Merge branch 'develop' into ci/issue-5289-update-peter-evans-create-p…

…ull-request-action

.github/workflows/benchmark.yml

@@ -50,9 +50,30 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: '3.8'
+
+    - name: Upgrade pip
+      run: |
+        pip install --upgrade pip
+        pip --version
+
+    - name: Build pymatgen with compatible numpy
+      run: |
+        # This step is necessary because certain versions of `pymatgen` will not specify an explicit version of
+        # `numpy` in its build requirements, and so the latest version will be used. This causes problems,
+        # however, because this means that the compiled version of `pymatgen` can only be used with that version
+        # of `numpy` or higher, since `numpy` only guarantees forward compatibility of the ABI. If we want to
+        # run with an older version of `numpy`, we need to ensure that `pymatgen` is built with that same
+        # version. This we can accomplish by installing the desired version of `numpy` manually and then calling
+        # the install command for `pymatgen` with the `--no-build-isolation` flag. This flag will ensure that
+        # build dependencies are ignored and won't be installed (preventing the most recent version of `numpy`
+        # to be installed) and the build relies on those requirements already being present in the environment.
+        # We also need to install `wheel` because otherwise the `pymatgen` build will fail because `bdist_wheel`
+        # will not be available.
+        pip install numpy==1.21.4 wheel
+        pip install pymatgen==2022.0.16 --no-cache-dir --no-build-isolation
+
     - name: Install python dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install -r requirements/requirements-py-3.8.txt
         pip install --no-deps -e .
         pip freeze

.github/workflows/ci-code.yml

@@ -89,11 +89,26 @@ jobs:
         sudo apt install postgresql graphviz
 
     - name: Upgrade pip and setuptools
-      # It is crucial to update `setuptools` or the installation of `pymatgen` can break
       run: |
-        pip install --upgrade pip setuptools
+        pip install --upgrade pip
         pip --version
 
+    - name: Build pymatgen with compatible numpy
+      run: |
+        # This step is necessary because certain versions of `pymatgen` will not specify an explicit version of
+        # `numpy` in its build requirements, and so the latest version will be used. This causes problems,
+        # however, because this means that the compiled version of `pymatgen` can only be used with that version
+        # of `numpy` or higher, since `numpy` only guarantees forward compatibility of the ABI. If we want to
+        # run with an older version of `numpy`, we need to ensure that `pymatgen` is built with that same
+        # version. This we can accomplish by installing the desired version of `numpy` manually and then calling
+        # the install command for `pymatgen` with the `--no-build-isolation` flag. This flag will ensure that
+        # build dependencies are ignored and won't be installed (preventing the most recent version of `numpy`
+        # to be installed) and the build relies on those requirements already being present in the environment.
+        # We also need to install `wheel` because otherwise the `pymatgen` build will fail because `bdist_wheel`
+        # will not be available.
+        pip install numpy==1.21.4 wheel
+        pip install pymatgen==2022.0.16 --no-cache-dir --no-build-isolation
+
     - name: Install aiida-core
       run: |
         pip install --use-feature=2020-resolver -r requirements/requirements-py-${{ matrix.python-version }}.txt

.github/workflows/ci-style.yml

@@ -29,7 +29,8 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        pip install -e .[all]
+        pip install -r requirements/requirements-py-3.8.txt
+        pip install -e .[pre-commit]
         pip freeze
 
     - name: Run pre-commit

.github/workflows/rabbitmq.yml

@@ -56,6 +56,22 @@ jobs:
                 pip install --upgrade pip
                 pip --version
 
+        -   name: Build pymatgen with compatible numpy
+            run: |
+                # This step is necessary because certain versions of `pymatgen` will not specify an explicit version of
+                # `numpy` in its build requirements, and so the latest version will be used. This causes problems,
+                # however, because this means that the compiled version of `pymatgen` can only be used with that version
+                # of `numpy` or higher, since `numpy` only guarantees forward compatibility of the ABI. If we want to
+                # run with an older version of `numpy`, we need to ensure that `pymatgen` is built with that same
+                # version. This we can accomplish by installing the desired version of `numpy` manually and then calling
+                # the install command for `pymatgen` with the `--no-build-isolation` flag. This flag will ensure that
+                # build dependencies are ignored and won't be installed (preventing the most recent version of `numpy`
+                # to be installed) and the build relies on those requirements already being present in the environment.
+                # We also need to install `wheel` because otherwise the `pymatgen` build will fail because `bdist_wheel`
+                # will not be available.
+                pip install numpy==1.21.4 wheel
+                pip install pymatgen==2022.0.16 --no-cache-dir --no-build-isolation
+
         -   name: Install aiida-core
             run: |
                 pip install -r requirements/requirements-py-3.8.txt

.github/workflows/release.yml

@@ -82,9 +82,30 @@ jobs:
       run: |
         sudo apt update
         sudo apt install postgresql graphviz
+
+    - name: Upgrade pip
+      run: |
+        pip install --upgrade pip
+        pip --version
+
+    - name: Build pymatgen with compatible numpy
+      run: |
+        # This step is necessary because certain versions of `pymatgen` will not specify an explicit version of
+        # `numpy` in its build requirements, and so the latest version will be used. This causes problems,
+        # however, because this means that the compiled version of `pymatgen` can only be used with that version
+        # of `numpy` or higher, since `numpy` only guarantees forward compatibility of the ABI. If we want to
+        # run with an older version of `numpy`, we need to ensure that `pymatgen` is built with that same
+        # version. This we can accomplish by installing the desired version of `numpy` manually and then calling
+        # the install command for `pymatgen` with the `--no-build-isolation` flag. This flag will ensure that
+        # build dependencies are ignored and won't be installed (preventing the most recent version of `numpy`
+        # to be installed) and the build relies on those requirements already being present in the environment.
+        # We also need to install `wheel` because otherwise the `pymatgen` build will fail because `bdist_wheel`
+        # will not be available.
+        pip install numpy==1.21.4 wheel
+        pip install pymatgen==2022.0.16 --no-cache-dir --no-build-isolation
+
     - name: Install aiida-core
       run: |
-        pip install --upgrade pip setuptools
         pip install -r requirements/requirements-py-3.8.txt
         pip install --no-deps -e .
     - name: Run sub-set of test suite

aiida/engine/daemon/execmanager.py

@@ -273,7 +273,8 @@ def upload_calculation(
     else:
 
         if remote_copy_list:
-            with open(os.path.join(workdir, '_aiida_remote_copy_list.txt'), 'w') as handle:  # pylint: disable=unspecified-encoding
+            filepath = os.path.join(workdir, '_aiida_remote_copy_list.txt')
+            with open(filepath, 'w', encoding='utf-8') as handle:  # type: ignore[assignment]
                 for remote_computer_uuid, remote_abs_path, dest_rel_path in remote_copy_list:
                     handle.write(
                         'would have copied {} to {} in working directory on remote {}'.format(
@@ -282,7 +283,8 @@ def upload_calculation(
                     )
 
         if remote_symlink_list:
-            with open(os.path.join(workdir, '_aiida_remote_symlink_list.txt'), 'w') as handle:  # pylint: disable=unspecified-encoding
+            filepath = os.path.join(workdir, '_aiida_remote_symlink_list.txt')
+            with open(filepath, 'w', encoding='utf-8') as handle:  # type: ignore[assignment]
                 for remote_computer_uuid, remote_abs_path, dest_rel_path in remote_symlink_list:
                     handle.write(
                         'would have created symlinks from {} to {} in working directory on remote {}'.format(
@@ -317,7 +319,7 @@ def upload_calculation(
             if relpath not in provenance_exclude_list and all(
                 dirname not in provenance_exclude_list for dirname in dirnames
             ):
-                with open(filepath, 'rb') as handle:
+                with open(filepath, 'rb') as handle:  # type: ignore[assignment]
                     node._repository.put_object_from_filelike(handle, relpath)  # pylint: disable=protected-access
 
     # Since the node is already stored, we cannot use the normal repository interface since it will raise a

aiida/engine/processes/builder.py

@@ -97,10 +97,10 @@ def __setattr__(self, attr: str, value: Any) -> None:
             except KeyError as exception:
                 if not self._port_namespace.dynamic:
                     raise AttributeError(f'Unknown builder parameter: {attr}') from exception
-                port = None  # type: ignore[assignment]
+                port = None
             else:
                 value = port.serialize(value)  # type: ignore[union-attr]
-                validation_error = port.validate(value)
+                validation_error = port.validate(value)  # type: ignore[union-attr]
                 if validation_error:
                     raise ValueError(f'invalid attribute value {validation_error.message}')
 

aiida/engine/processes/ports.py

@@ -41,7 +41,7 @@ class WithNonDb:
     def __init__(self, *args, **kwargs) -> None:
         self._non_db_explicitly_set: bool = bool('non_db' in kwargs)
         non_db = kwargs.pop('non_db', False)
-        super().__init__(*args, **kwargs)  # type: ignore[call-arg]
+        super().__init__(*args, **kwargs)
         self._non_db: bool = non_db
 
     @property
@@ -76,7 +76,7 @@ class WithSerialize:
 
     def __init__(self, *args, **kwargs) -> None:
         serializer = kwargs.pop('serializer', None)
-        super().__init__(*args, **kwargs)  # type: ignore[call-arg]
+        super().__init__(*args, **kwargs)
         self._serializer: Callable[[Any], 'Data'] = serializer
 
     def serialize(self, value: Any) -> 'Data':

aiida/orm/implementation/entities.py

@@ -77,7 +77,7 @@ def from_dbmodel(cls, dbmodel: Any, backend: 'Backend') -> EntityType:
 class BackendCollection(Generic[EntityType]):
     """Container class that represents a collection of entries of a particular backend entity."""
 
-    ENTITY_CLASS: ClassVar[Type[EntityType]]
+    ENTITY_CLASS: ClassVar[Type[EntityType]]  # type: ignore[misc]
 
     def __init__(self, backend: 'Backend'):
         """

aiida/orm/implementation/sqlalchemy/backend.py

@@ -154,7 +154,7 @@ def bulk_insert(self, entity_type: EntityTypes, rows: List[dict], allow_defaults
         # https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#orm-batch-inserts-with-psycopg2-now-batch-statements-with-returning-in-most-cases
         # by contrast, in sqlite, bulk_insert is faster: https://docs.sqlalchemy.org/en/14/faq/performance.html
         session = self.get_session()
-        with (nullcontext() if self.in_transaction else self.transaction()):  # type: ignore[attr-defined]
+        with (nullcontext() if self.in_transaction else self.transaction()):
             session.bulk_insert_mappings(mapper, rows, render_nulls=True, return_defaults=True)
         return [row['id'] for row in rows]
 
@@ -168,7 +168,7 @@ def bulk_update(self, entity_type: EntityTypes, rows: List[dict]) -> None:  # py
             if not keys.issuperset(row):
                 raise IntegrityError(f'Incorrect fields given for {entity_type}: {set(row)} not subset of {keys}')
         session = self.get_session()
-        with (nullcontext() if self.in_transaction else self.transaction()):  # type: ignore[attr-defined]
+        with (nullcontext() if self.in_transaction else self.transaction()):
             session.bulk_update_mappings(mapper, rows)
 
     def delete_nodes_and_connections(self, pks_to_delete: Sequence[int]) -> None:  # pylint: disable=no-self-use

aiida/orm/nodes/node.py

@@ -835,7 +835,7 @@ def _get_objects_to_hash(self) -> List[Any]:
         assert self._repository is not None, 'repository not initialised'
         top_level_module = self.__module__.split('.', 1)[0]
         try:
-            version = importlib.import_module(top_level_module).__version__  # type: ignore[attr-defined]
+            version = importlib.import_module(top_level_module).__version__
         except (ImportError, AttributeError) as exc:
             raise exceptions.HashingError("The node's package version could not be determined") from exc
         objects = [

aiida/orm/nodes/process/calculation/calcjob.py

@@ -122,7 +122,7 @@ def _get_objects_to_hash(self) -> List[Any]:
         """
         from importlib import import_module
         objects = [
-            import_module(self.__module__.split('.', 1)[0]).__version__,  # type: ignore[attr-defined]
+            import_module(self.__module__.split('.', 1)[0]).__version__,
             {
                 key: val
                 for key, val in self.attributes_items()

aiida/plugins/factories.py

@@ -100,8 +100,8 @@ def CalcJobImporterFactory(entry_point_name: str, load: bool = True) -> Optional
     entry_point = BaseFactory(entry_point_group, entry_point_name, load=load)
     valid_classes = (CalcJobImporter,)
 
