Update kb_SPAdesImpl.py

.github/workflows/kb_sdk_test.yaml

@@ -1,62 +1,33 @@
-name: KBase SDK Tests
+name: Run KBase SDK Tests
 
 on:
   push:
-    branches:
-    - master
-    - main
   pull_request:
-    branches:
-    - master
-    - main
-    - develop
 
 jobs:
-
-  sdk_tests:
+  test:
     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)
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download kb-sdk, set up path, and modify kb-sdk helper script
+        run: |
+          mkdir -p $(pwd)/bin
+          docker run ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 genscript > $(pwd)/bin/kb-sdk
+          docker tag ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 kbase/kb-sdk:latest
+          chmod 755 $(pwd)/bin/kb-sdk
+          echo "$(pwd)/bin" >> $GITHUB_PATH
+          sed -i 's/docker run -it/docker run /g' $(pwd)/bin/kb-sdk
+
+      - name: Setup KBase SDK Tests and inject kbase token
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          kb-sdk test || true
+          mkdir -p ./test_local
+          sed -i "s/^test_token=.*$/test_token=$KBASE_TEST_TOKEN/g" ./test_local/test.cfg
+        continue-on-error: true
+
+      - name: Run KBase SDK Tests
+        run: kb-sdk test

Dockerfile

@@ -1,4 +1,4 @@
-FROM kbase/sdkbase2:python
+FROM kbase/sdkpython:3.8.0
 MAINTAINER KBase Developer
 # -----------------------------------------
 # In this section, you can install any system dependencies required
@@ -14,13 +14,13 @@ RUN apt-get update \
     && apt-get -y install gcc
 
 RUN pip install --upgrade pip \
-    && pip3 install psutil \
+    && pip3 install psutil numpy pyyaml \
     && python --version
 
 ENV SPADES_VERSION='3.15.3'
 
 RUN cd /opt \
-    && wget http://cab.spbu.ru/files/release${SPADES_VERSION}/SPAdes-${SPADES_VERSION}-Linux.tar.gz \
+    && wget https://github.com/ablab/spades/releases/download/v3.15.3/SPAdes-3.15.3-Linux.tar.gz \
     && tar -xvzf SPAdes-${SPADES_VERSION}-Linux.tar.gz \
     && rm SPAdes-${SPADES_VERSION}-Linux.tar.gz
 

lib/kb_SPAdes/kb_SPAdesImpl.py

@@ -81,8 +81,8 @@ class kb_SPAdes:
     MAX_THREADS_META = 128  # Increase threads for metagenomic assemblies
     MEMORY_OFFSET_GB = 1  # 1GB
     MIN_MEMORY_GB = 4
-    MAX_MEMORY_GB_SPADES = 500
-    MAX_MEMORY_GB_META_SPADES = 1000
+    MAX_MEMORY_GB_SPADES = 200
+    MAX_MEMORY_GB_META_SPADES = 490
     GB = 1000000000
 
     URL_WS = 'workspace-url'