Merge pull request #156 from favreau/master

Documentation update and preparation for v1.3.4

CMakeLists.txt

@@ -1,13 +1,25 @@
-# Copyright (c) 2020-2022, Cyrille Favreau
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+# scientific data from visualization
 #
-# This file is part of https://github.com/BlueBrain/BioExplorer
+# Copyright 2020-2022 Blue BrainProject / EPFL
+# 
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
 
 cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
 
 set(NAME BIOEXPLORER)
-set(PACKAGE_VERSION 1.3.2)
+set(PACKAGE_VERSION 1.4.0)
 project(${NAME} VERSION ${PACKAGE_VERSION})
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)

Dockerfile

@@ -2,7 +2,7 @@
 # scientific data from visualization
 #
 # Copyright 2020-2022 Blue BrainProject / EPFL
-#
+# 
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU General Public License as published by the Free Software
 # Foundation, either version 3 of the License, or (at your option) any later

README.md

@@ -52,7 +52,7 @@ Check out the movie by clicking on the following image, and see the coronavirus
 
 <div align="center">
       <a href="https://youtu.be/Czn-YGLGfiA"/>
-         <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/movie_preview.png" style="width:50%;">
+         <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/covid19_movie_preview.png" style="width:50%;">
       </a>
 </div>
 
@@ -202,7 +202,7 @@ When a ray hits a geometry, a random secondary ray is sent in a direction belong
 
 White matter is composed of bundles, which connect various grey matter areas (the locations of nerve cell bodies) of the brain to each other, and carry nerve impulses between neurons. Myelin acts as an insulator, which allows electrical signals to jump, rather than coursing through the axon, increasing the speed of transmission of all nerve signals.
 
-A [Python notebook example](./bioexplorer/pythonsdk/notebooks/connectomics/BioExplorer_import_white_matter_allen_brain.ipynb) demonstrates how to download and import white matter streamlines from the Allen Brain Institute website into the _BBBE_ database. Another [Python notebook](./bioexplorer/pythonsdk/notebooks/connectomics/BioExplorer_white_matter.ipynb) demonstrates how to visualize the streamlines with the _BBBE_.
+A [Python notebook example](./bioexplorer/pythonsdk/notebooks/connectomics/BioExplorer_import_white_matter_allen_brain.ipynb) demonstrates how to download and import white matter streamlines from the [Allen Brain Institute website](https://alleninstitute.org) into the _BBBE_ database. Another [Python notebook](./bioexplorer/pythonsdk/notebooks/connectomics/BioExplorer_white_matter.ipynb) demonstrates how to visualize the streamlines with the _BBBE_.
 
 ```python
 white_matter_model = be.add_white_matter(
@@ -215,6 +215,14 @@ References:
 * [Allen Brain Institute: mouse connectivity projections](http://connectivity.brain-map.org/)
 * [Allen Brain Institute: mouse connectivity atlas](https://alleninstitute.github.io/AllenSDK/connectivity.html)
 
+The white matter feature contributed to generating images for the [null model of the mouse whole-neocortex micro-connectome](https://www.nature.com/articles/s41467-019-11630-x) publication and produce the corresponding movie.
+
+<div align="center">
+      <a href="https://www.youtube.com/watch?v=6cBNdAn04Qw"/>
+         <img src="https://github.com/BlueBrain/BioExplorer/blob/master/bioexplorer/pythonsdk/doc/source/images/connectomics_movie_preview.png" style="width:50%;">
+      </a>
+</div>
+
 
 ### Enzyme reactions
 

bioexplorer/core/CMakeLists.txt

@@ -1,8 +1,20 @@
-# Copyright (c) 2020-2022, Cyrille Favreau
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+# scientific data from visualization
 #
-# This file is part of https://github.com/BlueBrain/BioExplorer
+# Copyright 2020-2022 Blue BrainProject / EPFL
+# 
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
 
 cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
 

bioexplorer/core/deps/CMakeLists.txt

@@ -1,7 +1,20 @@
-# Copyright (c) 2020-2022, Cyrille Favreau
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# Copyright (c) 2020-2022, Blue Brain Project
+#                          Cyrille Favreau <[email protected]>
 #
-# This file is part of https://github.com/BlueBrain/BioExplorer
+# This file is part of BioExplorer <https://github.com/BlueBrain/BioExplorer>
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License version 3.0 as published
+# by the Free Software Foundation.
+#
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+# All rights reserved. Do not distribute without further notice.
 
 include(FetchContent)

bioexplorer/core/tests/CMakeLists.txt

@@ -1,9 +1,21 @@
-# Copyright (c) 2020-2022, Cyrille Favreau
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+# scientific data from visualization
 #
-# This file is part of https://github.com/BlueBrain/BioExplorer
-
+# Copyright 2020-2022 Blue BrainProject / EPFL
+# 
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
+
 find_package(Boost REQUIRED COMPONENTS unit_test_framework)
 find_package(Brayns REQUIRED)
 

bioexplorer/core/tests/Glycans.cpp

@@ -1,19 +1,21 @@
-/* Copyright (c) 2020-2022, EPFL/Blue Brain Project
- * All rights reserved. Do not distribute without permission.
- * Responsible Author: [email protected]
+/*
+ * The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+ * scientific data from visualization
  *
- * This library is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License version 3.0 as published
- * by the Free Software Foundation.
+ * Copyright 2020-2022 Blue BrainProject / EPFL
  *
- * This library is distributed in the hope that it will be useful, but WITHOUT
+ * This program is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
  * details.
  *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this library; if not, write to the Free Software Foundation, Inc.,
- * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 #include <plugin/common/Logs.h>

bioexplorer/core/tests/MeshBasedMembrane.cpp

@@ -1,19 +1,21 @@
-/* Copyright (c) 2020-2022, EPFL/Blue Brain Project
- * All rights reserved. Do not distribute without permission.
- * Responsible Author: [email protected]
+/*
+ * The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+ * scientific data from visualization
  *
- * This library is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License version 3.0 as published
- * by the Free Software Foundation.
+ * Copyright 2020-2022 Blue BrainProject / EPFL
  *
- * This library is distributed in the hope that it will be useful, but WITHOUT
+ * This program is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
  * details.
  *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this library; if not, write to the Free Software Foundation, Inc.,
- * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 #include <plugin/common/Assembly.h>

bioexplorer/core/tests/Protein.cpp

@@ -1,19 +1,21 @@
-/* Copyright (c) 2020-2022, EPFL/Blue Brain Project
- * All rights reserved. Do not distribute without permission.
- * Responsible Author: [email protected]
+/*
+ * The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+ * scientific data from visualization
  *
- * This library is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License version 3.0 as published
- * by the Free Software Foundation.
+ * Copyright 2020-2022 Blue BrainProject / EPFL
  *
- * This library is distributed in the hope that it will be useful, but WITHOUT
+ * This program is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
  * details.
  *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this library; if not, write to the Free Software Foundation, Inc.,
- * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 #include <plugin/common/Logs.h>

bioexplorer/core/tests/RNASequence.cpp

@@ -1,19 +1,21 @@
-/* Copyright (c) 2020-2022, EPFL/Blue Brain Project
- * All rights reserved. Do not distribute without permission.
- * Responsible Author: [email protected]
+/*
+ * The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+ * scientific data from visualization
  *
- * This library is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License version 3.0 as published
- * by the Free Software Foundation.
+ * Copyright 2020-2022 Blue BrainProject / EPFL
  *
- * This library is distributed in the hope that it will be useful, but WITHOUT
+ * This program is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
  * details.
  *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this library; if not, write to the Free Software Foundation, Inc.,
- * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ * You should have received a copy of the GNU General Public License along with
+ * this program.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 #include <plugin/common/Assembly.h>

bioexplorer/pythonsdk/Dockerfile

@@ -1,24 +1,21 @@
 
-# Copyright (c) 2020, EPFL/Blue Brain Project
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+# scientific data from visualization
 #
-# This file is part of BioExplorer
-# <https://github.com/BlueBrain/BioExplorer>
+# Copyright 2020-2022 Blue BrainProject / EPFL
+# 
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
 #
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License version 3.0 as published
-# by the Free Software Foundation.
-#
-# This library is distributed in the hope that it will be useful, but WITHOUT
+# This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
 # details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-# All rights reserved. Do not distribute without further notice.
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
 
 FROM debian:buster-slim as builder
 LABEL maintainer="[email protected]"

bioexplorer/pythonsdk/bioexplorer/version.py

@@ -21,4 +21,4 @@
 # You should have received a copy of the GNU General Public License along with
 # this program.  If not, see <https://www.gnu.org/licenses/>.
 
-VERSION = '1.3.2'
+VERSION = '1.4.0'

bioexplorer/pythonsdk/setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-version = 1.3.2
+version = 1.4.0
 name = bioexplorer
 summary = Blue Brain BioExplorer python API
 long_description = file: README.md

bioexplorer/pythonsdk/tests/test_widgets.py

@@ -3,26 +3,23 @@
 
 # -*- coding: utf-8 -*-
 
-# Copyright (c) 2020, EPFL/Blue Brain Project
-# All rights reserved. Do not distribute without permission.
-# Responsible Author: Cyrille Favreau <[email protected]>
+# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
+# scientific data from visualization
 #
-# This file is part of BioExplorer
-# <https://github.com/BlueBrain/BioExplorer>
+# Copyright 2020-2022 Blue BrainProject / EPFL
+# 
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
 #
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License version 3.0 as published
-# by the Free Software Foundation.
-#
-# This library is distributed in the hope that it will be useful, but WITHOUT
+# This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
 # details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-# All rights reserved. Do not distribute without further notice.
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
 
 
 from bioexplorer import BioExplorer, Widgets