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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy
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freiburgermsu committed Aug 24, 2023
2 parents 0afb525 + af1a4e6 commit 494e45d
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28 changes: 15 additions & 13 deletions docs/conf.py
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Expand Up @@ -40,8 +40,8 @@
master_doc = "index"

# General information about the project.
project = "sample"
copyright = "2012, Kenneth Reitz"
project = "ModelSEEDpy"
copyright = "2023, Henry Lab"

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
Expand Down Expand Up @@ -181,7 +181,7 @@
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
("index", "sample.tex", "sample Documentation", "Kenneth Reitz", "manual"),
# ("index", "sample.tex", "sample Documentation", "Kenneth Reitz", "manual"),
]

# The name of an image file (relative to this directory) to place at the top of
Expand Down Expand Up @@ -209,7 +209,9 @@

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [("index", "sample", "sample Documentation", ["Kenneth Reitz"], 1)]
man_pages = [
# ("index", "sample", "sample Documentation", ["Kenneth Reitz"], 1)
]

# If true, show URL addresses after external links.
# man_show_urls = False
Expand All @@ -221,15 +223,15 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(
"index",
"sample",
"sample Documentation",
"Kenneth Reitz",
"sample",
"One line description of project.",
"Miscellaneous",
),
# (
# "index",
# "sample",
# "sample Documentation",
# "Kenneth Reitz",
# "sample",
# "One line description of project.",
# "Miscellaneous",
# ),
]

# Documents to append as an appendix to all manuals.
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4 changes: 2 additions & 2 deletions docs/source/community/mssmetana_api.rst
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Expand Up @@ -143,14 +143,14 @@ All of the defined scores can be simulated on the initalized community system th
--------------------------
kbase_output()
report_generation()
--------------------------

The scores can be calculated over a large range of models, either for specified pairs or for all combinations of all models. This process can be expedited with optional parallelization. This function is a **Staticmethod**, and therefore cannot access any content that is loaded in the class object of the aforementioned functions.

