Cookpa patch 6

.github/workflows/ci-pytest.yml

@@ -0,0 +1,86 @@
+name: ci-pytest
+
+on: pull_request
+
+env:
+  # Changing either of these two things will invalidate the cache and cause a full re-install
+  # of ANTsPy and its dependencies
+  # Update this hash whenever there is a change that affects ANTsPy libraries or dependencies
+  # Updates or changes to the runner OS or arch will also invalidate the cache
+  python_version: '3.9' # Python version to use for testing - update when needed
+
+jobs:
+  test:
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: ${{ env.python_version }}
+        activate-environment: antspy-env
+
+    - name: Load conda environment from cache if available
+      id: cache-env
+      uses: actions/cache@v4
+      with:
+        path: ~/conda-env.tar.gz
+        key: >-
+            ${{ runner.os }}-conda-${{ env.python_version }}-
+            ${{ hashFiles('environment.yml', 'requirements.txt', 'setup.py',
+            'scripts/configure_ITK.sh', 'scripts/configure_ANTsPy.sh') }}
+
+    - name: Unpack cached environment
+      if: steps.cache-env.outputs.cache-hit == 'true'
+      run: |
+        tar -xzf ~/conda-env.tar.gz -C ${CONDA}/envs/antspy-env
+
+    - name: Checkout ANTsPy at specific commit
+      if: steps.cache-env.outputs.cache-hit != 'true'
+      uses: actions/checkout@v4
+      with:
+        repository: ANTsX/ANTsPy
+        ref: ${{ env.antspy_ref_hash }}
+        token: ${{ secrets.GITHUB_TOKEN }}
+        path: antspy-temp
+
+    - name: Install dependencies and ANTsPy from commit
+      if: steps.cache-env.outputs.cache-hit != 'true'
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda install -c conda-forge conda-pack
+        conda create -n antspy-env python=${{ env.python_version }} -y
+        conda activate antspy-env
+        pip install ./antspy-temp
+        # Pack the environment
+        conda deactivate
+        conda pack -n antspy-env -o ~/conda-env.tar.gz
+
+    - name: Cache Conda environment
+      if: steps.cache-env.outputs.cache-hit != 'true'
+      uses: actions/cache@v4
+      with:
+        path: ~/conda-env.tar.gz
+        key: >-
+            ${{ runner.os }}-conda-${{ env.python_version }}-
+            ${{ hashFiles('environment.yml', 'requirements.txt', 'setup.py',
+            'scripts/configure_ITK.sh', 'scripts/configure_ANTsPy.sh') }}
+
+    - uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr'
+      with:
+        path: antspy-pr
+
+    - name: Replace installed ANTsPy with PR code
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate antspy-env
+        ANTS_SITE_PACKAGES=$(python -c "import os, ants; print(os.path.dirname(ants.__file__))")
+        rm -rf $ANTS_SITE_PACKAGES/ants
+        cp -r antspy-pr/ants $ANTS_SITE_PACKAGES/ants
+
+    - name: Run tests
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate antspy-env
+        bash antspy-pr/tests/run_tests.sh

README.md

@@ -1,5 +1,6 @@
 # Advanced Normalization Tools in Python
 
+Hashin'
 
 [![Coverage Status](https://coveralls.io/repos/github/ANTsX/ANTsPy/badge.svg?branch=master)](https://coveralls.io/github/ANTsX/ANTsPy?branch=master)
 <a href='http://antspyx.readthedocs.io/en/latest/?badge=latest'>