[med-svn] [Git][med-team/python-cobra][upstream] New upstream version 0.26.2
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Feb 5 21:16:39 GMT 2023
Étienne Mollier pushed to branch upstream at Debian Med / python-cobra
Commits:
3de80761 by Étienne Mollier at 2023-02-05T21:49:10+01:00
New upstream version 0.26.2
- - - - -
13 changed files:
- + .readthedocs.yaml
- INSTALL.rst
- documentation_builder/conf.py
- documentation_builder/index.rst
- documentation_builder/requirements.txt
- + release-notes/0.26.1.md
- + release-notes/0.26.2.md
- setup.cfg
- setup.py
- src/cobra/__init__.py
- src/cobra/io/sbml.py
- + tests/data/mini_history.xml
- tests/test_io/test_sbml.py
Changes:
=====================================
.readthedocs.yaml
=====================================
@@ -0,0 +1,31 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+ os: ubuntu-22.04
+ tools:
+ python: "3.10"
+ # You can also specify other tool versions:
+ # nodejs: "16"
+ # rust: "1.55"
+ # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+ configuration: documentation_builder/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+# - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+ install:
+ - requirements: documentation_builder/requirements.txt
+ - method: pip
+ path: .
=====================================
INSTALL.rst
=====================================
@@ -6,9 +6,9 @@ For installation help, please use the `Google Group
<http://groups.google.com/group/cobra-pie>`_. For usage instructions, please see
the `documentation <https://cobrapy.readthedocs.org/en/latest/>`_.
-We only test against Python 3.6+, however, Python 3.4 or higher and even 2.7
-should work mostly. For Windows users and possibly also Mac OS users, we
-recommend using the `Anaconda Python <https://www.anaconda.com/>`_ distribution.
+We only test against Python 3.7+, however, Python 3.4 or higher work mostly.
+For Windows users and possibly also Mac OS users, we recommend using the
+`Anaconda Python <https://www.anaconda.com/>`_ distribution.
Stable version installation
===========================
=====================================
documentation_builder/conf.py
=====================================
@@ -36,7 +36,11 @@ extensions = [
"nbsphinx",
]
# Document Python Code
-autoapi_dirs = [SRC_PATH]
+autoapi_dirs = [join(SRC_PATH, "cobra")]
+autoapi_add_toctree_entry = False
+
+# Enable typehints
+autodoc_typehints = "signature"
# Napoleon settings
napoleon_numpy_docstring = True
@@ -46,7 +50,7 @@ master_doc = "index"
# General information about the project.
project = "cobra"
-copyright = "2016-2019, The cobrapy core team"
+copyright = "2016-2022, The cobrapy core team"
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
=====================================
documentation_builder/index.rst
=====================================
@@ -2,14 +2,14 @@ Documentation for COBRApy
=========================
For installation instructions, please see `INSTALL.rst
-<https://github.com/opencobra/cobrapy/blob/stable/INSTALL.rst>`_.
+<https://github.com/opencobra/cobrapy/blob/devel/INSTALL.rst>`_.
Many of the examples below are viewable as IPython notebooks, which can
be viewed at `nbviewer
<http://nbviewer.ipython.org/github/opencobra/cobrapy/tree/stable/documentation_builder/>`_.
.. toctree::
- :numbered:
+ :numbered: 3
:maxdepth: 2
getting_started
@@ -29,7 +29,7 @@ be viewed at `nbviewer
dfba
pymatbridge
faq
- _autogen/modules
+ API </autoapi/cobra/index.rst>
Indices and tables
=====================================
documentation_builder/requirements.txt
=====================================
@@ -1,4 +1,4 @@
-Sphinx~=2.2
+Sphinx~=5.3
sphinxcontrib-napoleon
sphinx-autoapi
nbsphinx>=0.2.4
=====================================
release-notes/0.26.1.md
=====================================
@@ -0,0 +1,18 @@
+# Release notes for cobrapy 0.26.1
+
+## New features
+
+## Fixes
+
+Fix automatic building of the documentation.
+
+Fix an issue where SBML models with a "created" date would break lots of the cobrapy
+functionality.