.. code-block:: python
scores_df, mets = mssmet.kbase_output(all_models:iter=None, pairs:dict=None, mem_media:dict=None,
scores_df, mets = mssmet.report_generation(all_models:iter=None, pairs:dict=None, mem_media:dict=None,
pair_limit:int=None, exclude_pairs:list=None, kbase_obj=None,
RAST_genomes:dict=None, see_media:bool=True,
environment:Union[dict]=None, # can be KBase media object
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2 changes: 1 addition & 1 deletion examples/Community Modeling/smetana/10-member_pairs_dev.ipynb
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Expand Up @@ -8092,7 +8092,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.9.12"
}
},
"nbformat": 4,
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16,410 changes: 16,286 additions & 124 deletions examples/Community Modeling/smetana/Vorholt_replication.ipynb
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56 changes: 56 additions & 0 deletions examples/Community Modeling/smetana/commscores_report.csv
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@@ -0,0 +1,56 @@
,model1,model2,media,model1 growth,model2 growth,community growth,MRO_model1,MRO_model2,CIP,MIP_model1 (costless),MIP_model2 (costless),BSS_model1,BSS_model2,PC_comm,PC_model1,PC_model2,BIT,GYD,FS
0,GCF_001421425.1.RAST.fbamodel,GCF_001423785.1.RAST.fbamodel,R2A_M,134.38,68.376,136.75,72.549% (37/51),82.222% (37/45),24,15 (3),4 (2),73.333%,66.667%,1.2025,1.0461,1.414,commensalism,0.35172,0.25651
1,GCF_001421425.1.RAST.fbamodel,GCF_001423565.1_Leaf145.fna_genome.fbamodel,R2A_M,65.365,48.135,96.27,64.706% (33/51),66.000% (33/50),21,1 (0),7 (3),78.0%,23.529%,0.85052,0.7364,1.0065,amensalism,0.36681,0.0
2,GCF_001421425.1.RAST.fbamodel,GCF_001422185.1.RAST.fbamodel,R2A_M,65.365,120.25,113.65,68.627% (35/51),92.105% (35/38),25,9 (3),3 (0),71.053%,68.627%,1.0277,0.86933,1.2567,parasitism,0.44565,0.34021
3,GCF_001421425.1.RAST.fbamodel,GCF_001421805.1.RAST.fbamodel,R2A_M,65.365,86.809,136.45,70.588% (36/51),76.596% (36/47),24,8 (3),2 (0),72.34%,68.627%,1.1348,1.0437,1.2434,commensalism,0.19126,0.34713
4,GCF_001421425.1.RAST.fbamodel,GCF_001421235.1_Leaf202.fna_genome.fbamodel,R2A_M,65.365,49.604,99.208,64.706% (33/51),68.750% (33/48),22,1 (1),7 (5),77.083%,19.608%,0.86576,0.75888,1.0077,amensalism,0.32786,0.0
5,GCF_001421425.1.RAST.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,65.365,51.069,92.928,64.706% (33/51),80.488% (33/41),24,11 (3),1 (1),78.049%,66.667%,0.84274,0.71083,1.0348,amensalism,0.45571,0.25436
6,GCF_001421425.1.RAST.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,65.365,59.161,118.32,68.627% (35/51),87.500% (35/40),21,11 (2),5 (2),75.0%,60.784%,1.8102,0.90509,,,,0.25368
7,GCF_001421425.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,65.365,92.093,138.0,74.510% (38/51),86.364% (38/44),25,11 (3),1 (1),70.455%,70.588%,1.1213,1.0556,1.1958,commensalism,0.13278,0.29827
8,GCF_001421425.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,65.365,63.018,126.04,66.667% (34/51),79.070% (34/43),23,9 (4),4 (1),72.093%,64.706%,1.0196,0.96408,1.0819,neutral,0.12222,0.25098
9,GCF_001421425.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,65.365,77.067,116.7,68.627% (35/51),77.778% (35/45),25,11 (3),3 (1),71.111%,68.627%,0.99996,0.89269,1.1365,parasitism,0.27317,0.25079
10,GCF_001423785.1.RAST.fbamodel,GCF_001423565.1_Leaf145.fna_genome.fbamodel,R2A_M,48.357,47.823,75.233,75.556% (34/45),68.000% (34/50),17,0 (0),5 (4),76.0%,33.333%,0.7822,0.77789,0.78657,competitive,0.011165,0.0
11,GCF_001423785.1.RAST.fbamodel,GCF_001422185.1.RAST.fbamodel,R2A_M,48.357,45.215,57.532,75.556% (34/45),89.474% (34/38),14,2 (1),4 (2),65.789%,71.111%,0.61484,0.59486,0.6362,competitive,0.06949,0.30249
12,GCF_001423785.1.RAST.fbamodel,GCF_001421805.1.RAST.fbamodel,R2A_M,48.357,54.871,69.48,80.000% (36/45),76.596% (36/47),17,2 (0),2 (1),68.085%,71.111%,0.67307,0.7184,0.63313,competitive,0.13469,0.30467
13,GCF_001423785.1.RAST.fbamodel,GCF_001421235.1_Leaf202.fna_genome.fbamodel,R2A_M,48.357,49.226,77.328,71.111% (32/45),66.667% (32/48),16,0 (0),5 (3),75.0%,28.889%,0.79243,0.79955,0.78544,competitive,0.017963,0.0
