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refactoring and fixes for MAT model parsing (#1220)
* changes in mat.py to read with the right terms changes to sbml.py to read annotations as list improved validate.py so it won't fail with new files modified annotation.xml, e_coli_core.xml to have more correct XML files and less errors compared to mat file modified true values in test_annotation.py and test_sbml.py * updated pickles got sbml to add the SBO term for subsystem updated wrong_key_caps.mat file and the associated test * tidying of mat.py mostly from_mat_struct() minor tidying of sbml.py, test_mat.py some tidying and flake8 correction of test_sbml.py * modified example_notes.xml to have no difference when saving/reading to MATLAB Fixed some issues in mat.py Made SBML read groups into subsystem. Made SBML have group annotations as list * subsystems should have group name if availabe SBML will set undefined formula and model name as None * black and updated pickles * forgot black on one file * fix gitignore * reverted list changes as discussed * changes in annotation of files * corrected according to comments * fixed typo Co-authored-by: uri.akavia <[email protected]>
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‎release-notes/next-release.md‎

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## Fixes
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* Reformatted example files (e_coli_core.xml, mini_cobra.xml, mini.json, mini.yml, textbook.xml.gz) to be more compliant with identifiers.org. ncbigi is not a valid identifiers.org, so it was replaced with ncbiprotein.
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* make sbml.py subsystem reading add partonomy, which matches the definition
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of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
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* Correct reading and writing of subsystem in mat.
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* General cleanup of code in mat.py
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## Other
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* Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (#1212).

‎src/cobra/data/mini.json‎

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},
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{
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"annotation": {
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"ncbigi": [
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"GI:1208453",
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"GI:1652654"
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"ncbiprotein": [
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"1652654"
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{
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"annotation": {
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"ncbiprotein": "1653839"
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"id": "b2779",
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"annotation": {
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"ncbiprotein": "1653609"
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"annotation": {
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},
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{
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"annotation": {
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"ncbigi": "GI:1653253"
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"ncbiprotein": "1653253"
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"pyr_c": 1.0
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"name": "D-lactate dehydrogenase",
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"subsystem": "Pyruvate Metabolism",
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"upper_bound": 1000.0
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},
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{

‎src/cobra/data/mini.mat‎

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‎src/cobra/data/mini.pickle‎

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‎src/cobra/data/mini.yml‎

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- lower_bound: -1000.0
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- gene_reaction_rule: b2133 or b1380
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- subsystem: Pyruvate Metabolism
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- annotation: !!omap
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- bigg.reaction: LDH_D
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- id: b1676
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- annotation: !!omap
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- ncbigi:
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- ncbiprotein:
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- annotation: !!omap
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- ncbiprotein: '1653839'
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‎src/cobra/data/mini_cobra.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" sboTerm="SBO:0000624" level="3" version="1" fbc:required="false">
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<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">
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<model metaid="meta_mini_textbook" id="mini_textbook" fbc:strict="true">
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<listOfUnitDefinitions>
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<unitDefinition id="mmol_per_gDW_per_hr">
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‎src/cobra/data/textbook.xml.gz‎

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