+
+Temporary fix of restricting numpy to <1.24 as that release introduces breaking changes both in cobrapy and dependencies
+
+## Other
+
+## Deprecated features
+
+## Backwards incompatible changes
=====================================
release-notes/0.26.2.md
=====================================
@@ -0,0 +1,13 @@
+# Release notes for cobrapy x.y.z
+
+## New features
+
+## Fixes
+
+Fix the version numbers, my bad - cd
+
+## Other
+
+## Deprecated features
+
+## Backwards incompatible changes
=====================================
setup.cfg
=====================================
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 0.26.0
+current_version = 0.26.2
commit = True
tag = True
parse = (?P<major>\d+)
@@ -60,7 +60,7 @@ install_requires =
future
httpx ~=0.14
importlib_resources
- numpy ~=1.13
+ numpy >=1.13,<1.24
optlang ~=1.5
pandas ~=1.0
pydantic ~=1.6
=====================================
setup.py
=====================================
@@ -19,4 +19,4 @@ if version_info[:2] < (3, 6):
# All other arguments are defined in `setup.cfg`.
if __name__ == "__main__":
- setup(version="0.26.0")
+ setup(version="0.26.2")
=====================================
src/cobra/__init__.py
=====================================
@@ -1,5 +1,5 @@
__author__ = "The cobrapy core development team."
-__version__ = "0.26.0"
+__version__ = "0.26.2"
from cobra.core import (
=====================================
src/cobra/io/sbml.py
=====================================
@@ -606,7 +606,7 @@ def _sbml_to_model(
history: "libsbml.ModelHistory" = model.getModelHistory()
if history.isSetCreatedDate():
- created = history.getCreatedDate()
+ created = history.getCreatedDate().getDateAsString()
c: "libsbml.ModelCreator"
for c in history.getListCreators():
@@ -1237,7 +1237,7 @@ def _model_to_sbml(
history: "libsbml.ModelHistory" = libsbml.ModelHistory()
if "created" in meta and meta["created"]:
- history.setCreatedDate(meta["created"])
+ history.setCreatedDate(libsbml.Date(meta["created"]))
else:
time = datetime.datetime.now()
timestr = time.strftime("%Y-%m-%dT%H:%M:%S")
=====================================
tests/data/mini_history.xml
=====================================
@@ -0,0 +1,1449 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" sboTerm="SBO:0000624" level="3" version="1" fbc:required="false">
+ <model metaid="meta_mini_textbook_history" id="mini_textbook" fbc:strict="true">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_mini_textbook_history">
+ <dcterms:creator>
+ <rdf:Bag>
+ <rdf:li rdf:parseType="Resource">
+ <vCard:ORG rdf:parseType="Resource">
+ <vCard:Orgname>The COBRAPY core development team</vCard:Orgname>
+ </vCard:ORG>
+ </rdf:li>
+ <rdf:li rdf:parseType="Resource">
+ <vCard:N rdf:parseType="Resource">
+ <vCard:Family>Diener</vCard:Family>
+ <vCard:Given>Christian</vCard:Given>
+ </vCard:N>
+ <vCard:EMAIL>mail [at] cdiener.com</vCard:EMAIL>
+ <vCard:ORG rdf:parseType="Resource">
+ <vCard:Orgname>COBRAPY core development team</vCard:Orgname>
+ </vCard:ORG>
+ </rdf:li>
+ </rdf:Bag>
+ </dcterms:creator>
+ <dcterms:created rdf:parseType="Resource">
+ <dcterms:W3CDTF>2022-11-17T11:00:00Z</dcterms:W3CDTF>
+ </dcterms:created>
+ <dcterms:modified rdf:parseType="Resource">
+ <dcterms:W3CDTF>2022-11-17T11:15:00Z</dcterms:W3CDTF>
+ </dcterms:modified>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr">
+ <listOfUnits>
+ <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+ <unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
+ <unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" name="cytosol" constant="true"/>
+ <compartment id="e" name="extracellular" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species metaid="meta_M_13dpg_c" id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4" fbc:chemicalFormula="C3H4O10P2">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_M_13dpg_c">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/13dpg"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/DPG"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:16001"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:1658"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:20189"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57604"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11881"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01270"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00236"/>
+ <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3535"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_29800"/>
+ <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00203"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00236"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_2pg_c" id="M_2pg_c" name="D-Glycerate 2-phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_M_2pg_c">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/2pg"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/2-PG"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:1267"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:58289"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:17835"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:21028"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11651"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:12986"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:24344"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:39868"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB03391"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB00362"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00631"/>
+ <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3904"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_30485"/>
