chromaquant 0.4.0__tar.gz → 0.5.0__tar.gz

chromaquant-0.5.0/.gitignore

@@ -0,0 +1,16 @@
+.conda/
+dist/
+.git/
+__pycache__/
+.pytest_cache/
+local-tests/
+.VSCodeCounter/
+.venv/
+.DS_Store
+.gitignore
+*.pyc
+*.pyo
+*.pyd
+report.xlsx
+tests/unit/report.xlsx
+~$report.xlsx

{chromaquant-0.4.0 → chromaquant-0.5.0}/LICENSE.txt

@@ -1,7 +1,7 @@
 
 ChromaQuant – A quantification software for complex gas chromatographic data
 
-Copyright (c) 2024, by Julia Hancock
+Copyright (c) 2026, by Julia Hancock
               Affiliation: Dr. Julie Elaine Rorrer
 	      URL: https://www.rorrerlab.com/
 

chromaquant-0.5.0/LICENSES_bundled.txt

@@ -0,0 +1,251 @@
+
+==========
+
+The ChromaQuant project uses Python as its primary language. The following is the Python license agreement as prepared by the Python Software Foundation:
+
+"1. This LICENSE AGREEMENT is between the Python Software Foundation
+("PSF"), and the Individual or Organization ("Licensee") accessing and
+otherwise using this software ("Python") in source or binary form and
+its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, PSF hereby
+grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
+analyze, test, perform and/or display publicly, prepare derivative works,
+distribute, and otherwise use Python alone or in any derivative version,
+provided, however, that PSF's License Agreement and PSF's notice of copyright,
+i.e., "Copyright (c) 2001-2024 Python Software Foundation; All Rights Reserved"
+are retained in Python alone or in any derivative version prepared by Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on
+or incorporates Python or any part thereof, and wants to make
+the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to Python.
+
+4. PSF is making Python available to Licensee on an "AS IS"
+basis.  PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
+OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any
+relationship of agency, partnership, or joint venture between PSF and
+Licensee.  This License Agreement does not grant permission to use PSF
+trademarks or trade name in a trademark sense to endorse or promote
+products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using Python, Licensee
+agrees to be bound by the terms and conditions of this License
+Agreement."
+
+==========
+
+The ChromaQuant repository and source depend on a number of libraries that are compatibly licensed. These are listed below:
+
+
+Name: Pandas
+License: BSD 3-Clause License
+
+"Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team
+All rights reserved.
+
+Copyright (c) 2011-2024, Open source contributors.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* 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.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+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 HOLDER 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."
+
+
+Name: molmass
+License: BSD 3-Clause License
+
+"Copyright (c) 1990-2024, Christoph Gohlke
+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 copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+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 HOLDER 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."
+
+
+Name: chemformula
+License: MIT License
+
+"Copyright (c) 2021 Axel Müller
+
+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."
+
+
+Name: XlsxWriter
+License: BSD 2-Clause
+
+"BSD 2-Clause License
+
+Copyright (c) 2013-2025, John McNamara <jmcnamara@cpan.org>
+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.
+
+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 HOLDER 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."
+
+
+Name: openpyxl
+License: MIT License
+
+"This software is under the MIT Licence
+======================================
+
+Copyright (c) 2010 openpyxl
+
+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."
+
+
+Name: pytest
+License: MIT License
+
+"The MIT License (MIT)
+
+Copyright (c) 2004 Holger Krekel and others
+
+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."
+
+
+Name: pre-commit
+License: MIT License
+
+"Copyright (c) 2014 pre-commit dev team: Anthony Sottile, Ken Struys
+
+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."

chromaquant-0.5.0/PKG-INFO

@@ -0,0 +1,61 @@
+Metadata-Version: 2.4
+Name: chromaquant
+Version: 0.5.0
+Summary: Analytical platform for gas chromatography
+Project-URL: Repository, https://github.com/JnliaH/ChromaQuant
+Author: Julia Hancock
+License: 
+        ChromaQuant – A quantification software for complex gas chromatographic data
+        
+        Copyright (c) 2026, by Julia Hancock
+                      Affiliation: Dr. Julie Elaine Rorrer
+        	      URL: https://www.rorrerlab.com/
+        
+        License: BSD 3-Clause License
+        
+        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 copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+        
+        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 HOLDER 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.
+License-File: LICENSE.txt
+License-File: LICENSES_bundled.txt
+Keywords: Analysis,Analytical Chemistry,Chromatography,Complex Hydrocarbon Analysis,Mass Spectrometry
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Environment :: MacOS X
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.14
+Requires-Dist: chemformula~=1.5.1
+Requires-Dist: molmass~=2025.12.12
+Requires-Dist: openpyxl~=3.1.5
+Requires-Dist: pandas~=2.3.3
+Requires-Dist: pre-commit~=4.5.1
+Requires-Dist: pytest~=9.0.2
+Requires-Dist: xlsxwriter~=3.2.9
+Description-Content-Type: text/markdown
+
+<h1>ChromaQuant</h1>
+<i>A solution for automated gas chromatographic peak assignment and quantification</i>
+
+<h4>Introduction</h4>
+<img style="float: right;" align="right" width="256" alt="ChromaQuant Logo" src="https://github.com/JnliaH/ChromaQuant/blob/rebrand/images/ChromaQuantIcon.png">
+ChromaQuant is an open-source toolkit designed to enable users to rapidly and precisely analyze chromatographic data. It offers tools for matching chromatographic signals to each other or to other tabulated data, writing formulas for dynamic Excel reporting, and peforming simple operations on tabulated data to produce properties like molecular weight.
+
+The development of ChromaQuant is associated with the <a href="https://www.rorrerlab.com/">Rorrer Lab</a> at the University of Washington Department of Chemical engineering.
+
+<h4>Installation</h4>
+Install ChromaQuant by running the following command in the terminal/command prompt:<br>
+
+
+> pip install chromaquant
+
+<h4>Usage</h4>
+
+ChromaQuant is currently under major renovations. Please tune back in for in-detail documentation on usage with examples!

