Fix CI

bio2zarr/vcf.py

@@ -1068,14 +1068,16 @@ def iter_alleles_and_genotypes(self, start, stop, shape, num_alleles):
             for variant_length, alleles in zip(
                 variant_lengths, self.iter_alleles(start, stop, num_alleles)
             ):
-                yield vcz.VariantData(variant_length, alleles, None, None)
+                # Stored ICF values are always at least 1D arrays; "rlen" is Number=1
+                # so we must extract the scalar to avoid NumPy scalar-conversion issues.
+                yield vcz.VariantData(variant_length[0], alleles, None, None)
         else:
             for variant_length, alleles, (gt, phased) in zip(
                 variant_lengths,
                 self.iter_alleles(start, stop, num_alleles),
                 self.iter_genotypes(shape, start, stop),
             ):
-                yield vcz.VariantData(variant_length, alleles, gt, phased)
+                yield vcz.VariantData(variant_length[0], alleles, gt, phased)
 
     def generate_schema(
         self, variants_chunk_size=None, samples_chunk_size=None, local_alleles=None

docs/Makefile

@@ -9,6 +9,7 @@ B2Z_VERSION:=$(shell PYTHONPATH=${PYPATH} \
 CASTS=_static/vcf2zarr_convert.cast\
 	_static/vcf2zarr_explode.cast
 
+ASCIINEMA_ARGS=-c "env PS1=\\$$\\  bash --noprofile --norc"
 
 BUILDDIR      = _build
 
@@ -36,15 +37,15 @@ sample.vcf.gz:
 
 _static/vcf2zarr_convert.cast: sample.vcf.gz
 	rm -fR sample.vcz
-	asciinema-automation -d cast_scripts/vcf2zarr_convert.sh $@
+	asciinema-automation -aa '$(ASCIINEMA_ARGS)' -d cast_scripts/vcf2zarr_convert.sh $@
 	cat _static/vcf2zarr_convert.log
 	asciinema play _static/vcf2zarr_convert.cast 
 	cp -R sample.vcz vcf2zarr
 
 # TODO rename this cast
 _static/vcf2zarr_explode.cast: sample.vcf.gz
 	rm -Rf sample.icf sample.vcz
-	asciinema-automation -d cast_scripts/vcf2zarr_explode.sh $@
+	asciinema-automation -aa '$(ASCIINEMA_ARGS)' -d cast_scripts/vcf2zarr_explode.sh $@
 	cat _static/vcf2zarr_explode.log
 	asciinema play _static/vcf2zarr_explode.cast 
 	cp -R sample.icf sample.vcz vcf2zarr

docs/build.sh

@@ -1,12 +1,12 @@
-#/bin/bash
+#!/usr/bin/env bash
 
 # Jupyter-build doesn't have an option to automatically show the 
 # saved reports, which makes it difficult to debug the reasons for 
 # build failures in CI. This is a simple wrapper to handle that.
 
 REPORTDIR=_build/html/reports
 
-jupyter-book build -Wn --keep-going .
+jupyter-book build -W -n --keep-going .
 RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then

docs/requirements.txt

@@ -1,4 +1,4 @@
 asciinema-automation
 bash_kernel
-jupyter-book
+jupyter-book<2
 sphinx-click

docs/vcf2zarr/tutorial.md

@@ -62,7 +62,7 @@ of these arrays is then stored hierarchically within
 these directories:
 
 ```{code-cell}
-tree sample.vcz
+find sample.vcz -maxdepth 2 -type d | sort
 ```
 
 You can get a better idea of what's being stored and the sizes

pyproject.toml

@@ -65,14 +65,14 @@ dev = [
   "pytest-xdist",
   "sgkit>=0.8.0",
   "tqdm",
-  "tskit>=0.6.4",
+  "tskit>=0.6.4,<1",
   "bed_reader",
   "cyvcf2"
 ]
-tskit = ["tskit>=0.6.4"]
+tskit = ["tskit>=0.6.4,<1"]
 vcf = ["cyvcf2"]
 all = [
-  "tskit>=0.6.4", 
+  "tskit>=0.6.4,<1",
   "cyvcf2"
 ]