Mckay/upsetplot port (#154) (#623)

Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com>

Author: Colelyman

.gitignore

@@ -6,6 +6,7 @@ __pycache__
 CRISPResso2.egg-info
 dist
 tests/CRISPResso*
+.coverage
 
 # Pixi
 .pixi/

CRISPResso2/CRISPRessoAggregateCORE.py

@@ -68,7 +68,7 @@ def main():
         args = parser.parse_args()
 
         if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
 

CRISPResso2/CRISPRessoBatchCORE.py

@@ -138,7 +138,7 @@ def main():
         _jp = lambda filename: os.path.join(OUTPUT_DIRECTORY, filename)  # handy function to put a file in the output directory
 
         if args.use_matplotlib or not C2PRO_INSTALLED:
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
         CRISPRessoPlot.setMatplotlibDefaults()

CRISPResso2/CRISPRessoCORE.py

@@ -2743,7 +2743,7 @@ def print_stacktrace_if_debug():
             raise CRISPRessoShared.BadParameterException("Needleman Wunsch gap extend penalty must be <= 0")
 
         if args.use_matplotlib or not C2PRO_INSTALLED:
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
         CRISPRessoPlot.setMatplotlibDefaults()

CRISPResso2/CRISPRessoCompareCORE.py

@@ -113,7 +113,7 @@ def main():
         info(compare_header)
 
         if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
 

CRISPResso2/CRISPRessoPooledCORE.py

@@ -288,7 +288,7 @@ def main():
         info(CRISPRessoShared.get_crispresso_header(description, pooled_string))
 
         if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
 

CRISPResso2/CRISPRessoWGSCORE.py

@@ -321,7 +321,7 @@ def print_stacktrace_if_debug():
         info(CRISPRessoShared.get_crispresso_header(description, wgs_string))
 
         if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
-            from CRISPResso2 import CRISPRessoPlot
+            from CRISPResso2.plots import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
 

CRISPResso2/__init__.py

@@ -0,0 +1,13 @@
+# Backward-compatible re-exports: CRISPRessoPlot and upsetplot moved to
+# CRISPResso2.plots but can still be imported from the top-level package.
+# We can remove this once we update CRISPRessoPro's importing
+import sys
+
+from CRISPResso2.plots import CRISPRessoPlot
+from CRISPResso2.plots import upsetplot
+
+# Register under old module paths so that `from CRISPResso2.CRISPRessoPlot import X`
+# and `from CRISPResso2.upsetplot import X` still work for downstream consumers
+# (e.g., CRISPRessoPro). Remove once all consumers are updated.
+sys.modules['CRISPResso2.CRISPRessoPlot'] = CRISPRessoPlot
+sys.modules['CRISPResso2.upsetplot'] = upsetplot

CRISPResso2/CRISPRessoPlot.py CRISPResso2/plots/CRISPRessoPlot.pyCRISPResso2/CRISPRessoPlot.py renamed to CRISPResso2/plots/CRISPRessoPlot.py

@@ -17,7 +17,7 @@
 import re
 from matplotlib import colors as colors_mpl
 import seaborn as sns
-import upsetplot
+from CRISPResso2.plots import upsetplot
 
 from CRISPResso2 import CRISPRessoShared