sbtabpy 1.0.8__tar.gz

sbtabpy-1.0.8/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2020 Timo Lubitz
+Copyright (c) 2020 Wolfram Liebermeister
+Copyright (c) 2020 Humboldt Universität zu Berlin
+Copyright (c) 2026 Elad Noor
+Copyright (c) 2026 Weizmann Institute of Science
+
+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.

sbtabpy-1.0.8/PKG-INFO

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+Metadata-Version: 2.4
+Name: sbtabpy
+Version: 1.0.8
+Summary: SBtab - Standardised Data Tables for Systems Biology
+Author-email: Timo Lubitz <timo.lubitz@gmail.com>, Elad Noor <elad.noor@weizmann.ac.il>
+License: MIT
+Project-URL: Homepage, https://www.sbtab.net
+Keywords: modelling,systems biology,standard format,data table
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: python-libsbml>=5.0
+Requires-Dist: numpy>=2.0
+Requires-Dist: scipy>=1.13
+Requires-Dist: openpyxl>=2.5
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyarrow>=14.0.1
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-raises; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: hypothesis; extra == "test"
+Provides-Extra: development
+Requires-Dist: ruff; extra == "development"
+Requires-Dist: pip-audit; extra == "development"
+Requires-Dist: tox; extra == "development"
+Requires-Dist: twine; extra == "development"
+Provides-Extra: deployment
+Requires-Dist: click; extra == "deployment"
+Requires-Dist: click-log; extra == "deployment"
+Requires-Dist: pyinstaller; extra == "deployment"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2.0; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Dynamic: license-file
+
+SBtab: a Table format for Systems Biology
+=========================================
+Python code and example files by
+Timo Lubitz, Elad Noor, Jens Hahn, Frank Bergmann (2018).
+
+[![PyPI version](https://img.shields.io/pypi/v/sbtab)](https://pypi.org/project/sbtab/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/sbtab)](https://pypi.org/project/sbtab/)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/sbtab)](https://pypi.org/project/sbtab/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Data tables in the form of spreadsheets or delimited text files are the most common data 
+format in Systems Biology. However, they are often not sufficiently structured and lack 
+clear naming conventions that would be required for modeling. We propose the **SBtab**
+format as an attempt to establish an easy-to-use table format that is both flexible and 
+clearly structured. It comprises defined table types for different kinds of data; syntax 
+rules for usage of names, shortnames, and database identifiers used for annotation;
+and standardized formulae for reaction stoichiometries. Predefined table types can be
+used to define biochemical network models and the biochemical constants therein. The users
+can also define their own table types, adjusting SBtab to other types of data.
+
+The SBtab specification can be found on the
+[SBtab homepage](https://www.sbtab.net/sbtab/default/downloads.html#spec).
+The homepage also provides various information on example files, frequently
+asked questions, online tools, and tutorials.
+
+Software tools
+--------------
+
+SBtab comes along with software tools which can be employed in three different ways:
+
+1. **SBtab online**
+
+    You can use the software tools that come with SBtab in the convenient online interface:
+    - [Validator](https://www.sbtab.net/sbtab/default/validator.html)
+    - [SBML Converter](https://www.sbtab.net/sbtab/default/converter.html)
+    - [Customize SBtab](https://www.sbtab.net/sbtab/default/def_files.html)
+  
+2. **Python package** (i.e., pip installer)
+  
+    The tools can be employed as a Python package. It needs to be installed via
+    [pypi](https://pypi.org/project/sbtab/). Please type on your commandline:
+    ```bash
+      sudo pip install sbtab
+    ```
+    You will then be able to import the SBtab library into your Python modules by adding
+    ```
+      import sbtab
+    ```
+    to them. See the code examples in this repository's directory `/examples`.
+  
+3. **From the commandline** (for experienced users)
+   
+    You can employ the SBtab commandline tools from the directory
+    `SBtab/python`. To use this option,
+    you will have to install the required packages on your own and put
+    the Python modules to their according directory. Details on the usage
+    of the commandline tools you can find in the directory `SBtab/python`.
+
+
+Repository contents
+-------------------
+The SBtab repository consists of the following directories and contents:
+
+- **Source Code `/src`**
+  
+  - Source scripts and commandline Python modules, including a file and object validator, and a converter to and from SBML.
+  - SQLite interface: Python interface for querying SQLite databases via SBtab.
+
+- **Unit Tests `/tests`**
+  
+  Some tests to ensure the correctness and functionality of the SBtab package.
+
+- **Definition Table `/definitions_table`**
+
+  Default definitions of predefined SBtab table types.
+
+- **Example Files `/examples`**
+  
+  Example SBtab files. These files can also be found including explanatory words in the [online SBtab Download Section](https://www.sbtab.net/sbtab/default/downloads.html)
+
+- **API documentation** `/api_documentation`
+  
+  HTML pydoc documentation of the SBtab interface and source code.

