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chore: update readthedocs config
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ivan-aksamentov committed Jul 17, 2023
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14 changes: 14 additions & 0 deletions .readthedocs.yml
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---
version: 2

conda:
environment: doc/python/environment.yml

sphinx:
configuration: doc/python/source/conf.py

build:
os: ubuntu-22.04
jobs:
pre_build:
- make clean swig python
32 changes: 32 additions & 0 deletions Makefile
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Expand Up @@ -361,3 +361,35 @@ $(PROFILE_OBJECT:%=$(PFLDIR)/%): $(PROFILE_SOURCE:%=$(PFLDIR)/%)
$(CXX) $(PROFILE_CXXFLAGS) -c $(@:.o=.cpp) -o $@

#############################################################################


export UID=$(shell id -u)
export GID=$(shell id -g)

docs:
@$(MAKE) --no-print-directory -C doc/python html

docs-clean:
rm -rf doc/python/build

SHELL := /bin/bash
.ONESHELL:
docker-docs:
set -euxo pipefail

docker build -t ffpopsim-docs-builder \
--network=host \
--build-arg UID=$(shell id -u) \
--build-arg GID=$(shell id -g) \
doc/python

docker run -it --rm \
--network=host \
--name=ffpopsim-docs-builder-$(shell date +%s) \
--init \
--user=$(shell id -u):$(shell id -g) \
--volume=$(shell pwd):/home/user/src \
--publish=8000:8000 \
--workdir=/home/user/src \
--env 'TERM=xterm-256colors' \
ffpopsim-docs-builder
86 changes: 86 additions & 0 deletions doc/python/Dockerfile
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FROM continuumio/miniconda3:23.3.1-0

SHELL ["bash", "-euxo", "pipefail", "-c"]

ARG DEBIAN_FRONTEND=noninteractive
ARG USER=user
ARG GROUP=user
ARG UID
ARG GID

ENV TERM="xterm-256color"
ENV HOME="/home/user"

# Install required packages if running Debian or Ubuntu
RUN set -euxo pipefail >/dev/null \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get update -qq --yes \
&& apt-get install -qq --no-install-recommends --yes \
apt-transport-https \
bash \
bash-completion \
ca-certificates \
curl \
git \
gnupg \
make \
sudo \
>/dev/null \
&& apt-get clean autoclean >/dev/null \
&& apt-get autoremove --yes >/dev/null \
&& rm -rf /var/lib/apt/lists/*

# Make a user and group
RUN set -euxo pipefail >/dev/null \
&& \
if [ -z "$(getent group ${GID})" ]; then \
addgroup --system --gid ${GID} ${GROUP}; \
else \
groupmod -n ${GROUP} $(getent group ${GID} | cut -d: -f1); \
fi \
&& \
if [ -z "$(getent passwd ${UID})" ]; then \
useradd \
--system \
--create-home --home-dir ${HOME} \
--shell /bin/bash \
--gid ${GROUP} \
--groups sudo \
--uid ${UID} \
${USER}; \
fi \
&& sed -i /etc/sudoers -re 's/^%sudo.*/%sudo ALL=(ALL:ALL) NOPASSWD:ALL/g' \
&& sed -i /etc/sudoers -re 's/^root.*/root ALL=(ALL:ALL) NOPASSWD:ALL/g' \
&& sed -i /etc/sudoers -re 's/^#includedir.*/## **Removed the include directive** ##"/g' \
&& echo "%sudo ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \
&& echo "${USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \
&& touch ${HOME}/.hushlogin \
&& chown -R ${UID}:${GID} "${HOME}"

RUN set -euxo pipefail >/dev/null \
&& chown -R ${USER}:${GROUP} ${HOME}

COPY environment.yml ${HOME}/src/

WORKDIR ${HOME}/src

RUN set -euxo pipefail >/dev/null \
&& cd ${HOME}/src \
&& conda install anaconda-client -n base \
&& conda env create -f environment.yml --name org.neherlab.ffpopsim.docs

USER ${USER}

RUN set -euxo pipefail >/dev/null \
&& conda init bash \
&& echo "conda activate org.neherlab.ffpopsim.docs" >> ${HOME}/.bashrc

ENV PATH="/opt/conda/envs/org.neherlab.ffpopsim.docs/bin:${PATH}"

CMD bash -c "set -euxo pipefail \
&& source ${HOME}/.bashrc \
&& make -j8 swig python \
&& cd doc/python \
&& rm -rf build \
&& make autobuild \
"
157 changes: 16 additions & 141 deletions doc/python/Makefile
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@@ -1,152 +1,27 @@
# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS =
PAPER =
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = source
BUILDDIR = build

# 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 gettext

# Put it first so that "make" without argument is like "make help".
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 " 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 " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in 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/FFPopSim.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/FFPopSim.qhc"

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

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 $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

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."
.PHONY: help Makefile

gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
autobuild:
cd source && sphinx-autobuild --host=0.0.0.0 --port=8000 . ../build/html

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."
sphinx-build -b linkcheck $(SOURCEDIR) $(BUILDDIR)/linkcheck $(SPHINXOPTS) $(O)

doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
53 changes: 53 additions & 0 deletions doc/python/README.md
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# FFPopSim Python documentation

Readthedocs project for FFPopSim

## Building the docs with Docker (recommended)

Once you have [Docker](https://docs.docker.com/get-docker/) installed, run from the root of the project:

make docker-docs

The HTML files will appear in `docs/build/html/` (for manual inspection) and served on `http://localhost:8000`. The package `sphinx-autobuild` will watch the files, rebuild the HTML and reload the page in the browser on changes.


## Building the docs locally

Build dependencies are managed with [Conda](https://conda.io).

Enter the docs directory:

cd doc/python

Install them into an isolated environment named `org.neherlab.ffpopsim.docs` with:

conda env create

Enter the environment with:

conda activate org.neherlab.ffpopsim.docs

You can now build the documentation with:

make html

which invokes Sphinx to build static HTML pages in `doc/python/build/html/`.

On some platforms you can view them in the default browser by running:

open build/html/index.html

or

xdg-open build/html/index.html


Alternatively, you can run

make autobuild

The HTML files will also appear in `doc/python/build/html/` (for manual inspection) and served on `http://localhost:8000`. The `sphinx-autobuild` will watch the files, rebuild the HTML and reload the page in the browser on changes.

Leave the environment with:

conda deactivate
25 changes: 25 additions & 0 deletions doc/python/environment.yml
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name: org.neherlab.ffpopsim.docs
channels:
- conda-forge
- defaults
dependencies:
- anaconda-client
- boost-cpp==1.82.0
- gcc
- gcc_linux-64
- gsl==2.7
- gxx
- gxx_linux-64
- make==4.3
- numpy
- pip
- recommonmark
- requests
- sphinx
- swig==4.0.2
- pip:
- sphinx-argparse
- sphinx-autobuild
- sphinx-markdown-tables
- sphinx-rtd-theme
- sphinx-tabs
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