diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..6887a69 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,28 @@ +# .coveragerc to control coverage.py +[run] +branch = True +source = scrnaseq +# omit = bad_file.py + +[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 + + # 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/pypi-publish.yml b/.github/workflows/pypi-publish.yml new file mode 100644 index 0000000..7b591a2 --- /dev/null +++ b/.github/workflows/pypi-publish.yml @@ -0,0 +1,51 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Publish to PyPI + +on: + push: + tags: "*" + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest tox + # - name: Lint with flake8 + # run: | + # # stop the build if there are Python syntax errors or undefined names + # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with tox + run: | + tox + - name: Build docs + run: | + tox -e docs + - run: touch ./docs/_build/html/.nojekyll + - name: GH Pages Deployment + uses: JamesIves/github-pages-deploy-action@4.1.3 + 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: Build Project and Publish + run: | + python -m tox -e clean,build + - name: Publish package + uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + with: + user: __token__ + password: ${{ secrets.PYPI_PASSWORD }} diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml new file mode 100644 index 0000000..f35fd23 --- /dev/null +++ b/.github/workflows/pypi-test.yml @@ -0,0 +1,37 @@ +name: Test the library + +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ] + + name: Python ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v2 + - name: Setup Python + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + cache: 'pip' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest tox + # - name: Lint with flake8 + # run: | + # # stop the build if there are Python syntax errors or undefined names + # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with tox + run: | + tox diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e9e1e9b --- /dev/null +++ b/.gitignore @@ -0,0 +1,54 @@ +# Temporary and binary files +*~ +*.py[cod] +*.so +*.cfg +!.isort.cfg +!setup.cfg +*.orig +*.log +*.pot +__pycache__/* +.cache/* +.*.swp +*/.ipynb_checkpoints/* +.DS_Store + +# Project files +.ropeproject +.project +.pydevproject +.settings +.idea +.vscode +tags + +# Package files +*.egg +*.eggs/ +.installed.cfg +*.egg-info + +# Unittest and coverage +htmlcov/* +.coverage +.coverage.* +.tox +junit*.xml +coverage.xml +.pytest_cache/ + +# Build and docs folder/files +build/* +dist/* +sdist/* +docs/api/* +docs/_rst/* +docs/_build/* +cover/* +MANIFEST + +# Per-project virtualenvs +.venv*/ +.conda*/ +.python-version diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..a2bcab3 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,27 @@ +# 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: + install: + - requirements: docs/requirements.txt + - {path: ., method: pip} diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..f21a024 --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,3 @@ +# Contributors + +* Jayaram Kancherla [jayaram.kancherla@gmail.com](mailto:jayaram.kancherla@gmail.com) diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..205cc5e --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,7 @@ +# Changelog + +## Version 0.1 (development) + +- Feature A added +- FIX: nasty bug #1729 fixed +- add your changes here! diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..1dba289 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,371 @@ +```{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 `scrnaseq` 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 `scrnaseq`, 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 `scrnaseq` docs by making them more readable and coherent, or +by adding missing information and correcting mistakes. + +`scrnaseq` 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 `scrnaseq`'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 scrnaseq python=3 six virtualenv pytest pytest-cov +conda activate scrnaseq +``` + +### 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/scrnaseq.git + cd scrnaseq + ``` + +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 + ``` + + `scrnaseq` 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 +`scrnaseq`: + +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. + + +[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/ + + +```{todo} Please review and change the following definitions: +``` + +[repository]: https://github.com//scrnaseq +[issue tracker]: https://github.com//scrnaseq/issues diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..a378847 