Merge pull request #720 from padix-key/docs

Fix failing examples in gallery

.github/workflows/test_and_deploy.yml

@@ -31,7 +31,7 @@ env:
   # mussllinux takes 6+ hrs to build and test so ignore it
   CIBW_TEST_SKIP: "*musllinux* *-macosx_arm64"
   # Configuration for the architecture-agnostic jobs
-  PY_VERSION: "3.12"  # Keep in sync with version in environment.yml
+  PY_VERSION: "3.11"  # Keep in sync with version in environment.yml
 
 
 jobs:

doc/switcher.py

@@ -92,6 +92,7 @@ def create_switcher_json(file_path, min_tag, n_versions):
             }
         )
     # Mark the latest version as preferred
-    version_config[-1]["preferred"] = True
+    if len(version_config) > 0:
+        version_config[-1]["preferred"] = True
     with open(file_path, "w") as file:
         json.dump(version_config, file, indent=4)

doc/tutorial/structure/io.rst

@@ -211,9 +211,9 @@ automatically - from a single :class:`BinaryCIFData` to an entire
 .. jupyter-execute::
 
     uncompressed_data = pdbx.BinaryCIFData(np.arange(100))
-    print(f"Uncompressed size: {len(uncompressed_data.serialize()["data"])} bytes")
+    print(f"Uncompressed size: {len(uncompressed_data.serialize()['data'])} bytes")
     compressed_data = pdbx.compress(uncompressed_data)
-    print(f"Compressed size: {len(compressed_data.serialize()["data"])} bytes")
+    print(f"Compressed size: {len(compressed_data.serialize()['data'])} bytes")
 
 
 Using structures from a PDBx file

environment.yml

@@ -10,7 +10,7 @@ channels:
   - salilab
 
 dependencies:
-  - python =3.12
+  - python =3.11
   # Package building
   - cython >=3.0
   - pip >=10.0
@@ -34,7 +34,7 @@ dependencies:
   - dssp =3
   - mafft
   - muscle =3
-  - sra-tools
+  - sra-tools =3
   - tantan
   - viennarna >=2.5.0
   # Documentation building

src/biotite/sequence/io/genbank/file.py

@@ -80,7 +80,7 @@ class GenBankFile(TextFile):
     >>> print(content)
     ['One line', 'A second line']
     >>> print(subfields)
-    OrderedDict({'SUBFIELD1': ['Single Line'], 'SUBFIELD2': ['Two', 'lines']})
+    OrderedDict([('SUBFIELD1', ['Single Line']), ('SUBFIELD2', ['Two', 'lines'])])
 
     Adding an additional field:
 

tests/application/test_sra.py

@@ -9,8 +9,12 @@
 from biotite.application.sra import FastaDumpApp, FastqDumpApp
 from biotite.sequence.io.fasta import FastaFile
 from biotite.sequence.io.fastq import FastqFile
+from tests.util import is_not_installed
 
 
+@pytest.mark.skipif(
+    is_not_installed("fasterq-dump"), reason="sra-tools is not installed"
+)
 @pytest.mark.parametrize(
     "app_class, custom_prefix",
     itertools.product([FastqDumpApp, FastaDumpApp], [False, True]),
@@ -42,6 +46,9 @@ def test_objects(app_class, custom_prefix):
             assert isinstance(fasta_file, FastaFile)
 
 
+@pytest.mark.skipif(
+    is_not_installed("fasterq-dump"), reason="sra-tools is not installed"
+)
 @pytest.mark.parametrize(
     "app_class, custom_prefix",
     itertools.product([FastqDumpApp, FastaDumpApp], [False, True]),