Commit 205bb2f6 authored by Martin Larralde's avatar Martin Larralde
Browse files

Fix broken links in documentation index

parent 24df3ad7
......@@ -33,37 +33,7 @@ sys.modules['peptides.tables'] = types.ModuleType('peptides.tables')
# -- Sphinx Setup ------------------------------------------------------------
# import docutils.nodes
# import docutils.utils
# import sphinx.transforms
#
# def doi_role(role, rawtext, text, lineno, inliner, options=None, content=None):
# node = docutils.nodes.reference(
# rawtext,
# "doi:{}".format(docutils.utils.unescape(text)),
# refuri="https://doi.org/{}".format(text),
# )
# return [node], []
#
# def pmid_role(row, rawtext, text, lineno, inliner, options=None, content=None):
# try:
# pmid = int(text)
# except ValueError:
# msg = inliner.reporter.error("Invalid PMID: {!r}".format(text), line=lineno)
# prb = inliner.problematic(rawtext, rawtext, msg)
# return [prb], [msg]
# node = docutils.nodes.reference(
# rawtext,
# "PMID:{}".format(pmid),
# refuri="https://pubmed.ncbi.nlm.nih.gov/{}".format(pmid),
# )
# return [node], []
#
def setup(app):
# Add roles for DOI and PMID
# app.add_role("doi", doi_role)
# app.add_role("pmid", pmid_role)
# Add custom stylesheet
app.add_css_file(os.path.join("_static/css/main.css"))
# app.add_js_file("js/apitoc.js")
......@@ -106,6 +76,10 @@ if "See Also:" in doc_lines:
# -- General configuration ---------------------------------------------------
# mock User-Agent for linkcheck builder (some publishers disallow robots,
# so link check of DOI-resolved publications may fail).
user_agent = 'Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
......
......@@ -23,13 +23,13 @@
:target: https://pypi.python.org/pypi/peptides
.. |Wheel| image:: https://img.shields.io/pypi/wheel/peptides?style=flat-square&maxAge=3600
:target: https://pypi.org/project/peptides.py/#files
:target: https://pypi.org/project/peptides/#files
.. |Versions| image:: https://img.shields.io/pypi/pyversions/peptides.svg?style=flat-square&maxAge=3600
:target: https://pypi.org/project/peptides.py/#files
:target: https://pypi.org/project/peptides/#files
.. |Implementations| image:: https://img.shields.io/badge/impl-universal-success.svg?style=flat-square&maxAge=3600&label=impl
:target: https://pypi.org/project/peptides.py/#files
:target: https://pypi.org/project/peptides/#files
.. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=3600
:target: https://choosealicense.com/licenses/gpl-3.0/
......@@ -81,7 +81,7 @@ A non-exhaustive list of available features:
- `MS-WHIM scores <https://doi.org/10.1021/ci980211b>`_
- `PCP descriptors <https://doi.org/10.1007/s00894-001-0058-5>`_
- `ProtFP descriptors <https://doi.org/10.1186/1758-2946-5-41>`_
- `Sneath vectors <10.1016/0022-5193(66)90112-3>`_
- `Sneath vectors <https://doi.org/10.1016/0022-5193(66)90112-3>`_
- `ST-scales <https://doi.org/10.1007/s00726-009-0287-y>`_
- `T-scales <https://doi.org/10.1016/j.molstruc.2006.07.004>`_
- `VHSE-scales <https://doi.org/10.1002/bip.20296>`_
......@@ -105,8 +105,9 @@ A non-exhaustive list of available features:
- Structural class using methods and reference data from either
`Nakashima, Nishikawa & Ooi (1985) <https://doi.org/10.1093/oxfordjournals.jbchem.a135454>`_,
`Chou (1989) <10.1007/978-1-4613-1571-1>`_,
or `Chou & Zhang (1992) <10.1111/j.1432-1033.1992.tb17067.x>`_.
`Chou (1989) <https://doi.org/10.1007/978-1-4613-1571-1>`_,
`Chou & Zhang (1992) <https://doi.org/10.1111/j.1432-1033.1992.tb17067.x>`_,
or `Chou, Liu, Maggiora & Zhang <https://pubmed.ncbi.nlm.nih.gov/9552161/>`_.
Setup
......
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