14,GCF_001423785.1.RAST.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,48.357,44.903,66.836,82.222% (37/45),90.244% (37/41),18,1 (1),1 (1),75.61%,66.667%,0.71666,0.69106,0.74423,competitive,0.076938,0.58231
15,GCF_001423785.1.RAST.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,48.357,0.0,0.0,84.444% (38/45),95.000% (38/40),17,,,70.0%,66.667%,0.0,0.0,,,,0.59298
16,GCF_001423785.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,48.357,57.704,60.993,86.667% (39/45),88.636% (39/44),16,3 (0),2 (1),63.636%,71.111%,0.57507,0.63065,0.5285,competitive,0.19327,0.46372
17,GCF_001423785.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,48.357,58.247,74.893,80.000% (36/45),83.721% (36/43),14,1 (1),3 (2),69.767%,64.444%,0.70254,0.77437,0.6429,competitive,0.2045,0.59201
18,GCF_001423785.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,48.357,51.341,57.925,88.889% (40/45),88.889% (40/45),14,2 (1),0 (0),66.667%,68.889%,0.58101,0.59893,0.56413,competitive,0.061693,0.58008
19,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001422185.1.RAST.fbamodel,R2A_M,47.823,45.215,68.732,62.000% (31/50),81.579% (31/38),14,4 (3),1 (0),26.316%,78.0%,0.73875,0.71861,0.76005,competitive,0.05768,0.0
20,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001421805.1.RAST.fbamodel,R2A_M,47.823,54.871,82.273,78.000% (39/50),82.979% (39/47),18,4 (3),0 (0),29.787%,78.0%,0.80115,0.86018,0.7497,competitive,0.14736,0.0
21,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001421235.1_Leaf202.fna_genome.fbamodel,R2A_M,47.823,49.226,68.4,92.000% (46/50),95.833% (46/48),9,0 (0),1 (1),33.333%,34.0%,0.70479,0.71513,0.69475,competitive,0.029329,0.0000
22,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,47.823,44.903,66.849,64.000% (32/50),78.049% (32/41),16,4 (3),1 (1),31.707%,72.0%,0.72093,0.69892,0.74438,competitive,0.065046,0.0
23,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,47.823,0.0,79.029,68.000% (34/50),85.000% (34/40),13,3 (1),1 (1),27.5%,66.0%,1.6525,0.82626,,,,0.0
24,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,47.823,57.704,93.497,66.000% (33/50),75.000% (33/44),17,7 (4),0 (0),25.0%,76.0%,0.886,0.97752,0.81015,amensalism,0.2066,0.0
25,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,47.823,58.247,87.065,68.000% (34/50),79.070% (34/43),16,4 (4),0 (0),30.233%,70.0%,0.82082,0.91027,0.74738,amensalism,0.21795,0.0
26,GCF_001423565.1_Leaf145.fna_genome.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,47.823,51.341,79.785,66.000% (33/50),73.333% (33/45),14,5 (3),1 (1),28.889%,74.0%,0.80458,0.83417,0.77702,competitive,0.073547,0.0
27,GCF_001422185.1.RAST.fbamodel,GCF_001421805.1.RAST.fbamodel,R2A_M,45.215,54.871,58.092,92.105% (35/38),74.468% (35/47),15,1 (0),2 (0),70.213%,68.421%,0.58042,0.64239,0.52936,competitive,0.21354,0.70211
28,GCF_001422185.1.RAST.fbamodel,GCF_001421235.1_Leaf202.fna_genome.fbamodel,R2A_M,45.215,49.226,69.962,84.211% (32/38),66.667% (32/48),15,1 (1),5 (5),75.0%,21.053%,0.74079,0.77365,0.71062,competitive,0.088701,0.0
29,GCF_001422185.1.RAST.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,45.215,44.903,63.188,81.579% (31/38),75.610% (31/41),17,1 (0),2 (0),70.732%,63.158%,0.70117,0.69875,0.70361,competitive,0.006964,0.30959
30,GCF_001422185.1.RAST.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,45.215,0.0,87.414,84.211% (32/38),80.000% (32/40),16,1 (1),2 (2),70.0%,60.526%,1.9333,0.96664,,,,0.31396
31,GCF_001422185.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,45.215,57.704,64.681,92.105% (35/38),79.545% (35/44),15,4 (1),2 (1),65.909%,68.421%,0.62846,0.71525,0.56046,competitive,0.27619,0.30953
32,GCF_001422185.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,45.215,58.247,81.229,86.842% (33/38),76.744% (33/43),16,1 (1),3 (2),69.767%,60.526%,0.78511,0.89824,0.69728,competitive,0.2882,0.30901
33,GCF_001422185.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,45.215,51.341,60.7,84.211% (32/38),71.111% (32/45),14,1 (0),3 (1),68.889%,63.158%,0.62865,0.67123,0.59115,competitive,0.13547,0.31512
