0.1.0 release bits

CHANGELOG.md

@@ -1,5 +1,21 @@
 # Changelog
 
+## [0.1.0] - 2025-05-29
+
+Improvements:
+
+- Support filtering by FILTER (#217), CHROM (#223) and general string values (#220)
+- Support regions (-r/-t), filter expressions (-i/-e) and samples (-s) in query command  (#205)
+- Various improvements to support VCZ datasets produced from tskit and plink files by bio2zarr.
+- Use a fully dynamically generated header via ``vcf_meta_information`` attributes
+(#208). Requires vcf-zarr version >= 0.4 (bio2zarr >= 0.1.6) to fully recover the original
+header.
+- Add --version (#197)
+
+Breaking:
+
+- Update minimum Click version to 8.2.0 (#206)
+
 ## [0.0.2] - 2025-04-04
 
 Important bugfixes for filtering language and sample subsetting.

README.md

@@ -1,4 +1,5 @@
 [![CI](https://github.com/sgkit-dev/vcztools/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/sgkit-dev/vcztools/actions/workflows/ci.yml)
+[![PyPI Downloads](https://static.pepy.tech/badge/vcztools)](https://pepy.tech/projects/vcztools)
 
 # vcztools
 Partial reimplementation of bcftools for [VCF Zarr](https://github.com/sgkit-dev/vcf-zarr-spec/)
@@ -17,24 +18,24 @@ python3 -m pip install vcztools
 ```
 vcztools view <path.vcz>
 ```
-or 
+or
 ```
 python -m vcztools view <path.vcz>
 ```
-should be equivalent to running 
+should be equivalent to running
 ```
 bcftools view <path.vcf.gz>
 ```
 
-See the [bio2zarr](https://sgkit-dev.github.io/bio2zarr/) project for help in 
+See the [bio2zarr](https://sgkit-dev.github.io/bio2zarr/) project for help in
 converting VCF files to Zarr.
 
 ## Goals
 
 Vcztools aims to be a drop-in replacement for a subset of bcftools functionality.
 Currently supported are the ``view``, ``query`` and ``index -s/-n`` commands.
 
-We aim for 100% compatibility so if you notice a difference between the output of 
+We aim for 100% compatibility so if you notice a difference between the output of
 vcztools and bcftools please do open an issue.
 
 ## Cloud stores
@@ -62,6 +63,6 @@ python -m vcztools view s3://<bucket-name>/path/to.vcz
 
 ## Development
 
-Vcztools is under active development and contributions are warmly welcomed. Please 
+Vcztools is under active development and contributions are warmly welcomed. Please
 see the project on [GitHub](https://github.com/sgkit-dev/vcztools).
 

vcztools/cli.py

@@ -111,6 +111,11 @@ def list_commands(self, ctx):
 )
 @handle_exception
 def index(path, nrecords, stats):
+    """
+    Query the number of records in a VCZ dataset. This subcommand only
+    implements the --nrecords and --stats options and does not build any
+    indexes.
+    """
     if nrecords and stats:
         raise click.UsageError("Expected only one of --stats or --nrecords options")
     if nrecords:
@@ -156,6 +161,15 @@ def query(
     include,
     exclude,
 ):
+    """
+    Transform VCZ into user-defined formats with efficient subsetting and
+    filtering. Intended as a drop-in replacement for bcftools query, where we
+    replace the VCF file path with a VCZ dataset URL.
+
+    This is an early version and not feature complete: if you are missing a
+    particular piece of functionality please open an issue at
+    https://github.com/sgkit-dev/vcztools/issues
+    """
     if list_samples:
         # bcftools query -l ignores the --output option and always writes to stdout
         output = sys.stdout
@@ -241,6 +255,15 @@ def view(
     include,
     exclude,
 ):
+    """
+    Convert VCZ dataset to VCF with efficient subsetting and filtering.
+    Intended as a drop-in replacement for bcftools view, where
+    we replace the VCF file path with a VCZ dataset URL.
+
+    This is an early version and not feature complete: if you are missing a
+    particular piece of functionality please open an issue at
+    https://github.com/sgkit-dev/vcztools/issues
+    """
     suffix = output.name.split(".")[-1]
     # Exclude suffixes which require bgzipped or BCF output:
     # https://github.com/samtools/htslib/blob/329e7943b7ba3f0af15b0eaa00a367a1ac15bd83/vcf.c#L3815