From 49af3330e7b84f5e2bb0f3edc3101484a143b07c Mon Sep 17 00:00:00 2001 From: Adam Li Date: Thu, 28 Apr 2022 14:57:12 -0400 Subject: [PATCH 1/5] Adding doc folder --- .flake8 | 26 ++ .gitignore | 3 + CONTRIBUTING.md | 177 ++++++++++++ LICENSE | 29 ++ MANIFEST.in | 12 +- Makefile | 21 +- README.md | 9 +- doc/Makefile | 190 ++++++++++++ doc/_static/favicon.ico | Bin 0 -> 7738 bytes doc/_static/js/copybutton.js | 63 ++++ doc/_static/mne_helmet.png | Bin 0 -> 27218 bytes doc/_static/mne_logo_small.png | Bin 0 -> 980 bytes doc/_static/style.css | 26 ++ doc/_templates/autosummary/class.rst | 10 + doc/_templates/autosummary/function.rst | 12 + doc/_templates/docs-navbar.html | 20 ++ doc/_templates/docs-toc.html | 13 + doc/_templates/layout.html | 19 ++ doc/_templates/version-switcher.html | 11 + doc/api.rst | 27 ++ doc/authors.inc | 1 + doc/bibliography.rst | 12 + doc/conf.py | 273 ++++++++++++++++++ doc/index.rst | 39 +++ doc/install.rst | 65 +++++ doc/make.bat | 242 ++++++++++++++++ doc/references.bib | 22 ++ doc/sphinxext/gh_substitutions.py | 33 +++ doc/whats_new.rst | 46 +++ doc/whats_new_previous_releases.rst | 20 ++ examples/automatic_artifact_correction_ica.py | 7 +- mne_icalabel/features.py | 38 +-- mne_icalabel/network.py | 6 +- mne_icalabel/tests/test_features.py | 95 ++---- mne_icalabel/tests/test_network.py | 35 +-- mne_icalabel/tests/test_utils.py | 26 +- mne_icalabel/utils.py | 24 +- pyproject.toml | 24 ++ requirements.txt | 3 +- requirements_testing.txt | 1 + setup.cfg | 9 + 41 files changed, 1523 insertions(+), 166 deletions(-) create mode 100644 .flake8 create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE create mode 100644 doc/Makefile create mode 100644 doc/_static/favicon.ico create mode 100644 doc/_static/js/copybutton.js create mode 100644 doc/_static/mne_helmet.png create mode 100644 doc/_static/mne_logo_small.png create mode 100644 doc/_static/style.css create mode 100644 doc/_templates/autosummary/class.rst create mode 100644 doc/_templates/autosummary/function.rst create mode 100644 doc/_templates/docs-navbar.html create mode 100644 doc/_templates/docs-toc.html create mode 100755 doc/_templates/layout.html create mode 100644 doc/_templates/version-switcher.html create mode 100644 doc/api.rst create mode 100644 doc/authors.inc create mode 100644 doc/bibliography.rst create mode 100644 doc/conf.py create mode 100644 doc/index.rst create mode 100644 doc/install.rst create mode 100644 doc/make.bat create mode 100644 doc/references.bib create mode 100644 doc/sphinxext/gh_substitutions.py create mode 100644 doc/whats_new.rst create mode 100644 doc/whats_new_previous_releases.rst create mode 100644 pyproject.toml diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..3e17d8ea --- /dev/null +++ b/.flake8 @@ -0,0 +1,26 @@ + +[flake8] +max-line-length = 115 + +ignore = + # these rules don't play well with black + # whitespace before : + E203 + # line break before binary operator + W503 + E241,E305,W504,W605,E731 + + +exclude = + .venv + .git + __pycache__ + docs/build + dist + .mypy_cache + __init__.py + +per-file-ignores = + # __init__.py files are allowed to have unused imports and lines-too-long + */__init__.py:F401 + */**/**/__init__.py:F401,E501 diff --git a/.gitignore b/.gitignore index 7050154d..dd0e8599 100644 --- a/.gitignore +++ b/.gitignore @@ -26,6 +26,9 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST +_build/ +generated/ +auto_examples/ # PyInstaller # Usually these files are written by a python script from a template diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..71c21b91 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,177 @@ +# Contributing + +Thanks for considering contributing! Please read this document to learn the various ways you can contribute to this project and how to go about doing it. + +## Bug reports and feature requests + +### Did you find a bug? + +First, do [a quick search](https://github.com/mne-tools/mne-icalabel/issues) to see whether your issue has already been reported. +If your issue has already been reported, please comment on the existing issue. + +Otherwise, open [a new GitHub issue](https://github.com/mne-tools/mne-icalabel/issues). Be sure to include a clear title +and description. The description should include as much relevant information as possible. The description should +explain how to reproduce the erroneous behavior as well as the behavior you expect to see. Ideally you would include a +code sample or an executable test case demonstrating the expected behavior. + +### Do you have a suggestion for an enhancement or new feature? + +We use GitHub issues to track feature requests. Before you create an feature request: + +* Make sure you have a clear idea of the enhancement you would like. If you have a vague idea, consider discussing +it first on a GitHub issue. +* Check the documentation to make sure your feature does not already exist. +* Do [a quick search](https://github.com/mne-tools/mne-icalabel/issues) to see whether your feature has already been suggested. + +When creating your request, please: + +* Provide a clear title and description. +* Explain why the enhancement would be useful. It may be helpful to highlight the feature in other libraries. +* Include code examples to demonstrate how the enhancement would be used. + +## Making a pull request + +When you're ready to contribute code to address an open issue, please follow these guidelines to help us be able to review your pull request (PR) quickly. + +1. **Initial setup** (only do this once) + +
Expand details 👇
+ + If you haven't already done so, please [fork](https://help.github.com/en/enterprise/2.13/user/articles/fork-a-repo) this repository on GitHub. + + Then clone your fork locally with + + git clone https://github.com/USERNAME/mne-icalabel.git + + or + + git clone git@github.com:USERNAME/mne-icalabel.git + + At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/mne-icalabel.git, but doesn't know anything the *main* repo, [https://github.com/mne-tools/mne-icalabel.git](https://github.com/mne-tools/mne-icalabel). You can see this by running + + git remote -v + + which will output something like this: + + origin https://github.com/USERNAME/mne-icalabel.git (fetch) + origin https://github.com/USERNAME/mne-icalabel.git (push) + + This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/mne-tools/mne-icalabel.git](https://github.com/mne-tools/mne-icalabel). To do this, run the following: + + git remote add upstream https://github.com/mne-tools/mne-icalabel.git + + Now if you do `git remote -v` again, you'll see + + origin https://github.com/USERNAME/mne-icalabel.git (fetch) + origin https://github.com/USERNAME/mne-icalabel.git (push) + upstream https://github.com/mne-tools/mne-icalabel.git (fetch) + upstream https://github.com/mne-tools/mne-icalabel.git (push) + + Finally, you'll need to create a Python 3 virtual environment suitable for working on this project. There a number of tools out there that making working with virtual environments easier. + The most direct way is with the [`venv` module](https://docs.python.org/3.7/library/venv.html) in the standard library, but if you're new to Python or you don't already have a recent Python 3 version installed on your machine, + we recommend [Miniconda](https://docs.conda.io/en/latest/miniconda.html). + + On Mac, for example, you can install Miniconda with [Homebrew](https://brew.sh/): + + brew install miniconda + + Then you can create and activate a new Python environment by running: + + conda create -n mne-icalabel python=3.9 + conda activate mne-icalabel + + Once your virtual environment is activated, you can install your local clone in "editable mode" with + + pip install -U pip setuptools wheel + pip install -e .