34,GCF_001421805.1.RAST.fbamodel,GCF_001421235.1_Leaf202.fna_genome.fbamodel,R2A_M,54.871,49.226,85.141,78.723% (37/47),77.083% (37/48),19,0 (0),4 (3),75.0%,25.532%,0.8179,0.77584,0.8648,competitive,0.11467,0.0
35,GCF_001421805.1.RAST.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,54.871,44.903,71.412,76.596% (36/47),87.805% (36/41),19,3 (3),4 (0),70.732%,65.957%,0.71574,0.65073,0.79519,competitive,0.22199,0.31434
36,GCF_001421805.1.RAST.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,54.871,0.0,98.741,74.468% (35/47),87.500% (35/40),20,1 (0),1 (1),70.0%,55.319%,1.7995,0.89976,,,,0.31926
37,GCF_001421805.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,54.871,57.704,77.358,82.979% (39/47),88.636% (39/44),19,4 (2),2 (0),65.909%,70.213%,0.68718,0.70491,0.67031,competitive,0.051628,0.32014
38,GCF_001421805.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,54.871,58.247,101.57,76.596% (36/47),83.721% (36/43),19,3 (2),4 (4),69.767%,63.83%,0.89795,0.92557,0.87193,amensalism,0.061523,0.31846
39,GCF_001421805.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,54.871,51.341,74.059,76.596% (36/47),80.000% (36/45),16,2 (1),4 (1),68.889%,65.957%,0.69728,0.67485,0.72125,competitive,0.068756,0.32181
40,GCF_001421235.1_Leaf202.fna_genome.fbamodel,GCF_001421165.1.RAST.fbamodel,R2A_M,49.226,44.903,70.18,64.583% (31/48),75.610% (31/41),16,4 (3),1 (1),26.829%,70.833%,0.74558,0.71284,0.78147,competitive,0.096283,0.0
41,GCF_001421235.1_Leaf202.fna_genome.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,49.226,0.0,82.046,68.750% (33/48),82.500% (33/40),12,4 (1),0 (0),22.5%,64.583%,1.6667,0.83336,,,,0.0
42,GCF_001421235.1_Leaf202.fna_genome.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,49.226,57.704,95.129,66.667% (32/48),72.727% (32/44),18,7 (4),0 (0),20.455%,75.0%,0.88964,0.96624,0.82429,amensalism,0.17222,0.0
43,GCF_001421235.1_Leaf202.fna_genome.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,49.226,58.247,89.509,68.750% (33/48),76.744% (33/43),15,2 (2),1 (0),25.581%,68.75%,0.83286,0.90916,0.76836,amensalism,0.18325,0.0
44,GCF_001421235.1_Leaf202.fna_genome.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,49.226,51.341,82.202,64.583% (31/48),68.889% (31/45),14,5 (2),0 (0),24.444%,72.917%,0.81739,0.83495,0.80056,competitive,0.042959,0.0
45,GCF_001421165.1.RAST.fbamodel,GCF_001423105.1.RAST.fbamodel,R2A_M,44.903,0.0,0.0,85.366% (35/41),87.500% (35/40),19,,,67.5%,65.854%,0.0,0.0,,,,0.72642
46,GCF_001421165.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,44.903,57.704,69.139,85.366% (35/41),79.545% (35/44),21,0 (0),4 (3),63.636%,75.61%,0.67383,0.76987,0.59909,competitive,0.28508,0.44533
47,GCF_001421165.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,44.903,58.247,77.23,87.805% (36/41),83.721% (36/43),18,0 (0),3 (3),65.116%,68.293%,0.74872,0.85997,0.66296,competitive,0.29717,0.7819
48,GCF_001421165.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,44.903,51.341,67.706,87.805% (36/41),80.000% (36/45),17,0 (0),3 (3),66.667%,73.171%,0.70348,0.75392,0.65938,competitive,0.14338,0.6918
49,GCF_001423105.1.RAST.fbamodel,GCF_001426165.RAST.fbamodel,R2A_M,0.0,57.704,80.191,92.500% (37/40),84.091% (37/44),19,3 (2),0 (0),61.364%,72.5%,1.3897,,0.69485,,,0.44941
50,GCF_001423105.1.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,0.0,58.247,0.0,92.500% (37/40),86.047% (37/43),16,,,62.791%,65.0%,0.0,,0.0,,,0.73411
51,GCF_001423105.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,0.0,51.341,0.0,92.500% (37/40),82.222% (37/45),15,,,64.444%,70.0%,0.0,,0.0,,,0.70353
52,GCF_001426165.RAST.fbamodel,GCF_001423665.1.RAST.fbamodel,R2A_M,57.704,58.247,75.719,86.364% (38/44),88.372% (38/43),18,2 (2),0 (0),69.767%,61.364%,0.65303,0.6561,0.64999,competitive,0.0094091,0.44441
53,GCF_001426165.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,57.704,51.341,61.254,88.636% (39/44),86.667% (39/45),17,4 (1),1 (0),68.889%,63.636%,0.56173,0.53076,0.59654,competitive,0.12393,0.44873
54,GCF_001423665.1.RAST.fbamodel,GCF_001424595.1.RAST.fbamodel,R2A_M,58.247,51.341,78.647,86.047% (37/43),82.222% (37/45),14,1 (0),2 (2),64.444%,67.442%,0.71767,0.67512,0.76593,competitive,0.13451,0.69979
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