rectanglepy 0.0.39__tar.gz → 0.0.43__tar.gz

{rectanglepy-0.0.39 → rectanglepy-0.0.43}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.39
+current_version = 0.0.43
 tag = True
 commit = True
 

{rectanglepy-0.0.39 → rectanglepy-0.0.43}/.github/workflows/build.yaml

@@ -59,6 +59,8 @@ jobs:
               uses: actions/setup-python@v2
               with:
                   python-version: "3.10"
+            - name: Install twine
+              run: pip install twine
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build
             - name: Build package

{rectanglepy-0.0.39 → rectanglepy-0.0.43}/.github/workflows/release.yaml

@@ -76,10 +76,11 @@ jobs:
             - name: Install hatch
               run: pip install hatch
 
+            - name: Install twine
+              run: pip install twine
+
             - name: Build project for distribution
               run: hatch build
 
             - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_API_TOKEN }}
+              run: twine upload dist/* -u __token__ -p ${{ secrets.PYPI_API_TOKEN }}

{rectanglepy-0.0.39 → rectanglepy-0.0.43}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: rectanglepy
-Version: 0.0.39
+Version: 0.0.43
 Summary: A very interesting piece of code
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/bernheder/Rectangle

rectanglepy-0.0.43/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal 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
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

rectanglepy-0.0.43/docs/_templates/autosummary/class.rst

@@ -0,0 +1,61 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes table
+~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in attributes %}
+    ~{{ fullname }}.{{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods table
+~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in methods %}
+    {%- if item != '__init__' %}
+    ~{{ fullname }}.{{ item }}
+    {%- endif -%}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block attributes_documentation %}
+{% if attributes %}
+Attributes
+~~~~~~~~~~~
+
+{% for item in attributes %}
+
+.. autoattribute:: {{ [objname, item] | join(".") }}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
+
+{% block methods_documentation %}
+{% if methods %}
+Methods
+~~~~~~~
+
+{% for item in methods %}
+{%- if item != '__init__' %}
+
+.. automethod:: {{ [objname, item] | join(".") }}
+{%- endif -%}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}

rectanglepy-0.0.43/docs/api.md

@@ -0,0 +1,15 @@
+# API
+
+## Rectangle
+
+```{eval-rst}
+.. currentmodule:: rectanglepy
+
+.. autosummary::
+    :toctree: generated
+
+    rectangle
+    pp.build_rectangle_signatures
+    pp.RectangleSignatureResult
+    tl.deconvolution
+```

rectanglepy-0.0.43/docs/changelog.md

@@ -0,0 +1,3 @@
+```{include} ../CHANGELOG.md
+
+```

rectanglepy-0.0.43/docs/conf.py

@@ -0,0 +1,140 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# 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
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
+
+HERE = Path(__file__).parent
+sys.path.insert(0, str(HERE / "extensions"))
+
+
+# -- Project information -----------------------------------------------------
+
+info = metadata("rectanglepy")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+repository_url = f"https://github.com/bernheder/{project_name}"
+
+# The full version, including alpha/beta/rc tags
+release = info["Version"]
+
+bibtex_bibfiles = ["references.bib"]
+templates_path = ["_templates"]
+nitpicky = True  # Warn about broken links
+needs_sphinx = "4.0"
+
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "bernheder",  # Username
+    "github_repo": project_name,  # Repo name
+    "github_version": "main",  # Version
+    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings.
+# They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+    "myst_nb",
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.bibtex",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.mathjax",
+    "IPython.sphinxext.ipython_console_highlighting",
+    *[p.stem for p in (HERE / "extensions").glob("*.py")],
+]
+
+autosummary_generate = True
+autodoc_member_order = "groupwise"
+default_role = "literal"
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_param = True
+myst_heading_anchors = 6  # create anchors for h1-h6
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+typehints_defaults = "braces"
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
+
+intersphinx_mapping = {
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "python": ("https://docs.python.org/3", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+
+# -- 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 = "sphinx_book_theme"
+html_static_path = ["_static"]
+html_title = project_name
+
+html_theme_options = {
+    "repository_url": repository_url,
+    "use_repository_button": True,
+    "path_to_docs": "docs/",
+}
+
+pygments_style = "emacs"
+
+nitpick_ignore = [
+    # If building the documentation fails because of a missing link that is outside your control,
+    # you can add an exception to this list.
+    #     ("py:class", "igraph.Graph"),
+]
+
+print("Pygments style:", pygments_style)
+
+
+def setup(app):
+    """App setup hook."""
+    app.add_config_value(
+        "recommonmark_config",
+        {
+            "auto_toc_tree_section": "Contents",
+            "enable_auto_toc_tree": True,
+            "enable_math": True,
+            "enable_inline_math": False,
+            "enable_eval_rst": True,
+        },
+        True,
+    )

