cellnition

View on PyPIReverse Dependencies (0)

0.3.0 cellnition-0.3.0-py3-none-any.whl

Wheel Details

Project: cellnition
Version: 0.3.0
Filename: cellnition-0.3.0-py3-none-any.whl
Download: [link]
Size: 240631
MD5: 0bab4b62340cdaf97c13c39b1055dce7
SHA256: a9b28c5cb737f4b190e05ed02da7856a0840cad50874a98746003443b224604c
Uploaded: 2025-03-25 15:38:39 +0000

dist-info

METADATA

Metadata-Version: 2.4
Name: cellnition
Version: 0.3.0
Summary: Open-source cross-platform biology simulator analyzing gene regulatory networks (GRNs) with Network Finite State Machines (NFSMs).
Author-Email: Alexis Pietak <alexis.pietak[at]gmail.com>
Maintainer-Email: Cecil Curry <leycec[at]gmail.com>
Project-Url: Docs, https://github.com/betsee/cellnition/blob/main/README.rst
Project-Url: GitHub, https://github.com/betsee/cellnition
Project-Url: Forums, https://github.com/betsee/cellnition/discussions
Project-Url: Issues, https://github.com/betsee/cellnition/issues
Project-Url: Releases, https://github.com/betsee/cellnition/releases
License: Tufts Open Source License Rider v.1 Academic Use Only Tufts University (“Licensor”) provides you a single copy of the Software identified below pursuant to the License identified below, subject to the following additional License conditions and terms, which are expressly made a part of and integrated with the below License. Notwithstanding anything to the contrary in the License, the license rights provided to you pursuant to the License may be exercised by you solely for academic, non-commercial, research purposes and for no other purpose. The rights granted to you in the License expressly do not include, and the License does not grant to you, the right to copy, modify, reproduce, distribute, display, perform, or otherwise exploit the Software for any commercial purpose. You may not use the Software to provide any product or service to any third party, whether for a fee or any other consideration, including without limitation any hosting, software as a service, consulting, or support services, and may not otherwise use the Software to develop, provide, maintain, or support any commercial product or service whose values derives, in whole or in part, from the Software or its features or functions. The Software is intended solely to support academic research purposes and any use outside this permitted purpose is prohibited. To this end, in the event you make or have made any modifications, updates, upgrades, or contributions to the Software (“Modifications”), Licensor asks that all such Modifications be disclosed and shared back to Licensor for potential use and consideration for updates and improvements to the Software for further use, disclosure, and licensing by Licensor in its discretion to further the associated research. At your request, in the event Licensor uses or incorporates your Modifications into future versions of the Software, Licensor will include attribution to you for such Modifications. Any license notice or attribution required by the License must also include the additional terms of this Tufts Open Source License Rider – Academic Use Only v. 1. Software: Cellnition License: Apache 2.0 Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS Copyright 2025 Alexis Pietak 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://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.
Keywords: biology,python,science,simulator
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: beartype (>=0.15.0)
Requires-Dist: networkx (>=3.4.0)
Requires-Dist: numpy (>=1.22.0)
Requires-Dist: pandas (>=1.5.0)
Requires-Dist: pygraphviz (>=1.10)
Requires-Dist: pyvista (>=0.42.0)
Requires-Dist: scipy (>=1.7.0)
Requires-Dist: sympy (>=1.9.0)
Requires-Dist: beartype[docs,test]; extra == "dev"
Requires-Dist: mkdocs-material (>=9.6.0); extra == "docs"
Requires-Dist: mkdocstrings-python (>=1.16.0); extra == "docs"
Requires-Dist: beartype[test-tox,test-tox-coverage]; extra == "test"
Requires-Dist: tox (>=3.20.1); extra == "test"
Requires-Dist: pytest (>=4.0.0); extra == "test-tox"
Requires-Dist: coverage (>=5.5); extra == "test-tox-coverage"
Provides-Extra: dev
Provides-Extra: docs
Provides-Extra: test
Provides-Extra: test-tox
Provides-Extra: test-tox-coverage
Description-Content-Type: text/x-rst
License-File: LICENSE
[Description omitted; length: 9741 characters]

