[FIX] update version in container (#1306)

* update dockerignore

* adapt apptainer image

* fixes

* print version apptainer

* fix doc

* fix doc

* make sure we have a clean working tree

* run git status to check worktree

* fix

* more git status

* typo

* clean

* fix

.circleci/config.yml

@@ -103,6 +103,10 @@ jobs:
                 name: create output directory
                 command: mkdir -p /home/circleci/outputs/ds000001/derivatives
 
+        -   run:
+                name: version
+                command: docker run -ti --rm << parameters.dh_orga >>/<< parameters.dh_repo >> --version
+
         -   run:
                 name: default model subject level
                 command: |

.dockerignore

@@ -1,18 +1,6 @@
-# ignoring this might speed up build
-# by preventing passing extra content to the docker daemon
-
-.github
-.mypy_cache
-.vscode
-binder
-coverage_html
-**/demos
-**/docs
-templates
-**/tests
-**/bids-examples
-lib/**/.git
+lib/spmup
 
+docs/posters/2023_ohbm/poster/betterposter-thumbnail-portrait.png
 
 # General
 .DS_Store
@@ -23,6 +11,8 @@ lib/**/.git
 *.html
 *.docx
 *.ps
+*.~lock.*
+*.ppt*
 
 new_events.tsv
 
@@ -38,21 +28,31 @@ skipped_roi_*.tsv
 # created by tests
 CHANGES
 README
+tests/data/tsv_files/moae_results_table.tsv
+htmlcov
 
 # Project specific
 onsets*_events.mat
 
-
 ## from running tests in root dir
 */group/*
 models/*
+derivatives/models
+derivatives/options
+
+# hatch
+src/bidspm/_version.py
 
 ###############################################################################
 # python
 **/*egg-info
 **/__pycache__
 **/build
 .coverage
+.pytest_cache
+.tox
+
+.mypy_cache
 
 # jupyter notebooks
 .ipynb_checkpoints

.github/workflows/apptainer_build.yml

@@ -26,3 +26,5 @@ jobs:
                 apptainer-version: 1.3.0
         -   name: build sif image
             run: apptainer build bidspm.sif bidspm.def
+        -   name: version
+            run: apptainer run bidspm.sif --version

.readthedocs.yml

@@ -6,6 +6,9 @@
 # Required
 version: 2
 
+submodules:
+    exclude: [lib/riksneurotools, lib/CPP_ROI]
+
 build:
     os: ubuntu-22.04
     tools:

Dockerfile

@@ -56,11 +56,17 @@ WORKDIR /home/neuro
 
 COPY . /home/neuro/bidspm
 WORKDIR /home/neuro/bidspm
-RUN pip install --no-cache-dir --upgrade pip && \
+RUN git restore . && \
+    git -C lib/CPP_ROI/atlas/HCPex reset --hard && \
+    git -C lib/CPP_ROI/atlas/HCPex clean --force -dfx && \
+    git status && \
+    pip install --no-cache-dir --upgrade pip && \
     pip3 --no-cache-dir install -r requirements.txt && \
     pip3 --no-cache-dir install . && \
-    octave --no-gui --eval "addpath('/opt/spm12/'); savepath ();" && \
-    octave --no-gui --eval "addpath(pwd); savepath(); bidspm(); path"
+    octave --no-gui --eval "addpath('/opt/spm12/'); savepath ('/usr/share/octave/site/m/startup/octaverc');" && \
+    octave --no-gui --eval "addpath(pwd); savepath('/usr/share/octave/site/m/startup/octaverc'); bidspm(); path" && \
+    octave --no-gui --eval "path"
+
 
 WORKDIR /home/neuro
 

Makefile

@@ -123,20 +123,6 @@ clean_docker:
 build_image: Dockerfile ## Build stable docker image from the main branch
 	docker build . -f Dockerfile -t cpplab/bidspm:unstable
 
-Dockerfile_matlab:
-	docker run --rm kaczmarj/neurodocker:0.9.1 generate docker \
-		--pkg-manager apt \
-		--base-image debian:stretch-slim \
-		--spm12 version=r7771 \
-		--install nodejs npm \
-		--run "node -v && npm -v && npm install -g bids-validator" \
-		--user neuro \
-		--run "mkdir code output bidspm" \
-		--copy ".", "/home/neuro/bidspm/" > 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
 

bidspm.def

@@ -50,11 +50,19 @@ From: bids/base_validator:1.13.1
     make -C /opt/spm12/src PLATFORM=octave install
     ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
 
+    git -C /opt/bidspm restore .
+    git -C /opt/bidspm/ submodule foreach --recursive 'git reset --hard'
+    git -C /opt/bidspm/ submodule foreach --recursive 'git clean --force -dfx'
+    git -C /opt/bidspm/ status
+
+
+
     pip install --upgrade pip
     pip install -r /opt/bidspm/requirements.txt
     pip install /opt/bidspm
     octave --no-gui --eval "addpath('/opt/spm12/'); savepath ('/usr/share/octave/site/m/startup/octaverc');" && \
-    octave --no-gui --eval "addpath('/opt/bidspm/'); savepath('/usr/share/octave/site/m/startup/octaverc'); bidspm(); path"
+    octave --no-gui --eval "addpath('/opt/bidspm/'); savepath('/usr/share/octave/site/m/startup/octaverc'); bidspm(); path"  && \
+    octave --no-gui --eval "path"
 
 %runscript
     bidspm "$@"

docs/Makefile

@@ -15,7 +15,7 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+SPHINXOPTS    ?= -v
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build

docs/source/conf.py

@@ -58,13 +58,10 @@
 exclude_patterns = [
     "**/examples/*",
     "**/images/*",
-    "**/lib/**",
     "demo",
     "defaults",
     "examples",
     "images",
-    "lib",
-    "tests/**/*.m",
 ]
 
 suppress_warnings = ["myst.header", "myst.xref_missing"]

docs/source/demos/openneuro.md

@@ -158,5 +158,5 @@ transformers cannot yet be appled to confounds
 ### Scripts
 
 ```{eval-rst}
-.. autoscript:: ds003379_run
+.. autoscript:: ds003397_run
 ```

pyproject.toml

@@ -36,7 +36,7 @@ dev = [
     'pandas'
 ]
 doc = [
-    "urllib3==1.26.15",
+    "urllib3",
     "faqtory",
     "myst-parser",
     "sphinx",
@@ -45,7 +45,7 @@ doc = [
     "pydata-sphinx-theme",
     "sphinx-togglebutton",
     "sphinxcontrib-bibtex",
-    "sphinxcontrib-matlabdomain",
+    "sphinxcontrib-matlabdomain>=0.22.1",
     "sphinxcontrib-mermaid",
     "setuptools"
 ]