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# Minimal makefile for Sphinx documentation | ||
# | ||
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# You can set these variables from the command line, and also | ||
# from the environment for the first two. | ||
SPHINXOPTS ?= | ||
SPHINXBUILD ?= sphinx-build | ||
SOURCEDIR = . | ||
BUILDDIR = _build | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile examples | ||
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examples: | ||
make -C examples notebooks | ||
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clean_examples: | ||
make -C examples clean | ||
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# 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) |
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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 | ||
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# -- Project information ----------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information | ||
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project = "cedalion" | ||
copyright = "2024, the cedalion developers" | ||
author = "the cedalion developers" | ||
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# -- General configuration --------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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extensions = [ | ||
"myst_parser", | ||
"nbsphinx", | ||
"sphinx.ext.autodoc", | ||
"sphinx.ext.autosummary", | ||
"sphinx.ext.napoleon", | ||
"sphinx_autodoc_typehints", | ||
] | ||
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myst_enable_extensions = [ | ||
"substitution", | ||
] | ||
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templates_path = ["_templates"] | ||
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] | ||
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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" | ||
html_static_path = ["_static"] | ||
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# -- Substitutions ----------------------------------------------------------- | ||
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myst_substitutions = {"docs_url": "https://eike.middell.net/share/cedalion/docs/"} |
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# Environments | ||
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TBD |
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EXAMPLE_NOTEBOOKS = new_conference_example1.ipynb \ | ||
new_conference_example2.ipynb \ | ||
pruning_and_motion_artifacts.ipynb \ | ||
photogrammetry.ipynb \ | ||
scalp_coupling_index.ipynb \ | ||
1010_system.ipynb | ||
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.PHONY: notebooks | ||
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notebooks: $(EXAMPLE_NOTEBOOKS) | ||
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$(EXAMPLE_NOTEBOOKS) : %.ipynb : ../../examples/%.ipynb | ||
jupyter nbconvert --ExecutePreprocessor.store_widget_state=True --to notebook \ | ||
--execute --output-dir=. $^ | ||
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clean: | ||
rm -f $(EXAMPLE_NOTEBOOKS) |
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# Examples | ||
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This section contains Jupyter notebooks that illustrate functionality of the toolbox. | ||
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```{toctree} | ||
:maxdepth: 2 | ||
:glob: | ||
* | ||
``` |
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# Getting started | ||
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```{toctree} | ||
installation.md | ||
contributing_code/contributing_code.md | ||
``` |
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# Installation | ||
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## Development | ||
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To create a conda environment with the necessary dependendencies run: | ||
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``` | ||
$ conda env create -n cedalion -f environment_dev.yml | ||
``` | ||
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Afterwards activate the environment and add an editable install of `cedalion` to it: | ||
``` | ||
$ conda activate cedalion | ||
$ pip install -e . | ||
``` | ||
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This will also install Jupyter Notebook to run the example notebooks. | ||
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```{admonition} If it's slow... | ||
:class: tip | ||
To create the environment conda needs to find a set of packages that fulfills all | ||
requirements. If conda needs too much time to find a solution, there are two ways to | ||
speed it up. | ||
1. Install [libmamba-solver](https://conda.github.io/conda-libmamba-solver/user-guide/) | ||
and configure conda to use it. (***recommended***) | ||
2. Install [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html), a drop-in replacement for conda. | ||
Additional guidance can be found in the the [environments section](environments.md). | ||
``` | ||
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## Production | ||
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- TBD | ||
- currently, no fixed release. not on pypi. |
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.. cedalion documentation master file, created by | ||
sphinx-quickstart on Tue Feb 20 04:43:23 2024. | ||
You can adapt this file completely to your liking, but it should at least | ||
contain the root `toctree` directive. | ||
Cedalion | ||
======== | ||
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A python-based framework for the data driven analysis of multimodal fNIRS and DOT in | ||
naturalistic environments. | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
:caption: Contents: | ||
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getting_started/index.md | ||
examples/index.md | ||
api.rst | ||
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Indices and tables | ||
================== | ||
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* :ref:`genindex` | ||
* :ref:`modindex` | ||
* :ref:`search` |
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@ECHO OFF | ||
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pushd %~dp0 | ||
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REM Command file for Sphinx documentation | ||
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if "%SPHINXBUILD%" == "" ( | ||
set SPHINXBUILD=sphinx-build | ||
) | ||
set SOURCEDIR=. | ||
set BUILDDIR=_build | ||
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%SPHINXBUILD% >NUL 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.https://www.sphinx-doc.org/ | ||
exit /b 1 | ||
) | ||
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if "%1" == "" goto help | ||
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
goto end | ||
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:help | ||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
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:end | ||
popd |
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