bio2zarr 0.1.2__tar.gz → 0.1.4__tar.gz

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/.github/workflows/ci.yml

@@ -138,7 +138,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        zarr: ["==2.18.3", ">=3"]
+        zarr: ["==2.18.3", ">=3.0.3"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -153,4 +153,4 @@ jobs:
           python -m pip install 'zarr${{ matrix.zarr }}'
       - name: Run tests
         run: |
-          python -m pytest -k "not test_double_encode_partition"
+          python -m pytest

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/CHANGELOG.md

@@ -1,3 +1,13 @@
+# 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
+
+- Support out-of-order field definitions in the VCF header (#322, @ACEnglish)
+
 # 0.1.2 2025-02-04
 
 - Reduce memory requirement for encoding genotypes with large sample sizes
@@ -20,7 +30,7 @@ Breaking changes
 
 Maintenance release:
 
-- Pin numpy to < 2 
+- Pin numpy to < 2
 - Pin Zarr to < 3
 
 # 0.1.0 2024-06-10

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bio2zarr
-Version: 0.1.2
+Version: 0.1.4
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/bio2zarr/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.2'
-__version_tuple__ = version_tuple = (0, 1, 2)
+__version__ = version = '0.1.4'
+__version_tuple__ = version_tuple = (0, 1, 4)

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/bio2zarr/vcf2zarr/icf.py

@@ -41,7 +41,7 @@ class VcfFieldSummary(core.JsonDataclass):
         return VcfFieldSummary(**d)
 
 
-@dataclasses.dataclass
+@dataclasses.dataclass(order=True)
 class VcfField:
     category: str
     name: str
@@ -192,6 +192,16 @@ class IcfMetadata(core.JsonDataclass):
         d["contigs"] = [Contig(**cd) for cd in d["contigs"]]
         return IcfMetadata(**d)
 
+    def __eq__(self, other):
+        if not isinstance(other, IcfMetadata):
+            return NotImplemented
+        return (
+            self.samples == other.samples
+            and self.contigs == other.contigs
+            and self.filters == other.filters
+            and sorted(self.fields) == sorted(other.fields)
+        )
+
 
 def fixed_vcf_field_definitions():
     def make_field_def(name, vcf_type, vcf_number):
@@ -1085,9 +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-0.1.2 → bio2zarr-0.1.4}/bio2zarr/zarr_utils.py

@@ -1,9 +1,8 @@
 import zarr
-from packaging.version import Version
 
 
 def zarr_v3() -> bool:
-    return Version(zarr.__version__).major >= 3
+    return zarr.__version__ >= "3"
 
 
 if zarr_v3():

{bio2zarr-0.1.2 → bio2zarr-0.1.4}/bio2zarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: bio2zarr
-Version: 0.1.2
+Version: 0.1.4
 Summary: Convert bioinformatics data to Zarr
 Author-email: sgkit Developers <project@sgkit.dev>
 License:                                  Apache License

{bio2zarr-0.1.2 → 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