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Testing for conflicts #84

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a061467
Merge pull request #99 from freiburgermsu/patch-1
Fxe Jan 2, 2023
ad70240
Checking in code for biomass reaction built into template
cshenry Jan 12, 2023
72d1ebb
Formatting in black
cshenry Jan 12, 2023
f63ec8a
Merge pull request #103 from cshenry/main
Fxe Jan 12, 2023
5ab95bf
fixes
Fxe Jan 17, 2023
44bba2b
run black
Fxe Jan 17, 2023
b3d6890
Merge pull request #104 from Fxe/dev
Fxe Jan 17, 2023
edc05ba
Minor fixes and adding some utility functionality
cshenry Jan 17, 2023
a4a8321
Merge commit 'b3d6890dbf5088dbd5c25c455218e9871c9f3c42'
cshenry Jan 17, 2023
7ae888a
biomass fix
Fxe Jan 17, 2023
eca4cc0
Merge pull request #105 from Fxe/dev
Fxe Jan 17, 2023
687e4ca
Merge commit 'eca4cc0d01ed551266214f65f0d095b02fef9b12'
cshenry Jan 17, 2023
3cba8e3
updated ML and scikit-learn version
Fxe Jan 18, 2023
2aa8a21
Merge pull request #106 from Fxe/dev
Fxe Jan 18, 2023
e0a7f4f
index fix
Fxe Jan 18, 2023
a27257c
missing import
Fxe Jan 31, 2023
6f4d57c
Merge pull request #109 from Fxe/dev
Fxe Jan 31, 2023
f2eb10e
fixed builder to detect biomass added compounds
Fxe Feb 1, 2023
c4bd08d
Merge pull request #110 from Fxe/dev
Fxe Feb 1, 2023
a858323
notebook update
Fxe Feb 3, 2023
fc5f584
Merge pull request #111 from Fxe/dev
Fxe Feb 3, 2023
f00dbc1
Fixes for new biomass code
cshenry Feb 9, 2023
cd7405f
Merge commit 'fc5f584bdb5f9ae6c1962de7e3d36c95372d33b4'
cshenry Feb 9, 2023
c22a8d6
Formatting with black
cshenry Feb 9, 2023
c61394c
biomass fix
Fxe Feb 14, 2023
dbdaa50
Merge branch 'ModelSEED:dev' into dev
Fxe Feb 14, 2023
0d82999
Merge pull request #114 from Fxe/dev
Fxe Feb 14, 2023
2915d77
bug fix
Fxe Feb 14, 2023
b32b9a2
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Feb 14, 2023
adf6bd0
Merge branch 'ModelSEED:dev' into dev
Fxe Feb 14, 2023
b42a04f
black
Fxe Feb 14, 2023
0e44ec6
Merge pull request #115 from Fxe/dev
Fxe Feb 14, 2023
27d353f
Merge pull request #113 from cshenry/main
Fxe Feb 14, 2023
d33bd9a
Updates to fix gapfilling and string concatenation
cshenry Feb 15, 2023
566b0a0
Merge pull request #116 from cshenry/main
cshenry Feb 15, 2023
906bb3e
genome feature aliases
Fxe Feb 20, 2023
98991c8
Merge branch 'ModelSEED:dev' into dev
Fxe Feb 20, 2023
3461c33
Merge pull request #117 from Fxe/dev
Fxe Feb 20, 2023
26d7b62
template.add_reaction update comcompound references
Fxe Feb 21, 2023
f1b1543
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Feb 21, 2023
218f2a1
Merge pull request #118 from Fxe/dev
Fxe Feb 21, 2023
34b4d81
Improving gapfilling and ATP correction
cshenry Mar 1, 2023
f6ac9a6
Merge commit '218f2a119a400c6ccfed29e92125b7c02e3c9659'
cshenry Mar 1, 2023
54f65d6
Merge pull request #119 from cshenry/main
Fxe Mar 1, 2023
64010b3
template species name
Fxe Mar 1, 2023
972920b
black
Fxe Mar 1, 2023
37f9d99
Merge pull request #120 from Fxe/dev
Fxe Mar 1, 2023
75c464a
x
Fxe Mar 13, 2023
e259296
Merge pull request #121 from Fxe/dev
Fxe Mar 13, 2023
cac909b
template format
Fxe Mar 28, 2023
fbc23f9
Merge branch 'ModelSEED:dev' into dev
Fxe Mar 28, 2023
dbe8c6d
black
Fxe Mar 28, 2023
bc94fd3
Merge pull request #123 from Fxe/dev
Fxe Mar 28, 2023
29e5c4d
examples
Fxe Apr 13, 2023
24ef228
lower/upper case fix
Fxe Apr 18, 2023
177d41f
Merge branch 'dev' of github.com:ModelSEED/ModelSEEDpy into dev
Fxe Apr 18, 2023
cf8fa78
Merge pull request #124 from Fxe/dev
Fxe Apr 18, 2023
b1e7ff4
Implementing multiple gapfill
cshenry May 3, 2023
9a6da45
Fixing test
cshenry May 16, 2023
b6671e7
Merge pull request #125 from cshenry/main
cshenry May 16, 2023
3256ea0
Renaming ATP
cshenry Jun 15, 2023
da33bd2
fixes
Fxe Jun 26, 2023
d13f6c2
black
Fxe Jun 26, 2023
2a9c02c
Merge pull request #126 from Fxe/dev
Fxe Jun 26, 2023
b7edac0
Changing zero threshold on gapfilling
cshenry Jul 2, 2023
97b5d4f
Adding version printing to ModelSEEDpy so I can be sure what version …
cshenry Jul 3, 2023
a27ba8f
Resetting gapfill threshold for zero
cshenry Jul 4, 2023
3dc662b
Restoring small gapfilling threshold
cshenry Jul 4, 2023
7f694bf
Fixing gapfilling target issue
cshenry Jul 4, 2023
a8563df
Fixing bug in ATP correction
cshenry Jul 4, 2023
7cc3c55
Fixing ATP correction
cshenry Jul 4, 2023
e76d824
Fixing ATP correction media selection
cshenry Jul 4, 2023
c456540
Running black
cshenry Jul 4, 2023
cb27e47
Merge pull request #127 from cshenry/main
Fxe Jul 4, 2023
c8b67b5
minor
Fxe Jul 4, 2023
01b9d16
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Jul 4, 2023
1851286
added e0 as extracell search for cobrapy
Fxe Jul 6, 2023
7e0e216
black
Fxe Jul 6, 2023
afcaa7a
pre-commit
Fxe Jul 6, 2023
8d23db0
Merge pull request #128 from Fxe/dev
Fxe Jul 6, 2023
38c5a7a
Fixing threshold and adding empty media and fixing thresholds
cshenry Jul 7, 2023
787c6be
Fixing empty media
cshenry Jul 7, 2023
82fd4a6
Merge branch 'dev' of https://github.com/ModelSEED/ModelSEEDpy
cshenry Jul 7, 2023
2f8aeee
Fixing git ignore
cshenry Jul 7, 2023
91ac499
Making thresholds on tests more flexible, including supporting media …
cshenry Jul 8, 2023
55ae63f
Improving commenting and improving multi gapfilling
cshenry Jul 10, 2023
32c590f
Fixing bug in log message
cshenry Jul 10, 2023
19f9f58
Update atp_medias.tsv
jplfaria Jul 10, 2023
45329c1
Merge pull request #6 from jplfaria/patch-1
Fxe Jul 10, 2023
5239078
Merge branch 'ModelSEED:dev' into dev
Fxe Jul 10, 2023
69d9a8d
Merge pull request #129 from Fxe/dev
Fxe Jul 10, 2023
432aaed
build biomass index fix
Fxe Jul 10, 2023
50714db
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Jul 10, 2023
ccfed7e
Merge pull request #130 from Fxe/dev
Fxe Jul 10, 2023
239ac6e
Fixing various media and element package
cshenry Jul 12, 2023
3f25882
Fixing weird import
cshenry Jul 12, 2023
b0311a3
Improving phenotype simulations and gapfilling
cshenry Jul 13, 2023
ea81a98
Fixing bug
cshenry Jul 13, 2023
abd998c
Adding MSGrowthPhenotype object
cshenry Jul 13, 2023
963f00a
Adding MSGrowthPhenotype
cshenry Jul 13, 2023
0d6e7af
Fixing error in simulate arguments
cshenry Jul 13, 2023
c0abcd1
Fixing attributes, improving phenotypes, improving gapfilling
cshenry Jul 17, 2023
de260ae
Fixing attritbute problem and fixing phenotypes
cshenry Jul 17, 2023
328c578
Improving phenotype simulations and enabling use of complete media
cshenry Jul 18, 2023
084054d
Fixing issue where attributes will be none
cshenry Jul 18, 2023
0d61497
atpcorrection
Fxe Jul 18, 2023
afb94cc
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Jul 18, 2023
b08f8f3
Improving phenotype simulation and making sure parameters are documen…
cshenry Jul 18, 2023
c45f798
Improved phenotype functions
cshenry Jul 22, 2023
a48f398
Removing failed ATP gapfillings from gapfilling sensitivity
cshenry Jul 24, 2023
6dca6d9
Adding ATP gapfilled reactions to gapfilling sensitivity
Jul 24, 2023
1be4674
Fixing bug in gapfill
cshenry Jul 25, 2023
148e3e6