WHEEL

Wheel-Version: 1.0
Generator: hatchling 1.27.0
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
cellnition/__init__.py sha256=1Ug9xuEORVYwdSKRutAJYHlHU8qqIsrssvNXAjQF92I 2538
cellnition/__main__.py sha256=DqbsSA9_p7ioiBgDSSPMrGEDu-5RFC36q8179N_mWUo 8390
cellnition/error.py sha256=y6iNhlOzOi2nyMFmF1hnKxrhphIAx12i0dY1wBZ3O7o 2261
cellnition/main_streamlit.py sha256=6rdnfClQ_RrZE0ACLjCGBUSMkw81DlWSPcw55RMyuFI 6030
cellnition/py.typed sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/types.py sha256=FpWa783LVyq7XGcKHSJEtML8tcIa315YZrM0NSxAiVQ 708
cellnition/_util/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/_util/cache/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/_util/cache/utilcachecall.py sha256=WfqilFLgl8AiCXv8vIk0DVEWxHqC3-sZ-QmfvDWFddk 1294
cellnition/_util/path/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/_util/path/utilpathmake.py sha256=ThiaBw5oS2KYAIicTo06It7hObop7bSpHsavdBYdJAE 4602
cellnition/_util/path/utilpathself.py sha256=lupFbXxtI6pyz3ON-QaChjAf0C9XW7Sbu2PTwcwvJCk 5679
cellnition/data/csv/.keep sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/data/csv/MAPK_Cancer_Mo.csv sha256=DENfw_YM2-0-UAli2naMMfPbvFbV5e6ONRh48rKBTog 5639
cellnition/data/png/cellnition_icon.png sha256=a4paQo_9R-dtxO8phKR7B0UKujzjaFT_v6uUDKkp0T8 76793
cellnition/data/png/glyph_stability/glyph_attractor.png sha256=NaVOaUO4pSri26MaLlzHuvJbOQjqeXIH-vSLSsHpjzY 7699
cellnition/data/png/glyph_stability/glyph_attractor_limit_cycle.png sha256=26U2cv-lX_v7tk-1e181OfC2UH3w9fGk4X0-Xzj1V0E 9683
cellnition/data/png/glyph_stability/glyph_hidden.png sha256=IIQdEbqJ4Y8AVKXuOVF1MeJu-TQiWQ00Ik6QInECQNo 7395
cellnition/data/png/glyph_stability/glyph_limit_cycle.png sha256=-W5Zrg15u7gAalixKIYrJzZNZk1bzFQWjjO9b8bKQPc 5713
cellnition/data/png/glyph_stability/glyph_repellor.png sha256=fFoJDvPT3H6U3uAhFqUVAbGpbdEjQSIIFUteOgUzack 7931
cellnition/data/png/glyph_stability/glyph_repellor_limit_cycle.png sha256=-SS87X8GrLRMx3mTmduEQyh4SA4ylNWyv93Nl_ptsLc 9796
cellnition/data/png/glyph_stability/glyph_saddle.png sha256=zoa344OaEbPkWyU3BI6oQa6Dg9B3tCKKvH1jn3zESpQ 4774
cellnition/data/png/glyph_stability/glyph_unknown.png sha256=8M5oyPwxmaxAkycPkco9_cPnEh2RISdFQuRT3nN_j3E 738
cellnition/science/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/science/network_workflow.py sha256=gXDJkDSvWYxNPMkAAG3-ZWjOn7eoMAEJaQh7X2UtxG0 49725
cellnition/science/network_models/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/science/network_models/basic_network.py sha256=FdCg-EqiA2fl22zZC6rAldHMqvfQCUl4rlyaIAHb2w8 533
cellnition/science/network_models/boolean_networks.py sha256=6OCgGQSeDqnSS6qspCDGXbxSZ-BguauDy4SvZy7ypQw 37748
cellnition/science/network_models/interaction_functions.py sha256=2dLnMLTohGgwn20W5QkmYtz6-khquNWLUI08Hz2MV7I 3727
cellnition/science/network_models/network_abc.py sha256=f7_ivxyCH_3d2f9AKDEaRzvlaquqzaw-gOtu4mkD9Gg 30317
cellnition/science/network_models/network_enums.py sha256=Gy_Csj8kOmYBpDCkfwhgSvqR9LgvKHA3sySo4RiBy_g 1373
cellnition/science/network_models/network_library.py sha256=GMWxJvvw-xkSLWeTVFCWyQFjW-vCUgBxhz4jKny7ArE 78232
cellnition/science/network_models/probability_networks.py sha256=9_YAuoUOlSjHs1MYdwEvOjo1hennaXRF1J09eSoDvS0 53936
cellnition/science/networks_toolbox/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/science/networks_toolbox/boolean_state_machine.py sha256=HA4ciDSqITqlAv-8jfJy2IRZTaC13voWB_14S5DsAw0 40732
cellnition/science/networks_toolbox/gene_knockout.py sha256=Nr1BDZPmISEeOeD2OPo6ZMEGGsE4heAzBfsAwNAdMt8 9734
cellnition/science/networks_toolbox/netplot.py sha256=TBgkVPCHC_hdK0D_dDuTs-a0xUyQNyg0UNH_ogfcqyk 6211
cellnition/science/networks_toolbox/phase_space_searches.py sha256=Ckpy3d-fn15HM5sUiIPxniVxBMi3zAoL4g0M6v425Ek 12695
cellnition/science/networks_toolbox/phase_space_viz.py sha256=ssP9SJSRpImcYbSNhyUFxwoaP1WVxr0jFU6sHbpDRqM 6966
cellnition/science/networks_toolbox/state_machine.py sha256=VxPXFmw9Opi0BytqJR842YOfM7naKAf9BurkZjexr3c 45293
cellnition/science/osmoadaptation/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cellnition/science/osmoadaptation/analytic_model.py sha256=5WuaeNVX6DF904c_hlIorJACPUQf9V3b3HVQPhGGgVw 16388
cellnition/science/osmoadaptation/model_params.py sha256=Yf-D8jwaD28IP9R28F4lnYn1ySf3WHk8uM1l_r0ucr4 7789
cellnition/science/osmoadaptation/osmo_model.py sha256=l6k2MvGWfnsEzbl_Y6wY75jYMVYtVTfKSXpaiYFMO3o 19940
cellnition-0.3.0.dist-info/METADATA sha256=xYpKNAmXADPmsnW28X7ypZ4tYPP9PXkp-TWsn75ZTmo 26410
cellnition-0.3.0.dist-info/WHEEL sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ 87
cellnition-0.3.0.dist-info/licenses/LICENSE sha256=5X5wLxhIni5TXcCMir0DTsDJGG1kZlKGSIY-OVUGXVk 12921
cellnition-0.3.0.dist-info/RECORD