-    if isclass(entry_point) and issubclass(entry_point, CalcJobImporter):  # type: ignore[arg-type]
-        return entry_point
+    if isclass(entry_point) and issubclass(entry_point, CalcJobImporter):
+        return entry_point  # type: ignore[return-value]
 
     raise_invalid_type_error(entry_point_name, entry_point_group, valid_classes)
 

aiida/repository/common.py

@@ -81,7 +81,7 @@ def from_serialized(cls, serialized: dict, name='') -> 'File':
             objects = {name: File.from_serialized(obj, name) for name, obj in serialized.get('o', {}).items()}
 
         instance = cls.__new__(cls)
-        instance.__init__(name, file_type, key, objects)
+        instance.__init__(name, file_type, key, objects)  # type: ignore[misc]
         return instance
 
     def serialize(self) -> dict:

aiida/repository/repository.py

@@ -66,7 +66,7 @@ def from_serialized(cls, backend: AbstractRepositoryBackend, serialized: Dict[st
         :param backend: instance of repository backend to use to actually store the file objects.
         """
         instance = cls.__new__(cls)
-        instance.__init__(backend)
+        instance.__init__(backend)  # type: ignore[misc]
 
         if serialized:
             for name, obj in serialized['o'].items():

aiida/tools/archive/create.py

@@ -345,7 +345,7 @@ def transform(row):
 
         if filename.exists():
             filename.unlink()
-        shutil.move(tmp_filename, filename)  # type: ignore
+        shutil.move(tmp_filename, filename)  # type: ignore[arg-type]
 
     EXPORT_LOGGER.report('Archive created successfully')
 

aiida/tools/archive/implementations/sqlite/backend.py

@@ -376,36 +376,36 @@ def get_backend_entity(dbmodel) -> Type[entities.SqlaModelEntity]:  # pylint: di
     raise TypeError(f'Cannot get backend entity for {dbmodel}')
 
 
-@get_backend_entity.register(DbAuthInfo)
+@get_backend_entity.register(DbAuthInfo)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(authinfos.SqlaAuthInfo, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbComment)  # type: ignore[no-redef]
+@get_backend_entity.register(DbComment)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(comments.SqlaComment, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbComputer)  # type: ignore[no-redef]
+@get_backend_entity.register(DbComputer)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(computers.SqlaComputer, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbGroup)  # type: ignore[no-redef]
+@get_backend_entity.register(DbGroup)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(groups.SqlaGroup, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbLog)  # type: ignore[no-redef]
+@get_backend_entity.register(DbLog)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(logs.SqlaLog, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbNode)  # type: ignore[no-redef]
+@get_backend_entity.register(DbNode)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(nodes.SqlaNode, dbmodel.__class__)
 
 
-@get_backend_entity.register(DbUser)  # type: ignore[no-redef]
+@get_backend_entity.register(DbUser)  # type: ignore[call-overload]
 def _(dbmodel):
     return create_backend_cls(users.SqlaUser, dbmodel.__class__)

aiida/tools/archive/implementations/sqlite/migrations/main.py

@@ -132,7 +132,7 @@ def path_callback(inpath, outpath) -> bool:
 
         if outpath.exists() and force:
             outpath.unlink()
-        shutil.move(Path(tmpdirname) / 'new.zip', outpath)  # type: ignore
+        shutil.move(Path(tmpdirname) / 'new.zip', outpath)  # type: ignore[arg-type]
 
 
 def _read_json(inpath: Path, filename: str, is_tar: bool) -> Dict[str, Any]: