Merge pull request #790 from Remi-Gau/mnt

[MNT] improve doc generation and remove dead code

Author: Remi-Gau

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = *.tsv,*.json,*.nii*,*.js,*.svg,*.eps,.git,env,*build,lib,outputs,inputs,bids-examples,stats_model,coverage_html
+skip = *.tsv,*.json,*.nii*,*.js,*.svg,*.eps,.git,env,*build,lib,outputs,inputs,bids-examples,stats_model,coverage_html,stats.md,preprocess.md
 ignore-words-list = fo,te,als,ane,nin,fot,fwe,commun
 builtin = clear,rare

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -80,7 +80,7 @@ body:
 
   - type: dropdown
     attributes:
-      label: BIDSpm version
+      label: bidspm version
       description: |
         In the MATLAB / Octave command line, try one of the following:
 
@@ -102,7 +102,7 @@ body:
 
   - type: textarea
     attributes:
-      label: BIDSpm branch / commit number
+      label: bidspm branch / commit number
       description: |
         In a terminal:
 

.github/workflows/codespell.yml

@@ -2,9 +2,9 @@ name: codespell
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

CITATION.cff

@@ -4,14 +4,14 @@ title: "bidspm"
 
 version: 2.2.0
 
-abstract: BIDSpm is a set pipelines and tools for Octave/MATLAB to process and analyze BIDS data sets using SPM.
+abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12.
 
 message: "If you use this software, please cite it as below."
 
 repository-code: "https://github.com/cpp-lln-lab/bidspm"
 
 identifiers:
-  - description: This is the collection of archived snapshots of all releases of BIDSpm
+  - description: This is the collection of archived snapshots of all releases of bidspm
     type: doi
     value: "10.5281/zenodo.3554331"
 

Dockerfile

@@ -20,30 +20,30 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
     build-essential \
     curl \
     octave \
-    liboctave-dev && \
-    apt-get clean && \
+    liboctave-dev &&
+    apt-get clean &&
     rm -rf \
         /tmp/hsperfdata* \
         /var/*/apt/*/partial \
         /var/lib/apt/lists/* \
         /var/log/apt/term*
 
-RUN mkdir /opt/spm12 && \
-    curl -SL https://github.com/spm/spm12/archive/r7771.tar.gz | \
-    tar -xzC /opt/spm12 --strip-components 1 && \
-    curl -SL https://raw.githubusercontent.com/spm/spm-docker/main/octave/spm12_r7771.patch | \
-    patch -p0 && \
-    make -C /opt/spm12/src PLATFORM=octave distclean && \
-    make -C /opt/spm12/src PLATFORM=octave && \
-    make -C /opt/spm12/src PLATFORM=octave install && \
+RUN mkdir /opt/spm12 &&
+    curl -SL https://github.com/spm/spm12/archive/r7771.tar.gz |
+    tar -xzC /opt/spm12 --strip-components 1 &&
+    curl -SL https://raw.githubusercontent.com/spm/spm-docker/main/octave/spm12_r7771.patch |
+    patch -p0 &&
+    make -C /opt/spm12/src PLATFORM=octave distclean &&
+    make -C /opt/spm12/src PLATFORM=octave &&
+    make -C /opt/spm12/src PLATFORM=octave install &&
     ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
 
 RUN octave --no-gui --eval "addpath('/opt/spm12/'); savepath ();"
 
 ## Install nods and bids validator
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
-    nodejs npm && \
-    apt-get clean && \
+    nodejs npm &&
+    apt-get clean &&
     rm -rf \
         /tmp/hsperfdata* \
         /var/*/apt/*/partial \
@@ -52,7 +52,7 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
 
 RUN node -v && npm -v && npm install -g bids-validator
 
-## Install BIDSpm in user folder
+## Install bidspm in user folder
 RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
 
 USER neuro

README.md

@@ -136,8 +136,7 @@ used to perform:
 -   GLM auto-correlation check
 
 Please see our
-[documentation](https://bidspm.readthedocs.io/en/latest/index.html) for more
-info.
+[documentation](https://bidspm.readthedocs.io/en/latest/index.html) for more info.
 
 ## Citation
 

bidspm.m

@@ -417,13 +417,13 @@ function initBidspm(dev)
       pathSep = ';';
     end
 
-    % add library first and then BIDSpm source code
+    % add library first and then bidspm source code
     % except for current folder
     run(fullfile(thisDirectory, 'lib', 'CPP_ROI', 'initCppRoi'));
     run(fullfile(thisDirectory, 'lib', 'spm_2_bids', 'init_spm_2_bids'));
     run(fullfile(thisDirectory, 'lib', 'octache', 'setup'));
 
-    % now add BIDSpm source code
+    % now add bidspm source code
     BIDSPM_PATHS = fullfile(thisDirectory);
     BIDSPM_PATHS = cat(2, BIDSPM_PATHS, ...
                        pathSep, ...

demos/vismotion/README.md

@@ -1,7 +1,7 @@
 Small demo using visual motion localizer data to show how to set up an analysis
-with BIDSpm from scratch with datalad.
+with bidspm from scratch with datalad.
 
-# Using BIDSpm and datalad
+# Using bidspm and datalad
 
 Ideally better to use the datalad fMRI template we have set up, this shows a set
 by step approach.
@@ -26,7 +26,7 @@ datalad create -c yoda visual_motion_localiser
 cd visual_motion_localiser
 ```
 
-Add the BIDSpm code as a sub-dataset, checkout the dev branch ands initializes
+Add the bidspm code as a sub-dataset, checkout the dev branch ands initializes
 
 all submodules.
 
@@ -47,7 +47,7 @@ cd code/bidspm
 git checkout dev
 git submodule update --init --recursive && git submodule update --recursive
 cd ..
-datalad save -m 'update BIDSpm submodules'
+datalad save -m 'update bidspm submodules'
 ```
 
 Now let's get the raw data as a subdataset and put it in an `inputs/raw` folder.

demos/vismotion/vismotion_demo.sh

@@ -18,7 +18,7 @@ root_directory="${PWD}/../.."
 datalad create -c yoda ~/visual_motion_localiser
 cd ~/visual_motion_localiser
 
-# get BIDSpm code from the dev branch
+# get bidspm code from the dev branch
 source="https://github.com/cpp-lln-lab/bidspm.git"
 
 # for debugging uncomment the following line

docs/.gitignore

@@ -1,2 +1,3 @@
 # documentation
 build/*
+reports