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check if file exist. then move to root dir for upload #424

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check if file exist. then move to root dir for upload

check if file exist. then move to root dir for upload #424

Workflow file for this run

.github/workflows/pytest.yml at 64592ba
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: Move .coverage to root
run: |
if [ -f atomsci/ddm/test/unit/.coverage ]; then
mv atomsci/ddm/test/unit/.coverage .
fi
- name: Check for .coverage file
run: ls -l .coverage || echo ".coverage not found"
- name: Upload coverage-part1
uses: actions/upload-artifact@v4
with:
name: coverage-part1
path: .coverage
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: 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: Move .coverage to root
run: |
if [ -f atomsci/ddm/test/integrative/.coverage ]; then
mv atomsci/ddm/test/integrative/.coverage .
fi
- name: Check for .coverage file
run: ls -l .coverage || echo ".coverage not found"
- name: Upload coverage-part2
uses: actions/upload-artifact@v4
with:
name: coverage-part2
path: .coverage
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 .
fi
- name: Check for .coverage file
run: ls -l .coverage || echo ".coverage not found"
- name: Upload coverage-part3
uses: actions/upload-artifact@v4
with:
name: coverage-part3
path: .coverage
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 .
fi
- name: Check for .coverage file
run: ls -l .coverage || echo ".coverage not found"
- name: Upload coverage-part4
uses: actions/upload-artifact@v4
with:
name: coverage-part4
path: .coverage
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 .
fi
- name: Check for .coverage file
run: ls -l .coverage || echo ".coverage not found"
- name: Upload coverage-part5
uses: actions/upload-artifact@v4
with:
name: coverage-part5
path: .coverage
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
# 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 }}