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Documentation should conform to that of the python-project template (#37
) * versioningit invoked when package is installed Signed-off-by: Jose Borreguero <[email protected]> * add make target to create documentation Signed-off-by: Jose Borreguero <[email protected]> * state how to build the docs Signed-off-by: Jose Borreguero <[email protected]> * add readthedocs configuration file Signed-off-by: Jose Borreguero <[email protected]> --------- Signed-off-by: Jose Borreguero <[email protected]>
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## Description of work: | ||
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Check all that apply: | ||
- [ ] added [release notes](https://github.com/neutrons/LiquidsReflectometer/blob/next/docs/source/releases.rst) | ||
(if not, provide an explanation in the work description) | ||
- [ ] updated documentation | ||
- [ ] Source added/refactored | ||
- [ ] Added unit tests | ||
- [ ] Added integration tests | ||
- [ ] Verified that tests requiring the /SNS and /HFIR filesystems pass without fail | ||
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**References:** | ||
- Links to IBM EWM items: | ||
- Links to related issues or pull requests: | ||
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## Manual test for the reviewer | ||
<!-- Instructions for testing here. --> | ||
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## Check list for the reviewer | ||
- [ ] [release notes](https://github.com/neutrons/LiquidsReflectometer/blob/next/docs/source/releases.rst) | ||
updated, or an explanation is provided as to why release notes are unnecessary | ||
- [ ] best software practices | ||
+ [ ] clearly named variables (better to be verbose in variable names) | ||
+ [ ] code comments explaining the intent of code blocks | ||
- [ ] All the tests are passing | ||
- [ ] The documentation is up to date | ||
- [ ] code comments added when explaining intent | ||
|
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version: 2 | ||
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build: | ||
os: ubuntu-22.04 | ||
tools: | ||
python: "mambaforge-4.10" | ||
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sphinx: | ||
builder: html | ||
configuration: docs/conf.py | ||
fail_on_warning: true | ||
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conda: | ||
environment: environment.yml |
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prefix := /SNS/REF_L/shared | ||
# bash sell to correctly interpret the double brackets in the conditions below | ||
SHELL=/bin/bash | ||
# https://www.gnu.org/software/make/manual/html_node/One-Shell.html | ||
# Required to prevent having to use "conda init" | ||
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all: | ||
@echo "Run 'make install' to install the automated reduction code for LR" | ||
# all the lines in a recipe are passed to a single invocation of the shell. | ||
.ONESHELL: | ||
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# list of all phony targets, alphabetically sorted | ||
.PHONY: help conda docs test install | ||
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install: | ||
cp -R scripts/livereduce/*.py $(prefix)/livereduce | ||
cp -R scripts/autoreduce/*.py $(prefix)/autoreduce | ||
cp -R scripts/shared/*.py $(prefix) | ||
cp -R scripts/shared/.*.conf $(prefix) | ||
cp -R launcher $(prefix) | ||
cp -R reduction $(prefix) | ||
cp -R xrr/xrr_processing.py $(prefix) | ||
help: | ||
# this nifty perl one-liner collects all commnents headed by the double "#" symbols next to each target and recycles them as comments | ||
@perl -nle'print $& if m{^[a-zA-Z_-]+:.*?## .*$$}' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-25s\033[0m %s\n", $$1, $$2}' | ||
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.PHONY: install | ||
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PREFIX := /SNS/REF_L/shared | ||
install: ## install the automated reduction code for LR | ||
cp -R scripts/livereduce/*.py $(PREFIX)/livereduce | ||
cp -R scripts/autoreduce/*.py $(PREFIX)/autoreduce | ||
cp -R scripts/shared/*.py $(PREFIX) | ||
cp -R scripts/shared/.*.conf $(PREFIX) | ||
cp -R launcher $(PREFIX) | ||
cp -R reduction $(PREFIX) | ||
cp -R xrr/xrr_processing.py $(PREFIX) | ||
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# Note that the extra activate is needed to ensure that the activate floats env to the front of PATH | ||
CONDA_ACTIVATE=source $$(conda info --base)/etc/profile.d/conda.sh ; conda activate | ||
conda-env: ## creates conda environment `lr_reduction` and installs package `lr_reduction` in editable mode | ||
conda env create --solver=libmamba --file ./environment.yml | ||
$(CONDA_ACTIVATE) lr_reduction | ||
pip install -e . | ||
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docs: ## generates HTML docs under `docs/_build/html/`, treating warnings as errors. Requires activation of the `lr_reduction` conda environment | ||
# this will fail on a warning | ||
@cd docs&& make html SPHINXOPTS="-W --keep-going -n" && echo -e "##########\n DOCS point your browser to file://$$(pwd)/build/html/index.html\n##########" | ||
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test-all: ## run all tests | ||
pytest ./test |
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# Makefile for Sphinx documentation | ||
# | ||
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# You can set these variables from the command line. | ||
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# Options should be aligned with how the documentation is built on RTD | ||
# (except for '--keep-going', failing fast is prefered on local builds) | ||
# We also remove '-E' to reduce the time of rebuilding reference indexes | ||
# on each build. | ||
SPHINXOPTS = -T -j auto -W | ||
SPHINXBUILD = sphinx-build | ||
PAPER = | ||
PROJECT ?= lr_reduction | ||
BUILDDIR = build | ||
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# Do not use local Django settings during the docs build | ||
export DJANGO_SETTINGS_SKIP_LOCAL = True | ||
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# User-friendly check for sphinx-build | ||
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 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 | ||
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# 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) . | ||
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext | ||
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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 " 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)" | ||
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clean: | ||
rm -rf $(BUILDDIR)/* | ||
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auto: | ||
sphinx-autobuild --port 8888 $(ALLSPHINXOPTS) $(BUILDDIR)/html | ||
@echo | ||
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html." | ||
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html: | ||
