Fix: compatibility with aiida-core 2.0.0 (#41)

.github/workflows/cd.yml

@@ -0,0 +1,128 @@
+name: cd
+
+on:
+    push:
+        tags:
+        -   'v[0-9]+.[0-9]+.[0-9]+*'
+
+jobs:
+
+    validate-release-tag:
+
+        if: github.repository == 'aiida-phonopy/aiida-phonopy'
+        runs-on: ubuntu-latest
+
+        steps:
+        -   name: Checkout source
+            uses: actions/checkout@v2
+
+        -   name: Set up Python 3.8
+            uses: actions/setup-python@v2
+            with:
+                python-version: '3.8'
+
+        -   name: Validate the tag version against the package version
+            run: python .github/workflows/validate_release_tag.py $GITHUB_REF
+
+    pre-commit:
+
+        needs: [validate-release-tag]
+        runs-on: ubuntu-latest
+
+        steps:
+        -   uses: actions/checkout@v2
+
+        -   name: Cache Python dependencies
+            uses: actions/cache@v1
+            with:
+                path: ~/.cache/pip
+                key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+                restore-keys:
+                    pip-pre-commit-
+
+        -   name: Set up Python
+            uses: actions/setup-python@v2
+            with:
+                python-version: '3.8'
+
+        -   name: Install Python dependencies
+            run: pip install -e .[pre-commit,tests]
+
+        -   name: Run pre-commit
+            run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+    tests:
+
+        needs: [validate-release-tag]
+        runs-on: ubuntu-latest
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                -   python-version: '3.8'
+                    phonopy-version: '2.14.0'
+                -   python-version: '3.9'
+                    phonopy-version: '2.15.0'
+                -   python-version: '3.10'
+                    phonopy-version: '2.16.3'
+                -   python-version: '3.11'
+                    phonopy-version: '2.16.3'
+
+        services:
+            postgres:
+                image: postgres:12
+            rabbitmq:
+                image: rabbitmq:latest
+                ports:
+                -   5672:5672
+
+        steps:
+        -   uses: actions/checkout@v2
+
+        -   name: Cache Python dependencies
+            uses: actions/cache@v1
+            with:
+                path: ~/.cache/pip
+                key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+                restore-keys:
+                    pip-${{ matrix.python-version }}-tests
+
+        -   name: Setup Conda
+            uses: s-weigand/setup-conda@v1
+            with:
+                python-version: ${{ matrix.python-version }}
+                conda-channels: conda-forge
+
+        -   name: Set up Phonopy ${{ matrix.phonopy-version }}
+            run: conda install -y phonopy==${{ matrix.phonopy-version }}
+
+        -   name: Install Python dependencies
+            run: pip install -e .[tests]
+
+        -   name: Run pytest
+            run: pytest -sv tests
+
+    publish:
+
+        name: Publish to PyPI
+        needs: [pre-commit, tests]
+        runs-on: ubuntu-latest
+
+        steps:
+        -   name: Checkout source
+            uses: actions/checkout@v2
+
+        -   name: Set up Python 3.8
+            uses: actions/setup-python@v2
+            with:
+                python-version: '3.8'
+
+        -   name: Install flit
+            run: pip install flit~=3.4
+
+        -   name: Build and publish
+            run: flit publish
+            env:
+                FLIT_USERNAME: __token__
+                FLIT_PASSWORD: ${{ secrets.PYPI_KEY }}

.github/workflows/ci.yml

@@ -36,8 +36,15 @@ jobs:
         runs-on: ubuntu-latest
 
         strategy:
+            fail-fast: false
             matrix:
-                python-version: ['3.8', '3.9']
+                include:
+                -   python-version: '3.8'
+                    phonopy-version: '2.14.0'
+                -   python-version: '3.9'
+                    phonopy-version: '2.15.0'
+                -   python-version: '3.10'
+                    phonopy-version: '2.16.3'
 
         services:
             rabbitmq:
@@ -57,19 +64,22 @@ jobs:
                 restore-keys:
                     pip-${{ matrix.python-version }}-tests
 
-        -   name: Set up Python ${{ matrix.python-version }}
-            uses: actions/setup-python@v2
+        -   name: Setup Conda
+            uses: s-weigand/setup-conda@v1
             with:
                 python-version: ${{ matrix.python-version }}
+                conda-channels: conda-forge
+
+        -   name: Set up Phonopy ${{ matrix.phonopy-version }}
+            run: conda install -y phonopy==${{ matrix.phonopy-version }}
 
-        -   name: Install system dependencies
-            run: sudo apt update && sudo apt install postgresql
+        # -   name: Set up Phonopy ${{ matrix.phonopy-version }}
+        #     run: pip install phonopy==${{ matrix.phonopy-version }}
 
         -   name: Install python dependencies
-            run: |
-                pip install --upgrade setuptools
-                pip install -e .[tests]
-                reentry scan
+            run: pip install -e .[tests]
 
         -   name: Run pytest
+            env:
+                AIIDA_WARN_v3: 1
             run: pytest -sv tests

.github/workflows/validate_release_tag.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+"""Validate that the version in the tag label matches the version of the package."""
+import argparse
+import ast
+from pathlib import Path
+
+
+def get_version_from_module(content: str) -> str:
+    """Get the ``__version__`` attribute from a module.
+
+    .. note:: This has been adapted from :mod:`setuptools.config`.
+    """
+    try:
+        module = ast.parse(content)
+    except SyntaxError as exception:
+        raise IOError('Unable to parse module.') from exception
+
+    try:
+        return next(
+            ast.literal_eval(statement.value) for statement in module.body if isinstance(statement, ast.Assign)
+            for target in statement.targets if isinstance(target, ast.Name) and target.id == '__version__'
+        )
+    except StopIteration as exception:
+        raise IOError('Unable to find the `__version__` attribute in the module.') from exception
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('GITHUB_REF', help='The GITHUB_REF environmental variable')
+    args = parser.parse_args()
+    assert args.GITHUB_REF.startswith('refs/tags/v'), f'GITHUB_REF should start with "refs/tags/v": {args.GITHUB_REF}'
+    tag_version = args.GITHUB_REF[11:]
+    package_version = get_version_from_module(Path('src/aiida_phonopy/__init__.py').read_text(encoding='utf-8'))
+    error_message = f'The tag version `{tag_version}` is different from the package version `{package_version}`'
+    assert tag_version == package_version, error_message

docs/phonopy.rst

@@ -84,7 +84,7 @@ aiida-phonopy calculation of rocksalt NaCl.
        PhononPhonopy = WorkflowFactory('phonopy.phonopy')
        builder = PhononPhonopy.get_builder()
        builder.structure = structure
-       builder.calculator_settings = Dict(dict={'forces': forces_config,
+       builder.calculator_settings = Dict({'forces': forces_config,
                                                 'nac': nac_config})
        builder.run_phonopy = Bool(True)
        builder.remote_phonopy = Bool(True)
@@ -95,7 +95,7 @@ aiida-phonopy calculation of rocksalt NaCl.
                  'distance': 0.01,
                  'is_nac': True})
        builder.symmetry_tolerance = Float(1e-5)
-       builder.options = Dict(dict=base_config['options'])
+       builder.options = Dict(base_config['options'])
        builder.metadata.label = "NaCl 2x2x2 phonon example"
        builder.metadata.description = "NaCl 2x2x2 phonon example"
 

examples/BaTiO3/script.py

@@ -25,7 +25,7 @@ def main():
 
     inputs = {
         'code': code,
-        'parameters': orm.Dict(dict=parameters),
+        'parameters': orm.Dict(parameters),
         'phonopy_data': phonopy_data,
         'metadata': {
             'options': {

pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 keywords = ['aiida', 'workflows']
 requires-python = '>=3.8'
 dependencies = [
-    "aiida-core>=1.6.0,<2.0.0",
+    "aiida-core>=2.0.0",
     "phonopy>=2.14,<3.0.0",
 ]
 
@@ -126,7 +126,6 @@ max-line-length = 120
 [tool.pylint.messages_control]
 disable = [
     'protected-access',
-    'bad-continuation',
     'duplicate-code',
     'import-outside-toplevel',
     'inconsistent-return-statements',

src/aiida_phonopy/__init__.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 """The official AiiDA plugin for Phonopy."""
-__version__ = '0.7.0'
+__version__ = '1.0.0'

src/aiida_phonopy/data/preprocess.py

@@ -48,7 +48,7 @@ def __init__(
     def displacement_dataset(self):
         """Get the dispacement dataset in a readible format for phonopy."""
         try:
-            the_displacement_dataset = self.get_attribute('displacement_dataset')
+            the_displacement_dataset = self.base.attributes.get('displacement_dataset')
         except AttributeError:
             the_displacement_dataset = None
         return the_displacement_dataset
@@ -107,7 +107,7 @@ def set_displacements(
         except ValueError as err:
             raise ValueError('one or more input types are not accepted') from err
 
-        self.set_attribute('displacement_dataset', copy.deepcopy(ph.dataset))
+        self.base.attributes.set('displacement_dataset', copy.deepcopy(ph.dataset))
 
     def set_displacements_from_dataset(self, dataset):
         """Set displacements for frozen phonon calculation from a dataset.
@@ -135,7 +135,7 @@ def set_displacements_from_dataset(self, dataset):
         else:
             raise ValueError('type not accepted')
 
-        self.set_attribute('displacement_dataset', copy.deepcopy(ph.dataset))
+        self.base.attributes.set('displacement_dataset', copy.deepcopy(ph.dataset))
 
     def get_supercells_with_displacements(self):
         """Get the supercells with displacements for frozen phonon calculation.