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base repository: hackingmaterials/atomate
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base: v0.8.5
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head repository: hackingmaterials/atomate
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compare: master
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Showing 827 changed files with 1,322,588 additions and 11,876 deletions.
74 changes: 44 additions & 30 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@ jobs:
py3test:
working_directory: ~/atomate
docker:
- image: materialsvirtuallab/circle-ci-pmg-py3:0.0.2
- image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
- image: circleci/mongo:3.4.15
steps:
- checkout
@@ -12,59 +12,73 @@ jobs:
- run:
command: |
export PATH=$HOME/miniconda3/bin:$PATH
conda create --quiet --yes --name test_env python=3.6
conda create --quiet --yes --name test_env python=3.7
source activate test_env
conda install --quiet --yes numpy scipy matplotlib sympy pandas
conda install --quiet --yes -c openbabel openbabel
conda install --quiet --yes -c clinicalgraphics vtk
conda install --quiet --yes -c conda-forge openbabel
# conda install --quiet --yes -c clinicalgraphics vtk
conda install --quiet --yes -c conda-forge python-igraph
conda update --quiet --all
mkdir coverage_reports
pip install --quiet -r requirements.txt -r requirements-optional.txt
wget https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
tar -zxvf vampire-5.0-linux.tar.gz
export PATH=/root/atomate/linux/:$PATH
pip install --quiet -r requirements.txt -r requirements-ci.txt
# Add executables and path.
for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
pip install --quiet -e .
nosetests --config=nose.cfg --cover-html --cover-html-dir=coverage_reports
pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate
no_output_timeout: 3600
- store_artifacts:
path: coverage_reports/
destination: tr1
- store_test_results:
path: coverage_reports/

py2test:
py3devtest:
working_directory: ~/atomate
docker:
- image: materialsvirtuallab/circle-ci-pmg-py2:0.0.2
- image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
- image: circleci/mongo:3.4.15

steps:
- checkout
- restore_cache:
key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
- run:
command: |
pip install virtualenv
virtualenv venv
. venv/bin/activate
apt-get -y -qq update
apt-get -y -qq install gfortran python-openbabel python-vtk python3-tk
pip install numpy
pip install -r requirements.txt
pip install -r requirements-optional.txt
- save_cache:
key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
paths:
- "venv"
- run:
command: |
. venv/bin/activate
python setup.py develop
ls
echo "PATH=$PATH"
nosetests --config=nose.cfg
export PATH=$HOME/miniconda3/bin:$PATH
conda create --quiet --yes --name test_env python=3.7
source activate test_env
conda install --quiet --yes numpy scipy matplotlib sympy pandas
conda install --quiet --yes -c conda-forge openbabel
# conda install --quiet --yes -c clinicalgraphics vtk
conda install --quiet --yes -c conda-forge python-igraph
conda update --quiet --all
wget https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
tar -zxvf vampire-5.0-linux.tar.gz
export PATH=/root/atomate/linux/:$PATH
pip install --quiet -r requirements.txt -r requirements-ci.txt
pip install git+https://github.com/materialsproject/pymatgen.git --upgrade
pip install git+https://github.com/materialsproject/custodian.git --upgrade
pip install git+https://github.com/materialsproject/fireworks.git --upgrade
# Add executables and path.
for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
pip install --quiet -e .
pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate
no_output_timeout: 3600
- store_artifacts:
path: coverage_reports/
destination: tr1
- store_test_results:
path: coverage_reports/

workflows:
version: 2
build_and_test:
jobs:
- py3test
- py3devtest:
filters: # don't run dev tests on master branch
branches:
ignore:
master


4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Please submit help issues to:
https://groups.google.com/forum/#!forum/atomate
https://matsci.org/atomate

The Github issues is no longer used except for internal development purposes.

If you are unable to use the Google Group, you may submit an issue here, but you must **clearly** state the reason you are unable to use the Google Group in your ticket. Otherwise, your issue will be **closed** without response.
If you are unable to use the Discourse forum, you may submit an issue here, but you must **clearly** state the reason you are unable to use the Discourse forum in your ticket. Otherwise, your issue will be **closed** without response.
6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -5,6 +5,7 @@
docs/_build/*
docs/_build/*/*
docs/_build/*/*/*
docs_rst/_build

# C extensions
*.so
@@ -31,6 +32,7 @@ pip-log.txt
.coverage
.tox
nosetests.xml
*.mypy_cache/*

# Translations
*.mo
@@ -45,6 +47,10 @@ nosetests.xml

.eggs/*

# VS Code
settings.json
.vscode

# scratch files
atomate/vasp/tests/scratch/*

19 changes: 19 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
repos:
- repo: git@github.com:humitos/mirrors-autoflake.git
rev: v1.1
hooks:
- id: autoflake
args: [ '--in-place', '--remove-all-unused-imports', '--remove-unused-variable' ]
- repo: https://github.com/ambv/black
rev: stable
hooks:
- id: black
language_version: python3.7
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v2.3.0
hooks:
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace
- id: flake8
args: ["--max-line-length=125"]
8 changes: 4 additions & 4 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -7,7 +7,7 @@ We love your input! We want to make contributing to atomate as easy and transpar
* Becoming a maintainer

## Reporting bugs, getting help, and discussion
At any time, feel free to start a thread on our [Google Group](https://groups.google.com/forum/#!forum/atomate).
At any time, feel free to start a thread on our [Discourse forum](https://discuss.matsci.org/c/atomate).

If you are making a bug report, incorporate as many elements of the following as possible to ensure a timely response and avoid the need for followups:
* A quick summary and/or background
@@ -35,10 +35,10 @@ We have a few tips for writing good PRs that are accepted into the main repo:
* Your code should have (4) spaces instead of tabs.
* If needed, update the documentation.
* **Write tests** for new features! Good tests are 100%, absolutely necessary for good code. We use the python `unittest` framework -- see some of the other tests in this repo for examples, or review the [Hitchhiker's guide to python](https://docs.python-guide.org/writing/tests/) for some good resources on writing good tests.
* Understand your contributions will fall under the same license as this repo.
* Understand your contributions will fall under the same license as this repo.

When you submit your PR, our CI service will automatically run your tests.
When you submit your PR, our CI service will automatically run your tests.
We welcome good discussion on the best ways to write your code, and the comments on your PR are an excellent area for discussion.

#### References
This document was adapted from the open-source contribution guidelines for Facebook's Draft, as well as briandk's [contribution template](https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62).
This document was adapted from the open-source contribution guidelines for Facebook's Draft, as well as briandk's [contribution template](https://gist.github.com/briandk/3d2e8b3ec8daf5a27a62).
12 changes: 6 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
@@ -3,16 +3,16 @@
atomate is a software for computational materials science that contains pre-built workflows to compute and analyze the properties of materials.

- **Website (including documentation):** https://hackingmaterials.github.io/atomate/
- **Help/Support:** https://groups.google.com/forum/#!forum/atomate
- **Help/Support:** https://discuss.matsci.org/c/atomate
- **Source:** https://github.com/hackingmaterials/atomate

If you find atomate useful, please encourage its development by citing the following paper in your research output:

```
Mathew, K., Montoya, J. H., Faghaninia, A., Dwarakanath, S., Aykol,
M., Tang, H., Chu, I., Smidt, T., Bocklund, B., Horton, M., Dagdelen,
J., Wood, B., Liu, Z.-K., Neaton, J., Ong, S. P., Persson, K., Jain,
A., Atomate: A high-level interface to generate, execute, and analyze
computational materials science workflows. Comput. Mater. Sci. 139,
Mathew, K., Montoya, J. H., Faghaninia, A., Dwarakanath, S., Aykol,
M., Tang, H., Chu, I., Smidt, T., Bocklund, B., Horton, M., Dagdelen,
J., Wood, B., Liu, Z.-K., Neaton, J., Ong, S. P., Persson, K., Jain,
A., Atomate: A high-level interface to generate, execute, and analyze
computational materials science workflows. Comput. Mater. Sci. 139,
140-152 (2017).
```
2 changes: 1 addition & 1 deletion atomate/__init__.py
Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.8.5"
__version__ = "0.9.6"
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