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2024 Jayaram Kancherla + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..847247d --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ + + +[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/) + +# scrnaseq + +> Add a short description here! + +A longer description of your project goes here... + + + + +## Note + +This project has been set up using PyScaffold 4.5. For details and usage +information on PyScaffold see https://pyscaffold.org/. diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..31655dd --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,29 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build +AUTODOCDIR = api + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1) +$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/") +endif + +.PHONY: help clean Makefile + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +clean: + rm -rf $(BUILDDIR)/* $(AUTODOCDIR) + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_static/.gitignore b/docs/_static/.gitignore new file mode 100644 index 0000000..3c96363 --- /dev/null +++ b/docs/_static/.gitignore @@ -0,0 +1 @@ +# Empty directory diff --git a/docs/authors.md b/docs/authors.md new file mode 100644 index 0000000..ced47d0 --- /dev/null +++ b/docs/authors.md @@ -0,0 +1,4 @@ +```{include} ../AUTHORS.md +:relative-docs: docs/ +:relative-images: +``` diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 0000000..6e2f0fb --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,4 @@ +```{include} ../CHANGELOG.md +:relative-docs: docs/ +:relative-images: +``` diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..023cb5d --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,304 @@ +# This file is execfile()d with the current directory set to its containing dir. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import os +import sys +import shutil + +# -- Path setup -------------------------------------------------------------- + +__location__ = os.path.dirname(__file__) + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +sys.path.insert(0, os.path.join(__location__, "../src")) + +# -- Run sphinx-apidoc ------------------------------------------------------- +# This hack is necessary since RTD does not issue `sphinx-apidoc` before running +# `sphinx-build -b html . _build/html`. See Issue: +# https://github.com/readthedocs/readthedocs.org/issues/1139 +# DON'T FORGET: Check the box "Install your project inside a virtualenv using +# setup.py install" in the RTD Advanced Settings. +# Additionally it helps us to avoid running apidoc manually + +try: # for Sphinx >= 1.7 + from sphinx.ext import apidoc +except ImportError: + from sphinx import apidoc + +output_dir = os.path.join(__location__, "api") +module_dir = os.path.join(__location__, "../src/scrnaseq") +try: + shutil.rmtree(output_dir) +except FileNotFoundError: + pass + +try: + import sphinx + + cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}" + + args = cmd_line.split(" ") + if tuple(sphinx.__version__.split(".")) >= ("1", "7"): + # This is a rudimentary parse_version to avoid external dependencies + args = args[1:] + + apidoc.main(args) +except Exception as e: + print("Running `sphinx-apidoc` failed!\n{}".format(e)) + +# -- General configuration --------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.intersphinx", + "sphinx.ext.todo", + "sphinx.ext.autosummary", + "sphinx.ext.viewcode", + "sphinx.ext.coverage", + "sphinx.ext.doctest", + "sphinx.ext.ifconfig", + "sphinx.ext.mathjax", + "sphinx.ext.napoleon", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + + +# Enable markdown +extensions.append("myst_parser") + +# Configure MyST-Parser +myst_enable_extensions = [ + "amsmath", + "colon_fence", + "deflist", + "dollarmath", + "html_image", + "linkify", + "replacements", + "smartquotes", + "substitution", + "tasklist", +] + +# The suffix of source filenames. +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "scrnaseq" +copyright = "2024, 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 +# built documents. +# +# version: The short X.Y version. +# release: The full version, including alpha/beta/rc tags. +# If you don’t need the separation provided between version and release, +# just set them both to the same value. +try: + from scrnaseq import __version__ as version +except ImportError: + version = "" + +if not version or version.lower() == "unknown": + version = os.getenv("READTHEDOCS_VERSION", "unknown") # automatically set by RTD + +release = version + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"] + +# The reST default role (used for this markup: `text`) to use for all documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +# modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +# keep_warnings = False + +# If this is True, todo emits a warning for each TODO entries. The default is False. +todo_emit_warnings = 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 = "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" +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = "" + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = "scrnaseq-doc" + + +# -- Options for LaTeX output ------------------------------------------------ + +latex_elements = { + # The paper size ("letterpaper" or "a4paper"). + # "papersize": "letterpaper", + # The font size ("10pt", "11pt" or "12pt"). + # "pointsize": "10pt", + # Additional stuff for the LaTeX preamble. + # "preamble": "", +} + +# 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", "scrnaseq Documentation", "Jayaram Kancherla", "manual") +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = "" + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + +# -- External mapping -------------------------------------------------------- +python_version = ".".join(map(str, sys.version_info[0:2])) +intersphinx_mapping = { + "sphinx": ("https://www.sphinx-doc.org/en/master", None), + "python": ("https://docs.python.org/" + python_version, None), + "matplotlib": ("https://matplotlib.org", None), + "numpy": ("https://numpy.org/doc/stable", None), + "sklearn": ("https://scikit-learn.org/stable", None), + "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) \ No newline at end of file diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..fc1b213 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,4 @@ +```{include} ../CONTRIBUTING.md +:relative-docs: docs/ +:relative-images: +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..26c9283 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,39 @@ +# scrnaseq + +Add a short description here! + + +## Note + +> This is the main page of your project's [Sphinx] documentation. It is +> formatted in [Markdown]. Add additional pages by creating md-files in +> `docs` or rst-files (formatted in [reStructuredText]) and adding links to +> them in the `Contents` section below. +> +> Please check [Sphinx] and [MyST] for more information +> about how to document your project and how to configure your preferences. + + +## Contents + +```{toctree} +:maxdepth: 2 + +Overview +Contributions & Help +License +Authors +Changelog +Module Reference +``` + +## Indices and tables + +* {ref}`genindex` +* {ref}`modindex` +* {ref}`search` + +[Sphinx]: http://www.sphinx-doc.org/ +[Markdown]: https://daringfireball.net/projects/markdown/ +[reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html +[MyST]: https://myst-parser.readthedocs.io/en/latest/ diff --git a/docs/license.md b/docs/license.md new file mode 100644 index 0000000..b231201 --- /dev/null +++ b/docs/license.md @@ -0,0 +1,5 @@ +# License + +```{literalinclude} ../LICENSE.txt +:language: text +``` diff --git a/docs/readme.md b/docs/readme.md new file mode 100644 index 0000000..2cb706b --- /dev/null +++ b/docs/readme.md @@ -0,0 +1,4 @@ +```{include} ../README.md +:relative-docs: docs/ +:relative-images: +``` diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..0990c2a --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,6 @@ +# 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 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..89a5bed --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,9 @@ +[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" + +[tool.setuptools_scm] +# For smarter version schemes and other configuration options, +# check out https://github.com/pypa/setuptools_scm +version_scheme = "no-guess-dev" diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..9f4d887 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,131 @@ +# 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 = scrnaseq +description = Collection of Public Single-Cell RNA-Seq Datasets +author = Jayaram Kancherla +author_email = jayaram.kancherla@gmail.com +license = MIT +license_files = LICENSE.txt +long_description = file: README.md +long_description_content_type = text/markdown; charset=UTF-8; variant=GFM +url = https://github.com/biocpy/scrnaseq +# Add here related links, for example: +project_urls = + Documentation = https://github.com/biocpy/scrnaseq +# Source = https://github.com/pyscaffold/pyscaffold/ +# 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 = >=3.8 + +# 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" + dolomite_base + dolomite_matrix + dolomite_sce + gypsum_client>=0.1.1 + delayedarray + summarizedexperiment + singlecellexperiment + +[options.packages.find] +where = src +exclude = + tests + +[options.extras_require] +# Add here additional requirements for extra features, to install with: +# `pip install scrnaseq[PDF]` like: +# PDF = ReportLab; RXP + +# Add here test requirements (semicolon/line-separated) +testing = + setuptools + pytest + pytest-cov + +[options.entry_points] +# Add here console scripts like: +# console_scripts = +# script_name = scrnaseq.module:function +# For example: +# console_scripts = +# fibonacci = scrnaseq.