WIP: Add jcvi.graphics.ribbon module (#733)

* Initialise dev branch

* Do not plot blocks/ribbons from lines beginning with *

* Add opt noline to suppress ribbon outlines

* Port style option for straight ribbons + various formating fixes

* Port xrange to Py3 and fix default strand colour selection

* Migrate Ribbon scripts to py3

* Beta support for PAF input

* pep8 fixes

* Black formatting

* add ribbon test case files

* log matplotlib backend

* add logging to ribbon

* Do not try to set usetex=False or resave
if savefig fails. Instead just return error msg.

* Replace check_call with check_out in sh()
Allows collection of outputs.
Added redirect_error arg so stderr can be
redirected to stdout and user in error logging.

* Collect stderr msgs from lastal for use in
informative logging.

* Log suggestion to use --notex if savefig fails

* Add cleanup empty pdf before exit if savefig fails

* Reorder imports

* Black formatting

* Add logging to clarify why latex use is
deactivated.

* Add logging to clarify why latex is
deactivated.

* rm trmp folder from tracking

* ignore dev files

* Use logger + minor pylance fixes

* sort imports

* Try checkout PR head instead of SHA

* Try PAT token

* disable black commits for forks

* add issues write permission

* test checkout fixes

* Disable for forks

.github/workflows/Black.yml

@@ -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:

.gitignore

@@ -1,5 +1,8 @@
 # Created by http://www.gitignore.io
 
+# Dev testing
+dev
+
 ### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -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.