From 58321ce018318935ee28f448b2c051d4b00f370e Mon Sep 17 00:00:00 2001
From: Peter Vegh <pvegh@posteo.uk>
Date: Sat, 17 Dec 2022 20:00:14 +0000
Subject: [PATCH] Fix DeprecationWarning

Remove `alpha` parameter.
---
 dnachisel/reports/optimization_reports.py     | 28 ++++++-------------
 .../generate_annotations.py                   | 15 ++--------
 2 files changed, 12 insertions(+), 31 deletions(-)

diff --git a/dnachisel/reports/optimization_reports.py b/dnachisel/reports/optimization_reports.py
index afd04fc..627363c 100644
--- a/dnachisel/reports/optimization_reports.py
+++ b/dnachisel/reports/optimization_reports.py
@@ -20,6 +20,7 @@
 
 try:
     import pandas
+
     PANDAS_AVAILABLE = True
 except ImportError:
     PANDAS_AVAILABLE = False
@@ -78,9 +79,7 @@ def ReportWriter(*a, **kw):
 )
 
 
-def write_no_solution_report(
-    target, problem, error, file_content=None, file_path=None
-):
+def write_no_solution_report(target, problem, error, file_content=None, file_path=None):
     """Write a report on incompatibility found in the problem's constraints.
 
     The report comprises a PDF of plots of the sequence (global constraints,
@@ -129,18 +128,15 @@ def write_no_solution_report(
         if error.location is None:
             raise error
         start, end, strand = error.location.to_tuple()
-        ax.fill_between(
-            [start, end], -10, 10, zorder=-1000, facecolor="#ffcccc"
-        )
+        ax.fill_between([start, end], -10, 10, zorder=-1000, facecolor="#ffcccc")
         title = "\n".join(
             textwrap.wrap(
-                "No solution found in zone [%d, %d]:%s"
-                % (start, end, str(error)),
+                "No solution found in zone [%d, %d]:%s" % (start, end, str(error)),
                 width=120,
             )
         )
         ax.set_title(title, fontdict=TITLE_FONTDICT)
-        pdf_io.savefig(ax.figure, bbox_inches="tight", alpha=0.5)
+        pdf_io.savefig(ax.figure, bbox_inches="tight")
         plt.close(ax.figure)
 
         # CREATE AND SAVE THE LOCAL CONSTRAINTS BREACHES RECORD
@@ -166,9 +162,7 @@ def is_in_focus(location):
             label_prefix="BREACH", locations_filter=is_in_focus
         )
         SeqIO.write(
-            record,
-            root._file("local_constraints_breaches.gb").open("w"),
-            "genbank",
+            record, root._file("local_constraints_breaches.gb").open("w"), "genbank",
         )
 
         # CREATE A FIGURE OF THE LOCAL CONSTRAINTS BREACHES AS A NEW PDF PAGE
@@ -184,7 +178,7 @@ def is_in_focus(location):
             fontdict=TITLE_FONTDICT,
         )
         ax.set_ylim(top=ax.get_ylim()[1] + 1)
-        pdf_io.savefig(ax.figure, bbox_inches="tight", alpha=0.5)
+        pdf_io.savefig(ax.figure, bbox_inches="tight")
         plt.close(ax.figure)
 
     root._file("logs.txt").write(problem.logger.dump_logs())
@@ -373,9 +367,7 @@ def write_optimization_report(
         problem=problem, constraints_evaluations=constraints_evaluations
     )
     filename = "constraints_before_and_after.csv"
-    constraints_before_after.to_csv(
-        root._file(filename).open("w"), index=False
-    )
+    constraints_before_after.to_csv(root._file(filename).open("w"), index=False)
 
     # GENERATE AND SAVE THE OBJECTIVES SUMMARY
 
@@ -415,9 +407,7 @@ def write_optimization_report(
         label_prefix="Breach from", merge_overlapping=True
     )
     record.features += breaches_locations
-    SeqIO.write(
-        record, root._file("final_sequence_with_edits.gb").open("w"), "genbank"
-    )
+    SeqIO.write(record, root._file("final_sequence_with_edits.gb").open("w"), "genbank")
 
     # CREATE THE "FINAL SEQUENCE" REPORT
 
diff --git a/docs/_static/images/genbank_annotations/generate_annotations.py b/docs/_static/images/genbank_annotations/generate_annotations.py
index fa14f60..0f5b4f6 100644
--- a/docs/_static/images/genbank_annotations/generate_annotations.py
+++ b/docs/_static/images/genbank_annotations/generate_annotations.py
@@ -14,11 +14,7 @@ def parse_locations(s):
     if "," not in s:
         start, end = map(int, s.strip().strip("+").split("-"))
         return [(start, end, 1 if s.endswith("+") else 0)]
-    return [
-        location
-        for sub in s.split(",")
-        for location in parse_locations(sub)
-    ]
+    return [location for sub in s.split(",") for location in parse_locations(sub)]
 
 
 def graphic_features_from_row(row):
@@ -28,7 +24,6 @@ def graphic_features_from_row(row):
     else:
         color = "#ededa7"
         fontdict = dict(size=14, color="black", family="Ubuntu")
-    
 
     return [
         dfv.GraphicFeature(
@@ -58,9 +53,7 @@ def plot_row_feature(row):
 
     if row.highlights != "none":
         for (start, end, _) in parse_locations(row.highlights):
-            ax.fill_between(
-                [start - 0.5, end - 0.5], -0.9, -0.5, facecolor="r", alpha=0.15
-            )
+            ax.fill_between([start - 0.5, end - 0.5], -0.9, -0.5, facecolor="r")
     ax.set_ylim(top=0.7)
     ax.figure.set_figheight(1)
     return ax
@@ -69,7 +62,5 @@ def plot_row_feature(row):
 data = pandas.read_csv("./examples.csv")
 for i, row in tqdm.tqdm(list(data.iterrows())):
     ax = plot_row_feature(row)
-    ax.figure.savefig(
-        "./%s.png" % row.filename, bbox_inches="tight", dpi=120
-    )
+    ax.figure.savefig("./%s.png" % row.filename, bbox_inches="tight", dpi=120)
     plt.close(ax.figure)