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Update from Hackathon/feb24 #329

Merged
merged 244 commits into from
Apr 15, 2024
Merged

Update from Hackathon/feb24 #329

merged 244 commits into from
Apr 15, 2024

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MatBarba
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@MatBarba MatBarba commented Mar 21, 2024 •
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Merge the hackathon improvements and fixes: xrefs, GFF3 parser, etc.

ens-LCampbell and others added 30 commits January 25, 2024 10:39
@ens-LCampbell
Merge pull request #278 from Ensembl/hackathon/jan24
49d7adf 
Small fix from black to hackathon_Jan24
@ens-LCampbell
Initalise dev test_download.py
d7a1e3d
@ens-LCampbell
Update change to usage example
5bbd162
@ens-LCampbell
Initial commit on assembly download unit test
0789fa4
@ens-LCampbell
Run Black
0aae4d7
@ens-LCampbell
Refactoring: FTP connection
368a042
@ens-LCampbell
Update dir name to fasta (process) test data
a5e4da7
@ens-LCampbell
get_checksum function test module
835a31b
@ens-LCampbell
Adding assembly download test data folder
0772d32
@ens-LCampbell
Add test test_md5_files
9347fbd
@ens-LCampbell
User specify md5sum filename or default
3a4bf94
@ens-LCampbell
Updated and added missing doc strings
54f4eec
@ens-LCampbell
Stashing attempt on download_file
76c147d
@MatBarba
Move methods to a new module standardize
8b2d3f9
@MatBarba
gene_to_cds to export a gene directly
84431f6
@MatBarba
Start test for standardize
4717450
@MatBarba
More tests
48b3d52
@ens-LCampbell
New changes to establish_ftp function and test
f6ffe3c
@ens-LCampbell
Modified ftp_connection and download_files functions
11be64c
@ens-LCampbell
Final test added on master function retrieve_assembly_data
07ab7b4
@ens-LCampbell
Cleanup of test arguments and test files used
33d9464
@ens-LCampbell
Clean up unused function params
01742a1
@ens-LCampbell
Round of cleaning
4a20475
@ens-LCampbell
Cleanup and blacked download sub module
3a1c3ad
@ens-LCampbell
Update md5 checksum file on test data checksums
3a55838
@ens-LCampbell
Adding all remaining test data files
5a40b8b
@ens-LCampbell
Remove unneeded test file
c406aa6
@ens-LCampbell
Remove unused FTP import
d4d2d7e
@JAlvarezJarreta
update fixture type hint
e384a90
@JAlvarezJarreta
update fixture name and docstring
faa87bc
MatBarba and others added 25 commits March 26, 2024 16:32
@MatBarba
format
42f1edd
@MatBarba
Merge branch 'mbarba/hack/gff_simplifier' into mbarba/hack/gff_mirna
70fcae0
@MatBarba
More tests
245d91f
@MatBarba
Test miRNA split support
cb5221b
@MatBarba
Add pseudogene check
36022b2
@MatBarba
Add pseudogene miRNA
412f59b
@MatBarba
Reorganize miRNA test files
230de4e
@MatBarba
Fix: no change, don't return modified gene
9803dd1
@MatBarba
Merge branch 'main' into hackathon/feb24
6a9f3d8
@MatBarba
Merge branch 'hackathon/feb24' into mbarba/hack/gff_simplifier
acf8e61
@MatBarba
Bugfix: properly store annotation for translations
4a5f251
@MatBarba
Add test for fix
61ffb3f
@JAlvarezJarreta @MatBarba
simplify code to avoid using flags
40ea4e6
@MatBarba
Restrict what is in the with section
c926678
@MatBarba
unify test_from_gff
5469ba7
@MatBarba
Restrict with
a6033ef
@MatBarba
simp creation outside with
58cf4c3
@MatBarba
tmp_dir -> tmp_path
aae6246
@MatBarba @JAlvarezJarreta
Apply suggestions from code review
3f89211 
Co-authored-by: J. Alvarez-Jarreta <[email protected]>
@MatBarba
Typo
d410b98
@MatBarba
Update doc
a948a90
@MatBarba
Exception instead of None for simpler_gff3_feature
a05f1de
@MatBarba
check_one_feature no return
2195607
@MatBarba @JAlvarezJarreta
Update src/python/ensembl/io/genomio/gff3/simplifier.py
efa874b 
Co-authored-by: J. Alvarez-Jarreta <[email protected]>
@MatBarba
Merge pull request #332 from Ensembl/mbarba/hack/gff_simplifier
d2e085f 
GFF3 simplifier refactoring and tests
JAlvarezJarreta
JAlvarezJarreta approved these changes Apr 15, 2024
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Re-approval!

@MatBarba MatBarba changed the title Update from Hackathon/feb24 (xrefs) Update from Hackathon/feb24 Apr 15, 2024
@MatBarba MatBarba merged commit 015c60c into main Apr 15, 2024
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@MatBarba MatBarba deleted the hackathon/feb24 branch April 17, 2024 14:48
@MatBarba MatBarba restored the hackathon/feb24 branch April 17, 2024 14:52
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@JAlvarezJarreta JAlvarezJarreta JAlvarezJarreta approved these changes

@Dishalodha Dishalodha Dishalodha approved these changes

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@MatBarba @JAlvarezJarreta @Dishalodha @ens-LCampbell