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Documentation should conform to that of the python-project template (#37
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* 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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jmborr authored Jul 29, 2024
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28 changes: 28 additions & 0 deletions .github/pull_request_template.md
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## Description of work:

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

**References:**
- Links to IBM EWM items:
- Links to related issues or pull requests:

## Manual test for the reviewer
<!-- Instructions for testing here. -->

## 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

14 changes: 14 additions & 0 deletions .readthedocs.yaml
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version: 2

build:
os: ubuntu-22.04
tools:
python: "mambaforge-4.10"

sphinx:
builder: html
configuration: docs/conf.py
fail_on_warning: true

conda:
environment: environment.yml
47 changes: 35 additions & 12 deletions Makefile
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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"

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:

# list of all phony targets, alphabetically sorted
.PHONY: help conda docs test install

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}'

.PHONY: install

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)

# 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 .

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##########"

test-all: ## run all tests
pytest ./test
195 changes: 195 additions & 0 deletions docs/Makefile
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# Makefile for Sphinx documentation
#

# You can set these variables from the command line.

# 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

# Do not use local Django settings during the docs build
export DJANGO_SETTINGS_SKIP_LOCAL = True

# 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 <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)"

clean:
rm -rf $(BUILDDIR)/*

auto:
sphinx-autobuild --port 8888 $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

livehtml:
sphinx-autobuild --port 4444 -b html $(ALLSPHINXOPTS) $(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/sdf.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sdf.qhc"

devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/sdf"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sdf"
@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."

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."
74 changes: 74 additions & 0 deletions docs/conf.py
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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

sys.path.insert(0, os.path.abspath("../reduction"))

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

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])

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

extensions = [
"sphinx.ext.duration",
"sphinx.ext.doctest",
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"sphinx.ext.intersphinx",
"sphinx.ext.viewcode",
"sphinx.ext.coverage",
]

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",
]

master_doc = "index"

intersphinx_mapping = {
"python": ("https://docs.python.org/3/", None),
"sphinx": ("https://www.sphinx-doc.org/en/master/", None),
}
intersphinx_disabled_domains = ["std"]

templates_path = ["_templates"]
exclude_patterns = ["_build"]
pygments_style = "sphinx"


# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

html_theme = "sphinx_rtd_theme" # pylint: disable=C0103

html_theme_options = {"style_nav_header_background": "#472375"}

epub_show_urls = "footnote" # pylint: disable=C0103
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