+ <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00482"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00631"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_3pg_c" id="M_3pg_c" name="3-Phospho-D-glycerate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_M_3pg_c">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/3pg"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/G3P"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:40016"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:58272"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57998"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11879"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:1657"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:1659"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:17050"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:21029"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11882"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:11880"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:12987"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:17794"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:24345"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB00807"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00197"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00597"/>
+ <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3497"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_29728"/>
+ <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00169"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00597"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00197"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_adp_c" id="M_adp_c" name="ADP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C10H12N5O10P2">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_M_adp_c">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/adp"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/ADP"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/ADP-GROUP"/>
+ <rdf:li rdf:resource="https://identifiers.org/cas/58-64-0"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13222"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:16761"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:2342"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22244"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:40553"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:456216"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB01341"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00008"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.glycan/G11113"/>
+ <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3310"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_190072"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_481002"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_211606"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_429160"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_29370"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_196180"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_113581"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_113582"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_114564"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_114565"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_429153"/>
+ <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00008"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00008"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_atp_c" id="M_atp_c" name="ATP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_M_atp_c">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/atp"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/ATP"/>
+ <rdf:li rdf:resource="https://identifiers.org/cas/56-65-5"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:40938"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15422"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:57299"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13236"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10789"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:30616"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22249"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10841"/>
+ <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:2359"/>
+ <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB00538"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00002"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.drug/D08646"/>
+ <rdf:li rdf:resource="https://identifiers.org/pubchem.substance/3304"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_190078"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_113592"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_113593"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_114570"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_29358"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_389573"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_139836"/>
+ <rdf:li rdf:resource="https://identifiers.org/reactome/REACT_211579"/>
+ <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00002"/>
+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00002"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_dhap_c" id="M_dhap_c" name="Dihydroxyacetone phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P">
+ <annotation>
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+ </annotation>
+ </species>
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+ <rdf:Description rdf:about="#meta_M_pi_e">
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+ <rdf:li rdf:resource="https://identifiers.org/biocyc/PHOSPHATE-GROUP"/>
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+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00009"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ <species metaid="meta_M_pyr_c" id="M_pyr_c" name="Pyruvate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C3H3O3">
+ <annotation>
