Merge remote-tracking branch 'upstream/main' into macs_gof

.dockerignore

@@ -11,7 +11,7 @@ coverage_html
 templates
 **/tests
 **/bids-examples
-lib/*/.git
+lib/**/.git
 
 
 # General

.github/workflows/tests_octave.yml

@@ -71,7 +71,7 @@ jobs:
     - name: Install python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Clone bidspm
       uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -56,7 +56,7 @@ repos:
     args: [--config=pyproject.toml]
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.11.0
   hooks:
   - id: pyupgrade
     args: [--py38-plus]
@@ -73,7 +73,7 @@ repos:
   - id: flynt
 
 - repo: https://github.com/asottile/reorder-python-imports
-  rev: v3.10.0
+  rev: v3.11.0
   hooks:
   - id: reorder-python-imports
     args: [--py38-plus, --add-import, from __future__ import annotations]

Makefile

@@ -34,7 +34,7 @@ ARG    = -nodisplay -nosplash -nodesktop
 
 install:
 	npm install -g bids-validator
-	pip3 install .
+	pip3 install .[dev]
 
 help: ## Show what this Makefile can do
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
@@ -122,7 +122,6 @@ clean_docker:
 
 build_image: Dockerfile ## Build stable docker image from the main branch
 	docker build . -f Dockerfile -t cpplab/bidspm:unstable
-	VERSION=$(cat version.txt | cut -c2-)
 
 Dockerfile_matlab:
 	docker run --rm kaczmarj/neurodocker:0.9.1 generate docker \
@@ -138,4 +137,7 @@ Dockerfile_matlab:
 build_image_matlab: Dockerfile_matlab
 	docker build . -f Dockerfile_matlab -t cpplab/bidspm_matlab:unstable
 
+docker_data:
+	make -C demos/openneuro data_ds000001
+
 ################################################################################

demos/MoAE/test_moae.m

@@ -84,13 +84,22 @@
 
   cd(WD);
 
-  % with Octave running more n-1 loop in CI is fine
+  % Octave
+  % running more n-1 loop in CI is fine
   % but not running crashes with a segmentation fault
   % /home/runner/work/_temp/fb8e9d58-fa9f-4f93-8c96-387973f3632e.sh: line 2:
   % 7487 Segmentation fault      (core dumped) octave $OCTFLAGS --eval "run system_tests_facerep;"
   %
   % not sure why
-  if bids.internal.is_octave()
+  %
+
+  % Windows
+  % Error using overwriteDir
+  %    C:\Users\runneradmin\AppData\Local\Temp\8f7c44ca98d0\outputs\derivatives\bidspm-stats\
+  %           sub-01\task-auditory_space-individual_FWHM-6 could not be removed.
+  % Error in setBatchSubjectLevelGLMSpec (line 73)
+  %    overwriteDir(ffxDir, opt);
+  if bids.internal.is_octave() || ispc()
     break
   end
 

pyproject.toml

@@ -69,6 +69,7 @@ dev = [
     "coverage",
     "pytest",
     "ruamel.yaml",
+    'pandas'
 ]
 
 [project.scripts]

tests/Makefile

@@ -10,7 +10,7 @@ clean_local:
 	rm -rf data/derivatives/bidspm-*/jobs
 
 create_dummy_dataset: clean_local
-	sh createDummyDataSet.sh
+	python create_dummy_dataset.py
 
 bids_examples:
 	rm -rf bids-examples/