Merge commit '9cc63ca' into molmd_fix_3-9

Author: mmbliss

.github/workflows/lint.yml

@@ -4,6 +4,8 @@ on: [push, pull_request]
 
 jobs:
   build:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 1
@@ -17,6 +19,12 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/release.yml

@@ -7,6 +7,8 @@ on:
 
 jobs:
   test:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
 
     strategy:
       max-parallel: 20
@@ -32,15 +34,14 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
       - uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
         with:
-          path: ~/Library/Caches/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          path: ~/Library/Caches/pip # needs to change if `runs-on: macos` changes
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install dependencies
@@ -59,7 +60,7 @@ jobs:
       max-parallel: 2
       matrix:
         os: [ macos-latest, windows-latest ]
-        python-version: [ 3.7, 3.8 ]
+        python-version: [ '3.8', '3.9', '3.10' ]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -68,10 +69,13 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Get pip cache dir
+        id: cache-dir
+        run: |
+          echo "::set-output name=dir::$(pip cache dir)"
       - uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
         with:
-          path: ~/Library/Caches/pip
+          path: ${{ steps.cache-dir.outputs.dir }}
           key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
@@ -86,6 +90,8 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
         run: |
           pip install setuptools wheel twine
+          rm -rf test_files
           python setup.py sdist bdist_wheel
-          twine upload dist/*.whl
+          twine upload --skip-existing dist/*.whl
           twine upload --skip-existing dist/*.tar.gz
+        continue-on-error: true

.github/workflows/test.yml renamed to .github/workflows/test-linux.yml

@@ -1,13 +1,15 @@
 # This workflow runs only on Ubuntu and aims to be more complete than the Mac and Windows workflows.
 # In particular, Openbabel and many of the external command line dependencies are included for testing.defaults:
 # The ext package is also only tested in this workflow. Coverage is also computed based on this platform.
-name: Testing
+name: Testing Linux
 
 on: [ push, pull_request ]
 
 jobs:
 
   test:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
     strategy:
       max-parallel: 20
       matrix:
@@ -17,7 +19,7 @@ jobs:
             pkg_id: 1
           - pkg: pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
             pkg_id: 2
-          - pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line
+          - pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext
             pkg_id: 3
           - pkg: pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line
             pkg_id: 4
@@ -34,12 +36,12 @@ jobs:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: Cache pip
         uses: actions/cache@v2
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install OpenBabel and Libs
@@ -73,10 +75,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: Install deps
         run: |
           python -m pip install --upgrade pip

.github/workflows/test-macwin.yml renamed to .github/workflows/test-mac.yml

@@ -1,20 +1,22 @@
-name: Testing Mac Windows
+name: Testing Mac
 
 on: [ pull_request ]
 
 jobs:
   test:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
 
     strategy:
       max-parallel: 20
       matrix:
-        os: [ macos-latest, windows-latest ]
-        python-version: [ 3.8 ]
+        os: [ macos-latest ]
+        python-version: [ '3.10' ]
         # This distribution of tests is designed to ensure an approximately even time to finish for parallel jobs.
         pkg:
           - pymatgen/analysis/defects pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism
           - pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
-          - pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line
+          - pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line  pymatgen/ext
           - pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line
 
     runs-on: ${{ matrix.os }}
@@ -32,24 +34,16 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
         with:
-          path: ~/Library/Caches/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'Windows')
-        with:
-          path: ~\AppData\Local\pip\Cache
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ~/Library/Caches/pip # needs to change if `runs-on: macos` changes
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements{,-dev}.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Install dependencies
         run: |
           pip install --upgrade pip wheel
           pip install -r requirements.txt
-          pip install -r requirements-optional.txt -r requirements-dev.txt
+          pip install -r requirements-dev.txt
           pip install -e .
       - name: pytest ${{ matrix.pkg }}
         run: |

.github/workflows/test-win.yml

@@ -0,0 +1,50 @@
+name: Testing Windows
+
+on: [ pull_request ]
+
+jobs:
+  test:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
+
+    strategy:
+      max-parallel: 20
+      matrix:
+        os: [ windows-latest ]
+        python-version: [ '3.9' ]
+        # This distribution of tests is designed to ensure an approximately even time to finish for parallel jobs.
+        pkg:
+          - pymatgen/analysis/defects pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism
+          - pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
+          - pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line  pymatgen/ext
+          - pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line
+
+    runs-on: ${{ matrix.os }}
+
+    env:
+      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+      MPLBACKEND: "Agg"
+      PMG_TEST_FILES_DIR: ${{ github.workspace }}/test_files
+      GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/cache@v2
+        with:
+          path: ~\AppData\Local\pip\Cache # needs to change if `runs-on: windows` changes
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements{,-dev}.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip wheel
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          pip install -e .
+      - name: pytest ${{ matrix.pkg }}
+        run: |
+          pytest ${{ matrix.pkg }}