chromaquant-0.5.0/README.md

@@ -0,0 +1,18 @@
+<h1>ChromaQuant</h1>
+<i>A solution for automated gas chromatographic peak assignment and quantification</i>
+
+<h4>Introduction</h4>
+<img style="float: right;" align="right" width="256" alt="ChromaQuant Logo" src="https://github.com/JnliaH/ChromaQuant/blob/rebrand/images/ChromaQuantIcon.png">
+ChromaQuant is an open-source toolkit designed to enable users to rapidly and precisely analyze chromatographic data. It offers tools for matching chromatographic signals to each other or to other tabulated data, writing formulas for dynamic Excel reporting, and peforming simple operations on tabulated data to produce properties like molecular weight.
+
+The development of ChromaQuant is associated with the <a href="https://www.rorrerlab.com/">Rorrer Lab</a> at the University of Washington Department of Chemical engineering.
+
+<h4>Installation</h4>
+Install ChromaQuant by running the following command in the terminal/command prompt:<br>
+
+
+> pip install chromaquant
+
+<h4>Usage</h4>
+
+ChromaQuant is currently under major renovations. Please tune back in for in-detail documentation on usage with examples!

{chromaquant-0.4.0 → chromaquant-0.5.0}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "hatchling.build"
 
 [project]
 name = "chromaquant"
-dynamic = ["version"]
+version = "0.5.0"
 description = "Analytical platform for gas chromatography"
 readme = "README.md"
 license = {file = "LICENSE.txt"}
-requires-python = ">=3.12"
+requires-python = ">=3.14"
 authors = [{name = "Julia Hancock"},]
 keywords = [
 	"Analysis",
@@ -26,18 +26,14 @@ classifiers = [
 	"Environment :: MacOS X",
 ]
 dependencies = [
-	"pandas~=2.2.2",
-	"molmass~=2024.5.24",
-	"numpy~=1.26.4",
-	"chemformula~=1.3.1",
-	"scipy~=1.13.1",
-	"ttkthemes~=3.2.2",
-	"pillow~=10.3.0",
-	"plotly~=5.22.0",
-	"pubchempy~=1.0.4",
-	"rdkit~=2024.3.5",
-	"XlsxWriter~=3.2.0",
+	"pandas~=2.3.3",
+	"molmass~=2025.12.12",
+	"chemformula~=1.5.1",
+	"XlsxWriter~=3.2.9",
 	"openpyxl~=3.1.5",
+	"pytest~=9.0.2",
+	"pre-commit~=4.5.1"
+
 ]
 
 [project.urls]
@@ -45,10 +41,6 @@ Repository = "https://github.com/JnliaH/ChromaQuant"
 
 [tool.hatch.build.targets.sdist]
 include	= [
-	"/forms",
-	"/images",
-	"/resources",
-	"/response-factors",
 	"/src",
 	"CONTRIBUTING.md",
 	"README.md",
@@ -58,20 +50,15 @@ include	= [
 
 exclude = [
 	"/__pycache__",
-	"/appdist",
-	"/build",
-	"/data",
-	"/shells",
-	"/spec",
-	"ChromaQuantIcon.icns",
-]
+	"/dist",
+	"/.venv",
+	"/.conda",
 
-[tool.hatch.version]
-path = "src/chromaquant/__main__.py"
+]
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/chromaquant"]
 
-[project.gui-scripts]
-chroma-ui = "chromaquant.__main__:runUI"
-
+[pytest]
+addopts = ["--import-mode=importlib"]
+testpaths = ["tests"]

chromaquant-0.5.0/src/chromaquant/__init__.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+chromaquant.utils package initialization
+
+Julia Hancock
+Created 10-20-2024
+
+"""
+
+from .results import Results
+from .formula import Formula
+from .match import MatchConfig
+from .data import Table
+from .data import Value
+from .data import Breakdown

chromaquant-0.5.0/src/chromaquant/data/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+ChromaQuant.data module initialization
+
+Julia Hancock
+Created 10-19-2024
+
+"""
+
+from .table import Table
+from .value import Value
+from .breakdown import Breakdown