Fix CI

Author: benjeffery

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