Merge branch 'main' of https://github.com/cshenry/ModelSEEDpy
cshenry Jul 25, 2023
2db54c6
Fixing bug in ATP media
cshenry Jul 26, 2023
ca7cc50
Fixing ATP correction
Jul 26, 2023
dba76e8
Merge branch 'main' of github.com:cshenry/ModelSEEDpy
Jul 26, 2023
03ad8cc
Adding MSModelReport object with Jose's report code
cshenry Jul 26, 2023
81dd30c
Adding filename for report output
cshenry Jul 26, 2023
6507666
Fixing report
cshenry Jul 26, 2023
28c7028
Fixing accuracy and output and baseline growth
cshenry Aug 2, 2023
21efcbc
Fixing gapfilling filter saving and complete media
cshenry Aug 2, 2023
ed04550
Fixing bug in phenotype accuracy computation
cshenry Aug 3, 2023
2649577
Fixing gapfilling filter attribute
cshenry Aug 3, 2023
8c70448
Fixing bug in saving of gapfilling filtering
cshenry Aug 3, 2023
f02a4a7
fixing filter saving in attributes
cshenry Aug 4, 2023
ca7dee2
Removing debugging from filtering code
cshenry Aug 4, 2023
0cdba7c
Adding support for building models from multiple annotations
cshenry Aug 8, 2023
cdea5d6
Fixing gene hash function
cshenry Aug 8, 2023
894cee0
Fixing add feature function
cshenry Aug 8, 2023
47de2c8
Fixing problem with ModelSEEDDatabase reactions
cshenry Aug 8, 2023
951bce1
Fixing annotation ontology and build from annotation ontology
cshenry Aug 10, 2023
be8dcd1
Correcting message output in ontology builder
cshenry Aug 10, 2023
0af0299
Checking in first draft of tempalte
cshenry Aug 17, 2023
58cc3c2
Fixing template
cshenry Aug 17, 2023
39fe14d
Updating template
cshenry Aug 17, 2023
de30b92
Adding probabilities for ensemble models
cshenry Aug 24, 2023
6ee54a2
Fixing bug
cshenry Aug 24, 2023
9c2cff1
Fixing bug in report when gapfilling isn't run
cshenry Aug 24, 2023
645be00
Updates to report code
Aug 24, 2023
7d3560f
Merge branch 'main' of github.com:cshenry/ModelSEEDpy
Aug 24, 2023
4d4cc53
Merge branch 'main' of https://github.com/cshenry/ModelSEEDpy into dev
jplfaria Aug 25, 2023
ec198d8
adding multi tab model report
jplfaria Aug 25, 2023
6210810
Merge pull request #133 from cshenry/main
Fxe Aug 26, 2023
61ecda1
changes to multitab report and redoing gapfilling and atp analysis re…
jplfaria Aug 28, 2023
eb785b2
Merge pull request #134 from jplfaria/dev
Fxe Aug 28, 2023
1f0ec94
Fixing bug in report
cshenry Aug 30, 2023
6496f65
Fixing report bug
cshenry Aug 30, 2023
c5b1f4f
Debugging media
cshenry Sep 7, 2023
ea4117a
Removing debugging
cshenry Sep 7, 2023
cfc3bec
Fixing report
cshenry Sep 9, 2023
1b038fd
Fixing report
cshenry Sep 9, 2023
4632303
Fixing report
cshenry Sep 9, 2023
4b5f573
Fixing report
cshenry Sep 9, 2023
c9ce470
Slight report correction
cshenry Sep 9, 2023
de064ab
Fixing report bugs
cshenry Sep 11, 2023
481d914
Fixing model report encoding
cshenry Sep 13, 2023
df44d59
Fixing report for empty gapfillling data
cshenry Sep 13, 2023
b4a62f4
Adding annotationontology class to module
cshenry Sep 13, 2023
2818366
Fixing report for models where gapfilling has an empty solution
cshenry Sep 13, 2023
1dd84b3
utl
Fxe Sep 14, 2023
b65c591
Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev
Fxe Sep 14, 2023
7112e17
balck
Fxe Sep 14, 2023
722d4dd
precommit
Fxe Sep 14, 2023
6151d17
ignore examples
Fxe Sep 14, 2023
06e05f3
no examples
Fxe Sep 14, 2023
9bcc3b4
version bump and atpcorrection media id check
Fxe Sep 15, 2023
a7de549
black
Fxe Sep 15, 2023
59f7c85
Merge pull request #136 from Fxe/dev
Fxe Sep 15, 2023
640118c
Adding function template for gapfilling function from PNNL team
cshenry Sep 21, 2023