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 scrnaseq --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 = scrnaseq +extensions = + markdown diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..26b2cdf --- /dev/null +++ b/setup.py @@ -0,0 +1,21 @@ +""" + Setup file for scrnaseq. + 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/scrnaseq/__init__.py b/src/scrnaseq/__init__.py new file mode 100644 index 0000000..5915d6e --- /dev/null +++ b/src/scrnaseq/__init__.py @@ -0,0 +1,18 @@ +import sys + +if sys.version_info[:2] >= (3, 8): + # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8` + from importlib.metadata import PackageNotFoundError, version # pragma: no cover +else: + from importlib_metadata import PackageNotFoundError, version # pragma: no cover + +try: + # Change here if project is renamed and does not equal the package name + dist_name = __name__ + __version__ = version(dist_name) +except PackageNotFoundError: # pragma: no cover + __version__ = "unknown" +finally: + del version, PackageNotFoundError + +from .fetch_dataset import fetch_dataset, fetch_metadata \ No newline at end of file diff --git a/src/scrnaseq/fetch_dataset.py b/src/scrnaseq/fetch_dataset.py new file mode 100644 index 0000000..02c4ccc --- /dev/null +++ b/src/scrnaseq/fetch_dataset.py @@ -0,0 +1,217 @@ +import atexit +import json +import os + +from delayedarray import is_sparse, to_dense_array, to_scipy_sparse_matrix +from dolomite_base import alt_read_object, alt_read_object_function, read_object +from gypsum_client import cache_directory, save_file, save_version +from singlecellexperiment import SingleCellExperiment +from summarizedexperiment import SummarizedExperiment + +__author__ = "Jayaram Kancherla" +__copyright__ = "Jayaram Kancherla" +__license__ = "MIT" + + +def fetch_dataset( + name: str, + version: str, + path: str = None, + package: str = "scRNAseq", + cache_dir: str = cache_directory(), + overwrite: bool = False, + realize_assays: bool = False, + realize_reduced_dims: bool = True, + **kwargs, +) -> SummarizedExperiment: + """Fetch a dataset from the gypsum backend. + + Args: + name: + Name of the dataset. + + version: + Version of the dataset. + + path: + Path to a subdataset, if name contains multiple datasets. + Defaults to None. + + package: + Name of the package. + Defaults to "scRNAseq". + + cache_dir: + Path to cache directory. + + overwrite: + Whether to overwrite existing files. + Defaults to False. + + realize_assays: + Whether to realize assays into memory. + Defaults to False. + + realize_reduced_dims: + Whether to realize reduced dimensions into memory. + Defaults to True. + + **kwargs: + Further arguments to pass to + :py:func:`~dolomite_base.read_object.read_object`. + + Returns: + The dataset as a + :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment` + or one of its subclasses. + """ + + cache_dir = cache_directory(cache_dir) + + version_path = save_version( + package, name, version, cache_dir=cache_dir, overwrite=overwrite + ) + obj_path = ( + version_path if path is None else os.path.join(version_path, path.rstrip("/")) + ) + + old = alt_read_object_function(single_cell_load_object) + + def reset_alt_read_func(): + alt_read_object_function(old) + + atexit.register(reset_alt_read_func) + return alt_read_object( + obj_path, + scrnaseq_realize_assays=realize_assays, + scrnaseq_realize_reduced_dims=realize_reduced_dims, + **kwargs, + ) + + +def fetch_metadata( + name: str, + version: str, + path: str = None, + package: str = "scRNAseq", + cache_dir: str = cache_directory(), + overwrite: bool = False, +): + """Fetch metadata for a dataset from the gypsum backend. + + Args: + name: + Name of the dataset. + + version: + Version of the dataset. + + path: + Path to a subdataset, if name contains multiple datasets. + Defaults to None. + + package: + Name of the package. + Defaults to "scRNAseq". + + cache: + Path to the cache directory. + + overwrite: + Whether to overwrite existing files. + Defaults to False. + + Returns: + Dictionary containing metadata for the specified dataset. + """ + remote_path = "_bioconductor.json" if