[dev] + + The "editable mode" comes from the `-e` argument to `pip`, and essential just creates a symbolic link from the site-packages directory of your virtual environment to the source code in your local clone. That way any changes you make will be immediately reflected in your virtual environment. + +
+ +2. **Ensure your fork is up-to-date** + +
Expand details 👇
+ + Once you've added an "upstream" remote pointing to [https://github.com/allenai/python-package-temlate.git](https://github.com/mne-tools/mne-icalabel), keeping your fork up-to-date is easy: + + git checkout main # if not already on main + git pull --rebase upstream main + git push + +
+ +3. **Create a new branch to work on your fix or enhancement** + +
Expand details 👇
+ + Committing directly to the main branch of your fork is not recommended. It will be easier to keep your fork clean if you work on a separate branch for each contribution you intend to make. + + You can create a new branch with + + # replace BRANCH with whatever name you want to give it + git checkout -b BRANCH + git push -u origin BRANCH + +
+ +4. **Test your changes** + +
Expand details 👇
+ + Our continuous integration (CI) testing runs [a number of checks](https://github.com/mne-tools/mne-icalabel/actions) for each pull request on [GitHub Actions](https://github.com/features/actions). You can run most of these tests locally, which is something you should do *before* opening a PR to help speed up the review process and make it easier for us. + + For convenience you can run a check for all style components necessary: + + make run-checks + + This will run isort, black, flake8, mypy, check-manifest, and pydocstyle on the entire repository. Please fix your errors if you see any. + + First, you should run [`isort`](https://github.com/PyCQA/isort) and [`black`](https://github.com/psf/black) to make sure you code is formatted consistently. + Many IDEs support code formatters as plugins, so you may be able to setup isort and black to run automatically every time you save. + For example, [`black.vim`](https://github.com/psf/black/tree/master/plugin) will give you this functionality in Vim. But both `isort` and `black` are also easy to run directly from the command line. + Just run this from the root of your clone: + + isort . + black . + + Our CI also uses [`flake8`](https://github.com/mne-tools/mne-icalabel/tree/main/tests) to lint the code base and [`mypy`](http://mypy-lang.org/) for type-checking. You should run both of these next with + + flake8 . + + and + + mypy . + + We also strive to maintain high test coverage, so most contributions should include additions to [the unit tests](https://github.com/mne-tools/mne-icalabel/tree/main/tests). These tests are run with [`pytest`](https://docs.pytest.org/en/latest/), which you can use to locally run any test modules that you've added or changed. + + For example, if you've fixed a bug in `causal_networkx/a/b.py`, you can run the tests specific to that module with + + pytest -v tests/a/b_test.py + + Our CI will automatically check that test coverage stays above a certain threshold (around 90%). To check the coverage locally in this example, you could run + + pytest -v --cov causal_networkx.a.b tests/a/b_test.py + + If your contribution involves additions to any public part of the API, we require that you write docstrings + for each function, method, class, or module that you add. + See the [Writing docstrings](#writing-docstrings) section below for details on the syntax. + You should test to make sure the API documentation can build without errors by running + + make docs + + If the build fails, it's most likely due to small formatting issues. If the error message isn't clear, feel free to comment on this in your pull request. + + And finally, please update the [CHANGELOG](https://github.com/mne-tools/mne-icalabel/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top. + + After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/mne-tools/mne-icalabel/pulls). + Make sure you have a clear description of the problem and the solution, and include a link to relevant issues. + + We look forward to reviewing your PR! + +
+ +### Writing docstrings + +We use [Sphinx](https://www.sphinx-doc.org/en/master/index.html) to build our API docs, which automatically parses all docstrings +of public classes and methods. All docstrings should adhere to the [Numpy styling convention](https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html). diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..e51514ef --- /dev/null +++ b/LICENSE @@ -0,0 +1,29 @@ +BSD 3-Clause License + +Copyright (c) 2022, MNE +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/MANIFEST.in b/MANIFEST.in index 31eca89c..cd7c8478 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,16 +1,22 @@ include *.png include *.txt +include *.md include Makefile + +# examples recursive-include examples *.py recursive-include examples *.txt + +# main files recursive-include mne_icalabel *.pt recursive-include mne_icalabel *.py -recursive-include test_data *.mat +exclude .circleci/config.yml + +# exclude all data files +recursive-exclude mne_icalabel *.txt recursive-exclude mne_icalabel *.fif recursive-exclude mne_icalabel *.m - -exclude .circleci/config.yml recursive-exclude mne_icalabel *.fdt recursive-exclude mne_icalabel *.mat recursive-exclude mne_icalabel *.set \ No newline at end of file diff --git a/Makefile b/Makefile index 57cfd69a..3c2de902 100644 --- a/Makefile +++ b/Makefile @@ -91,7 +91,7 @@ flake: black: @if command -v black > /dev/null; then \ echo "Running black"; \ - black --check mne_icalabel examples; \ + black mne_icalabel examples; \ else \ echo "black not found, please install it!"; \ exit 1; \ @@ -114,11 +114,30 @@ check-manifest: check-readme: python setup.py check --restructuredtext --strict +isort: + @if command -v isort > /dev/null; then \ + echo "Running isort"; \ + isort mne_icalabel examples; \ + else \ + echo "isort not found, please install it!"; \ + exit 1; \ + fi; + @echo "isort passed" + pep: @$(MAKE) -k black pydocstyle codespell-error check-manifest docstyle: pydocstyle +run-checks: + isort --check . + black --check mne_icalabel examples + flake8 . + mypy . + @$(MAKE) pydocstyle + check-manifest + @$(MAKE) codespell-error + build-doc: @echo "Building documentation" make -C doc/ clean diff --git a/README.md b/README.md index c3b72e81..883403b2 100644 --- a/README.md +++ b/README.md @@ -19,22 +19,23 @@ This package aims at automating that process conforming to the popular MNE-Pytho TBD. Add example code for how this works. # Documentation -TBD +[Stable version](https://mne.tools/mne-icalabel/stable/index.html) documentation. +[Dev version](https://mne.tools/mne-icalabel/dev/index.html) documentation. # Installation To get the latest code using [git](https://git-scm.com/), open a terminal and type: - git clone git://github.com/jacobf18/iclabel-python.git + git clone git://github.com/mne-tools/mne-icalabel.git cd iclabel-python pip install -e . or one can install directly using pip - pip install --user -U https://api.github.com/repos/jacobf18/iclabel-python/zipball/main + pip install --user -U https://api.github.com/repos/mne-tools/mne-icalabel/zipball/main Alternatively, you can also download a -`zip file of the latest development version `__. +`zip file of the latest development version `__. ## Converting MatConvNet to PyTorch diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 00000000..51a51428 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,190 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = -nWT --keep-going +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(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 http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + -rm -rf auto_examples/ + -rm -rf generated/* + -rm -rf modules/generated/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +html-noplot: + $(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/project-template.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/project-template.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/project-template" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/project-template" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. 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+ On this page +
+{%- endif %} + + + +{% include "edit_this_page.html" %} diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html new file mode 100755 index 00000000..6b3d45b5 --- /dev/null +++ b/doc/_templates/layout.html @@ -0,0 +1,19 @@ +{%- extends "pydata_sphinx_theme/layout.html" %} + +{% block fonts %} + + + + + +{% endblock %} + +{% block extrahead %} + + + +{{ super() }} +{% endblock %} diff --git a/doc/_templates/version-switcher.html b/doc/_templates/version-switcher.html new file mode 100644 index 00000000..add61722 --- /dev/null +++ b/doc/_templates/version-switcher.html @@ -0,0 +1,11 @@ +
+ +
+ {%- for ver, txt in versions_dropdown.items() %} + {{ txt }} + {%- endfor %} +
+
diff --git a/doc/api.rst b/doc/api.rst new file mode 100644 index 00000000..819023b3 --- /dev/null +++ b/doc/api.rst @@ -0,0 +1,27 @@ +### +API +### + +:py:mod:`mne_icalabel`: + +.. automodule:: mne_icalabel + :no-members: + :no-inherited-members: + +This is the application programming interface (API) reference +for classes (``CamelCase`` names) and functions +(``underscore_case`` names) of MNE-Connectivity, grouped thematically by analysis +stage. The data structure classes contain different types of connectivity data +and are described below. + +Most-used functions +=================== + +.. currentmodule:: mne_icalabel + +.. autosummary:: + :toctree: generated/ + + label_components + generate_features + ICLabelNet \ No newline at end of file diff --git a/doc/authors.inc b/doc/authors.inc new file mode 100644 index 00000000..14975a20 --- /dev/null +++ b/doc/authors.inc @@ -0,0 +1 @@ +.. _Adam Li: https://github.com/adam2392 diff --git a/doc/bibliography.rst b/doc/bibliography.rst new file mode 100644 index 00000000..4a310352 --- /dev/null +++ b/doc/bibliography.rst @@ -0,0 +1,12 @@ +:orphan: + +.. _general_bibliography: + +General bibliography +==================== + +The references below are arranged alphabetically by first author. + +.. bibliography:: ./references.bib + :all: + :list: enumerated diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 00000000..7f7a6550 --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,273 @@ +"""Configure details for documentation with sphinx.""" +from datetime import date +import os +import sys +import warnings + +import sphinx_gallery # noqa: F401 +from sphinx_gallery.sorting import ExampleTitleSortKey + +import mne +sys.path.insert(0, os.path.abspath("..")) +import mne_icalabel # noqa: E402 + +# 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. +curdir = os.path.dirname(__file__) +sys.path.append(os.path.abspath(os.path.join(curdir, '..'))) +sys.path.append(os.path.abspath(os.path.join(curdir, '..', 'mne_icalabel'))) +sys.path.append(os.path.abspath(os.path.join(curdir, 'sphinxext'))) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +needs_sphinx = '4.0' + +# 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.autosummary', + 'sphinx.ext.doctest', + 'sphinx.ext.intersphinx', + 'sphinx_autodoc_typehints', + 'sphinx.ext.mathjax', + 'sphinx.ext.viewcode', + 'sphinx_gallery.gen_gallery', + 'sphinxcontrib.bibtex', + 'numpydoc', + 'sphinx_copybutton', + 'gh_substitutions', # custom extension, see sphinxext/gh_substitutions.py +] + +# configure sphinx-copybutton +copybutton_prompt_text = r">>> |\.\.\. |\$ " +copybutton_prompt_is_regexp = True + +# generate autosummary even if no references +# -- sphinx.ext.autosummary +autosummary_generate = True + +autodoc_default_options = {'inherited-members': None} +autodoc_typehints = 'signature' + +# prevent jupyter notebooks from being run even if empty cell +# nbsphinx_execute = 'never' +# nbsphinx_allow_errors = True + +error_ignores = { + # These we do not live by: + 'GL01', # Docstring should start in the line immediately after the quotes + 'EX01', 'EX02', # examples failed (we test them separately) + 'ES01', # no extended summary + 'SA01', # no see also + 'YD01', # no yields section + 'SA04', # no description in See Also + 'PR04', # Parameter "shape (n_channels" has no type + 'RT02', # The first line of the Returns section should contain only the type, unless multiple values are being returned # noqa + # XXX should also verify that | is used rather than , to separate params + # XXX should maybe also restore the parameter-desc-length < 800 char check +} + +# -- numpydoc +# Below is needed to prevent errors +numpydoc_xref_param_type = True +numpydoc_class_members_toctree = False +numpydoc_attributes_as_param_list = True +numpydoc_use_blockquotes = True +numpydoc_xref_ignore = { + # words + 'instance', 'instances', 'of', 'default', 'shape', 'or', + 'with', 'length', 'pair', 'matplotlib', 'optional', 'kwargs', 'in', + 'dtype', 'object', 'self.verbose', + # shapes + 'n_times', 'obj', 'n_chan', 'n_epochs', 'n_picks', 'n_ch_groups', + 'n_node_names', 'n_tapers', 'n_signals', 'n_step', 'n_freqs', + 'epochs', 'freqs', 