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Issues to resolve before release 2.0 #121

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4 of 8 tasks
GwennyGit opened this issue Apr 22, 2024 · 0 comments · Fixed by #133
Open
4 of 8 tasks

Issues to resolve before release 2.0 #121

GwennyGit opened this issue Apr 22, 2024 · 0 comments · Fixed by #133
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@cb-Hades @GwennyGit
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documentation Improvements or additions to documentation enhancement New feature or request help wanted Extra attention is needed refactoring changes in the code functionality

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@GwennyGit
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GwennyGit commented Apr 22, 2024 •
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Dependancies:

  • check if all dependancies are imported
  • problem with BOFdat: script for changing the files or try and make a pull request? (rather easy fix honestly...)
@GwennyGit GwennyGit added documentation Improvements or additions to documentation enhancement New feature or request help wanted Extra attention is needed refactoring changes in the code functionality labels Apr 22, 2024
cb-Hades added a commit that referenced this issue Apr 29, 2024
@cb-Hades
Small EGC update #121
b68dc2b
cb-Hades added a commit that referenced this issue Apr 29, 2024
@cb-Hades
Fixed DB validation #121
577d972
cb-Hades added a commit that referenced this issue May 6, 2024
@cb-Hades
small fixes #121
4598cd7
GwennyGit added a commit that referenced this issue May 22, 2024
@GwennyGit
Updated cmd_access for gap analysis & filling #121
2f53116
GwennyGit added a commit that referenced this issue May 23, 2024
@GwennyGit
Updated gapfill & cmd_access to fit together #118 #121
e17bf58
niinina added a commit that referenced this issue May 27, 2024
@niinina
Update pyproject.toml
e108618 
#121
cb-Hades added a commit that referenced this issue Jun 4, 2024
@cb-Hades
Bug fix #121
2f675a1
niinina added a commit that referenced this issue Jun 7, 2024
@niinina
Update core_pan.py
50ee36f 
#121
cb-Hades added a commit that referenced this issue Jun 7, 2024
@cb-Hades
Added deprecation warning #120 #121
65d292c
cb-Hades added a commit that referenced this issue Jun 18, 2024
@cb-Hades
updated dependancies #121
ff966c6
cb-Hades added a commit that referenced this issue Jun 18, 2024
@cb-Hades
Update pyproject.toml #121
4af3fce
cb-Hades added a commit that referenced this issue Jun 25, 2024
@cb-Hades
Added correct MCC branch #121
5563061
niinina added a commit that referenced this issue Jun 27, 2024
@niinina
Fix medium.py
490f9a0 
#121
niinina added a commit that referenced this issue Jun 27, 2024
@niinina
Update polish.py
6508315 
#121
cb-Hades added a commit that referenced this issue Jun 28, 2024
@cb-Hades
Bug fixes #121
3db323f
cb-Hades added a commit that referenced this issue Jul 5, 2024
@cb-Hades
update dependancies #121
65ab258
GwennyGit added a commit that referenced this issue Jul 10, 2024
@GwennyGit
Removed typo in growth.py #121
d41ef26
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Update cmd_access.py #120 #121
a84509b
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Updated colours for admonitions #120 #121
6d9d07f
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Finalised intro, index & installation #120 #121
1f5b026
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Updated api.rst #120 #121
721b416
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Adjusted deprecation warnings in curate.py for docs #120 #121
9c9717d
GwennyGit added a commit that referenced this issue Jul 15, 2024
@GwennyGit
Started clean-up in cmd_desc.rst #120 #121
55234f1
GwennyGit added a commit that referenced this issue Aug 15, 2024
@GwennyGit
Added depreaction comment to parse_fasta_headers #121 #130
