Skip to content
Code-Analysis

mol2rdkit_phys_chem: catch and log exceptions #77

Sign in to view logs

mol2rdkit_phys_chem: catch and log exceptions

mol2rdkit_phys_chem: catch and log exceptions #77

Workflow file for this run

.github/workflows/linting.yml at 998bdb8
name: Code-Analysis
on: [push]
jobs:
pylint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install $(find . -name "requirement*" -type f -printf ' -r %p')
pip install pylint
- name: Analysing the code with pylint
run: |
pylint -d C0301,R0913,W1202 $(git ls-files '*.py') --ignored-modules "rdkit"
mypy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install mypy
mypy . || exit_code=$?
mypy --install-types --non-interactive
- name: Analysing the code with mypy
run: |
mypy --ignore-missing-imports --disallow-any-generics --disallow-untyped-defs --no-implicit-optional --disallow-incomplete-defs .
pydocstyle:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pydocstyle
- name: Analysing the code with pydocstyle
run: |
pydocstyle .
docsig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install docsig
- name: Analysing the code with docsig
run: |
docsig --check-class-constructor --check-dunders --check-protected-class-methods --check-nested --check-overridden --check-protected --check-property-returns .
black:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install black[jupyter]
- name: Analysing the code with black
run: |
black --check .
flake8:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8
- name: Analysing the code with flake8
run: |
flake8 --extend-ignore=D203,E203,E501,W503 .
interrogate:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install interrogate
- name: Analysing the code with interrogate
run: |
interrogate --ignore-overloaded-functions -vv .
bandit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install bandit
- name: Analysing the code with bandit
run: |
bandit -r --skip=B404,B603,B602 .
isort:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install isort
- name: Analysing the code with isort
run: |
isort --profile black .
test_basis:
needs:
- pylint
- mypy
- pydocstyle
- docsig
- black
- flake8
- interrogate
- bandit
- isort
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install package
run: |
python -m pip install --upgrade pip
pip install .
- name: Run unit-tests
run: |
python -m unittest discover -v -s tests -t .
test_chemprop:
needs:
- test_basis
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.11
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install package
run: |
python -m pip install --upgrade pip
pip install torch
pip install .[chemprop]
- name: Run unit-tests for chemprop
run: |
python -m unittest discover -v -s test_extras/test_chemprop -t .
test_notebooks:
needs:
- test_basis
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.11
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install package
run: |
python -m pip install --upgrade pip
pip install "pandas<2.2.0"
pip install .[notebooks]
- name: Run unit-tests for notebooks
run: |
python test_extras/test_notebooks/test_notebooks.py --continue-on-failure