Merge pull request #196 from jeromekelleher/improve-casts

Improve cast infrastructure

Author: jeromekelleher

.github/workflows/docs.yml

@@ -34,10 +34,6 @@ jobs:
       - name: Install package
         run: |
           python3 -m pip install .
-          
-      - name: Record casts
-        run: |
-          asciinema-automation docs/cast_scripts/vcf2zarr_convert.sh docs/_static/demo.cast
 
       - name: Build Docs
         run: |

docs/Makefile

@@ -5,14 +5,21 @@ B2Z_VERSION:=$(shell PYTHONPATH=${PYPATH} \
 
 BUILDDIR      = _build
 
-dev:
+dev: _static/vcf2zarr_convert.cast
 	PYTHONPATH=${PYPATH} ./build.sh
 
-dist:
+dist: _static/vcf2zarr_convert.cast
 	@echo Building distribution for bio2zarr version ${B2Z_VERSION}
 	cd doxygen && doxygen
 	sed -i -e s/__BIO2ZARR_VERSION__/${B2Z_VERSION}/g _config.yml
 	PYTHONPATH=${PYPATH} ./build.sh
 
 clean:
 	rm -fR $(BUILDDIR)
+
+
+_static/vcf2zarr_convert.cast:
+	rm -fR sample.zarr
+	cp ../tests/data/vcf/sample.vcf.gz ./
+	cp ../tests/data/vcf/sample.vcf.gz.tbi ./
+	asciinema-automation cast_scripts/vcf2zarr_convert.sh _static/vcf2zarr_convert.cast

docs/cast_scripts/vcf2zarr_convert.sh

@@ -1,3 +1,3 @@
 #$ delay 10
-vcf2zarr convert tests/data/vcf/sample.bcf tmp.zarr -p 4
+vcf2zarr convert sample.vcf.gz sample.zarr -p 4
 #$ expect \$ 

docs/vcf2zarr_tutorial.md

@@ -11,9 +11,9 @@ kernelspec:
 ---
 # Vcf2zarr tutorial
 
-This is a step-by-step tutorial showing you how to convert your 
-VCF data into Zarr format. There's three different ways to 
-convert your data, basically providing different levels of 
+This is a step-by-step tutorial showing you how to convert your
+VCF data into Zarr format. There's three different ways to
+convert your data, basically providing different levels of
 convenience and flexibility corresponding to what you might
 need for small, intermediate and large datasets.
 
@@ -23,10 +23,11 @@ need for small, intermediate and large datasets.
 <!-- vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf -->
 <!-- ``` -->
 
- <div id="demo"></div>
+ <div id="vcf2zarr_convert"></div>
  <script>
- AsciinemaPlayer.create('_static/demo.cast', document.getElementById('demo'), {
-    cols:80, 
+ AsciinemaPlayer.create('_static/vcf2zarr_convert.cast',
+    document.getElementById('vcf2zarr_convert'), {
+    cols:80,
     rows:12
  });
  </script>