Merge pull request #7 from pyiron/migrate_yaff_quickff

Migrate quickff and yaff to pyiron_gpl

.ci_support/environment.yml

@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+dependencies:
+  - coveralls
+  - coverage
+  - codacy-coverage
+  - molmod =1.4.8
+  - numpy =1.20.1
+  - pyiron_atomistics =0.2.7
+  - scipy =1.6.0
+  - spglib =1.16.1
+  - sqlalchemy =1.3.23  # 1.4.0 is broken on conda
+  - quickff =2.2.4
+  - tamkin =1.2.6
+  - yaff =1.4.2

.ci_support/pyironconfig.py

@@ -0,0 +1,19 @@
+import os
+
+
+def main():
+    current_path = os.path.abspath(os.path.curdir)
+    top_level_path = current_path.replace('\\', '/')
+    resource_path = os.path.join(current_path, "tests", "static").replace('\\', '/')
+    pyiron_config = os.path.expanduser('~/.pyiron').replace('\\', '/')
+    if not os.path.exists(pyiron_config):
+        with open(pyiron_config, 'w') as f:
+            f.writelines(['[DEFAULT]\n',
+                          'TOP_LEVEL_DIRS = ' + top_level_path + '\n',
+                          'RESOURCE_PATHS = ' + resource_path + '\n'])
+    else:
+        print('config exists')
+
+
+if __name__ == '__main__':
+    main()

.coveralls.yml

@@ -0,0 +1 @@
+repo_token: dLxjhAmj4DHMiWimt2eqTHaA41qSlIUA9

.github/workflows/coverage.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Coverage
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    env: 
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.9
+        environment-file: .ci_support/environment.yml
+    - name: Setup
+      shell: bash -l {0}
+      run: |
+        python .ci_support/pyironconfig.py
+        pip install --no-deps .
+    - name: Test
+      shell: bash -l {0}
+      run: coverage run --omit pyiron_atomistics/_version.py -m unittest discover tests
+    - name: Coverage
+      shell: bash -l {0}
+      run: |
+        coveralls
+        coverage xml
+        python-codacy-coverage -r coverage.xml

.github/workflows/unittests.yml

@@ -0,0 +1,36 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.operating-system }}
+    strategy:
+      matrix:
+        operating-system: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        environment-file: .ci_support/environment.yml
+    - name: Setup
+      shell: bash -l {0}
+      run: |
+        python .ci_support/pyironconfig.py
+        pip install --no-deps .
+        pip check
+    - name: Tests
+      shell: bash -l {0}
+      run: coverage run --omit pyiron_gpl/_version.py -m unittest discover tests

pyiron_gpl/__init__.py

@@ -5,8 +5,10 @@
 from pyiron_base import Notebook, install_dialog, JOB_CLASS_DICT
 
 # Make classes available for new pyiron version
-JOB_CLASS_DICT['ElasticMatrixJob'] = 'pyiron_gpl.elastic.elastic'
-JOB_CLASS_DICT['PaceMakerJob'] = 'pyiron_gpl.pacemaker.pacemaker'
+JOB_CLASS_DICT["ElasticMatrixJob"] = "pyiron_gpl.elastic.elastic"
+JOB_CLASS_DICT["PaceMakerJob"] = "pyiron_gpl.pacemaker.pacemaker"
+JOB_CLASS_DICT["QuickFF"] = "pyiron_gpl.quickff.quickff"
+JOB_CLASS_DICT["Yaff"] = "pyiron_gpl.yaff.yaff"
 
 from ._version import get_versions