Migrate from circleci to github actions

.github/workflows/ci.yml

@@ -0,0 +1,134 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pre_commit_check:
+    name: Pre-Commit Check
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: tiktorch-server-env
+          environment-file: environment.yml
+          channel-priority: flexible
+          miniforge-variant: Miniforge3
+      - name: Run Pre-Commit
+        run: |
+          echo $BRANCH_NAME
+          echo ${{ github.event.pull_request.base.ref }}
+          echo ${{ github.event.pull_request.head.sha }}
+          git fetch origin
+          pre-commit run --from-ref origin/${{ github.event.pull_request.base.ref }} --to-ref ${{ github.event.pull_request.head.sha }}
+
+  conda-noarch-build:
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.version.outputs.version }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          channel-priority: flexible
+          miniforge-variant: Miniforge3
+      - name: install common conda dependencies
+        run: mamba install -n base -c conda-forge conda-build setuptools_scm -y
+      - name: Cache Conda Packages
+        uses: actions/cache@v4
+        with:
+          path: |
+            pkgs/noarch
+            pkgs/channeldata.json
+          key: ${{ github.sha }}-packages
+      - id: version
+        run: |
+          vers=$( python setup.py --version )
+          echo "version=${vers}" >> $GITHUB_OUTPUT
+      - name: Linux Conda Build Test
+        run: |
+          mkdir -p ./pkgs/noarch
+          conda build -c conda-forge conda-recipe --no-test --output-folder ./pkgs
+
+  test-conda-packages:
+    needs: [conda-noarch-build]
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    env:
+      TIKTORCH_PACKAGE_NAME: tiktorch-${{ needs.conda-noarch-build.outputs.version }}-py_0.tar.bz2
+    steps:
+      # Use GNU tar instead of BSD tar on Windows
+      - name: "Use GNU tar instead of BSD tar"
+        if: matrix.os == 'windows-latest'
+        shell: cmd
+        run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%"
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          channel-priority: flexible
+          miniforge-variant: Miniforge3
+      - name: install common conda dependencies
+        run: mamba install -n base -c conda-forge conda-build setuptools_scm -y
+      - name: Cache Conda Packages
+        uses: actions/cache@v4
+        with:
+          path: |
+            pkgs/noarch
+            pkgs/channeldata.json
+          key: ${{ github.sha }}-packages
+          enableCrossOsArchive: true
+      - name: Linux Test
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          conda build --test --override-channels \
+            -c ./pkgs -c pytorch -c ilastik-forge -c conda-forge \
+            ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
+      - name: macOS Test
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: |
+          conda build --test --override-channels \
+            -c ./pkgs -c pytorch -c ilastik-forge -c conda-forge \
+            ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
+      - name: Windows Test
+        if: matrix.os == 'windows-latest'
+        # HACK: due to a bug in conda-build need to point to
+        # libarchive explicitly.
+        # https://github.com/conda/conda/issues/12563#issuecomment-1494264704
+        env:
+          LIBARCHIVE: C:\Miniconda\Library\bin\archive.dll
+        shell: cmd /C CALL {0}
+        run: |
+          conda build --test --override-channels ^
+            -c %CD%\pkgs -c pytorch -c ilastik-forge -c conda-forge ^
+            .\pkgs\noarch\%TIKTORCH_PACKAGE_NAME%

conda-recipe/meta.yaml

@@ -30,13 +30,11 @@ requirements:
     - {{ dep.lower() }}
     {% endfor %}
   run_constrained:
+    - mkl <2024.1.0  # [linux] until pytorch is compatible with the current version
     - cudatoolkit >=10.2
     {% for dep in setup_py_data['extras_require']['server-pytorch'] %}
     - {{ dep.lower() }}
     {% endfor %}
-    {% for dep in setup_py_data['extras_require']['server-tensorflow'] %}
-    - {{ dep.lower() }}
-    {% endfor %}
 
 about:
   home: https://github.com/ilastik/tiktorch
@@ -52,12 +50,10 @@ test:
     {% for dep in setup_py_data['extras_require']['server-pytorch'] %}
     - {{ dep.lower() }}
     {% endfor %}
-    {% for dep in setup_py_data['extras_require']['server-tensorflow'] %}
-    - {{ dep.lower() }}
-    {% endfor %}
     # this is still necessary, torchvision doesn't work properly with cpuonly mutex
     - torchvision=*=*cpu
     - cpuonly
+    - pytest
   imports:
     # client
     - tiktorch
@@ -70,3 +66,11 @@ test:
     # server
     - tiktorch.server.base
     - tiktorch.server.session
+
+  sources:
+    - tests
+    - tiktorch
+
+  command:
+    - pytest -v
+

environment.yml

@@ -25,12 +25,11 @@ dependencies:
 
   # pytorch
   # remove cpuonly, add cudatoolkit and cudnn for gpu support
-  - pytorch=1.13.*
-  - inferno=v0.4.*
+  - pytorch=2.4.*
   # currently it's necessary to force the cpu version, remove
   # torchvision pin when going for gpu
   # - torchvision
-  #- cpuonly
+  - cpuonly
   # - cudatoolkit >=10.2
   # - cudnn
   # - tochvision
@@ -50,6 +49,8 @@ dependencies:
   - mypy
   - pre_commit
 
+  - mkl <2024.1.0  # [linux] until pytorch is compatible with the current version
+
+  - setuptools
   - pip
 
-  - mkl <2024.1.0  # [linux] until pytorch is compatible with the current version

setup.py

@@ -37,14 +37,9 @@
     ],
     extras_require={
         "server-pytorch": [
-            "inferno",
             "pytorch>=1.6",
             "scikit-learn",
-        ],
-        "server-tensorflow": [
-            "tensorflow>=2.9",
-            "scikit-learn",
-        ],
+        ]
     },
     entry_points={"console_scripts": ["tiktorch=tiktorch.server.base:main"]},
     # extras_require={"test": ["pytest"]},