Commit 19997d5d authored by Martino Bertoni's avatar Martino Bertoni 🌋
Browse files

finally a working autogenerated API reference

parent 634aa28c
......@@ -64,6 +64,7 @@ instance/
# Sphinx documentation
docs/_build/
docs/_autosummary/
docs/source/
# PyBuilder
......
......@@ -63,7 +63,9 @@ coverage: ## check code coverage quickly with the default Python
$(BROWSER) htmlcov/index.html
docs: ## generate Sphinx HTML documentation, including API docs
sphinx-apidoc -o docs/source chemicalchecker -f -M
rm -fr docs/_build/
rm -fr docs/_autosummary/
##sphinx-apidoc -o docs/source chemicalchecker -f -M -e ## updating sphinx made this useless
$(MAKE) -C docs clean
$(MAKE) -C docs html
$(BROWSER) docs/_build/html/index.html
......
......@@ -18,3 +18,4 @@ help:
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
{{ fullname | escape | underline}}
.. currentmodule:: {{ module }}
.. autoclass:: {{ objname }}
:members:
:show-inheritance:
:inherited-members:
:special-members: __call__, __add__, __mul__
{% block methods %}
{% if methods %}
.. rubric:: {{ _('Methods') }}
.. autosummary::
:nosignatures:
{% for item in methods %}
{%- if not item.startswith('_') %}
~{{ name }}.{{ item }}
{%- endif -%}
{%- endfor %}
{% endif %}
{% endblock %}
{% block attributes %}
{% if attributes %}
.. rubric:: {{ _('Attributes') }}
.. autosummary::
{% for item in attributes %}
~{{ name }}.{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
{{ fullname | escape | underline}}
.. automodule:: {{ fullname }}
{% block attributes %}
{% if attributes %}
.. rubric:: Module attributes
.. autosummary::
:toctree:
{% for item in attributes %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
{% block functions %}
{% if functions %}
.. rubric:: {{ _('Functions') }}
.. autosummary::
:toctree:
:nosignatures:
{% for item in functions %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
{% block classes %}
{% if classes %}
.. rubric:: {{ _('Classes') }}
.. autosummary::
:toctree:
:template: custom-class-template.rst
:nosignatures:
{% for item in classes %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
{% block exceptions %}
{% if exceptions %}
.. rubric:: {{ _('Exceptions') }}
.. autosummary::
:toctree:
{% for item in exceptions %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
{% block modules %}
{% if modules %}
.. autosummary::
:toctree:
:template: custom-module-template.rst
:recursive:
{% for item in modules %}
{{ item }}
{%- endfor %}
{% endif %}
{% endblock %}
......@@ -87,7 +87,7 @@ language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '_templates']
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
......@@ -109,6 +109,7 @@ html_theme = 'sphinx_rtd_theme'
#
# html_theme_options = {}
html_logo = 'img/logo.svg'
html_favicon = 'img/favicon.ico'
html_theme_options = {
'logo_only': True,
'display_version': False,
......@@ -195,4 +196,4 @@ napoleon_use_param = True
napoleon_use_rtype = True
def setup(app):
app.add_stylesheet('css/logo.css')
app.add_css_file('css/logo.css')
The Chemical Checker repository
===============================
The Chemical Checker package
============================
The Chemical Checker (CC) is a data-driven resource of small molecule
bioactivity data. The main goal of the CC is to express data in a format
......@@ -24,55 +24,38 @@ patrick.aloy@irbbarcelona.org.
This project was first presented to the scientific community in the
following paper:
Duran-Frigola et al., Extending the small molecule similarity principle to all levels of biology (2019)
Duran-Frigola M, et al
"**Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker.**"
Nature Biotechnology (2020) [`link`_]
and has since
produced a number of :doc:`related publications <publications>`.
and has since produced a number of `related publications`_.
.. _Structural Bioinformatics & Network Biology Laboratory: https://sbnb.irbbarcelona.org/
.. _IRB Barcelona: https://www.irbbarcelona.org/en
Quick Start
-----------
Assuming you have Python already, Install the Chemical Checker package:
.. prompt:: bash $
export DEVPI_HOST=10.7.108.15
export DEVPI_PORT=3141
pip install --index http://$DEVPI_HOST:$DEVPI_PORT/root/dev/ --trusted-host $DEVPI_HOST chemicalchecker
This will install the *lite* version of the package
.. code-block:: python
from chemicalchecker import ChemicalChecker
cc = ChemicalChecker()
.. _related publications: https://www.bioactivitysignatures.org/publications.html
.. _link: https://www.nature.com/articles/s41587-020-0502-7
.. toctree::
:maxdepth: 2
:caption: Manifesto
:caption: Contents:
manifesto
.. toctree::
:maxdepth: 2
:caption: Publications
API Refernce
''''''''''''
publications
.. autosummary::
:toctree: _autosummary
:caption: API Reference
:template: custom-module-template.rst
:recursive:
chemicalchecker
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
\ No newline at end of file
* :ref:`genindex`
Publications
============
CC publications
---------------
- Duran-Frigola et al. *Extending the small molecule similarity
principle to all levels of biology*, in preparation
- Duran-Frigola et al. *Formatting biological big data for modern
machine learning in drug discovery*, WIREs Comput Mol Sci
[`paper <http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS1408.html>`__]
Previous related publications from SB&NB
----------------------------------------
*Sorted by relevance to the CC*
- Duran-Frigola et al., *A chemo-centric view of human health and
disease*, Nature Communications (2014)
[`paper <https://www.nature.com/articles/ncomms6676>`__]
- Duran-Frigola et al., *Drug repositioning beyond the low-hanging
fruits*, Current Opinion in Systems Biology (2017)
[`paper <https://www.sciencedirect.com/science/article/pii/S2452310016300142>`__]
- Duran-Frigola and Aloy, *Analysis of chemical and biological features
yields mechanistic insights into drug side effects*, Chemistry and
Biology (2013)
[`paper <https://www.sciencedirect.com/science/article/pii/S107455211300121X>`__]
- Jaeger, Duran-Frigola et al., *Drug sensitivity in cancer cell lines
is not tissue specific*, Molecular cancer (2015)
[`paper <https://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-015-0312-6>`__]
- Fernández-Torras et al., *Encircling the regions of the
pharmacogenomic landscape that determine drug response*, under
revision
[`paper <https://www.biorxiv.org/content/early/2018/08/02/383588>`__]
- Juan-Blanco et al., *Rationalizing drug response in cancer cell
lines*, Journal of Molecular Biology (2018)
[`paper <https://www.sciencedirect.com/science/article/pii/S0022283618301700>`__]
- Duran-Frigola, Mosca and Aloy, *Structural systems pharmacology: the
role of 3D structures in next-generation drug development*, Chemistry
and Biology (2013)
[`paper <https://www.sciencedirect.com/science/article/pii/S1074552113000872>`__]
- Duran-Frigola, Siragusa et al., *Detecting similar binding pockets to
enable systems polypharmacology*, PLOS Computational Biology (2017)
[`paper <http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005522>`__]
- Juan-Blanco et al., *IntSide: a web server for the chemical and
biological examination of drug side effects*, Bioinformatics (2014)
[`paper <https://academic.oup.com/bioinformatics/article-abstract/31/4/612/2748228>`__]
- Persi, Duran-Frigola, Damaghi, et al., *Systems analysis of
intracellular pH vulnerabilities for cancer therapy*, Nature
Communications (2018)
[`paper <https://www.nature.com/articles/s41467-018-05261-x>`__]
.. _paper: http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS1408.html
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