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WIP: Add jcvi.graphics.ribbon module #733

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Dec 26, 2024
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8178517
Initialise dev branch
Adamtaranto Sep 18, 2019
08b1110
Merge branch 'master' into dev
Adamtaranto Sep 19, 2019
3b53422
Merge branch 'master' into dev
Adamtaranto Sep 19, 2019
f711d54
Do not plot blocks/ribbons from lines beginning with *
Adamtaranto Sep 20, 2019
20822ff
Add opt noline to suppress ribbon outlines
Adamtaranto Sep 25, 2019
a6481dc
Merge branch 'master' into dev
Adamtaranto Dec 11, 2019
29845fc
Port style option for straight ribbons + various formating fixes
Adamtaranto Dec 12, 2019
a052c78
Port xrange to Py3 and fix default strand colour selection
Adamtaranto Feb 19, 2020
33f915d
Merge branch 'master' into dev
Adamtaranto Feb 21, 2020
cef3130
Merge branch 'master' into dev
Adamtaranto Jun 30, 2021
88bed6a
Migrate Ribbon scripts to py3
Adamtaranto Jul 1, 2021
40ae6b7
Beta support for PAF input
Adamtaranto Jul 5, 2021
90ac8b7
pep8 fixes
Adamtaranto Jul 5, 2021
da8113d
Merge branch 'master' into dev
Adamtaranto Jul 6, 2021
333fc2e
Merge branch 'master' into dev
Adamtaranto Jul 13, 2021
65057ad
Black formatting
Adamtaranto Feb 15, 2023
6c6da04
Merge branch 'master' into dev
Adamtaranto Feb 15, 2023
9a0cf01
add ribbon test case files
Adamtaranto Feb 17, 2023
37ea56b
log matplotlib backend
Adamtaranto Feb 17, 2023
b265c46
add logging to ribbon
Adamtaranto Feb 17, 2023
e36ab91
Merge branch 'dev' of github.com:Adamtaranto/jcvi into dev
Adamtaranto Feb 17, 2023
b4a44fb
Merge branch 'master' into dev
Adamtaranto Feb 17, 2023
8e4c872
Do not try to set usetex=False or resave
Adamtaranto Feb 19, 2023
8029175
Replace check_call with check_out in sh()
Adamtaranto Feb 19, 2023
a5225ec
Collect stderr msgs from lastal for use in
Adamtaranto Feb 19, 2023
3f7ad6d
Log suggestion to use --notex if savefig fails
Adamtaranto Feb 19, 2023
7abd51e
Merge branch 'master' into dev
Adamtaranto Feb 19, 2023
00ff793
Add cleanup empty pdf before exit if savefig fails
Adamtaranto Feb 20, 2023
6b986bb
Merge branch 'main' of https://github.com/tanghaibao/jcvi
Adamtaranto Feb 20, 2023
2dc790c
Merge branch 'master' into dev
Adamtaranto Feb 20, 2023
cecfab7
Reorder imports
Adamtaranto Feb 20, 2023
bf49be0
Black formatting
Adamtaranto Feb 20, 2023
642c0ba
Add logging to clarify why latex use is
Adamtaranto Feb 21, 2023
e378e6f
Add logging to clarify why latex is
Adamtaranto Feb 21, 2023
ad0c3d2
Merge branch 'master' into dev
Adamtaranto Feb 21, 2023
2daf3dc
Merge branch 'main' of https://github.com/tanghaibao/jcvi
Adamtaranto Feb 23, 2023
ae7c0ef
Merge remote-tracking branch 'upstream/main'
Adamtaranto Nov 14, 2024
9043e99
Merge branch 'main' into dev
Adamtaranto Nov 14, 2024
aef18d5
Merge branch 'tanghaibao:main' into dev
Adamtaranto Dec 25, 2024
b37a74a
Merge branch 'tanghaibao:main' into dev
Adamtaranto Dec 26, 2024
bdecf60
rm trmp folder from tracking
Adamtaranto Dec 26, 2024
efb0dba
ignore dev files
Adamtaranto Dec 26, 2024
eb9e35e
Use logger + minor pylance fixes
Adamtaranto Dec 26, 2024
75530e8
sort imports
Adamtaranto Dec 26, 2024
ec9adac
Try checkout PR head instead of SHA
Adamtaranto Dec 26, 2024
49ee148
Try PAT token
Adamtaranto Dec 26, 2024
0bc954a
disable black commits for forks
Adamtaranto Dec 26, 2024
e622804
add issues write permission
Adamtaranto Dec 26, 2024
9221608
test checkout fixes
Adamtaranto Dec 26, 2024
691b470
Disable for forks
Adamtaranto Dec 26, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/Black.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@ name: Black Formatting
on: [pull_request]
jobs:
black:
if: ${{ github.actor != 'dependabot[bot]' }} # Do not run on commits created by dependabot
# Only run if not from dependabot AND not from a fork
if: ${{ github.actor != 'dependabot[bot]' && github.event.pull_request.head.repo.fork != true }}
runs-on: ubuntu-latest
permissions:
# Give the default GITHUB_TOKEN write permission to commit and push the changed files.
contents: write # Allows reading and writing repository contents (e.g., commits)
pull-requests: write # Allows reading and writing pull requests
contents: write
pull-requests: write
steps:
- uses: actions/checkout@v4
with:
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3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
# Created by http://www.gitignore.io

# Dev testing
dev

### Python ###
# Byte-compiled / optimized / DLL files
__pycache__/
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1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ methods.
- Histogram using R and ASCII art.
- Paint regions on set of chromosomes.
- Macro-synteny and micro-synteny plots.
- Ribbon plots from whole genome alignments.

- <kbd>utils</kbd>
- Grouper can be used as disjoint set data structure.
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