Merge branch 'rc'

.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,33 @@
+name: publish PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Make sdist and bdist_wheel
+      run: |
+        pip install wheel
+        python setup.py sdist bdist_wheel
+    - name: Publish package to TestPyPI
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/rc')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+    - name: Publish package to PyPI
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/master')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+# See https://pre-commit.com for more informatio
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.4.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+
+- repo: https://github.com/pycqa/flake8
+  rev: 3.8.4
+  hooks:
+  - id: flake8
+    args:
+    - "--max-line-length=88"
+    - "--ignore=E203,W503"
+
+- repo: https://github.com/psf/black
+  rev: 21.9b0
+  hooks:
+  - id: black
+    args:
+    - --line-length=88

MANIFEST.in

@@ -0,0 +1,4 @@
+graft example
+include setup.json
+include LICENSE
+include pyproject.toml

README.md

@@ -1,6 +1,7 @@
-AiiDA Phonopy plugin
-====================
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/aiida-phonopy/aiida-phonopy/develop.svg)](https://results.pre-commit.ci/latest/github/aiida-phonopy/aiida-phonopy/develop)
 
-This a phonopy plugin for AiiDA. This plugin includes workflows to
-calculate phonons with supercell and finite displacement approaches.
-Currently it provides interfaces only to VASP.
+# AiiDA Phonopy plugin
+
+This a phonopy plugin for AiiDA. This plugin includes workflows to calculate
+phonons with supercell and finite displacement approaches. Currently VASP and QE
+are supported.

aiida_phonopy/calcs/base.py

@@ -1,62 +1,63 @@
+"""Base class of PhonopyCalculation and Phono3pyCalculation."""
+
 from aiida.engine import CalcJob
 from aiida.common import CalcInfo, CodeInfo
 from aiida.plugins import DataFactory
-from aiida.orm import Bool
 from aiida_phonopy.common.file_generators import get_BORN_txt
 
-Dict = DataFactory('dict')
-StructureData = DataFactory('structure')
-ArrayData = DataFactory('array')
+Dict = DataFactory("dict")
+StructureData = DataFactory("structure")
+ArrayData = DataFactory("array")
+Float = DataFactory("float")
+Bool = DataFactory("bool")
 
 
 class BasePhonopyCalculation(CalcJob):
-    """
-    A basic plugin for calculating force constants using Phonopy.
+    """A basic plugin for calculating force constants using Phonopy.
+
     Requirement: the node should be able to import phonopy if NAC is used
+
     """
 
-    _INPUT_NAC = 'BORN'
+    _INPUT_NAC = "BORN"
 
     @classmethod
     def define(cls, spec):
-        """
-
-        dataset : Dict, ArrayData, optional
-            In Dict, this is similar to phonopy.dataset. This can be either
-            type-I or type-II. In ArrayData, this can contain arrays of forces
-            and displacements like type-II phonopy dataset, for which the array
-            names are 'forces' and 'displacements'.
-
-        """
-
+        """Define inputs, outputs, and outline."""
         super().define(spec)
-
-        spec.input('settings', valid_type=Dict,
-                   help='Phonopy parameters')
-        spec.input('structure', valid_type=StructureData,
-                   help='Unit cell structure')
-        spec.input('fc_only', valid_type=Bool,
-                   help='Only force constants are calculated.',
-                   default=lambda: Bool(False))
-        spec.input('force_sets', valid_type=ArrayData, required=False,
-                   help='Sets of forces in supercells')
-        spec.input('dataset', valid_type=ArrayData, required=False,
-                   help='Sets of displacements and forces in supercells')
-        spec.input('nac_params', valid_type=ArrayData, required=False,
-                   help='NAC parameters')
-        spec.input('primitive', valid_type=StructureData, required=False,
-                   help='Primitive cell structure')
-        spec.input('dataset', valid_type=(Dict, ArrayData), required=False,
-                   help='Displacements and forces dataset')
-        spec.inputs['metadata']['options']['withmpi'].default = False
+        spec.input("settings", valid_type=Dict, help="Phonopy parameters.")
+        spec.input("structure", valid_type=StructureData, help="Unit cell structure.")
+        spec.input("symmetry_tolerance", valid_type=Float, default=lambda: Float(1e-5))
+        spec.input(
+            "fc_only",
+            valid_type=Bool,
+            help="Only force constants are calculated.",
+            default=lambda: Bool(False),
+        )
+        spec.input(
+            "force_sets",
+            valid_type=ArrayData,
+            required=False,
+            help="Sets of forces in supercells",
+        )
+        spec.input(
+            "nac_params", valid_type=ArrayData, required=False, help="NAC parameters."
+        )
+        spec.input(
+            "primitive",
+            valid_type=StructureData,
+            required=False,
+            help="Primitive cell structure only necessary NAC is applied.",
+        )
+        spec.input(
+            "dataset",
+            valid_type=(Dict, ArrayData),
+            required=False,
+            help="Displacements and forces dataset.",
+        )
 
     def prepare_for_submission(self, folder):
-        """Create the input files from the input nodes passed to this instance of the `CalcJob`.
-
-        :param folder: an `aiida.common.folders.Folder` to temporarily write files on disk
-        :return: `aiida.common.datastructures.CalcInfo` instance
-        """
-
+        """Prepare calcinfo."""
         self.logger.info("prepare_for_submission")
 
         # These three lists are updated in self._create_additional_files(folder)
@@ -68,18 +69,22 @@ def prepare_for_submission(self, folder):
         # ================= prepare the python input files =================
 
         # BORN
-        if (not self.inputs.fc_only and
-            'nac_params' in self.inputs and
-            'primitive' in self.inputs and
-            'symmetry_tolerance' in self.inputs.settings.attributes):
+        if (
+            not self.inputs.fc_only
+            and "nac_params" in self.inputs
+            and "primitive" in self.inputs
+        ):
             born_txt = get_BORN_txt(
                 self.inputs.nac_params,
                 self.inputs.primitive,
-                self.inputs.settings['symmetry_tolerance'])
-            with folder.open(self._INPUT_NAC, 'w', encoding='utf8') as handle:
+                self.inputs.symmetry_tolerance,
+            )
+            with folder.open(self._INPUT_NAC, "w", encoding="utf8") as handle:
                 handle.write(born_txt)
             for params in self._additional_cmd_params:
-                params.append('--nac')
+                params.append("--nac")
+
+        self.inputs.metadata.options.withmpi = False
 
         # ============================ calcinfo ===============================
 
@@ -93,13 +98,13 @@ def prepare_for_submission(self, folder):
         calcinfo.retrieve_list = self._internal_retrieve_list
 
         calcinfo.codes_info = []
-        for i, (default_params, additional_params) in enumerate(zip(
-                self._calculation_cmd, self._additional_cmd_params)):
+        for i, (default_params, additional_params) in enumerate(
+            zip(self._calculation_cmd, self._additional_cmd_params)
+        ):
             codeinfo = CodeInfo()
-            codeinfo.cmdline_params = default_params + additional_params
+            cmdline_params = default_params + additional_params
+            codeinfo.cmdline_params = cmdline_params
             codeinfo.code_uuid = self.inputs.code.uuid
-            codeinfo.stdout_name = "%s%d" % (
-                self.options.output_filename, i + 1)
             codeinfo.withmpi = False
             calcinfo.codes_info.append(codeinfo)