bio2zarr 0.1.3__tar.gz → 0.1.4__tar.gz

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/CHANGELOG.md

@@ -1,3 +1,7 @@
+# 0.1.4 2025-03-10
+
+- Fix bug in handling all-missing genotypes (#328)
+
 # 0.1.3 2025-03-04
 
 - Fix missing dependency issue for packaging

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bio2zarr
-Version: 0.1.3
+Version: 0.1.4
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/bio2zarr/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.3'
-__version_tuple__ = version_tuple = (0, 1, 3)
+__version__ = version = '0.1.4'
+__version_tuple__ = version_tuple = (0, 1, 4)

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/bio2zarr/vcf2zarr/icf.py

@@ -1095,9 +1095,8 @@ class IntermediateColumnarFormatWriter:
                     for field in info_fields:
                         tcw.append(field.full_name, variant.INFO.get(field.name, None))
                     if has_gt:
-                        if variant.genotype is None:
-                            val = None
-                        else:
+                        val = None
+                        if "GT" in variant.FORMAT and variant.genotype is not None:
                             val = variant.genotype.array()
                         tcw.append("FORMAT/GT", val)
                     for field in format_fields:

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/bio2zarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bio2zarr
-Version: 0.1.3
+Version: 0.1.4
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License

{bio2zarr-0.1.3 → bio2zarr-0.1.4}/docs/_config.yml

@@ -2,9 +2,8 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: bio2zarr Documentation
-author: sgkit developers
+author: the sgkit developers
 logo: logo.png
-copyright: "2024"
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
@@ -22,12 +21,19 @@ repository:
 html:
   use_issues_button: true
   use_repository_button: true
+  extra_footer: |
+      <p>
+      Documentation available under the terms of the
+      <a href="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0</a> 
+      license.
+      </p>
 
 sphinx:
   extra_extensions:
     - sphinx_click.ext
     - sphinx.ext.todo
   config:
+    html_show_copyright: false
     # This is needed to make sure that text is output in single block from
     # bash cells.
     nb_merge_streams: true