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Tests Cross-Platform

Tests Cross-Platform #143

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Tests Cross-Platform

Tests Cross-Platform #143

Workflow file for this run

.github/workflows/tests-conda.yml at 564e3f4
name: Tests Cross-Platform
on:
workflow_dispatch:
pull_request:
branches:
- dev
- master
push:
branches:
- dev
- master
jobs:
build:
runs-on: windows-latest
strategy:
max-parallel: 5
matrix:
python-version: [3.9]
timeout-minutes: 60
steps:
- uses: actions/checkout@v2
- name: Set up JDK 17
uses: actions/setup-java@v2
with:
java-version: '17'
distribution: 'temurin'
id: setup-java
- name: Debug JAVA_HOME
run: |
echo $env:JAVA_HOME
echo $env:PATH
shell: pwsh
- name: Set JDK_HOME environment variable
run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
shell: bash
- name: Print JAVA_HOME and JDK_HOME
run: |
echo "JAVA_HOME: $env:JAVA_HOME"
echo "JDK_HOME: $env:JDK_HOME"
shell: pwsh
- name: Setup Miniconda
uses: conda-incubator/setup-miniconda@v2
with:
auto-activate-base: false
activate-environment: pathml
environment-file: '.github/ci-environments/env-py39.yml'
mamba-version: "*"
python-version: ${{ matrix.python-version }}
- name: Debugging
shell: bash -l {0}
run: |
echo "Checking the status of mamba..."
mamba --version
echo "Checking the available disk space..."
df -h
- name: Conda info
shell: bash -l {0}
run: |
conda info
conda list
- name: Install PathML
shell: bash -l {0}
run: pip install -e .
- name: Install torchvision
shell: bash -l {0}
run: pip install torchvision==0.14.1
- name: Download and Setup OpenSlide
run: |
Invoke-WebRequest -Uri "https://github.com/openslide/openslide-bin/releases/download/v20231011/openslide-win64-20231011.zip" -OutFile "openslide-win64-20231011.zip"
Expand-Archive -Path "openslide-win64-20231011.zip" -DestinationPath "${{ github.workspace }}/openslide-binaries"
echo "${{ github.workspace }}/openslide-binaries/openslide-win64-20231011" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
shell: pwsh
- name: Test tile_stitcher with pytest and generate coverage
shell: bash -l {0}
run: |
coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py
continue-on-error: true
- name: Test other modules with pytest and generate coverage
shell: bash -l {0}
run: |
coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude"
continue-on-error: true
# name: Tests Cross-Platform
# on:
# workflow_dispatch:
# pull_request:
# branches:
# - dev
# - master
# push:
# branches:
# - dev
# - master
# jobs:
# build:
# runs-on: windows-latest # Use Ubuntu if you're building on Linux, or keep windows-latest if you're targeting Windows.
# strategy:
# max-parallel: 5
# matrix:
# python-version: [3.9]
# timeout-minutes: 60
# steps:
# - uses: actions/checkout@v2
# - name: Set up JDK 17
# uses: actions/setup-java@v2
# with:
# java-version: '17'
# distribution: 'temurin' # Use 'temurin' for Eclipse Temurin distribution
# id: setup-java
# - name: Debug JAVA_HOME
# run: |
# echo $env:JAVA_HOME
# echo $env:PATH
# shell: pwsh
# - name: Set JDK_HOME environment variable
# shell: bash
# run: echo "JDK_HOME=${JAVA_HOME}" >> $GITHUB_ENV
# - name: Print JAVA_HOME and JDK_HOME
# run: |
# echo "JAVA_HOME: $env:JAVA_HOME"
# echo "JDK_HOME: $env:JDK_HOME"
# shell: pwsh
# - name: vcpkg build
# uses: johnwason/vcpkg-action@v6
# id: vcpkg
# with:
# pkgs: openslide
# triplet: x64-windows
# token: ${{ github.token }}
# github-binarycache: true
# - name: Setup Miniconda
# uses: conda-incubator/setup-miniconda@v2
# with:
# auto-activate-base: false
# activate-environment: pathml
# environment-file: '.github/ci-environments/env-py39.yml' # Directly specify the env-py39.yml file
# mamba-version: "*"
# python-version: ${{ matrix.python-version }}
# - name: Debugging
# shell: bash -l {0}
# run: |
# echo "Checking the status of mamba..."
# mamba --version
# echo "Checking the available disk space..."
# df -h
# - name: Conda info
# shell: bash -l {0}
# run: |
# conda info
# conda list
# - name: Install PathML
# shell: bash -l {0}
# run: pip install -e .
# # - name: Install python-spams
# # shell: bash -l {0}
# # run: pip install spams
# - name: Install torchvision
# shell: bash -l {0}
# run: pip install torchvision==0.14.1
# - name: Set up vcpkg
# uses: lukka/run-vcpkg@v10
# with:
# # Setup vcpkg directory
# vcpkgDirectory: '${{ github.workspace }}/vcpkg'
# # Clone vcpkg repo
# setupOnly: true
# - name: Install OpenSlide with vcpkg
# run: |
# ./vcpkg/vcpkg install openslide
# working-directory: ${{ github.workspace }}
# - name: Test tile_stitcher with pytest and generate coverage
# shell: bash -l {0}
# run: |
# # COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py
# coverage run --data-file=.coverage_tilestitcher -m pytest tests/preprocessing_tests/test_tilestitcher.py
# - name: Test other modules with pytest and generate coverage
# shell: bash -l {0}
# run: coverage run --data-file=.coverage_others -m pytest -m "not slow and not exclude"
# # COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude"