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Release 3.19 #474

Merged
merged 74 commits into from
May 6, 2024
Merged

Release 3.19 #474

merged 74 commits into from
May 6, 2024

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lldelisle
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3.9

Changes in dependencies:

  • This version drops support for python 3.7.
  • This version is compatible with matplotlib 3.8.

Enhancement:

  • pyGenomeTracks now uses font type 42 for pdf and ps which helps modification with illustrator.

  • 2 new display for bed: deletions which is helpful when you need to show a deletion with precise coordinates and inversions which displays arrows.

  • New style to display bed: exonarrows which displays arrows with orientation in the exons.

  • For the UCSC stlyle, the color of arrows on introns in customable

  • Do not hesistate to check the updated documentation: here <https://pygenometracks.readthedocs.io/en/latest/content/examples.html#examples-with-bed-and-gtf>_

  • Allow to rasterize rectangles/lines of maf tracks with rasterize = true.

Bugfix:

  • Fix the UTR/Coding of BED8/BED9.
  • Fix a typo in options help text of bedgraph and bigwig: tranform instead of transform.

lldelisle and others added 30 commits February 7, 2023 17:30
@lldelisle
change fonttype for illustrator
2c0ae8c
@lldelisle
fix python_requires
8584b7a
@lldelisle
explicitly test style
5389351
@lldelisle
more info in docstring
f2d20b6
@lldelisle
fix CDS/UTR in BED8 and BED9
83f9898
@lldelisle
update outputs
35694dd
@lldelisle
fix broken bed6 and tssarrow
82f04d0
@lldelisle
add release message
b4eebc7
@bgruening
Merge pull request #448 from lldelisle/fix_installation_setup
aea296d 
Fix installation setup
@lldelisle
add demo figure
5cea2eb
@lldelisle
fix initiation of block_starts for non bed12
e467ae9
@lldelisle
add color_utr when needed
993ad04
@lldelisle
fix CDS of invalid rgb
73951c0
@lldelisle
update outputs
db4198d
@lldelisle
fix fasta output
c3aab09
@lldelisle
add new style: exonarrow
b817b2a
@lldelisle
add tests
3092f10
@lldelisle
update GtfTrack
48870b1
@lldelisle
update doc
77c1af8
@bgruening @lldelisle
fix linting
376a352
@lldelisle
add release text
a07d9d4
@lldelisle
update release message
d460c8b
@lldelisle
add new display: deletions
dad0801
@lldelisle
improve doc
d5eaac1
@lldelisle
update help text
f35c5ac
@lldelisle
update doc
3b70404
@lldelisle
fix linting
9d65dbe
@lldelisle
adjust deletions plot to be overlayed with collapsed bed
aac0c4c
@lldelisle
add new style inversions
1a25680
@lldelisle
arrowhead_fraction is not defined for domains
db02d42
lldelisle added 27 commits May 2, 2024 12:02
@lldelisle
keep edges in exonarrows style
ce0e5fc
@lldelisle
Merge pull request #450 from lldelisle/new_style_exonarrows
d537fe8 
New style for bed exonarrows
@lldelisle
Merge branch 'develop' of github.com:deeptools/pyGenomeTracks into ne…
79c856f 
…w_style_deletion
@lldelisle
Merge pull request #451 from lldelisle/new_style_deletion
156784a 
New display: deletions
@lldelisle
Merge branch 'develop' of github.com:deeptools/pyGenomeTracks into ne…
12b1046 
…w_style_inversion
@lldelisle
Merge pull request #456 from lldelisle/new_style_inversion
470d90c 
New display inversions
@lldelisle
Merge branch 'develop' of github.com:deeptools/pyGenomeTracks into fi…
f439c81 
…x_typo_transform
@lldelisle
add message in release
fdd9abc
@lldelisle
add new option to rasterize rectangles/lines in maf
9da0168
@lldelisle
Merge pull request #459 from lldelisle/fix_typo_transform
6b14a6d 
fix typo tranform to transform
@lldelisle
update README [no ci]
765af85
@lldelisle
change setup.py to project.toml
8fdca5b
@lldelisle
fix test matplotlib
a33fda6
@lldelisle
try newer versions of matplotlib
2796ff7
@lldelisle
put param names for Arc
c029d9f
@lldelisle
still restrict matplotlib<3.9
f90d1f3
@lldelisle
use the last supported version for new plots
68ef312
@lldelisle
add note to release
c1718c2
@lldelisle
put back test on low matplotlib linux
1267fa1
@lldelisle
Merge pull request #473 from deeptools/test_matplotlib
17f3f94 
Relax matplotlib versions compatible
@lldelisle
use shutil instead of system cp
9a1fa37
@lldelisle
Merge branch 'develop' of github.com:deeptools/pyGenomeTracks into re…
1c3a1fe 
…move_setup_py
@lldelisle
update requirement for matplotlib in pyproject.toml
83026ca
@lldelisle
Merge pull request #471 from lldelisle/rasterize_maf
105919b 
add new option to rasterize rectangles/lines in maf
@lldelisle
Merge branch 'develop' of github.com:deeptools/pyGenomeTracks into re…
89baa12 
…move_setup_py
@lldelisle
Merge pull request #472 from lldelisle/remove_setup_py
21d3a53 
change setup.py to project.toml
@lldelisle
bump version
e588397
@lldelisle
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Ready for release.

bgruening
bgruening approved these changes May 6, 2024
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Cool, so many new tests!

@lldelisle lldelisle merged commit 8b0c96b into master May 6, 2024
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@bgruening bgruening bgruening approved these changes

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@lldelisle @bgruening