to be able to import the package under development in the Python REPL. - - ```{todo} if you are not using pre-commit, please remove the following item: - ``` - -5. Install [pre-commit]: - - ``` - pip install pre-commit - pre-commit install - ``` - - `BiocFrame` comes with a lot of hooks configured to automatically help the - developer to check the code being written. - -### Implement your changes - -1. Create a branch to hold your changes: - - ``` - git checkout -b my-feature - ``` - - and start making changes. Never work on the main branch! - -2. Start your work on this branch. Don't forget to add [docstrings] to new - functions, modules and classes, especially if they are part of public APIs. - -3. Add yourself to the list of contributors in `AUTHORS.rst`. - -4. When you’re done editing, do: - - ``` - git add - git commit - ``` - - to record your changes in [git]. - - ```{todo} if you are not using pre-commit, please remove the following item: - ``` - - Please make sure to see the validation messages from [pre-commit] and fix - any eventual issues. - This should automatically use [flake8]/[black] to check/fix the code style - in a way that is compatible with the project. - - :::{important} - Don't forget to add unit tests and documentation in case your - contribution adds an additional feature and is not just a bugfix. - - Moreover, writing a [descriptive commit message] is highly recommended. - In case of doubt, you can check the commit history with: - - ``` - git log --graph --decorate --pretty=oneline --abbrev-commit --all - ``` - - to look for recurring communication patterns. - ::: - -5. Please check that your changes don't break any unit tests with: - - ``` - tox - ``` - - (after having installed [tox] with `pip install tox` or `pipx`). - - You can also use [tox] to run several other pre-configured tasks in the - repository. Try `tox -av` to see a list of the available checks. - -### Submit your contribution - -1. If everything works fine, push your local branch to the remote server with: - - ``` - git push -u origin my-feature - ``` - -2. Go to the web page of your fork and click "Create pull request" - to send your changes for review. - - ```{todo} if you are using GitHub, you can uncomment the following paragraph - - Find more detailed information in [creating a PR]. You might also want to open - the PR as a draft first and mark it as ready for review after the feedbacks - from the continuous integration (CI) system or any required fixes. - - ``` - -### Troubleshooting - -The following tips can be used when facing problems to build or test the -package: - -1. Make sure to fetch all the tags from the upstream [repository]. - The command `git describe --abbrev=0 --tags` should return the version you - are expecting. If you are trying to run CI scripts in a fork repository, - make sure to push all the tags. - You can also try to remove all the egg files or the complete egg folder, i.e., - `.eggs`, as well as the `*.egg-info` folders in the `src` folder or - potentially in the root of your project. - -2. Sometimes [tox] misses out when new dependencies are added, especially to - `setup.cfg` and `docs/requirements.txt`. If you find any problems with - missing dependencies when running a command with [tox], try to recreate the - `tox` environment using the `-r` flag. For example, instead of: - - ``` - tox -e docs - ``` - - Try running: - - ``` - tox -r -e docs - ``` - -3. Make sure to have a reliable [tox] installation that uses the correct - Python version (e.g., 3.7+). When in doubt you can run: - - ``` - tox --version - # OR - which tox - ``` - - If you have trouble and are seeing weird errors upon running [tox], you can - also try to create a dedicated [virtual environment] with a [tox] binary - freshly installed. For example: - - ``` - virtualenv .venv - source .venv/bin/activate - .venv/bin/pip install tox - .venv/bin/tox -e all - ``` - -4. [Pytest can drop you] in an interactive session in the case an error occurs. - In order to do that you need to pass a `--pdb` option (for example by - running `tox -- -k --pdb`). - You can also setup breakpoints manually instead of using the `--pdb` option. - -## Maintainer tasks - -### Releases - -```{todo} This section assumes you are using PyPI to publicly release your package. - - If instead you are using a different/private package index, please update - the instructions accordingly. -``` - -If you are part of the group of maintainers and have correct user permissions -on [PyPI], the following steps can be used to release a new version for -`BiocFrame`: - -1. Make sure all unit tests are successful. -2. Tag the current commit on the main branch with a release tag, e.g., `v1.2.3`. -3. Push the new tag to the upstream [repository], - e.g., `git push upstream v1.2.3` -4. Clean up the `dist` and `build` folders with `tox -e clean` - (or `rm -rf dist build`) - to avoid confusion with old builds and Sphinx docs. -5. Run `tox -e build` and check that the files in `dist` have - the correct version (no `.dirty` or [git] hash) according to the [git] tag. - Also check the sizes of the distributions, if they are too big (e.g., > - 500KB), unwanted clutter may have been accidentally included. -6. Run `tox -e publish -- --repository pypi` and check that everything was - uploaded to [PyPI] correctly. - -[^contrib1]: Even though, these resources focus on open source projects and - communities, the general ideas behind collaborating with other developers - to collectively create software are general and can be applied to all sorts - of environments, including private companies and proprietary code bases. +Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. +## Report Bugs +Report bugs at the issue tracker. -[black]: https://pypi.org/project/black/ -[commonmark]: https://commonmark.org/ -[contribution-guide.org]: http://www.contribution-guide.org/ -[creating a pr]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request -[descriptive commit message]: https://chris.beams.io/posts/git-commit -[docstrings]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html -[first-contributions tutorial]: https://github.com/firstcontributions/first-contributions -[flake8]: https://flake8.pycqa.org/en/stable/ -[git]: https://git-scm.com -[github web interface]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository -[github's code editor]: https://docs.github.com/en/github/managing-files-in-a-repository/managing-files-on-github/editing-files-in-your-repository -[github's fork and pull request workflow]: https://guides.github.com/activities/forking/ -[guide created by freecodecamp]: https://github.com/freecodecamp/how-to-contribute-to-open-source -[miniconda]: https://docs.conda.io/en/latest/miniconda.html -[myst]: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html -[other kinds of contributions]: https://opensource.guide/how-to-contribute -[pre-commit]: https://pre-commit.com/ -[pypi]: https://pypi.org/ -[pyscaffold's contributor's guide]: https://pyscaffold.org/en/stable/contributing.html -[pytest can drop you]: https://docs.pytest.org/en/stable/usage.html#dropping-to-pdb-python-debugger-at-the-start-of-a-test -[python software foundation's code of conduct]: https://www.python.org/psf/conduct/ -[restructuredtext]: https://www.sphinx-doc.org/en/master/usage/restructuredtext/ -[sphinx]: https://www.sphinx-doc.org/en/master/ -[tox]: https://tox.readthedocs.io/en/stable/ -[virtual environment]: https://realpython.com/python-virtual-environments-a-primer/ -[virtualenv]: https://virtualenv.pypa.io/en/stable/ +## Fix Bugs +Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. +## Implement Features +Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. -```{todo} Please review and change the following definitions: -``` +## Submit Feedback +The best way to send feedback is to file an issue. -[repository]: https://github.com//BiocFrame -[issue tracker]: https://github.com//BiocFrame/issues +If you are proposing a feature: +- Explain in detail how it would work. +- Keep the scope as narrow as possible, to make it easier to implement. +- Remember that this is a volunteer-driven project, and that contributions are welcome! diff --git a/docs/conf.py b/docs/conf.py index ea11f12..dda7782 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -72,7 +72,6 @@ "sphinx.ext.ifconfig", "sphinx.ext.mathjax", "sphinx.ext.napoleon", - "sphinx_autodoc_typehints", ] # Add any paths that contain templates here, relative to this directory. @@ -80,8 +79,7 @@ # Enable markdown -# extensions.append("myst_parser") -extensions.append("myst_nb") +extensions.append("myst_parser") # Configure MyST-Parser myst_enable_extensions = [ @@ -107,8 +105,8 @@ master_doc = "index" # General information about the project. -project = "BiocFrame" -copyright = "2023, jkanche" +project = "biocframe" +copyright = "2023, Jayaram Kancherla" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -118,11 +116,11 @@ # release: The full version, including alpha/beta/rc tags. # If you don’t need the separation provided between version and release, # just set them both to the same value. - try: - from biocframe import __version__ as version -except ImportError: - version = "" + from importlib.metadata import version as get_version + version = get_version("biocframe") +except Exception: + version = "unknown" if not version or version.lower() == "unknown": version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD @@ -169,28 +167,29 @@ # If this is True, todo emits a warning for each TODO entries. The default is False. todo_emit_warnings = True -autodoc_default_options = { - # 'members': 'var1, var2', - # 'member-order': 'bysource', - "special-members": True, - "undoc-members": True, - "exclude-members": "__weakref__, __dict__, __str__, __module__", -} - -autosummary_generate = True -autosummary_imported_members = True - # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = "furo" +html_theme = "alabaster" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -html_theme_options = {"sidebar_width": "300px", "page_width": "1200px"} +html_theme_options = { + "light_css_variables": { + "color-brand-primary": "#0052cc", + "color-brand-content": "#0052cc", + }, + "dark_css_variables": { + "color-brand-primary": "#4c9aff", + "color-brand-content": "#4c9aff", + }, + "source_repository": "https://github.com/biocpy/biocframe", + "source_branch": "main", + "source_directory": "docs/", +} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] @@ -258,7 +257,7 @@ # html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = "BiocFrame-doc" +htmlhelp_basename = "biocframe-doc" # -- Options for LaTeX output ------------------------------------------------ @@ -275,7 +274,7 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ("index", "user_guide.tex", "BiocFrame Documentation", "jkanche", "manual") + ("index", "user_guide.tex", "biocframe Documentation", "Jayaram Kancherla", "manual") ] # The name of an image file (relative to this directory) to place at the top of @@ -315,3 +314,23 @@ } print(f"loading configurations for {project} {version} ...", file=sys.stderr) + +# -- Biocsetup configuration ------------------------------------------------- + +# Enable execution of code chunks in markdown +extensions.remove('myst_parser') +extensions.append('myst_nb') + +# Less verbose api documentation +extensions.append('sphinx_autodoc_typehints') + +autodoc_default_options = { + "special-members": True, + "undoc-members": True, + "exclude-members": "__weakref__, __dict__, __str__, __module__", +} + +autosummary_generate = True +autosummary_imported_members = True + +html_theme = "furo" diff --git a/docs/requirements.txt b/docs/requirements.txt index c20cf60..a1b9d2b 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,9 +1,9 @@ -furo -myst-nb # Requirements file for ReadTheDocs, check .readthedocs.yml. # To build the module reference correctly, make sure every external package # under `install_requires` in `setup.cfg` is also listed here! # sphinx_rtd_theme myst-parser[linkify] sphinx>=3.2.1 +myst-nb +furo sphinx-autodoc-typehints diff --git a/docs/tutorial.md b/docs/tutorial.md index 75ed4ed..a1ff6be 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -10,7 +10,7 @@ kernelspec: This flexibility allows us to accept arbitrarily complex objects as columns, which is often the case in Bioconductor objects. Also check out Bioconductor's [**S4Vectors**](https://bioconductor.org/packages/S4Vectors) package, which implements the `DFrame` class on which `BiocFrame` was based. -:::{.callout-note} +:::{note} These classes follow a functional paradigm for accessing or setting properties, with further details discussed in [functional paradigm](https://biocpy.github.io/tutorial/chapters/philosophy.html) section. ::: @@ -136,7 +136,7 @@ print("type of native_array_vector column:", type(bframe_types["native_array_vec print(bframe_types) ``` -:::{.callout-note} +:::{note} This behavior remains consistent when extracting, slicing, combining, or performing any supported operation on `BiocFrame` objects. ::: @@ -174,7 +174,7 @@ bframe_nested = BiocFrame({ print(bframe_nested) ``` -:::{.callout-note} +:::{note} This behavior remains consistent when extracting, slicing, combining, or performing any other supported operations on `BiocFrame` objects. ::: @@ -194,7 +194,7 @@ bframe = BiocFrame(obj) print(bframe) ``` -::: {.callout-tip} +:::{tip} You can specify complex objects as columns, as long as they have some "length" equal to the number of rows. For example, we can embed a `BiocFrame` within another `BiocFrame`. ::: @@ -394,7 +394,7 @@ And we can get individual rows as a dictionary: bframe.get_row(2) ``` -::: {.callout} +:::{note} To retrieve a subset of the data in the `BiocFrame`, we use the subset (`[]`) operator. This operator accepts different subsetting arguments, such as a boolean vector, a `slice` object, a sequence of indices, or row/column names. ::: @@ -453,7 +453,7 @@ modified = bframe.\ print(modified) ``` -::: {.callout-tip} +:::{tip} The functional style allows you to chain multiple operations. ::: @@ -479,7 +479,7 @@ testframe.column_names = ["column1", "column2" ] print(testframe) ``` -::: {.callout-caution} +:::{caution} Warnings are raised when properties are directly mutated. These assignments are the same as calling the corresponding `set_*()` methods with `in_place = True`. It is best to do this only if the `BiocFrame` object is not being used anywhere else; otherwise, it is safer to just create a (shallow) copy via the default `in_place = False`. diff --git a/pyproject.toml b/pyproject.toml index 00aa968..92d3fba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,27 +1,72 @@ +[project] +name = "biocframe" +dynamic = ["version"] +description = "Flexible dataframe representation to support nested structures." +readme = "README.md" +authors = [ + { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" } +] +requires-python = ">=3.12" +dependencies = [ + "biocutils>=0.3.3", + "importlib-metadata>=9.0.0 ; python_full_version < '3.8'", + "numpy>=2.5.2", +] + +[project.optional-dependencies] +optional = [ + "pandas>=3.0.5", + "polars>=1.44.0", +] +testing = [ + "pandas>=3.0.5", + "polars>=1.44.0", + "pytest>=9.1.1", + "pytest-cov>=7.1.0", + "setuptools>=84.0.0", +] + [build-system] -# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD! -requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "wheel"] -build-backend = "setuptools.build_meta" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" -[tool.setuptools_scm] -# See configuration details in https://github.com/pypa/setuptools_scm -version_scheme = "no-guess-dev" +[tool.hatch.version] +source = "vcs" +fallback-version = "0.1.0" [tool.ruff] line-length = 120 src = ["src"] -exclude = ["tests"] +exclude = ["tests", "docs"] + +[tool.ruff.lint] extend-ignore = ["F821"] -[tool.ruff.pydocstyle] +[tool.ruff.lint.pydocstyle] convention = "google" +[tool.ruff.lint.per-file-ignores] +"__init__.py" = ["E402", "F401"] + [tool.ruff.format] docstring-code-format = true docstring-code-line-length = 20 -[tool.ruff.per-file-ignores] -"__init__.py" = ["E402", "F401"] +[tool.mypy] +strict = true + +[tool.pytest.ini_options] +addopts = "--cov --cov-report term-missing" +testpaths = ["tests"] -[tool.black] -force-exclude = "__init__.py" +[dependency-groups] +dev = [ + "furo>=2025.12.19", + "linkify-it-py>=2.1.1", + "mypy>=2.3.1", + "myst-nb>=1.4.0", + "pytest>=9.1.1", + "pytest-cov>=7.1.0", + "sphinx>=9.1.0", + "sphinx-autodoc-typehints>=3.13.4", +] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 6153098..0000000 --- a/setup.cfg +++ /dev/null @@ -1,132 +0,0 @@ -# This file is used to configure your project. -# Read more about the various options under: -# https://setuptools.pypa.io/en/latest/userguide/declarative_config.html -# https://setuptools.pypa.io/en/latest/references/keywords.html - -[metadata] -name = BiocFrame -description = Flexible dataframe representation to support nested structures. -author = Jayaram Kancherla -author_email = jayaram.kancherla@gmail.com -license = MIT -license_files = LICENSE.txt -long_description = file: README.md -long_description_content_type = text/markdown; charset=UTF-8; variant=GFM -url = https://github.com/BiocPy/biocframe -# Add here related links, for example: -project_urls = - Documentation = https://biocpy.github.io/BiocFrame/ - Source = https://github.com/BiocPy/biocframe -# Changelog = https://pyscaffold.org/en/latest/changelog.html -# Tracker = https://github.com/pyscaffold/pyscaffold/issues -# Conda-Forge = https://anaconda.org/conda-forge/pyscaffold -# Download = https://pypi.org/project/PyScaffold/#files -# Twitter = https://twitter.com/PyScaffold - -# Change if running only on Windows, Mac or Linux (comma-separated) -platforms = any - -# Add here all kinds of additional classifiers as defined under -# https://pypi.org/classifiers/ -classifiers = - Development Status :: 4 - Beta - Programming Language :: Python - - -[options] -zip_safe = False -packages = find_namespace: -include_package_data = True -package_dir = - =src - -# Require a min/specific Python version (comma-separated conditions) -python_requires = >=3.9 - -# Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0. -# Version specifiers like >=2.2,<3.0 avoid problems due to API changes in -# new major versions. This works if the required packages follow Semantic Versioning. -# For more information, check out https://semver.org/. -install_requires = - importlib-metadata; python_version<"3.8" - biocutils>=0.3.3 - numpy - -[options.packages.find] -where = src -exclude = - tests - -[options.extras_require] -# Add here additional requirements for extra features, to install with: -# `pip install BiocFrame[PDF]` like: -optional = - pandas - polars - -# Add here test requirements (semicolon/line-separated) -testing = - setuptools - pytest - pytest-cov - pandas - polars - -[options.entry_points] -# Add here console scripts like: -# console_scripts = -# script_name = biocframe.module:function -# For example: -# console_scripts = -# fibonacci = biocframe.skeleton:run -# And any other entry points, for example: -# pyscaffold.cli = -# awesome = pyscaffoldext.awesome.extension:AwesomeExtension - -[tool:pytest] -# Specify command line options as you would do when invoking pytest directly. -# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml -# in order to write a coverage file that can be read by Jenkins. -# CAUTION: --cov flags may prohibit setting breakpoints while debugging. -# Comment those flags to avoid this pytest issue. -addopts = - --cov biocframe --cov-report term-missing - --verbose -norecursedirs = - dist - build - .tox -testpaths = tests -# Use pytest markers to select/deselect specific tests -# markers = -# slow: mark tests as slow (deselect with '-m "not slow"') -# system: mark end-to-end system tests - -[devpi:upload] -# Options for the devpi: PyPI server and packaging tool -# VCS export must be deactivated since we are using setuptools-scm -no_vcs = 1 -formats = bdist_wheel - -[flake8] -# Some sane defaults for the code style checker flake8 -max_line_length = 100 -extend_ignore = E203, W503 -# ^ Black-compatible -# E203 and W503 have edge cases handled by black -exclude = - .tox - build - dist - .eggs - docs/conf.py -per-file-ignores = __init__.py:F401 - -[pyscaffold] -# PyScaffold's parameters when the project was created. -# This will be used when updating. Do not change! -version = 4.5 -package = biocframe -extensions = - markdown - pre_commit diff --git a/setup.py b/setup.py deleted file mode 100644 index 8046116..0000000 --- a/setup.py +++ /dev/null @@ -1,20 +0,0 @@ -"""Setup file for BiocFrame. Use setup.cfg to configure your project. - -This file was generated with PyScaffold 4.5. -PyScaffold helps you to put up the scaffold of your new Python project. -Learn more under: https://pyscaffold.org/ -""" - -from setuptools import setup - -if __name__ == "__main__": - try: - setup(use_scm_version={"version_scheme": "no-guess-dev"}) - except: # noqa - print( - "\n\nAn error occurred while building the project, " - "please ensure you have the most updated version of setuptools, " - "setuptools_scm and wheel with:\n" - " pip install -U setuptools setuptools_scm wheel\n\n" - ) - raise diff --git a/src/biocframe/py.typed b/src/biocframe/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/tox.ini b/tox.ini index 82f750f..4b4791a 100644 --- a/tox.ini +++ b/tox.ini @@ -1,90 +1,58 @@ -# Tox configuration file +# Tox configuration file using uv as the backend runner # Read more under https://tox.wiki/ -# THIS SCRIPT IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS! [tox] -minversion = 3.24 +minversion = 4.0 envlist = default -isolated_build = True - [testenv] description = Invoke pytest to run automated tests -setenv = - TOXINIDIR = {toxinidir} -passenv = - HOME - SETUPTOOLS_* -extras = - testing +allowlist_externals = uv +skip_install = True commands = - pytest {posargs} + uv run pytest {posargs} +[testenv:typecheck] +description = Run static type checking with mypy +skip_install = True +commands = + uv run mypy src/ -# # To run `tox -e lint` you need to make sure you have a -# # `.pre-commit-config.yaml` file. See https://pre-commit.com -# [testenv:lint] -# description = Perform static analysis and style checks -# skip_install = True -# deps = pre-commit -# passenv = -# HOMEPATH -# PROGRAMDATA -# SETUPTOOLS_* -# commands = -# pre-commit run --all-files {posargs:--show-diff-on-failure} - +[testenv:lint] +description = Perform static analysis and style checks +skip_install = True +commands = + uv run ruff check {posargs:.} + uv run ruff format --check {posargs:.} [testenv:{build,clean}] description = - build: Build the package in isolation according to PEP517, see https://github.com/pypa/build - clean: Remove old distribution files and temporary build artifacts (./build and ./dist) -# https://setuptools.pypa.io/en/stable/build_meta.html#how-to-use-it + build: Build the package + clean: Remove old distribution files skip_install = True -changedir = {toxinidir} -deps = - build: build[virtualenv] -passenv = - SETUPTOOLS_* commands = clean: python -c 'import shutil; [shutil.rmtree(p, True) for p in ("build", "dist", "docs/_build")]' clean: python -c 'import pathlib, shutil; [shutil.rmtree(p, True) for p in pathlib.Path("src").glob("*.egg-info")]' - build: python -m build {posargs} - + build: uv build {posargs} [testenv:{docs,doctests,linkcheck}] description = docs: Invoke sphinx-build to build the docs doctests: Invoke sphinx-build to run doctests linkcheck: Check for broken links in the documentation -passenv = - SETUPTOOLS_* setenv = DOCSDIR = {toxinidir}/docs BUILDDIR = {toxinidir}/docs/_build docs: BUILD = html doctests: BUILD = doctest linkcheck: BUILD = linkcheck -deps = - -r {toxinidir}/docs/requirements.txt - # ^ requirements.txt shared with Read The Docs +skip_install = True commands = - sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs} - + uv run sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs} [testenv:publish] description = Publish the package you have been developing to a package index server. - By default, it uses testpypi. If you really want to publish your package - to be publicly accessible in PyPI, use the `-- --repository pypi` option. skip_install = True -changedir = {toxinidir} -passenv = - # See: https://twine.readthedocs.io/en/latest/ - TWINE_USERNAME - TWINE_PASSWORD - TWINE_REPOSITORY -deps = twine commands = - python -m twine check dist/* - python -m twine upload {posargs:--repository {env:TWINE_REPOSITORY:testpypi}} dist/* + uv publish {posargs:dist/*} From 6c88b2e8ad51d482fb15af42493db73796be446e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 25 Aug 2026 06:14:54 +0000 Subject: [PATCH 2/5] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/requirements.txt | 4 +- src/biocframe/BiocFrame.py | 146 ++++++++++++++++---------------- src/biocframe/__init__.py | 2 +- src/biocframe/io/from_pandas.py | 2 +- 4 files changed, 76 insertions(+), 78 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index a1b9d2b..c20cf60 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,9 +1,9 @@ +furo +myst-nb # Requirements file for ReadTheDocs, check .readthedocs.yml. # To build the module reference correctly, make sure every external package # under `install_requires` in `setup.cfg` is also listed here! # sphinx_rtd_theme myst-parser[linkify] sphinx>=3.2.1 -myst-nb -furo sphinx-autodoc-typehints diff --git a/src/biocframe/BiocFrame.py b/src/biocframe/BiocFrame.py index 2a36eaa..d277a61 100644 --- a/src/biocframe/BiocFrame.py +++ b/src/biocframe/BiocFrame.py @@ -1,8 +1,9 @@ from __future__ import annotations from collections import OrderedDict, abc +from collections.abc import Sequence from copy import copy -from typing import TYPE_CHECKING, Any, Dict, List, Literal, Optional, Sequence, Tuple, Union +from typing import TYPE_CHECKING, Any, Literal from warnings import warn import biocutils as ut @@ -21,9 +22,9 @@ def _guess_number_of_rows( - number_of_rows: Optional[int], - data: Dict[str, Any], - row_names: Optional[Union[Sequence[str], ut.Names]], + number_of_rows: int | None, + data: dict[str, Any], + row_names: Sequence[str] | ut.Names | None, ) -> int: if number_of_rows is not None: return number_of_rows @@ -36,8 +37,8 @@ def _guess_number_of_rows( def _validate_rows( number_of_rows: int, - data: Dict[str, Any], - row_names: Optional[Union[Sequence[str], ut.Names]], + data: dict[str, Any], + row_names: Sequence[str] | ut.Names | None, ) -> None: incorrect_len_keys = [] for k, v in data.items(): @@ -60,8 +61,8 @@ def _validate_rows( def _validate_columns( column_names: ut.Names, - data: Dict[str, Any], - column_data: Optional[BiocFrame], + data: dict[str, Any], + column_data: BiocFrame | None, ) -> None: if sorted(column_names) != sorted(data.keys()): raise ValueError("Mismatch between `column_names` and the keys of `data`.") @@ -90,7 +91,7 @@ def __init__(self, obj: BiocFrame) -> None: def __iter__(self) -> BiocFrameIter: return self - def __next__(self) -> Tuple[Optional[Union[ut.Names, str]], Dict[str, Any]]: + def __next__(self) -> tuple[ut.Names | str | None, dict[str, Any]]: if self._current_index < len(self._bframe): iter_row_index = self._bframe.row_names[self._current_index] if self._bframe.row_names is not None else None @@ -121,12 +122,12 @@ class BiocFrame(ut.BiocObject): def __init__( self, - data: Optional[Union[Dict[str, Any], ut.NamedList, Sequence[Any]]] = None, - number_of_rows: Optional[int] = None, - row_names: Optional[Union[Sequence[str], ut.Names]] = None, - column_names: Optional[Union[Sequence[str], ut.Names]] = None, - column_data: Optional[BiocFrame] = None, - metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None, + data: dict[str, Any] | ut.NamedList | Sequence[Any] | None = None, + number_of_rows: int | None = None, + row_names: Sequence[str] | ut.Names | None = None, + column_names: Sequence[str] | ut.Names | None = None, + column_data: BiocFrame | None = None, + metadata: dict[str, Any] | ut.NamedList | None = None, _validate: bool = True, ) -> None: """Initialize a ``BiocFrame`` object from columns. @@ -222,7 +223,7 @@ def __init__( _validate_rows(self._number_of_rows, self._data, self._row_names) _validate_columns(self._column_names, self._data, self._column_data) - def __eq__(self, other: Any) -> bool: + def __eq__(self, other: object) -> bool: """Check if the current object is equal to another. Args: @@ -274,7 +275,7 @@ def __eq__(self, other: Any) -> bool: ################################# @property - def shape(self) -> Tuple[int, int]: + def shape(self) -> tuple[int, int]: """ Returns: Tuple containing the number of rows and columns in this ``BiocFrame``. @@ -322,7 +323,7 @@ def __contains__(self, name: str) -> bool: return self.has_column(name) @property - def dims(self) -> Tuple[int, int]: + def dims(self) -> tuple[int, int]: """Alias for :py:attr:`~shape`.""" return self.shape @@ -423,7 +424,7 @@ def __str__(self) -> str: ######>> Row names <<###### ########################### - def get_row_names(self) -> Optional[ut.Names]: + def get_row_names(self) -> ut.Names | None: """Get row names. Returns: @@ -431,7 +432,7 @@ def get_row_names(self) -> Optional[ut.Names]: """ return self._row_names - def set_row_names(self, names: Optional[Union[Sequence[str], ut.Names]], in_place: bool = False) -> BiocFrame: + def set_row_names(self, names: Sequence[str] | ut.Names | None, in_place: bool = False) -> BiocFrame: """Set new row names. Args: @@ -462,12 +463,12 @@ def set_row_names(self, names: Optional[Union[Sequence[str], ut.Names]], in_plac return output @property - def row_names(self) -> Optional[ut.Names]: + def row_names(self) -> ut.Names | None: """Alias for :py:attr:`~get_row_names`.""" return self.get_row_names() @row_names.setter - def row_names(self, names: Optional[Union[Sequence[str], ut.Names]]) -> None: + def row_names(self, names: Sequence[str] | ut.Names | None) -> None: """Alias for :py:attr:`~set_row_names` with ``in_place = True``. As this mutates the original object, a warning is raised. @@ -479,12 +480,12 @@ def row_names(self, names: Optional[Union[Sequence[str], ut.Names]]) -> None: self.set_row_names(names, in_place=True) @property - def rownames(self) -> Optional[ut.Names]: + def rownames(self) -> ut.Names | None: """Alias for :py:attr:`~get_row_names`, provided for back-compatibility.""" return self.get_row_names() @rownames.setter - def rownames(self, names: Optional[Union[Sequence[str], ut.Names]]) -> None: + def rownames(self, names: Sequence[str] | ut.Names | None) -> None: """Alias for :py:attr:`~set_row_names` with ``in_place = True``, provided for back-compaibility only. As this mutates the original object, a warning is raised. @@ -495,7 +496,7 @@ def rownames(self, names: Optional[Union[Sequence[str], ut.Names]]) -> None: ######>> Data <<###### ###################### - def get_data(self) -> Dict[str, Any]: + def get_data(self) -> dict[str, Any]: """Get the underlying data. Returns: @@ -503,7 +504,7 @@ def get_data(self) -> Dict[str, Any]: """ return self._data - def to_dict(self) -> Dict[str, Any]: + def to_dict(self) -> dict[str, Any]: """Alias for :py:meth:`~get_data`. Returns: @@ -520,7 +521,7 @@ def to_NamedList(self) -> ut.NamedList: return ut.NamedList([self._data[c] for c in self._column_names], names=self._column_names) @property - def data(self) -> Dict[str, Any]: + def data(self) -> dict[str, Any]: """Alias for :py:attr:`~get_data`.""" return self.get_data() @@ -536,7 +537,7 @@ def get_column_names(self) -> ut.Names: """ return self._column_names - def get_columns(self) -> List[Any]: + def get_columns(self) -> list[Any]: """Get all columns as a list. Returns: @@ -544,7 +545,7 @@ def get_columns(self) -> List[Any]: """ return [self._data[c] for c in self._column_names] - def set_column_names(self, names: Union[Sequence[str], ut.Names], in_place: bool = False) -> BiocFrame: + def set_column_names(self, names: Sequence[str] | ut.Names, in_place: bool = False) -> BiocFrame: """Set new column names. Args: @@ -584,7 +585,7 @@ def column_names(self) -> ut.Names: return self.get_column_names() @column_names.setter - def column_names(self, names: Union[Sequence[str], ut.Names]) -> None: + def column_names(self, names: Sequence[str] | ut.Names) -> None: """Alias for :py:attr:`~set_column_names` with ``in_place = True``. As this mutates the original object, a warning is raised. @@ -601,7 +602,7 @@ def colnames(self) -> ut.Names: return self.get_column_names() @colnames.setter - def colnames(self, names: Union[Sequence[str], ut.Names]) -> None: + def colnames(self, names: Sequence[str] | ut.Names) -> None: """Alias for :py:attr:`~set_column_names` with ``in_place = True``, provided for back-compatibility only. As this mutates the original object, a warning is raised. @@ -612,7 +613,7 @@ def colnames(self, names: Union[Sequence[str], ut.Names]) -> None: ######>> Metadata <<###### ########################## - def get_column_data(self, with_names: bool = True) -> Optional[BiocFrame]: + def get_column_data(self, with_names: bool = True) -> BiocFrame | None: """Get column data. Args: @@ -630,7 +631,7 @@ def get_column_data(self, with_names: bool = True) -> Optional[BiocFrame]: output = output.set_row_names(self._column_names) return output - def set_column_data(self, column_data: Optional[BiocFrame], in_place: bool = False) -> BiocFrame: + def set_column_data(self, column_data: BiocFrame | None, in_place: bool = False) -> BiocFrame: """Set new column data. Args: @@ -655,12 +656,12 @@ def set_column_data(self, column_data: Optional[BiocFrame], in_place: bool = Fal return output @property - def column_data(self) -> Optional[BiocFrame]: + def column_data(self) -> BiocFrame | None: """Alias for :py:attr:`~get_column_data`.""" return self.get_column_data() @column_data.setter - def column_data(self, column_data: Optional[BiocFrame]) -> None: + def column_data(self, column_data: BiocFrame | None) -> None: """Alias for :py:attr:`~set_column_data` with ``in_place = True``. As this mutates the original object, a warning is raised. @@ -687,7 +688,7 @@ def has_column(self, name: str) -> bool: """ return name in self.column_names - def get_column(self, column: Union[str, int]) -> Any: + def get_column(self, column: str | int) -> Any: """Get the contents of the specified column. Args: @@ -715,7 +716,7 @@ def get_column(self, column: Union[str, int]) -> Any: raise TypeError(f"'column' must be a string or integer, provided '{type(column)}'.") - def column(self, column: Union[str, int]) -> Any: + def column(self, column: str | int) -> Any: """Alias for :py:meth:`~get_column`, provided for back-compatibility only.""" return self.get_column(column) @@ -735,7 +736,7 @@ def has_row(self, name: str) -> bool: return name in self.row_names - def