Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

…gram_big

.coveragerc

@@ -1,10 +1,11 @@
 [run]
 branch = True
 concurrency = multiprocessing
-data_file = .test_reports/.coverage
-source =
-    scilpy/
-    scripts/
+data_file = .coverage
+source_pkgs = 
+    scilpy
+    scripts
+relative_files = True
 omit =
     scripts/tests/*.py
     scilpy/tests/**/*.py
@@ -15,6 +16,11 @@ omit =
 
 [report]
 skip_empty = True
+skip_covered = True
 
 [html]
 title = Scilpy Coverage Report
+directory = .test_reports/coverage.html
+
+[xml]
+output = .test_reports/coverage.xml

.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 +1,73 @@
+name: Scilpy test suite
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    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
+    if: github.repository == 'scilus/scilpy'
+    steps:
+      - name: Checkout repository for merge
+        uses: actions/checkout@v4
+
+      - 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@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests
+          name: scilpy-unittests-${{ github.run_id }}
+          verbose: true
+          fail_ci_if_error: true
+          plugin: pycoverage
+
+      - 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"

pytest.ini

@@ -33,8 +33,7 @@ junit_logging = out-err
 
 addopts =
     --html=.test_reports/pytest.html
-    --cov-report=html:.test_reports/coverage.html
     --junit-xml=.test_reports/junit.xml
-    --cov-report=xml:.test_reports/coverage.xml
-    --cov=scilpy/
-    --cov=scripts/    
+    --cov
+    --cov-report html
+    --cov-report xml