Merge pull request #439 from kbase/develop

D->Main

.github/workflows/ee2-tests.yml

@@ -11,7 +11,7 @@
 name: Execution Engine 2 Test Suite
 
 on:
-  [push, pull_request]
+  [pull_request]
 
 jobs:
   build:
@@ -43,4 +43,3 @@ jobs:
         cp test/env/test.travis.env test.env
         make test-coverage
         codecov
-

.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
+      - merged
+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/prod_release.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

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
 -   repo: https://github.com/ambv/black
-    rev: 21.5b0
+    rev: 22.1.0
     hooks:
     - id: black
       exclude: '.+Impl.py'
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: ''
+    rev: '3.9.2'
     hooks:
     - id: flake8

Dockerfile

@@ -1,7 +1,7 @@
-FROM quay.io/kbase/sdkbase2:python
+FROM kbase/sdkpython:3.8.0
 MAINTAINER KBase Developer
 
-RUN apt-get clean all && apt-get update --fix-missing -y
+RUN apt-get clean all && apt-get update --fix-missing -y && apt-get upgrade -y
 
 # -----------------------------------------
 # In this section, you can install any system dependencies required
@@ -11,21 +11,19 @@ RUN apt-get clean all && apt-get update --fix-missing -y
 RUN apt-get install -y gcc wget vim htop tmpreaper
 RUN mkdir -p /etc/apt/sources.list.d
 
+# Install condor
+RUN curl -fsSL https://get.htcondor.org | /bin/bash -s -- --no-dry-run
 
-RUN DEBIAN_FRONTEND=noninteractive wget -qO - https://research.cs.wisc.edu/htcondor/debian/HTCondor-Release.gpg.key | apt-key add - \
-    && echo "deb http://research.cs.wisc.edu/htcondor/debian/8.8/stretch stretch contrib" >> /etc/apt/sources.list \
-    && echo "deb-src http://research.cs.wisc.edu/htcondor/debian/8.8/stretch stretch contrib" >> /etc/apt/sources.list \
-    && apt-get update -y \
-    && apt-get install -y condor
+# Install jars for testing purposes
+# Uncomment this if you want to run tests inside the ee2 container on MacOSX
+# RUN cd /opt && git clone https://github.com/kbase/jars && cd -
 
-# install jars
-# perhaps we should have test and prod dockerfiles to avoid jars and mongo installs in prod
-RUN cd /opt \
-    && git clone https://github.com/kbase/jars \
-    && cd -
-
-# Remove due to cve-2021-4104 issue in spin (log4j)
-RUN rm /opt/jars/lib/jars/dockerjava/docker-java-shaded-3.0.14.jar
+
+# Install DOCKERIZE
+RUN curl -o /tmp/dockerize.tgz https://raw.githubusercontent.com/kbase/dockerize/dist/dockerize-linux-amd64-v0.5.0.tar.gz && \
+      cd /usr/bin && \
+      tar xvzf /tmp/dockerize.tgz && \
+      rm /tmp/dockerize.tgz
 
 
 # install mongodb
@@ -65,6 +63,10 @@ RUN mkdir -p /kb/module/work && chmod -R a+rw /kb/module && mkdir -p /etc/condor
 WORKDIR /kb/module
 RUN make all
 
+# Remove Jars and old Conda for Trivy Scans and after compilation is done
+RUN rm -rf /sdk && rm -rf /opt
+RUN rm -rf /miniconda-latest/pkgs/conda-4.12.0-py39h06a4308_0/info/test/tests/data/env_metadata
+
 WORKDIR /kb/module/scripts
 RUN chmod +x download_runner.sh && ./download_runner.sh
 

Pipfile

@@ -64,7 +64,7 @@ slackclient = "==2.7.1"
 toml = "==0.10.1"
 tqdm = "==4.42.1"
 typing-extensions = "==3.7.4.3"
-ujson = "==1.35"
+ujson = "==5.2.0"
 urllib3 = "==1.25.8"
 uvloop = "==0.12.2"
 websockets = "==6.0"