merging of scilus#1201

.coveragerc

@@ -2,17 +2,16 @@
 branch = True
 concurrency = multiprocessing
 data_file = .coverage
-source_pkgs =
-    scilpy
-    scripts
+source = src
 relative_files = True
 omit =
-    scripts/tests/*.py
-    scilpy/tests/**/*.py
-    scilpy/**/tests/*.py
-    scilpy/**/tests/**/*.py
-    scripts/tests/*.py
-    scripts/tests/**/*.py
+    src/scilpy/tests/**/*.py
+    src/scilpy/**/tests/*.py
+    src/scilpy/**/tests/**/*.py
+    src/scilpy/cli/tests/*.py
+    src/scilpy/cli/tests/**/*.py
+    src/scilpy/cli/scil_data_download.py
+    src/scilpy/io/deprecator.py
 
 [report]
 skip_empty = True

.github/workflows/test.yml

@@ -12,14 +12,14 @@ on:
 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
+    runs-on: scilus-bigmem-runners
     if: github.repository == 'scilus/scilpy'
 
     steps:
@@ -30,11 +30,12 @@ jobs:
         id: python-selector
         run: echo "python-version=$(head -1 .python-version)" >> $GITHUB_OUTPUT
 
-      - name: Set up Python for Scilpy
-        uses: actions/setup-[email protected]
+      - name: Set up Python and uv for Scilpy
+        uses: astral-sh/setup-[email protected]
         with:
           python-version: ${{ steps.python-selector.outputs.python-version }}
-          cache: 'pip'
+          activate-environment: true
+          enable-cache: true
 
       - name: Install non-python dependencies
         run: |
@@ -46,19 +47,30 @@ jobs:
             libblas-dev \
             liblapack-dev \
             libfreetype6-dev \
-            libdrm-dev
+            libdrm-dev \
+            libgl1-mesa-dev \
+            libosmesa6-dev
 
-      - name: Install Scilpy
+      - name: stdlib checkout
+        if: ${{ !contains(steps.python-selector.outputs.python-version, '3.12') }}
         run: |
-          export SETUPTOOLS_USE_DISTUTILS=stdlib
-          python -m pip install --upgrade pip wheel
-          python -m pip install --upgrade "setuptools<71.0.0" 
-          python -m pip install -e .
+          echo "SETUPTOOLS_USE_DISTUTILS=stdlib" >> "$GITHUB_ENV"
 
+      - name: Install Scilpy
+        run: |
+          uv pip install --upgrade pip wheel
+          uv pip install --upgrade "setuptools<71.0.0" 
+          uv pip install -e .
+          # TODO: to adapt once Scilpy passes to VTK 9.4.0, which selects OSMesa at runtime
+          # https://discourse.vtk.org/t/status-update-runtime-opengl-render-window-selection-in-vtk/14583
+          VTK_VERSION=$(cat pyproject.toml | grep 'vtk==' | sed 's/vtk==//g' | sed 's/\"//g' )
+          uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
+          uv pip install pytest-xdist pytest-cov
       - 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
+          scil_data_download
+          uv run --active pytest --cov-report term-missing:skip-covered
 
       - name: Save test results and coverage
         uses: actions/upload-artifact@v4
@@ -80,27 +92,16 @@ jobs:
       - name: Checkout repository at merge
         uses: actions/checkout@v4
 
-      - name: Set up Python for codecov upload
-        uses: actions/[email protected]
-        with:
-          python-version: '3.10'
-          cache: 'pip'
-
-      - name: Install pycoverage
-        run: pip install coverage
-
       - name: Download test results and coverage
         uses: actions/download-artifact@v4
         with:
           name: test-coverage-${{ github.run_id }}
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5.4.3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests
           name: scilpy-unittests-${{ github.run_id }}-${{ github.run_attempt }}
           verbose: true
           fail_ci_if_error: true
-          plugin: pycoverage
-

.python-version

@@ -1,2 +1,2 @@
-3.10
->=3.9,<3.12
+3.12
+>=3.10, < 3.13

MANIFEST.in

@@ -3,7 +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
+recursive-include src/scilpy/data *
+recursive-include src/scilpy *.c
+recursive-include src/scilpy *.cpp
+recursive-include src/scilpy *.pyx

README.md

@@ -14,22 +14,10 @@
 **Scilpy** mainly comprises tools and utilities to quickly work with diffusion MRI. Most of the tools are based
 on or are wrappers of the [DIPY] library, and most of them will eventually be migrated to [DIPY]. Those tools implement the recommended workflows and parameters used in the lab.
 
-## Install scilpy as a user
-
-We highly encourage to install scilpy in a virtual environnement. Once done and you're in your virtual environnement you can run this command:
-
-```
-export SETUPTOOLS_USE_DISTUTILS=stdlib
-pip install scilpy
-```
-
-## Install scilpy as a developer
-
-The library is now built for Python 3.9/3.10 and 3.11. Please, be sure to create a virtual environnement. 
-If none of these versions are installed on your computer, we suggest you to install python3.10:
+The library is now built for Python 3.12 so be sure to create a virtual environnement for Python 3.12. If this version is not installed on your computer:
 ```
 sudo add-apt-repository ppa:deadsnakes/ppa
-sudo apt-get install python3.10 python3.10-dev python3.10-venv python3.10-minimal python3.10-tk
+sudo apt-get install python3.12 python3.12-dev python3.12-venv python3.12-tk
 ```
 
 Make sure your pip is up-to-date before trying to install:
@@ -39,19 +27,34 @@ pip install --upgrade pip
 
 The library's structure is mostly aligned on that of [DIPY].
 
-The library and scripts can be installed locally by using:
+We highly encourage to install scilpy in a virtual environnement. Once done and you're in your virtual environnement, the library and scripts can be installed locally by running these commands:
+
+## Install scilpy as a user
+
 ```
+# If you are using Python3.10 or Python3.11, export this variable before installing
 export SETUPTOOLS_USE_DISTUTILS=stdlib
-pip install -e .
+
+# If you don't want to install legacy scripts
+export SCILPY_LEGACY='False'
+
+pip install scilpy # For the most recent release from PyPi
 ```
 
-If you don't want to install legacy scripts:
+## Install scilpy as a developer
+
 ```
+# If you are using Python3.10 or Python3.11, export this variable before installing
+export SETUPTOOLS_USE_DISTUTILS=stdlib
+
+# If you don't want to install legacy scripts
 export SCILPY_LEGACY='False'
-pip install -e .
+pip install -e . # Install from source code (for development)
 ```
 
-(Then, without the legacy scripts, if you want to use pytest, use:)
+## EXTRAS
+
+Then, without the legacy scripts, if you want to use pytest, use:
 ```
 pytest --ignore=scripts/legacy
 ```

codecov.yml

@@ -24,11 +24,11 @@ component_management:
     - component_id: scilpy_scripts
       name: Scripts
       paths:
-        - scripts/
+        - src/scilpy/cli/
     - component_id: scilpy_library
       name: Library
       paths:
-        - scilpy/
+        - "^src/scilpy/(?!cli)/.*$"
 
 comment:
   layout: "condensed_header, diff, components"