Merge pull request #31 from MetaSys-LISBP/dev

Dev

.github/workflows/test_suite.yml

@@ -2,7 +2,7 @@ name: Launch tests
 
 on:
   pull_request:
-    types: [opened, synchronize]
+    types: [synchronize]
   push:
     branches:
       - dev

doc/conf.py

@@ -11,13 +11,16 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
 import datetime
+import os
+import sys
+
+import isocor  # NB: the *installed* version that is used in the notebooks
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -41,7 +44,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -53,8 +56,6 @@
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
-#
-import isocor  # NB: the *installed* version that is used in the notebooks
 
 full_version = isocor.__version__  # x.y.z
 # The short X.Y version.
@@ -65,42 +66,41 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ['_build']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # sphinx.ext.todo options
 todo_include_todos = True
 
-
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -110,26 +110,26 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -138,49 +138,48 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'isocordoc'
 
-
 # -- Options for LaTeX output --------------------------------------------------
 # Warning: as of Nov 18, ReadTheDocs hardcode the use of pdflatex
 # so there is no use of Sphinx's 'latex_engine' option.
@@ -189,18 +188,18 @@
 #   https://github.com/rtfd/readthedocs.org/issues/1556
 
 latex_elements = {
-# The paper size ('letter' or 'a4').
-'papersize': 'a4',
+    # The paper size ('letter' or 'a4').
+    'papersize': 'a4',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# remove blank pages (between the title page and the TOC, etc.)
-'classoptions': ',openany,oneside',
-'babel' : '\\usepackage[english]{babel}',
+    # remove blank pages (between the title page and the TOC, etc.)
+    'classoptions': ',openany,oneside',
+    'babel': '\\usepackage[english]{babel}',
 
-# Additional stuff for the LaTeX preamble.
-'preamble': r'''
+    # Additional stuff for the LaTeX preamble.
+    'preamble': r'''
   \usepackage{hyperref}
   \usepackage{upquote}
   \setcounter{tocdepth}{3}
@@ -210,29 +209,29 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual], toctree_only).
 latex_documents = [
-  ('index', 'isocor.tex', u'IsoCor Documentation',
-   "Baudoin Del\\'epine, Matthieu Guionnet, Pierre Millard", 'manual', False),
+    ('index', 'isocor.tex', u'IsoCor Documentation',
+     "Baudoin Del\\'epine, Matthieu Guionnet, Pierre Millard", 'manual', False),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 latex_use_modindex = True
 
 # -- Options for manual page output --------------------------------------------
@@ -245,7 +244,7 @@
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ------------------------------------------------
@@ -254,16 +253,17 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'IsoCor', u'IsoCor Documentation',
-   u'Baudoin Delépine, Matthieu Guionnet, Pierre Millard', 'IsoCor', 'Isotope Correction for mass spectrometry labeling experiments.',
-   'Miscellaneous'),
+    ('index', 'IsoCor', u'IsoCor Documentation',
+     u'Baudoin Delépine, Matthieu Guionnet, Pierre Millard', 'IsoCor',
+     'Isotope Correction for mass spectrometry labeling experiments.',
+     'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'

readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: requirements.txt
+    - method: pip
+      path: .
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  builder: html
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf