Merge pull request #192 from jeromekelleher/first-tutorial-infra

First pass at executable tutorial

Author: jeromekelleher

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Build Docs
+name: Docs
 
 on:
   pull_request:
@@ -10,7 +10,7 @@ on:
 
 jobs:
   build-docs:
-    name: Docs
+    name: Build
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
@@ -29,6 +29,11 @@ jobs:
         run: |
           pip install --upgrade pip wheel
           pip install -r docs/requirements.txt
+          python3 -m bash_kernel.install
+
+      - name: Install package
+        run: |
+          python3 -m pip install .
 
       - name: Build Docs
         run: |

docs/_toc.yml

@@ -1,4 +1,5 @@
 format: jb-book
 root: intro
 chapters:
+- file: vcf2zarr_tutorial
 - file: cli

docs/requirements.txt

@@ -1,11 +1,3 @@
-bed_reader
-click
-cyvcf2
+bash_kernel
 jupyter-book
-msprime
-pysam
-sgkit
 sphinx-click
-tabulate
-tqdm
-zarr>=2.17

docs/vcf2zarr_tutorial.md

@@ -0,0 +1,28 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+kernelspec:
+  display_name: Bash
+  language: bash
+  name: bash
+---
+# 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 
+convenience and flexibility corresponding to what you might
+need for small, intermediate and large datasets.
+
+## Small
+
+```{code-cell} bash
+vcf2zarr convert ../tests/data/vcf/sample.vcf.gz sample.zarr -vf
+```
+
+## Intermediate
+
+## Large