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Update atoms, old prototype back. #1405

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Update atoms, old prototype back.

Update atoms, old prototype back. #1405

Workflow file for this run

.github/workflows/action_build.yml at a11d1ec
name: JARVIS-Tools 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 --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
- name: Run pytest
shell: bash -l {0}
run: |
conda install pytest coverage codecov
python setup.py develop
coverage run -m pytest
coverage report -m -i
codecov
codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
rm POSCAR* *.png
# 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