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html | ||
@echo | ||
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html." | ||
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livehtml: | ||
sphinx-autobuild --port 4444 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html | ||
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dirhtml: | ||
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml | ||
@echo | ||
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." | ||
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singlehtml: | ||
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml | ||
@echo | ||
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." | ||
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pickle: | ||
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle | ||
@echo | ||
@echo "Build finished; now you can process the pickle files." | ||
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json: | ||
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json | ||
@echo | ||
@echo "Build finished; now you can process the JSON files." | ||
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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." | ||
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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/sdf.qhcp" | ||
@echo "To view the help file:" | ||
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sdf.qhc" | ||
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devhelp: | ||
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp | ||
@echo | ||
@echo "Build finished." | ||
@echo "To view the help file:" | ||
@echo "# mkdir -p $$HOME/.local/share/devhelp/sdf" | ||
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sdf" | ||
@echo "# devhelp" | ||
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epub: | ||
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub | ||
@echo | ||
@echo "Build finished. The epub file is in $(BUILDDIR)/epub." | ||
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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)." | ||
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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." | ||
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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." | ||
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text: | ||
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text | ||
@echo | ||
@echo "Build finished. The text files are in $(BUILDDIR)/text." | ||
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man: | ||
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man | ||
@echo | ||
@echo "Build finished. The manual pages are in $(BUILDDIR)/man." | ||
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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)." | ||
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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." | ||
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gettext: | ||
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale | ||
@echo | ||
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." | ||
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changes: | ||
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes | ||
@echo | ||
@echo "The overview file is in $(BUILDDIR)/changes." | ||
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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." | ||
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doctest: | ||
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest | ||
@echo "Testing of doctests in the sources finished, look at the " \ | ||
"results in $(BUILDDIR)/doctest/output.txt." | ||
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xml: | ||
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml | ||
@echo | ||
@echo "Build finished. The XML files are in $(BUILDDIR)/xml." | ||
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pseudoxml: | ||
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml | ||
@echo | ||
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." |
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"""Configuration file for the Sphinx documentation builder. | ||
For the full list of built-in configuration values, see the documentation: | ||
https://www.sphinx-doc.org/en/master/usage/configuration.html | ||
""" | ||
import os | ||
import sys | ||
import versioningit | ||
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sys.path.insert(0, os.path.abspath("../reduction")) | ||
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# -- Project information ----------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information | ||
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project = "lr_reduction" | ||
copyright = "2024, ORNL" # noqa A001 | ||
author = "ORNL" | ||
version = versioningit.get_version("../") | ||
# The full version, including alpha/beta/rc tags | ||
release = "source/".join(version.split("source/")[:-1]) | ||
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# -- General configuration --------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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extensions = [ | ||
"sphinx.ext.duration", | ||
"sphinx.ext.doctest", | ||
"sphinx.ext.autodoc", | ||
"sphinx.ext.autosummary", | ||
"sphinx.ext.intersphinx", | ||
"sphinx.ext.viewcode", | ||
"sphinx.ext.coverage", | ||
] | ||
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autodoc_mock_imports = [ | ||
"mantid", | ||
"mantid.api", | ||
"mantid.kernel", | ||
"mantid.utils", | ||
"mantid.utils.logging", | ||
"mantid.simpleapi", | ||
"mantid.geometry", | ||
"mantidqt.widgets", | ||
"mantidqt.widgets.algorithmprogress", | ||
"qtpy", | ||
"qtpy.uic", | ||
"qtpy.QtWidgets", | ||
"mantidqt", | ||
"mantid.plots", | ||
"mantid.plots.plotfunctions", | ||
"mantid.plots.datafunctions", | ||
"mantid.plots.utility", | ||
] | ||
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master_doc = "index" | ||
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intersphinx_mapping = { | ||
"python": ("https://docs.python.org/3/", None), | ||
"sphinx": ("https://www.sphinx-doc.org/en/master/", None), | ||
} | ||
intersphinx_disabled_domains = ["std"] | ||
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templates_path = ["_templates"] | ||
exclude_patterns = ["_build"] | ||
pygments_style = "sphinx" | ||
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# -- Options for HTML output ------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output | ||
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html_theme = "sphinx_rtd_theme" # pylint: disable=C0103 | ||
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html_theme_options = {"style_nav_header_background": "#472375"} | ||
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epub_show_urls = "footnote" # pylint: disable=C0103 |
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