From e79b25a87f51db6282531db514d81cf62b84aed1 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Sat, 29 Aug 2026 23:09:30 -0700 Subject: [PATCH 01/14] update to hatchit --- .coveragerc | 21 +- .gitattributes | 10 + .github/dependabot.yml | 15 + .github/workflows/pre-commit.yml | 16 + .github/workflows/publish-pypi.yml | 107 +- .github/workflows/run-tests.yml | 22 +- .gitignore | 56 + .pre-commit-config.yaml | 15 +- .readthedocs.yml | 26 +- .zenodo.json | 14 + CITATION.cff | 10 + CONTRIBUTING.md | 377 +---- docs/conf.py | 61 +- docs/requirements.txt | 4 +- pyproject.toml | 86 +- setup.cfg | 129 -- setup.py | 20 - src/biocutils/mcols.py | 84 ++ src/biocutils/melt.py | 25 + src/biocutils/pminmax.py | 46 + src/biocutils/py.typed | 0 src/biocutils/relist.py | 45 + src/biocutils/rle.py | 40 + src/biocutils/unlist.py | 29 + src/biocutils/xtfrm.py | 47 + tests/test_melt_dispatcher.py | 61 + tests/test_new_generics.py | 87 ++ tests/test_xtfrm.py | 88 ++ tox.ini | 80 +- uv.lock | 2103 ++++++++++++++++++++++++++++ 30 files changed, 3040 insertions(+), 684 deletions(-) create mode 100644 .gitattributes create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/pre-commit.yml create mode 100644 .zenodo.json create mode 100644 CITATION.cff delete mode 100644 setup.cfg delete mode 100644 setup.py create mode 100644 src/biocutils/mcols.py create mode 100644 src/biocutils/melt.py create mode 100644 src/biocutils/pminmax.py create mode 100644 src/biocutils/py.typed create mode 100644 src/biocutils/relist.py create mode 100644 src/biocutils/rle.py create mode 100644 src/biocutils/unlist.py create mode 100644 src/biocutils/xtfrm.py create mode 100644 tests/test_melt_dispatcher.py create mode 100644 tests/test_new_generics.py create mode 100644 tests/test_xtfrm.py create mode 100644 uv.lock diff --git a/.coveragerc b/.coveragerc index 30f1dae..a920d99 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,28 +1,13 @@ -# .coveragerc to control coverage.py [run] -branch = True -source = biocutils -# 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/.gitattributes b/.gitattributes new file mode 100644 index 0000000..0b7360d --- /dev/null +++ b/.gitattributes @@ -0,0 +1,10 @@ +# Enforce Unix line endings +* text=auto eol=lf + +# Git LFS configurations for large scientific datasets +*.h5 filter=lfs diff=lfs merge=lfs -text +*.hdf5 filter=lfs diff=lfs merge=lfs -text +*.rds filter=lfs diff=lfs merge=lfs -text +*.rda filter=lfs diff=lfs merge=lfs -text +*.csv.gz filter=lfs diff=lfs merge=lfs -text +*.bam filter=lfs diff=lfs merge=lfs -text 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..3e93b84 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -1,52 +1,101 @@ -name: Publish to PyPI +name: Publish to PyPI and GitHub Pages on: push: tags: "*" jobs: - build: + build-and-test: + name: Build and Test runs-on: ubuntu-latest - permissions: - id-token: write - repository-projects: write - contents: write - pages: write - steps: - uses: actions/checkout@v4 + + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true - name: Set up Python 3.12 uses: actions/setup-python@v5 with: python-version: 3.12 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install tox + - name: Install tox + run: uv tool install tox --with tox-uv - - name: Test with tox - run: | - tox + - name: Test + run: tox -e default - - name: Build Project and Publish - run: | - python -m tox -e clean,build + - name: Build Project + run: tox -e build - # This uses the trusted publisher workflow so no token is required. - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Store the distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + build-docs: + name: Build Documentation + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Set up Python 3.12 + uses: actions/setup-python@v5 + with: + python-version: 3.12 + + - name: Install tox + run: uv tool install tox --with tox-uv - name: Build docs - run: | - tox -e docs + run: tox -e docs + + - name: Add .nojekyll + run: touch ./docs/_build/html/.nojekyll - - run: touch ./docs/_build/html/.nojekyll + - name: Upload Pages artifact + uses: actions/upload-pages-artifact@v3 + with: + path: ./docs/_build/html - - name: GH Pages Deployment - uses: JamesIves/github-pages-deploy-action@v4 + publish-pypi: + name: Publish to PyPI + needs: build-and-test + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/biocutils + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 with: - branch: gh-pages # The branch the action should deploy to. - folder: ./docs/_build/html - clean: true # Automatically remove deleted files from the deploy branch + name: python-package-distributions + path: dist/ + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + deploy-pages: + name: Deploy GitHub Pages + needs: build-docs + runs-on: ubuntu-latest + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index e0f247d..662c96f 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -38,21 +38,25 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - id: setup-python + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + + - name: Set up Python + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python }} + - name: Install tox + run: uv tool install tox --with tox-uv + - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install tox coverage + run: uv sync --all-extras --python ${{ matrix.python }} - name: Run tests - run: >- - pipx run --python '${{ 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 ff68130..1ae9c43 100644 --- a/.gitignore +++ b/.gitignore @@ -53,3 +53,59 @@ docs/html .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..af3eb03 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: @@ -51,3 +53,10 @@ repos: # rev: v2.2.5 # hooks: # - id: codespell + +- repo: https://github.com/PyCQA/bandit + rev: 1.7.9 + hooks: + - id: bandit + args: ["-c", "pyproject.toml"] + additional_dependencies: ["bandit[toml]"] diff --git a/.readthedocs.yml b/.readthedocs.yml index a2bcab3..da89049 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,27 +1,21 @@ # 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 - build: os: ubuntu-22.04 tools: - python: "3.11" + python: "3.12" + jobs: + post_install: + - curl -LsSf https://astral.sh/uv/install.sh | sh + - uv sync + +sphinx: + configuration: docs/conf.py python: install: - - requirements: docs/requirements.txt - - {path: ., method: pip} + - method: pip + path: . diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..c0eb26d --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,14 @@ +{ + "title": "biocutils", + "description": "Utilities to use across the biocpy packages.", + "creators": [ + { + "name": "Jayaram Kancherla", + "affiliation": "YOUR_AFFILIATION", + "orcid": "0000-0000-0000-0000" + } + ], + "access_right": "open", + "license": "MIT", + "upload_type": "software" +} diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..10eef90 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,10 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +authors: +- family-names: "Kancherla" + given-names: "Jayaram" + orcid: "https://orcid.org/0000-0000-0000-0000" +title: "biocutils" +version: 0.1.0 +date-released: 2026-08-24 +url: "https://github.com/YOUR_ORG_OR_USERNAME/biocutils" diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index aaa1e60..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 `biocutils` 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 `biocutils`, 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 `biocutils` docs by making them more readable and coherent, or -by adding missing information and correcting mistakes. - -`biocutils` 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 `biocutils`'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 biocutils python=3 six virtualenv pytest pytest-cov -conda activate biocutils -``` - -### 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/biocutils.git - cd biocutils - ``` - -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 - ``` - - `biocutils` 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 -`biocutils`: - -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//biocutils -[issue tracker]: https://github.com//biocutils/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 528312d..7f64459 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. @@ -80,7 +79,7 @@ # Enable markdown -extensions.append("myst_nb") +extensions.append("myst_parser") # Configure MyST-Parser myst_enable_extensions = [ @@ -107,7 +106,7 @@ # General information about the project. project = "biocutils" -copyright = "2023, Aaron Lun" +copyright = "2026, 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 @@ -118,9 +117,10 @@ # If you don’t need the separation provided between version and release, # just set them both to the same value. try: - from biocutils import __version__ as version -except ImportError: - version = "" + from importlib.metadata import version as get_version + version = get_version("biocutils") +except Exception: + version = "unknown" if not version or version.lower() == "unknown": version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD @@ -167,30 +167,28 @@ # 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__, __init__' -} - -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" + "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/biocutils", + "source_branch": "main", + "source_directory": "docs/", } # Add any paths that contain custom themes here, relative to this directory. @@ -276,7 +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", "biocutils Documentation", "Aaron Lun", "manual") + ("index", "user_guide.tex", "biocutils Documentation", "Jayaram Kancherla", "manual") ] # The name of an image file (relative to this directory) to place at the top of @@ -310,7 +308,26 @@ "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None), "scipy": ("https://docs.scipy.org/doc/scipy/reference", None), "setuptools": ("https://setuptools.pypa.io/en/stable/", None), - "pyscaffold": ("https://pyscaffold.org/en/stable", None), } 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/pyproject.toml b/pyproject.toml index 45716dd..3f487b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,28 +1,84 @@ +[project] +name = "biocutils" +dynamic = [ + "version", +] +description = "Utilities to use across the biocpy packages." +readme = "README.md" +authors = [ + { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" }, +] +requires-python = ">=3.12" +dependencies = [ + "importlib-metadata>=9.0.0 ; python_full_version < '3.8'", + "numpy>=2.5.2", +] + +[project.optional-dependencies] +testing = [ + "pandas>=3.0.5", + "pytest>=9.1.1", + "pytest-cov>=7.1.0", + "scipy>=1.18.1", + "setuptools>=84.0.0", +] + [build-system] -# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD! -requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"] -build-backend = "setuptools.build_meta" +requires = [ + "hatchling", + "hatch-vcs", +] +build-backend = "hatchling.build" -[tool.setuptools_scm] -# For smarter version schemes and other configuration options, -# check out 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"] -extend-ignore = ["F821"] +src = [ + "src", +] +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 = [ + "pytest", + "pytest-cov", + "sphinx", + "myst-nb", + "furo", + "sphinx-autodoc-typehints", + "linkify-it-py", + "mypy", +] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 289856f..0000000 --- a/setup.cfg +++ /dev/null @@ -1,129 +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 = biocutils -description = Utilities to use across the biocpy packages. -author = Aaron Lun -author_email = infinite.monkeys.with.keyboards@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/biocutils -# Add here related links, for example: -project_urls = - Documentation = https://biocpy.github.io/BiocUtils/ - Source = https://github.com/biocpy/biocutils -# 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" - numpy - - -[options.packages.find] -where = src -exclude = - tests - -[options.extras_require] -# Add here additional requirements for extra features, to install with: -# `pip install biocutils[PDF]` like: -# PDF = ReportLab; RXP - -# Add here test requirements (semicolon/line-separated) -testing = - setuptools - pytest - pytest-cov - pandas - scipy - -[options.entry_points] -# Add here console scripts like: -# console_scripts = -# script_name = biocutils.module:function -# For example: -# console_scripts = -# fibonacci = biocutils.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 biocutils --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 = 88 -extend_ignore = E203, W503 -# ^ Black-compatible -# E203 and W503 have edge cases handled by black -exclude = - .tox - build - dist - .eggs - docs/conf.py - -[pyscaffold] -# PyScaffold's parameters when the project was created. -# This will be used when updating. Do not change! -version = 4.5 -package = biocutils -extensions = - markdown - pre_commit diff --git a/setup.py b/setup.py deleted file mode 100644 index 4fbfd79..0000000 --- a/setup.py +++ /dev/null @@ -1,20 +0,0 @@ -"""Setup file for biocutils. 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/biocutils/mcols.py b/src/biocutils/mcols.py new file mode 100644 index 0000000..99047fc --- /dev/null +++ b/src/biocutils/mcols.py @@ -0,0 +1,84 @@ +from functools import singledispatch +from typing import Any + +@singledispatch +def mcols(x: Any) -> Any: + """Retrieve metadata columns from an object. + + Args: + x: + The object to retrieve mcols from. + + Returns: + The metadata columns (usually a BiocFrame or None). + """ + if hasattr(x, "mcols"): + val = x.mcols + if callable(val): + return val() + return val + return None + +@singledispatch +def set_mcols(x: Any, value: Any) -> Any: + """Set or replace metadata columns on an object. + + Args: + x: + The target object. + value: + The new metadata columns. + + Returns: + A modified object. + """ + if hasattr(x, "set_mcols"): + return x.set_mcols(value) + if hasattr(x, "mcols"): + try: + x.mcols = value + return x + except AttributeError: + pass + raise TypeError(f"Cannot set mcols on type '{type(x).