'times', 'arrays', 'lists', 'func', 'n_nodes', + 'n_estimated_nodes', 'n_samples', 'n_channels', 'Renderer', + 'n_ytimes', 'n_ychannels', 'n_events' +} +numpydoc_xref_aliases = { + # Python + 'file-like': ':term:`file-like `', + # Matplotlib + 'colormap': ':doc:`colormap `', + 'color': ':doc:`color `', + 'collection': ':doc:`collections `', + 'Axes': 'matplotlib.axes.Axes', + 'Figure': 'matplotlib.figure.Figure', + 'Axes3D': 'mpl_toolkits.mplot3d.axes3d.Axes3D', + 'PolarAxes': 'matplotlib.projections.polar.PolarAxes', + 'ColorbarBase': 'matplotlib.colorbar.ColorbarBase', + # joblib + 'joblib.Parallel': 'joblib.Parallel', + # MNE + 'Label': 'mne.Label', 'Forward': 'mne.Forward', 'Evoked': 'mne.Evoked', + 'Info': 'mne.Info', 'SourceSpaces': 'mne.SourceSpaces', + 'SourceMorph': 'mne.SourceMorph', + 'Epochs': 'mne.Epochs', 'Layout': 'mne.channels.Layout', + 'EvokedArray': 'mne.EvokedArray', 'BiHemiLabel': 'mne.BiHemiLabel', + 'AverageTFR': 'mne.time_frequency.AverageTFR', + 'EpochsTFR': 'mne.time_frequency.EpochsTFR', + 'Raw': 'mne.io.Raw', 'ICA': 'mne.preprocessing.ICA', +} +numpydoc_validate = True +numpydoc_validation_checks = {'all'} | set(error_ignores) +numpydoc_validation_exclude = { # set of regex + # dict subclasses + r'\.clear', r'\.get$', r'\.copy$', r'\.fromkeys', r'\.items', r'\.keys', + r'\.pop', r'\.popitem', r'\.setdefault', r'\.update', r'\.values', + # list subclasses + r'\.append', r'\.count', r'\.extend', r'\.index', r'\.insert', r'\.remove', + r'\.sort', + # we currently don't document these properly (probably okay) + r'\.__getitem__', r'\.__contains__', r'\.__hash__', r'\.__mul__', + r'\.__sub__', r'\.__add__', r'\.__iter__', r'\.__div__', r'\.__neg__', + r'plot_circle' +} + + +default_role = 'py:obj' + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'MNE-ICALabel' +td = date.today() +copyright = u'2021-%s, MNE Developers. Last updated on %s' % (td.year, + td.isoformat()) + +author = u'Adam Li' + +# 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. +# +# The short X.Y version. +version = mne_icalabel.__version__ +# The full version, including alpha/beta/rc tags. +release = version + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', "**.ipynb_checkpoints"] + +# HTML options (e.g., theme) +# see: https://sphinx-bootstrap-theme.readthedocs.io/en/latest/README.html +# Clean up sidebar: Do not show "Source" link +html_show_sourcelink = False +html_copy_source = False + +html_theme = 'pydata_sphinx_theme' + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] +html_static_path = ['_static'] +html_css_files = ['style.css'] + +# 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 = { + 'icon_links': [ + dict(name='GitHub', + url='https://github.com/mne-tools/MNE-ICALabel', + icon='fab fa-github-square'), + ], + 'use_edit_page_button': False, + 'navigation_with_keys': False, + 'show_toc_level': 1, + 'navbar_end': ['version-switcher', 'navbar-icon-links'], +} +# Custom sidebar templates, maps document names to template names. +html_sidebars = { + 'index': ['search-field.html'], +} + +html_context = { + 'versions_dropdown': { + 'dev': 'v0.1 (devel)', + }, +} + +# html_sidebars = {'**': ['localtoc.html']} + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = { + 'python': ('https://docs.python.org/3', None), + 'mne': ('https://mne.tools/dev', None), + 'numpy': ('https://numpy.org/devdocs', None), + 'scipy': ('https://scipy.github.io/devdocs', None), + 'matplotlib': ('https://matplotlib.org/stable', None), + 'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None), + 'sklearn': ('https://scikit-learn.org/stable', None), + 'joblib': ('https://joblib.readthedocs.io/en/latest', None), + "torch": ("https://pytorch.org/docs/stable", None), +} +intersphinx_timeout = 5 + +# Resolve binder filepath_prefix. From the docs: +# "A prefix to append to the filepath in the Binder links. You should use this +# if you will store your built documentation in a sub-folder of a repository, +# instead of in the root." +# we will store dev docs in a `dev` subdirectory and all other docs in a +# directory "v" + version_str. E.g., "v0.3" +if 'dev' in version: + filepath_prefix = 'dev' +else: + filepath_prefix = 'v{}'.format(version) + +os.environ['_MNE_BUILDING_DOC'] = 'true' +scrapers = ('matplotlib',) +try: + with warnings.catch_warnings(): + warnings.filterwarnings("ignore", category=DeprecationWarning) + import pyvista + pyvista.OFF_SCREEN = False +except Exception: + pass +else: + scrapers += ('pyvista',) +if 'pyvista' in scrapers: + brain_scraper = mne.viz._brain._BrainScraper() + scrapers = list(scrapers) + scrapers.insert(scrapers.index('pyvista'), brain_scraper) + scrapers = tuple(scrapers) + +sphinx_gallery_conf = { + 'doc_module': 'mne_icalabel', + 'reference_url': { + 'mne_icalabel': None, + }, + 'backreferences_dir': 'generated', + 'plot_gallery': 'True', # Avoid annoying Unicode/bool default warning + 'within_subsection_order': ExampleTitleSortKey, + 'examples_dirs': ['../examples'], + 'gallery_dirs': ['auto_examples'], + 'filename_pattern': '^((?!sgskip).)*$', + 'matplotlib_animations': True, + 'compress_images': ('images', 'thumbnails'), + 'image_scrapers': scrapers, +} + +# sphinxcontrib-bibtex +bibtex_bibfiles = ['./references.bib'] +bibtex_style = 'unsrt' +bibtex_footbibliography_header = '' + + +# Enable nitpicky mode - which ensures that all references in the docs +# resolve. +nitpicky = True +nitpick_ignore = [] diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 00000000..20e931be --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,39 @@ +**mne-icalabel** +=================== + +mne-icalabel is a Python package for labeling independent components that stem +from an `Independent Component Analysis (ICA) `. + +We encourage you to use the package for your research and also build on top +with relevant Pull Requests. See our examples for walk-throughs of how to use the package. + +Contents +-------- + +.. toctree:: + :maxdepth: 2 + :caption: Getting started: + + whats_new + install + api + auto_examples/index + +.. toctree:: + :hidden: + :caption: Development + + License + Contributing + +License +------- + +**mne-icalabel** is licensed under `BSD 3.0 `_. +A full copy of the license can be found `on GitHub `_. + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` diff --git a/doc/install.rst b/doc/install.rst new file mode 100644 index 00000000..db0d5f60 --- /dev/null +++ b/doc/install.rst @@ -0,0 +1,65 @@ +:orphan: + +Installation +============ + +Dependencies +------------ + +* ``mne`` (>=1.0) +* ``numpy`` (>=1.14) +* ``scipy`` (>=1.5.0) +* ``joblib`` (>=1.0.0) +* ``scikit-learn`` (>=1.1) +* ``torch`` (for running pytorch neural networks) +* ``python-picard`` (for running ICA) +* ``matplotlib`` (optional, for using the interactive data inspector) + +We require that you use Python 3.8 or higher. +You may choose to install ``mne-icalabel`` `via pip <#Installation via pip>`_, +or conda. + +Installation via Conda +---------------------- + +To