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tests #436

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tests

tests #436

Workflow file for this run

.github/workflows/pytest.yml at 7990eaf
name: tests
on:
push:
branches: ["**"]
pull_request:
types:
- opened
- reopened
- ready_for_review
jobs:
# pytest-unit:
# runs-on: ubuntu-24.04
# strategy:
# matrix:
# python-version: ["3.9"]
# steps:
# - name: System Dependencies
# run: |
# sudo apt install -y build-essential \
# libcairo2-dev \
# pkg-config \
# python3-dev \
# python3-openssl
# - uses: actions/checkout@v4
# - name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v5
# with:
# python-version: ${{ matrix.python-version }}
# - name: Cache Python dependencies
# uses: actions/cache@v4
# with:
# path: ~/.cache/pip
# key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
# restore-keys: |
# ${{ runner.os }}-pip-
# - name: Install dependencies
# run: |
# python3.9 -m pip install --upgrade pip
# pip install -e .
# if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
# if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi
# - name: pytest
# run: |
# # python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/unit
# python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/modac/test/unit
# cd atomsci/ddm/test/unit && python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv
# env:
# ENV: test
# - name: combine/move .coverage files (for parallel test run)
# run: |
# cd atomsci/ddm/test/unit
# if ls -a .coverage* 1> /dev/null 2>&1; then
# coverage combine .coverage*
# mv .coverage* $GITHUB_WORKSPACE
# fi
# - name: Upload coverage-part1
# uses: actions/upload-artifact@v4
# with:
# name: coverage-part1
# path: .coverage
# if-no-files-found: ignore
pytest-integrative-1:
runs-on: ubuntu-24.04
strategy:
matrix:
python-version: ["3.9"]
steps:
- name: System Dependencies
run: |
sudo apt install -y build-essential \
libcairo2-dev \
pkg-config \
python3-dev \
python3-openssl
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache Python dependencies
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install dependencies
run: |
python3.9 -m pip install --upgrade pip
pip install -e .
if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi
- name: Install sqlite3
run: sudo apt-get update && sudo apt-get install -y sqlite3
- name: pytest
run: |
# TODO: Run this test with pytest for paralell testing
# python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 0
env:
ENV: test
- name: Combine coverage files
run: |
find . -name '.coverage*' | while read covfile; do
echo "Report for $covfile"
done
# combine the coverage files
coverage combine $(find . -name '.coverage')
if ls -a .coverage* 1> /dev/null 2>&1; then
command="pwd && ls -lsa .coverage*"
echo "Executing: $command"
eval "$command"
coverage report
else
echo ".coverage files not found"
fi
working-directory: ${{ github.workspace }}
- name: Upload coverage-part2
uses: actions/upload-artifact@v4
with:
name: coverage-part2
path: ${{ github.workspace }}/.coverage
if-no-files-found: ignore
# pytest-integrative-2:
# runs-on: ubuntu-24.04
# strategy:
# matrix:
# python-version: ["3.9"]
# steps:
# - name: System Dependencies
# run: |
# sudo apt install -y build-essential \
# libcairo2-dev \
# pkg-config \
# python3-dev \
# python3-openssl
# - uses: actions/checkout@v4
# - name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v4
# with:
# python-version: ${{ matrix.python-version }}
# - name: Cache Python dependencies
# uses: actions/cache@v4
# with:
# path: ~/.cache/pip
# key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
# restore-keys: |
# ${{ runner.os }}-pip-
# - name: Install dependencies
# run: |
# python3.9 -m pip install --upgrade pip
# pip install -e .
# if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
# if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi
# - name: pytest
# run: |
# # TODO: Run this test with pytest for paralell testing
# # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
# cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 1
# env:
# ENV: test
# - name: Move .coverage to root
# run: |
# if [ -f atomsci/ddm/test/integrative/.coverage* ]; then
# mv atomsci/ddm/test/integrative/.coverage* $GITHUB_WORKSPACE
# fi
# - name: Check for .coverage file
# run: ls -la .coverage* || echo ".coverage not found"
# - name: Combine coverage files
# run: |
# if ls .coverage* 1> /dev/null 2>&1; then
# coverage combine .coverage*
# fi
# - name: Upload coverage-part3
# uses: actions/upload-artifact@v4
# with:
# name: coverage-part3
# path: .coverage
# if-no-files-found: ignore
# pytest-integrative-3:
# runs-on: ubuntu-24.04
# strategy:
# matrix:
# python-version: ["3.9"]
# steps:
# - name: System Dependencies
# run: |
# sudo apt install -y build-essential \
# libcairo2-dev \
# pkg-config \
# python3-dev \
# python3-openssl
# - uses: actions/checkout@v4
# - name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v4
# with:
# python-version: ${{ matrix.python-version }}
# - name: Cache Python dependencies
# uses: actions/cache@v4
# with:
# path: ~/.cache/pip
# key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
# restore-keys: |
# ${{ runner.os }}-pip-
# - name: Install dependencies
# run: |
# python3.9 -m pip install --upgrade pip
# pip install -e .