rectanglepy-0.0.43/docs/contributing.md

@@ -0,0 +1,197 @@
+# Contributing guide
+
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this repo, too.
+This document will not reproduce the entire content from there. Instead, it aims at summarizing the most important
+information to get you started on contributing.
+
+We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
+to the [scanpy developer guide][].
+
+## Installing dev dependencies
+
+In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
+the documentation_. It's easy to install them using `pip`:
+
+```bash
+cd Rectangle
+pip install -e ".[dev,test,doc]"
+```
+
+## Code-style
+
+This template uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either
+automatically fix issues with the code, or raise an error message. See [pre-commit checks](template_usage.md#pre-commit-checks) for
+a full list of checks enabled for this repository.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub. If you didn't run `pre-commit` before
+pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+
+If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
+
+```bash
+git pull --rebase
+```
+
+to integrate the changes into yours.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+
+Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [black][black-editors]
+and [prettier][prettier-editors].
+
+[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
+[prettier-editors]: https://prettier.io/docs/en/editors.html
+
+## Writing tests
+
+```{note}
+Remember to first install the package with `pip install '-e[dev,test]'`
+```
+
+This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
+to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the
+command line by executing
+
+```bash
+pytest
+```
+
+in the root of the repository. Continuous integration will automatically run the tests on all pull requests.
+
+[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+
+## Publishing a release
+
+### Updating the version number
+
+Before making a release, you need to update the version number. Please adhere to [Semantic Versioning][semver], in brief
+
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1.  MAJOR version when you make incompatible API changes,
+> 2.  MINOR version when you add functionality in a backwards compatible manner, and
+> 3.  PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
+
+We use [bump2version][] to automatically update the version number in all places and automatically create a git tag.
+Run one of the following commands in the root of the repository
+
+```bash
+bump2version patch
+bump2version minor
+bump2version major
+```
+
+Once you are done, run
+
+```
+git push --tags
+```
+
+to publish the created tag on GitHub.
+
+[bump2version]: https://github.com/c4urself/bump2version
+
+### Building and publishing the package on PyPI
+
+Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run
+
+```bash
+python -m build
+```
+
+This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.
+
+Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
+
+```bash
+twine check dist/*
+```
+
+and finally publishing it with:
+
+```bash
+twine upload dist/*
+```
+
+Provide your username and password when requested and then go check out your package on [PyPI][]!
+
+For more information, follow the [Python packaging tutorial][].
+
+It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
+in the cookiecutter-scverse template.
+
+[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
+[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
+
+-   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+-   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+-   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+-   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+
+See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
+on how to write documentation.
+
+### Tutorials with myst-nb and jupyter notebooks
+
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
+Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
+It is your reponsibility to update and re-run the notebook whenever necessary.
+
+If you are interested in automatically running notebooks as part of the continuous integration, please check
+out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
+repository.
+
+#### Hints
+
+-   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+    if you do so can sphinx automatically create a link to the external documentation.
+-   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+    the `nitpick_ignore` list in `docs/conf.py`
+
+#### Building the docs locally
+
+```bash
+cd docs
+make html
+open _build/html/index.html
+```
+
+<!-- Links -->
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
+[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
+[codecov]: https://about.codecov.io/sign-up/
+[codecov docs]: https://docs.codecov.com/docs
+[codecov bot]: https://docs.codecov.com/docs/team-bot
+[codecov app]: https://github.com/apps/codecov
+[pre-commit.ci]: https://pre-commit.ci/
+[readthedocs.org]: https://readthedocs.org/
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[jupytext]: https://jupytext.readthedocs.io/en/latest/
+[pre-commit]: https://pre-commit.com/
+[anndata]: https://github.com/scverse/anndata
+[mudata]: https://github.com/scverse/mudata
+[pytest]: https://docs.pytest.org/
+[semver]: https://semver.org/
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
+[pypi]: https://pypi.org/

rectanglepy-0.0.43/docs/extensions/typed_returns.py

@@ -0,0 +1,32 @@
+# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
+# with some minor adjustment
+from __future__ import annotations
+
+import re
+from collections.abc import Generator, Iterable
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+    for line in lines:
+        if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
+            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+        else:
+            yield line
+
+
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = self._dedent(self._consume_to_next_section())
+    if lines_raw[0] == ":":
+        del lines_raw[0]
+    lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
+    if lines and lines[-1]:
+        lines.append("")
+    return lines
+
+
+def setup(app: Sphinx):
+    """Set app."""
+    NumpyDocstring._parse_returns_section = _parse_returns_section

rectanglepy-0.0.43/docs/index.md

@@ -0,0 +1,16 @@
+```{include} ../README.md
+
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+
+api.md
+notebooks/example
+changelog.md
+contributing.md
+references.md
+
+
+```

rectanglepy-0.0.43/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd