Merge pull request #23 from USDA-ARS-GBRU/dockerpatch

Dockerpatch

CHANGELOG.md

@@ -1,11 +1,11 @@
 # v0.4.0
 
-* changed the cli flag `--filter_by_locus` to `--filter_by_attribute`  and added the flag `--attribute_key` so that keys other than the addribute key "locus_tag" can be filtered.
-* Changed the cli to add `--raw_output_only`. This option allows the user to just get hte guides that met LSR and distance criteria without doing any parsing of the genome annotation files.
-* updated caching for Streamlit 1.26
-* updated GC and position methods for Biopython 1.8.1
-* replaced append methods with concat methods for Pandas 2.1.1
-* output data is now gzipped
-* updated Dockerfile to use minimamba base image
-* 
+*  changed the cli flag `--filter_by_locus` to `--filter_by_attribute`  and added the flag `--attribute_key` so that keys other than the addribute key "locus_tag" can be filtered.
+*  Changed the cli to add `--raw_output_only`. This option allows the user to just get hte guides that met LSR and distance criteria without doing any parsing of the genome annotation files.
+*  updated caching for Streamlit 1.26
+*  updated GC and position methods for Biopython 1.8.1
+*  replaced append methods with concat methods for Pandas 2.1.1
+*  output data is now gzipped
+*  updated Dockerfile to use minimamba base image
+*  Updates to python dependencies
 

README.md

@@ -40,7 +40,6 @@ docker pull ghcr.io/usda-ars-gbru/guidemaker-webapp
 docker pull ghcr.io/usda-ars-gbru/guidemaker-nonavx
 ```
 
-
 ### Bioconda
 
 ```bash
@@ -71,10 +70,6 @@ guidemaker -h
     guidemaker -h
 ```
 
-
-```
-
-
 ### Dependencies
 
 *   ``pybedtools``

coverage.xml

@@ -1,12 +1,12 @@
 <?xml version="1.0" ?>
-<coverage version="7.3.1" timestamp="1694793608190" lines-valid="1164" lines-covered="683" line-rate="0.5868" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.3.1" timestamp="1694802720014" lines-valid="1163" lines-covered="682" line-rate="0.5864" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.3.1 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
 		<source>/Users/rivers/Documents/guidemaker/guidemaker</source>
 	</sources>
 	<packages>
-		<package name="." line-rate="0.681" branch-rate="0" complexity="0">
+		<package name="." line-rate="0.6806" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -70,7 +70,7 @@
 						<line number="85" hits="1"/>
 					</lines>
 				</class>
-				<class name="cli.py" filename="cli.py" complexity="0" line-rate="0.08152" branch-rate="0">
+				<class name="cli.py" filename="cli.py" complexity="0" line-rate="0.0765" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="6" hits="1"/>
@@ -80,7 +80,6 @@
 						<line number="11" hits="1"/>
 						<line number="12" hits="1"/>
 						<line number="13" hits="1"/>
-						<line number="14" hits="1"/>
 						<line number="16" hits="1"/>
 						<line number="17" hits="1"/>
 						<line number="19" hits="1"/>

docker-images/nonavx/Dockerfile

@@ -16,12 +16,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     python3-dev \
     zlib1g-dev \
-    git
+    git && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
 USER $MAMBA_USER
 
 # RUN pip install --no-binary :all: nmslib
 
-RUN git clone -b https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install .
+RUN git clone https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install .
 
 # port on the docker container
 EXPOSE 8501 

docker-images/webapp/Dockerfile

@@ -13,15 +13,16 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 USER root
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential \
-    python3-dev \
-    zlib1g-dev \
-    git
+    build-essential=12.9 \
+    python3-dev=3.9 \
+    zlib1g-dev=1.2 \
+    git=2.30 && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
 USER $MAMBA_USER
 
 RUN pip install --no-binary :all: nmslib
 
-RUN git clone -b https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install .
+RUN git clone https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install .
 
 # port on the docker container
 EXPOSE 8501 

guidemaker/cli.py

@@ -11,7 +11,7 @@
 import os
 import yaml
 import textwrap
-import pandas as pd
+
 
 import pybedtools
 from Bio import SeqIO