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Gapfill update #73

Merged
merged 55 commits into from
Mar 7, 2023
Merged

Gapfill update #73

merged 55 commits into from
Mar 7, 2023

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GwennyGit
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I think we can merge gapfill now completely into dev and main. I tested it on two of my models, and it runs through without any issues now. Additionally, the gap filled model is valid according to COBRApy.

GwennyGit and others added 30 commits February 24, 2023 15:32
@GwennyGit
Added BiGG ID filtering #52
1e2b0eb
@GwennyGit
Changed a test line in analysis_db #52
71454cb 
In line 200 the official code was not used for testing due to making the rest of the process faster. Changed that line back to the official code.
@GwennyGit
Changed output format for gapfill #52
9721f62
@GwennyGit
Changed output handling for gapfill in main #52
b8e83a9
@GwennyGit
Fixed issue with KEGG gapfill analysis #52
9aaa366
@famosab
setup include ratelimit and sqlalchemy #52
204113f
@famosab
How to get BioCyc smart tables docs #52
18950f9
@famosab
Update Docs
5b8f040
@famosab
Modify auto-imports
6bcb3ac
@famosab
Update Docs
b6cd6ab
@famosab
change gitignore
d9801fc
@famosab
Update Docs
e66bbf7
@GwennyGit
Completed function gapfill_model #52
1f1649f 
Now gapfill should be able to do the gap filling via an Excel table.
@GwennyGit
Adjusted main for gapfill #52
103d98f
@GwennyGit
Did some minor changes to improve code #52
68a251a
@GwennyGit
Adjusted config file for gapfill #52
3229ffc
@GwennyGit
Created example file for Excel table #52
6d0ae6f
@GwennyGit
Changed mapping in cvterms dicts for BioCyc #59
3f812ed
@GwennyGit
Adjusted entities for gapfill #52
c50c0de
@GwennyGit
Adjusted curate, growth & polish for the docs
e7603d3
@GwennyGit
Updated Docs
2c496e8
@famosab
Update Docs
f1697be
@GwennyGit
Merge branch 'dev' of https://github.com/draeger-lab/refinegems into …
462a0fa 
…gapfill-update
@GwennyGit
Updated documentation website
3ec25cc 
- Added Development
- Added logo
- Refined appearance
@GwennyGit
Updated README
ec14a32
@GwennyGit
Added missing comma to setup.py
3de4ccb
@GwennyGit
Update README.md
c9c8273
@GwennyGit
Fixed some major issues #52
6735d90
@GwennyGit
Commented gff part out as currently not working #52
ee815bc
@GwennyGit
Fixed all remaining problems #52
622c6ac
@famosab
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famosab commented Mar 4, 2023

For most modules the correct imports should already be defined on the dev branch.

famosab
famosab requested changes Mar 4, 2023
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I would suggest merging #72 first, then adopting the new main.py, the io.py and the config to include everything gapfill related.

@GwennyGit GwennyGit linked an issue Mar 5, 2023 that may be closed by this pull request
Improvement of gap-filling in refineGEMs #52
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@famosab
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famosab commented Mar 6, 2023 •
edited by GwennyGit
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I resolved the merge conflicts and accepted changes from dev when neccessary. What still needs to be done is:

  • include gapfill in the new main.py
  • include gapfill in the new config
  • include gapfill in io.save_user_input

famosab
famosab approved these changes Mar 7, 2023
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Looks good, the remaining docs can be updated directly on dev.

@famosab famosab merged commit 2b11e20 into dev Mar 7, 2023
@famosab famosab deleted the gapfill-update branch March 7, 2023 12:21
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Improvement of gap-filling in refineGEMs
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@GwennyGit @famosab