36f9c3f
cb-Hades added a commit that referenced this issue Aug 22, 2024
@cb-Hades
Fixed issue with gene duplicates #52 #121
182719b
cb-Hades added a commit that referenced this issue Aug 23, 2024
@cb-Hades
Bug fixed and solved tags #121
d5e17c7
GwennyGit added a commit that referenced this issue Aug 26, 2024
@GwennyGit
Adjusted version for new pre-release #121 #
76bcb6e 
- Added handling of autodoc to exclude specific members
GwennyGit added a commit that referenced this issue Aug 26, 2024
@GwennyGit
Resolved naming issues in egcs #121
abc374b
cb-Hades added a commit that referenced this issue Aug 27, 2024
@cb-Hades
Improved decorators #121
08e4ac3
GwennyGit added a commit that referenced this issue Aug 27, 2024
@GwennyGit
Added files for artificial sebum #16 #121
742445f 
- Python Notebook to generate oil content from VMH specs & specs in the paper
- Files used for the generation in a ZIP-archive
GwennyGit added a commit that referenced this issue Aug 27, 2024
@GwennyGit
Added TODOs in decorators & entities #121
384d467
GwennyGit added a commit that referenced this issue Aug 27, 2024
@GwennyGit
Finalised docs for pre-release 2.0.0 #120 #121
d093457
GwennyGit added a commit that referenced this issue Aug 27, 2024
@GwennyGit
Adjusted columns for missing_reactions & extended docs #120 #121 #126
174ce36
@GwennyGit GwennyGit linked a pull request Aug 27, 2024 that will close this issue
Merge dev-2 into dev to get refactoring ready for main #133
Merged
GwennyGit added a commit that referenced this issue Aug 28, 2024
@GwennyGit
Deleted accidently added testing files #121
1fbee36
cb-Hades added a commit that referenced this issue Aug 28, 2024
@cb-Hades
bug fixes #121
548868d
GwennyGit added a commit that referenced this issue Aug 28, 2024
@GwennyGit
Fixed some bugs #126 #121
266f1f4
GwennyGit added a commit that referenced this issue Aug 28, 2024
@GwennyGit
Updated gapfill-testing.ipynb #126 #121
c3369ac
@cb-Hades cb-Hades reopened this Aug 28, 2024
GwennyGit added a commit that referenced this issue Aug 28, 2024
@GwennyGit
Updated README & docs with new installation instructions #121
dd50de8
GwennyGit added a commit that referenced this issue Sep 1, 2024
@GwennyGit
Fixed fill_model for BioCycGapFiller #121 #126
4e76f63
GwennyGit added a commit that referenced this issue Sep 1, 2024
@GwennyGit
Fixed test_auxotrophies #121
bb564e7 
Changed infeasible status of optimisation to be handled as 0
GwennyGit added a commit that referenced this issue Sep 1, 2024
@GwennyGit
Added tutorial #121
c42b7bc
GwennyGit added a commit that referenced this issue Sep 1, 2024
@GwennyGit
Adjusted versions for new pre-release 2.0.0a1 #121
25e6990
GwennyGit added a commit that referenced this issue Nov 15, 2024
@GwennyGit
Opened a discussion & a deprecation #121
3056065 
- Discussion: write_model_to_file currently only accepts strings
- Deprecation: parse_gff_for_refseq_info can be deleted
GwennyGit added a commit that referenced this issue Nov 15, 2024
@GwennyGit
Bug fix in cmd_access.py #121
53c9834 
write_model_to_file only accepts strings and no pathlib.Path objects!
GwennyGit added a commit that referenced this issue Nov 15, 2024
@GwennyGit
Bug fix in polish.py #121
0580ae6 
Bug is fixed now but handling of duplicate RefSeq/Protein IDs needs to be discussed for cv_ncbiprotein and probably also for add_gp_id_from_gff!
GwennyGit added a commit that referenced this issue Nov 18, 2024
@GwennyGit
Added TODO to utility.io #121
d0a8176
GwennyGit added a commit that referenced this issue Nov 20, 2024
@GwennyGit
Update of the gapfill.rst #52 #121 #126
5470523
niinina added a commit that referenced this issue Nov 25, 2024
@niinina
Update pyproject.toml #121
4024bd4
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Merge dev-2 into dev to get refactoring ready for main draeger-lab/refinegems
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@cb-Hades @GwennyGit