.gitignore

@@ -10,6 +10,7 @@ dependencies/spglib*/build
 *.swp
 *.swo
 *.pyd
+*.c
 pymatgen/pymatgen.cfg
 dist
 _build

.pre-commit-config.yaml

@@ -1,18 +1,17 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
+    rev: 21.11b1
     hooks:
-    - id: black
-      language_version: python3 # Should be a command that runs python3.6+
+      - id: black
   - repo: https://github.com/pre-commit/mirrors-pylint
-    rev: '36ae6523465f8ba6936f6b63c3df94ab237eda00'  # Use the sha / tag you want to point at
+    rev: v3.0.0a4
     hooks:
-    - id: pylint
+      - id: pylint
   - 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=120"]
+        args: [--max-line-length=120]

ADMIN.rst

@@ -1,7 +1,7 @@
 Introduction
 ============
 
-This docmentation provides a guide for pymatgen administrators. The following 
+This documentation provides a guide for pymatgen administrators. The following
 assumes you are using miniconda or Anaconda.
 
 Releases
@@ -23,18 +23,18 @@ Install some conda tools first::
 	conda install --yes conda-build anaconda-client
 	conda config --add channels matsci
 
-Pymatgen uses `invoke <http://www.pyinvoke.org/>`_ to automate releases. You will 
+Pymatgen uses `invoke <http://www.pyinvoke.org/>`_ to automate releases. You will
 also need sphinx and doc2dash. Install these using::
 
 	pip install --upgrade invoke sphinx doc2dash
 
-For 2018, we will release both py27 and py37 versions of pymatgen. Create 
+For 2018, we will release both py27 and py37 versions of pymatgen. Create
 environments for py27 and py37 using conda::
 
 	conda create --yes -n py37 python=3.7
 	conda create --yes -n py27 python=2.7
 
-For each env, install some packages using conda followed by dev install for 
+For each env, install some packages using conda followed by dev install for
 pymatgen::
 
 	conda activate py37
@@ -50,43 +50,43 @@ pymatgen::
 	pip install invoke sphinx doc2dash
 	python setup.py develop
 
-Add your PyPI username and password and GITHUB_RELEASE_TOKEN into your 
+Add your PyPI username and password and GITHUB_RELEASE_TOKEN into your
 environment::
 
 	export TWINE_USERNAME=PYPIUSERNAME
 	export TWINE_PASSWORD=PYPIPASSWORD
 	export GITHUB_RELEASES_TOKEN=TOKEN_YOU_GET_FROM_GITHUB
 
-You may want to add these to your .bash_profile to avoid having to type these 
+You may want to add these to your .bash_profile to avoid having to type these
 each time.
 
 Machine-specific issues
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-The above instructions are general, but there are some known issues that are 
+The above instructions are general, but there are some known issues that are
 machine-specific:
 
-* Installing lxml via pip required `STATIC_DEPS=true pip install lxml` on 
+* Installing lxml via pip required `STATIC_DEPS=true pip install lxml` on
   macOS 10.13.
-* It can be useful to `pip install --upgrade pip twine setuptools` (this may 
+* It can be useful to `pip install --upgrade pip twine setuptools` (this may
   be necessary if there are authentication errors when connecting to PyPI).
 * You may have to `brew install hdf5 netcdf` or similar to be able to pip
   install the optional requirement `netCDF4`.
 
 Doing the release
 -----------------
 
-Ensure appropriate environment variabels are set including `DISCOURSE_API_USERNAME`,
+Ensure appropriate environment variables are set including `DISCOURSE_API_USERNAME`,
 `DISCOURSE_API_KEY` and `GITHUB_RELEASES_TOKEN`.
 
-First update the change log. The autogenerated change log is simply a list of 
+First update the change log. The autogenerated change log is simply a list of
 commit messages since the last version.  Make sure to edit the log for brevity
 and to attribute significant features to appropriate developers::
 
     conda activate py37
     invoke update-changelog
 
-Then, do the release with the following sequence of commands (you can put them 
+Then, do the release with the following sequence of commands (you can put them
 in a bash script in your PATH somewhere)::
 
     conda activate py37
@@ -97,7 +97,7 @@ in a bash script in your PATH somewhere)::
     python setup.py develop
 
 Double check that the releases are properly done on Pypi. If you are releasing
-on a Mac, you should see a pymatgen.version.tar.gz and two wheels (Py37 and 
+on a Mac, you should see a pymatgen.version.tar.gz and two wheels (Py37 and
 P). There will be a py37 wheel for Windows that is generated by Appveyor.
 
 Materials.sh