Merge branch 'main' into fix_boundingbox_transformation

.github/workflows/_e2e.yaml

@@ -8,6 +8,10 @@ on:
       python-version:
         required: true
         type: string
+      use-cfg:
+        required: false
+        type: string
+        default: ''
 
 jobs:
   e2e:
@@ -18,7 +22,12 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ inputs.python-version }}
-
+
+    - if: ${{ inputs.use-cfg != '' }}
+      uses: './.github/workflows/setup-custom-cfg'
+      with:
+        siibra-cfg-ref: ${{ inputs.use-cfg }}
+
     - name: Install dependencies
       shell: bash
       run: |

.github/workflows/_importable.yaml

@@ -8,6 +8,10 @@ on:
       python-version:
         required: true
         type: string
+      use-cfg:
+        required: false
+        type: string
+        default: ''
 
 jobs:
   check-importable:
@@ -18,6 +22,12 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ inputs.python-version }}
+
+    - if: ${{ inputs.use-cfg != '' }}
+      uses: './.github/workflows/setup-custom-cfg'
+      with:
+        siibra-cfg-ref: ${{ inputs.use-cfg }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/_unittest.yaml

@@ -8,6 +8,10 @@ on:
       python-version:
         required: true
         type: string
+      use-cfg:
+        required: false
+        type: string
+        default: ''
 
 jobs:
   unit-tests:
@@ -18,6 +22,12 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: '${{ inputs.python-version }}'
+
+    - if: ${{ inputs.use-cfg != '' }}
+      uses: './.github/workflows/setup-custom-cfg'
+      with:
+        siibra-cfg-ref: ${{ inputs.use-cfg }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/cron-siibra-tutorials.yml

@@ -1,6 +1,7 @@
 name: '[cron] test siibra-tutorials'
 
 on:
+  workflow_dispatch:
   schedule:
     - cron: '30 6 1,11,21 * *' # every 1st, 11th, and 21th of every month at 6:30
 
@@ -19,6 +20,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install -U .
+          pip install -r requirements.txt
+          pip install siibra_jugex
+          pip install matplotlib
           pip install pytest nbmake
 
       - name: checkout siibra-tutorials
@@ -31,4 +35,4 @@ jobs:
           ref: 'main'
 
       - name: Test tutorial notebooks with nbmake
-        run: pytest --nbmake ./siibra-tutorials-${{ github.run_id }}-${{ github.run_number }}
+        run: pytest --nbmake --nbmake-timeout=1200 ./siibra-tutorials-${{ github.run_id }}-${{ github.run_number }}

.github/workflows/docs.yml

@@ -1,7 +1,7 @@
-name: '[Docs and examples] Create docs and run examples'
-on: 
-  pull_request:
-    branches: [ 'main' ]
+name: '[Docs] Build docs and upload artifacts'
+on:
+  push:
+    branches: [ 'main', 'doc_*' ] 
   release:
     types: [ 'published' ]
 

.github/workflows/push-to-mirror.yml

@@ -2,7 +2,7 @@ name: '[mirror] push to mirror'
 
 on:
   push:
-    branches: ["master"]
+    branches: ["main"]
     tags: ["**"]
 
 env:
@@ -22,7 +22,7 @@ jobs:
     - name: mirror to remote
       run: |
         git fetch --tags -f
-        git fetch origin master
+        git fetch origin main
         if ! git ls-remote ebrains > /dev/null; then git remote add ebrains https://jugitpusher:${{ secrets.EBRAINS_GITLAB_PUSH_TOKEN }}@${{ vars.EBRAINS_GITLAB_HOST }}/${{ env.EBRAINS_GITLAB_REPO }}; fi
         git push ebrains --tags -f
-        git push ebrains HEAD:master -f 
+        git push ebrains HEAD:main -f 

.github/workflows/setup-custom-cfg/action.yml

@@ -0,0 +1,19 @@
+name: '[siibra-cfg] setup custom config'
+author: 'Xiao Gui <xgui3783@gmail.com>'
+description: 'Setup siibra custom config for tests'
+inputs:
+  siibra-cfg-ref:
+    description: 'git ref of siibra configuration to use'
+    required: true
+runs:
+  using: composite
+  steps:
+  - uses: 'actions/checkout@v4'
+    with:
+      repository: 'fzj-inm1-bda/siibra-configurations'
+      ref: ${{ inputs.siibra-cfg-ref }}
+      path: ${{ github.workspace }}/siibra-configurations
+  - id: 'set-env'
+    run: |
+      echo "SIIBRA_USE_CONFIGURATION=${{ github.workspace }}/siibra-configurations" >> $GITHUB_ENV
+    shell: bash

.github/workflows/siibra-testing.yml

@@ -10,58 +10,107 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  USE_CONFIG_COMMIT_KW: "[ci:usecfg]"
+
 jobs:
 
+  use-custom-cfg:
+    runs-on: ubuntu-latest
+    outputs:
+      USE_REF: ${{ steps.use-ref.outputs.USE_REF }}
+    env:
+      # see https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+      COMMIT_MSG: ${{ github.event.head_commit.message }}
+    steps:
+    - uses: actions/checkout@v4
+    - id: 'use-ref'
+      run: |
+        SED_S_PATTERN=$(echo '${{ env.USE_CONFIG_COMMIT_KW }}' | sed 's/\[/\\[/' | sed 's/]/\\]/')
+        echo "$COMMIT_MSG" | while IFS= read -r line
+        do
+          if [[ "$line" == "${{ env.USE_CONFIG_COMMIT_KW }}"* ]]
+          then
+            echo "Found usecfg line in commit message: $line"
+            USE_REF=$(echo $line | sed "s/$SED_S_PATTERN *//")
+            echo "Use Ref: $USE_REF"
+            echo USE_REF=$USE_REF >> $GITHUB_OUTPUT
+          fi
+        done
+
   lint:
     uses: ./.github/workflows/_lint.yaml
     with:
       os: ubuntu-latest
       python-version: '3.8'
 