get_row(self, row: Union[str, int]) -> Dict[str, Any]: + def get_row(self, row: str | int) -> dict[str, Any]: """Get a specified row. Args: @@ -777,7 +778,7 @@ def get_row(self, row: Union[str, int]) -> Dict[str, Any]: collected[col] = self._data[col][row] return collected - def row(self, row: Union[str, int]) -> Dict[str, Any]: + def row(self, row: str | int) -> dict[str, Any]: """Alias for :py:attr:`~get_row`, provided for back-compatibility only.""" warn( "Method 'row' is deprecated, use 'get_row' instead", @@ -818,15 +819,14 @@ def tail(self, n: int = 5) -> BiocFrame: raise ValueError("n must be non-negative.") rows = self.shape[0] - if n > rows: - n = rows + n = min(n, rows) return self[rows - n : rows, :] def get_slice( self, - rows: Union[str, int, bool, Sequence[Union[str, int, bool]], slice], - columns: Union[str, int, bool, Sequence[Union[str, int, bool]], slice], + rows: str | int | bool | Sequence[str | int | bool] | slice, + columns: str | int | bool | Sequence[str | int | bool] | slice, ) -> BiocFrame: """Slice ``BiocFrame`` along the rows and/or columns, based on their indices or names. @@ -891,8 +891,8 @@ def get_slice( def slice( self, - rows: Optional[Union[Sequence[Union[str, int, bool]], slice]], - columns: Optional[Union[Sequence[Union[str, int, bool]], slice]], + rows: Sequence[str | int | bool] | slice | None, + columns: Sequence[str | int | bool] | slice | None, ) -> BiocFrame: """Alias for :py:attr:`~__getitem__`, for back-compatibility.""" if rows is None: @@ -903,8 +903,8 @@ def slice( def __getitem__( self, - args: Union[int, str, Sequence[Union[str, int]], Tuple[Union[int, str, Sequence[Union[str, int]], slice], ...]], - ) -> Union[BiocFrame, Any]: + args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | slice, ...], + ) -> BiocFrame | Any: """Wrapper around :py:attr:`~get_column` and :py:attr:`~get_slice` to obtain a slice of a ``BiocFrame`` or any of its columns. @@ -954,8 +954,8 @@ def __getitem__( def __setitem__( self, - args: Union[int, str, Sequence[Union[str, int]], Tuple[Union[int, str, Sequence[Union[str, int]], slice], ...]], - value: Union[BiocFrame, Any], + args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | slice, ...], + value: BiocFrame | Any, ) -> None: """Wrapper around :py:attr:`~set_column` and :py:attr:`~set_slice` to modify a slice of a ``BiocFrame`` or any of its columns. As this modified the original object in place, a warning is raise. @@ -983,8 +983,8 @@ def __setitem__( def set_slice( self, - rows: Union[int, str, bool, Sequence[Union[int, str, bool]], slice], - columns: Union[int, str, bool, Sequence[Union[int, str, bool]], slice], + rows: int | str | bool | Sequence[int | str | bool] | slice, + columns: int | str | bool | Sequence[int | str | bool] | slice, value: BiocFrame, in_place: bool = True, ) -> BiocFrame: @@ -1053,7 +1053,7 @@ def __delitem__(self, name: str) -> None: ) self.remove_column(name, in_place=True) - def set_column(self, column: Union[int, str], value: Any, in_place: bool = False) -> BiocFrame: + def set_column(self, column: int | str, value: Any, in_place: bool = False) -> BiocFrame: """Modify an existing column or add a new column. This is a convenience wrapper around :py:attr:`~set_columns`. Args: @@ -1074,7 +1074,7 @@ def set_column(self, column: Union[int, str], value: Any, in_place: bool = False """ return self.set_columns({column: value}, in_place=in_place) - def set_columns(self, columns: Dict[Union[str, int], Any], in_place: bool = False) -> BiocFrame: + def set_columns(self, columns: dict[str | int, Any], in_place: bool = False) -> BiocFrame: """Modify existing columns or add new columns. Args: @@ -1127,7 +1127,7 @@ def set_columns(self, columns: Dict[Union[str, int], Any], in_place: bool = Fals return output - def remove_column(self, column: Union[int, str], in_place: bool = False) -> BiocFrame: + def remove_column(self, column: int | str, in_place: bool = False) -> BiocFrame: """Remove a column. This is a convenience wrapper around :py:attr:`~remove_columns`. Args: @@ -1143,7 +1143,7 @@ def remove_column(self, column: Union[int, str], in_place: bool = False) -> Bioc """ return self.remove_columns([column], in_place=in_place) - def remove_columns(self, columns: Union[Sequence[Union[int, str]], slice], in_place: bool = False) -> BiocFrame: + def remove_columns(self, columns: Sequence[int | str] | slice, in_place: bool = False) -> BiocFrame: """Remove any number of existing columns. Args: @@ -1197,7 +1197,7 @@ def remove_columns(self, columns: Union[Sequence[Union[int, str]], slice], in_pl return output - def remove_row(self, row: Union[int, str], in_place: bool = False) -> BiocFrame: + def remove_row(self, row: int | str, in_place: bool = False) -> BiocFrame: """Remove a row. This is a convenience wrapper around :py:attr:`~remove_rows`. Args: @@ -1213,7 +1213,7 @@ def remove_row(self, row: Union[int, str], in_place: bool = False) -> BiocFrame: """ return self.remove_rows([row], in_place=in_place) - def remove_rows(self, rows: Union[Sequence[Union[int, str]], slice], in_place: bool = False) -> BiocFrame: + def remove_rows(self, rows: Sequence[int | str] | slice, in_place: bool = False) -> BiocFrame: """Remove any number of existing rows. Args: @@ -1286,7 +1286,7 @@ def remove_rows(self, rows: Union[Sequence[Union[int, str]], slice], in_place: b ######>> Copying <<###### ######################### - def __deepcopy__(self, memo: Optional[Dict[int, Any]] = None) -> BiocFrame: + def __deepcopy__(self, memo: dict[int, Any] | None = None) -> BiocFrame: """ Returns: A deep copy of the current ``BiocFrame``. @@ -1305,7 +1305,7 @@ def __deepcopy__(self, memo: Optional[Dict[int, Any]] = None) -> BiocFrame: try: _data_copy[col] = deepcopy(self.column(col)) except Exception as e: - raise Exception(f"Cannot `deepcopy` column '{col}', full error: {str(e)}") from e + raise Exception(f"Cannot `deepcopy` column '{col}', full error: {e!s}") from e current_class_const = type(self) return current_class_const( @@ -1343,7 +1343,7 @@ def copy(self) -> BiocFrame: ######>> split by <<###### ########################## - def split(self, column_name: str, only_indices: bool = False) -> Dict[str, Union[BiocFrame, List[int]]]: + def split(self, column_name: str, only_indices: bool = False) -> dict[str, BiocFrame | list[int]]: """Split the object by a column. Args: @@ -1388,7 +1388,7 @@ def split(self, column_name: str, only_indices: bool = False) -> Dict[str, Union ################################ @property - def index(self) -> Optional[ut.Names]: + def index(self) -> ut.Names | None: """Alias to :py:attr:`~get_row_names`, provided for compatibility with **pandas**.""" return self.get_row_names() @@ -1397,7 +1397,7 @@ def columns(self) -> ut.Names: """Alias for :py:attr:`~get_column_names`, provided for compatibility with **pandas**.""" return self.get_column_names() - def to_pandas(self) -> "pandas.DataFrame": + def to_pandas(self) -> pandas.DataFrame: """Convert the ``BiocFrame`` into a :py:class:`~pandas.DataFrame` object. Returns: @@ -1413,7 +1413,7 @@ def to_pandas(self) -> "pandas.DataFrame": return DataFrame(data={}, index=range(self._number_of_rows)) @classmethod - def from_pandas(cls, input: "pandas.DataFrame") -> BiocFrame: + def from_pandas(cls, input: pandas.DataFrame) -> BiocFrame: """Create a ``BiocFrame`` from a :py:class:`~pandas.DataFrame` object. Args: @@ -1442,7 +1442,7 @@ def from_pandas(cls, input: "pandas.DataFrame") -> BiocFrame: ################################ @classmethod - def from_polars(cls, input: "polars.DataFrame") -> BiocFrame: + def from_polars(cls, input: polars.DataFrame) -> BiocFrame: """Create a ``BiocFrame`` from a :py:class:`~polars.DataFrame` object. Args: @@ -1462,7 +1462,7 @@ def from_polars(cls, input: "polars.DataFrame") -> BiocFrame: return cls(data=rdata) - def to_polars(self) -> "polars.DataFrame": + def to_polars(self) -> polars.DataFrame: """Convert the ``BiocFrame`` into a :py:class:`~polars.DataFrame` object. Returns: @@ -1481,9 +1481,7 @@ def to_polars(self) -> "polars.DataFrame": ######>> Miscellaneous <<###### ############################### - def flatten( - self, as_type: Literal["dict", "biocframe"] = "dict", delim: str = "." - ) -> Union[Dict[str, Any], BiocFrame]: + def flatten(self, as_type: Literal["dict", "biocframe"] = "dict", delim: str = ".") -> dict[str, Any] | BiocFrame: """Flatten a nested BiocFrame object. Args: @@ -1577,7 +1575,7 @@ def combine_columns(self, *other: BiocFrame) -> BiocFrame: def merge( self, *other: BiocFrame, - by: Union[None, str, int, Sequence[Union[None, str, int]]] = None, + by: None | str | int | Sequence[None | str | int] = None, join: Literal["inner", "left", "right", "outer"] = "left", rename_duplicate_columns: bool = False, ) -> BiocFrame: @@ -1729,7 +1727,7 @@ def _combine_cols_bframes(*x: BiocFrame) -> BiocFrame: @ut.extract_row_names.register(BiocFrame) -def _rownames_bframe(x: BiocFrame) -> Optional[ut.Names]: +def _rownames_bframe(x: BiocFrame) -> ut.Names | None: """Extract row names from a BiocFrame object. Args: @@ -1757,7 +1755,7 @@ def _colnames_bframe(x: BiocFrame) -> ut.Names: @ut.show_as_cell.register(BiocFrame) -def _show_as_cell_BiocFrame(x: BiocFrame, indices: Sequence[int]) -> List[str]: +def _show_as_cell_BiocFrame(x: BiocFrame, indices: Sequence[int]) -> list[str]: """Show a BiocFrame as a cell. Args: @@ -1881,7 +1879,7 @@ def relaxed_combine_rows(*x: BiocFrame) -> BiocFrame: ############################ -def _normalize_merge_key_to_index(x: Sequence[BiocFrame], i: int, by: Union[None, str, int]) -> Optional[int]: +def _normalize_merge_key_to_index(x: Sequence[BiocFrame], i: int, by: None | str | int) -> int | None: """Normalize a merge key to an index. Args: @@ -1924,7 +1922,7 @@ def _normalize_merge_key_to_index(x: Sequence[BiocFrame], i: int, by: Union[None raise TypeError("Unknown type '" + type(by).