__name__}'") + +@singledispatch +def metadata(x: Any) -> Any: + """Retrieve general metadata from an object. + + Args: + x: + The object to retrieve metadata from. + + Returns: + A dictionary or NamedList containing metadata. + """ + if hasattr(x, "metadata"): + val = x.metadata + if callable(val): + return val() + return val + return None + +@singledispatch +def set_metadata(x: Any, value: Any) -> Any: + """Set or replace general metadata on an object. + + Args: + x: + The target object. + value: + The new metadata. + + Returns: + A modified object. + """ + if hasattr(x, "set_metadata"): + return x.set_metadata(value) + if hasattr(x, "metadata"): + try: + x.metadata = value + return x + except AttributeError: + pass + raise TypeError(f"Cannot set metadata on type '{type(x).__name__}'") diff --git a/src/biocutils/melt.py b/src/biocutils/melt.py new file mode 100644 index 0000000..b8093a0 --- /dev/null +++ b/src/biocutils/melt.py @@ -0,0 +1,25 @@ +from functools import singledispatch +from typing import Any +import pandas as pd + +@singledispatch +def melt(x: Any, **kwargs) -> pd.DataFrame: + """Melt a container into a tidy long-format pandas DataFrame. + + Args: + x: + The object/container to melt. + **kwargs: + Optional keyword arguments passed to the specific implementation. + + Returns: + A pandas DataFrame in long format. + """ + if hasattr(x, "melt"): + return x.melt(**kwargs) + + if hasattr(x, "to_pandas"): + df = x.to_pandas() + return df.melt(**kwargs) + + raise TypeError(f"No melt implementation found for class '{type(x).__name__}'") diff --git a/src/biocutils/pminmax.py b/src/biocutils/pminmax.py new file mode 100644 index 0000000..aea39b1 --- /dev/null +++ b/src/biocutils/pminmax.py @@ -0,0 +1,46 @@ +from typing import Any +import numpy as np + +def pmin(*x: Any, **kwargs) -> Any: + """Calculate the parallel element-wise minimum of multiple sequences. + + Args: + *x: + Sequence objects or vectors of equal length. + + Returns: + The element-wise minimum. + """ + if not x: + raise ValueError("Must specify at least one sequence/vector.") + + arrays = [np.asarray(item) for item in x] + res = arrays[0] + for arr in arrays[1:]: + res = np.minimum(res, arr) + + if isinstance(x[0], (list, tuple)): + return type(x[0])(res.tolist()) + return res + +def pmax(*x: Any, **kwargs) -> Any: + """Calculate the parallel element-wise maximum of multiple sequences. + + Args: + *x: + Sequence objects or vectors of equal length. + + Returns: + The element-wise maximum. + """ + if not x: + raise ValueError("Must specify at least one sequence/vector.") + + arrays = [np.asarray(item) for item in x] + res = arrays[0] + for arr in arrays[1:]: + res = np.maximum(res, arr) + + if isinstance(x[0], (list, tuple)): + return type(x[0])(res.tolist()) + return res diff --git a/src/biocutils/py.typed b/src/biocutils/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/src/biocutils/relist.py b/src/biocutils/relist.py new file mode 100644 index 0000000..ce4ce9f --- /dev/null +++ b/src/biocutils/relist.py @@ -0,0 +1,45 @@ +from typing import Any + +_relist_registry = {} + +def relist(flesh: Any, skeleton: Any, **kwargs) -> Any: + """Relist a flat sequence into the structure/shape of a skeleton. + + Args: + flesh: + The flat sequence/vector to reshape. + skeleton: + The template container whose structure should be replicated. + + Returns: + A reshaped nested container of the same class/type as skeleton. + """ + for cls in type(skeleton).__mro__: + if cls in _relist_registry: + return _relist_registry[cls](flesh, skeleton, **kwargs) + + if hasattr(skeleton, "relist"): + return skeleton.relist(flesh, **kwargs) + + if isinstance(skeleton, (list, tuple)): + res = [] + curr = 0 + for item in skeleton: + if isinstance(item, (list, tuple)): + nested_len = len(item) + res.append(relist(flesh[curr : curr + nested_len], item)) + curr += nested_len + else: + res.append(flesh[curr]) + curr += 1 + return type(skeleton)(res) + + raise TypeError(f"No relist implementation found for skeleton type '{type(skeleton).__name__}'") + +def register(cls): + def decorator(func): + _relist_registry[cls] = func + return func + return decorator + +relist.register = register diff --git a/src/biocutils/rle.py b/src/biocutils/rle.py new file mode 100644 index 0000000..f8412a8 --- /dev/null +++ b/src/biocutils/rle.py @@ -0,0 +1,40 @@ +import numpy as np +from typing import Any, List, Union + +class Rle: + def __init__(self, values: Any, lengths: Any = None): + """Initialize Run-Length Encoded vector. + + Args: + values: + Sequence of values, or a single value if lengths is specified. + lengths: + Sequence of run lengths matching each value, or None if values should be run-length compressed. + """ + if lengths is None: + vals = np.asarray(values) + if len(vals) == 0: + self.values = np.array([], dtype=vals.dtype) + self.lengths = np.array([], dtype=np.int32) + else: + change_indices = np.where(vals[:-1] != vals[1:])[0] + runs = np.diff(np.concatenate([[-1], change_indices, [len(vals) - 1]])) + self.values = np.concatenate([[vals[0]], vals[change_indices + 1]]) + self.lengths = runs.astype(np.int32) + else: + self.values = np.asarray(values) + self.lengths = np.asarray(lengths, dtype=np.int32) + + def __len__(self) -> int: + return int(np.sum(self.lengths)) + + def to_numpy(self) -> np.ndarray: + """Decompress Rle back to a dense numpy array.""" + return np.repeat(self.values, self.lengths) + + def __getitem__(self, idx: Union[int, slice]) -> Any: + dense = self.to_numpy() + return dense[idx] + + def __repr__(self) -> str: + return f"Rle(values={self.values.tolist()}, lengths={self.lengths.tolist()})" diff --git a/src/biocutils/unlist.py b/src/biocutils/unlist.py new file mode 100644 index 0000000..ef951e3 --- /dev/null +++ b/src/biocutils/unlist.py @@ -0,0 +1,29 @@ +from functools import singledispatch +from typing import Any + +@singledispatch +def unlist(x: Any, **kwargs) -> Any: + """Unlist a structured list-like container into a flat sequence. + + Args: + x: + The structured object/container to flatten. + **kwargs: + Optional keyword arguments passed to the specific implementation. + + Returns: + A flat representation of the sequence. + """ + if hasattr(x, "unlist"): + return x.unlist(**kwargs) + + if isinstance(x, (list, tuple)): + flat = [] + for item in x: + if isinstance(item, (list, tuple)): + flat.extend(unlist(item)) + else: + flat.append(item) + return type(x)(flat) + + return x diff --git a/src/biocutils/xtfrm.py b/src/biocutils/xtfrm.py new file mode 100644 index 0000000..5d664ad --- /dev/null +++ b/src/biocutils/xtfrm.py @@ -0,0 +1,47 @@ +from functools import singledispatch +from typing import Any + +import numpy + +from .Factor import Factor + + +@singledispatch +def xtfrm(x: Any) -> Any: + """Obtain a numeric representation of the elements of ``x`` that can be sorted. + + Args: + x: + Values to be transformed. + + Returns: + A numeric representation (usually a NumPy array or a sequence of numbers) + whose elements sort in the same relative order as ``x``. + """ + if hasattr(x, "__xtfrm__"): + return x.__xtfrm__() + + if isinstance(x, numpy.ndarray) and numpy.issubdtype(x.dtype, numpy.number): + return x + + from .order import order + from .subset import subset + + o = order(x) + ranks = numpy.empty(len(x), dtype=int) + if len(x) == 0: + return ranks + + sorted_x = subset(x, o) + current_rank = 0 + for i, idx in enumerate(o): + if i > 0 and sorted_x[i] != sorted_x[i - 1]: + current_rank += 1 + ranks[idx] = current_rank + + return ranks + + +@xtfrm.register +def _xtfrm_Factor(x: Factor) -> numpy.ndarray: + return x.get_codes() diff --git a/tests/test_melt_dispatcher.py b/tests/test_melt_dispatcher.py new file mode 100644 index 0000000..1ddf1f8 --- /dev/null +++ b/tests/test_melt_dispatcher.py @@ -0,0 +1,61 @@ +import pytest +import numpy as np +import pandas as pd +import biocframe +from biocframe import BiocFrame +from genomicranges import GenomicRanges +from summarizedexperiment import SummarizedExperiment +from multiassayexperiment import MultiAssayExperiment +import biocutils as ut + +def test_melt_biocframe(): + bf = BiocFrame({"A": [1, 2], "B": [3, 4]}) + res = ut.melt(bf) + assert isinstance(res, pd.DataFrame) + assert list(res["variable"]) == ["A", "A", "B", "B"] + assert list(res["value"]) == [1, 2, 3, 4] + +def test_melt_genomicranges(): + gr = GenomicRanges.from_pandas(pd.DataFrame({ + "seqnames": ["chr1"], + "starts": [10], + "ends": [15], + "strand": ["+"] + })) + res = ut.melt(gr) + assert isinstance(res, pd.DataFrame) + # Check that coordinate variables are in the melted DataFrame + # self.to_pandas() returns a DataFrame with seqnames, starts, ends, strand, names + assert "variable" in res.columns + assert "value" in res.columns + +def test_melt_summarizedexperiment(): + se = SummarizedExperiment( + assays={"counts": np.array([[1, 2], [3, 4]])}, + row_names=["gene_A", "gene_B"], + column_names=["sample_1", "sample_2"] + ) + res = ut.melt(se, assay=0) + assert isinstance(res, pd.DataFrame) + assert len(res) == 4 + assert list(res["value"]) == [1, 2, 3, 4] + +def test_melt_multiassayexperiment(): + se1 = SummarizedExperiment( + assays={"counts": np.array([[1, 2], [3, 4]])}, + row_names=["gene_A", "gene_B"], + column_names=["sample_1", "sample_2"] + ) + se2 = SummarizedExperiment( + assays={"counts": np.array([[5, 6], [7, 8]])}, + row_names=["gene_A", "gene_B"], + column_names=["sample_1", "sample_2"] + ) + mae = MultiAssayExperiment( + experiments={"assay1": se1, "assay2": se2} + ) + res = ut.melt(mae) + assert isinstance(res, pd.DataFrame) + assert len(res) == 8 + assert "assay" in res.columns + assert list(res["assay"]) == ["assay1"] * 4 + ["assay2"] * 4 diff --git a/tests/test_new_generics.py b/tests/test_new_generics.py new file mode 100644 index 0000000..7151d12 --- /dev/null +++ b/tests/test_new_generics.py @@ -0,0 +1,87 @@ +import pytest +import numpy as np +import pandas as pd +import biocframe +from biocframe import BiocFrame +from genomicranges import GenomicRanges, CompressedGenomicRangesList +from biostrings import DNAString, DNAStringSet +import biocutils as ut + +def test_unlist_relist_lists(): + lst = [[1, 2], [3, 4, 5]] + flat = ut.unlist(lst) + assert flat == [1, 2, 3, 4, 5] + + rel = ut.relist(flat, lst) + assert rel == [[1, 2], [3, 4, 5]] + +def test_unlist_relist_genomicranges(): + gr1 = GenomicRanges.from_pandas(pd.DataFrame({ + "seqnames": ["chr1", "chr1"], + "starts": [10, 20], + "ends": [15, 25], + "strand": ["+", "-"] + })) + gr2 = GenomicRanges.from_pandas(pd.DataFrame({ + "seqnames": ["chr2"], + "starts": [100], + "ends": [105], + "strand": ["+"] + })) + + grl = CompressedGenomicRangesList.from_list([gr1, gr2], names=["a", "b"]) + + flat = ut.unlist(grl) + assert isinstance(flat, GenomicRanges) + assert len(flat) == 3 + assert list(flat.get_start()) == [10, 20, 100] + + rel = ut.relist(flat, grl) + assert isinstance(rel, CompressedGenomicRangesList) + assert len(rel) == 2 + assert len(rel[0]) == 2 + assert len(rel[1]) == 1 + +def test_unlist_relist_biostrings(): + ds = DNAStringSet(["ACGT", "AAAA"]) + + flat = ut.unlist(ds) + assert isinstance(flat, DNAString) + assert str(flat) == "ACGTAAAA" + + rel = ut.relist(flat, ds) + assert isinstance(rel, DNAStringSet) + assert len(rel) == 2 + assert rel.to_list() == ["ACGT", "AAAA"] + +def test_pmin_pmax(): + v1 = [1, 5, 3] + v2 = [2, 4, 6] + + min_res = ut.pmin(v1, v2) + assert list(min_res) == [1, 4, 3] + + max_res = ut.pmax(v1, v2) + assert list(max_res) == [2, 5, 6] + +def test_mcols_metadata(): + gr = GenomicRanges.from_pandas(pd.DataFrame({ + "seqnames": ["chr1"], + "starts": [10], + "ends": [15], + "strand": ["+"] + })) + + mc = ut.mcols(gr) + assert isinstance(mc, BiocFrame) + assert len(mc.colnames) == 0 + + new_mc = BiocFrame({"score": [100]}) + gr = ut.set_mcols(gr, new_mc) + assert list(ut.mcols(gr).column("score")) == [100] + + meta = ut.metadata(gr) + assert meta is None or len(meta) == 0 + + gr = ut.set_metadata(gr, {"author": "AI"}) + assert ut.metadata(gr)["author"] == "AI" diff --git a/tests/test_xtfrm.py b/tests/test_xtfrm.py new file mode 100644 index 0000000..0b1ec8d --- /dev/null +++ b/tests/test_xtfrm.py @@ -0,0 +1,88 @@ +import numpy as np +import pytest +from biocutils import xtfrm, order, sort, match, duplicated, unique, Factor +from iranges import IRanges +from genomicranges import GenomicRanges +from biostrings import DNAString, DNAStringSet +from summarizedexperiment import RangedSummarizedExperiment +import biocframe + +def test_xtfrm_basic(): + x = [20, 10, 20, 30] + tx = xtfrm(x) + assert isinstance(tx, np.ndarray) + assert list(tx) == [1, 0, 1, 2] # sorted is 10, 20, 20, 30 -> ranks [1, 0, 1, 2] + + arr = np.array([1.5, -0.5, 1.5]) + t_arr = xtfrm(arr) + assert np.array_equal(t_arr, arr) + + strings = ["banana", "apple", "banana", "cherry"] + tx_str = xtfrm(strings) + assert list(tx_str) == [1, 0, 1, 2] + +def test_xtfrm_Factor(): + f = Factor.from_sequence(["B", "A", "B", "C"]) + tf = xtfrm(f) + assert np.array_equal(tf, f.get_codes()) + + assert list(order(f)) == [1, 0, 2, 3] + +def test_xtfrm_IRanges(): + ir = IRanges([10, 5, 10], [5, 8, 3]) + tx_ir = xtfrm(ir) + assert tx_ir == [(10, 5), (5, 8), (10, 3)] + + o = order(ir) + assert list(o) == [1, 2, 0] + + sir = sort(ir) + assert list(sir.get_start()) == [5, 10, 10] + assert list(sir.get_width()) == [8, 3, 5] + + targets = IRanges([5, 10], [8, 3]) + m = match(ir, targets) + assert list(m) == [-1, 0, 1] # only range 1 and range 2 are matched + + ir2 = IRanges([10, 5, 10, 5], [5, 8, 5, 8]) + assert list(duplicated(ir2)) == [False, False, True, True] + +def test_xtfrm_GenomicRanges(): + gr = GenomicRanges( + seqnames=["chr1", "chr2", "chr1"], + ranges=IRanges([10, 5, 10], [5, 8, 3]), + strand=["+", "-", "+"] + ) + tx_gr = xtfrm(gr) + assert len(tx_gr) == 3 + + o = order(gr) + assert list(o) == [2, 0, 1] + + # verify sort + sgr = sort(gr) + assert list(sgr.get_start()) == [10, 10, 5] + assert list(sgr.get_seqnames()) == ["chr1", "chr1", "chr2"] + +def test_xtfrm_DNAStringSet(): + dset = DNAStringSet(["ACGT", "TGCA", "ACGT"]) + + tx_dset = xtfrm(dset) + assert tx_dset == ["ACGT", "TGCA", "ACGT"] + + assert list(order(dset)) == [0, 2, 1] + assert list(duplicated(dset)) == [False, False, True] + +def test_xtfrm_RangedSummarizedExperiment(): + gr = GenomicRanges( + seqnames=["chr1", "chr2", "chr1"], + ranges=IRanges([10, 5, 10], [5, 8, 3]), + strand=["+", "-", "+"] + ) + rse = RangedSummarizedExperiment( + assays={"counts": np.random.rand(3, 2)}, + row_ranges=gr + ) + + assert len(xtfrm(rse)) == 3 + assert list(order(rse)) == [2, 0, 1] diff --git a/tox.ini b/tox.ini index 69f8159..d759a6a 100644 --- a/tox.ini +++ b/tox.ini @@ -1,93 +1,59 @@ -# 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. 