[DOC] minor doc fixes (#1020)

* minor doc fixes

* update badges

* update ignore pattern dead links

* fix dead links

Author: Remi-Gau

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -41,7 +41,7 @@ body:
   attributes:
     label: Operating system version
     value: |
-      - Linux Ubuntu 18.04 "bionic beaver"
+      - Linux Ubuntu 22.04 "jammy jellyfish"
       - Mac OS Version 12 "monterey"
   validations:
     required: false
@@ -114,7 +114,7 @@ body:
       In the MATLAB command line
 
        - `[branch, commit] = getRepoInfo()`
-    value: |
+    placeholder: |
       - main 29b689dd
       - dev 1bda0162
 
@@ -144,7 +144,11 @@ body:
       Also add the error.log that might have been generated.
     value: |
       ```matlab
-      % this is the error I got
+      % copy the error you got below
+      % before the three backticks (```)
+
+
+
 
       ```
   validations:

.github/workflows/mlc_config.json

@@ -1,7 +1,7 @@
 {
     "ignorePatterns": [
         {
-            "pattern": "^https://www.fil.ion.ucl.ac.uk/spm"
+            "pattern": "fil.ion.ucl.ac.uk|mybinder.org"
         }
     ]
 }

.pre-commit-config.yaml

@@ -108,5 +108,11 @@ repos:
   hooks:
   - id: codespell
 
+# - repo: https://github.com/tcort/markdown-link-check
+#   rev: v3.11.2
+#   hooks:
+#   - id: markdown-link-check
+#     args: [-q, -c, .github/workflows/mlc_config.json]
+
 ci:
   skip: [hadolint-docker]

README.md

@@ -5,7 +5,8 @@
   [![miss hit](https://img.shields.io/badge/code%20style-miss_hit-000000.svg)](https://misshit.org/)
   [![Documentation Status: main](https://readthedocs.org/projects/bidspm/badge/?version=stable)](https://bidspm.readthedocs.io/en/stable/?badge=stable)
   [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/main)
-  [![tests](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml)
+  [![tests matlab](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests_matlab.yml)
+  [![tests octave](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests_octave.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests_octave.yml)
   [![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
   [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)
   [![GitHub last commit](https://img.shields.io/github/last-commit/cpp-lln-lab/bidspm)](https://github.com/cpp-lln-lab/bidspm.git)

docs/generate_doc.py

@@ -65,7 +65,7 @@ def main():
 
 .. _dev_doc:
 
-developer documentation
+Developer documentation
 ***********************
 """
 

docs/source/dev_doc.rst

@@ -2,7 +2,7 @@
 
 .. _dev_doc:
 
-developer documentation
+Developer documentation
 ***********************
 
 

src/workflows/stats/bidsRFX.m

@@ -1,8 +1,5 @@
 function matlabbatch = bidsRFX(varargin)
   %
-  % - smooths all contrast images created at the subject level
-  %
-  % OR
   %
   % - creates a mean structural image and mean mask over the sample
   %
@@ -15,7 +12,7 @@
   %
   %  bidsRFX(action, opt, 'nodeName', '')
   %
-  % :param action: Action to be conducted: ``'smoothContrasts'`` or ``'RFX'`` or
+  % :param action: Action to be conducted: ``'RFX'`` or
   %                ``'meanAnatAndMask'`` or ``'contrast'``
   % :type action: char
   %