sbtabpy-1.0.8/README.md

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+SBtab: a Table format for Systems Biology
+=========================================
+Python code and example files by
+Timo Lubitz, Elad Noor, Jens Hahn, Frank Bergmann (2018).
+
+[![PyPI version](https://img.shields.io/pypi/v/sbtab)](https://pypi.org/project/sbtab/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/sbtab)](https://pypi.org/project/sbtab/)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/sbtab)](https://pypi.org/project/sbtab/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Data tables in the form of spreadsheets or delimited text files are the most common data 
+format in Systems Biology. However, they are often not sufficiently structured and lack 
+clear naming conventions that would be required for modeling. We propose the **SBtab**
+format as an attempt to establish an easy-to-use table format that is both flexible and 
+clearly structured. It comprises defined table types for different kinds of data; syntax 
+rules for usage of names, shortnames, and database identifiers used for annotation;
+and standardized formulae for reaction stoichiometries. Predefined table types can be
+used to define biochemical network models and the biochemical constants therein. The users
+can also define their own table types, adjusting SBtab to other types of data.
+
+The SBtab specification can be found on the
+[SBtab homepage](https://www.sbtab.net/sbtab/default/downloads.html#spec).
+The homepage also provides various information on example files, frequently
+asked questions, online tools, and tutorials.
+
+Software tools
+--------------
+
+SBtab comes along with software tools which can be employed in three different ways:
+
+1. **SBtab online**
+
+    You can use the software tools that come with SBtab in the convenient online interface:
+    - [Validator](https://www.sbtab.net/sbtab/default/validator.html)
+    - [SBML Converter](https://www.sbtab.net/sbtab/default/converter.html)
+    - [Customize SBtab](https://www.sbtab.net/sbtab/default/def_files.html)
+  
+2. **Python package** (i.e., pip installer)
+  
+    The tools can be employed as a Python package. It needs to be installed via
+    [pypi](https://pypi.org/project/sbtab/). Please type on your commandline:
+    ```bash
+      sudo pip install sbtab
+    ```
+    You will then be able to import the SBtab library into your Python modules by adding
+    ```
+      import sbtab
+    ```
+    to them. See the code examples in this repository's directory `/examples`.
+  
+3. **From the commandline** (for experienced users)
+   
+    You can employ the SBtab commandline tools from the directory
+    `SBtab/python`. To use this option,
+    you will have to install the required packages on your own and put
+    the Python modules to their according directory. Details on the usage
+    of the commandline tools you can find in the directory `SBtab/python`.
+
+
+Repository contents
+-------------------
+The SBtab repository consists of the following directories and contents:
+
+- **Source Code `/src`**
+  
+  - Source scripts and commandline Python modules, including a file and object validator, and a converter to and from SBML.
+  - SQLite interface: Python interface for querying SQLite databases via SBtab.
+
+- **Unit Tests `/tests`**
+  
+  Some tests to ensure the correctness and functionality of the SBtab package.
+
+- **Definition Table `/definitions_table`**
+
+  Default definitions of predefined SBtab table types.
+
+- **Example Files `/examples`**
+  
+  Example SBtab files. These files can also be found including explanatory words in the [online SBtab Download Section](https://www.sbtab.net/sbtab/default/downloads.html)
+
+- **API documentation** `/api_documentation`
+  
+  HTML pydoc documentation of the SBtab interface and source code.

sbtabpy-1.0.8/pyproject.toml

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+[project]
+name = "sbtabpy"
+version = "1.0.8"
+description = "SBtab - Standardised Data Tables for Systems Biology"
+readme = "README.md"
+license = { text = "MIT" }
+authors = [{ name = "Timo Lubitz", email = "timo.lubitz@gmail.com" },
+           { name = "Elad Noor", email = "elad.noor@weizmann.ac.il" }]
+keywords = ["modelling", "systems biology", "standard format", "data table"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Topic :: Software Development",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "python-libsbml>=5.0",
+    "numpy>=2.0",
+    "scipy>=1.13",
+    "openpyxl>=2.5",
+    "pandas>=2.0",
+    "pyarrow>=14.0.1",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-raises",
+    "pytest-mock",
+    "hypothesis"
+]
+development = [
+    "ruff",
+    "pip-audit",
+    "tox",
+    "twine"
+]
+deployment = [
+    "click",
+    "click-log",
+    "pyinstaller",
+]
+docs = [
+    "sphinx>=7.0",
+    "sphinx-rtd-theme>=2.0",
+    "myst-parser>=2.0",
+]
+
+[project.scripts]
+sbtab = "sbtab.__main__:main"
+
+[project.urls]
+Homepage = "https://www.sbtab.net"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"sbtab" = ["data/*.html", "data/*.tsv"]
+
+
+[build-system]
+requires = [ "setuptools>=61", "wheel", "setuptools-git-versioning>=2.0,<3", ]
+build-backend = "setuptools.build_meta"
+
+[tool.distutils.bdist_wheel]
+universal = true
+
+[tool.setuptools-git-versioning]
+enabled = true
+
+[tool.isort]
+profile = "black"
+
+[tool.black]
+target-version = ["py314"]
+exclude = '''
+(
+    __init__.py
+)
+'''
+
+[tool.ruff]
+target-version = "py314"
+
+[tool.ruff.lint]
+ignore = ["F401"]

sbtabpy-1.0.8/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+