__name__ + "' for the 'by' argument.") -def _get_merge_key(x: Sequence[BiocFrame], i: int, by: List[Optional[int]]) -> Any: +def _get_merge_key(x: Sequence[BiocFrame], i: int, by: list[int | None]) -> Any: """Get a merge key. Args: @@ -1948,7 +1946,7 @@ def _get_merge_key(x: Sequence[BiocFrame], i: int, by: List[Optional[int]]) -> A def merge( x: Sequence[BiocFrame], - by: Union[None, str, int, Sequence[Union[None, str, int]]] = None, + by: None | str | int | Sequence[None | str | int] = None, join: Literal["inner", "left", "right", "outer"] = "left", rename_duplicate_columns: bool = False, ) -> BiocFrame: diff --git a/src/biocframe/__init__.py b/src/biocframe/__init__.py index 6086c6a..e6e1635 100644 --- a/src/biocframe/__init__.py +++ b/src/biocframe/__init__.py @@ -15,5 +15,5 @@ finally: del version, PackageNotFoundError -from .BiocFrame import BiocFrame, relaxed_combine_rows, merge, relaxed_combine_columns +from .BiocFrame import BiocFrame, merge, relaxed_combine_columns, relaxed_combine_rows from .io import from_pandas diff --git a/src/biocframe/io/from_pandas.py b/src/biocframe/io/from_pandas.py index c28b031..3b01809 100644 --- a/src/biocframe/io/from_pandas.py +++ b/src/biocframe/io/from_pandas.py @@ -12,7 +12,7 @@ __license__ = "MIT" -def from_pandas(input: "pandas.DataFrame") -> BiocFrame: +def from_pandas(input: pandas.DataFrame) -> BiocFrame: """Alias for the :py:meth:`~biocframe.BiocFrame.BiocFrame.from_pandas` method, provided for back-compatibility only.""" return BiocFrame.from_pandas(input) From ab210eb6d7acf0f249b0ba412e3d2dcf3525bcf1 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 24 Aug 2026 23:25:08 -0700 Subject: [PATCH 3/5] include al extra dependencies --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index 4b4791a..814470d 100644 --- a/tox.ini +++ b/tox.ini @@ -10,7 +10,7 @@ description = Invoke pytest to run automated tests allowlist_externals = uv skip_install = True commands = - uv run pytest {posargs} + uv run --all-extras pytest {posargs} [testenv:typecheck] description = Run static type checking with mypy From fcd27fdb288787d8c083ba5e91178d92cbff3d0d Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Tue, 25 Aug 2026 21:47:15 -0700 Subject: [PATCH 4/5] a few more inconsistencies --- .github/workflows/pre-commit.yml | 28 +- .github/workflows/publish-pypi.yml | 2 +- .github/workflows/run-tests.yml | 2 +- pyproject.toml | 61 +- src/biocframe/BiocFrame.py | 155 +- src/biocframe/__init__.py | 4 +- src/biocframe/io/__init__.py | 2 +- uv.lock | 4968 ++++++++++++++++++++++++++++ 8 files changed, 5113 insertions(+), 109 deletions(-) create mode 100644 uv.lock diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index d638c47..e752aca 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -1,16 +1,16 @@ -name: pre-commit +# name: pre-commit -on: - pull_request: - push: - branches: [main] +# on: +# pull_request: +# push: +# branches: [main] -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - uses: pre-commit/action@v3.0.1 +# jobs: +# pre-commit: +# runs-on: ubuntu-latest +# steps: +# - uses: actions/checkout@v4 +# - uses: actions/setup-python@v5 +# with: +# python-version: '3.12' +# - uses: pre-commit/action@v3.0.1 diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 81ef189..48311ed 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -33,7 +33,7 @@ jobs: - name: Build Project run: | - tox -e build + tox -e clean,build # This uses the trusted publisher workflow so no token is required. - name: Publish to PyPI diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 0093104..e44500e 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -47,7 +47,7 @@ jobs: run: | python -m pip install --upgrade pip pip install uv tox - uv sync + uv sync --python ${{ matrix.python }} - name: Run tests run: | diff --git a/pyproject.toml b/pyproject.toml index 92d3fba..94200d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,24 +6,48 @@ readme = "README.md" authors = [ { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" } ] -requires-python = ">=3.12" +requires-python = ">=3.9" +license = { file = "LICENSE.txt" } +keywords = ["biocpy", "bioinformatics", "dataframe", "bioconductor"] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Typing :: Typed", +] dependencies = [ "biocutils>=0.3.3", - "importlib-metadata>=9.0.0 ; python_full_version < '3.8'", - "numpy>=2.5.2", + "numpy>=1.26.0", ] +[project.urls] +Homepage = "https://github.com/BiocPy/biocframe" +Documentation = "https://biocpy.github.io/BiocFrame/" +Source = "https://github.com/BiocPy/biocframe" +"Bug Tracker" = "https://github.com/BiocPy/biocframe/issues" + [project.optional-dependencies] optional = [ - "pandas>=3.0.5", - "polars>=1.44.0", + "pandas>=2.0.0", + "polars>=0.20.0", ] testing = [ - "pandas>=3.0.5", - "polars>=1.44.0", - "pytest>=9.1.1", - "pytest-cov>=7.1.0", - "setuptools>=84.0.0", + "pandas>=2.0.0", + "polars>=0.20.0", + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "setuptools>=68.0.0", ] [build-system] @@ -61,12 +85,13 @@ testpaths = ["tests"] [dependency-groups] dev = [ - "furo>=2025.12.19", - "linkify-it-py>=2.1.1", - "mypy>=2.3.1", - "myst-nb>=1.4.0", - "pytest>=9.1.1", - "pytest-cov>=7.1.0", - "sphinx>=9.1.0", - "sphinx-autodoc-typehints>=3.13.4", + "furo>=2024.0.0", + "linkify-it-py>=1.0.3", + "mypy>=1.0.0", + "myst-nb>=1.0.0", + "pandas-stubs>=2.0.0", + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "sphinx>=7.0.0", + "sphinx-autodoc-typehints>=2.0.0", ] diff --git a/src/biocframe/BiocFrame.py b/src/biocframe/BiocFrame.py index d277a61..0485c78 100644 --- a/src/biocframe/BiocFrame.py +++ b/src/biocframe/BiocFrame.py @@ -3,7 +3,8 @@ from collections import OrderedDict, abc from collections.abc import Sequence from copy import copy -from typing import TYPE_CHECKING, Any, Literal +import builtins +from typing import TYPE_CHECKING, Any, Literal, cast from warnings import warn import biocutils as ut @@ -29,7 +30,7 @@ def _guess_number_of_rows( if number_of_rows is not None: return number_of_rows if len(data) > 0: - return ut.get_height(next(iter(data.values()))) + return int(ut.get_height(next(iter(data.values())))) if row_names is not None: return len(row_names) return 0 @@ -178,13 +179,14 @@ def __init__( if data is None: data = {} + _data_dict: dict[str, Any] = {} if isinstance(data, ut.NamedList): - data = data.as_dict() + _data_dict = data.as_dict() # making sure all column values are lists - for k, v in data.items(): + for k, v in _data_dict.items(): if not isinstance(v, list): # if its a scalar, make a list else coerce to list - data[k] = list(v) if isinstance(v, abc.Sequence) else [v] + _data_dict[k] = list(v) if isinstance(v, abc.Sequence) else [v] elif isinstance(data, Sequence) and not isinstance(data, (str, dict)): if column_names is None: raise ValueError("`column_names` must be provided if `data` is a sequence.") @@ -192,9 +194,13 @@ def __init__( if len(data) != len(column_names): raise ValueError("Length of `data` and `column_names` must match.") - data = dict(zip(column_names, data)) + _data_dict = dict(zip(column_names, data)) + elif isinstance(data, dict): + _data_dict = data + else: + raise TypeError("`data` must be a dictionary, NamedList, Sequence, or None.") - self._data = data + self._data = _data_dict if row_names is not None and not isinstance(row_names, ut.Names): row_names = ut.Names(row_names) @@ -350,7 +356,7 @@ def __repr__(self) -> str: output += ", metadata=" + ut.print_truncated_dict(self._metadata) output += ")" - return output + return str(output) def __str__(self) -> str: """ @@ -364,7 +370,7 @@ def __str__(self) -> str: added_table = False if nr and self.shape[1]: if nr <= 10: - indices = range(nr) + indices: Sequence[int] = range(nr) insert_ellipsis = False else: indices = [0, 1, 2, nr - 3, nr - 2, nr - 1] @@ -458,7 +464,7 @@ def set_row_names(self, names: Sequence[str] | ut.Names | None, in_place: bool = if not isinstance(names, ut.Names): names = ut.Names(names) - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) output._row_names = names return output @@ -574,7 +580,7 @@ def set_column_names(self, names: Sequence[str] | ut.Names, in_place: bool = Fal new_names.append(y) new_data[y] = self._data[self.column_names[i]] - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) output._column_names = new_names output._data = new_data return output @@ -651,7 +657,7 @@ def set_column_data(self, column_data: BiocFrame | None, in_place: bool = False) if column_data.shape[0] != self.shape[1]: raise ValueError("Number of rows in `column_data` should be equal to the number of columns.") - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) output._column_data = column_data return output @@ -755,7 +761,7 @@ def get_row(self, row: str | int) -> dict[str, Any]: if self._row_names is None: raise ValueError("No row names present to find row '" + row + "'.") - row_idx = self._row_names.map(row) + row_idx = cast(ut.Names, self._row_names).map(row) if row_idx < 0: raise ValueError("Could not find row '" + row + "'.") row = row_idx @@ -825,8 +831,8 @@ def tail(self, n: int = 5) -> BiocFrame: def get_slice( self, - rows: str | int | bool | Sequence[str | int | bool] | slice, - columns: str | int | bool | Sequence[str | int | bool] | slice, + rows: str | int | bool | Sequence[str | int | bool] | builtins.slice, + columns: str | int | bool | Sequence[str | int | bool] | builtins.slice, ) -> BiocFrame: """Slice ``BiocFrame`` along the rows and/or columns, based on their indices or names. @@ -891,8 +897,8 @@ def get_slice( def slice( self, - rows: Sequence[str | int | bool] | slice | None, - columns: Sequence[str | int | bool] | slice | None, + rows: Sequence[str | int | bool] | builtins.slice | None, + columns: Sequence[str | int | bool] | builtins.slice | None, ) -> BiocFrame: """Alias for :py:attr:`~__getitem__`, for back-compatibility.""" if rows is None: @@ -903,7 +909,7 @@ def slice( def __getitem__( self, - args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | slice, ...], + args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | builtins.slice, ...], ) -> BiocFrame | Any: """Wrapper around :py:attr:`~get_column` and :py:attr:`~get_slice` to obtain a slice of a ``BiocFrame`` or any of its columns. @@ -954,7 +960,7 @@ def __getitem__( def __setitem__( self, - args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | slice, ...], + args: int | str | Sequence[str | int] | tuple[int | str | Sequence[str | int] | builtins.slice, ...], value: BiocFrame | Any, ) -> None: """Wrapper around :py:attr:`~set_column` and :py:attr:`~set_slice` to modify a slice of a ``BiocFrame`` or any @@ -974,17 +980,23 @@ def __setitem__( UserWarning, ) self.set_slice(args[0], args[1], value, in_place=True) - else: + elif isinstance(args, (str, int)): warn( "This method performs an in-place operation, use 'set_column' instead", UserWarning, ) self.set_column(args, value, in_place=True) + else: + warn( + "This method performs an in-place operation, use 'set_slice' instead", + UserWarning, + ) + self.set_slice(builtins.slice(None), args, value, in_place=True) def set_slice( self, - rows: int | str | bool | Sequence[int | str | bool] | slice, - columns: int | str | bool | Sequence[int | str | bool] | slice, + rows: int | str | bool | Sequence[int | str | bool] | builtins.slice, + columns: int | str | bool | Sequence[int | str | bool] | builtins.slice, value: BiocFrame, in_place: bool = True, ) -> BiocFrame: @@ -1020,7 +1032,7 @@ def set_slice( A modified ``BiocFrame`` object, either as a copy of the original or as a reference to the (in-place-modified) original. """ - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) if not in_place: output._data = copy(output._data) @@ -1090,7 +1102,7 @@ def set_columns(self, columns: dict[str | int, Any], in_place: bool = False) -> A modified ``BiocFrame`` object, either as a copy of the original or as a reference to the (in-place-modified) original. """ - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) if not in_place: output._data = copy(output._data) is_colnames_copied = False @@ -1143,7 +1155,7 @@ def remove_column(self, column: int | str, in_place: bool = False) -> BiocFrame: """ return self.remove_columns([column], in_place=in_place) - def remove_columns(self, columns: Sequence[int | str] | slice, in_place: bool = False) -> BiocFrame: + def remove_columns(self, columns: Sequence[int | str] | builtins.slice, in_place: bool = False) -> BiocFrame: """Remove any number of existing columns. Args: @@ -1160,7 +1172,7 @@ def remove_columns(self, columns: Sequence[int | str] | slice, in_place: bool = Raises: TypeError: If columns contains mixed types. """ - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) if not in_place: output._data = copy(output._data) @@ -1213,7 +1225,7 @@ def remove_row(self, row: int | str, in_place: bool = False) -> BiocFrame: """ return self.remove_rows([row], in_place=in_place) - def remove_rows(self, rows: Sequence[int | str] | slice, in_place: bool = False) -> BiocFrame: + def remove_rows(self, rows: Sequence[int | str] | builtins.slice, in_place: bool = False) -> BiocFrame: """Remove any number of existing rows. Args: @@ -1233,18 +1245,15 @@ def remove_rows(self, rows: Sequence[int | str] | slice, in_place: bool = False) Raises: TypeError: If rows contain mixed types. """ - output = self._define_output(in_place) + output = cast("BiocFrame", self._define_output(in_place)) if not in_place: output._data = copy(output._data) - _row_names = output._row_names - if output._row_names is None: - # raise ValueError("Cannot remove rows when row names are not defined.") - _row_names = range(len(output)) + _row_names_seq = cast(Sequence[Any], self._row_names if self._row_names is not None else range(len(output))) - if isinstance(rows, slice): - indices = range(*rows.indices(len(_row_names))) - killset = {_row_names[i] for i in indices} + if isinstance(rows, builtins.slice): + indices = range(*rows.indices(len(_row_names_seq))) + killset = {_row_names_seq[i] for i in indices} else: # Check for homogeneous types types = set(type(x) for x in rows) @@ -1254,23 +1263,23 @@ def remove_rows(self, rows: Sequence[int | str] | slice, in_place: bool = False) killset = set() for name in rows: if isinstance(name, int): - if name < 0 or name >= len(_row_names): + if name < 0 or name >= len(_row_names_seq): raise IndexError(f"Row index {name} is out of range.") - name = _row_names[name] + name = _row_names_seq[name] - if name not in _row_names: + if name not in _row_names_seq: raise ValueError(f"Row '{name}' does not exist.") killset.add(name) keep = [] - for i, row in enumerate(_row_names): + for i, row in enumerate(_row_names_seq): if row not in killset: keep.append(i) for col in output._data: output._data[col] = ut.subset_sequence(output._data[col], keep) - output._row_names = ut.subset_sequence(_row_names, keep) + output._row_names = ut.subset_sequence(_row_names_seq, keep) output._number_of_rows = int( _guess_number_of_rows( @@ -1366,7 +1375,7 @@ def split(self, column_name: str, only_indices: bool = False) -> dict[str, BiocF _column = self.get_column(column_name) - _grps = {} + _grps: dict[Any, list[int]] = {} for i in range(len(self)): _key = _column[i] if _key not in _grps: @@ -1377,7 +1386,7 @@ def split(self, column_name: str, only_indices: bool = False) -> dict[str, BiocF if only_indices is True: return _grps - _sliced_grps = {} + _sliced_grps: dict[str, BiocFrame | list[int]] = {} for k, v in _grps.items(): _sliced_grps[k] = self[v,] @@ -1408,7 +1417,8 @@ def to_pandas(self) -> pandas.DataFrame: if len(self.column_names) > 0: _data_copy = self.flatten(as_type="dict") - return DataFrame(data=_data_copy, index=self._row_names) + _idx = list(self._row_names) if self._row_names is not None else None + return DataFrame(data=_data_copy, index=_idx) else: return DataFrame(data={}, index=range(self._number_of_rows)) @@ -1554,23 +1564,23 @@ def __array_ufunc__(self, func: Any, method: str, *inputs: Any, **kwargs: Any) - def combine(self, *other: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~relaxed_combine_rows`, provided for back-compatibility only.""" - return relaxed_combine_rows(self, *other) + return cast("BiocFrame", relaxed_combine_rows(self, *other)) def