[INFRA] use code cov token (#125)

* use code cov token * update circle ci * unlock data before running * add git config * do not unlock * check version * same but more * bump up python things * retry
cpp-lln-lab · Jan 20, 2023 · a02df1d · a02df1d
1 parent c0b3c78
commit a02df1d
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Showing 5 changed files with 32 additions and 10 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -28,28 +28,31 @@ jobs:
                 name: Install dependencies
                 command: |
                     sudo apt-get update
-                    sudo apt-get install -y git-annex
-                    python -m pip install --upgrade pip setuptools
-                    pip install datalad
+                    sudo apt-get install -y python3 git-annex
+                    python3 -m pip install --upgrade pip setuptools
+                    pip3 install datalad
+                    datalad wtf
         -   restore_cache:
                 keys:
                 -   my_cache
         -   run:
                 name: Get ds002799
                 command: |
+                    # Git set up: to keep datalad warnings away
+                    git config --global --add user.name "Ford Escort"
+                    git config --global --add user.email 42@H2G2.com
                     mkdir -p ${HOME}/data/
                     datalad install -s ///openneuro/ds002799 ${HOME}/data/ds002799
                     cd ${HOME}/data/ds002799/derivatives/fmriprep
-                    datalad get sub-30[27]/ses-*/func/*run-*preproc*bold*
+                    datalad get sub-30[27]/ses-*/func/*run-*MNI152NLin2009cAsym*preproc*bold*
+                    datalad unlock sub-30[27]/ses-*/func/*run-*MNI152NLin2009cAsym*preproc*bold*
         -   save_cache:
                 key: my_cache
                 paths:
-
                 -   ~/data
         -   persist_to_workspace:
                 root: /home/circleci
                 paths:
-
                 -   data/ds002799
 
 
@@ -76,8 +79,10 @@ jobs:
                       -v ${HOME}/outputs:/outputs \
                         cpp-lln-lab/bidsmreye \
                           /bids_dataset \
-                          /outputs participant \
+                          /outputs \
+                          participant \
                           --participant_label 302 307 \
+                          --space MNI152NLin2009cAsym \
                           --action all
                 no_output_timeout: 6h
         -   store_artifacts:

diff --git a/.github/workflows/test_and_coverage.yml b/.github/workflows/test_and_coverage.yml
@@ -19,6 +19,7 @@ jobs:
             matrix:
                 os: [ubuntu-latest, macOS-latest] # windows-latest: does not work because antspyx is not available for windows
                 python-version: ['3.8', '3.9', '3.10'] # '3.11' : some dependencies are not yet available for python 3.11
+            fail-fast: false
 
         steps:
 
@@ -45,3 +46,4 @@ jobs:
                 flags: tests
                 name: codecov-umbrella
                 fail_ci_if_error: true
+                token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/Makefile b/Makefile
@@ -217,7 +217,6 @@ docker_demo: docker_build clean-demo
 
 docker_prepare_data:
 	docker run --rm -it \
-				--user "$$(id -u):$$(id -g)" \
 				-v $$PWD/tests/data/moae_fmriprep:/home/neuro/data \
 				-v $$PWD/outputs/moae_fmriprep/derivatives:/home/neuro/outputs/ \
 				cpplab/bidsmreye:unstable \
@@ -230,11 +229,26 @@ docker_prepare_data:
 
 docker_generalize:
 	docker run --rm -it \
-				--user "$$(id -u):$$(id -g)" \
 				-v $$PWD/tests/data/moae_fmriprep:/home/neuro/data \
 				-v $$PWD/outputs/moae_fmriprep/derivatives:/home/neuro/outputs/ \
 				cpplab/bidsmreye:unstable \
 				/home/neuro/data/ \
 				/home/neuro/outputs/ \
 				participant \
 				--action generalize
+
+docker_ds002799: get_ds002799
+	datalad unlock $$PWD/tests/data/ds002799/derivatives/fmriprep/sub-30[27]/ses-*/func/*run-*preproc*bold*
+	docker run --rm -it \
+				-v $$PWD/tests/data/ds002799/derivatives/fmriprep:/home/neuro/data \
+				-v $$PWD/outputs/ds002799/derivatives:/home/neuro/outputs/ \
+				cpplab/bidsmreye:unstable \
+				/home/neuro/data/ \
+				/home/neuro/outputs/ \
+				participant \
+				--action all \
+				--debug \
+				--participant_label 302 307 \
+				--space MNI152NLin2009cAsym \
+				--run 1 2 \
+				-vv
diff --git a/README.md b/README.md
@@ -155,7 +155,7 @@ eyes from the fMRI images.
 If your data is not in MNI space, bidsmreye will also register the data to MNI.
 
 ```bash
-bidsmreye --action prepapre \
+bidsmreye --action prepare \
           bids_dir \
           output_dir
 ```

diff --git a/tests/data/.gitignore b/tests/data/.gitignore
@@ -1,2 +1,3 @@
 moae_fmriprep
 ds000201-der/derivatives
+ds002799