   check-importable:
+    needs: 'use-custom-cfg'
+    uses: ./.github/workflows/_importable.yaml
+    with:
+      os: ubuntu-20.04
+      python-version: ${{ matrix.python-version }}
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ '3.12', '3.11', '3.10', '3.9', '3.8' ]
+
+  check-importable-python-3_7:
+    needs: 'use-custom-cfg'
     uses: ./.github/workflows/_importable.yaml
     with:
       os: ubuntu-latest
       python-version: ${{ matrix.python-version }}
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.12', '3.11', '3.10', '3.9', '3.8', '3.7' ]
+        python-version: [ '3.7' ]
 
   unit-tests-full:
     if: ${{ github.event_name == 'pull_request' }}
+    needs: 'use-custom-cfg'
     uses: ./.github/workflows/_unittest.yaml
     with:
       os: ubuntu-latest
       python-version: ${{ matrix.python-version }}
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
     strategy:
       fail-fast: false
       matrix:
         python-version: [ '3.12', '3.11', '3.10', '3.9', '3.8', '3.7' ]
 
   unit-tests-fast:
     if: ${{ github.event_name != 'pull_request' }}
+    needs: 'use-custom-cfg'
     uses: ./.github/workflows/_unittest.yaml
     with:
       os: ubuntu-latest
       python-version: '3.8'
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
 
 
   e2e-tests-full:
     if: ${{ github.event_name == 'pull_request' }}
+    needs: 'use-custom-cfg'
     uses: ./.github/workflows/_e2e.yaml
     with:
       os: ubuntu-latest
       python-version: ${{ matrix.python-version }}
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
     strategy:
       fail-fast: false
       matrix:
         python-version: [ '3.12', '3.11', '3.10', '3.9', '3.8', '3.7' ]
 
   e2e-tests-fast:
     if: ${{ github.event_name != 'pull_request' }}
+    needs: 'use-custom-cfg'
     uses: ./.github/workflows/_e2e.yaml
     with:
       os: ubuntu-latest
       python-version: '3.8'
+      use-cfg: ${{ needs.use-custom-cfg.outputs.USE_REF }}
+
 

.github/workflows/validate-citation.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install cffconvert
@@ -31,7 +31,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install cffconvert

CITATION.cff

@@ -15,9 +15,9 @@ license: Apache-2.0
 
 repository-code: https://github.com/FZJ-INM1-BDA/siibra-python
 
-version: v1.0a09
+version: v1.0a14
 
-date-released: 2024-03-14
+date-released: 2024-07-03
 
 doi: 10.5281/zenodo.7885728
 

config_schema/has_ebrainsrefs.json

@@ -27,6 +27,9 @@
                 },
                 "openminds/BrainAtlasVersion": {
                     "$ref": "#/definitions/ebrainsdef"
+                },
+                "openminds/AtlasAnnotation": {
+                    "$ref": "#/definitions/ebrainsdef"
                 }
             },
             "additionalProperties": false

e2e/features/activity_timeseries/test_activity_timeseries.py

@@ -4,30 +4,11 @@
 import sys
 from siibra.features.tabular.regional_timeseries_activity import RegionalBOLD
 from siibra.features.feature import CompoundFeature
-from e2e.util import check_duplicate
 
 skip_on_windows = pytest.mark.skipif(sys.platform == "win32", reason="Fails due to memory limitation issues on Windows on Github actions. (Passes on local machines.)")
 
 jba_29 = siibra.parcellations["julich 2.9"]
 
-
-all_bold_instances = [
-    f
-    for Cls in siibra.features.feature.Feature._SUBCLASSES[RegionalBOLD]
-    for f in Cls._get_instances()
-]
-
-
-def test_id_unique():
-    duplicates = check_duplicate([f.id for f in all_bold_instances])
-    assert len(duplicates) == 0
-
-
-def test_feature_unique():
-    duplicates = check_duplicate([f for f in all_bold_instances])
-    assert len(duplicates) == 0
-
-
 bold_cfs = [
     *siibra.features.get(jba_29, "bold"),
     *siibra.features.get(siibra.parcellations["julich 3"], "bold")

e2e/features/connectivity/test_connectivity.py

@@ -3,7 +3,6 @@
 from typing import List
 from siibra.features.feature import CompoundFeature
 from siibra.features.connectivity.regional_connectivity import RegionalConnectivity
-from e2e.util import check_duplicate
 from zipfile import ZipFile
 import os
 
@@ -13,17 +12,7 @@
     for f in Cls._get_instances()
 ]
 
-compound_conns = siibra.features.get(siibra.parcellations['julich 3'], RegionalConnectivity)
-
-
-def test_id_unique():
-    duplicates = check_duplicate([f.id for f in all_conn_instances])
-    assert len(duplicates) == 0
-
-
-def test_feature_unique():
-    duplicates = check_duplicate([f for f in all_conn_instances])
-    assert len(duplicates) == 0
+compound_conns = siibra.features.get(siibra.parcellations['julich 3.0.3'], RegionalConnectivity)
 
 
 @pytest.mark.parametrize("cf", compound_conns)
@@ -38,7 +27,7 @@ def test_connectivity_get_data(cf: CompoundFeature):
 
 
 jba_29 = siibra.parcellations["julich 2.9"]
-jba_3 = siibra.parcellations["julich 3"]
+jba_3 = siibra.parcellations["julich 3.0.3"]
 
 args = [
     (jba_29, "StreamlineCounts"),