Merge pull request #50 from broadinstitute/ct-update-viral-core-2.3.3

bump viral-core version 2.3.1 -> 2.3.3

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.3.1
+FROM quay.io/broadinstitute/viral-core:2.3.3
 
 LABEL maintainer "[email protected]"
 

docs/requirements.txt

@@ -1,8 +1,8 @@
-jinja2==3.1.2 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
-Sphinx==5.3.0 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
-sphinx-argparse
-sphinx-rtd-theme==1.1.1
+jinja2==3.1.4 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
+Sphinx==7.4.7 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
+sphinx-argparse==0.5.2
+sphinx-rtd-theme>=2.0.0
 matplotlib>=2.2.4
-PyYAML==6.0
+PyYAML==6.0.1
 mock==5.0.1
 recommonmark

test/unit/test_integration_kaiju.py

@@ -10,7 +10,7 @@
 import shutil
 import tempfile
 
-import lxml.html.clean
+#import lxml.html.clean
 import pytest
 from Bio import SeqIO
 

test/unit/test_integration_kraken2.py

@@ -5,7 +5,7 @@
 import os.path
 from os.path import join
 
-import lxml.html.clean
+#import lxml.html.clean
 import pytest
 
 import metagenomics