[ENH] improve bids validation

.github/workflows/run_system_tests_matlab.yml

@@ -64,12 +64,23 @@ jobs:
           # MATLAB release to set up R2020a
           release: R2020a
 
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
       - name: Clone bidspm
         uses: actions/checkout@v3
         with:
           submodules: recursive
           fetch-depth: 0
 
+      - name: Install validators
+        run: make install
+
       - name: Get moae fmriprep data from OSF
         run: |
           mkdir -p demos/MoAE/inputs/

.github/workflows/run_system_tests_octave.yml

@@ -59,6 +59,14 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install octave liboctave-dev
 
+    - uses: actions/setup-node@v3
+      with:
+        node-version: 18
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
     - name: Info
       run: |
         octave --version
@@ -69,6 +77,9 @@ jobs:
         submodules: recursive
         fetch-depth: 0
 
+    - name: Install validators
+      run: make install
+
     - name: Get moae fmriprep data from OSF
       run: |
         mkdir -p demos/MoAE/inputs/

.github/workflows/run_tests_matlab.yml

@@ -29,12 +29,23 @@ jobs:
           # MATLAB release to set up R2020a
           release: R2020a
 
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 18
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
       - name: Clone bidspm
         uses: actions/checkout@v3
         with:
           submodules: recursive
           fetch-depth: 0
 
+      - name: Install validators
+        run: make install
+
       - name: Install SPM
         run: |
           git clone https://github.com/spm/spm12.git --depth 1

.github/workflows/run_tests_octave.yml

@@ -39,12 +39,23 @@ jobs:
       run: |
         octave --version
 
+    - uses: actions/setup-node@v3
+      with:
+        node-version: 18
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
     - name: Clone bidspm
       uses: actions/checkout@v3
       with:
         submodules: recursive
         fetch-depth: 0
 
+    - name: Install validators
+      run: make install
+
     - name: Install SPM
       run: |
         git clone https://github.com/spm/spm12.git --depth 1

.gitmodules

@@ -31,6 +31,3 @@
 	path = lib/octache
 	url = https://github.com/Remi-Gau/Octache.git
 	datalad-url = https://github.com/Remi-Gau/Octache.git
-[submodule "tools/stats_model"]
-	path = tools/stats_model
-	url = https://github.com/bids-standard/stats-models.git

.pre-commit-config.yaml

@@ -53,8 +53,20 @@ repos:
   rev: 22.10.0
   hooks:
   - id: black
+    args: [--config=pyproject.toml]
 
 - repo: https://github.com/asottile/reorder_python_imports
   rev: v3.9.0
   hooks:
   - id: reorder-python-imports
+
+- repo: https://github.com/asottile/setup-cfg-fmt
+  rev: v2.1.0
+  hooks:
+  - id: setup-cfg-fmt
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.1.0
+  hooks:
+  - id: pyupgrade
+    args: [--py38-plus]

.readthedocs.yml

@@ -21,6 +21,6 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: "3.8"
   install:
     - requirements: requirements_doc.txt

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "bidspm"
 
-version: 2.1.0dev
+version: 2.2.0
 
 abstract: BIDSpm is a set pipelines and tools for Octave/MATLAB to process and analyze BIDS data sets using SPM.
 

Dockerfile

@@ -1,4 +1,6 @@
-# Creates a docker image of bidspm with
+# Creates a docker image of bidspm
+
+# version number are updated automatically with tbe bump version script
 
 # this is mostly taken from the spm docker files: https://github.com/spm/spm-docker
 FROM ubuntu:22.04
@@ -8,62 +10,59 @@ USER root
 ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 
-#TODO how to update this with the content of the current version
-LABEL version="1.1.5dev"
+LABEL version="2.2.0"
 
 LABEL maintainer="Rémi Gau <remi.gau@gmail.com>"
 
-## Install SPM
-# basic OS tools install and also octave
+## basic OS tools install, node, npm also octave
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
-    build-essential \
+    build-essential software-properties-common\
     curl \
-    octave \
-    liboctave-dev &&
-    apt-get clean &&
+    octave liboctave-dev \
+    nodejs npm
+
+## add python
+RUN add-apt-repository ppa:deadsnakes/ppa && apt-get update
+RUN apt-get -y install python3.10 python3-pip
+
+RUN 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 &&
+## Install SPM
+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 &&
-    rm -rf \
-        /tmp/hsperfdata* \
-        /var/*/apt/*/partial \
-        /var/lib/apt/lists/* \
-        /var/log/apt/term*
-
 RUN node -v && npm -v && npm install -g bids-validator
 
 ## Install BIDSpm in user folder
 RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
 
-USER neuro
-
 WORKDIR /home/neuro
+RUN mkdir code input output
 
-RUN mkdir code output bidspm
+# COPY . /home/neuro/bidspm # this is for local development
+RUN git clone --branch v2.2.0 --depth 1 --recursive https://github.com/cpp-lln-lab/bidspm.git
 
-WORKDIR /home/neuro/
+RUN cd bidspm && pip3 install .
+RUN echo '\n'
+RUN python3 --version && pip3 list
+RUN echo '\n'
 