# if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
# if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi
# - name: pytest
# run: |
# # TODO: Run this test with pytest for paralell testing
# # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
# cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 2
# env:
# ENV: test
# - name: Move .coverage to root
# run: |
# if [ -f atomsci/ddm/test/integrative/.coverage* ]; then
# mv atomsci/ddm/test/integrative/.coverage* $GITHUB_WORKSPACE
# fi
# - name: Check for .coverage file
# run: ls -la .coverage* || echo ".coverage not found"
# - name: Combine coverage files
# run: |
# if ls .coverage* 1> /dev/null 2>&1; then
# coverage combine .coverage*
# fi
# - name: Upload coverage-part4
# uses: actions/upload-artifact@v4
# with:
# name: coverage-part4
# path: .coverage
# if-no-files-found: ignore
# pytest-integrative-4:
# runs-on: ubuntu-24.04
# strategy:
# matrix:
# python-version: ["3.9"]
# steps:
# - name: System Dependencies
# run: |
# sudo apt install -y build-essential \
# libcairo2-dev \
# pkg-config \
# python3-dev \
# python3-openssl
# - uses: actions/checkout@v4
# - name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v4
# with:
# python-version: ${{ matrix.python-version }}
# - name: Cache Python dependencies
# uses: actions/cache@v4
# with:
# path: ~/.cache/pip
# key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
# restore-keys: |
# ${{ runner.os }}-pip-
# - name: Install dependencies
# run: |
# python3.9 -m pip install --upgrade pip
# pip install -e .
# if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
# if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi
# - name: pytest
# run: |
# # TODO: Run this test with pytest for paralell testing
# # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
# cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 3
# env:
# ENV: test
# - name: Move .coverage to root
# run: |
# if [ -f atomsci/ddm/test/integrative/.coverage* ]; then
# mv atomsci/ddm/test/integrative/.coverage* $GITHUB_WORKSPACE
# fi
# - name: Check for .coverage file
# run: ls -la .coverage* || echo ".coverage not found"
# - name: Combine coverage files
# run: |
# if ls .coverage* 1> /dev/null 2>&1; then
# coverage combine .coverage*
# fi
# - name: Upload coverage-part5
# uses: actions/upload-artifact@v4
# with:
# name: coverage-part5
# path: .coverage
# if-no-files-found: ignore
# combine-and-upload:
# name: Combine codecov and upload
# runs-on: ubuntu-latest
# needs: [pytest-unit, pytest-integrative-1, pytest-integrative-2, pytest-integrative-3, pytest-integrative-4]
# steps:
# - uses: actions/checkout@v4
# - uses: actions/setup-python@v5
# with:
# python-version: "3.9"
# - run: pip install coverage codecov
# - name: Check current directory
# run: pwd
# - name: Check for .coverage file
# run: ls -la .coverage* coverage* || echo ".coverage not found"
# # Download all coverage artifacts
# - uses: actions/download-artifact@v4
# with:
# name: coverage-part1
# path: coverage1
# - uses: actions/download-artifact@v4
# with:
# name: coverage-part2
# path: coverage2
# - uses: actions/download-artifact@v4
# with:
# name: coverage-part3
# path: coverage3
# - uses: actions/download-artifact@v4
# with:
# name: coverage-part4
# path: coverage4
# - uses: actions/download-artifact@v4
# with:
# name: coverage-part5
# path: coverage5
# # Move and rename .coverage files
# - name: Move and rename coverage files
# run: |
# mv coverage1/.coverage .coverage.1
# mv coverage2/.coverage .coverage.2
# mv coverage3/.coverage .coverage.3
# mv coverage4/.coverage .coverage.4
# mv coverage5/.coverage .coverage.5
# # Combine coverage data
# - name: Combine coverage data
# run: coverage combine .coverage.1 .coverage.2 .coverage.3 .coverage.4 .coverage.5
# # Generate XML report
# - name: Generate XML report
# run: coverage xml
# # Upload to Codecov
# - name: Upload coverage reports to Codecov
# uses: codecov/codecov-action@v4
# with:
# files: ./coverage.xml
# fail_ci_if_error: true
# env:
# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}