Merge pull request #383 from favreau/master

Version 2.0.0

Author: Cyrille Favreau

.github/workflows/deploy.yml

@@ -0,0 +1,33 @@
+name: Build and Deploy Jekyll Site
+
+on:
+  push:
+    branches:
+      - main  # Remplace par ta branche principale si nécessaire
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Setup Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '2.7'
+
+    - name: Install dependencies
+      run: |
+        gem install bundler
+        bundle install
+
+    - name: Build site
+      run: bundle exec jekyll build
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./_site

.gitmodules

@@ -1,15 +1,9 @@
-[submodule "platorm/deps/uvw"]
-path = platorm/deps/uvw
-url = https://github.com/skypjack/uvw.git
-[submodule "platform/deps/perceptualdiff"]
-path = platform/deps/perceptualdiff
-url = https://github.com/myint/perceptualdiff.git
-[submodule "platform/deps/rapidjson"]
-path = platform/deps/rapidjson
-url = https://github.com/Tencent/rapidjson.git
 [submodule "platform/deps/uvw"]
-path = platform/deps/uvw
-url = https://github.com/skypjack/uvw.git
+	path = platform/deps/uvw
+	url = https://github.com/skypjack/uvw.git
+[submodule "platform/deps/rapidjson"]
+	path = platform/deps/rapidjson
+	url = https://github.com/Tencent/rapidjson.git
 [submodule "common/deps/async++"]
-path = common/deps/async++
-url = https://github.com/Amanieu/asyncplusplus.git
+	path = common/deps/async++
+	url = https://github.com/Amanieu/asyncplusplus.git

CMake/FindFreeImage.cmake

@@ -16,8 +16,8 @@ cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
 set(NAME BIOEXPLORER)
 
 set(PACKAGE_VERSION_ABI 1)
-set(PACKAGE_VERSION_MAJOR 1)
-set(PACKAGE_VERSION_MINOR 8)
+set(PACKAGE_VERSION_MAJOR 2)
+set(PACKAGE_VERSION_MINOR 0)
 set(PACKAGE_VERSION_PATCH 0)
 
 # Get the Git revision using the git command

CMakeLists.txt

@@ -477,7 +477,7 @@ be.add_sars_cov_2(name=name, resource_folder=resource_folder)
 
 # License
 
-_BBBE_ is available to download and use under the GNU General Public License ([GPL](https://www.gnu.org/licenses/gpl.html), or “free software”). The code is open sourced with approval from the open sourcing committee and principal coordinators of the Blue Brain Project in February 2022.
+_BBBE_ is available to download and use under the [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0). The code is open sourced with approval from the open sourcing committee and principal coordinators of the Blue Brain Project in February 2022.
 
 
 # Contact

README.md

@@ -248,7 +248,7 @@ include_directories(
 set(${NAME}_LINK_LIBRARIES
     PUBLIC ${${NAME}_PUBLIC_MODULE_LIBRARIES}
     PRIVATE CoreParameters CoreCommon CoreEngine CoreIO mpfr stdc++fs
-    ${${NAME}_PRIVATE_MODULE_LIBRARIES} ${FreeImage_LIBRARIES} ${PQXX_LIBRARIES} ${OpenMP_CXX_LIBRARIES}
+    ${${NAME}_PRIVATE_MODULE_LIBRARIES} ${PQXX_LIBRARIES} ${OpenMP_CXX_LIBRARIES}
 )
 
 if(${CGAL_FOUND})

bioexplorer/backend/CMakeLists.txt

@@ -9,7 +9,7 @@ maintainers: Cyrille Favreau
 name: BioExplorer
 license: Apache 2.0
 issuesurl: https://github.com/BlueBrain/BioExplorer/issues
-version: 1.8.0
+version: 2.0.0
 contributors: Cyrille Favreau
 minor: 1
 ---

bioexplorer/backend/doc/metadata.md

@@ -1,21 +1,16 @@
-
-# The Blue Brain BioExplorer is a tool for scientists to extract and analyse
-# scientific data from visualization
+# Copyright 2020 - 2023 Blue Brain Project / EPFL
 #
-# Copyright 2020-2023 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.
+# 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
 #
-# 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.
+#     http://www.apache.org/licenses/LICENSE-2.0
 #
-# You should have received a copy of the GNU General Public License along with
-# this program.  If not, see <https://www.gnu.org/licenses/>.
+# 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 debian:buster-slim as builder
 LABEL maintainer="cyrille.favreau@epfl.ch"

bioexplorer/pythonsdk/Dockerfile

@@ -1,33 +1,28 @@
-# Copyright (c) 2020-2023, Blue Brain Project
-#                          Cyrille Favreau <cyrille.favreau@epfl.ch>
+# Copyright 2020 - 2023 Blue Brain Project / EPFL
 #
-# This file is part of BioExplorer <https://github.com/BlueBrain/BioExplorer>
+# 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
 #
-# 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.
+#     http://www.apache.org/licenses/LICENSE-2.0
 #
-# 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.
+# 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.
 
 ROOT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
 
-#see if we're in a virtualenv, and use that, otherwise use the default
+# See if we're in a virtualenv, and use that, otherwise use the default
 ifdef VIRTUAL_ENV
    VENV=$(VIRTUAL_ENV)
 else
    VENV:=venv
 endif
 VENV_BIN:=$(VENV)/bin
 
-# simulate running in headless mode
+# Simulate running in headless mode
 unexport DISPLAY
 
 # Test coverage pass threshold (percent)

bioexplorer/pythonsdk/Makefile

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 # Copyright 2020 - 2024 Blue Brain Project / EPFL
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,15 +14,37 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+"""
+BioExplorer module
+
+This package provides tools for exploring biological data, including utilities for molecular system
+animations, displacement parameters for eurons and astrocytes, report parameters, movie making, and
+more.
+
+Modules included:
+- Vector2, Vector3, Quaternion, Bounds, Transformation
+- MolecularSystemAnimationParams, CellAnimationParams
+- NeuronDisplacementParams, AstrocyteDisplacementParams, VasculatureDisplacementParams,
+SynapseDisplacementParams
+- Volume, Membrane, Protein, Sugar, RNASequence, Cell, Surfactant, Virus, EnzymeReaction
+- NeuronReportParams
+- MovieMaker, MovieScenario
+- Metabolism
+- SonataExplorer
+- Widgets
+- TransferFunction
+- BioExplorer
+
+For more information, please refer to the individual module docstrings.
+"""
+
 from .version import VERSION as __version__
 from .math_utils import (Vector2, Vector3, Quaternion, Bounds, Transformation)
-from .animation_parameters import (
-    MolecularSystemAnimationParams, CellAnimationParams)
-from .displacement_parameters import (
-    NeuronDisplacementParams, AstrocyteDisplacementParams, VasculatureDisplacementParams,
-    SynapseDisplacementParams)
-from .molecular_systems import (Volume, Membrane, Protein, Sugar, RNASequence,
-    Cell, Surfactant, Virus, EnzymeReaction)
+from .animation_parameters import (MolecularSystemAnimationParams, CellAnimationParams)
+from .displacement_parameters import (NeuronDisplacementParams, AstrocyteDisplacementParams,
+                                      VasculatureDisplacementParams, SynapseDisplacementParams)
+from .molecular_systems import (Volume, Membrane, Protein, Sugar, RNASequence, Cell, Surfactant,
+                                Virus, EnzymeReaction)
 from .report_parameters import NeuronReportParams
 from .movie_maker import MovieMaker
 from .movie_scenario import MovieScenario
@@ -35,6 +59,7 @@
     "BioExplorer",
     "Vector2",
     "Vector3",
+    "Quaternion",
     "Bounds",
     "Transformation",
     "Membrane",

bioexplorer/pythonsdk/bioexplorer/__init__.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env
+
 # Copyright 2020 - 2024 Blue Brain Project / EPFL
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,10 +14,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+"""
+Module animation_parameters
+
+This module provides classes to define animation parameters for molecular systems and cells.
+These parameters are used to introduce randomness and sinusoidal motion to make animations appear
+more realistic.
+"""
+
 
 class MolecularSystemAnimationParams:
     """
     Parameters used to introduce some randomness in the position and orientation of the protein.
+
     This approach is used to make assemblies appear more realistic and for animation purposes.
     """
 
@@ -33,9 +44,11 @@ def __init__(
 
         :param seed: int, optional: Randomization seed for initial setup. Defaults to 0.
         :param position_seed: int, optional: Seed for position randomization. Defaults to 0.
-        :param position_strength: float, optional: Strength of position randomization. Defaults to 0.0.
+        :param position_strength: float, optional: Strength of position randomization. Defaults to
+        0.0.
         :param rotation_seed: int, optional: Seed for rotation randomization. Defaults to 0.
-        :param rotation_strength: float, optional: Strength of rotation randomization. Defaults to 0.0.
+        :param rotation_strength: float, optional: Strength of rotation randomization. Defaults to
+        0.0.
         :param morphing_step: float, optional: Step for morphing between shapes. Defaults to 0.0.
         """
         self.components = {
@@ -74,15 +87,15 @@ def copy(self):
         return MolecularSystemAnimationParams(**self.components)
 
     def __repr__(self):
-        """
-        Return the official string representation of the object for debugging and logging purposes.
-        """
-        return f"MolecularSystemAnimationParams({', '.join(f'{k}={v}' for k, v in self.components.items())})"
+        """Return the string representation of the object for debugging and logging purposes."""
+        return f"MolecularSystemAnimationParams(\
+            {', '.join(f'{k}={v}' for k, v in self.components.items())})"
 
 
 class CellAnimationParams:
     """
     Parameters used to introduce some sinusoidal function in a cell structure.
+
     This class is used to define how cells should be animated using sinusoidal motion.
     """
 
@@ -129,7 +142,5 @@ def copy(self):
         return CellAnimationParams(**self.components)
 
     def __repr__(self):
-        """
-        Return the official string representation of the object for debugging and logging purposes.
-        """
+        """Return the string representation of the object for debugging and logging purposes."""
         return f"CellAnimationParams({', '.join(f'{k}={v}' for k, v in self.components.items())})"