From 4d944b629d0fd70d023019a93a2ff179d5c769b0 Mon Sep 17 00:00:00 2001
From: Daniel Bolin <axbolin@iu.edu>
Date: Wed, 2 Oct 2024 14:09:40 -0400
Subject: [PATCH 1/2] feat: Enable onclass annotation method in popv

Popv has fixed the bug that made onclass fail in fast mode annotations
---
 containers/popv/context/main.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/containers/popv/context/main.py b/containers/popv/context/main.py
index b6e357a..1fa8549 100644
--- a/containers/popv/context/main.py
+++ b/containers/popv/context/main.py
@@ -126,14 +126,12 @@ def do_run(
         data = self.prepare_query(data, organ, metadata["model"], options)
         popv.annotation.annotate_data(
             data,
-            # TODO: onclass has been removed due to error in fast mode
-            # seen_result_key is not added to the result in fast mode but still expected during compute_consensus
             methods=[
                 "knn_on_scvi",
                 "scanvi",
                 "svm",
                 "rf",
-                # "onclass",
+                "onclass",
                 "celltypist",
             ],
         )

From 6719457e9bf42d507463fe5b9815c94e8ce4ebb1 Mon Sep 17 00:00:00 2001
From: Daniel Bolin <axbolin@iu.edu>
Date: Wed, 2 Oct 2024 14:10:56 -0400
Subject: [PATCH 2/2] refactor: Skip python install in popv docker

Base image already provides python & pip
---
 containers/popv/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/containers/popv/Dockerfile b/containers/popv/Dockerfile
index 1467a68..d3415e3 100644
--- a/containers/popv/Dockerfile
+++ b/containers/popv/Dockerfile
@@ -1,6 +1,6 @@
 FROM tensorflow/tensorflow:2.16.1
 
-RUN apt-get -y update && apt-get -y install python3-dev python3-pip g++ git wget && apt-get clean
+RUN apt-get -y update && apt-get -y install git && apt-get clean
 
 COPY context/download-ontology.sh .
 RUN ./download-ontology.sh