PUBLIC-2591: App code extraction, test improvement

.github/workflows/kb_sdk_test.yaml

@@ -2,9 +2,6 @@ name: KBase SDK Tests
 
 on:
     pull_request:
-        branches:
-            - main
-            - develop
 
 jobs:
     sdk_tests:

Dockerfile

@@ -4,25 +4,24 @@ LABEL maintainer="KBase Developers [[email protected]]"
 WORKDIR /kb/module
 # Update
 RUN apt-get update \
-    && apt-get upgrade -y \
-    && sed -i 's/\(.*DST_Root_CA_X3.crt\)/!\1/' /etc/ca-certificates.conf \
-    && update-ca-certificates \
-    && apt-get -y install xvfb \
-    && pip install --upgrade pip && \
+    && apt-get upgrade -y && \
+    update-ca-certificates && \
+    apt-get -y install xvfb curl && \
     # Install FastTree
     mkdir -p /kb/module/FastTree/bin && \
     cd /kb/module/FastTree/bin && \
     curl -o FastTree http://www.microbesonline.org/fasttree/FastTree && \
-    chmod 555 FastTree
+    chmod 555 FastTree && \
+    pip install --upgrade pip && \
+    # install the python requirements
+    # Note: You must use PyQt5==5.11.3 on debian
+    pip install ete3==3.1.2 PyQt5==5.11.3 numpy==1.23.1 pytest coverage pytest-cov vcrpy
 
 COPY ./ /kb/module
 
 RUN mkdir -p /kb/module/work && \
     chmod -R a+rw /kb/module && \
-    mv /kb/module/compile_report.json /kb/module/work/compile_report.json && \
-    # install the python requirements
-    # Note: You must use PyQt5==5.11.3 on debian
-    pip install ete3==3.1.2 PyQt5==5.11.3 numpy==1.23.1 pytest coverage pytest-cov
+    mv /kb/module/compile_report.json /kb/module/work/compile_report.json
 
 WORKDIR /kb/module
 ENTRYPOINT [ "./scripts/entrypoint.sh" ]

deploy.cfg

@@ -1,23 +1,4 @@
 [kb_fasttree]
 kbase-endpoint = {{ kbase_endpoint }}
-job-service-url = {{ job_service_url }}
 workspace-url = {{ workspace_url }}
-shock-url = {{ shock_url }}
-{% if handle_url %}
-handle-service-url = {{ handle_url }}
-{% else %}
-handle-service-url = {{ kbase_endpoint }}/handle_service
-{% endif %}
-{% if srv_wiz_url %}
-service-wizard-url = {{ srv_wiz_url }}
-{% else %}
-service-wizard-url = {{ kbase_endpoint }}/service_wizard
-{% endif %}
-njsw-url = {{ njsw_url }}
-{% if auth_service_url %}
-auth-service-url = {{ auth_service_url }}
-{% endif %}
-{% if auth_service_url_allow_insecure %}
-auth-service-url-allow-insecure = {{ auth_service_url_allow_insecure }}
-{% endif %}
 scratch = /kb/module/work/tmp