Merge pull request #691 from padix-key/examples

Refactor some examples

doc/examples/scripts/sequence/annotation/plasmid_map.py

@@ -25,9 +25,8 @@
 import biotite.sequence.io.genbank as gb
 
 PLASMID_URL = (
-    "https://media.addgene.org/snapgene-media/v1.7.9-0-g88a3305/"
-    "sequences/12250/9998fdbe-051f-4dc6-ba0f-24e65127a0c5/"
-    "addgene-plasmid-26092-sequence-12250.gbk"
+    "https://media.addgene.org/snapgene-media/v2.0.0/sequences/12250/"
+    "9998fdbe-051f-4dc6-ba0f-24e65127a0c5/addgene-plasmid-26092-sequence-12250.gbk"
 )
 
 
@@ -46,12 +45,6 @@
     ],
 )
 _, seq_length, _, _, _, _ = gb.get_locus(gb_file)
-# AddGene stores the plasmid name in the 'KEYWORDS' field
-# [0][0][0] ->
-# The first (and only) 'KEYWORDS' field
-# The first entry in the tuple
-# The first (and only) line in the field
-plasmid_name = gb_file.get_fields("KEYWORDS")[0][0][0]
 
 
 def custom_feature_formatter(feature):
@@ -79,7 +72,7 @@ def custom_feature_formatter(feature):
     ax,
     annotation,
     plasmid_size=seq_length,
-    label=plasmid_name,
+    label="pET15-MHL",
     feature_formatter=custom_feature_formatter,
 )
 fig.tight_layout()

doc/examples/scripts/sequence/homology/genome_comparison.py

@@ -335,7 +335,7 @@ def draw_arrow(ax, feature, loc):
 annotation = gb.get_annotation(gb_file, include_only=["CDS", "rRNA", "tRNA"])
 
 n_rows = int(np.ceil(len(unique_alignments) / N_COL))
-fig, axes = plt.subplots(n_rows, N_COL, figsize=(8.0, 24.0), constrained_layout=True)
+fig, axes = plt.subplots(n_rows, N_COL, figsize=(8.0, 1.5 * n_rows))
 
 for (alignment, log_evalue), ax in zip(unique_alignments, axes.flatten()):
     # Transform 0-based sequence index to 1-based sequence position

environment.yml

@@ -45,7 +45,7 @@ dependencies:
   - sphinxcontrib-bibtex >=2.3
   - sphinx-copybutton >=0.5
   - sphinx-design >=0.5
-  - sphinx-gallery =0.15.0
+  - sphinx-gallery =0.18.0
   - sphinx-notfound-page >=1.0
   # Extra packages used in example gallery
   - pandas >=1.5.2