TST download mapper for testing

Author: TomDLT

.github/workflows/run_tests.yml

@@ -26,7 +26,11 @@ jobs:
 
     - name: Install dependencies
       run: |
+        pip install -U setuptools
+        pip install -U wheel
+        pip install git+https://github.com/gallantlab/pycortex.git
         pip install -e ."[github]"
+        $CONDA/bin/conda install -c conda-forge git-annex=*=alldep*
 
     - name: Lint with flake8
       run: |
@@ -36,10 +40,21 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --ignore=E402,C901 --max-line-length=127 --statistics
 
+    - name: Config git-annex
+      run: |
+        # change of path not in effect before next action
+        echo "${CONDA}/bin" >> $GITHUB_PATH
+        # add back python to avoid using conda's
+        echo $(dirname $(which python)) >> $GITHUB_PATH
+        # add some git config for git-annex
+        git config --global user.email "github-actions@example.com"
+        git config --global user.name "Github Actions"
+
     - name: Test with pytest
       run: |
+        # run the tests
         pip install -q pytest pytest-cov codecov
-        pytest --cov=./  --reruns 2
+        pytest --cov=./
 
     - name: Run codecov
       run: |

setup.py

@@ -31,7 +31,7 @@
 
 extras_require = {
     "docs": ["sphinx", "sphinx_gallery", "numpydoc"],
-    "github": ["pytest", "pytest-rerunfailures"],
+    "github": ["pytest"],
 }
 
 

voxelwise_tutorials/tests/test_mappers.py

@@ -12,9 +12,16 @@
 from voxelwise_tutorials.viz import plot_flatmap_from_mapper
 from voxelwise_tutorials.viz import plot_2d_flatmap_from_mapper
 
-dataset_directory = '/data1/tutorials/vim-4/'
+from voxelwise_tutorials.io import get_data_home
+from voxelwise_tutorials.io import download_datalad
+
+dataset_directory = get_data_home(dataset="shortclips")
 subject_id = "S01"
 
+# download mapper if not already present
+download_datalad("mappers/S01_mappers.hdf", destination=dataset_directory,
+                 source="https://gin.g-node.org/gallantlab/shortclips")
+
 
 def test_flatmap_mappers():