7debbb4
Fixing bug in model reconstruction
cshenry Sep 23, 2023
1449464
Running black
cshenry Sep 23, 2023
67eb8c2
Beginning implementation of global gapfill method
cshenry Sep 23, 2023
e44ea1e
Merge commit '59f7c857b38f55de4ca86b5fc97f07b1e98d8553'
cshenry Sep 23, 2023
ac7c82d
Merge pull request #137 from cshenry/main
Fxe Sep 24, 2023
9de1e73
Enabling phenotypes to ignore growth data
cshenry Sep 24, 2023
0f8ddc8
fixing bug in msatpcorrection
cshenry Oct 4, 2023
1e7b63a
Fixing ID in phenotype simulation output
cshenry Oct 4, 2023
a3d13c7
Fixing threshold for pyruvate and fixing bug in multigapfilling
cshenry Oct 4, 2023
967239d
Fixing phenotype id code
cshenry Oct 5, 2023
5b321ee
Setting debug messages to understanding hanging during sensitivity an…
cshenry Oct 6, 2023
a523de8
Fixing problem with solution integration during multigapfill
cshenry Oct 8, 2023
dfca462
update rast call
Fxe Oct 10, 2023
0769975
Merge branch 'ModelSEED:dev' into dev
Fxe Oct 10, 2023
e08b372
Merge pull request #138 from Fxe/dev
Fxe Oct 10, 2023
7aa4d46
Adding function to build modelutl from file
cshenry Oct 11, 2023
d99441a
Adding some utility functions and adding current_media to KBase media…
cshenry Oct 13, 2023
f5d1d3d
Adding reaction links for obsolete reactions to reaction annotations
cshenry Oct 13, 2023
d037644
Fixing none linked reactions
cshenry Oct 13, 2023
8951c96
adding another utility function
cshenry Oct 13, 2023
4b6520c
Checking in improved gapfilling
cshenry Nov 10, 2023
7b1a0fa
Fixing bug in ATP code
cshenry Nov 10, 2023
0178590
Created Weighting function for gap fill. Example data required for te…
jjacobson95 Dec 4, 2023
fb9f116
updated cobra version and template reaction type fix
Fxe Dec 7, 2023
ea79000
format
Fxe Dec 7, 2023
8a6157e
Merge pull request #141 from Fxe/dev
Fxe Dec 7, 2023
b06d221
Fixing phenotype calling
cshenry Dec 21, 2023
76d2013
debugging growth calls
cshenry Dec 21, 2023
74a333e
Fixing FBA package and phenotyping
cshenry Dec 28, 2023
7132c50
Linted
jjacobson95 Jan 4, 2024
d36463f
Checking in gapfilling improvements for PNNL use in developing gapfil…
cshenry Jan 25, 2024
ebaaaf7
Updating code for gapfilling and annotation ontology support
cshenry Feb 6, 2024
491a200
Major updates to weighting / expression data function
jjacobson95 Feb 14, 2024
0a45528
Adding ensemble class and uploading fixes to gapfilling
cshenry Mar 11, 2024
c68740c
Adding fba object and fixing ontology object
cshenry Mar 11, 2024
d38ce28
Integrating Andrew Freiburger's community modeling code for GROW proj…
cshenry Mar 11, 2024
13274cc
Updates to support mscommunity and probabiliy and fixes to ModelSEEDpy
cshenry Mar 17, 2024
ea73824
Checking in the stripping out of flux limits
cshenry Mar 19, 2024
917bf84
Restoring old MSCommunity for now because refactor to new code is too…
cshenry Mar 19, 2024
4300bec
Fixing
cshenry Mar 19, 2024
6ac6e6b
Fixing bug
cshenry Mar 19, 2024
5003789
Fixing bug
cshenry Mar 19, 2024
4898d5d
Fixing
cshenry Mar 19, 2024
221fe72
Fixing community
cshenry Mar 19, 2024
a22b9e3
Fixing
cshenry Mar 19, 2024
4ae878e
Rolling back to old reconstruction code
cshenry Mar 19, 2024
3efd02e
Fixing basemodel support
cshenry Mar 19, 2024
5cd37e9
Fixing
cshenry Mar 19, 2024
3e94867
Fixing
cshenry Mar 19, 2024
f85fba1
Merge pull request #140 from jjacobson95/dev
cshenry Mar 21, 2024
0d7d955
Merge commit 'f85fba105a6d081c1589e1f4f0c098d097ac2c29'
cshenry Mar 21, 2024
95d45c2
Updates to improve annotation ontology support
