Initial Release

.github/workflows/manual-build.yml

@@ -0,0 +1,11 @@
+---
+name: Manual Build & Push
+on:
+ workflow_dispatch:
+jobs:
+  build-push:
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: br-${{ github.ref_name }}
+    secrets: inherit

.github/workflows/pr_build.yml

@@ -0,0 +1,43 @@
+---
+name: Pull Request Build, Tag, & Push
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+jobs:
+  build-develop-open:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build.yml@main
+    secrets: inherit
+  build-develop-merge:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: pr-${{ github.event.number }},latest
+    secrets: inherit
+  build-main-open:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }}
+    secrets: inherit
+  build-main-merge:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }},latest-rc
+    secrets: inherit
+  trivy-scans:
+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit

.github/workflows/release-main.yml

@@ -0,0 +1,25 @@
+---
+name: Release - Build & Push Image
+on:
+  release:
+    branches:
+      - main
+      - master
+    types: [ published ]
+jobs:
+  check-source-branch:
+    uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
+    with:
+      build_branch: '${{ github.event.release.target_commitish }}'
+  validate-release-tag:
+    needs: check-source-branch
+    uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
+    with:
+      release_tag: '${{ github.event.release.tag_name }}'
+  build-push:
+    needs: validate-release-tag
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: '${{ github.event.release.tag_name }},latest'
+    secrets: inherit

Dockerfile

@@ -1,36 +1,54 @@
 FROM ubuntu:20.04
 
+# Note that these labels need to be manually updated with the actual contents of the image
 LABEL maintainer="[email protected]"
 LABEL us.kbase.ubuntu="20.04"
-LABEL us.kbase.python="3.8.4"
-LABEL us.kbase.sdk="1.0.18"
+LABEL us.kbase.python="3.9.12"
+LABEL us.kbase.sdk="1.2.1"
+LABEL us.kbase.sdkcommit="8def489f648a7ff5657d33ed05f41c60f4766e1b"
 
+# Fix KBase Catalog Registration Issue
+ENV PIP_PROGRESS_BAR=off
+
+# Install system dependencies
 RUN \
     apt-get -y update && \
+    apt-get -y upgrade && \
     export DEBIAN_FRONTEND=noninteractive && \
     export TZ=Etc/UTC && \
-    apt-get -y install gcc make curl git openjdk-8-jre
+    apt-get -y install gcc make curl git openjdk-8-jre unzip htop
 
 # Copy in the SDK
-COPY --from=kbase/kb-sdk:20180808 /src /sdk
+COPY --from=kbase/kb-sdk:1.2.1 /src /sdk
 RUN sed -i 's|/src|/sdk|g' /sdk/bin/*
 
+
+# Install Conda version py39_4.12.0 and Python 3.9.12
+ENV CONDA_VERSION=py39_4.12.0
+ENV CONDA_INSTALL_DIR=/opt/conda/py39_4.12.0
+
 RUN \
-    V=py38_4.10.3 && \
-    curl -o conda.sh -s https://repo.anaconda.com/miniconda/Miniconda3-${V}-Linux-x86_64.sh && \
-    sh ./conda.sh -b -p /opt/conda3 && \
+    echo "Installing to ${CONDA_INSTALL_DIR}"  && \
+    curl -o conda.sh -s https://repo.anaconda.com/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh && \
+    sh ./conda.sh -b -p ${CONDA_INSTALL_DIR} && \
     rm conda.sh
 
-ENV PATH=/opt/conda3/bin:$PATH:/sdk/bin
+# Add in some legacy modules
 
-# Install packages including mamba
-RUN \
-    conda install -c conda-forge mamba
+ADD biokbase $CONDA_INSTALL_DIR/lib/biokbase
+ADD biokbase/user-env.sh /kb/deployment/user-env.sh
+ADD requirements.txt /tmp/requirements.txt
 
-ADD ./requirements.txt /tmp/
-RUN \
-    pip install -r /tmp/requirements.txt
+ENV PATH=$CONDA_INSTALL_DIR/bin:/sdk/bin:$PATH
+run env
 
-# Add in some legacy modules
-ADD biokbase /opt/conda3/lib/python3.8/site-packages/biokbase
+# Configure Conda and Install Mamba 
+RUN \
+    conda config --add channels conda-forge  && \
+    conda config --set channel_priority strict && \
+    conda install -y mamba=0.15.3
 
+#Install packages required for base image
+RUN \ 
+    which pip && \
+    pip install -r /tmp/requirements.txt

README.md

@@ -1,6 +1,6 @@
 # SDK Base Python Image
 
-This is a very minimal base python image for building KBase SDK apps.
+This is a very minimal base python image for building KBase SDK apps. It also contains a copy of the KBase SDK.
 
 
 ## Contents
@@ -9,7 +9,7 @@ This image just contains the basics.
 
 * Ubuntu 20.04 base image
 * Dependencies packages:  gcc make curl git openjdk-8-jre
-* Installation of the kb-sdk tool (1.0.18)
-* Python 3.8 via Conda
+* Installation of the kb-sdk tool (1.2.1)
+* Python 3.9.13 via Conda
 * Mamba for Conda package installation
-* A select set of python modules 
+* A select set of python modules in the requirements.txt 

biokbase/user-env.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+# In order to avoid `./scripts/entrypoint.sh: line 3: /kb/deployment/user-env.sh: No such file or directory`
+# This file is now here
+echo "user-env.sh is ignored"

requirements.txt

@@ -1,5 +1,7 @@
-requests
-coverage
-nose
-sphinx
-jsonrpcbase
+requests==2.27.1
+coverage==6.3.3
+nose==1.3.7
+sphinx==4.5.0
+jsonrpcbase==0.2.0
+pytest==7.1.1
+pytest-cov==3.0.0