Chore: Add license headers

.copyright.tmpl

@@ -0,0 +1,6 @@
+Copyright (c) 2023-${edit_year} Blue Brain Project, EPFL.
+
+This file is part of region-grower.
+See https://github.com/BlueBrain/region-grower for further info.
+
+SPDX-License-Identifier: Apache-2.0

.pre-commit-config.yaml

@@ -39,3 +39,11 @@ repos:
     rev: 7.1.1
     hooks:
       - id: flake8
+  - repo: https://github.com/arkinmodi/add-license-header
+    rev: v2.2.0
+    hooks:
+      - id: add-license-header
+        args:
+            - --license-file
+            - .copyright.tmpl
+        files: \.py$

docs/source/conf.py

@@ -1,5 +1,15 @@
 """Configuration file for the Sphinx documentation builder."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html

region_grower/__init__.py

@@ -3,6 +3,16 @@
 Synthesize cells in a given spatial context.
 """
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import importlib.metadata
 
 __version__ = importlib.metadata.version("region-grower")

region_grower/atlas_helper.py

@@ -3,6 +3,16 @@
 This helper allows simple lookups without having to reason in term of [PH][1-6] and [PH]y.
 """
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import operator
 from pathlib import Path
 from typing import List

region_grower/cli.py

@@ -1,5 +1,15 @@
 """Command Line Interface for the region_grower package."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=redefined-outer-name
 import importlib.metadata
 import json

region_grower/context.py

@@ -7,6 +7,16 @@
 the placement_algorithm package to synthesize circuit morphologies.
 """
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import os
 from collections import defaultdict
 from copy import deepcopy

region_grower/generate.py

@@ -1,5 +1,15 @@
 """Functions to generate parameters and distributions."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import json
 import logging
 import multiprocessing

region_grower/modify.py

@@ -1,5 +1,15 @@
 """Use spatial properties to modify synthesis input."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 from typing import Dict
 from typing import List
 from typing import Optional

region_grower/morph_io.py

@@ -1,5 +1,15 @@
 """Module to load and write morphologies."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import os
 import random
 import uuid

region_grower/synthesize_morphologies.py

@@ -7,6 +7,16 @@
 - optional axon grafting "on-the-fly"
 """
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import json
 import logging
 import os

region_grower/utils.py

@@ -1,5 +1,15 @@
 """Utils module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import json
 import logging
 import os

region_grower/version.py

@@ -1,3 +1,13 @@
 """Version of the region-grower package."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 VERSION = "1.4.0"  # pragma: no cover

scripts/distribution_definition/add_diameter_info.py

@@ -1,5 +1,15 @@
 """Script to add the diameter distributions to another distribution."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import argparse
 import json
 import os

scripts/distribution_definition/generate_synthesis_distributions.py

@@ -1,5 +1,15 @@
 """Extract TNS distributions used by NeuroTS."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 from __future__ import print_function
 
 import argparse

scripts/parameter_definition/generate_synthesis_recipe.py

@@ -1,5 +1,15 @@
 """Script to generate a synthesis recipe."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 import copy
 import json
 

setup.py

@@ -1,5 +1,15 @@
 """Setup for the region-grower package."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 from pathlib import Path
 
 from setuptools import find_namespace_packages

tests/__init__.py

@@ -1 +1,11 @@
 """Tests suite for the region-grower package."""
+
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#

tests/conftest.py

@@ -1,5 +1,15 @@
 """Configuration for the pytest test suite."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=redefined-outer-name
 # pylint: disable=missing-function-docstring
 from pathlib import Path

tests/data_factories.py

@@ -1,5 +1,15 @@
 """Generate atlas for tests."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=missing-function-docstring
 import json
 import os

tests/test_atlas_helper.py

@@ -1,5 +1,15 @@
 """Test the region_grower.atlas_helper.AtlasHelper module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 from pathlib import Path
 
 import pytest

tests/test_cli.py

@@ -1,5 +1,15 @@
 """Tests for the region_grower.cli module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=missing-function-docstring
 import json
 from pathlib import Path

tests/test_context.py

@@ -1,5 +1,15 @@
 """Test the region_grower.context module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=missing-function-docstring
 # pylint: disable=use-implicit-booleaness-not-comparison
 

tests/test_modify.py

@@ -1,5 +1,15 @@
 """Test the region_grower.modify module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=missing-function-docstring
 from copy import deepcopy
 

tests/test_morph_io.py

@@ -1,5 +1,15 @@
 """Test the region_grower.utils module."""
 
+# LICENSE HEADER MANAGED BY add-license-header
+#
+# Copyright (c) 2023-2024 Blue Brain Project, EPFL.
+#
+# This file is part of region-grower.
+# See https://github.com/BlueBrain/region-grower for further info.
+#
+# SPDX-License-Identifier: Apache-2.0
+#
+
 # pylint: disable=missing-function-docstring
 # pylint: disable=protected-access
 from pathlib import Path