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Merge pull request #14 from nipype/add-docs
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add docs to ci/cd and readme
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tclose authored Mar 26, 2024
2 parents 672d5c2 + d17e2d4 commit 1386dec
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65 changes: 57 additions & 8 deletions .github/workflows/ci-cd.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,11 @@ env:
FREESURFER_HOME: /opt/freesurfer
DOWNLOADS_DIR: /downloads/freesurfer

permissions:
contents: read
pages: write
id-token: write

jobs:

nipype-conv:
Expand All @@ -36,6 +41,8 @@ jobs:

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.x'

- name: Install build dependencies
run: python -m pip install --upgrade pip
Expand Down Expand Up @@ -131,19 +138,20 @@ jobs:
sudo mkdir -p $FREESURFER_HOME
sudo chown $USER $FREESURFER_HOME
- name: Cache Freesurfer Install
id: cache-install
uses: actions/cache@v4
with:
path: ${{ env.DOWNLOADS_DIR }}
key: freesurfer-${{ env.FREESURFER_VERSION }}-${{ runner.os }}
# - name: Cache Freesurfer Download
# id: cache-install
# uses: actions/cache@v4
# with:
# path: ${{ env.DOWNLOADS_DIR }}
# key: freesurfer-${{ env.FREESURFER_VERSION }}-${{ runner.os }}

- name: Download FreeSurfer
if: steps.cache-install.outputs.cache-hit != 'true'
# if: steps.cache-install.outputs.cache-hit != 'true'
run: |
sudo mkdir -p $DOWNLOADS_DIR
sudo chown $USER $DOWNLOADS_DIR
curl -s -o $DOWNLOADS_DIR/freesurfer-linux-ubuntu22_amd64-${{ env.FREESURFER_VERSION }}.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${{ env.FREESURFER_VERSION }}/freesurfer-linux-ubuntu22_amd64-${{ env.FREESURFER_VERSION }}.tar.gz
curl -s -o $DOWNLOADS_DIR/freesurfer-linux-ubuntu22_amd64-${{ env.FREESURFER_VERSION }}.tar.gz \
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${{ env.FREESURFER_VERSION }}/freesurfer-linux-ubuntu22_amd64-${{ env.FREESURFER_VERSION }}.tar.gz
shell: bash

- name: Install Freesurfer
Expand Down Expand Up @@ -394,6 +402,47 @@ jobs:
draft: false
prerelease: false

# docs:
# # needs: deploy
# environment:
# name: github-pages
# url: ${{ steps.deployment.outputs.page_url }}
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - uses: actions/setup-python@v5
# with:
# python-version: '3.x'

# - name: Download tasks converted from Nipype
# uses: actions/download-artifact@v4
# with:
# name: converted-nipype
# path: pydra/tasks/freesurfer/auto

# - name: Install dependencies
# run: python -m pip install related-packages/fileformats .[doc]

# - name: Build docs
# run: |
# pushd docs
# make html
# popd

# - name: Upload artifact
# uses: actions/upload-pages-artifact@v3
# with:
# path: 'docs/build/html'

# - name: Setup GitHub Pages
# if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
# uses: actions/configure-pages@v4

# - name: Deploy to GitHub Pages
# if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
# id: deployment
# uses: actions/deploy-pages@v4

# report_progress:
# needs: [deploy]
# runs-on: ubuntu-latest
Expand Down
16 changes: 10 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
[![PyPI - Version][pypi-version]][pypi-project]
[![PyPI - Python Version][pypi-pyversions]][pypi-project]
[![PyPI - Downloads][pypi-downloads]][pypi-project]
![][status-docs]
![][status-cicd]
[![Status-docs][status-docs-badge]][status-docs-link]
[![Status-CICD][status-cicd-badge]][status-cicd-link]

----

Expand Down Expand Up @@ -136,10 +136,10 @@ ready for use, where v* corresponds to the version of Freesurfer that you have t
it against e.g.

```console
from pydra.tasks.freesurfer.auto import <the-task-you-have-validated>
from pydra.tasks.freesurfer.auto import <the-task-you-have-validated>
```

and copy the test file `pydra/tasks/freesurfer/auto/tests/test_<validated-task>.py
and copy the test file `pydra/tasks/freesurfer/auto/tests/test_<validated-task>.py`
into `pydra/tasks/freesurfer/v*/tests`.


Expand Down Expand Up @@ -189,6 +189,10 @@ This project is distributed under the terms of the [Apache License, Version 2.0]

[pypi-version]: https://img.shields.io/pypi/v/pydra-freesurfer.svg

[status-docs]: https://github.com/nipype/pydra-freesurfer/actions/workflows/docs.yaml/badge.svg
[status-docs-badge]: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat

[status-cicd]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg
[status-cicd-badge]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg

[status-docs-link]: https://nipype.github.io/pydra-freesurfer/

[status-cicd-link]: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
192 changes: 192 additions & 0 deletions docs/Makefile
Original file line number Diff line number Diff line change
@@ -0,0 +1,192 @@
# Makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS =
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) source
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source

.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext

help:
@echo "Please use \`make <target>' where <target> 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 " applehelp to make an Apple Help Book"
@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)"
@echo " coverage to run coverage check of the documentation (if enabled)"

clean:
rm -rf $(BUILDDIR)/*

html:
$(SPHINXBUILD) -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/Pype9.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Pype9.qhc"

applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."

devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/Pype9"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Pype9"
@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. The message catalogs are in $(BUILDDIR)/locale."

changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."

linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."

doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."

coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."

xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."

pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
File renamed without changes.
14 changes: 4 additions & 10 deletions docs/conf.py → docs/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,21 +3,15 @@
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

import sys
from pathlib import Path

from sphinx_pyproject import SphinxConfig

config = SphinxConfig(globalns=globals())
sys.path.insert(0, str(Path.cwd().parent / "src"))
from pydra.tasks.freesurfer import __version__ # noqa

# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = config.name
author = "The Aramis Lab"
project = "pydra-freesurfer"
author = "Pydra Developers"
copyright = f"2022-2023, {author}"
release = config.version
release = __version__

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
Expand Down
File renamed without changes.
3 changes: 2 additions & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ build-backend = "hatchling.build"
[project]
name = "pydra-freesurfer"
description = "Pydra tasks package for freesurfer"
readme = "README.rst"
readme = "README.md"
requires-python = ">=3.8"
dependencies = [
"pydra >=0.22",
Expand Down Expand Up @@ -41,6 +41,7 @@ doc = [
"sphinxcontrib-apidoc ~=0.3.0",
"sphinxcontrib-napoleon",
"sphinxcontrib-versioning",
"pydata-sphinx-theme >=0.13",
]
test = [
"nipype2pydra",
Expand Down

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