Merge pull request #700 from the-virtual-brain/TVB-3103

TVB-3103. Update siibra version to 1.0a5
the-virtual-brain · Feb 11, 2024 · fcaf759 · fcaf759
2 parents bc81607 + 42a4af9
commit fcaf759
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Showing 13 changed files with 230 additions and 807 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -72,7 +72,6 @@ jobs:
 
       - name: run framework tests
         env:
-          HBP_AUTH_TOKEN: ${{ secrets.HBP_AUTH_TOKEN }}   # token or (secret+id) are needed for siibra tests
           KEYCLOAK_CLIENT_ID: ${{ secrets.KEYCLOAK_CLIENT_ID }} # KEYCLOAK_CLIENT_ID & SECRET have priority in tests
           KEYCLOAK_CLIENT_SECRET: ${{ secrets.KEYCLOAK_CLIENT_SECRET }}
         run: pytest -v tvb_framework  --cov --cov-report=xml --ignore=tvb_framework/tvb/interfaces/rest/client/tests/rest_test.py && mv coverage.xml coverage-framework.xml

diff --git a/.github/workflows/notebooks.yml b/.github/workflows/notebooks.yml
@@ -58,7 +58,5 @@ jobs:
           python setup.py develop
 
       - name: run notebooks
-        env:
-          HBP_AUTH_TOKEN: ${{ secrets.HBP_AUTH_TOKEN }}   # token or (secret+id) are needed for siibra tests
         run: |
-          python ./tvb_build/notebook_runner.py ./tvb_documentation/demos siibra
+          python ./tvb_build/notebook_runner.py ./tvb_documentation/demos
diff --git a/tvb_build/docker/requirements_group b/tvb_build/docker/requirements_group
@@ -49,7 +49,7 @@ lxml
 pylems
 docutils
 Pillow
-siibra==0.4a35
+siibra==1.0a5
 bctpy
 Deprecated
 kubernetes

diff --git a/tvb_build/notebook_runner.py b/tvb_build/notebook_runner.py
@@ -45,13 +45,16 @@ def execute_notebook(notebook):
 
 if __name__ == '__main__':
 
+    if len(sys.argv) < 1:
+        raise AttributeError("please insert the input path")
+    in_path = sys.argv[1]
+
     if len(sys.argv) >= 2:
-        in_path = sys.argv[1]
         sub_folders = sys.argv[2:]
         # compute relative paths
         sub_folders = [os.path.join(in_path, folder) for folder in sub_folders]
     else:
-        raise AttributeError("please insert the input path")
+        sub_folders = []
 
     skipped_notebooks = [
         'exploring_time_series_interactive.ipynb',  # run separately because of other notebook dependency

diff --git a/tvb_build/tvb_build/third_party_licenses/packages_accepted.xml b/tvb_build/tvb_build/third_party_licenses/packages_accepted.xml
@@ -2846,11 +2846,11 @@
     <dependency env="[win,mac,linux]" name="siibra">
         <full-name value="siibra"/>
         <project-home value="https://github.com/FZJ-INM1-BDA/siibra-python"/>
-        <version value="0.4a35"/>
+        <version value="1.0a5"/>
         <usage value="dynamic linking"/>
         <license value="LICENSE_siibra.txt"/>
         <license-type value="Apache_ 2"/>
-        <copyright-notice value="Copyright 2020-2021, Forschungszentrum J&#252;lich GmbH"/>
+        <copyright-notice value="Copyright 2020-2023, Forschungszentrum J&#252;lich GmbH"/>
         <description value="Software interface for interacting with brain atlases."/>
     </dependency>
     <dependency env="[win,linux]" name="simplegeneric">