Merge pull request #217 from ilastik/ci-multiple-os

Migrate from circleci to github actions

.github/workflows/ci.yml

@@ -0,0 +1,172 @@
+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 }}
+
+  test-dev:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    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: conda diagnostics
+        run: |
+          conda list
+          conda info
+      - name: install submodules
+        run: |
+          git submodule init
+          git submodule update
+          make install_submodules
+      - name: Run tests
+        run: |
+          pytest -v -s --cov=tiktorch --cov-report=xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+
+  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: conda 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
+        run: |
+          mkdir -p ./pkgs/noarch
+          conda build -c ilastik-forge -c pytorch -c conda-forge \
+          conda-recipe --no-test --output-folder ./pkgs
+
+  test-build-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: conda 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: ${{ github.sha }}-packages
+          enableCrossOsArchive: true
+      - name: Linux Test
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          conda build --test --override-channels \
+            -c ./pkgs -c ilastik-forge -c pytorch -c conda-forge \
+            ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
+      - name: macOS Test
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: |
+          conda build --test --override-channels \
+            -c ./pkgs -c ilastik-forge -c pytorch -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 ilastik-forge -c pytorch -c conda-forge ^
+            .\pkgs\noarch\%TIKTORCH_PACKAGE_NAME%

Makefile

@@ -28,5 +28,4 @@ install_submodules:
 remove_devenv:
 	conda env remove --yes --name $(TIKTORCH_ENV_NAME)
 
-
 .PHONY: *

README.md

@@ -2,6 +2,7 @@
 [![CircleCI](https://circleci.com/gh/ilastik/tiktorch.svg?style=shield)](https://circleci.com/gh/ilastik/tiktorch)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Conda](https://anaconda.org/ilastik-forge/tiktorch/badges/version.svg)](https://anaconda.org/ilastik-forge/tiktorch)
+[![codecov](https://codecov.io/gh/ilastik/tiktorch/branch/main/graph/badge.svg)](https://codecov.io/gh/ilastik/tiktorch)
 
 `tiktorch` is the neural network prediction server for [`ilastik`](https://ilastik.org).
 The server is used in the [Neural Network Workflow](https://www.ilastik.org/documentation/nn/nn).

conda-recipe/meta.yaml

@@ -15,28 +15,26 @@ source:
 build:
   noarch: python
   number: 0
-  script: python -m pip install --no-deps --ignore-installed .
+  script:
+    - python -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
   entry_points:
     - tiktorch-server = tiktorch.server.base:main
 
 requirements:
   host:
     - pip
-    - python >=3.7
+    - python >=3.8
   run:
-    - python >=3.7
-    - pickle5  # [py37]
+    - python >=3.8
     {% for dep in setup_py_data['install_requires'] %}
     - {{ 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 +50,11 @@ 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
+    - python 3.9.*
+    - pytest
+    - pytest-grpc
     - cpuonly
+    - ilastik-pytorch-version-helper-cpu
   imports:
     # client
     - tiktorch
@@ -70,3 +67,12 @@ test:
     # server
     - tiktorch.server.base
     - tiktorch.server.session
+
+  source_files:
+    - tests
+    - tiktorch
+    - pytest.ini
+
+  commands:
+    - pytest
+