install mne-icalabel using conda in a virtual environment, +simply run the following at the root of the repository: + +.. code-block:: bash + + # with python>=3.8 at least + conda create -n mne + conda activate mne + conda install -c conda-forge mne-icalabel + + +Installation via Pip +-------------------- + +To install mne-icalabel including all dependencies required to use all features, +simply run the following at the root of the repository: + +.. code-block:: bash + + python -m venv .venv + pip install -U mne-icalabel + +If you want to install a snapshot of the current development version, run: + +.. code-block:: bash + + pip install --user -U https://api.github.com/repos/mne-tools/mne-icalabel/zipball/main + +To check if everything worked fine, the following command should not give any +error messages: + +.. code-block:: bash + + python -c 'import mne_icalabel' + +mne-icalabel works best with the latest stable release of MNE-Python. To ensure +MNE-Python is up-to-date, run: + +.. code-block:: bash + + pip install --user -U mne diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 00000000..79c1e198 --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,242 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. xml to make Docutils-native XML files + echo. pseudoxml to make pseudoxml-XML files for display purposes + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + + +%SPHINXBUILD% 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.http://sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\project-template.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\project-template.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdf" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdfja" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf-ja + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +if "%1" == "xml" ( + %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The XML files are in %BUILDDIR%/xml. + goto end +) + +if "%1" == "pseudoxml" ( + %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. + goto end +) + +:end diff --git a/doc/references.bib b/doc/references.bib new file mode 100644 index 00000000..4dd8060e --- /dev/null +++ b/doc/references.bib @@ -0,0 +1,22 @@ +% Encoding: UTF-8 +@article{AvantsEtAl2008, + author = {Avants, Brian B. and Epstein, Charles L. and Grossman, Murray C. and Gee, James C.}, + doi = {10.1016/j.media.2007.06.004}, + journal = {Medical Image Analysis}, + number = {1}, + pages = {26-41}, + shorttitle = {Symmetric Diffeomorphic Image Registration with Cross-Correlation}, + title = {Symmetric Diffeomorphic Image Registration with Cross-Correlation: Evaluating Automated Labeling of Elderly and Neurodegenerative Brain}, + volume = {12}, + year = {2008} +} + +@book{OppenheimEtAl1999, + address = {Upper Saddle River, NJ}, + edition = {2 edition}, + title = {Discrete-{Time} {Signal} {Processing}}, + isbn = {978-0-13-754920-7}, + publisher = {Prentice Hall}, + author = {Oppenheim, Alan V. and Schafer, Ronald W. and Buck, John R.}, + year = {1999} +} diff --git a/doc/sphinxext/gh_substitutions.py b/doc/sphinxext/gh_substitutions.py new file mode 100644 index 00000000..a1eddfbc --- /dev/null +++ b/doc/sphinxext/gh_substitutions.py @@ -0,0 +1,33 @@ +"""Provide a convenient way to link to GitHub issues and pull requests. + +Link to any issue or PR using :gh:`issue-or-pr-number`. + +Adapted from: +https://doughellmann.com/blog/2010/05/09/defining-custom-roles-in-sphinx/ + +""" +from docutils.nodes import reference +from docutils.parsers.rst.roles import set_classes + + +def gh_role(name, rawtext, text, lineno, inliner, options={}, content=[]): + """Link to a GitHub issue.""" + try: + # issue/PR mode (issues/PR-num will redirect to pull/PR-num) + int(text) + except ValueError: + # direct link mode + slug = text + else: + slug = 'issues/' + text + text = '#' + text + ref = 'https://github.com/mne-tools/mne-connectivity/' + slug + set_classes(options) + node = reference(rawtext, text, refuri=ref, **options) + return [node], [] + + +def setup(app): + """Do setup.""" + app.add_role('gh', gh_role) + return diff --git a/doc/whats_new.rst b/doc/whats_new.rst new file mode 100644 index 00000000..49a80c9a --- /dev/null +++ b/doc/whats_new.rst @@ -0,0 +1,46 @@ +:orphan: + +.. _whats_new: + + +What's new? +=========== + +Here we list a changelog of MNE-ICALabel. + +.. contents:: Contents + :local: + :depth: 3 + +.. currentmodule:: mne_icalabel + +.. _current: + +Version 0.1 (Unreleased) +------------------------ + +... + +Enhancements +~~~~~~~~~~~~ + + +Bug +~~~ + +- + +API +~~~ + +- + +Authors +~~~~~~~ + +* `Adam Li`_ +* `TODO fill in other authors name and add to authors.inc` + +:doc:`Find out what was new in previous releases ` + +.. include:: authors.inc diff --git a/doc/whats_new_previous_releases.rst b/doc/whats_new_previous_releases.rst new file mode 100644 index 00000000..a328fc16 --- /dev/null +++ b/doc/whats_new_previous_releases.rst @@ -0,0 +1,20 @@ +:orphan: + +.. _whats_new_in_previous_releases: + +.. currentmodule:: mne_connectivity + +What was new in previous releases? +================================== + +Version 0.1 (2022-03-01) +------------------------ + +Authors +~~~~~~~ + +People who contributed to this release (in alphabetical order): + +* `Adam Li`_ + +.. include:: authors.inc diff --git a/examples/automatic_artifact_correction_ica.py b/examples/automatic_artifact_correction_ica.py index d26d7a73..32f7dfc9 100644 --- a/examples/automatic_artifact_correction_ica.py +++ b/examples/automatic_artifact_correction_ica.py @@ -21,8 +21,9 @@ # %% import os + import mne -from mne.preprocessing import ICA, create_eog_epochs, create_ecg_epochs +from mne.preprocessing import ICA, create_ecg_epochs, create_eog_epochs sample_data_folder = mne.datasets.sample.data_path() sample_data_raw_file = os.path.join( @@ -204,7 +205,5 @@ ica.apply(reconst_raw) raw.plot(order=artifact_picks, n_channels=len(artifact_picks), show_scrollbars=False) -reconst_raw.plot( - order=artifact_picks, n_channels=len(artifact_picks), show_scrollbars=False -) +reconst_raw.plot(order=artifact_picks, n_channels=len(artifact_picks), show_scrollbars=False) del reconst_raw diff --git a/mne_icalabel/features.py b/mne_icalabel/features.py index c18b4f01..8330f702 100644 --- a/mne_icalabel/features.py +++ b/mne_icalabel/features.py @@ -1,13 +1,13 @@ -from typing import Union, Tuple +from typing import Tuple, Union +import numpy as np from mne import BaseEpochs from mne.io import BaseRaw from mne.preprocessing import ICA -import numpy as np from numpy.typing import NDArray from scipy.signal import resample_poly -from .utils import pol2cart, mne_to_eeglab_locs, gdatav4, _next_power_of_2 +from .utils import _next_power_of_2, gdatav4, mne_to_eeglab_locs, pol2cart def get_features(inst: Union[BaseRaw, BaseEpochs], ica: ICA): @@ -75,9 +75,7 @@ def retrieve_eeglab_icawinv( return icawinv, weights -def compute_ica_activations( - inst: Union[BaseRaw, BaseEpochs], ica: