update FastTree to v2.1.11

.github/workflows/kb_sdk_test.yaml

@@ -0,0 +1,62 @@
+name: KBase SDK Tests
+
+on:
+  push:
+    branches:
+    - master
+    - main
+  pull_request:
+    branches:
+    - master
+    - main
+    - develop
+
+jobs:
+
+  sdk_tests:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Check out GitHub repo
+      if: "!contains(github.event.head_commit.message, 'skip ci')"
+      uses: actions/checkout@v2
+
+    - name: Check out Actions CI files
+      if: "!contains(github.event.head_commit.message, 'skip ci')"
+      uses: actions/checkout@v2
+      with:
+        repository: 'kbaseapps/kb_sdk_actions'
+        path: 'kb_sdk_actions'
+
+
+    - name: Set up test environment
+      if: "!contains(github.event.head_commit.message, 'skip ci')"
+      shell: bash
+      env:
+        KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+      run: |
+        # Verify kb_sdk_actions clone worked
+        test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned"
+        # Pull kb-sdk & create startup script
+        docker pull kbase/kb-sdk
+
+        sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local"
+        test -f "test_local/test.cfg" && echo "Confirmed config exists"
+
+    - name: Configure authentication
+      if: "!contains(github.event.head_commit.message, 'skip ci')"
+      shell: bash
+      env:
+        KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+      run: |
+        # Add token to config
+        sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg
+
+    - name: Run tests
+      if: "!contains(github.event.head_commit.message, 'skip ci')"
+      shell: bash
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      run: |
+        sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
+        bash <(curl -s https://codecov.io/bash)

Dockerfile

@@ -1,4 +1,4 @@
-FROM kbase/kbase:sdkbase2.latest
+FROM kbase/sdkpython:3.8.10
 MAINTAINER KBase Developer [Dylan Chivian ([email protected])]
 
 # -----------------------------------------
@@ -7,15 +7,21 @@ MAINTAINER KBase Developer [Dylan Chivian ([email protected])]
 # install line here, a git checkout to download code, or run any other
 # installation scripts.
 
-#RUN apt-get update
+# Update
+RUN apt-get update
+
+# udpate certs
+RUN apt-get upgrade -y
+RUN sed -i 's/\(.*DST_Root_CA_X3.crt\)/!\1/' /etc/ca-certificates.conf
+RUN update-ca-certificates
+
 
 # Install ETE3
-#RUN apt-get -y --fix-missing install python-numpy python-qt4 python-lxml python-six
-# only need qt4
-#RUN apt-get -y install python-qt4
 RUN apt-get update && \
-    apt-get -y install xvfb python-qt4 && \
-    pip install ete3==3.0.0b35
+    apt-get -y install xvfb
+RUN pip install --upgrade pip
+# Note: You must use PyQt5==5.11.3 on debian
+RUN pip install ete3==3.1.2 PyQt5==5.11.3 numpy==1.23.1
 
 # -----------------------------------------
 
@@ -31,17 +37,12 @@ RUN make all
 #
 RUN mkdir -p /kb/module/FastTree/bin
 WORKDIR /kb/module/FastTree/bin
-#RUN curl http://www.microbesonline.org/fasttree/FastTree > FastTree2.1.9_64
-RUN \
-    git clone https://github.com/kbaseapps/kb_fasttree && \
-    cp kb_fasttree/src/FastTree2.1.9_64 . && \
-# INCLUDES ARE FAILING
-#     gcc -Wall -O3 -finline-functions -funroll-loops -o FastTree2.1.9_64 -lm kb_fasttree/src/FastTree.c && \
-#    cp kb_fasttree/src/FastTree2.1.9_64_DEBUG ./FastTree2.1.9_64 && \
+RUN curl -o FastTree2.1.11_64 http://www.microbesonline.org/fasttree/FastTree && \
 #RUN \
-#    curl https://github.com/dcchivian/kb_fasttree/blob/master/src/FastTree2.1.9_64 > FastTree2.1.9_64 && \
-    chmod 555 FastTree2.1.9_64 && \
-    ln -s FastTree2.1.9_64 FastTree
+#    git clone https://github.com/kbaseapps/kb_fasttree && \
+#    cp kb_fasttree/src/FastTree2.1.11_64 . && \
+    chmod 555 FastTree2.1.11_64 && \
+    ln -s FastTree2.1.11_64 FastTree
 
 
 WORKDIR /kb/module

RELEASE_NOTES.md

@@ -1,3 +1,10 @@
+### Version 1.1.0
+- update FastTree to v2.1.11
+- update Docker base image to kbase/sdkpython:3.8.10
+- update ETE3 to 3.1.2
+- update PyQt5 (note: must use PyQt5==5.11.3 on debian)
+- added Github Actions testing
+
 ### Version 1.0.3
 - update base image to sdkbase2
 

dependencies.json

@@ -0,0 +1,13 @@
+[ {
+  "module_name" : "DataFileUtil",
+  "type" : "sdk",
+  "version_tag" : "release"
+}, {
+  "module_name" : "KBaseReport",
+  "type" : "sdk",
+  "version_tag" : "release"
+}, {
+  "module_name" : "Workspace",
+  "type" : "core",
+  "file_path" : "https://raw.githubusercontent.com/kbase/workspace_deluxe/master/workspace.spec"
+} ]

kbase.yml

@@ -8,7 +8,7 @@ service-language:
     python
 
 module-version:
-    1.0.3
+    1.1.0
 
 owners:
     [dylan]