path is None else f"{path}/_bioconductor.json" + local_path = save_file( + package, name, version, remote_path, cache_dir=cache_dir, overwrite=overwrite + ) + + with open(local_path, "r") as f: + metadata = json.load(f) + + return metadata + + +def single_cell_load_object( + path: str, + metadata: dict = None, + scrnaseq_realize_assays: bool = False, + scrnaseq_realize_reduced_dims: bool = True, + **kwargs, +): + """Load a ``SummarizedExperiment`` or ``SingleCellExperiment`` object from a file. + + Args: + path: + Path to the dataset. + + metadata: + Metadata for the dataset. + Defaults to None. + + scrnaseq_realize_assays: + Whether to realize assays into memory. + Defaults to False. + + scrnaseq_realize_reduced_dims: + Whether to realize reduced dimensions into memory. + Defaults to True. + + **kwargs: + Further arguments to pass to + :py:func:`~dolomite_base.read_object.read_object`. + + Returns: + A `SummarizedExperiment` of the object. + """ + obj = read_object( + path, + metadata=metadata, + scrnaseq_realize_assays=scrnaseq_realize_assays, + scrnaseq_realize_reduced_dims=scrnaseq_realize_reduced_dims, + **kwargs, + ) + + if isinstance(obj, SummarizedExperiment): + if scrnaseq_realize_assays: + _assays = {} + for y in obj.get_assay_names(): + _assays[y] = realize_array(obj.assay(y)) + + obj = obj.set_assays(_assays) + + if isinstance(obj, SingleCellExperiment): + if scrnaseq_realize_reduced_dims: + _red_dims = {} + for z in obj.get_reduced_dim_names(): + _red_dims[z] = realize_array(obj.reduced_dim(z)) + + obj = obj.set_reduced_dims(_red_dims) + + return obj + + +def realize_array(x): + """ + Realize a `ReloadedArray` into a dense array or sparse matrix. + + Args: + x: + `ReloadedArray` object. + + Returns: + + Realized array or matrix. + """ + from dolomite_matrix import ReloadedArray + + if isinstance(x, ReloadedArray): + if is_sparse(x): + x = to_scipy_sparse_matrix(x, "csr") + else: + x = to_dense_array(x) + + return x diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..72c29e9 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,10 @@ +""" + Dummy conftest.py for scrnaseq. + + If you don't know what this is for, just leave it empty. + Read more about conftest.py under: + - https://docs.pytest.org/en/stable/fixture.html + - https://docs.pytest.org/en/stable/writing_plugins.html +""" + +# import pytest diff --git a/tests/test_fetch_dataset.py b/tests/test_fetch_dataset.py new file mode 100644 index 0000000..753a815 --- /dev/null +++ b/tests/test_fetch_dataset.py @@ -0,0 +1,14 @@ +import pytest +from scrnaseq import fetch_dataset +from singlecellexperiment import SingleCellExperiment + +__author__ = "Jayaram Kancherla" +__copyright__ = "Jayaram Kancherla" +__license__ = "MIT" + + +def test_fetch_dataset(): + sce = fetch_dataset("zeisel-brain-2015", "2023-12-14") + + print(sce) + assert isinstance(sce, SingleCellExperiment) diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..69f8159 --- /dev/null +++ b/tox.ini @@ -0,0 +1,93 @@ +# Tox configuration file +# Read more under https://tox.wiki/ +# THIS SCRIPT IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS! + +[tox] +minversion = 3.24 +envlist = default +isolated_build = True + + +[testenv] +description = Invoke pytest to run automated tests +setenv = + TOXINIDIR = {toxinidir} +passenv = + HOME + SETUPTOOLS_* +extras = + testing +commands = + pytest {posargs} + + +# # To run `tox -e lint` you need to make sure you have a +# # `.pre-commit-config.yaml` file. See https://pre-commit.com +# [testenv:lint] +# description = Perform static analysis and style checks +# skip_install = True +# deps = pre-commit +# passenv = +# HOMEPATH +# PROGRAMDATA +# SETUPTOOLS_* +# commands = +# pre-commit run --all-files {posargs:--show-diff-on-failure} + + +[testenv:{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 +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` + + +[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 +commands = + sphinx-build --color -b {env:BUILD} -d "{env:BUILDDIR}/doctrees" "{env:DOCSDIR}" "{env:BUILDDIR}/{env:BUILD}" {posargs} + + +[testenv:publish] +description = + Publish the package you have been developing to a package index server. + By default, it uses testpypi. If you really want to publish your package + to be publicly accessible in PyPI, use the `-- --repository pypi` option. +skip_install = True +changedir = {toxinidir} +passenv = + # See: https://twine.readthedocs.io/en/latest/ + TWINE_USERNAME + TWINE_PASSWORD + TWINE_REPOSITORY + TWINE_REPOSITORY_URL +deps = twine +commands = + python -m twine check dist/* + python -m twine upload {posargs:--repository {env:TWINE_REPOSITORY:testpypi}} dist/*