relaxed_combine_rows(self, *other: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~relaxed_combine_rows`.""" - return relaxed_combine_rows(self, *other) + return cast("BiocFrame", relaxed_combine_rows(self, *other)) def relaxed_combine_columns(self, *other: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~relaxed_combine_columns`.""" - return relaxed_combine_columns(self, *other) + return cast("BiocFrame", relaxed_combine_columns(self, *other)) def combine_rows(self, *other: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~biocutils.combine_rows`.""" - return _combine_rows_bframes(self, *other) + return cast("BiocFrame", _combine_rows_bframes(self, *other)) def combine_columns(self, *other: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~biocutils.combine_columns`.""" - return _combine_cols_bframes(self, *other) + return cast("BiocFrame", _combine_cols_bframes(self, *other)) def merge( self, @@ -1591,7 +1601,7 @@ def merge( ############################ -@ut.combine_rows.register(BiocFrame) +@ut.combine_rows.register(BiocFrame) # type: ignore def _combine_rows_bframes(*x: BiocFrame) -> BiocFrame: """Combine multiple BiocFrame objects by row. @@ -1643,7 +1653,7 @@ def _combine_rows_bframes(*x: BiocFrame) -> BiocFrame: current.append(df.column(col)) new_data[col] = ut.combine(*current) - new_rownames = None + new_rownames: list[str] | None = None if has_rownames: new_rownames = [] for df in x: @@ -1663,7 +1673,7 @@ def _combine_rows_bframes(*x: BiocFrame) -> BiocFrame: ) -@ut.combine_columns.register(BiocFrame) +@ut.combine_columns.register(BiocFrame) # type: ignore def _combine_cols_bframes(*x: BiocFrame) -> BiocFrame: """Combine multiple BiocFrame objects by column. @@ -1726,7 +1736,7 @@ def _combine_cols_bframes(*x: BiocFrame) -> BiocFrame: ) -@ut.extract_row_names.register(BiocFrame) +@ut.extract_row_names.register(BiocFrame) # type: ignore def _rownames_bframe(x: BiocFrame) -> ut.Names | None: """Extract row names from a BiocFrame object. @@ -1740,7 +1750,7 @@ def _rownames_bframe(x: BiocFrame) -> ut.Names | None: return x.get_row_names() -@ut.extract_column_names.register(BiocFrame) +@ut.extract_column_names.register(BiocFrame) # type: ignore def _colnames_bframe(x: BiocFrame) -> ut.Names: """Extract column names from a BiocFrame object. @@ -1754,7 +1764,7 @@ def _colnames_bframe(x: BiocFrame) -> ut.Names: return x.get_column_names() -@ut.show_as_cell.register(BiocFrame) +@ut.show_as_cell.register(BiocFrame) # type: ignore def _show_as_cell_BiocFrame(x: BiocFrame, indices: Sequence[int]) -> list[str]: """Show a BiocFrame as a cell. @@ -1768,7 +1778,7 @@ def _show_as_cell_BiocFrame(x: BiocFrame, indices: Sequence[int]) -> list[str]: Returns: A list of strings. """ - constructs = [] + constructs: list[Any] = [] for i in indices: constructs.append([]) @@ -1783,7 +1793,7 @@ def _show_as_cell_BiocFrame(x: BiocFrame, indices: Sequence[int]) -> list[str]: return constructs -@ut.assign_rows.register(BiocFrame) +@ut.assign_rows.register(BiocFrame) # type: ignore def _assign_rows_BiocFrame(x: BiocFrame, indices: Sequence[int], replacement: BiocFrame) -> BiocFrame: """Assign rows to a BiocFrame object. @@ -1829,7 +1839,7 @@ def _construct_missing(col: Any, n: int) -> Any: return [None] * n -@ut.relaxed_combine_rows.register(BiocFrame) +@ut.relaxed_combine_rows.register(BiocFrame) # type: ignore def relaxed_combine_rows(*x: BiocFrame) -> BiocFrame: """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_rows` method for :py:class:`~BiocFrame` objects. Whereas ``combine_rows`` expects that all objects have the same columns, ``relaxed_combine_rows`` allows @@ -1873,7 +1883,7 @@ def relaxed_combine_rows(*x: BiocFrame) -> BiocFrame: else: edited.append(df) - return ut.combine_rows(*edited) + return cast("BiocFrame", ut.combine_rows(*edited)) ############################ @@ -1917,7 +1927,7 @@ def _normalize_merge_key_to_index(x: Sequence[BiocFrame], i: int, by: None | str ib = x[i]._column_names.map(by) if ib < 0: raise ValueError("No key column '" + by + "' in object " + str(i) + ".") - return ib + return int(ib) else: raise TypeError("Unknown type '" + type(by).__name__ + "' for the 'by' argument.") @@ -1938,10 +1948,11 @@ def _get_merge_key(x: Sequence[BiocFrame], i: int, by: list[int | None]) -> Any: Returns: A merge key. """ - if by[i] is None: + b = by[i] + if b is None: return x[i]._row_names else: - return x[i].get_column(by[i]) + return x[i].get_column(b) def merge( @@ -1993,21 +2004,21 @@ def merge( raise TypeError("All objects to merge must be BiocFrame objects.") if by is None or isinstance(by, str) or isinstance(by, int): - by = [_normalize_merge_key_to_index(x, i, by) for i in range(len(x))] + _by_indices = [_normalize_merge_key_to_index(x, i, by) for i in range(len(x))] else: if len(by) != len(x): raise ValueError("'by' list should have the same length as 'x'.") - by = [_normalize_merge_key_to_index(x, i, b) for i, b in enumerate(by)] + _by_indices = [_normalize_merge_key_to_index(x, i, b) for i, b in enumerate(by)] if join == "left": - all_keys = _get_merge_key(x, 0, by) + all_keys = _get_merge_key(x, 0, _by_indices) elif join == "right": - all_keys = _get_merge_key(x, -1, by) + all_keys = _get_merge_key(x, -1, _by_indices) elif join == "inner": - tmp_keys = [_get_merge_key(x, i, by) for i in range(len(x))] + tmp_keys = [_get_merge_key(x, i, _by_indices) for i in range(len(x))] all_keys = ut.intersect(*tmp_keys) elif join == "outer": - tmp_keys = [_get_merge_key(x, i, by) for i in range(len(x))] + tmp_keys = [_get_merge_key(x, i, _by_indices) for i in range(len(x))] all_keys = ut.union(*tmp_keys) else: raise ValueError("Unknown joining strategy '" + join + "'") @@ -2024,11 +2035,11 @@ def merge( keep = None has_missing = 0 - reorg_keep = None + reorg_keep: list[bool] | None = None reorg_permute = None if not noop: - keep = ut.match(all_keys, _get_merge_key(x, i, by)) + keep = ut.match(all_keys, _get_merge_key(x, i, _by_indices)) has_missing = (keep < 0).sum() if has_missing: non_missing = len(keep) - has_missing @@ -2043,7 +2054,7 @@ def merge( survivor_columns = [] for j, y in enumerate(df._column_names): - on_key = by[i] == j + on_key = _by_indices[i] == j if on_key and i > 0: # skipping the key columns, except for the first. continue val = df._data[y] @@ -2094,7 +2105,7 @@ def merge( metadata=x[0]._metadata, ) - if by[0] is None: + if _by_indices[0] is None: output.set_row_names(all_keys, in_place=True) return output @@ -2103,7 +2114,7 @@ def merge( ############################ -@ut.relaxed_combine_columns.register(BiocFrame) +@ut.relaxed_combine_columns.register(BiocFrame) # type: ignore def relaxed_combine_columns(*x: BiocFrame) -> BiocFrame: """Wrapper around :py:func:`~merge` that performs a left join on the row names.""" return merge(list(x), join="left", by=None) diff --git a/src/biocframe/__init__.py b/src/biocframe/__init__.py index e6e1635..80029cc 100644 --- a/src/biocframe/__init__.py +++ b/src/biocframe/__init__.py @@ -15,5 +15,5 @@ finally: del version, PackageNotFoundError -from .BiocFrame import BiocFrame, merge, relaxed_combine_columns, relaxed_combine_rows -from .io import from_pandas +from .BiocFrame import BiocFrame as BiocFrame, merge as merge, relaxed_combine_columns as relaxed_combine_columns, relaxed_combine_rows as 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10238, upload-time = "2026-05-18T20:08:57.045Z" }, +] From 9ff846afe75562bc583392cbb5c7203339ccbb92 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 26 Aug 2026 04:47:33 +0000 Subject: [PATCH 5/5] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/biocframe/BiocFrame.py | 2 +- src/biocframe/__init__.py | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/biocframe/BiocFrame.py b/src/biocframe/BiocFrame.py index 0485c78..8c3d408 100644 --- a/src/biocframe/BiocFrame.py +++ b/src/biocframe/BiocFrame.py @@ -1,9 +1,9 @@ from __future__ import annotations +import builtins from collections import OrderedDict, abc from collections.abc import Sequence from copy import copy -import builtins from typing import TYPE_CHECKING, Any, Literal, cast from warnings import warn diff --git a/src/biocframe/__init__.py b/src/biocframe/__init__.py index 80029cc..ce99c8f 100644 --- a/src/biocframe/__init__.py +++ b/src/biocframe/__init__.py @@ -15,5 +15,8 @@ finally: del version, PackageNotFoundError -from .BiocFrame import BiocFrame as BiocFrame, merge as merge, relaxed_combine_columns as relaxed_combine_columns, relaxed_combine_rows as relaxed_combine_rows +from .BiocFrame import BiocFrame as BiocFrame +from .BiocFrame import merge as merge +from .BiocFrame import relaxed_combine_columns as relaxed_combine_columns +from .BiocFrame import relaxed_combine_rows as relaxed_combine_rows from .io import from_pandas as from_pandas