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Mat cleanup #1220

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merged 12 commits into from
Jul 5, 2022
Merged

Mat cleanup #1220

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c14b306
changes in mat.py to read with the right terms
Apr 27, 2022
a9d7f18
updated pickles
Apr 27, 2022
a77f773
tidying of mat.py mostly from_mat_struct()
May 4, 2022
219360b
modified example_notes.xml to have no difference when saving/reading …
May 5, 2022
307ec41
subsystems should have group name if availabe
May 5, 2022
77a1359
black and updated pickles
May 10, 2022
f6244f2
forgot black on one file
May 10, 2022
ffd375a
fix gitignore
Jun 19, 2022
f47a655
reverted list changes as discussed
Jun 28, 2022
878486e
changes in annotation of files
Jun 28, 2022
c9c84d0
corrected according to comments
Jul 1, 2022
ee4842b
fixed typo
Jul 1, 2022
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -92,6 +92,7 @@ ipython_config.py
.idea/**/usage.statistics.xml
.idea/**/dictionaries
.idea/**/shelf
.idea/

# Generated files
.idea/**/contentModel.xml
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6 changes: 6 additions & 0 deletions release-notes/next-release.md
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Expand Up @@ -4,6 +4,12 @@

## Fixes

* 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.
* make sbml.py subsystem reading add partonomy, which matches the definition
of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
* Correct reading and writing of subysstem in mat.
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* General cleanup of code in mat.py

## Other

* Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (#1212).
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19 changes: 10 additions & 9 deletions src/cobra/data/mini.json
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Expand Up @@ -26,9 +26,9 @@
},
{
"annotation": {
"ncbigi": [
"GI:1208453",
"GI:1652654"
"ncbiprotein": [
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What's the difference between the mini.json in src/cobra/data and the one in tests/data. Couldn't the tests just use the first one?

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None.
The tests are using the one in tests, because that's how the functions are designed. The ones in src/cobra/data are example files for users installing cobra without development and without tests.
If we want to have tests rely on the files in src/cobra/data we can rewrite tests and update_pickles.py, which I'd be happy to do in a different PR.

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That sounds good to me 👍

"1208453",
"1652654"
]
},
"id": "b1676",
Expand Down Expand Up @@ -84,7 +84,7 @@
},
{
"annotation": {
"ncbigi": "GI:1653839"
"ncbiprotein": "1653839"
},
"id": "b2779",
"name": "eno"
Expand All @@ -95,7 +95,7 @@
},
{
"annotation": {
"ncbigi": "GI:1653609"
"ncbiprotein": "1653609"
},
"id": "b2926",
"name": "pgk"
Expand All @@ -114,9 +114,9 @@
},
{
"annotation": {
"ncbigi": [
"GI:1006614",
"GI:1651919"
"ncbiprotein": [
"1006614",
"1651919"
]
},
"id": "b3916",
Expand All @@ -128,7 +128,7 @@
},
{
"annotation": {
"ncbigi": "GI:1653253"
"ncbiprotein": "1653253"
},
"id": "b4025",
"name": "pgi"
Expand Down Expand Up @@ -1278,6 +1278,7 @@
"pyr_c": 1.0
},
"name": "D-lactate dehydrogenase",
"subsystem": "Pyruvate Metabolism",
"upper_bound": 1000.0
},
{
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19 changes: 10 additions & 9 deletions src/cobra/data/mini.yml
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Expand Up @@ -960,6 +960,7 @@
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2133 or b1380
- subsystem: Pyruvate Metabolism
- annotation: !!omap
- bigg.reaction: LDH_D
- biocyc: META:DLACTDEHYDROGNAD-RXN
Expand Down Expand Up @@ -1080,9 +1081,9 @@
- id: b1676
- name: pykF
- annotation: !!omap
- ncbigi:
- GI:1208453
- GI:1652654
- ncbiprotein:
- '1208453'
- '1652654'
- !!omap
- id: b1723
- name: pfkB
Expand Down Expand Up @@ -1123,15 +1124,15 @@
- id: b2779
- name: eno
- annotation: !!omap
- ncbigi: GI:1653839
- ncbiprotein: '1653839'
- !!omap
- id: b2925
- name: fbaA
- !!omap
- id: b2926
- name: pgk
- annotation: !!omap
- ncbigi: GI:1653609
- ncbiprotein: '1653609'
- !!omap
- id: b2987
- name: pitB
Expand All @@ -1145,17 +1146,17 @@
- id: b3916
- name: pfkA
- annotation: !!omap
- ncbigi:
- GI:1006614
- GI:1651919
- ncbiprotein:
- '1006614'
- '1651919'
- !!omap
- id: b3919
- name: tpiA
- !!omap
- id: b4025
- name: pgi
- annotation: !!omap
- ncbigi: GI:1653253
- ncbiprotein: '1653253'
- !!omap
- id: b4395
- name: ytjC
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16 changes: 8 additions & 8 deletions src/cobra/data/mini_cobra.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<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">
<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" id="mini_textbook" fbc:strict="true">
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
Expand Down Expand Up @@ -1333,8 +1333,8 @@
<rdf:Description rdf:about="#meta_G_b1676">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1208453"/>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1652654"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1208453"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1652654"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand All @@ -1359,7 +1359,7 @@
<rdf:Description rdf:about="#meta_G_b2779">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1653839"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653839"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand All @@ -1373,7 +1373,7 @@
<rdf:Description rdf:about="#meta_G_b2926">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1653609"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653609"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand All @@ -1389,8 +1389,8 @@
<rdf:Description rdf:about="#meta_G_b3916">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1006614"/>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1651919"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1006614"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1651919"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand All @@ -1404,7 +1404,7 @@
<rdf:Description rdf:about="#meta_G_b4025">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ncbigi/GI:1653253"/>
<rdf:li rdf:resource="https://identifiers.org/ncbiprotein/1653253"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
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