Merge remote-tracking branch 'upstream/master' into atheb/fix_connect…

…ivity_visualize

.github/workflows/freeze_requirements.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   freeze_requirements:
-    runs-on: ubuntu-latest
+    runs-on: scilus-runners
     steps:
       - 
         name: Checkout scilpy

.github/workflows/test.yml

@@ -0,0 +1,74 @@
+name: Scilpy test suite
+
+on:
+  push:
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  MPLBACKEND: agg
+  OPENBLAS_NUM_THREADS: 1
+
+jobs:
+  test:
+    runs-on: scilus-runners
+    steps:
+      - name: Checkout repository
+        uses: actions/[email protected]
+
+      - name: Fetch python version from repository
+        id: python-selector
+        run: echo "python-version=$(cat .python-version)" >> $GITHUB_OUTPUT
+
+      - name: Set up Python for Scilpy
+        uses: actions/[email protected]
+        with:
+          python-version: ${{ steps.python-selector.outputs.python-version }}
+          cache: 'pip'
+
+      - name: Install non-python dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            curl \
+            git \
+            libblas-dev \
+            liblapack-dev \
+            libfreetype6-dev
+
+      - name: Install Scilpy
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install -e .
+
+      - name: Run tests
+        run: |
+          export C_INCLUDE_PATH=$pythonLocation/include/python${{ steps.python-selector.outputs.python-version }}:$C_INCLUDE_PATH
+          pytest --cov-report term-missing:skip-covered
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          flags: unittests
+          name: scilpy-unittests-${{ github.run_id }}
+          verbose: true
+          directory: .test_reports/
+          fail_ci_if_error: true
+          root_dir: $GITHUB_WORKSPACE/scilpy/
+
+      - name: Upload test reports and coverage to artifacts
+        uses: actions/[email protected]
+        with:
+          name: test-reports
+          path: |
+            .test_reports/*

MANIFEST.in

@@ -3,6 +3,7 @@ include LICENSE
 include requirements.txt
 include .python-version
 
+recursive-include data/LUT *
 recursive-include scilpy *.c
 recursive-include scilpy *.cpp
 recursive-include scilpy *.pyx

codecov.yml

@@ -0,0 +1,34 @@
+codecov:
+  allow_coverage_offsets: True
+
+coverage:
+  status:
+    project:
+      default:
+        target: 75%
+        threshold: 2%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+    patch:
+      default:
+        target: 90%
+        branches: 
+          - master
+        if_ci_failed: error
+        only_pulls: false
+
+component_management:
+  individual_components:
+    - component_id: scilpy_scripts
+      name: Scripts
+      paths:
+        - scripts/
+    - component_id: scilpy_library
+      name: Library
+      paths:
+        - scilpy/
+
+comment:
+  layout: "condensed_header, diff, components"

scripts/scil_tractogram_assign_custom_color.py

@@ -200,7 +200,9 @@ def main():
                 data = np.clip(data, np.quantile(data, 0.05),
                                np.quantile(data, 0.95))
         elif args.use_dpp:
-            data = np.squeeze(sft.data_per_point[args.use_dpp]._data)
+            tmp = [np.squeeze(sft.data_per_point[args.use_dpp][s]) for s in
+                   range(len(sft))]
+            data = np.hstack(tmp)
         elif args.load_dps:
             data = np.squeeze(load_matrix_in_any_format(args.load_dps))
             if len(data) != len(sft):

scripts/scil_tractogram_filter_by_anatomy.py

@@ -49,7 +49,7 @@
 import json
 import logging
 import os
-import pkg_resources
+import importlib.resources as resources
 
 from dipy.io.streamline import save_tractogram
 from dipy.io.utils import is_header_compatible
@@ -142,9 +142,8 @@ def load_wmparc_labels():
     Load labels dictionary of different parcellations from the
     Desikan-Killiany atlas
     """
-    resource_package = pkg_resources.get_distribution('scilpy').location
-    labels_path = os.path.join(
-        resource_package, 'data/LUT/dk_aggregate_structures.json')
+    lut_package = resources.files('data').joinpath('LUT')
+    labels_path = lut_package.joinpath('dk_aggregate_structures.json')
     with open(labels_path) as labels_file:
         labels = json.load(labels_file)
     return labels

scripts/tests/test_assign_custom_color_to_tractogram.py → scripts/tests/test_tractogram_assign_custom_color.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_assign_custom_color_to_tractogram.py',
+    ret = script_runner.run('scil_tractogram_assign_custom_color.py',
                             '--help')
     assert ret.success
 
@@ -24,7 +24,7 @@ def test_execution_tractometry(script_runner):
                              'IFGWM.trk')
     in_anat = os.path.join(get_home(), 'tractometry',
                            'IFGWM_labels_map.nii.gz')
-    ret = script_runner.run('scil_assign_custom_color_to_tractogram.py',
+    ret = script_runner.run('scil_tractogram_assign_custom_color.py',
                             in_bundle, 'colored.trk', '--from_anatomy',
                             in_anat)
     assert ret.success

scripts/tests/test_assign_uniform_color_to_tractograms.py → scripts/tests/test_tractogram_assign_uniform_color.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_assign_uniform_color_to_tractograms.py',
+    ret = script_runner.run('scil_tractogram_assign_uniform_color.py',
                             '--help')
     assert ret.success
 
@@ -22,7 +22,7 @@ def test_execution_tractometry(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_bundle = os.path.join(get_home(), 'tractometry',
                              'IFGWM.trk')
-    ret = script_runner.run('scil_assign_uniform_color_to_tractograms.py',
+    ret = script_runner.run('scil_tractogram_assign_uniform_color.py',
                             in_bundle, '--fill_color', '0x000000',
                             '--out_tractogram', 'colored.trk')
     assert ret.success