Merge branch 'main' of https://github.com/hackingmaterials/atomate

Author: rkingsbury

.circleci/config.yml

@@ -1,69 +1,30 @@
-version: 2
+version: 2.1
 jobs:
-  py3test:
+  test:
     working_directory: ~/atomate
     docker:
-      - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
+      - image: continuumio/miniconda3
+      - image: circleci/mongo
     steps:
       - checkout
       - restore_cache:
-          key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
+          key: deps-{{ checksum "requirements-ci.txt" }}-{{ checksum "setup.py" }}
       - run:
+          name: Install dependencies
           command: |
             export PATH=$HOME/miniconda3/bin:$PATH
-            conda create --quiet --yes --name test_env python=3.7
+            conda create --name test_env python=3.8
             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/:$PATH
-            pip install --quiet -r requirements.txt -r requirements-ci.txt
-            # Add executables and path.
-            for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
-            pip install --quiet -e .
-            pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate
-          no_output_timeout: 3600
-      - store_artifacts:
-          path: coverage_reports/
-          destination: tr1
-      - store_test_results:
-          path: coverage_reports/
-  py3devtest:
-    working_directory: ~/atomate
-    docker:
-      - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
-    steps:
-      - checkout
-      - restore_cache:
-          key: deps1-{{ .Branch }}-{{ checksum "requirements.txt" }}
+            conda install -c conda-forge openbabel pymatgen
+            pip install -r requirements-ci.txt
+            pip install .
+          no_output_timeout: 1h
       - run:
+          name: pytest
           command: |
-            export PATH=$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
+          no_output_timeout: 1h
       - store_artifacts:
           path: coverage_reports/
           destination: tr1
@@ -74,11 +35,4 @@ workflows:
   version: 2
   build_and_test:
     jobs:
-      - py3test
-      - py3devtest:
-          filters:  # don't run dev tests on main branch
-              branches:
-                  ignore:
-                      main
-
-
+      - test

.circleci/images/py3/Dockerfile

@@ -3,4 +3,4 @@ FROM python:3.6.4
 RUN apt-get update && apt-get install -y gfortran python-openbabel python-vtk python3-tk
 RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 RUN bash Miniconda3-latest-Linux-x86_64.sh -b
-RUN export PATH=$HOME/miniconda3/bin:$PATH
+RUN export PATH=$HOME/miniconda3/bin:$PATH

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 ## Summary
 
-<Short few sentences, and summary of the major changes in bullet 
+<Short few sentences, and summary of the major changes in bullet
 points>
 
 * Feature 1
@@ -10,7 +10,7 @@ points>
 
 ## TODO (if any)
 
-<If this is a work-in-progress, write something about what else needs 
+<If this is a work-in-progress, write something about what else needs
 to be done>
 
-* Feature 1 supports a, but not b.
+* Feature 1 supports a, but not b.

.github/workflows/test.yml

@@ -0,0 +1,50 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    if: github.repository_owner == 'hackingmaterials' # don't run on forks
+    runs-on: ubuntu-latest
+    services:
+      mongodb:
+        image: mongo
+        ports:
+          - 27017:27017
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install OpenBabel
+        run: |
+          # underlying C++ lib needed for Python openbabel wrapper installed by `pip install .`
+          sudo apt-get install libopenbabel-dev
+          # https://github.com/openbabel/openbabel/issues/2408#issuecomment-1014466193
+          sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements-ci.txt', 'setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements-ci.txt
+          pip install .[complete]
+
+      - name: pytest
+        run: |
+          pytest --ignore=atomate/qchem/test_files --cov=atomate --cov-report html:coverage_reports atomate

.pre-commit-config.yaml

@@ -1,21 +1,37 @@
+exclude: ^(docs/|.*test_files/|.*tests/)
+
 repos:
   - repo: https://github.com/myint/autoflake
     rev: v1.4
     hooks:
-    - id: autoflake
-      args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+
   - repo: https://github.com/psf/black
-    rev: 21.4b2
+    rev: 22.1.0
     hooks:
-    - id: black
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
     hooks:
       - id: flake8
         args: [--max-line-length=125]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.1.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort

CHANGES.txt

@@ -1 +1 @@
-(see changelog in the docs) 
+(see changelog in the docs)

LICENSE

@@ -43,4 +43,4 @@ for such Enhancements, then you hereby grant the following license:
 a  non-exclusive, royalty-free perpetual license to install, use,
 modify, prepare derivative works, incorporate into other computer
 software, distribute, and sublicense such enhancements or derivative
-works thereof, in binary and source code form.
+works thereof, in binary and source code form.

README.md

@@ -1,4 +1,9 @@
-# <img alt="atomate" src="docs_rst/_static/atomate_logo_small.png" width="250">
+# <img alt="atomate" src="https://raw.githubusercontent.com/hackingmaterials/atomate/main/docs_rst/_static/atomate_logo_small.png" width="250">
+
+[![Tests](https://github.com/hackingmaterials/atomate/actions/workflows/test.yml/badge.svg)](https://github.com/hackingmaterials/atomate/actions/workflows/test.yml)
+[![PyPI Downloads](https://img.shields.io/pypi/dm/atomate?label=PyPI%20Downloads)](https://pypi.org/project/atomate)
+[![PyPI](https://img.shields.io/pypi/v/atomate?label=PyPI%20Release)](https://pypi.org/project/atomate)
+[![Requires Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?label=Requires%20Python)](https://python.org/downloads)
 
 atomate is a software for computational materials science that contains pre-built workflows to compute and analyze the properties of materials.
 
@@ -8,7 +13,7 @@ atomate is a software for computational materials science that contains pre-buil
 
 If you find atomate useful, please encourage its development by citing the following paper in your research output:
 
-```
+```txt
 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,

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.3"

atomate/common/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"