diff --git a/LICENSE b/LICENSE index 0037300..c8cb256 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,16 @@ -MIT License - -Copyright (c) 2026 ViroSync Development Team - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +License Agreement +Lawrence Berkeley National Laboratory +NON-COMMERCIAL USE ONLY LICENSE +ViroSync Copyright (c) 2026, The Regents of the University of California, through Lawrence Berkeley National Laboratory (“Berkeley Lab”) subject to receipt of any required approvals from the U.S. Dept. of Energy. All rights reserved. +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: +(1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +(2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +(3) Neither the name of the University of California, Berkeley Lab, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission of Berkeley Lab. +(4) Use of the software, in source or binary form is for NON-COMMERCIAL USE purposes ONLY. The software is not available for commercial use. If you have any questions regarding this software, please contact Berkeley Lab at IPO@lbl.gov. +(5) User agrees to indemnify, defend, and hold harmless Berkeley Lab, the U.S. Government, the software developers, the software sponsors, and their agents, officers, and employees, against any and all claims, suits, losses, damage, costs, fees, and expenses arising out of or in connection with this Agreement. User agrees to pay all costs incurred by Berkeley Lab in enforcing this provision, including reasonable attorney fees. +(6) In the event User creates any bug fixes, patches, upgrades, updates, modifications, derivative works or enhancements to the source code or binary code of the software ("Enhancements") User hereby grants Berkeley Lab and the U.S. Government a paid-up, non-exclusive, irrevocable, worldwide license in the Enhancements to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +Copyright Notice +ViroSync Copyright (c) 2026, The Regents of the University of California, through Lawrence Berkeley National Laboratory (“Berkeley Lab”) subject to receipt of any required approvals from the U.S. Dept. of Energy. All rights reserved. +If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov. +NOTICE: This Software was developed under Contract No. DE-AC02-05CH11231 with the Department of Energy (“DOE”). During the period of commercialization or such other time period specified by DOE, the U.S. Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly, by or on behalf of the U.S. Government. Subsequent to that period, the U.S. Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. The specific term of the license can be identified by inquiry made to Lawrence Berkeley National Laboratory or DOE. NEITHER THE UNITED STATES NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY DATA, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS. diff --git a/README.md b/README.md index 06ba51d..fb100c6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # ViroSync ![Version](https://img.shields.io/badge/version-1.0.0-blue) -[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) +[![License: non-commercial use only](https://img.shields.io/badge/license-non--commercial-orange.svg)](LICENSE) ViroSync detects candidate endogenous viral elements (EVEs) in assembled eukaryotic genomes. The active pipeline combines hallmark-marker discovery, taxonomy-guided boundary refinement, host-aware trimming, and multi-evidence confidence scoring to prioritize regions for downstream review. diff --git a/pyproject.toml b/pyproject.toml index 14d9f1e..c699011 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ version = "1.0.0" description = "Framework for discovering and characterizing ancient viral elements in eukaryotic genomes" readme = "README.md" requires-python = ">=3.11,<3.12" -license = { text = "MIT" } +license = { file = "LICENSE" } authors = [ { name = "ViroSync Development Team" } ]