ICA -) -> NDArray[float]: +def compute_ica_activations(inst: Union[BaseRaw, BaseEpochs], ica: ICA) -> NDArray[float]: """Compute the ICA activations 'icaact' variable from an MNE ICA instance. Parameters @@ -119,9 +117,7 @@ def compute_ica_activations( # ---------------------------------------------------------------------------- -def eeg_topoplot( - inst: Union[BaseRaw, BaseEpochs], icawinv: NDArray[float] -) -> NDArray[float]: +def eeg_topoplot(inst: Union[BaseRaw, BaseEpochs], icawinv: NDArray[float]) -> NDArray[float]: """Topoplot feature.""" # TODO: Selection of channels is missing. ncomp = icawinv.shape[-1] @@ -135,9 +131,7 @@ def eeg_topoplot( return topo.astype(np.float32) -def _topoplotFast( - values: NDArray[float], rd: NDArray[float], th: NDArray[float] -) -> NDArray[float]: +def _topoplotFast(values: NDArray[float], rd: NDArray[float], th: NDArray[float]) -> NDArray[float]: """Implements topoplotFast.m from MATLAB. Each topographic map is a 32x32 images.""" # constants @@ -194,9 +188,7 @@ def _topoplotFast( # ---------------------------------------------------------------------------- -def eeg_rpsd( - inst: Union[BaseRaw, BaseEpochs], ica: ICA, icaact: NDArray[float] -) -> NDArray[float]: +def eeg_rpsd(inst: Union[BaseRaw, BaseEpochs], ica: ICA, icaact: NDArray[float]) -> NDArray[float]: """PSD feature.""" assert isinstance(inst, (BaseRaw, BaseEpochs)) # sanity-check constants = _eeg_rpsd_constants(inst, ica) @@ -271,9 +263,7 @@ def _eeg_rpsd_compute_psdmed( temp = np.hstack([icaact[it, index[:, k]] for k in range(index.shape[-1])]) temp = temp.reshape(*index.shape, order="F") elif isinstance(inst, BaseEpochs): - temp = np.hstack( - [icaact[it, index[:, k], :] for k in range(index.shape[-1])] - ) + temp = np.hstack([icaact[it, index[:, k], :] for k in range(index.shape[-1])]) temp = temp.reshape(index.shape[0], len(inst), order="F") else: raise RuntimeError # should never happen @@ -326,9 +316,7 @@ def _eeg_rpsd_format( return psd[:, :, np.newaxis, np.newaxis].transpose([2, 1, 3, 0]).astype(np.float32) -def eeg_autocorr_welch( - raw: BaseRaw, ica: ICA, icaact: NDArray[float] -) -> NDArray[float]: +def eeg_autocorr_welch(raw: BaseRaw, ica: ICA, icaact: NDArray[float]) -> NDArray[float]: """Autocorrelation feature applied on raw object with at least 5 * fs samples (5 seconds). MATLAB: 'eeg_autocorr_welch.m'.""" @@ -438,9 +426,7 @@ def eeg_autocorr(raw: BaseRaw, ica: ICA, icaact: NDArray[float]) -> NDArray[floa return resamp.astype(np.float32) -def eeg_autocorr_fftw( - epochs: BaseEpochs, ica: ICA, icaact: NDArray[float] -) -> NDArray[float]: +def eeg_autocorr_fftw(epochs: BaseEpochs, ica: ICA, icaact: NDArray[float]) -> NDArray[float]: """Autocorrelation feature applied on epoch object. MATLAB: 'eeg_autocorr_fftw.m'.""" assert isinstance(epochs, BaseEpochs) # sanity-check @@ -458,9 +444,7 @@ def eeg_autocorr_fftw( ac = np.fft.ifft(ac) if epochs.times.size < epochs.info["sfreq"]: - zeros = np.zeros( - (ac.shape[0], int(epochs.info["sfreq"]) - epochs.times.size + 1) - ) + zeros = np.zeros((ac.shape[0], int(epochs.info["sfreq"]) - epochs.times.size + 1)) ac = np.hstack([ac[:, : epochs.times.size], zeros]) else: ac = ac[:, : int(epochs.info["sfreq"]) + 1] diff --git a/mne_icalabel/network.py b/mne_icalabel/network.py index 969f01ee..b402992b 100644 --- a/mne_icalabel/network.py +++ b/mne_icalabel/network.py @@ -1,11 +1,11 @@ try: from importlib.resources import files except ImportError: - from importlib_resources import files + from importlib_resources import files # type: ignore -import torch.nn as nn -import torch import numpy as np +import torch +import torch.nn as nn from numpy.typing import ArrayLike diff --git a/mne_icalabel/tests/test_features.py b/mne_icalabel/tests/test_features.py index c538b607..3d212148 100644 --- a/mne_icalabel/tests/test_features.py +++ b/mne_icalabel/tests/test_features.py @@ -1,79 +1,60 @@ -try: - from importlib.resources import files -except ImportError: - from importlib_resources import files from pathlib import Path +import numpy as np +import pytest from mne import read_epochs_eeglab from mne.io import read_raw from mne.io.eeglab.eeglab import _check_load_mat from mne.preprocessing import read_ica_eeglab -import numpy as np from scipy.io import loadmat -import pytest from mne_icalabel.features import ( - retrieve_eeglab_icawinv, - compute_ica_activations, - get_features, - eeg_topoplot, - _topoplotFast, - _eeg_rpsd_constants, _eeg_rpsd_compute_psdmed, + _eeg_rpsd_constants, _eeg_rpsd_format, - eeg_autocorr_welch, + _topoplotFast, + compute_ica_activations, eeg_autocorr, eeg_autocorr_fftw, + eeg_autocorr_welch, + eeg_topoplot, + get_features, + retrieve_eeglab_icawinv, ) from mne_icalabel.utils import mne_to_eeglab_locs +try: + from importlib.resources import files +except ImportError: + from importlib_resources import files # type: ignore + # Raw/Epochs files with ICA decomposition -raw_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/datasets/sample-raw.set") -) +raw_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/datasets/sample-raw.set")) raw_short_eeglab_path = str( files("mne_icalabel.tests").joinpath("data/datasets/sample-short-raw.set") ) raw_very_short_eeglab_path = str( files("mne_icalabel.tests").joinpath("data/datasets/sample-very-short-raw.set") ) -epo_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/datasets/sample-epo.set") -) +epo_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/datasets/sample-epo.set")) # ICA activation matrix for raw/epochs -raw_icaact_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/icaact/icaact-raw.mat") -) -epo_icaact_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/icaact/icaact-epo.mat") -) +raw_icaact_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/icaact/icaact-raw.mat")) +epo_icaact_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/icaact/icaact-epo.mat")) # Topography raw_topo1_path = str(files("mne_icalabel.tests").joinpath("data/topo/topo1-raw.mat")) epo_topo1_path = str(files("mne_icalabel.tests").joinpath("data/topo/topo1-epo.mat")) -raw_topo_feature_path = str( - files("mne_icalabel.tests").joinpath("data/topo/topo-feature-raw.mat") -) -epo_topo_feature_path = str( - files("mne_icalabel.tests").joinpath("data/topo/topo-feature-epo.mat") -) +raw_topo_feature_path = str(files("mne_icalabel.tests").joinpath("data/topo/topo-feature-raw.mat")) +epo_topo_feature_path = str(files("mne_icalabel.tests").joinpath("data/topo/topo-feature-epo.mat")) # PSD -psd_constants_raw_path = str( - files("mne_icalabel.tests").joinpath("data/psd/constants-raw.mat") -) -psd_steps_raw_path = str( - files("mne_icalabel.tests").joinpath("data/psd/psd-step-by-step-raw.mat") -) +psd_constants_raw_path = str(files("mne_icalabel.tests").joinpath("data/psd/constants-raw.mat")) +psd_steps_raw_path = str(files("mne_icalabel.tests").joinpath("data/psd/psd-step-by-step-raw.mat")) psd_raw_path = str(files("mne_icalabel.tests").joinpath("data/psd/psd-raw.mat")) -psd_constants_epo_path = str( - files("mne_icalabel.tests").joinpath("data/psd/constants-epo.mat") -) -psd_steps_epo_path = str( - files("mne_icalabel.tests").joinpath("data/psd/psd-step-by-step-epo.mat") -) +psd_constants_epo_path = str(files("mne_icalabel.tests").joinpath("data/psd/constants-epo.mat")) +psd_steps_epo_path = str(files("mne_icalabel.tests").joinpath("data/psd/psd-step-by-step-epo.mat")) psd_epo_path = str(files("mne_icalabel.tests").joinpath("data/psd/psd-epo.mat")) # Autocorrelations @@ -86,17 +67,11 @@ autocorr_very_short_raw_path = str( files("mne_icalabel.tests").joinpath("data/autocorr/autocorr-very-short-raw.mat") ) -autocorr_epo_path = str( - files("mne_icalabel.tests").joinpath("data/autocorr/autocorr-epo.mat") -) +autocorr_epo_path = str(files("mne_icalabel.tests").joinpath("data/autocorr/autocorr-epo.mat")) # Complete features -features_raw_path = str( - files("mne_icalabel.tests").joinpath("data/features/features-raw.mat") -) -features_epo_path = str( - files("mne_icalabel.tests").joinpath("data/features/features-epo.mat") -) +features_raw_path = str(files("mne_icalabel.tests").joinpath("data/features/features-raw.mat")) +features_epo_path = str(files("mne_icalabel.tests").joinpath("data/features/features-epo.mat")) # General readers @@ -114,9 +89,7 @@ (epo_eeglab_path, psd_constants_epo_path, features_epo_path), ], ) -def test_get_features_from_precomputed_ica( - file, psd_constant_file, eeglab_feature_file -): +def test_get_features_from_precomputed_ica(file, psd_constant_file, eeglab_feature_file): """Test that we get the correct set of features from an MNE instance. Corresponds to the output from 'ICL_feature_extractor.m'.""" type_ = str(Path(file).stem)[-3:] @@ -242,9 +215,7 @@ def test_eeg_rpsd_constants(): # Raw -------------------------------------------------------------------- raw = read_raw(raw_eeglab_path, preload=True) ica = read_ica_eeglab(raw_eeglab_path) - ncomp, nfreqs, n_points, nyquist, index, window, subset = _eeg_rpsd_constants( - raw, ica - ) + ncomp, nfreqs, n_points, nyquist, index, window, subset = _eeg_rpsd_constants(raw, ica) constants_eeglab = loadmat(psd_constants_raw_path)["constants"][0, 0] ncomp_eeglab = constants_eeglab["ncomp"][0, 0] @@ -273,9 +244,7 @@ def test_eeg_rpsd_constants(): # Epochs ----------------------------------------------------------------- epochs = read_epochs_eeglab(epo_eeglab_path) ica = read_ica_eeglab(epo_eeglab_path) - ncomp, nfreqs, n_points, nyquist, index, window, subset = _eeg_rpsd_constants( - epochs, ica - ) + ncomp, nfreqs, n_points, nyquist, index, window, subset = _eeg_rpsd_constants(epochs, ica) constants_eeglab = loadmat(psd_constants_epo_path)["constants"][0, 0] ncomp_eeglab = constants_eeglab["ncomp"][0, 0] @@ -361,9 +330,7 @@ def test_eeg_rpsd(): subset_eeglab = constants_eeglab["subset"][0, :] - 1 # retrieve the rest from python - ncomp, nfreqs, n_points, nyquist, index, window, _ = _eeg_rpsd_constants( - epochs, ica - ) + ncomp, nfreqs, n_points, nyquist, index, window, _ = _eeg_rpsd_constants(epochs, ica) # compute psdmed psdmed = _eeg_rpsd_compute_psdmed( diff --git a/mne_icalabel/tests/test_network.py b/mne_icalabel/tests/test_network.py index d0f740f8..cbb7e807 100644 --- a/mne_icalabel/tests/test_network.py +++ b/mne_icalabel/tests/test_network.py @@ -1,21 +1,18 @@ try: from importlib.resources import files except ImportError: - from importlib_resources import files + from importlib_resources import files # type: ignore import numpy as np -from scipy.io import loadmat -import torch import pytest +import torch +from scipy.io import loadmat from mne_icalabel.network import ICLabelNet, format_input, run_iclabel - # Network weights torch_iclabel_path = str(files("mne_icalabel").joinpath("assets/iclabelNet.pt")) -matconvnet_iclabel_path = str( - files("mne_icalabel.tests").joinpath("data/network/netICL.mat") -) +matconvnet_iclabel_path = str(files("mne_icalabel.tests").joinpath("data/network/netICL.mat")) # Network forward pass input/output matconvnet_fw_input_path = str( @@ -26,12 +23,8 @@ ) # Features (similar to network_input) -features_raw_path = str( - files("mne_icalabel.tests").joinpath("data/features/features-raw.mat") -) -features_epo_path = str( - files("mne_icalabel.tests").joinpath("data/features/features-epo.mat") -) +features_raw_path = str(files("mne_icalabel.tests").joinpath("data/features/features-raw.mat")) +features_epo_path = str(files("mne_icalabel.tests").joinpath("data/features/features-epo.mat")) # Features formatted features_formatted_raw_path = str( @@ -42,12 +35,8 @@ ) # ICLabel output -iclabel_output_raw_path = str( - files("mne_icalabel.tests").joinpath("data/iclabel-output-raw.mat") -) -iclabel_output_epo_path = str( - files("mne_icalabel.tests").joinpath("data/iclabel-output-epo.mat") -) +iclabel_output_raw_path = str(files("mne_icalabel.tests").joinpath("data/iclabel-output-raw.mat")) +iclabel_output_epo_path = str(files("mne_icalabel.tests").joinpath("data/iclabel-output-epo.mat")) def test_weights(): @@ -64,9 +53,7 @@ def test_weights(): elif weight.ndim == 3: weights_matlab[k] = weight.transpose((2, 0, 1)) - network_python_layers = [ - layer for layer in network_python.keys() if "seq" not in layer - ] + network_python_layers = [layer for layer in network_python.keys() if "seq" not in layer] network_matlab_layers = [elt[0] for elt in network_matlab["params"]["name"][0, :]] # match layer names torch -> matconvnet @@ -181,9 +168,7 @@ def test_run_iclabel(eeglab_feature_file, eeglab_output_file): features retrieved in python in 'test_features.py:test_get_features'.""" features_eeglab = loadmat(eeglab_feature_file)["features"] # run the forward pass on pytorch - labels = run_iclabel( - features_eeglab[0, 0], features_eeglab[0, 1], features_eeglab[0, 2] - ) + labels = run_iclabel(features_eeglab[0, 0], features_eeglab[0, 1], features_eeglab[0, 2]) # load the labels from EEGLAB matlab_labels = loadmat(eeglab_output_file)["labels"] # (30, 7) diff --git a/mne_icalabel/tests/test_utils.py b/mne_icalabel/tests/test_utils.py index 2c898403..a705d749 100644 --- a/mne_icalabel/tests/test_utils.py +++ b/mne_icalabel/tests/test_utils.py @@ -1,25 +1,21 @@ try: from importlib.resources import files except ImportError: - from importlib_resources import files + from importlib_resources import files # type: ignore + from pathlib import Path +import numpy as np +import pytest from mne import read_epochs_eeglab from mne.io import read_raw -import numpy as np from scipy.io import loadmat -import pytest - -from mne_icalabel.utils import mne_to_eeglab_locs, gdatav4, _next_power_of_2 +from mne_icalabel.utils import _next_power_of_2, gdatav4, mne_to_eeglab_locs # Raw/Epochs files with ICA decomposition -raw_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/datasets/sample-raw.set") -) -epo_eeglab_path = str( - files("mne_icalabel.tests").joinpath("data/datasets/sample-epo.set") -) +raw_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/datasets/sample-raw.set")) +epo_eeglab_path = str(files("mne_icalabel.tests").joinpath("data/datasets/sample-epo.set")) # Electrode locations @@ -27,12 +23,8 @@ loc_epo_path = str(files("mne_icalabel.tests").joinpath("data/utils/loc-raw.mat")) # Grid data interpolation -gdatav4_raw_path = str( - files("mne_icalabel.tests").joinpath("data/utils/gdatav4-raw.mat") -) -gdatav4_epo_path = str( - files("mne_icalabel.tests").joinpath("data/utils/gdatav4-epo.mat") -) +gdatav4_raw_path = str(files("mne_icalabel.tests").joinpath("data/utils/gdatav4-raw.mat")) +gdatav4_epo_path = str(files("mne_icalabel.tests").joinpath("data/utils/gdatav4-epo.mat")) # General readers diff --git a/mne_icalabel/utils.py b/mne_icalabel/utils.py index bc3890a8..7095ce0b 100644 --- a/mne_icalabel/utils.py +++ b/mne_icalabel/utils.py @@ -1,8 +1,8 @@ -from typing import Tuple, List +from typing import List, Tuple -from mne.io import BaseRaw -from numpy.typing import NDArray, ArrayLike import numpy as np +from mne.io import BaseRaw +from numpy.typing import ArrayLike, NDArray def mne_to_eeglab_locs(raw: BaseRaw) -> Tuple[NDArray[float], NDArray[float]]: @@ -77,9 +77,7 @@ def _cart2sph(_x, _y, _z): return rd.reshape([1, -1]), np.degrees(th).reshape([1, -1]) -def pol2cart( - theta: NDArray[float], rho: NDArray[float] -) -> Tuple[NDArray[float], NDArray[float]]: +def pol2cart(theta: NDArray[float], rho: NDArray[float]) -> Tuple[NDArray[float], NDArray[float]]: """ Converts polar coordinates to cartesian coordinates. @@ -145,9 +143,7 @@ def gdatav4( g = np.square(d) * (np.log(d) - 1) # Value of Green's function at zero g[np.where(np.isclose(d, 0))] = 0 - vq[i, j] = (np.expand_dims(g, axis=0) @ np.expand_dims(weights, axis=1))[0][ - 0 - ] + vq[i, j] = (np.expand_dims(g, axis=0) @ np.expand_dims(weights, axis=1))[0][0] return xq, yq, vq @@ -197,9 +193,7 @@ def mergepoints2D( return x, y, v -def mergesimpts( - data: ArrayLike, tols: List[ArrayLike], mode: str = "average" -) -> ArrayLike: +def mergesimpts(data: ArrayLike, tols: List[ArrayLike], mode: str = "average") -> ArrayLike: """ Args: @@ -213,15 +207,13 @@ def mergesimpts( data_ = data.copy()[np.argsort(data[:, 0])] newdata = [] tols_ = np.array(tols) - idxs_ready = [] + idxs_ready: List[int] = [] point = 0 for point in range(data_.shape[0]): if point in idxs_ready: continue else: - similar_pts = np.where( - np.prod(np.abs(data_ - data_[point]) < tols_, axis=-1) - ) + similar_pts = np.where(np.prod(np.abs(data_ - data_[point]) < tols_, axis=-1)) similar_pts = np.array(list(set(similar_pts[0].tolist()) - set(idxs_ready))) idxs_ready += similar_pts.tolist() if mode == "average": diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..e2f335cf --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,24 @@ +[tool.black] +line-length = 100 + +include = '\.pyi?$' + +exclude = ''' +( + __pycache__ + | \.git + | \.mypy_cache + | \.pytest_cache + | \.vscode + | \.venv + | \bdist\b + | \bdoc\b +) +''' +[tool.isort] +profile = "black" +multi_line_output = 3 + +[build-system] +requires = ["setuptools", "wheel"] +build-backend = "setuptools.build_meta" diff --git a/requirements.txt b/requirements.txt index effab43c..0bd6558b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,5 +5,4 @@ joblib mne python-picard scikit-learn -torch -sklearn \ No newline at end of file +torch \ No newline at end of file diff --git a/requirements_testing.txt b/requirements_testing.txt index 62e5d53c..4f269d73 100644 --- a/requirements_testing.txt +++ b/requirements_testing.txt @@ -16,3 +16,4 @@ mne-bids importlib_resources pymatreader black +isort \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index c8d70f18..06f990c6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -70,6 +70,15 @@ filterwarnings = # This is for Python 3.10+ and MNE <1.0 ignore:The distutils package is deprecated.*:DeprecationWarning +[mypy] +ignore_missing_imports = true +no_site_packages = true +allow_redefinition = True +exclude = _script.py + +[mypy-tests.*] +strict_optional = false + [pydocstyle] convention = pep257 match_dir = ^(?!\.|doc|examples).*$ From 29ada692a586ac3d968e0d0a7b6d5c2859ea136b Mon Sep 17 00:00:00 2001 From: Adam Li Date: Thu, 28 Apr 2022 16:13:26 -0400 Subject: [PATCH 2/5] Fix gh actions --- .github/workflows/unit_tests.yml | 2 +- requirements_doc.txt | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 76e04a52..8f953f7c 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -31,7 +31,7 @@ jobs: pip install --upgrade --upgrade-strategy eager -r requirements.txt pip install --upgrade --upgrade-strategy eager -r requirements_testing.txt - name: Run style & documentation tests - run: make pep + run: make run-checks # Run installation tests build: diff --git a/requirements_doc.txt b/requirements_doc.txt index 49330528..f1e36012 100644 --- a/requirements_doc.txt +++ b/requirements_doc.txt @@ -4,8 +4,6 @@ sphinx-gallery sphinx_rtd_theme sphinx-copybutton numpydoc -nibabel -nilearn pydata-sphinx-theme typing-extensions sphinx-autodoc-typehints From a1efd0a1bb43ccef2f8da7f4ee9b9e9205bf5f18 Mon Sep 17 00:00:00 2001 From: Adam Li Date: Thu, 28 Apr 2022 16:16:49 -0400 Subject: [PATCH 3/5] Fix sort --- doc/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 7f7a6550..2cbafd9b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -1,13 +1,13 @@ """Configure details for documentation with sphinx.""" -from datetime import date import os import sys import warnings +from datetime import date +import mne import sphinx_gallery # noqa: F401 from sphinx_gallery.sorting import ExampleTitleSortKey -import mne sys.path.insert(0, os.path.abspath("..")) import mne_icalabel # noqa: E402 From 9d681654995bbcdd802c8e27f71ce839a6615fbb Mon Sep 17 00:00:00 2001 From: Adam Li Date: Thu, 28 Apr 2022 16:18:54 -0400 Subject: [PATCH 4/5] Fix manfiest --- MANIFEST.in | 3 +++ Makefile | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/MANIFEST.in b/MANIFEST.in index cd7c8478..28fe1416 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -12,6 +12,9 @@ recursive-include mne_icalabel *.pt recursive-include mne_icalabel *.py exclude .circleci/config.yml +exclude .flake8 + +recursive-exclude doc * # exclude all data files recursive-exclude mne_icalabel *.txt diff --git a/Makefile b/Makefile index 3c2de902..f6220f93 100644 --- a/Makefile +++ b/Makefile @@ -133,7 +133,7 @@ run-checks: isort --check . black --check mne_icalabel examples flake8 . - mypy . + mypy ./mne_icalabel @$(MAKE) pydocstyle check-manifest @$(MAKE) codespell-error From 7839bbb191a1700153fec7183df77622474aa002 Mon Sep 17 00:00:00 2001 From: Adam Li Date: Thu, 28 Apr 2022 16:29:04 -0400 Subject: [PATCH 5/5] Add mypy --- requirements_testing.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements_testing.txt b/requirements_testing.txt index 4f269d73..d02253bd 100644 --- a/requirements_testing.txt +++ b/requirements_testing.txt @@ -16,4 +16,5 @@ mne-bids importlib_resources pymatreader black -isort \ No newline at end of file +isort +mypy \ No newline at end of file