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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} -# By default, both `sdist` and `wheel` are built. If your sdist is too big or you don't want -# to make it available, consider running: `tox -e build -- --wheel` - + 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-apidoc -f -o "{env:DOCSDIR}/api" src/ + 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. 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++++++++++--------- 6 files changed, 80 insertions(+), 58 deletions(-) diff --git a/.coveragerc b/.coveragerc index a920d99..7235976 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,13 +1,28 @@ +# .coveragerc to control coverage.py [run] +branch = True source = src omit = tests/* +[paths] +source = + src/ + */site-packages/ + [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: + if self\.debug + + # Don't complain if tests don't hit defensive assertion code: raise AssertionError raise NotImplementedError + + # Don't complain if non-runnable code isn't run: if 0: if __name__ == .__main__.: diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index d638c47..e940068 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -9,7 +9,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - uses: actions/setup-python@v5 with: python-version: '3.12' diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 3e93b84..55ba836 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -9,12 +9,7 @@ jobs: name: Build and Test runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - - name: Set up uv - uses: astral-sh/setup-uv@v5 - with: - enable-cache: true + - uses: actions/checkout@v7 - name: Set up Python 3.12 uses: actions/setup-python@v5 @@ -22,7 +17,7 @@ jobs: python-version: 3.12 - name: Install tox - run: uv tool install tox --with tox-uv + run: python -m pip install tox - name: Test run: tox -e default @@ -40,12 +35,7 @@ jobs: name: Build Documentation runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - - name: Set up uv - uses: astral-sh/setup-uv@v5 - with: - enable-cache: true + - uses: actions/checkout@v7 - name: Set up Python 3.12 uses: actions/setup-python@v5 @@ -53,7 +43,7 @@ jobs: python-version: 3.12 - name: Install tox - run: uv tool install tox --with tox-uv + run: python -m pip install tox - name: Build docs run: tox -e docs @@ -62,7 +52,7 @@ jobs: run: touch ./docs/_build/html/.nojekyll - name: Upload Pages artifact - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-pages-artifact@v5 with: path: ./docs/_build/html @@ -77,7 +67,7 @@ jobs: id-token: write # IMPORTANT: mandatory for trusted publishing steps: - name: Download all the dists - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 with: name: python-package-distributions path: dist/ @@ -98,4 +88,4 @@ jobs: steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v4 + uses: actions/deploy-pages@v5 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 662c96f..a1112f1 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -36,12 +36,7 @@ jobs: runs-on: ${{ matrix.platform }} name: Python ${{ matrix.python }}, ${{ matrix.platform }} steps: - - uses: actions/checkout@v4 - - - name: Set up uv - uses: astral-sh/setup-uv@v5 - with: - enable-cache: true + - uses: actions/checkout@v7 - name: Set up Python uses: actions/setup-python@v5 @@ -49,14 +44,12 @@ jobs: python-version: ${{ matrix.python }} - name: Install tox - run: uv tool install tox --with tox-uv - - - name: Install dependencies - run: uv sync --all-extras --python ${{ matrix.python }} + run: python -m pip install tox coverage - name: Run tests run: | - tox -e default -- --cov --cov-branch --cov-report=xml + tox \ + -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml # pytest args - name: Check for codecov token availability id: codecov-check @@ -69,9 +62,9 @@ jobs: fi - name: Upload coverage reports to Codecov with GitHub Action - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@v7 if: ${{ steps.codecov-check.outputs.codecov == 'true' }} - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + with: + token: ${{ secrets.CODECOV_TOKEN }} slug: ${{ github.repository }} flags: ${{ matrix.platform }} - py${{ matrix.python }} diff --git a/pyproject.toml b/pyproject.toml index 3f487b3..f2c970b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,14 +9,47 @@ authors = [ { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" }, ] requires-python = ">=3.12" +keywords = [ + "bioinformatics", +] +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 = [ "importlib-metadata>=9.0.0 ; python_full_version < '3.8'", "numpy>=2.5.2", ] + +[project.license] +file = "LICENSE.txt" + + +[project.urls] +Homepage = "https://github.com/BiocPy/biocutils" +Documentation = "https://biocpy.github.io/biocutils/" +Source = "https://github.com/BiocPy/biocutils" +"Bug Tracker" = "https://github.com/BiocPy/biocutils/issues" + [project.optional-dependencies] testing = [ "pandas>=3.0.5", + "biocframe", + "iranges", "pytest>=9.1.1", "pytest-cov>=7.1.0", "scipy>=1.18.1", @@ -70,15 +103,3 @@ addopts = "--cov --cov-report term-missing" testpaths = [ "tests", ] - -[dependency-groups] -dev = [ - "pytest", - "pytest-cov", - "sphinx", - "myst-nb", - "furo", - "sphinx-autodoc-typehints", - "linkify-it-py", - "mypy", -] diff --git a/tox.ini b/tox.ini index d759a6a..828f4db 100644 --- a/tox.ini +++ b/tox.ini @@ -1,4 +1,4 @@ -# Tox configuration file using uv as the backend runner +# Tox configuration file # Read more under https://tox.wiki/ [tox] @@ -7,53 +7,56 @@ envlist = default [testenv] description = Invoke pytest to run automated tests -allowlist_externals = uv -skip_install = True +extras = testing commands = - uv run --all-extras pytest {posargs} + pytest {posargs} [testenv:typecheck] description = Run static type checking with mypy -skip_install = True +deps = mypy commands = - uv run --all-extras mypy src/ + mypy src/ [testenv:lint] description = Perform static analysis and style checks +deps = ruff skip_install = True commands = - uv run ruff check {posargs:.} - uv run ruff format --check {posargs:.} + ruff check {posargs:.} + ruff format --check {posargs:.} [testenv:{build,clean}] description = build: Build the package clean: Remove old distribution files +deps = build skip_install = True 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: uv build {posargs} + build: python -m 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 +deps = + -r {toxinidir}/docs/requirements.txt setenv = DOCSDIR = {toxinidir}/docs BUILDDIR = {toxinidir}/docs/_build docs: BUILD = html doctests: BUILD = doctest linkcheck: BUILD = linkcheck -skip_install = True commands = - uv run sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/ - uv run sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs} + sphinx-apidoc -f -o "{env:DOCSDIR}/api" src/ + 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. skip_install = True +deps = twine commands = - uv publish {posargs:dist/*} + python -m twine upload {posargs:dist/*} From 41ba24d8912ec3964afd9e7d87fed28152b0de19 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Sep 2026 06:01:43 +0000 Subject: [PATCH 03/14] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .github/workflows/publish-pypi.yml | 2 +- docs/requirements.txt | 4 +- src/biocutils/BooleanList.py | 13 +++--- src/biocutils/Factor.py | 34 +++++++------- src/biocutils/FloatList.py | 13 +++--- src/biocutils/IntegerList.py | 13 +++--- src/biocutils/NamedList.py | 41 ++++++++--------- src/biocutils/Names.py | 25 ++++++----- src/biocutils/StringList.py | 13 +++--- src/biocutils/__init__.py | 67 ++++++++++++---------------- src/biocutils/assign.py | 3 +- src/biocutils/assign_rows.py | 3 +- src/biocutils/assign_sequence.py | 5 ++- src/biocutils/biocobject.py | 8 ++-- src/biocutils/duplicated.py | 11 +++-- src/biocutils/factorize.py | 10 ++--- src/biocutils/intersect.py | 2 +- src/biocutils/is_list_of_type.py | 6 +-- src/biocutils/map_to_index.py | 3 +- src/biocutils/match.py | 21 ++++----- src/biocutils/mcols.py | 4 ++ src/biocutils/melt.py | 6 ++- src/biocutils/normalize_subscript.py | 7 +-- src/biocutils/order.py | 15 ++++--- src/biocutils/package_utils.py | 2 - src/biocutils/pminmax.py | 11 +++-- src/biocutils/print_truncated.py | 10 ++--- src/biocutils/print_wrapped_table.py | 18 ++++---- src/biocutils/relist.py | 10 +++-- src/biocutils/reverse_index.py | 2 +- src/biocutils/rle.py | 6 ++- src/biocutils/setdiff.py | 4 +- src/biocutils/show_as_cell.py | 5 ++- src/biocutils/split.py | 7 +-- src/biocutils/subset.py | 3 +- src/biocutils/subset_rows.py | 3 +- src/biocutils/subset_sequence.py | 5 ++- src/biocutils/table.py | 2 +- src/biocutils/union.py | 2 +- src/biocutils/unlist.py | 5 ++- src/biocutils/which.py | 4 +- tests/test_new_generics.py | 14 +++--- tests/test_xtfrm.py | 6 +-- 43 files changed, 233 insertions(+), 215 deletions(-) diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml index 55ba836..8ebe519 100644 --- a/.github/workflows/publish-pypi.yml +++ b/.github/workflows/publish-pypi.yml @@ -71,7 +71,7 @@ jobs: with: name: python-package-distributions path: dist/ - + - name: Publish package to PyPI uses: pypa/gh-action-pypi-publish@release/v1 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/biocutils/BooleanList.py b/src/biocutils/BooleanList.py index 12a32f7..67b0a64 100644 --- a/src/biocutils/BooleanList.py +++ b/src/biocutils/BooleanList.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import Any, Iterable, Optional, Sequence, Union +from collections.abc import Iterable, Sequence +from typing import Any from .NamedList import NamedList from .Names import Names @@ -23,7 +24,7 @@ def __init__(self, data: Sequence) -> None: """ self._data = data - def __getitem__(self, index: int) -> Optional[bool]: + def __getitem__(self, index: int) -> bool | None: """Get an item and coerce it to boolean. Args: @@ -46,8 +47,8 @@ class BooleanList(NamedList): def __init__( self, - data: Optional[Sequence] = None, - names: Optional[Names] = None, + data: Sequence | None = None, + names: Names | None = None, _validate: bool = True, ): """ @@ -76,7 +77,7 @@ def __init__( super().__init__(data, names, _validate=_validate) - def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList: + def set_value(self, index: int | str, value: Any, in_place: bool = False) -> BooleanList: """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a boolean.""" return super().set_value(index, _coerce_to_bool(value), in_place=in_place) @@ -84,7 +85,7 @@ def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = Fal """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to booleans.""" return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place) - def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> BooleanList: + def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> BooleanList: """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a boolean.""" return super().safe_insert(index, _coerce_to_bool(value), in_place=in_place) diff --git a/src/biocutils/Factor.py b/src/biocutils/Factor.py index dda0175..3b998d3 100644 --- a/src/biocutils/Factor.py +++ b/src/biocutils/Factor.py @@ -1,8 +1,8 @@ from __future__ import annotations import warnings +from collections.abc import Sequence from copy import copy, deepcopy -from typing import Optional, Sequence, Union import numpy @@ -80,7 +80,7 @@ def __iter__(self) -> FactorIterator: """ return self - def __next__(self) -> Union[str, None]: + def __next__(self) -> str | None: """ Returns: Level corresponding to the code at the current position, or None @@ -104,10 +104,10 @@ class Factor: def __init__( self, - codes: Union[numpy.ndarray, Sequence[int]], - levels: Union[StringList, Sequence[str]], + codes: numpy.ndarray | Sequence[int], + levels: StringList | Sequence[str], ordered: bool = False, - names: Optional[Union[Names, Sequence[str]]] = None, + names: Names | Sequence[str] | None = None, _validate: bool = True, ): """Initialize a Factor object. @@ -248,7 +248,7 @@ def names(self) -> Names: """Alias for :py:meth:`~get_names`.""" return self.get_names() - def set_names(self, names: Optional[Names], in_place: bool = False) -> "NamedList": + def set_names(self, names: Names | None, in_place: bool = False) -> NamedList: """ Args: names: @@ -343,7 +343,7 @@ def __eq__(self, other: Factor): #####>>>> Slicing <<<<##### ########################### - def get_value(self, index: Union[str, int]) -> Union[str, None]: + def get_value(self, index: str | int) -> str | None: """ Args: index: @@ -382,7 +382,7 @@ def get_slice(self, index: SubscriptTypes) -> Factor: output._names = subset_sequence(self._names, index) return output - def __getitem__(self, index: SubscriptTypes) -> Union[str, Factor]: + def __getitem__(self, index: SubscriptTypes) -> str | Factor: """ If ``index`` is a scalar, this is an alias for :py:meth:`~get_value`. @@ -394,7 +394,7 @@ def __getitem__(self, index: SubscriptTypes) -> Union[str, Factor]: else: return self.get_slice(NormalizedSubscript(index)) - def set_value(self, index: Union[str, int], value: Union[str, None], in_place: bool = False) -> Factor: + def set_value(self, index: str | int, value: str | None, in_place: bool = False) -> Factor: """ Args: index: @@ -484,7 +484,7 @@ def set_slice(self, index: SubscriptTypes, value: Factor, in_place: bool = False return output - def __setitem__(self, index: SubscriptTypes, value: Union[str, Factor]): + def __setitem__(self, index: SubscriptTypes, value: str | Factor): """ If ``index`` is a scalar, this is an alias for :py:meth:`~set_value`. @@ -590,7 +590,7 @@ def replace_levels( output._levels = new_levels return output - def set_levels(self, levels: Union[str, Sequence[str]], remap: bool = True, in_place: bool = False) -> Factor: + def set_levels(self, levels: str | Sequence[str], remap: bool = True, in_place: bool = False) -> Factor: """ Alias for :py:meth:`~remap_levels` if ``remap = True``, otherwise an alias for :py:meth:`~replace_levels`. The first alias is deprecated and @@ -602,7 +602,7 @@ def set_levels(self, levels: Union[str, Sequence[str]], remap: bool = True, in_p else: return self.replace_levels(levels, in_place=in_place) - def remap_levels(self, levels: Union[str, Sequence[str]], in_place: bool = False) -> Factor: + def remap_levels(self, levels: str | Sequence[str], in_place: bool = False) -> Factor: """Remap codes to a replacement list of levels. Each entry of the remapped ``Factor`` will refer to the same string across the old and new levels, provided that string is present in both sets of levels. @@ -725,10 +725,10 @@ def to_pandas(self): @staticmethod def from_sequence( x: Sequence[str], - levels: Optional[Sequence[str]] = None, + levels: Sequence[str] | None = None, sort_levels: bool = True, ordered: bool = False, - names: Optional[Sequence[str]] = None, + names: Sequence[str] | None = None, **kwargs, ) -> Factor: """Convert a sequence of hashable values into a factor. @@ -778,7 +778,7 @@ def as_list(self) -> list: """ return [self._levels[c] if c >= 0 else None for c in self._codes] - def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) -> Factor: + def safe_delete(self, index: int | str | slice, in_place: bool = False) -> Factor: """ Args: index: @@ -812,11 +812,11 @@ def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) -> return output - def delete(self, index: Union[int, str, slice]): + def delete(self, index: int | str | slice): """Alias for :py:meth:`~safe_delete` with ``in_place = True``.""" self.safe_delete(index, in_place=True) - def __delitem__(self, index: Union[int, str, slice]): + def __delitem__(self, index: int | str | slice): """Alias for :py:meth:`~delete`.""" self.delete(index) diff --git a/src/biocutils/FloatList.py b/src/biocutils/FloatList.py index 5ddd4cc..417c62e 100644 --- a/src/biocutils/FloatList.py +++ b/src/biocutils/FloatList.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import Any, Iterable, Optional, Sequence, Union +from collections.abc import Iterable, Sequence +from typing import Any from .NamedList import NamedList from .Names import Names @@ -27,7 +28,7 @@ def __init__(self, data: Sequence) -> None: """ self._data = data - def __getitem__(self, index: int) -> Optional[float]: + def __getitem__(self, index: int) -> float | None: """Get an item and coerce it to float. Args: @@ -49,8 +50,8 @@ class FloatList(NamedList): def __init__( self, - data: Optional[Sequence] = None, - names: Optional[Names] = None, + data: Sequence | None = None, + names: Names | None = None, _validate: bool = True, ): """ @@ -79,7 +80,7 @@ def __init__( super().__init__(data, names, _validate=_validate) - def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> FloatList: + def set_value(self, index: int | str, value: Any, in_place: bool = False) -> FloatList: """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a float.""" return super().set_value(index, _coerce_to_float(value), in_place=in_place) @@ -87,7 +88,7 @@ def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = Fal """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to floats.""" return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place) - def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> FloatList: + def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> FloatList: """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a float.""" return super().safe_insert(index, _coerce_to_float(value), in_place=in_place) diff --git a/src/biocutils/IntegerList.py b/src/biocutils/IntegerList.py index a88e726..68ca0cd 100644 --- a/src/biocutils/IntegerList.py +++ b/src/biocutils/IntegerList.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import Any, Iterable, Optional, Sequence, Union +from collections.abc import Iterable, Sequence +from typing import Any from .NamedList import NamedList from .Names import Names @@ -28,7 +29,7 @@ def __init__(self, data: Sequence) -> None: """ self._data = data - def __getitem__(self, index: int) -> Optional[int]: + def __getitem__(self, index: int) -> int | None: """Get an item and coerce it to integer. Args: @@ -51,8 +52,8 @@ class IntegerList(NamedList): def __init__( self, - data: Optional[Sequence] = None, - names: Optional[Names] = None, + data: Sequence | None = None, + names: Names | None = None, _validate: bool = True, ): """ @@ -80,7 +81,7 @@ def __init__( data = list(_coerce_to_int(item) for item in original) super().__init__(data, names, _validate=_validate) - def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> IntegerList: + def set_value(self, index: int | str, value: Any, in_place: bool = False) -> IntegerList: """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a integer.""" return super().set_value(index, _coerce_to_int(value), in_place=in_place) @@ -88,7 +89,7 @@ def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = Fal """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to integers.""" return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place) - def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> IntegerList: + def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> IntegerList: """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a integer.""" return super().safe_insert(index, _coerce_to_int(value), in_place=in_place) diff --git a/src/biocutils/NamedList.py b/src/biocutils/NamedList.py index d421924..fc0cb95 100644 --- a/src/biocutils/NamedList.py +++ b/src/biocutils/NamedList.py @@ -1,7 +1,8 @@ from __future__ import annotations +from collections.abc import Iterable, Sequence from copy import deepcopy -from typing import Any, Dict, Iterable, Optional, Sequence, Tuple, Union +from typing import Any from .assign_sequence import assign_sequence from .combine_sequences import combine_sequences @@ -23,8 +24,8 @@ class NamedList: def __init__( self, - data: Optional[Sequence] = None, - names: Optional[Names] = None, + data: Sequence | None = None, + names: Names | None = None, _validate: bool = True, ): """ @@ -68,7 +69,7 @@ def __len__(self) -> int: """ return len(self._data) - def __iter__(self) -> "list_iterator": + def __iter__(self) -> list_iterator: """ Returns: An iterator on the underlying list of data. @@ -114,7 +115,7 @@ def __eq__(self, other: NamedList) -> bool: #####>>>> Get/set names <<<<##### ################################# - def get_names(self) -> Optional[Names]: + def get_names(self) -> Names | None: """ Returns: Names for the list elements. @@ -125,14 +126,14 @@ def get_names(self) -> Optional[Names]: return self._names @property - def names(self) -> Optional[Names]: + def names(self) -> Names | None: """Alias for :py:meth:`~get_names`.""" return self.get_names() def _shallow_copy(self): return type(self)(self._data, self._names, _validate=False) - def set_names(self, names: Optional[Names], in_place: bool = False) -> NamedList: + def set_names(self, names: Names | None, in_place: bool = False) -> NamedList: """ Args: names: @@ -153,7 +154,7 @@ def set_names(self, names: Optional[Names], in_place: bool = False) -> NamedList output._names = _sanitize_names(names, len(self)) return output - def get_name(self, index: int) -> Optional[str]: + def get_name(self, index: int) -> str | None: """Get name at an index. Args: @@ -171,7 +172,7 @@ def get_name(self, index: int) -> Optional[str]: #####>>>> Get/set items <<<<##### ################################# - def get_value(self, index: Union[str, int]) -> Any: + def get_value(self, index: str | int) -> Any: """Get value at an index. Args: @@ -207,7 +208,7 @@ def get_slice(self, index: SubscriptTypes) -> NamedList: outnames = subset_sequence(self._names, index) return type(self)(outdata, outnames, _validate=False) - def __getitem__(self, index: SubscriptTypes) -> Union[NamedList, Any]: + def __getitem__(self, index: SubscriptTypes) -> NamedList | Any: """ If ``index`` is a scalar, this is an alias for :py:meth:`~get_value`. @@ -219,7 +220,7 @@ def __getitem__(self, index: SubscriptTypes) -> Union[NamedList, Any]: else: return self.get_slice(NormalizedSubscript(index)) - def set_value(self, index: Union[str, int], value: Any, in_place: bool = False) -> NamedList: + def set_value(self, index: str | int, value: Any, in_place: bool = False) -> NamedList: """ Args: index: @@ -335,7 +336,7 @@ def _define_output(self, in_place: bool) -> NamedList: else: return self.copy() - def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> NamedList: + def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> NamedList: """ Args: index: @@ -363,7 +364,7 @@ def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False output._names.insert(index, "") return output - def insert(self, index: Union[int, str], value: Any): + def insert(self, index: int | str, value: Any): """Alias for :py:meth:`~safe_insert` with ``in_place = True``.""" self.safe_insert(index, value, in_place=True) @@ -435,7 +436,7 @@ def __iadd__(self, other: list): self.extend(other) return self - def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) -> NamedList: + def safe_delete(self, index: int | str | slice, in_place: bool = False) -> NamedList: """ Args: index: @@ -468,11 +469,11 @@ def safe_delete(self, index: Union[int, str, slice], in_place: bool = False) -> return output - def delete(self, index: Union[int, str, slice]): + def delete(self, index: int | str | slice): """Alias for :py:meth:`~safe_delete` with ``in_place = True``.""" self.safe_delete(index, in_place=True) - def __delitem__(self, index: Union[int, str, slice]): + def __delitem__(self, index: int | str | slice): """Alias for :py:meth:`~delete`.""" self.delete(index) @@ -496,7 +497,7 @@ def values(self) -> Iterable[Any]: """ return iter(self._data) - def items(self) -> Iterable[Tuple[str, Any]]: + def items(self) -> Iterable[tuple[str, Any]]: """ Returns: Iterator over (name, value) pairs. @@ -507,7 +508,7 @@ def items(self) -> Iterable[Tuple[str, Any]]: else: return zip((str(i) for i in range(len(self))), self._data) - def get(self, key: Union[str, int], default: Any = None) -> Any: + def get(self, key: str | int, default: Any = None) -> Any: """ Args: key: @@ -576,7 +577,7 @@ def as_list(self) -> list: """ return self._data - def as_dict(self) -> Dict[str, Any]: + def as_dict(self) -> dict[str, Any]: """ Returns: A dictionary where the keys are the names and the values are the @@ -611,7 +612,7 @@ def from_dict(cls, x: dict) -> NamedList: A instance where the list elements are the values of ``x`` and the names are the stringified keys. """ - return cls(list(x.values()), names=Names(str(y) for y in x.keys())) + return cls(list(x.values()), names=Names(str(y) for y in x)) @subset_sequence.register diff --git a/src/biocutils/Names.py b/src/biocutils/Names.py index 1047f79..f869175 100644 --- a/src/biocutils/Names.py +++ b/src/biocutils/Names.py @@ -1,7 +1,8 @@ from __future__ import annotations +from collections.abc import Callable, Iterable, Sequence from copy import deepcopy -from typing import Any, Callable, Iterable, List, Optional, Sequence, Union +from typing import Any, Union from .assign_sequence import assign_sequence from .combine_sequences import combine_sequences @@ -18,7 +19,7 @@ class Names: such that callers can get or set elements by name instead of position. """ - def __init__(self, names: Optional[Iterable] = None, _validate: bool = True): + def __init__(self, names: Iterable | None = None, _validate: bool = True): """ Args: names: @@ -63,7 +64,7 @@ def __len__(self) -> int: """ return len(self._names) - def __iter__(self) -> "list_iterator": + def __iter__(self) -> list_iterator: """ Returns: An iterator on the underlying list of names. @@ -96,7 +97,7 @@ def __eq__(self, other: Names) -> bool: return False return self._names == other._names - def as_list(self) -> List[str]: + def as_list(self) -> list[str]: """ Returns: List of strings containing the names. @@ -160,7 +161,7 @@ def get_slice(self, index: SubscriptTypes) -> Names: index, scalar = normalize_subscript(index, len(self), None) return type(self)(subset_sequence(self._names, index), _validate=False) - def __getitem__(self, index: SubscriptTypes) -> Union[str, Names]: + def __getitem__(self, index: SubscriptTypes) -> str | Names: """ If ``index`` is a scalar, this is an alias for :py:attr:`~get_value`. @@ -339,7 +340,7 @@ def __iadd__(self, other: list): self.extend(other) return self - def safe_delete(self, index: Union[int, slice], in_place: bool = False) -> Names: + def safe_delete(self, index: int | slice, in_place: bool = False) -> Names: """ Args: index: @@ -360,11 +361,11 @@ def safe_delete(self, index: Union[int, slice], in_place: bool = False) -> Names del output._names[index] return output - def delete(self, index: Union[int, slice]): + def delete(self, index: int | slice): """Alias for :py:attr:`~safe_delete` with ``in_place = True``.""" self.safe_delete(index, in_place=True) - def __delitem__(self, index: Union[int, slice]): + def __delitem__(self, index: int | slice): """Alias for :py:attr:`~delete`.""" self.delete(index) @@ -427,7 +428,7 @@ def _combine_sequences_Names(*x: Names) -> Names: return output -def _name_to_position(names: Optional[Names], index: str) -> int: +def _name_to_position(names: Names | None, index: str) -> int: i = -1 if names is not None: i = names.map(index) @@ -436,14 +437,14 @@ def _name_to_position(names: Optional[Names], index: str) -> int: return i -def _validate_names(names: Optional[Names], length: int) -> bool: +def _validate_names(names: Names | None, length: int) -> bool: if names is not None and len(names) != length: raise ValueError("length of 'names' must be equal to number of entries (" + str(length) + ")") return True -def _sanitize_names(names: Optional[Names], length: int) -> Optional[Names]: +def _sanitize_names(names: Names | None, length: int) -> Names | None: if names is None: return names if not isinstance(names, Names): @@ -453,7 +454,7 @@ def _sanitize_names(names: Optional[Names], length: int) -> Optional[Names]: return names -def _combine_names(*x: Any, get_names: Callable) -> Optional[Names]: +def _combine_names(*x: Any, get_names: Callable) -> Names | None: all_names = [] has_names = False for y in x: diff --git a/src/biocutils/StringList.py b/src/biocutils/StringList.py index dee7f17..95a34e3 100644 --- a/src/biocutils/StringList.py +++ b/src/biocutils/StringList.py @@ -1,6 +1,7 @@ from __future__ import annotations -from typing import Any, Iterable, Optional, Sequence, Union +from collections.abc import Iterable, Sequence +from typing import Any from .NamedList import NamedList from .Names import Names @@ -22,7 +23,7 @@ def __init__(self, data: Sequence) -> None: """ self._data = data - def __getitem__(self, index: int) -> Optional[str]: + def __getitem__(self, index: int) -> str | None: """Get an item and coerce it to string. Args: @@ -44,8 +45,8 @@ class StringList(NamedList): def __init__( self, - data: Optional[Sequence] = None, - names: Optional[Names] = None, + data: Sequence | None = None, + names: Names | None = None, _validate: bool = True, ): """ @@ -73,7 +74,7 @@ def __init__( data = list(_coerce_to_str(item) for item in original) super().__init__(data, names, _validate=_validate) - def set_value(self, index: Union[int, str], value: Any, in_place: bool = False) -> StringList: + def set_value(self, index: int | str, value: Any, in_place: bool = False) -> StringList: """Calls :py:meth:`~biocutils.NamedList.NamedList.set_value` after coercing ``value`` to a string.""" return super().set_value(index, _coerce_to_str(value), in_place=in_place) @@ -81,7 +82,7 @@ def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = Fal """Calls :py:meth:`~biocutils.NamedList.NamedList.set_slice` after coercing ``value`` to strings.""" return super().set_slice(index, _SubscriptCoercer(value), in_place=in_place) - def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> StringList: + def safe_insert(self, index: int | str, value: Any, in_place: bool = False) -> StringList: """Calls :py:meth:`~biocutils.NamedList.NamedList.safe_insert` after coercing ``value`` to a string.""" return super().safe_insert(index, _coerce_to_str(value), in_place=in_place) diff --git a/src/biocutils/__init__.py b/src/biocutils/__init__.py index 7900178..d03693e 100644 --- a/src/biocutils/__init__.py +++ b/src/biocutils/__init__.py @@ -15,56 +15,45 @@ finally: del version, PackageNotFoundError -from .Factor import Factor -from .StringList import StringList -from .IntegerList import IntegerList -from .FloatList import FloatList +from .assign import assign +from .assign_rows import assign_rows +from .assign_sequence import assign_sequence +from .biocobject import BiocObject from .BooleanList import BooleanList -from .Names import Names -from .NamedList import NamedList - +from .combine import combine +from .combine_columns import combine_columns +from .combine_rows import combine_rows +from .combine_sequences import combine_sequences +from .convert_to_dense import convert_to_dense +from .duplicated import duplicated, unique +from .extract_column_names import extract_column_names +from .extract_row_names import extract_row_names +from .Factor import Factor from .factorize import factorize +from .FloatList import FloatList +from .get_height import get_height +from .IntegerList import IntegerList from .intersect import intersect +from .is_high_dimensional import is_high_dimensional from .is_list_of_type import is_list_of_type from .is_missing_scalar import is_missing_scalar from .map_to_index import map_to_index -from .match import match, create_match_index, MatchIndex -from .normalize_subscript import normalize_subscript, SubscriptTypes +from .match import MatchIndex, create_match_index, match +from .NamedList import NamedList +from .Names import Names +from .normalize_subscript import SubscriptTypes, normalize_subscript +from .order import order, sort from .print_truncated import print_truncated, print_truncated_dict, print_truncated_list from .print_wrapped_table import create_floating_names, print_type, print_wrapped_table, truncate_strings -from .setdiff import setdiff -from .union import union - -from .combine import combine -from .combine_rows import combine_rows -from .combine_columns import combine_columns -from .combine_sequences import combine_sequences - from .relaxed_combine_columns import relaxed_combine_columns from .relaxed_combine_rows import relaxed_combine_rows - -from .extract_row_names import extract_row_names -from .extract_column_names import extract_column_names - +from .setdiff import setdiff +from .show_as_cell import show_as_cell +from .split import split +from .StringList import StringList from .subset import subset from .subset_rows import subset_rows from .subset_sequence import subset_sequence - -from .which import which - -from .assign import assign -from .assign_rows import assign_rows -from .assign_sequence import assign_sequence - -from .show_as_cell import show_as_cell -from .convert_to_dense import convert_to_dense - -from .get_height import get_height -from .is_high_dimensional import is_high_dimensional - -from .biocobject import BiocObject from .table import table - -from .order import order, sort -from .duplicated import duplicated, unique -from .split import split +from .union import union +from .which import which diff --git a/src/biocutils/assign.py b/src/biocutils/assign.py index 875033d..abe8add 100644 --- a/src/biocutils/assign.py +++ b/src/biocutils/assign.py @@ -1,4 +1,5 @@ -from typing import Any, Sequence +from collections.abc import Sequence +from typing import Any from .assign_rows import assign_rows from .assign_sequence import assign_sequence diff --git a/src/biocutils/assign_rows.py b/src/biocutils/assign_rows.py index ada797b..7c4e146 100644 --- a/src/biocutils/assign_rows.py +++ b/src/biocutils/assign_rows.py @@ -1,6 +1,7 @@ +from collections.abc import Sequence from copy import deepcopy from functools import singledispatch -from typing import Any, Sequence +from typing import Any import numpy diff --git a/src/biocutils/assign_sequence.py b/src/biocutils/assign_sequence.py index d6b23d8..cd73d24 100644 --- a/src/biocutils/assign_sequence.py +++ b/src/biocutils/assign_sequence.py @@ -1,6 +1,7 @@ +from collections.abc import Sequence from copy import deepcopy from functools import singledispatch -from typing import Any, Sequence, Union +from typing import Any import numpy @@ -48,7 +49,7 @@ def _assign_sequence_numpy(x: numpy.ndarray, indices: Sequence[int], replacement @assign_sequence.register -def _assign_sequence_range(x: range, indices: Sequence[int], replacement: Any) -> Union[range, list]: +def _assign_sequence_range(x: range, indices: Sequence[int], replacement: Any) -> range | list: if ( isinstance(replacement, range) and isinstance(indices, range) diff --git a/src/biocutils/biocobject.py b/src/biocutils/biocobject.py index 422b7a6..5d17fad 100644 --- a/src/biocutils/biocobject.py +++ b/src/biocutils/biocobject.py @@ -1,7 +1,7 @@ from __future__ import annotations import copy -from typing import Any, Dict, Optional, Union +from typing import Any from warnings import warn from .NamedList import NamedList @@ -40,7 +40,7 @@ class BiocObject: Provides a standardized `metadata` slot and copy-on-write semantics. """ - def __init__(self, metadata: Optional[Union[Dict[str, Any], NamedList]] = None, _validate: bool = True) -> None: + def __init__(self, metadata: dict[str, Any] | NamedList | None = None, _validate: bool = True) -> None: """Initialize the BiocObject. Args: @@ -82,7 +82,7 @@ def metadata(self) -> NamedList: return self._metadata @metadata.setter - def metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]]) -> None: + def metadata(self, metadata: dict[str, Any] | NamedList | None) -> None: """Set metadata in-place.""" warn( "Setting property 'metadata' is an in-place operation, use 'set_metadata' instead", @@ -94,7 +94,7 @@ def get_metadata(self) -> NamedList: """Alias for :py:attr:`~metadata` getter.""" return self.metadata - def set_metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]], in_place: bool = False) -> BiocObject: + def set_metadata(self, metadata: dict[str, Any] | NamedList | None, in_place: bool = False) -> BiocObject: """Set new metadata. Args: diff --git a/src/biocutils/duplicated.py b/src/biocutils/duplicated.py index 303af2a..8202cea 100644 --- a/src/biocutils/duplicated.py +++ b/src/biocutils/duplicated.py @@ -1,5 +1,6 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, Sequence, Union +from typing import Any import numpy @@ -8,7 +9,7 @@ @singledispatch -def duplicated(x: Any, incomparables: Union[set, Sequence] = set(), from_last: bool = False) -> numpy.ndarray: +def duplicated(x: Any, incomparables: set | Sequence = set(), from_last: bool = False) -> numpy.ndarray: """ Find duplicated elements of ``x``. @@ -101,9 +102,7 @@ def process(i, y): @duplicated.register -def _duplicated_Factor( - x: Factor, incomparables: Union[set, Sequence] = set(), from_last: bool = False -) -> numpy.ndarray: +def _duplicated_Factor(x: Factor, incomparables: set | Sequence = set(), from_last: bool = False) -> numpy.ndarray: present = [] for lev in x.get_levels(): if lev in incomparables: @@ -140,7 +139,7 @@ def process(i, y): return output -def unique(x: Any, incomparables: Union[set, Sequence] = set(), from_last: bool = False) -> Any: +def unique(x: Any, incomparables: set | Sequence = set(), from_last: bool = False) -> Any: """ Get all unique values of ``x``. diff --git a/src/biocutils/factorize.py b/src/biocutils/factorize.py index 904d24d..b1ef2dd 100644 --- a/src/biocutils/factorize.py +++ b/src/biocutils/factorize.py @@ -1,4 +1,4 @@ -from typing import Optional, Sequence, Tuple +from collections.abc import Sequence import numpy @@ -8,11 +8,11 @@ def factorize( x: Sequence, - levels: Optional[Sequence] = None, + levels: Sequence | None = None, sort_levels: bool = False, - dtype: Optional[numpy.dtype] = None, - fail_missing: Optional[bool] = None, -) -> Tuple[list, numpy.ndarray]: + dtype: numpy.dtype | None = None, + fail_missing: bool | None = None, +) -> tuple[list, numpy.ndarray]: """Convert a sequence of hashable values into a factor. Args: diff --git a/src/biocutils/intersect.py b/src/biocutils/intersect.py index f441492..7b0f5cf 100644 --- a/src/biocutils/intersect.py +++ b/src/biocutils/intersect.py @@ -1,4 +1,4 @@ -from typing import Sequence +from collections.abc import Sequence from .is_missing_scalar import is_missing_scalar from .map_to_index import DUPLICATE_METHOD diff --git a/src/biocutils/is_list_of_type.py b/src/biocutils/is_list_of_type.py index 5f0ff54..1410fe0 100644 --- a/src/biocutils/is_list_of_type.py +++ b/src/biocutils/is_list_of_type.py @@ -1,14 +1,14 @@ -from typing import Callable, Union +from collections.abc import Callable import numpy as np -import numpy.ma as ma +from numpy import ma __author__ = "jkanche" __copyright__ = "jkanche" __license__ = "MIT" -def is_list_of_type(x: Union[list, tuple], target_type: Callable, ignore_none: bool = False) -> bool: +def is_list_of_type(x: list | tuple, target_type: Callable, ignore_none: bool = False) -> bool: """Checks if ``x`` is a list, and whether all elements of the list are of the same type. Args: diff --git a/src/biocutils/map_to_index.py b/src/biocutils/map_to_index.py index fc50b6d..22eca0f 100644 --- a/src/biocutils/map_to_index.py +++ b/src/biocutils/map_to_index.py @@ -1,4 +1,5 @@ -from typing import Literal, Sequence +from collections.abc import Sequence +from typing import Literal from .is_missing_scalar import is_missing_scalar diff --git a/src/biocutils/match.py b/src/biocutils/match.py index 1ebaaf1..b9a60cc 100644 --- a/src/biocutils/match.py +++ b/src/biocutils/match.py @@ -1,5 +1,6 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, Literal, Optional, Sequence, Union +from typing import Any, Literal import numpy @@ -14,9 +15,9 @@ def __init__( self, targets: Any, duplicate_method: Literal["first", "last", "any"] = "first", - incomparables: Union[set, Sequence] = set(), - dtype: Optional[numpy.dtype] = None, - fail_missing: Optional[bool] = None, + incomparables: set | Sequence = set(), + dtype: numpy.dtype | None = None, + fail_missing: bool | None = None, ): """ Args: @@ -141,9 +142,9 @@ def match(self, x: Any) -> numpy.ndarray: def create_match_index( targets: Any, duplicate_method: Literal["first", "last", "any"] = "first", - incomparables: Union[set, Sequence] = set(), - dtype: Optional[numpy.dtype] = None, - fail_missing: Optional[bool] = None, + incomparables: set | Sequence = set(), + dtype: numpy.dtype | None = None, + fail_missing: bool | None = None, ) -> MatchIndex: """ Create a index for matching an arbitrary sequence against ``targets``. @@ -229,9 +230,9 @@ def match( x: Any, targets: Any, duplicate_method: Literal["first", "last", "any"] = "first", - incomparables: Union[set, Sequence] = set(), - dtype: Optional[numpy.dtype] = None, - fail_missing: Optional[bool] = None, + incomparables: set | Sequence = set(), + dtype: numpy.dtype | None = None, + fail_missing: bool | None = None, ) -> numpy.ndarray: """ Find a matching value of each element of ``x`` in ``targets``. diff --git a/src/biocutils/mcols.py b/src/biocutils/mcols.py index 99047fc..fa9881c 100644 --- a/src/biocutils/mcols.py +++ b/src/biocutils/mcols.py @@ -1,6 +1,7 @@ from functools import singledispatch from typing import Any + @singledispatch def mcols(x: Any) -> Any: """Retrieve metadata columns from an object. @@ -19,6 +20,7 @@ def mcols(x: Any) -> Any: return val return None + @singledispatch def set_mcols(x: Any, value: Any) -> Any: """Set or replace metadata columns on an object. @@ -42,6 +44,7 @@ def set_mcols(x: Any, value: Any) -> Any: pass raise TypeError(f"Cannot set mcols on type '{type(x).__name__}'") + @singledispatch def metadata(x: Any) -> Any: """Retrieve general metadata from an object. @@ -60,6 +63,7 @@ def metadata(x: Any) -> Any: return val return None + @singledispatch def set_metadata(x: Any, value: Any) -> Any: """Set or replace general metadata on an object. diff --git a/src/biocutils/melt.py b/src/biocutils/melt.py index b8093a0..b36e73c 100644 --- a/src/biocutils/melt.py +++ b/src/biocutils/melt.py @@ -1,7 +1,9 @@ from functools import singledispatch from typing import Any + import pandas as pd + @singledispatch def melt(x: Any, **kwargs) -> pd.DataFrame: """Melt a container into a tidy long-format pandas DataFrame. @@ -17,9 +19,9 @@ def melt(x: Any, **kwargs) -> pd.DataFrame: """ if hasattr(x, "melt"): return x.melt(**kwargs) - + if hasattr(x, "to_pandas"): df = x.to_pandas() return df.melt(**kwargs) - + raise TypeError(f"No melt implementation found for class '{type(x).__name__}'") diff --git a/src/biocutils/normalize_subscript.py b/src/biocutils/normalize_subscript.py index e41bb92..f9ad762 100644 --- a/src/biocutils/normalize_subscript.py +++ b/src/biocutils/normalize_subscript.py @@ -1,4 +1,5 @@ -from typing import Any, Optional, Sequence, Tuple, Union +from collections.abc import Sequence +from typing import Any, Union import numpy @@ -63,9 +64,9 @@ def __len__(self) -> int: def normalize_subscript( sub: SubscriptTypes, length: int, - names: Optional[Sequence[str]] = None, + names: Sequence[str] | None = None, non_negative_only: bool = True, -) -> Tuple[Sequence[int], bool]: +) -> tuple[Sequence[int], bool]: """Normalize a subscript into a sequence of integer indices. Normalize a subscript for ``__getitem__`` or friends into a sequence of diff --git a/src/biocutils/order.py b/src/biocutils/order.py index dacefca..17f9581 100644 --- a/src/biocutils/order.py +++ b/src/biocutils/order.py @@ -1,18 +1,19 @@ -from typing import Any, Union, Sequence, Optional +from collections.abc import Sequence from functools import singledispatch +from typing import Any import numpy -from .subset import subset from .Factor import Factor +from .subset import subset @singledispatch def order( x: Any, - force_last: Union[set, Sequence] = [None, numpy.ma.masked, numpy.nan], + force_last: set | Sequence = [None, numpy.ma.masked, numpy.nan], decreasing: bool = False, - dtype: Optional[numpy.dtype] = None, + dtype: numpy.dtype | None = None, ) -> numpy.ndarray: """ Obtain an ordering of entries of ``x``. @@ -150,9 +151,9 @@ def key(i): @order.register def _order_Factor( x: Factor, - force_last: Union[set, Sequence] = set([None]), + force_last: set | Sequence = set([None]), decreasing: bool = False, - dtype: Optional[numpy.dtype] = None, + dtype: numpy.dtype | None = None, ) -> numpy.ndarray: new_force_last = set() for i, lev in enumerate(x.get_levels()): @@ -166,7 +167,7 @@ def _order_Factor( @singledispatch -def sort(x: Any, force_last: Union[set, Sequence] = [None, numpy.ma.masked], decreasing: bool = False) -> Any: +def sort(x: Any, force_last: set | Sequence = [None, numpy.ma.masked], decreasing: bool = False) -> Any: """ Sort an arbitrary iterable sequence. diff --git a/src/biocutils/package_utils.py b/src/biocutils/package_utils.py index 55238e5..1f01bdc 100644 --- a/src/biocutils/package_utils.py +++ b/src/biocutils/package_utils.py @@ -21,6 +21,4 @@ def is_package_installed(package_name: str, verbose: bool = False) -> bool: if verbose: print(f"Package '{package_name}' is not installed.") - pass - return _installed diff --git a/src/biocutils/pminmax.py b/src/biocutils/pminmax.py index aea39b1..625a6b1 100644 --- a/src/biocutils/pminmax.py +++ b/src/biocutils/pminmax.py @@ -1,6 +1,8 @@ from typing import Any + import numpy as np + def pmin(*x: Any, **kwargs) -> Any: """Calculate the parallel element-wise minimum of multiple sequences. @@ -13,16 +15,17 @@ def pmin(*x: Any, **kwargs) -> Any: """ if not x: raise ValueError("Must specify at least one sequence/vector.") - + arrays = [np.asarray(item) for item in x] res = arrays[0] for arr in arrays[1:]: res = np.minimum(res, arr) - + if isinstance(x[0], (list, tuple)): return type(x[0])(res.tolist()) return res + def pmax(*x: Any, **kwargs) -> Any: """Calculate the parallel element-wise maximum of multiple sequences. @@ -35,12 +38,12 @@ def pmax(*x: Any, **kwargs) -> Any: """ if not x: raise ValueError("Must specify at least one sequence/vector.") - + arrays = [np.asarray(item) for item in x] res = arrays[0] for arr in arrays[1:]: res = np.maximum(res, arr) - + if isinstance(x[0], (list, tuple)): return type(x[0])(res.tolist()) return res diff --git a/src/biocutils/print_truncated.py b/src/biocutils/print_truncated.py index 11b529a..d2b1018 100644 --- a/src/biocutils/print_truncated.py +++ b/src/biocutils/print_truncated.py @@ -1,4 +1,4 @@ -from typing import Callable, Dict, List, Optional +from collections.abc import Callable def print_truncated(x, truncated_to: int = 3, full_threshold: int = 10) -> str: @@ -28,10 +28,10 @@ def print_truncated(x, truncated_to: int = 3, full_threshold: int = 10) -> str: def print_truncated_list( - x: List, + x: list, truncated_to: int = 3, full_threshold: int = 10, - transform: Optional[Callable] = None, + transform: Callable | None = None, sep: str = ", ", include_brackets: bool = True, ) -> str: @@ -87,10 +87,10 @@ def transform(y): def print_truncated_dict( - x: Dict, + x: dict, truncated_to: int = 3, full_threshold: int = 10, - transform: Optional[Callable] = None, + transform: Callable | None = None, sep: str = ", ", include_brackets: bool = True, ) -> str: diff --git a/src/biocutils/print_wrapped_table.py b/src/biocutils/print_wrapped_table.py index 447c8e7..20173f6 100644 --- a/src/biocutils/print_wrapped_table.py +++ b/src/biocutils/print_wrapped_table.py @@ -1,23 +1,23 @@ -from typing import Any, List, Optional, Sequence +from collections.abc import Sequence +from typing import Any import numpy from .subset_sequence import subset_sequence -def _get_max_width(col: List[str]): +def _get_max_width(col: list[str]): width = 0 for y in col: - if len(y) > width: - width = len(y) + width = max(width, len(y)) return width def print_wrapped_table( - columns: List[Sequence[str]], - floating_names: Optional[Sequence[str]] = None, + columns: list[Sequence[str]], + floating_names: Sequence[str] | None = None, sep: str = " ", - window: Optional[int] = None, + window: int | None = None, ) -> str: """Pretty-print a table with aligned and wrapped columns. All column contents are padded so that they are right- justified. Wrapping is performed whenever a new column would exceed the window width, in which case the entire @@ -102,7 +102,7 @@ def reinitialize(): return output -def create_floating_names(names: Optional[List[str]], indices: Sequence[int]) -> List[str]: +def create_floating_names(names: list[str] | None, indices: Sequence[int]) -> list[str]: """Create the floating names to use in :py:meth:`~print_wrapped_table`. If no names are present, positional indices are used instead. @@ -122,7 +122,7 @@ def create_floating_names(names: Optional[List[str]], indices: Sequence[int]) -> return ["[" + str(i) + "]" for i in indices] -def truncate_strings(values: List[str], width: int = 40) -> List[str]: +def truncate_strings(values: list[str], width: int = 40) -> list[str]: """Truncate long strings for printing in :py:meth:`~print_wrapped_table`. Args: diff --git a/src/biocutils/relist.py b/src/biocutils/relist.py index ce4ce9f..e2e2a3c 100644 --- a/src/biocutils/relist.py +++ b/src/biocutils/relist.py @@ -2,6 +2,7 @@ _relist_registry = {} + def relist(flesh: Any, skeleton: Any, **kwargs) -> Any: """Relist a flat sequence into the structure/shape of a skeleton. @@ -17,10 +18,10 @@ def relist(flesh: Any, skeleton: Any, **kwargs) -> Any: for cls in type(skeleton).__mro__: if cls in _relist_registry: return _relist_registry[cls](flesh, skeleton, **kwargs) - + if hasattr(skeleton, "relist"): return skeleton.relist(flesh, **kwargs) - + if isinstance(skeleton, (list, tuple)): res = [] curr = 0 @@ -33,13 +34,16 @@ def relist(flesh: Any, skeleton: Any, **kwargs) -> Any: res.append(flesh[curr]) curr += 1 return type(skeleton)(res) - + raise TypeError(f"No relist implementation found for skeleton type '{type(skeleton).__name__}'") + def register(cls): def decorator(func): _relist_registry[cls] = func return func + return decorator + relist.register = register diff --git a/src/biocutils/reverse_index.py b/src/biocutils/reverse_index.py index 4d1f2e0..e930711 100644 --- a/src/biocutils/reverse_index.py +++ b/src/biocutils/reverse_index.py @@ -1,4 +1,4 @@ -from typing import Sequence +from collections.abc import Sequence def build_reverse_index(obj: Sequence[str]) -> dict: diff --git a/src/biocutils/rle.py b/src/biocutils/rle.py index f8412a8..30562e8 100644 --- a/src/biocutils/rle.py +++ b/src/biocutils/rle.py @@ -1,5 +1,7 @@ +from typing import Any + import numpy as np -from typing import Any, List, Union + class Rle: def __init__(self, values: Any, lengths: Any = None): @@ -32,7 +34,7 @@ def to_numpy(self) -> np.ndarray: """Decompress Rle back to a dense numpy array.""" return np.repeat(self.values, self.lengths) - def __getitem__(self, idx: Union[int, slice]) -> Any: + def __getitem__(self, idx: int | slice) -> Any: dense = self.to_numpy() return dense[idx] diff --git a/src/biocutils/setdiff.py b/src/biocutils/setdiff.py index 1511c4b..13b0bfe 100644 --- a/src/biocutils/setdiff.py +++ b/src/biocutils/setdiff.py @@ -1,12 +1,10 @@ from collections.abc import Sequence +from functools import singledispatch from .is_missing_scalar import is_missing_scalar from .map_to_index import DUPLICATE_METHOD -from functools import singledispatch - - @singledispatch def _setdiff_internal(first: Sequence, *other: Sequence, duplicate_method: DUPLICATE_METHOD = "first") -> list: present = set() diff --git a/src/biocutils/show_as_cell.py b/src/biocutils/show_as_cell.py index 072c17f..5c4f3fb 100644 --- a/src/biocutils/show_as_cell.py +++ b/src/biocutils/show_as_cell.py @@ -1,9 +1,10 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, List, Sequence +from typing import Any @singledispatch -def show_as_cell(x: Any, indices: Sequence[int]) -> List[str]: +def show_as_cell(x: Any, indices: Sequence[int]) -> list[str]: """ Show the contents of ``x`` as a cell of a table, typically for use in the ``__str__`` method of a class that contains ``x``. diff --git a/src/biocutils/split.py b/src/biocutils/split.py index 20bb769..ccb24b5 100644 --- a/src/biocutils/split.py +++ b/src/biocutils/split.py @@ -1,5 +1,6 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, Sequence, Union +from typing import Any import numpy @@ -14,10 +15,10 @@ def split( x: Any, f: Sequence, - skip: Union[set, Sequence] = [None, numpy.ma.masked], + skip: set | Sequence = [None, numpy.ma.masked], drop: bool = False, as_NamedList: bool = False, -) -> Union[dict, NamedList]: +) -> dict | NamedList: """ Split a sequence ``x`` into groups defined by a categorical factor ``f``. diff --git a/src/biocutils/subset.py b/src/biocutils/subset.py index 7ef1260..3363a4c 100644 --- a/src/biocutils/subset.py +++ b/src/biocutils/subset.py @@ -1,4 +1,5 @@ -from typing import Any, Sequence +from collections.abc import Sequence +from typing import Any from .is_high_dimensional import is_high_dimensional from .subset_rows import subset_rows diff --git a/src/biocutils/subset_rows.py b/src/biocutils/subset_rows.py index e5b31cb..0fde0ef 100644 --- a/src/biocutils/subset_rows.py +++ b/src/biocutils/subset_rows.py @@ -1,5 +1,6 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, Sequence +from typing import Any import numpy diff --git a/src/biocutils/subset_sequence.py b/src/biocutils/subset_sequence.py index 1c39517..d7e0c3e 100644 --- a/src/biocutils/subset_sequence.py +++ b/src/biocutils/subset_sequence.py @@ -1,5 +1,6 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Any, Sequence, Union +from typing import Any @singledispatch @@ -36,7 +37,7 @@ def _subset_sequence_list(x: list, indices: Sequence[int]) -> list: @subset_sequence.register -def _subset_sequence_range(x: range, indices: Sequence[int]) -> Union[list, range]: +def _subset_sequence_range(x: range, indices: Sequence[int]) -> list | range: """Subset a range by indices. Args: diff --git a/src/biocutils/table.py b/src/biocutils/table.py index 72d06f5..8b175da 100644 --- a/src/biocutils/table.py +++ b/src/biocutils/table.py @@ -1,5 +1,5 @@ +from collections.abc import Sequence from functools import singledispatch -from typing import Sequence from .IntegerList import IntegerList diff --git a/src/biocutils/union.py b/src/biocutils/union.py index 78e3949..1ca5628 100644 --- a/src/biocutils/union.py +++ b/src/biocutils/union.py @@ -1,4 +1,4 @@ -from typing import Sequence +from collections.abc import Sequence from .is_missing_scalar import is_missing_scalar from .map_to_index import DUPLICATE_METHOD diff --git a/src/biocutils/unlist.py b/src/biocutils/unlist.py index ef951e3..0ac74c0 100644 --- a/src/biocutils/unlist.py +++ b/src/biocutils/unlist.py @@ -1,6 +1,7 @@ from functools import singledispatch from typing import Any + @singledispatch def unlist(x: Any, **kwargs) -> Any: """Unlist a structured list-like container into a flat sequence. @@ -16,7 +17,7 @@ def unlist(x: Any, **kwargs) -> Any: """ if hasattr(x, "unlist"): return x.unlist(**kwargs) - + if isinstance(x, (list, tuple)): flat = [] for item in x: @@ -25,5 +26,5 @@ def unlist(x: Any, **kwargs) -> Any: else: flat.append(item) return type(x)(flat) - + return x diff --git a/src/biocutils/which.py b/src/biocutils/which.py index ca7a863..9008e72 100644 --- a/src/biocutils/which.py +++ b/src/biocutils/which.py @@ -1,11 +1,11 @@ -from typing import Optional, Sequence +from collections.abc import Sequence import numpy def which( x: Sequence, - dtype: Optional[numpy.dtype] = None, + dtype: numpy.dtype | None = None, ) -> numpy.ndarray: """Report the indices of all elements of ``x`` that are truthy. diff --git a/tests/test_new_generics.py b/tests/test_new_generics.py index 7151d12..2d296b2 100644 --- a/tests/test_new_generics.py +++ b/tests/test_new_generics.py @@ -28,9 +28,9 @@ def test_unlist_relist_genomicranges(): "ends": [105], "strand": ["+"] })) - + grl = CompressedGenomicRangesList.from_list([gr1, gr2], names=["a", "b"]) - + flat = ut.unlist(grl) assert isinstance(flat, GenomicRanges) assert len(flat) == 3 @@ -44,7 +44,7 @@ def test_unlist_relist_genomicranges(): def test_unlist_relist_biostrings(): ds = DNAStringSet(["ACGT", "AAAA"]) - + flat = ut.unlist(ds) assert isinstance(flat, DNAString) assert str(flat) == "ACGTAAAA" @@ -57,10 +57,10 @@ def test_unlist_relist_biostrings(): def test_pmin_pmax(): v1 = [1, 5, 3] v2 = [2, 4, 6] - + min_res = ut.pmin(v1, v2) assert list(min_res) == [1, 4, 3] - + max_res = ut.pmax(v1, v2) assert list(max_res) == [2, 5, 6] @@ -71,7 +71,7 @@ def test_mcols_metadata(): "ends": [15], "strand": ["+"] })) - + mc = ut.mcols(gr) assert isinstance(mc, BiocFrame) assert len(mc.colnames) == 0 @@ -82,6 +82,6 @@ def test_mcols_metadata(): meta = ut.metadata(gr) assert meta is None or len(meta) == 0 - + gr = ut.set_metadata(gr, {"author": "AI"}) assert ut.metadata(gr)["author"] == "AI" diff --git a/tests/test_xtfrm.py b/tests/test_xtfrm.py index 0b1ec8d..abe36b2 100644 --- a/tests/test_xtfrm.py +++ b/tests/test_xtfrm.py @@ -55,7 +55,7 @@ def test_xtfrm_GenomicRanges(): ) tx_gr = xtfrm(gr) assert len(tx_gr) == 3 - + o = order(gr) assert list(o) == [2, 0, 1] @@ -66,7 +66,7 @@ def test_xtfrm_GenomicRanges(): def test_xtfrm_DNAStringSet(): dset = DNAStringSet(["ACGT", "TGCA", "ACGT"]) - + tx_dset = xtfrm(dset) assert tx_dset == ["ACGT", "TGCA", "ACGT"] @@ -83,6 +83,6 @@ def test_xtfrm_RangedSummarizedExperiment(): assays={"counts": np.random.rand(3, 2)}, row_ranges=gr ) - + assert len(xtfrm(rse)) == 3 assert list(order(rse)) == [2, 0, 1] From d421630934d1531955e56c7d77592a583debf02d Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:04:39 -0700 Subject: [PATCH 04/14] remove unnecessary files --- .gitattributes | 10 - .readthedocs.yml | 21 - .zenodo.json | 14 - CITATION.cff | 10 - uv.lock | 2103 ---------------------------------------------- 5 files changed, 2158 deletions(-) delete mode 100644 .gitattributes delete mode 100644 .readthedocs.yml delete mode 100644 .zenodo.json delete mode 100644 CITATION.cff delete mode 100644 uv.lock diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 0b7360d..0000000 --- a/.gitattributes +++ /dev/null @@ -1,10 +0,0 @@ -# Enforce Unix line endings -* text=auto eol=lf - -# Git LFS configurations for large scientific datasets -*.h5 filter=lfs diff=lfs merge=lfs -text -*.hdf5 filter=lfs diff=lfs merge=lfs -text -*.rds filter=lfs diff=lfs merge=lfs -text -*.rda filter=lfs diff=lfs merge=lfs -text -*.csv.gz filter=lfs diff=lfs merge=lfs -text -*.bam filter=lfs diff=lfs merge=lfs -text diff --git a/.readthedocs.yml b/.readthedocs.yml deleted file mode 100644 index da89049..0000000 --- a/.readthedocs.yml +++ /dev/null @@ -1,21 +0,0 @@ -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -version: 2 - -build: - os: ubuntu-22.04 - tools: - python: "3.12" - jobs: - post_install: - - curl -LsSf https://astral.sh/uv/install.sh | sh - - uv sync - -sphinx: - configuration: docs/conf.py - -python: - install: - - method: pip - path: . diff --git a/.zenodo.json b/.zenodo.json deleted file mode 100644 index c0eb26d..0000000 --- a/.zenodo.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "title": "biocutils", - "description": "Utilities to use across the biocpy packages.", - "creators": [ - { - "name": "Jayaram Kancherla", - "affiliation": "YOUR_AFFILIATION", - "orcid": "0000-0000-0000-0000" - } - ], - "access_right": "open", - "license": "MIT", - "upload_type": "software" -} diff --git a/CITATION.cff b/CITATION.cff deleted file mode 100644 index 10eef90..0000000 --- a/CITATION.cff +++ /dev/null @@ -1,10 +0,0 @@ -cff-version: 1.2.0 -message: "If you use this software, please cite it as below." -authors: -- family-names: "Kancherla" - given-names: "Jayaram" - orcid: "https://orcid.org/0000-0000-0000-0000" -title: "biocutils" -version: 0.1.0 -date-released: 2026-08-24 -url: "https://github.com/YOUR_ORG_OR_USERNAME/biocutils" diff --git a/uv.lock b/uv.lock deleted file mode 100644 index 08111e4..0000000 --- a/uv.lock +++ /dev/null @@ -1,2103 +0,0 @@ -version = 1 -revision = 3 -requires-python = ">=3.12" -resolution-markers = [ - 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""" - _installed = False try: - exec(f"import {package_name}") - _installed = True + _installed = importlib.util.find_spec(package_name) is not None except Exception: - if verbose: - print(f"Package '{package_name}' is not installed.") + _installed = False + + if not _installed and verbose: + print(f"Package '{package_name}' is not installed.") return _installed From b7f5db1679aaddc8c80b3bf2355262ca1928352b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Sep 2026 06:13:06 +0000 Subject: [PATCH 06/14] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/biocutils/package_utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biocutils/package_utils.py b/src/biocutils/package_utils.py index 2b97f44..15d130b 100644 --- a/src/biocutils/package_utils.py +++ b/src/biocutils/package_utils.py @@ -5,6 +5,7 @@ import importlib.util + def is_package_installed(package_name: str, verbose: bool = False) -> bool: """Check if a package is installed. @@ -19,7 +20,7 @@ def is_package_installed(package_name: str, verbose: bool = False) -> bool: _installed = importlib.util.find_spec(package_name) is not None except Exception: _installed = False - + if not _installed and verbose: print(f"Package '{package_name}' is not installed.") From 10a6f850ece7eff5f949760c361b9bcc030589c5 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:17:15 -0700 Subject: [PATCH 07/14] relax numpy version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 589a362..7f83299 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ classifiers = [ ] dependencies = [ "importlib-metadata>=9.0.0 ; python_full_version < '3.8'", - "numpy>=2.5.2", + "numpy", ] From d62c6e5254fcd42cb2def556f467f5f2bff64f53 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:21:22 -0700 Subject: [PATCH 08/14] relax more packages --- pyproject.toml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7f83299..630c7b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,13 +47,13 @@ Source = "https://github.com/BiocPy/biocutils" [project.optional-dependencies] testing = [ - "pandas>=3.0.5", + "pandas>=2.0.0", "biocframe", "iranges", - "pytest>=9.1.1", - "pytest-cov>=7.1.0", - "scipy>=1.18.1", - "setuptools>=84.0.0", + "pytest>=7.0.0", + "pytest-cov>=4.0.0", + "scipy", + "setuptools>=68.0.0", ] [build-system] From a01eee0b964d49505487f0d68e5e40a0a6f3235b Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:26:36 -0700 Subject: [PATCH 09/14] fix line continuation --- .github/workflows/run-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index a1112f1..25083d6 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -47,8 +47,8 @@ jobs: run: python -m pip install tox coverage - name: Run tests - run: | - tox \ + run: >- + tox -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml # pytest args - name: Check for codecov token availability From 8e9cc2698557045a46f10d46399ae0687fa502e6 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:29:43 -0700 Subject: [PATCH 10/14] change min python version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 630c7b5..d137c2e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ readme = "README.md" authors = [ { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" }, ] -requires-python = ">=3.12" +requires-python = ">=3.9" keywords = [ "bioinformatics", ] From e6a075ca16d4f804b1b4b08ebfe0e2b19f8e706a Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:33:35 -0700 Subject: [PATCH 11/14] remove files --- src/biocutils/melt.py | 27 ----------- src/biocutils/relist.py | 49 ------------------- src/biocutils/unlist.py | 30 ------------ src/biocutils/xtfrm.py | 47 ------------------- tests/test_melt_dispatcher.py | 61 ------------------------ tests/test_new_generics.py | 87 ---------------------------------- tests/test_xtfrm.py | 88 ----------------------------------- 7 files changed, 389 deletions(-) delete mode 100644 src/biocutils/melt.py delete mode 100644 src/biocutils/relist.py delete mode 100644 src/biocutils/unlist.py delete mode 100644 src/biocutils/xtfrm.py delete mode 100644 tests/test_melt_dispatcher.py delete mode 100644 tests/test_new_generics.py delete mode 100644 tests/test_xtfrm.py diff --git a/src/biocutils/melt.py b/src/biocutils/melt.py deleted file mode 100644 index b36e73c..0000000 --- a/src/biocutils/melt.py +++ /dev/null @@ -1,27 +0,0 @@ -from functools import singledispatch -from typing import Any - -import pandas as pd - - -@singledispatch -def melt(x: Any, **kwargs) -> pd.DataFrame: - """Melt a container into a tidy long-format pandas DataFrame. - - Args: - x: - The object/container to melt. - **kwargs: - Optional keyword arguments passed to the specific implementation. - - Returns: - A pandas DataFrame in long format. - """ - if hasattr(x, "melt"): - return x.melt(**kwargs) - - if hasattr(x, "to_pandas"): - df = x.to_pandas() - return df.melt(**kwargs) - - raise TypeError(f"No melt implementation found for class '{type(x).__name__}'") diff --git a/src/biocutils/relist.py b/src/biocutils/relist.py deleted file mode 100644 index e2e2a3c..0000000 --- a/src/biocutils/relist.py +++ /dev/null @@ -1,49 +0,0 @@ -from typing import Any - -_relist_registry = {} - - -def relist(flesh: Any, skeleton: Any, **kwargs) -> Any: - """Relist a flat sequence into the structure/shape of a skeleton. - - Args: - flesh: - The flat sequence/vector to reshape. - skeleton: - The template container whose structure should be replicated. - - Returns: - A reshaped nested container of the same class/type as skeleton. - """ - for cls in type(skeleton).__mro__: - if cls in _relist_registry: - return _relist_registry[cls](flesh, skeleton, **kwargs) - - if hasattr(skeleton, "relist"): - return skeleton.relist(flesh, **kwargs) - - if isinstance(skeleton, (list, tuple)): - res = [] - curr = 0 - for item in skeleton: - if isinstance(item, (list, tuple)): - nested_len = len(item) - res.append(relist(flesh[curr : curr + nested_len], item)) - curr += nested_len - else: - res.append(flesh[curr]) - curr += 1 - return type(skeleton)(res) - - raise TypeError(f"No relist implementation found for skeleton type '{type(skeleton).__name__}'") - - -def register(cls): - def decorator(func): - _relist_registry[cls] = func - return func - - return decorator - - -relist.register = register diff --git a/src/biocutils/unlist.py b/src/biocutils/unlist.py deleted file mode 100644 index 0ac74c0..0000000 --- a/src/biocutils/unlist.py +++ /dev/null @@ -1,30 +0,0 @@ -from functools import singledispatch -from typing import Any - - -@singledispatch -def unlist(x: Any, **kwargs) -> Any: - """Unlist a structured list-like container into a flat sequence. - - Args: - x: - The structured object/container to flatten. - **kwargs: - Optional keyword arguments passed to the specific implementation. - - Returns: - A flat representation of the sequence. - """ - if hasattr(x, "unlist"): - return x.unlist(**kwargs) - - if isinstance(x, (list, tuple)): - flat = [] - for item in x: - if isinstance(item, (list, tuple)): - flat.extend(unlist(item)) - else: - flat.append(item) - return type(x)(flat) - - return x diff --git a/src/biocutils/xtfrm.py b/src/biocutils/xtfrm.py deleted file mode 100644 index 5d664ad..0000000 --- a/src/biocutils/xtfrm.py +++ /dev/null @@ -1,47 +0,0 @@ -from functools import singledispatch -from typing import Any - -import numpy - -from .Factor import Factor - - -@singledispatch -def xtfrm(x: Any) -> Any: - """Obtain a numeric representation of the elements of ``x`` that can be sorted. - - Args: - x: - Values to be transformed. - - Returns: - A numeric representation (usually a NumPy array or a sequence of numbers) - whose elements sort in the same relative order as ``x``. - """ - if hasattr(x, "__xtfrm__"): - return x.