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Merge dev branch into master to release version 2.2.0 #298

Merged
merged 61 commits into from
Oct 29, 2024
Merged

Merge dev branch into master to release version 2.2.0 #298

merged 61 commits into from
Oct 29, 2024

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JeanMainguy
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This pull request merges the dev branch into the master branch to release version 2.2.0

This includes previous PR that have been merged to dev:

  • Partial genes now properly handled (#290)
  • Non-ASCII characters filtered (#291).
  • Better memory for ppanggolin fasta (#283)
  • Black linter added (#295)
  • Reduced log noise (#296).
  • Corrected Chao formula (#284)
  • Fixed empty metadata tags (#287).

JeanMainguy and others added 30 commits September 16, 2024 17:27
@JeanMainguy
write fasta by reading directly from the pangenome file
96ec865
@JeanMainguy
add module filter in gene_families writing
1b3b35f
@JeanMainguy
fix none manageemnt
c14eac4
@JeanMainguy
write module and rgp family genes
1ac566c
@ggautreau
fix an error in the formula to calculate chao displayed on the ucurve…
7b8c6c2 
… plot
@JeanMainguy
add possibility to write module and rgp in prot fasta
2518942
@JeanMainguy
Add possibility to write genes by reading pangenome file directly
1157761
@JeanMainguy
reset genes var if it has been handle by writting fct
3a6840c
@fchapoton
remove trailing whitespaces
cae0c4a
@fchapoton
a few more fixes by hand
b0d5d19
@axbazin
Merge pull request #284 from labgem/fix_ucurve_chao
6bae993 
fix an error in the formula to calculate chao displayed on the ucurve…
@JeanMainguy
add softcore and core filter in gene_families output
825e1e7
@JeanMainguy
add softcore and core filter in prot_families output
25c61bc
@JeanMainguy
handle proteins in faster way
baa9a0f
@JeanMainguy
clean region seq writting
cfc9073
@JeanMainguy
add docstring and clean fct not used
bd592d0
@JeanMainguy
clean import
cd30d15
@JeanMainguy
use set instead of list to speed gene selection
bc18e15
@JeanMainguy
improve error management and refactor code for more clarity
06e47df
@JeanMainguy
ignore empty metadata tag in annotation file
dd84093
@axbazin
Merge pull request #287 from labgem/fix_genome_metadata_handeling
4706587 
Fix empty metadata tag in annotation file
@axbazin
Merge pull request #283 from labgem/improve_fasta_cmd
2923c56 
Improved Memory Efficiency for `ppanggolin fasta` Command
@JeanMainguy
Merge pull request #286 from fchapoton/trailing_spaces
0c1b85e 
remove trailing whitespaces
@JeanMainguy
identify starting and ending partiality of gene
7bb83ce
@JeanMainguy
fix coordinates for partial genes
ad44264
@JeanMainguy
add pytest for fixing coordinates fct
b8b1f42
@JeanMainguy
refactor shifting function to handle tricky coordinates and reuse code
2a62ee8
@JeanMainguy
update tests to match refactoring and tricky cases
aa4e988
@JeanMainguy
do not ignore CDS with trans_except instead give a warning
0507a4b
@JeanMainguy
simplify fct fix_partial_gene_coordinates
1e99584
JeanMainguy and others added 27 commits October 15, 2024 10:21
@JeanMainguy
rm debug
d99404c
@JeanMainguy
use locus_tag in GFF parsing
e802d5e
@JeanMainguy
update CI
7cb227c
@JeanMainguy
update expected files with new genes and cluster
6507c57
@JeanMainguy
Revert "update CI"
498b033 
This reverts commit 7cb227c.
@JeanMainguy
update CI
0ed382a
@JeanMainguy
rm cluster file not used in CI anymore
760b0f0
@jpjarnoux
Fix how frame getter/setter attribute is handled
a9a251f
@jpjarnoux
Update docstring and typing
6940253
@jpjarnoux
Merge pull request #290 from labgem/handle_partial_genes
561d81b 
Handling of partial genes in PPanGGOLiN
@JeanMainguy
filter out non ascii character when found in product
0b6d1df
@JeanMainguy
add some pytest to test ascii filtering fct
fbe6132
@jpjarnoux
Merge pull request #291 from labgem/filter_non_ascii_char
1fd1092 
Filter non ASCII character
@JeanMainguy
apply black to ppanggolin python code
70155bd
@JeanMainguy
add black to test deps in toml
73dd3df
@JeanMainguy
add CI lint
5d8305a
@JeanMainguy
fix synthax error in toml
348a7af
@JeanMainguy
test black
de47131
@JeanMainguy
test black revert
99249ed
@JeanMainguy
update doc with black
798f850
@JeanMainguy
add black github link in doc
4e2b9df
@JeanMainguy
add missing disable bar flag in fast projection
ac13ec7
@JeanMainguy
use debug to inform on missing translation table in input files
af0c675
@JeanMainguy
Merge pull request #295 from labgem/add_linter
9526e46 
Add linter to PPanGGOLIN code base
@JeanMainguy
Bump to version 2.2.0
e3713ca
@axbazin
Merge pull request #296 from labgem/adjust_log_and_bar
92263af 
Adjust logging and fix unwanted progress bar
@axbazin
Merge pull request #297 from labgem/update_version
23c4fd7 
Update version to 2.2.0
@axbazin axbazin self-requested a review October 29, 2024 16:33
@axbazin axbazin merged commit 8cacb1b into master Oct 29, 2024
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5 participants
@JeanMainguy @axbazin @ggautreau @fchapoton @jpjarnoux