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main.yml
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name: ALIGNN github action
on: [push, pull_request]
jobs:
miniconda:
name: Miniconda ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest"]
steps:
- uses: actions/checkout@v2
- uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: test
environment-file: environment.yml
python-version: "3.10"
auto-activate-base: false
- shell: bash -l {0}
run: |
conda info
conda list
- name: Lint
shell: bash -l {0}
run: |
conda install flake8 pycodestyle pydocstyle
flake8 --ignore E203,W503 --exclude=examples,tests,scripts --statistics --count --exit-zero alignn
pycodestyle --ignore E203,W503 --exclude=examples,tests,scripts alignn
pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count alignn
- name: Run pytest
shell: bash -l {0}
run: |
#source ~/.bashrc
find . -type f > before_test_files.txt
conda env create -f environment.yml
conda activate my_alignn
conda install pytest coverage codecov pandas numpy matplotlib phonopy scikit-learn jarvis-tools --quiet
export DGLBACKEND=pytorch
export CUDA_VISIBLE_DEVICES="-1"
pip install phonopy flake8 pytest pycodestyle pydocstyle codecov pytest-cov coverage
python setup.py develop
echo 'environment.yml'
conda env export
coverage run -m pytest
coverage report -m -i
codecov
codecov --token="85bd9c5d-9e55-4f6d-bd69-350ee5e3bb41"
echo 'Train alignn'
train_alignn.py -h
echo 'Pre-trained models'
pretrained.py -h
find . -type f > after_test_files.txt
# name: JARVIS-Tools github action
# on: [push, pull_request]
# jobs:
# checks:
# name: Checks
# runs-on: ubuntu-latest
# defaults:
# run:
# shell: bash -l {0}
# strategy:
# matrix:
# python-version: ["3.10"]
# steps:
# - uses: actions/checkout@v2
# - name: Setup Python ${{ matrix.python-version }}
# uses: actions/setup-python@v2
# with:
# python-version: ${{ matrix.python-version }}
# - uses: actions/cache@v2
# with:
# path: ${{ env.pythonLocation }}
# key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
# - name: Install requirements
# run: |
# source ~/.bashrc
# echo "begin: PATH=$PATH;"
# find . -type f > before_test_files.txt
# conda env create -f environment.yml
# conda activate my_jarvis
# conda install pandas numpy matplotlib phonopy scikit-learn --quiet
# pip install --upgrade pip
# pip install pycodestyle flake8 pydocstyle coverage pytest codecov qiskit==0.41.1
# flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis
# pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
# pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis
# #python setup.py develop
# #pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
# #conda install -c ambermd pytraj
# #pip install numpy scipy matplotlib
# #pip install -r dev-requirements.txt
# pip install -e .
# echo 'CONDA LIST'
# conda list
# echo 'PIP FREEZE'
# pip freeze
# #echo 'PYTEST-COV'
# #pytest --cov-config=.coveragerc --cov=jarvis -n 2
# coverage run -m pytest
# coverage report -m -i
# codecov
# codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
# find . -type f > after_test_files.txt
# #comm -13 <(sort before_test_files.txt) <(sort after_test_files.txt) > new_files.txt
# #cat new_files.txt | xargs rm
# #rm before_test_files.txt after_test_files.txt new_files.txt
# # git clone https://github.com/QEF/q-e.git
# # cd q-e
# # ./configure
# # make pw
# jobs:
# checks:
# name: Checks
# runs-on: ubuntu-latest
# strategy:
# matrix:
# python-version: ["3.9","3.10"]
# steps:
# - uses: actions/checkout@v2
# - name: Setup Python ${{ matrix.python-version }}
# uses: actions/setup-python@v2
# with:
# python-version: ${{ matrix.python-version }}
# - uses: actions/cache@v2
# with:
# path: ${{ env.pythonLocation }}
# key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
# - name: Install requirements
# run: |
# python setup.py develop
# pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
# #conda install -c ambermd pytraj
# echo 'CONDA LIST'
# conda list
# echo 'PIP FREEZE'
# pip freeze
# #echo 'PYTEST-COV'
# #pytest --cov-config=.coveragerc --cov=jarvis -n 2
# coverage run -m pytest
# coverage report -m -i
# codecov
# codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
# # git clone https://github.com/QEF/q-e.git
# # cd q-e
# # ./configure
# # make pw
#jobs:
# miniconda:
# name: Miniconda ${{ matrix.os }}
# runs-on: ${{ matrix.os }}
# strategy:
# matrix:
# os: ["ubuntu-latest"]
# steps:
# - uses: actions/checkout@v2
# - uses: conda-incubator/setup-miniconda@v2
# with:
# activate-environment: test
# python-version: 3.8
# auto-activate-base: false
# - shell: bash -l {0}
# run: |
# conda info
# conda list
# - uses: actions/cache@v2
# with:
# path: ~/.cache/pip
# key: ${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
# - name: Run pytest
# shell: bash -l {0}
# run: |
# python setup.py develop
# #pip uninstall qiskit
# # pip install qiskit ase numpy==1.18.5 scipy==1.4.1 matplotlib>=3.0.0 phonopy==2.8.1 coverage lightgbm==2.1.0 flask joblib networkx scikit-learn pandas pennylane==0.14.1 dgl tqdm codecov torch keras tensorflow==2.3.0 pytest pytest-cov bokeh pytest-xdist
# # pip install git+https://github.com/aspuru-guzik-group/tequila.git
# # pip install -r requirements-for-ci-only.txt
# # pip install -r dev-requirements.txt
# pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
# echo 'CONDA LIST'
# conda list
# echo 'PIP FREEZE'
# pip freeze
# #echo 'PYTEST-COV'
# #pytest --cov-config=.coveragerc --cov=jarvis -n 2
# coverage run -m pytest
# coverage report -m
# codecov
# codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
# # git clone https://github.com/QEF/q-e.git
# # cd q-e
# # ./configure
# # make pw
# name: alignn-action
# on: [push, pull_request]
# jobs:
# build:
# runs-on: ubuntu-latest
# strategy:
# matrix:
# python-version: ['3.10']
# steps:
# - uses: actions/checkout@v2
# - name: Set up Python ${{ matrix.python-version }}
# uses: actions/setup-python@v2
# with:
# python-version: ${{ matrix.python-version }}
# - name: Install dependencies
# run: |
# python -m pip install --upgrade pip
# python -m pip install numpy
# python setup.py install
# - name: Lint
# run: |
# pip install flake8 pytest pycodestyle pydocstyle
# pycodestyle --ignore E203,W503 --exclude=tests alignn
# pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count alignn
# flake8 --ignore E203,W503 --exclude=tests,scripts --statistics --count --exit-zero alignn
# - name: Test with pytest
# run: |
# export DGLBACKEND=pytorch
# export CUDA_VISIBLE_DEVICES="-1"
# #pip install dgl-cu111
# pip install phonopy flake8 pytest pycodestyle pydocstyle codecov pytest-cov coverage
# pip install -e .
# #pip uninstall -y torch nvidia-cublas-cu11 nvidia-cuda-nvrtc-cu11 nvidia-cuda-runtime-cu11 nvidia-cudnn-cu11
# #conda install -y pytorch-cpu
# #pip install torch==2.0.0
# #pip install attrs==22.1.0 certifi==2022.9.24 charset-normalizer==2.1.1 codecov==2.1.12 contourpy==1.0.5 coverage==6.5.0 cycler==0.11.0 dgl==0.9.1 flake8==5.0.4 fonttools==4.38.0 idna==3.4 iniconfig==1.1.1 jarvis-tools==2022.9.16 joblib==1.2.0 kiwisolver==1.4.4 matplotlib==3.6.1 mccabe==0.7.0 networkx==3.0b1 numpy==1.23.4 packaging==21.3 pandas==1.5.1 Pillow==9.2.0 pluggy==1.0.0 psutil==5.9.3 py==1.11.0 pycodestyle==2.9.1 pydantic==1.10.2 pydocstyle==6.1.1 pyflakes==2.5.0 pyparsing==2.4.7 pytest==7.1.3 pytest-cov==4.0.0 python-dateutil==2.8.2 pytorch-ignite==0.5.0.dev20221024 pytz==2022.5 requests==2.28.1 scikit-learn==1.1.2 scipy==1.9.3 six==1.16.0 snowballstemmer==2.2.0 spglib==2.0.1 threadpoolctl==3.1.0 tomli==2.0.1 toolz==0.12.0 torch==1.12.1 tqdm==4.64.1 typing_extensions==4.4.0 urllib3==1.26.12 xmltodict==0.13.0
# echo 'PIP freeze'
# pip freeze
# echo 'environment.yml start'
# conda env export
# echo 'environment.yml end'
# coverage run -m pytest
# coverage report -m -i
# codecov
# codecov --token="85bd9c5d-9e55-4f6d-bd69-350ee5e3bb41"
# echo 'Train alignn'
# train_alignn.py -h
# echo 'Pre-trained models'
# pretrained.py -h
# #train_folder.py --root_dir "alignn/examples/sample_data" --config "alignn/examples/sample_data/config_example.json" --output_dir=temp