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+ <rdf:Description rdf:about="#meta_M_pyr_c">
+ <bqbiol:is>
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+ <rdf:li rdf:resource="https://identifiers.org/biocyc/PYRUVATE"/>
+ <rdf:li rdf:resource="https://identifiers.org/cas/127-17-3"/>
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+ <rdf:li rdf:resource="https://identifiers.org/unipathway.compound/UPC00022"/>
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+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/>
+ <parameter sboTerm="SBO:0000626" id="cobra_default_ub" value="1000" constant="true"/>
+ <parameter sboTerm="SBO:0000626" id="cobra_0_bound" value="0" constant="true"/>
+ <parameter sboTerm="SBO:0000626" id="minus_inf" value="-INF" constant="true"/>
+ <parameter sboTerm="SBO:0000626" id="plus_inf" value="INF" constant="true"/>
+ <parameter sboTerm="SBO:0000625" id="R_ATPM_lower_bound" value="8.39" units="mmol_per_gDW_per_hr" constant="true"/>
+ <parameter sboTerm="SBO:0000625" id="R_EX_glc__D_e_lower_bound" value="-10" units="mmol_per_gDW_per_hr" constant="true"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction metaid="meta_R_ATPM" id="R_ATPM" name="ATP maintenance requirement" reversible="false" fast="false" fbc:lowerFluxBound="R_ATPM_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
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+ <rdf:Description rdf:about="#meta_R_ATPM">
+ <bqbiol:is>
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+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_D_LACt2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"/>
+ <reaction metaid="meta_R_ENO" id="R_ENO" name="enolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_ENO">
+ <bqbiol:is>
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+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2779"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_EX_glc__D_e" sboTerm="SBO:0000627" id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true" fast="false" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_EX_glc__D_e">
+ <bqbiol:is>
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+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction metaid="meta_R_EX_h_e" sboTerm="SBO:0000627" id="R_EX_h_e" name="H+ exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
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+ <rdf:Description rdf:about="#meta_R_EX_h_e">
+ <bqbiol:is>
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+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction metaid="meta_R_EX_lac__D_e" sboTerm="SBO:0000627" id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_EX_lac__D_e">
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+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/lac__D"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ <reaction metaid="meta_R_FBA" id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_FBA">
+ <bqbiol:is>
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+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
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+ <fbc:geneProductRef fbc:geneProduct="G_b2925"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_GAPD" id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_GAPD">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GAPD"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1779"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_GLCpts" id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_GLCpts">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLCpts"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1101"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1621"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1818"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1819"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b2416"/>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_H2Ot" id="R_H2Ot" name="R H2O transport via - diffusion" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_H2Ot">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/H2Ot"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0875"/>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_LDH_D" sboTerm="SBO:0000375" id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_LDH_D">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/LDH_D"/>
+ <rdf:li rdf:resource="https://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN"/>
+ <rdf:li rdf:resource="https://identifiers.org/ec-code/1.1.1.28"/>
+ <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R00704"/>
+ <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR101037"/>
+ <rdf:li rdf:resource="https://identifiers.org/rhea/16369"/>
+ <rdf:li rdf:resource="https://identifiers.org/rhea/16370"/>
+ <rdf:li rdf:resource="https://identifiers.org/rhea/16371"/>
+ <rdf:li rdf:resource="https://identifiers.org/rhea/16372"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2133"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1380"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PFK" id="R_PFK" name="phosphofructokinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PFK">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PFK"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1723"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PGI" id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PGI">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGI"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4025"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PGK" id="R_PGK" name="phosphoglycerate kinase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PGK">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGK"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2926"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PGM" id="R_PGM" name="phosphoglycerate mutase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PGM">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PGM"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4395"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b3612"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b0755"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PIt2r" id="R_PIt2r" name="R phosphate reversible transport via - symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PIt2r">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PIt2r"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2987"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b3493"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_PYK" id="R_PYK" name="pyruvate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_PYK">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PYK"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1854"/>
+ <fbc:geneProductRef fbc:geneProduct="G_b1676"/>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction metaid="meta_R_TPI" id="R_TPI" name="triose-phosphate isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_R_TPI">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/TPI"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ <listOfReactants>
+ <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3919"/>
+ </fbc:geneProductAssociation>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfObjectives fbc:activeObjective="obj">
+ <fbc:objective fbc:id="obj" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:reaction="R_ATPM" fbc:coefficient="1"/>
+ <fbc:fluxObjective fbc:reaction="R_PFK" fbc:coefficient="1"/>
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ <fbc:listOfGeneProducts>
+ <fbc:geneProduct fbc:id="G_b0755" fbc:name="gpmA" fbc:label="G_b0755"/>
+ <fbc:geneProduct fbc:id="G_b0875" fbc:name="aqpZ" fbc:label="G_b0875"/>
+ <fbc:geneProduct fbc:id="G_b1101" fbc:name="ptsG" fbc:label="G_b1101"/>
+ <fbc:geneProduct fbc:id="G_b1380" fbc:name="ldhA" fbc:label="G_b1380"/>
+ <fbc:geneProduct fbc:id="G_b1621" fbc:name="malX" fbc:label="G_b1621"/>
+ <fbc:geneProduct metaid="meta_G_b1676" fbc:id="G_b1676" fbc:name="pykF" fbc:label="G_b1676">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_G_b1676">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1208453"/>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652654"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct fbc:id="G_b1723" fbc:name="pfkB" fbc:label="G_b1723"/>
+ <fbc:geneProduct fbc:id="G_b1773" fbc:name="ydjI" fbc:label="G_b1773"/>
+ <fbc:geneProduct fbc:id="G_b1779" fbc:name="gapA" fbc:label="G_b1779"/>
+ <fbc:geneProduct fbc:id="G_b1817" fbc:name="manX" fbc:label="G_b1817"/>
+ <fbc:geneProduct fbc:id="G_b1818" fbc:name="manY" fbc:label="G_b1818"/>
+ <fbc:geneProduct fbc:id="G_b1819" fbc:name="manZ" fbc:label="G_b1819"/>
+ <fbc:geneProduct fbc:id="G_b1854" fbc:name="pykA" fbc:label="G_b1854"/>
+ <fbc:geneProduct fbc:id="G_b2097" fbc:name="fbaB" fbc:label="G_b2097"/>
+ <fbc:geneProduct fbc:id="G_b2133" fbc:name="dld" fbc:label="G_b2133"/>
+ <fbc:geneProduct fbc:id="G_b2415" fbc:name="ptsH" fbc:label="G_b2415"/>
+ <fbc:geneProduct fbc:id="G_b2416" fbc:name="ptsI" fbc:label="G_b2416"/>
+ <fbc:geneProduct fbc:id="G_b2417" fbc:name="crr" fbc:label="G_b2417"/>
+ <fbc:geneProduct metaid="meta_G_b2779" fbc:id="G_b2779" fbc:name="eno" fbc:label="G_b2779">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_G_b2779">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653839"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct fbc:id="G_b2925" fbc:name="fbaA" fbc:label="G_b2925"/>
+ <fbc:geneProduct metaid="meta_G_b2926" fbc:id="G_b2926" fbc:name="pgk" fbc:label="G_b2926">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_G_b2926">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653609"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct fbc:id="G_b2987" fbc:name="pitB" fbc:label="G_b2987"/>
+ <fbc:geneProduct fbc:id="G_b3493" fbc:name="pitA" fbc:label="G_b3493"/>
+ <fbc:geneProduct fbc:id="G_b3612" fbc:name="gpmM" fbc:label="G_b3612"/>
+ <fbc:geneProduct metaid="meta_G_b3916" fbc:id="G_b3916" fbc:name="pfkA" fbc:label="G_b3916">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_G_b3916">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1006614"/>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1651919"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct fbc:id="G_b3919" fbc:name="tpiA" fbc:label="G_b3919"/>
+ <fbc:geneProduct metaid="meta_G_b4025" fbc:id="G_b4025" fbc:name="pgi" fbc:label="G_b4025">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#meta_G_b4025">
+ <bqbiol:is>
+ <rdf:Bag>
+ <rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653253"/>
+ </rdf:Bag>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </fbc:geneProduct>
+ <fbc:geneProduct fbc:id="G_b4395" fbc:name="ytjC" fbc:label="G_b4395"/>
+ <fbc:geneProduct fbc:id="G_s0001" fbc:name="G_s0001" fbc:label="G_s0001"/>
+ </fbc:listOfGeneProducts>
+ </model>
+</sbml>
=====================================
tests/test_io/test_sbml.py
=====================================
@@ -704,3 +704,13 @@ def test_stable_gprs(data_directory: Path, tmp_path: Path) -> None:
assert (
fixed_model.reactions.GLCpts.gene_reaction_rule == "(b2415 and b2417) or b2416"
)
+
+
+def test_history(data_directory: Path) -> None:
+ """Test that the history is read from the model."""
+ mini = read_sbml_model(join(data_directory, "mini_history.xml"))
+ assert "creators" in mini._sbml
+ assert "organisation" in mini._sbml["creators"][0]
+ assert "created" in mini._sbml
+ assert isinstance(mini._sbml["created"], str)
+ assert "2022" in mini._sbml["created"]
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/3de80761171b971f88e473d8fd685b45cd3069a3
--
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/3de80761171b971f88e473d8fd685b45cd3069a3
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