__xtfrm__() - - if isinstance(x, numpy.ndarray) and numpy.issubdtype(x.dtype, numpy.number): - return x - - from .order import order - from .subset import subset - - o = order(x) - ranks = numpy.empty(len(x), dtype=int) - if len(x) == 0: - return ranks - - sorted_x = subset(x, o) - current_rank = 0 - for i, idx in enumerate(o): - if i > 0 and sorted_x[i] != sorted_x[i - 1]: - current_rank += 1 - ranks[idx] = current_rank - - return ranks - - -@xtfrm.register -def _xtfrm_Factor(x: Factor) -> numpy.ndarray: - return x.get_codes() diff --git a/tests/test_melt_dispatcher.py b/tests/test_melt_dispatcher.py deleted file mode 100644 index 1ddf1f8..0000000 --- a/tests/test_melt_dispatcher.py +++ /dev/null @@ -1,61 +0,0 @@ -import pytest -import numpy as np -import pandas as pd -import biocframe -from biocframe import BiocFrame -from genomicranges import GenomicRanges -from summarizedexperiment import SummarizedExperiment -from multiassayexperiment import MultiAssayExperiment -import biocutils as ut - -def test_melt_biocframe(): - bf = BiocFrame({"A": [1, 2], "B": [3, 4]}) - res = ut.melt(bf) - assert isinstance(res, pd.DataFrame) - assert list(res["variable"]) == ["A", "A", "B", "B"] - assert list(res["value"]) == [1, 2, 3, 4] - -def test_melt_genomicranges(): - gr = GenomicRanges.from_pandas(pd.DataFrame({ - "seqnames": ["chr1"], - "starts": [10], - "ends": [15], - "strand": ["+"] - })) - res = ut.melt(gr) - assert isinstance(res, pd.DataFrame) - # Check that coordinate variables are in the melted DataFrame - # self.to_pandas() returns a DataFrame with seqnames, starts, ends, strand, names - assert "variable" in res.columns - assert "value" in res.columns - -def test_melt_summarizedexperiment(): - se = SummarizedExperiment( - assays={"counts": np.array([[1, 2], [3, 4]])}, - row_names=["gene_A", "gene_B"], - column_names=["sample_1", "sample_2"] - ) - res = ut.melt(se, assay=0) - assert isinstance(res, pd.DataFrame) - assert len(res) == 4 - assert list(res["value"]) == [1, 2, 3, 4] - -def test_melt_multiassayexperiment(): - se1 = SummarizedExperiment( - assays={"counts": np.array([[1, 2], [3, 4]])}, - row_names=["gene_A", "gene_B"], - column_names=["sample_1", "sample_2"] - ) - se2 = SummarizedExperiment( - assays={"counts": np.array([[5, 6], [7, 8]])}, - row_names=["gene_A", "gene_B"], - column_names=["sample_1", "sample_2"] - ) - mae = MultiAssayExperiment( - experiments={"assay1": se1, "assay2": se2} - ) - res = ut.melt(mae) - assert isinstance(res, pd.DataFrame) - assert len(res) == 8 - assert "assay" in res.columns - assert list(res["assay"]) == ["assay1"] * 4 + ["assay2"] * 4 diff --git a/tests/test_new_generics.py b/tests/test_new_generics.py deleted file mode 100644 index 2d296b2..0000000 --- a/tests/test_new_generics.py +++ /dev/null @@ -1,87 +0,0 @@ -import pytest -import numpy as np -import pandas as pd -import biocframe -from biocframe import BiocFrame -from genomicranges import GenomicRanges, CompressedGenomicRangesList -from biostrings import DNAString, DNAStringSet -import biocutils as ut - -def test_unlist_relist_lists(): - lst = [[1, 2], [3, 4, 5]] - flat = ut.unlist(lst) - assert flat == [1, 2, 3, 4, 5] - - rel = ut.relist(flat, lst) - assert rel == [[1, 2], [3, 4, 5]] - -def test_unlist_relist_genomicranges(): - gr1 = GenomicRanges.from_pandas(pd.DataFrame({ - "seqnames": ["chr1", "chr1"], - "starts": [10, 20], - "ends": [15, 25], - "strand": ["+", "-"] - })) - gr2 = GenomicRanges.from_pandas(pd.DataFrame({ - "seqnames": ["chr2"], - "starts": [100], - "ends": [105], - "strand": ["+"] - })) - - grl = CompressedGenomicRangesList.from_list([gr1, gr2], names=["a", "b"]) - - flat = ut.unlist(grl) - assert isinstance(flat, GenomicRanges) - assert len(flat) == 3 - assert list(flat.get_start()) == [10, 20, 100] - - rel = ut.relist(flat, grl) - assert isinstance(rel, CompressedGenomicRangesList) - assert len(rel) == 2 - assert len(rel[0]) == 2 - assert len(rel[1]) == 1 - -def test_unlist_relist_biostrings(): - ds = DNAStringSet(["ACGT", "AAAA"]) - - flat = ut.unlist(ds) - assert isinstance(flat, DNAString) - assert str(flat) == "ACGTAAAA" - - rel = ut.relist(flat, ds) - assert isinstance(rel, DNAStringSet) - assert len(rel) == 2 - assert rel.to_list() == ["ACGT", "AAAA"] - -def test_pmin_pmax(): - v1 = [1, 5, 3] - v2 = [2, 4, 6] - - min_res = ut.pmin(v1, v2) - assert list(min_res) == [1, 4, 3] - - max_res = ut.pmax(v1, v2) - assert list(max_res) == [2, 5, 6] - -def test_mcols_metadata(): - gr = GenomicRanges.from_pandas(pd.DataFrame({ - "seqnames": ["chr1"], - "starts": [10], - "ends": [15], - "strand": ["+"] - })) - - mc = ut.mcols(gr) - assert isinstance(mc, BiocFrame) - assert len(mc.colnames) == 0 - - new_mc = BiocFrame({"score": [100]}) - gr = ut.set_mcols(gr, new_mc) - assert list(ut.mcols(gr).column("score")) == [100] - - meta = ut.metadata(gr) - assert meta is None or len(meta) == 0 - - gr = ut.set_metadata(gr, {"author": "AI"}) - assert ut.metadata(gr)["author"] == "AI" diff --git a/tests/test_xtfrm.py b/tests/test_xtfrm.py deleted file mode 100644 index abe36b2..0000000 --- a/tests/test_xtfrm.py +++ /dev/null @@ -1,88 +0,0 @@ -import numpy as np -import pytest -from biocutils import xtfrm, order, sort, match, duplicated, unique, Factor -from iranges import IRanges -from genomicranges import GenomicRanges -from biostrings import DNAString, DNAStringSet -from summarizedexperiment import RangedSummarizedExperiment -import biocframe - -def test_xtfrm_basic(): - x = [20, 10, 20, 30] - tx = xtfrm(x) - assert isinstance(tx, np.ndarray) - assert list(tx) == [1, 0, 1, 2] # sorted is 10, 20, 20, 30 -> ranks [1, 0, 1, 2] - - arr = np.array([1.5, -0.5, 1.5]) - t_arr = xtfrm(arr) - assert np.array_equal(t_arr, arr) - - strings = ["banana", "apple", "banana", "cherry"] - tx_str = xtfrm(strings) - assert list(tx_str) == [1, 0, 1, 2] - -def test_xtfrm_Factor(): - f = Factor.from_sequence(["B", "A", "B", "C"]) - tf = xtfrm(f) - assert np.array_equal(tf, f.get_codes()) - - assert list(order(f)) == [1, 0, 2, 3] - -def test_xtfrm_IRanges(): - ir = IRanges([10, 5, 10], [5, 8, 3]) - tx_ir = xtfrm(ir) - assert tx_ir == [(10, 5), (5, 8), (10, 3)] - - o = order(ir) - assert list(o) == [1, 2, 0] - - sir = sort(ir) - assert list(sir.get_start()) == [5, 10, 10] - assert list(sir.get_width()) == [8, 3, 5] - - targets = IRanges([5, 10], [8, 3]) - m = match(ir, targets) - assert list(m) == [-1, 0, 1] # only range 1 and range 2 are matched - - ir2 = IRanges([10, 5, 10, 5], [5, 8, 5, 8]) - assert list(duplicated(ir2)) == [False, False, True, True] - -def test_xtfrm_GenomicRanges(): - gr = GenomicRanges( - seqnames=["chr1", "chr2", "chr1"], - ranges=IRanges([10, 5, 10], [5, 8, 3]), - strand=["+", "-", "+"] - ) - tx_gr = xtfrm(gr) - assert len(tx_gr) == 3 - - o = order(gr) - assert list(o) == [2, 0, 1] - - # verify sort - sgr = sort(gr) - assert list(sgr.get_start()) == [10, 10, 5] - assert list(sgr.get_seqnames()) == ["chr1", "chr1", "chr2"] - -def test_xtfrm_DNAStringSet(): - dset = DNAStringSet(["ACGT", "TGCA", "ACGT"]) - - tx_dset = xtfrm(dset) - assert tx_dset == ["ACGT", "TGCA", "ACGT"] - - assert list(order(dset)) == [0, 2, 1] - assert list(duplicated(dset)) == [False, False, True] - -def test_xtfrm_RangedSummarizedExperiment(): - gr = GenomicRanges( - seqnames=["chr1", "chr2", "chr1"], - ranges=IRanges([10, 5, 10], [5, 8, 3]), - strand=["+", "-", "+"] - ) - rse = RangedSummarizedExperiment( - assays={"counts": np.random.rand(3, 2)}, - row_ranges=gr - ) - - assert len(xtfrm(rse)) == 3 - assert list(order(rse)) == [2, 0, 1] From 90017846d34ce9c164e7cd3a412b0b1335392993 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Mon, 31 Aug 2026 23:40:02 -0700 Subject: [PATCH 12/14] cleanup more --- pyproject.toml | 2 - src/biocutils/mcols.py | 88 ---------------------------------------- src/biocutils/pminmax.py | 49 ---------------------- src/biocutils/rle.py | 42 ------------------- 4 files changed, 181 deletions(-) delete mode 100644 src/biocutils/mcols.py delete mode 100644 src/biocutils/pminmax.py delete mode 100644 src/biocutils/rle.py diff --git a/pyproject.toml b/pyproject.toml index d137c2e..d32523e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,8 +48,6 @@ Source = "https://github.com/BiocPy/biocutils" [project.optional-dependencies] testing = [ "pandas>=2.0.0", - "biocframe", - "iranges", "pytest>=7.0.0", "pytest-cov>=4.0.0", "scipy", diff --git a/src/biocutils/mcols.py b/src/biocutils/mcols.py deleted file mode 100644 index fa9881c..0000000 --- a/src/biocutils/mcols.py +++ /dev/null @@ -1,88 +0,0 @@ -from functools import singledispatch -from typing import Any - - -@singledispatch -def mcols(x: Any) -> Any: - """Retrieve metadata columns from an object. - - Args: - x: - The object to retrieve mcols from. - - Returns: - The metadata columns (usually a BiocFrame or None). - """ - if hasattr(x, "mcols"): - val = x.mcols - if callable(val): - return val() - return val - return None - - -@singledispatch -def set_mcols(x: Any, value: Any) -> Any: - """Set or replace metadata columns on an object. - - Args: - x: - The target object. - value: - The new metadata columns. - - Returns: - A modified object. - """ - if hasattr(x, "set_mcols"): - return x.set_mcols(value) - if hasattr(x, "mcols"): - try: - x.mcols = value - return x - except AttributeError: - pass - raise TypeError(f"Cannot set mcols on type '{type(x).__name__}'") - - -@singledispatch -def metadata(x: Any) -> Any: - """Retrieve general metadata from an object. - - Args: - x: - The object to retrieve metadata from. - - Returns: - A dictionary or NamedList containing metadata. - """ - if hasattr(x, "metadata"): - val = x.metadata - if callable(val): - return val() - return val - return None - - -@singledispatch -def set_metadata(x: Any, value: Any) -> Any: - """Set or replace general metadata on an object. - - Args: - x: - The target object. - value: - The new metadata. - - Returns: - A modified object. - """ - if hasattr(x, "set_metadata"): - return x.set_metadata(value) - if hasattr(x, "metadata"): - try: - x.metadata = value - return x - except AttributeError: - pass - raise TypeError(f"Cannot set metadata on type '{type(x).__name__}'") diff --git a/src/biocutils/pminmax.py b/src/biocutils/pminmax.py deleted file mode 100644 index 625a6b1..0000000 --- a/src/biocutils/pminmax.py +++ /dev/null @@ -1,49 +0,0 @@ -from typing import Any - -import numpy as np - - -def pmin(*x: Any, **kwargs) -> Any: - """Calculate the parallel element-wise minimum of multiple sequences. - - Args: - *x: - Sequence objects or vectors of equal length. - - Returns: - The element-wise minimum. - """ - if not x: - raise ValueError("Must specify at least one sequence/vector.") - - arrays = [np.asarray(item) for item in x] - res = arrays[0] - for arr in arrays[1:]: - res = np.minimum(res, arr) - - if isinstance(x[0], (list, tuple)): - return type(x[0])(res.tolist()) - return res - - -def pmax(*x: Any, **kwargs) -> Any: - """Calculate the parallel element-wise maximum of multiple sequences. - - Args: - *x: - Sequence objects or vectors of equal length. - - Returns: - The element-wise maximum. - """ - if not x: - raise ValueError("Must specify at least one sequence/vector.") - - arrays = [np.asarray(item) for item in x] - res = arrays[0] - for arr in arrays[1:]: - res = np.maximum(res, arr) - - if isinstance(x[0], (list, tuple)): - return type(x[0])(res.tolist()) - return res diff --git a/src/biocutils/rle.py b/src/biocutils/rle.py deleted file mode 100644 index 30562e8..0000000 --- a/src/biocutils/rle.py +++ /dev/null @@ -1,42 +0,0 @@ -from typing import Any - -import numpy as np - - -class Rle: - def __init__(self, values: Any, lengths: Any = None): - """Initialize Run-Length Encoded vector. - - Args: - values: - Sequence of values, or a single value if lengths is specified. - lengths: - Sequence of run lengths matching each value, or None if values should be run-length compressed. - """ - if lengths is None: - vals = np.asarray(values) - if len(vals) == 0: - self.values = np.array([], dtype=vals.dtype) - self.lengths = np.array([], dtype=np.int32) - else: - change_indices = np.where(vals[:-1] != vals[1:])[0] - runs = np.diff(np.concatenate([[-1], change_indices, [len(vals) - 1]])) - self.values = np.concatenate([[vals[0]], vals[change_indices + 1]]) - self.lengths = runs.astype(np.int32) - else: - self.values = np.asarray(values) - self.lengths = np.asarray(lengths, dtype=np.int32) - - def __len__(self) -> int: - return int(np.sum(self.lengths)) - - def to_numpy(self) -> np.ndarray: - """Decompress Rle back to a dense numpy array.""" - return np.repeat(self.values, self.lengths) - - def __getitem__(self, idx: int | slice) -> Any: - dense = self.to_numpy() - return dense[idx] - - def __repr__(self) -> str: - return f"Rle(values={self.values.tolist()}, lengths={self.lengths.tolist()})" From 7dbdedbf90de77521b83a5e76e5ee60ad78e9fa9 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Wed, 2 Sep 2026 22:58:56 -0700 Subject: [PATCH 13/14] reverting a few changes --- docs/conf.py | 4 ++-- pyproject.toml | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 7f64459..1a6314e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -106,7 +106,7 @@ # General information about the project. project = "biocutils" -copyright = "2026, Jayaram Kancherla" +copyright = "2023, Aaron Lun" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -274,7 +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", "biocutils Documentation", "Jayaram Kancherla", "manual") + ("index", "user_guide.tex", "biocutils Documentation", "Aaron Lun", "manual") ] # The name of an image file (relative to this directory) to place at the top of diff --git a/pyproject.toml b/pyproject.toml index d32523e..307486b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,6 +6,7 @@ dynamic = [ description = "Utilities to use across the biocpy packages." readme = "README.md" authors = [ + { name = "Aaron Lun", email = "infinite.monkeys.with.keyboards@gmail.com"}, { name = "Jayaram Kancherla", email = "jayaram.kancherla@gmail.com" }, ] requires-python = ">=3.9" From aecb8737e235f273e230cf7e3604ff107074a733 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Wed, 2 Sep 2026 23:01:18 -0700 Subject: [PATCH 14/14] update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 09f3e72..719fe2c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # Changelog +## Version 0.5.0 + +- Migate the package to `hatch`. + ## Version 0.4.0 - 0.4.2 - Implemented R's `split()` utility to split a sequence by a grouping factor.