From f6bf7baebb256bdd21cad6ff48a3e36bb69f104c Mon Sep 17 00:00:00 2001
From: John Huddleston <huddlej@gmail.com>
Date: Mon, 31 Jul 2023 14:10:53 -0700
Subject: [PATCH] Use vl-convert to save altair figures for reports

---
 notebooks/plot-counts-per-lineage.py.ipynb | 21 +++++++--------------
 workflow/envs/notebook.yaml                |  6 +++---
 2 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/notebooks/plot-counts-per-lineage.py.ipynb b/notebooks/plot-counts-per-lineage.py.ipynb
index 44effd4d..904755d0 100644
--- a/notebooks/plot-counts-per-lineage.py.ipynb
+++ b/notebooks/plot-counts-per-lineage.py.ipynb
@@ -4,7 +4,6 @@
    "cell_type": "markdown",
    "id": "0c5449d8-365a-4292-a772-6c1a79f5e43d",
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Plot counts per lineage through time"
    ]
@@ -13,7 +12,6 @@
    "cell_type": "markdown",
    "id": "4e0df709-e102-488f-8829-fe71a8433ae6",
    "metadata": {},
-   "outputs": [],
    "source": [
     "## Imports"
    ]
@@ -26,7 +24,6 @@
    "outputs": [],
    "source": [
     "import altair as alt\n",
-    "from altair_saver import save\n",
     "import pandas as pd"
    ]
   },
@@ -34,7 +31,6 @@
    "cell_type": "markdown",
    "id": "06cbed4f-f94d-4d33-9b83-7354626d791f",
    "metadata": {},
-   "outputs": [],
    "source": [
     "## Configuration"
    ]
@@ -46,14 +42,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "min_date = \"2021-08-01\""
+    "min_date = \"2022-01-01\""
    ]
   },
   {
    "cell_type": "markdown",
    "id": "43c90ae7-2cac-44d1-9f8f-da40a0db7f20",
    "metadata": {},
-   "outputs": [],
    "source": [
     "## Load metadata"
    ]
@@ -217,9 +212,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "038b9332-fcf1-49ac-9342-4e9503fe8ec2",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "all_lineages_chart = alt.Chart(binned_counts).mark_line(point=alt.OverlayMarkDef(size=100)).encode(\n",
@@ -243,11 +236,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "72a0bb83",
+   "id": "03d21429-ec5e-4bf6-b4fc-108d6f3a6e72",
    "metadata": {},
    "outputs": [],
    "source": [
-    "save(all_lineages_chart, snakemake.output.total_sample_count_by_lineage)"
+    "all_lineages_chart.save(snakemake.output.total_sample_count_by_lineage, scale_factor=2.0)"
    ]
   },
   {
@@ -306,7 +299,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "save(h1n1pdm_chart, snakemake.output.total_sample_count_h1n1pdm)"
+    "h1n1pdm_chart.save(snakemake.output.total_sample_count_h1n1pdm, scale_factor=2.0)"
    ]
   },
   {
@@ -365,7 +358,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "save(h3n2_chart, snakemake.output.total_sample_count_h3n2)"
+    "h3n2_chart.save(snakemake.output.total_sample_count_h3n2, scale_factor=2.0)"
    ]
   },
   {
@@ -414,7 +407,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "save(vic_chart, snakemake.output.total_sample_count_vic)"
+    "vic_chart.save(snakemake.output.total_sample_count_vic, scale_factor=2.0)"
    ]
   },
   {
diff --git a/workflow/envs/notebook.yaml b/workflow/envs/notebook.yaml
index 2f5cc0fb..fb8ad8c2 100644
--- a/workflow/envs/notebook.yaml
+++ b/workflow/envs/notebook.yaml
@@ -3,9 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - altair=4.2.0
-  - altair_saver=0.5.0
+  - altair=5.0.1
   - jupyter=1.0
-  - jupyterlab_code_formatter=1.4
+  - jupyterlab_code_formatter=2.2.1
   - pandas=1.5.0
   - python=3.9*
+  - vl-convert-python=0.11.1