Add License notice to all modules.

MANIFEST.in

@@ -0,0 +1 @@
+include LICENCE.txt

setup.py

@@ -35,7 +35,7 @@
  "pandas>=1.0.0",
  "morphio>=3.0.0",
  "libsonata>=0.1.8",
- "click>=7.0",
+ "click>=8.0",
  ],
  extras_require={"convert-vtk": DEPS_VTK, "all": DEPS_VTK + ["python-igraph>=0.8.0"]},
  packages=find_packages(),

tox.ini

@@ -1,31 +1,23 @@
 [base]
 name = vascpy
 testdeps =
- mock
- pytest
- vtk
- click
+ mock
+ pytest
+ vtk
 extras = all
 
 [tox]
+minversion = 3.1.0
 envlist =
- check-version
- lint
- coverage
- py{38}
-
-indexserver =
-default = https://bbpteam.epfl.ch/repository/devpi/simple
+ py{37,38,39}
+ py39-lint
+ py39-coverage
+ignore_basepython_conflict = true
 
 [testenv]
 deps = {[base]testdeps}
 commands = py.test {posargs} tests
 
-[testenv:check-version]
-skip_install = true
-deps = bbp-nse-ci
-commands = do_release.py -p . check-version
-
 [testenv:format]
 deps =
  black==21.9b0
@@ -34,28 +26,20 @@ commands =
  isort -l 100 --profile black {[base]name} tests setup.py
  black -l 100 {[base]name} tests setup.py
 
-[testenv:check-packaging]
-deps =
- wheel
- twine
-commands =
- python setup.py sdist bdist_wheel -d {envtmpdir}/dist
- twine check {envtmpdir}/dist/*
-
-[testenv:lint]
+[testenv:py39-lint]
 deps =
- isort
- black==20.8b1
- pycodestyle
- pylint
- click
+  isort
+  black==20.8b1
+  pycodestyle
+  pylint
+  click
 commands =
- isort -l 100 --profile black --check-only --diff {[base]name} tests setup.py
- black -l 100 --check {[base]name} tests setup.py
- pycodestyle {[base]name}
- pylint -j2 {[base]name}
+  isort -l 100 --profile black --check-only --diff {[base]name} tests setup.py
+  black -l 100 --check {[base]name} tests setup.py
+  pycodestyle {[base]name}
+  pylint -j2 {[base]name}
 
-[testenv:coverage]
+[testenv:py39-coverage]
 deps =
  {[base]testdeps}
  pytest-cov

vascpy/__init__.py

@@ -1,3 +1,17 @@
-""" Vasculature API """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 vascpy.point_vasculature import PointVasculature
 from vascpy.section_vasculature import SectionVasculature

vascpy/cli.py

@@ -1,4 +1,18 @@
-""" vasculatureapo app """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 logging
 
 import click

vascpy/conversion.py

@@ -1,4 +1,18 @@
-""" Graph conversion """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 logging
 import tempfile
 from collections import deque

vascpy/point_graph/__init__.py

@@ -1 +1,15 @@
-""" Point vasculature subpackage """
+""""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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.
+"""

vascpy/point_graph/curation.py

@@ -1,5 +1,18 @@
-"""Curation of point graphs, which is mutative"""
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 logging
 
 import numpy as np

vascpy/point_graph/features.py

@@ -1,5 +1,18 @@
-""" Contains features that can be extracted from a vasculature object """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 numpy as np
 
 

vascpy/point_graph/io.py

@@ -1,5 +1,18 @@
-""" Lazy IO for vtk and h5 loaders and writers """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 logging
 from collections import OrderedDict
 from typing import Tuple

vascpy/point_vasculature.py

@@ -1,4 +1,18 @@
-""" Point graph representation of the vasculature """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 logging
 import warnings
 from dataclasses import dataclass

vascpy/section_graph/__init__.py

@@ -1 +1,15 @@
-""" Section graph representation of vasculature """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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.
+"""

vascpy/section_graph/io.py

@@ -1,5 +1,18 @@
-""" Lazy IO for vtk and h5 loaders and writers """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 logging
 
 import numpy as np

vascpy/section_vasculature.py

@@ -1,4 +1,18 @@
-""" Vasculature representation as a Section Graph """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 morphio.vasculature import Vasculature
 
 from vascpy.section_graph import io

vascpy/specs.py

@@ -1,5 +1,17 @@
-"""Specifications for the various vasculature data structures
-and file formats.
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 collections import namedtuple
 

vascpy/utils/__init__.py

@@ -0,0 +1,15 @@
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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.
+"""

vascpy/utils/adjacency.py

@@ -1,4 +1,18 @@
-""" Adjacency """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
+
+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:https://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 numpy as np
 from scipy import sparse
 

vascpy/utils/geometry.py

@@ -1,5 +1,18 @@
-""" Geometry helpers """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 numpy as np
 
 

vascpy/utils/section_creation.py

@@ -1,5 +1,18 @@
-""" Section creation from point graph representation """
+"""
+Copyright (c) 2021 Blue Brain Project/EPFL
 
+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:https://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 logging
 from collections import defaultdict, deque