126 minor fixes (#127)

* Fix warning spectral_profile

Fix README

Move testing files to subfolders to mimic src structure

* Deleted copyright notice at the beginning of each file

* Changed __eq__ (and __ne__) for function is_equal_cell

* Fix conftest imports

README.md

@@ -8,14 +8,20 @@
 
 # `nomad-simulations`
 
-This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base sections definitions for materials science simulations. This schema can be used at any prefered level by the user, it can be modified and extended, and we welcome external collaborators.
+The `nomad-simulations` is an open-source Python package for managing Materials Science simulation data. It is following the plugin architechture of [NOMAD](https://nomad-lab.eu). This package contains a set of section definitions (Python classes) with quantities (attributes) and methods defined to automate data extraction from different simulation codes. These section definitions can be used at any prefered level by the user, they can be modified and extended, and we welcome external collaborators.
+
+Read more in the [official documentation](https://nomad-coe.github.io/nomad-simulations/) page.
 
 
 ## Getting started
 
 `nomad-simulations` can be installed as a PyPI package using `pip`:
+
+> [!WARNING]
+> Unfortunately, the current plugin mechanism is not supported by the latest nomad-lab version on PyPI and therefore an index url pointing to the NOMAD Gitlab registry needs to be added.
+
 ```sh
-pip install nomad-simulations
+pip install nomad-simulations --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
 
@@ -49,6 +55,11 @@ The plugin is still under development. If you would like to contribute, install
 uv pip install -e '.[dev]'
 ```
 
+**Note:** If you do not use `uv`, you need to add the `--index-url` flag as in the PyPI command for installing the package:
+```sh
+pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+```
+
 
 ### Run the tests
 
@@ -139,7 +150,7 @@ Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/
 Modify the script under `/nomad/scripts/install_default_plugins.sh` and add the path to this repository pointing to the `@develop` branch:
 ```sh
 <other-content-in-install_default_plugins.sh...>
-pip install git+https://github.com/nomad-coe/nomad-simulations.git@develop
+git+https://github.com/nomad-coe/nomad-simulations.git@develop
 ```
 
 Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:

src/nomad_simulations/schema_packages/__init__.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from nomad.config.models.plugins import SchemaPackageEntryPoint
 from pydantic import Field
 

src/nomad_simulations/schema_packages/atoms_state.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING, Any, Optional, Union
 
 import ase

src/nomad_simulations/schema_packages/general.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/nomad_simulations/schema_packages/model_method.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 import re
 from typing import TYPE_CHECKING, Optional
 

src/nomad_simulations/schema_packages/model_system.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 import re
 from typing import TYPE_CHECKING, Optional
 
@@ -308,7 +290,14 @@ def _check_positions(self, positions_1, positions_2) -> list:
                     break
         return check_positions
 
-    def __eq__(self, other) -> bool:
+    def is_equal_cell(self, other) -> bool:
+        """
+        Check if the cell is equal to an`other` cell by comparing the `positions`.
+        Args:
+            other: The other cell to compare with.
+        Returns:
+            bool: True if the cells are equal, False otherwise.
+        """
         # TODO implement checks on `lattice_vectors` and other quantities to ensure the equality of primitive cells
         if not isinstance(other, Cell):
             return False
@@ -322,14 +311,13 @@ def __eq__(self, other) -> bool:
             return False
         n_positions = len(self.positions)
 
-        check_positions = self._check_positions(self.positions, other.positions)
+        check_positions = self._check_positions(
+            positions_1=self.positions, positions_2=other.positions
+        )
         if len(check_positions) != n_positions:
             return False
         return True
 
-    def __ne__(self, other) -> bool:
-        return not self.__eq__(other)
-
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)
 
@@ -373,16 +361,26 @@ def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwarg
         # Set the name of the section
         self.name = self.m_def.name
 
-    def __eq__(self, other) -> bool:
+    def is_equal_cell(self, other) -> bool:
+        """
+        Check if the atomic cell is equal to an`other` atomic cell by comparing the `positions` and
+        the `AtomsState[*].chemical_symbol`.
+        Args:
+            other: The other atomic cell to compare with.
+        Returns:
+            bool: True if the atomic cells are equal, False otherwise.
+        """
         if not isinstance(other, AtomicCell):
             return False
 
         # Compare positions using the parent sections's `__eq__` method
-        if not super().__eq__(other):
+        if not super().is_equal_cell(other=other):
             return False
 
         # Check that the `chemical_symbol` of the atoms in `cell_1` match with the ones in `cell_2`
-        check_positions = self._check_positions(self.positions, other.positions)
+        check_positions = self._check_positions(
+            positions_1=self.positions, positions_2=other.positions
+        )
         try:
             for atom in check_positions:
                 element_1 = self.atoms_state[atom[0]].chemical_symbol
@@ -393,9 +391,6 @@ def __eq__(self, other) -> bool:
             return False
         return True
 
-    def __ne__(self, other) -> bool:
-        return not self.__eq__(other)
-
     def to_ase_atoms(self, logger: 'BoundLogger') -> Optional[ase.Atoms]:
         """
         Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`

src/nomad_simulations/schema_packages/numerical_settings.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from itertools import accumulate, chain, tee
 from typing import TYPE_CHECKING, Optional, Union
 

src/nomad_simulations/schema_packages/outputs.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING, Optional
 
 import numpy as np

src/nomad_simulations/schema_packages/physical_property.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from functools import wraps
 from typing import TYPE_CHECKING, Any, Optional
 

src/nomad_simulations/schema_packages/properties/__init__.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD.
-# See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
 from .band_gap import ElectronicBandGap
 from .band_structure import ElectronicBandStructure, ElectronicEigenvalues, Occupancy
 from .energies import (

src/nomad_simulations/schema_packages/properties/band_gap.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING, Optional
 
 import numpy as np

src/nomad_simulations/schema_packages/properties/band_structure.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING, Optional, Union
 
 import numpy as np

src/nomad_simulations/schema_packages/properties/energies.py

@@ -1,21 +1,3 @@
-#
-# Copyright The NOMAD Authors.
-#
-# This file is part of NOMAD. See https://nomad-lab.eu for further info.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
 from typing import TYPE_CHECKING
 
 import numpy as np