From b5e1ab01fbfcdf32f0c8a2c03be23ac1016b98c7 Mon Sep 17 00:00:00 2001 From: adrianciu Date: Wed, 13 Nov 2024 19:01:29 +0200 Subject: [PATCH] TVB-3109 created pyproject.toml for tvb-library, tvb-framework, tvb-storage and tvb-contrib --- tvb_contrib/pyproject.toml | 72 ++++++++++++ tvb_contrib/{setup.py => setup_old.py} | 0 tvb_framework/pyproject.toml | 134 +++++++++++++++++++++++ tvb_framework/{setup.py => setup_old.py} | 0 tvb_library/pyproject.toml | 107 ++++++++++++++++++ tvb_library/{setup.py => setup_old.py} | 0 tvb_storage/pyproject.toml | 82 ++++++++++++++ tvb_storage/{setup.py => setup_old.py} | 0 8 files changed, 395 insertions(+) create mode 100644 tvb_contrib/pyproject.toml rename tvb_contrib/{setup.py => setup_old.py} (100%) create mode 100644 tvb_framework/pyproject.toml rename tvb_framework/{setup.py => setup_old.py} (100%) create mode 100644 tvb_library/pyproject.toml rename tvb_library/{setup.py => setup_old.py} (100%) create mode 100644 tvb_storage/pyproject.toml rename tvb_storage/{setup.py => setup_old.py} (100%) diff --git a/tvb_contrib/pyproject.toml b/tvb_contrib/pyproject.toml new file mode 100644 index 0000000000..6e72a41fa3 --- /dev/null +++ b/tvb_contrib/pyproject.toml @@ -0,0 +1,72 @@ +# -*- coding: utf-8 -*- +# +# +# TheVirtualBrain-Contributors Package. This package holds simulator extensions. +# See also http://www.thevirtualbrain.org +# +# (c) 2012-2024, Baycrest Centre for Geriatric Care ("Baycrest") and others +# +# 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 . +# +# +# CITATION: +# When using The Virtual Brain for scientific publications, please cite it as explained here: +# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications +# +# + + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "tvb-contrib" +version = "2.9.2" +description = "A package with TVB contributed additions to the simulator, useful for scripting." +readme = "README.rst" +license = { file = "LICENSE" } +authors = [ + { name = "Stuart Knock" }, + { name = "Dionysios Perdikis" }, + { name = "Paula Sanz Leon" }, + { name = "Bogdan Valean" }, + { name = "Marmaduke Woodman" }, + { name = "Michiel van der Vlag" }, +] +maintainers = [ + { name = "Codemart", email = "tvb.admin@thevirtualbrain.org" } +] +keywords = [ + "brain", + "contrib", + "neuroscience", + "simulator", + "tvb", +] +dependencies = [ + "lxml", + "pylems", + "scikit-learn", + "tvb-library", + "xarray", +] + +[project.urls] +Download = "https://github.com/the-virtual-brain/tvb-root" +Homepage = "https://www.thevirtualbrain.org" + +[tool.hatch.version] +path = "tvb/__init__.py" + +[tool.hatch.build.targets.sdist] +include = [ + "/tvb", +] diff --git a/tvb_contrib/setup.py b/tvb_contrib/setup_old.py similarity index 100% rename from tvb_contrib/setup.py rename to tvb_contrib/setup_old.py diff --git a/tvb_framework/pyproject.toml b/tvb_framework/pyproject.toml new file mode 100644 index 0000000000..0722bc2c98 --- /dev/null +++ b/tvb_framework/pyproject.toml @@ -0,0 +1,134 @@ +# -*- coding: utf-8 -*- +# +# +# TheVirtualBrain-Framework Package. This package holds all Data Management, and +# Web-UI helpful to run brain-simulations. To use it, you also need to download +# TheVirtualBrain-Scientific Package (for simulators). See content of the +# documentation-folder for more details. See also http://www.thevirtualbrain.org +# +# (c) 2012-2024, Baycrest Centre for Geriatric Care ("Baycrest") and others +# +# 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 . +# +# +# CITATION: +# When using The Virtual Brain for scientific publications, please cite it as explained here: +# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications +# +# + + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "tvb-framework" +version = "2.9.2" +description = "A package for performing whole brain simulations" +readme = "README.rst" +license = { file = "LICENSE" } +requires-python = ">=3.8" +authors = [ + { name = "Mihai Andrei" }, + { name = "Lia Domide" }, + { name = "Stuart Knock" }, + { name = "Bogdan Neacsa" }, + { name = "Paula Prodan" }, + { name = "Paula Sansz Leon" }, + { name = "Marmaduke Woodman" }, +] +maintainers = [ + { name = "Codemart", email = "tvb.admin@thevirtualbrain.org" } +] +keywords = [ + "animal", + "brain", + "delay", + "dynamics", + "human", + "models", + "neuronal", + "neuroscience", + "simulator", + "tvb", +] +classifiers = [ + "Development Status :: 6 - Mature", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +dependencies = [ + "alembic", + "bctpy", + "cherrypy", + "docutils", + "flask", + "flask-restx", + "formencode", + "gevent", + "h5py", + "Jinja2", + "matplotlib", + "nibabel", + "numpy<2.0", + "pandas", + "Pillow", + "psutil", + "python-keycloak", + "requests", + "requests-toolbelt>=0.10", + "scikit-learn", + "scipy", + "siibra", + "simplejson", + "six", + "sqlalchemy", + "tvb-data", + "tvb-gdist", + "tvb-library", + "tvb-storage", + "werkzeug", +] + +[project.optional-dependencies] +extra = [ + "allensdk", +] +hpc = [ + "elasticsearch", + "pyunicore", +] +postgres = [ + "psycopg2", +] +test = [ + "BeautifulSoup4", + "pytest", + "pytest-benchmark", + "pytest-mock", +] + +[project.urls] +Download = "https://github.com/the-virtual-brain/tvb-root" +Homepage = "https://www.thevirtualbrain.org" + +[tool.hatch.version] +path = "tvb/__init__.py" + +[tool.hatch.build.targets.sdist] +include = [ + "/tvb", +] diff --git a/tvb_framework/setup.py b/tvb_framework/setup_old.py similarity index 100% rename from tvb_framework/setup.py rename to tvb_framework/setup_old.py diff --git a/tvb_library/pyproject.toml b/tvb_library/pyproject.toml new file mode 100644 index 0000000000..8177ca77be --- /dev/null +++ b/tvb_library/pyproject.toml @@ -0,0 +1,107 @@ +# -*- coding: utf-8 -*- +# +# +# TheVirtualBrain-Scientific Package. This package holds all simulators, and +# analysers necessary to run brain-simulations. You can use it stand alone or +# in conjunction with TheVirtualBrain-Framework Package. See content of the +# documentation-folder for more details. See also http://www.thevirtualbrain.org +# +# (c) 2012-2024, Baycrest Centre for Geriatric Care ("Baycrest") and others +# +# 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 . +# +# +# CITATION: +# When using The Virtual Brain for scientific publications, please cite it as explained here: +# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications +# +# + + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "tvb-library" +version = "2.9.2" +dynamic = ["version"] +description = "A package for performing whole brain simulations" +readme = "README.rst" +license = { file = "LICENSE" } +requires-python = ">=3.8" +authors = [ + { name = "Marmaduke Woodman" }, + { name = "Jan Fousek" }, + { name = "Stuart Knock" }, + { name = "Paula Sanz Leon" }, + { name = "Viktor Jirsa" }, +] +maintainers = [ + { name = "Codemart", email = "tvb.admin@thevirtualbrain.org" } +] +keywords = [ + "animal", + "brain", + "delay", + "dynamics", + "human", + "models", + "neuronal", + "neuroscience", + "simulator", + "tvb", +] +classifiers = [ + "Development Status :: 6 - Mature", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +dependencies = [ + "autopep8", + "Deprecated", + "docutils", + "ipywidgets", + "mako>=1.1.4", + "matplotlib", + "networkx", + "numba", + "numexpr", + "numpy<2.0", + "scipy", + "six", +] + +[project.optional-dependencies] +test = [ + "h5py", + "pytest", + "pytest-benchmark", + "pytest-xdist", + "tvb-data", + "tvb-gdist", +] + +[project.urls] +Download = "https://github.com/the-virtual-brain/tvb-root" +Homepage = "https://www.thevirtualbrain.org" + +[tool.hatch.version] +path = "tvb/__init__.py" + +[tool.hatch.build.targets.sdist] +include = [ + "/tvb", +] diff --git a/tvb_library/setup.py b/tvb_library/setup_old.py similarity index 100% rename from tvb_library/setup.py rename to tvb_library/setup_old.py diff --git a/tvb_storage/pyproject.toml b/tvb_storage/pyproject.toml new file mode 100644 index 0000000000..834cb94268 --- /dev/null +++ b/tvb_storage/pyproject.toml @@ -0,0 +1,82 @@ +# -*- coding: utf-8 -*- +# +# +# TheVirtualBrain-Framework Package. This package holds all Data Management, and +# Web-UI helpful to run brain-simulations. To use it, you also need to download +# TheVirtualBrain-Scientific Package (for simulators). See content of the +# documentation-folder for more details. See also http://www.thevirtualbrain.org +# +# (c) 2012-2024, Baycrest Centre for Geriatric Care ("Baycrest") and others +# +# 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 . +# +# +# CITATION: +# When using The Virtual Brain for scientific publications, please cite it as explained here: +# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications +# +# + + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "tvb-storage" +version = "2.9.2" +description = "A package which handles the storage of TVB data" +readme = "README.rst" +license = "GPL-3.0-or-later" +authors = [ + { name = "Lia Domide" }, + { name = "Paula Prodan" }, + { name = "Bogdan Valean" }, + { name = "Robert Vincze" }, +] +maintainers = [ + { name = "Codemart", email = "tvb.admin@thevirtualbrain.org" } +] +keywords = [ + "brain", + "h5", + "storage", + "tvb", +] +dependencies = [ + "cryptography", + "h5py", + "kubernetes", + "numpy", + "pyAesCrypt", + "requests", + "tvb-library", +] + +[project.optional-dependencies] +encrypt = [ + "syncrypto", +] +test = [ + "decorator", + "pytest", +] + +[project.urls] +Download = "https://github.com/the-virtual-brain/tvb-root" +Homepage = "https://www.thevirtualbrain.org" + +[tool.hatch.version] +path = "tvb/__init__.py" + +[tool.hatch.build.targets.sdist] +include = [ + "/tvb", +] diff --git a/tvb_storage/setup.py b/tvb_storage/setup_old.py similarity index 100% rename from tvb_storage/setup.py rename to tvb_storage/setup_old.py