-COPY [".", "/home/neuro/bidspm/"]
+RUN cd bidspm && octave --no-gui --eval "bidspm; savepath();"
 
-RUN cd bidspm && octave --no-gui --eval "initCppSpm(false); savepath();"
+USER neuro
 
 ENTRYPOINT ["octave"]

Makefile

@@ -24,18 +24,24 @@ endef
 export PRINT_HELP_PYSCRIPT
 
 # TODO make more general to use the local matlab version
-MATLAB = /usr/local/MATLAB/R2017a/bin/matlab
+MATLAB = /usr/local/MATLAB/R2018a/bin/matlab
 ARG    = -nodisplay -nosplash -nodesktop
 
 ################################################################################
 #   General
 
 .PHONY: help clean clean_demos clean_test update fix_submodule
 
+install:
+	npm install -g bids-validator
+	pip install .
+
 help: ## Show what this Makefile can do
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
 clean: clean_demos clean_doc clean_test ## Remove all the clutter
 	rm -rf version.txt
+
 clean_demos: ## Remove all the output of the demo
 	rm -rf demos/*/cfg
 	rm -rf demos/*/outputs/derivatives
@@ -46,28 +52,25 @@ clean_demos: ## Remove all the output of the demo
 clean_test:	## Remove all the output of the tests
 	rm *.log
 	rm -rf coverage_html
+
 update: update.sh ## Tries to get the latest version of the current branch from upstream
-	bash update.sh
+	bash tools/update.sh
 
 fix_submodule: ## Fix any submodules that would not be checked out
 	git submodule update --init --recursive && git submodule update --recursive
 
-# TODO should update the version in
-# - the doc conf.py
-# - in the reference in the README
-# - dockerfile
-version.txt: CITATION.cff
-	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
+bump_version:
+	bash tools/bump_version.sh
 
 validate_cff: ## Validate the citation file
 	cffconvert --validate
 
+release: validate_cff bump_version lint manual
+
 
 ################################################################################
 #   doc
 
-.PHONY: clean_doc manual
-
 clean_doc:
 	cd docs && make clean
 
@@ -78,8 +81,6 @@ manual: ## Build PDF version of the doc
 ################################################################################
 #   lint
 
-.PHONY: lint lint_matlab lint_python
-
 lint: lint_matlab lint_python ## Clean MATLAB and python code
 
 lint_matlab: ## Clean MATLAB code
@@ -93,11 +94,12 @@ lint_python: ## Clean python code
 ################################################################################
 #   test
 
-.PHONY: test system_test
-test: run_tests.m initCppSpm.m src tests ## Run tests with coverage
+test: ## Run tests with coverage
 	$(MATLAB) $(ARG) -r "run_tests; exit()"
-system_test: manualTests/test_moae.m initCppSpm.m src demos/MoAE/options demos/MoAE/models ## Run system tests
-	$(MATLAB) $(ARG) -r "cd manualTests; test_moae; exit()"
+
+system_test: ## Run system tests
+	$(MATLAB) $(ARG) -r "cd demos/face_repetition/; test_face_rep; exit()"
+	$(MATLAB) $(ARG) -r "cd demos/MoAE/; test_moae; exit()"
 
 
 ################################################################################

README.md

@@ -1,4 +1,5 @@
-<!-- .. only:: html -->
+<!-- needed to ignore badges when building doc -->
+<!-- .. only:: not latex -->
 
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/cpp-lln-lab/bidspm/main.svg)](https://results.pre-commit.ci/latest/github/cpp-lln-lab/bidspm/main)
 [![miss hit](https://img.shields.io/badge/code%20style-miss_hit-000000.svg)](https://misshit.org/)
@@ -35,15 +36,41 @@ git clone \
 ```
 
 To start using bidspm, you just need to initialize it for this MATLAB / Octave
-session with::
+session with:
 
 ```matlab
 bidspm()
 ```
 
 Please see our
-[documentation](https://bidspm.readthedocs.io/en/latest/general_information.html)
-for more info.
+[documentation](https://bidspm.readthedocs.io/en/latest/installation.html) for
+more info.
+
+### Validation dependencies
+
+If you want to validate bids dataset and bids stats model through bidspm, you
+will need:
+
+-   [python3](https://www.python.org/downloads/)
+-   [node.js and npm](https://docs.npmjs.com/downloading-and-installing-node-js-and-npm)
+
+You can then install:
+
+-   the bids validator
+-   the bidspm package
+
+by running from the command line in the root folder of the repository:
+
+```bash
+make install
+```
+
+or
+
+```bash
+npm install -g bids-validator
+pip install .
+```
 
 ## Usage
 
@@ -146,7 +173,7 @@ info.
   license = {GPL-3.0},
   title   = {bidspm},
   url = {https://github.com/cpp-lln-lab/bidspm},
-  version = {2.1.0dev},
+  version = {2.2.0}
   doi     = {10.5281/zenodo.3554331},
   publisher = {Zenodo},
   journal = {Software}