cshenry Mar 22, 2024
0ad47c4
Fixing annoopt bug
cshenry Mar 22, 2024
24ae847
Fixing genome
cshenry Mar 22, 2024
1e83b45
Fixing genome
cshenry Mar 22, 2024
cb50084
Update msgapfill.py
jjacobson95 Mar 22, 2024
fc1019b
linted
jjacobson95 Mar 22, 2024
6738874
re-linted msgapfill.py
jjacobson95 Mar 22, 2024
e59adab
Adding function for creating new features
cshenry Mar 23, 2024
7d433a5
Fixing genome info bug
cshenry Mar 23, 2024
f9feaf6
Fixing feature
cshenry Mar 23, 2024
76804cc
Merge pull request #142 from jjacobson95/dev
cshenry Mar 25, 2024
884b162
Merge commit '76804cca89e5ee34ca104c63773083e54355cbc6'
cshenry Mar 25, 2024
3391b5c
Finalizing omegga
cshenry Mar 28, 2024
a6fc4b9
Fixing omegga capabilities
cshenry Mar 30, 2024
92a59ff
Working on fbareport for community FBA app and adding debug message w…
cshenry Apr 1, 2024
48fde20
Temporarily removing dependency
cshenry Apr 28, 2024
f133947
Fixes to support simulation of uptake and excretion phenotypes
cshenry May 21, 2024
742c514
Improving gapfilling and modelutl
cshenry May 22, 2024
cff2a9e
Checking in fixes to support phenotype simulations
cshenry Jun 3, 2024
f8ef961
Fixing minimum value for phenotype
cshenry Jun 3, 2024
17ceafd
Fixing phenotype simulation
cshenry Jun 3, 2024
b8eb006
Disabling phenotype call adjustment
cshenry Jun 3, 2024
35e3b33
Adjusting where growth constraint is being removed
cshenry Jun 4, 2024
213fe4e
Checking in various code updates from recent project work.
Aug 6, 2024
0e84a2b
Fixes for expression fba and ATP
Oct 8, 2024
78fda49
Fixing error with bio reaction, fixing check for compounds in templat…
Nov 5, 2024
c2c1168
Fixing media forcing; fixing ensemble modeling; fixing aliases in gen…
Nov 20, 2024
02319e0
Removing pyeda dependency
Nov 21, 2024
3d4d79f
Removing solution printing that was used for debugging
Nov 21, 2024
3749d67
Setting config for KBase deploy
Nov 21, 2024
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2 changes: 2 additions & 0 deletions .github/workflows/pre-commit.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@ name: Run Pre-Commit
on:
pull_request: {}
push:
paths-ignore:
- 'examples/**'
branches:
- dev
- main
Expand Down
28 changes: 28 additions & 0 deletions .github/workflows/tox.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
name: Run Tox

on:
pull_request: {}
push:
branches: [main]

jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: ['3.8', '3.9', '3.10']
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip setuptools wheel build
python -m pip install tox tox-gh-actions
- name: Test with tox
run: |
tox
python -m build .
5 changes: 5 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -131,3 +131,8 @@ dmypy.json

# Pyre type checker
.pyre/

.pydevproject
.settings/*
*data/*
*.lp
2 changes: 2 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,9 @@ repos:
args:
- --pytest-test-first
- id: check-json
exclude: examples/
- id: pretty-format-json
exclude: examples/
args:
- --autofix
- --top-keys=_id
Expand Down
2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
language: python
python:
- 3.6
- 3.7
- 3.8
- 3.9
before_install:
- python --version
- pip install -U pip
Expand Down
2 changes: 1 addition & 1 deletion examples/Flux Analysis/FullThermodynamicsExample.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -1373,7 +1373,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.9"
"version": "3.9.12"
}
},
"nbformat": 4,
Expand Down
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