update doc

Author: Remi-Gau

.all-contributorsrc

@@ -7,7 +7,7 @@
   "contributors": [
     {
       "login": "CerenB",
-      "name": "CerenB",
+      "name": "Ceren Battal",
       "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
       "profile": "https://github.com/CerenB",
       "contributions": [
@@ -21,7 +21,7 @@
     },
     {
       "login": "marcobarilari",
-      "name": "marcobarilari",
+      "name": "Marco Barilari",
       "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
       "profile": "https://github.com/marcobarilari",
       "contributions": [
@@ -64,7 +64,7 @@
     },
     {
       "login": "iqrashahzad14",
-      "name": "iqrashahzad14",
+      "name": "Iqra Shahzad",
       "avatar_url": "https://avatars.githubusercontent.com/u/75671348?v=4",
       "profile": "https://github.com/iqrashahzad14",
       "contributions": [

docs/source/conf.py

@@ -12,17 +12,19 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'CPP BIDS'
-copyright = '2020, the CPP BIDS dev team'
-author = 'the CPP BIDS dev team'
+project = "CPP BIDS"
+copyright = "2020, the CPP BIDS dev team"
+author = "the CPP BIDS dev team"
 
 # The full version, including alpha/beta/rc tags
-release = 'v2.1.2dev'
+with open("../../version.txt", encoding="utf-8") as version_file:
+    release = version_file.read()
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,42 +33,45 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinxcontrib.matlab',
-    'sphinx.ext.autodoc']
-matlab_src_dir = os.path.dirname(os.path.abspath('../../src'))
-primary_domain = 'mat'
+    "sphinxcontrib.matlab",
+    "sphinx.ext.autodoc",
+    "myst_parser",
+    "sphinx_copybutton",
+]
+matlab_src_dir = os.path.dirname(os.path.abspath("../../src"))
+primary_domain = "mat"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
-html_logo = '_static/cpp_lab_logo.png'
+html_logo = "_static/cpp_lab_logo.png"
 
 # html_theme_options = {
 #     'github_user': 'cpp-lln-lab',
@@ -81,11 +86,11 @@
 # }
 
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+        "donate.html",
     ]
 }

miss_hit.cfg

@@ -2,7 +2,7 @@
 project_root
 
 line_length: 100
-regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+regex_function_name: "[a-z]+(_*[a-zA-Z0-9]+[a-z]*)*"
 regex_parameter_name: "[a-z0-9]+(([A-Z]){1}[A-Za-z]+)*"
 
 exclude_dir: "lib"

requirements.txt

@@ -2,6 +2,10 @@ Sphinx
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
 sphinx_rtd_theme
+myst-parser
+
 miss_hit==0.9.29
+pre-commit
+
 notebook
 octave_kernel