Adding GHAs for building module and code QC

.coveragerc

@@ -0,0 +1,5 @@
+[html]
+directory = ./python-coverage
+
+[xml]
+output = ./python-coverage/coverage.xml

.github/dependabot.yml

@@ -0,0 +1,19 @@
+version: 2
+updates:
+- package-ecosystem: docker
+  directory: "/"
+  schedule:
+    interval: monthly
+    time: '11:00'
+  open-pull-requests-limit: 10
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: monthly
+    time: '11:00'
+  open-pull-requests-limit: 10
+- package-ecosystem: "github-actions"
+  directory: ".github/workflows"
+  schedule:
+    interval: "monthly"
+  open-pull-requests-limit: 10

.github/workflows/codeql.yml

@@ -0,0 +1,47 @@
+name: "CodeQL"
+
+on:
+    push:
+        branches:
+            - develop
+            - main
+            - master
+    pull_request:
+        types:
+            - opened
+            - reopened
+            - synchronize
+            - closed
+
+jobs:
+    analyze:
+        name: Analyze
+        runs-on: ubuntu-latest
+        permissions:
+            actions: read
+            contents: read
+            security-events: write
+
+        strategy:
+            fail-fast: false
+            matrix:
+                language: [python]
+
+        steps:
+            - name: Checkout
+              uses: actions/checkout@master
+
+            - name: Initialize CodeQL
+              uses: github/codeql-action/init@main
+              with:
+                  languages: ${{ matrix.language }}
+                  queries: +security-and-quality
+
+            - name: Autobuild
+              uses: github/codeql-action/autobuild@main
+              if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }}
+
+            - name: Perform CodeQL Analysis
+              uses: github/codeql-action/analyze@main
+              with:
+                  category: "/language:${{ matrix.language }}"

.github/workflows/kb_sdk_test.yaml

@@ -1,62 +1,49 @@
 name: KBase SDK Tests
 
 on:
-  push:
-    branches:
-    - master
-    - main
-  pull_request:
-    branches:
-    - master
-    - main
-    - develop
+    pull_request:
+        branches:
+            - 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)
+    sdk_tests:
+        runs-on: ubuntu-latest
+        steps:
+            - name: Check out GitHub repo
+              uses: actions/checkout@master
+
+            - name: Set up test environment
+              shell: bash
+              run: |
+                  # Cache the group for the docker file
+                  if [ ! -e $HOME/.kbsdk.cache ] ; then
+                    docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache
+                  fi
+
+
+                  # ignore the exit code
+                  docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock  -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test || true
+
+            - name: Confirm config exists and add token
+              shell: bash
+              env:
+                  KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+              run: |
+                  test -f "test_local/test.cfg" && echo "Confirmed config exists"
+                  # Add token to config
+                  sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg
+
+            - name: Run tests
+              shell: bash
+              run: |
+                  docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test --verbose
+
+            - name: Upload coverage to Codecov
+              id: send_to_codecov
+              uses: codecov/codecov-action@main
+              continue-on-error: true
+              with:
+                  files: ./python-coverage/coverage.xml
+                  fail_ci_if_error: true
+                  token: ${{ secrets.CODECOV_TOKEN }}

Dockerfile

@@ -17,11 +17,10 @@ RUN update-ca-certificates
 
 
 # Install ETE3
-RUN apt-get update && \
-    apt-get -y install xvfb
+RUN 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
+RUN pip install ete3==3.1.2 PyQt5==5.11.3 numpy==1.23.1 pytest coverage pytest-cov
 
 # -----------------------------------------
 
@@ -37,16 +36,11 @@ RUN make all
 #
 RUN mkdir -p /kb/module/FastTree/bin
 WORKDIR /kb/module/FastTree/bin
-RUN curl -o FastTree2.1.11_64 http://www.microbesonline.org/fasttree/FastTree && \
-#RUN \
-#    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
+RUN curl -o FastTree http://www.microbesonline.org/fasttree/FastTree && \
+    chmod 555 FastTree
 
 
 WORKDIR /kb/module
 ENTRYPOINT [ "./scripts/entrypoint.sh" ]
 
 CMD [ ]
-

Makefile

@@ -10,15 +10,18 @@ LBIN_DIR = bin
 EXECUTABLE_SCRIPT_NAME = run_$(SERVICE_CAPS)_async_job.sh
 STARTUP_SCRIPT_NAME = start_server.sh
 TEST_SCRIPT_NAME = run_tests.sh
+COMPILE_REPORT = ./compile_report.json
 
 .PHONY: test
 
 default: compile
 
-all: compile build build-startup-script build-executable-script build-test-script
+all: build compile
 
 compile:
-	kb-sdk compile $(SPEC_FILE) \
+	rm $(COMPILE_REPORT) || true
+	KB_SDK_COMPILE_REPORT_FILE=$(COMPILE_REPORT) kb-sdk compile $(SPEC_FILE) \
+		--verbose \
 		--out $(LIB_DIR) \
 		--plclname $(SERVICE_CAPS)::$(SERVICE_CAPS)Client \
 		--jsclname javascript/Client \
@@ -31,33 +34,6 @@ compile:
 build:
 	chmod +x $(SCRIPTS_DIR)/entrypoint.sh
 
-build-executable-script:
-	mkdir -p $(LBIN_DIR)
-	echo '#!/bin/bash' > $(LBIN_DIR)/$(EXECUTABLE_SCRIPT_NAME)
-	echo 'script_dir=$$(dirname "$$(readlink -f "$$0")")' >> $(LBIN_DIR)/$(EXECUTABLE_SCRIPT_NAME)
-	echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(LBIN_DIR)/$(EXECUTABLE_SCRIPT_NAME)
-	echo 'python -u $$script_dir/../$(LIB_DIR)/$(SERVICE_CAPS)/$(SERVICE_CAPS)Server.py $$1 $$2 $$3' >> $(LBIN_DIR)/$(EXECUTABLE_SCRIPT_NAME)
-	chmod +x $(LBIN_DIR)/$(EXECUTABLE_SCRIPT_NAME)
-
-build-startup-script:
-	mkdir -p $(LBIN_DIR)
-	echo '#!/bin/bash' > $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-	echo 'script_dir=$$(dirname "$$(readlink -f "$$0")")' >> $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-	echo 'export KB_DEPLOYMENT_CONFIG=$$script_dir/../deploy.cfg' >> $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-	echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-	echo 'uwsgi --master --processes 5 --threads 5 --http :5000 --wsgi-file $$script_dir/../$(LIB_DIR)/$(SERVICE_CAPS)/$(SERVICE_CAPS)Server.py' >> $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-	chmod +x $(SCRIPTS_DIR)/$(STARTUP_SCRIPT_NAME)
-
-build-test-script:
-	echo '#!/bin/bash' > $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'script_dir=$$(dirname "$$(readlink -f "$$0")")' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'export KB_DEPLOYMENT_CONFIG=$$script_dir/../deploy.cfg' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'export KB_AUTH_TOKEN=`cat /kb/module/work/token`' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'cd $$script_dir/../$(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'python -m nose --with-coverage --cover-package=$(SERVICE_CAPS) --cover-html --cover-html-dir=/kb/module/work/test_coverage --nocapture  --nologcapture .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	chmod +x $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-
 test:
 	if [ ! -f /kb/module/work/token ]; then echo -e '\nOutside a docker container please run "kb-sdk test" rather than "make test"\n' && exit 1; fi
 	xvfb-run bash $(TEST_DIR)/$(TEST_SCRIPT_NAME)

compile_report.json

@@ -0,0 +1 @@
+{"functions":{"run_FastTree":{"name":"run_FastTree","comment":"Method for Tree building of either DNA or PROTEIN sequences\n**\n**        input_type: MSA\n**        output_type: Tree","place":null,"input":[{"type":"kb_fasttree.FastTree_Params","comment":"FastTree Input Params"}],"output":[{"type":"kb_fasttree.FastTree_Output","comment":"FastTree Output"}]}},"module_name":"kb_fasttree","sdk_version":"1.2.6","sdk_git_commit":"cedcfc2326db32bbdb09eb6d031838a93853c530","impl_file_path":"lib/kb_fasttree/kb_fasttreeImpl.py","spec_files":[{"content":"/*\n** A KBase module: kb_fasttree\n**\n** This module runs FastTree to make Trees for either DNA or PROTEIN MSAs\n** \n*/\n\nmodule kb_fasttree {\n\n    /* \n    ** The workspace object refs are of form:\n    **\n    **    objects = ws.get_objects([{'ref': params['workspace_id']+'/'+params['obj_name']}])\n    **\n    ** \"ref\" means the entire name combining the workspace id and the object name\n    ** \"id\" is a numerical identifier of the workspace or object, and should just be used for workspace\n    ** \"name\" is a string identifier of a workspace or object.  This is received from Narrative.\n    */\n    typedef string workspace_name;\n    typedef string data_obj_name;\n    typedef string data_obj_ref;\n\n\n    /* FastTree Input Params\n    */\n    typedef structure {\n        workspace_name workspace_name;\n\tstring         desc;\n\tdata_obj_ref   input_ref;\n        data_obj_name  output_name;\n\tint            species_tree_flag;  /* boolean */\n\tdata_obj_ref   intree_ref;\n\tint            fastest;  /* boolean */\n\tint            pseudo;   /* boolean */\n\tint            gtr;      /* boolean */\n\tint            wag;      /* boolean */\n\tint            noml;     /* boolean */\n\tint            nome;     /* boolean */\n        int            cat;      /* actually is an int */\n\tint            nocat;    /* boolean */\n        int            gamma;    /* boolean */\n    } FastTree_Params;\n\n\n    /* FastTree Output\n    */\n    typedef structure {\n\tdata_obj_name report_name;\n\tdata_obj_ref  report_ref;\n        data_obj_ref  output_ref;\n    } FastTree_Output;\n\t\n\n    /*  Method for Tree building of either DNA or PROTEIN sequences\n    **\n    **        input_type: MSA\n    **        output_type: Tree\n    */\n    funcdef run_FastTree (FastTree_Params params)  returns (FastTree_Output) authentication required;\n};\n","file_name":"kb_fasttree.spec","is_main":1}],"function_places":{}}

pyproject.toml

@@ -0,0 +1,123 @@
+[tool.ruff]
+line-length = 100
+
+extend-exclude = [
+    "lib/installed_clients/*"
+]
+
+# Assume Python 3.12.
+target-version = "py312"
+
+[tool.ruff.lint]
+select = [
+    # core
+    "F", # Pyflakes
+    "E", # pycodestyle errors
+    "W", # pycodestyle warnings
+    "C90", # mccabe +
+    "I", # isort
+    "N", # pep8-naming
+    "D", # pydocstyle
+    "UP", # pyupgrade
+    # extensions
+    "YTT", # flake8-2020
+    "ANN", # flake8-annotations
+    "ASYNC", # flake8-async
+    "S", # flake8-bandit
+    "BLE", # flake8-blind-except
+    "FBT", # flake8-boolean-trap
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    # "COM", # flake8-commas
+    "CPY", # flake8-copyright
+    "C4", # flake8-comprehensions
+    "DTZ", # flake8-datetimez
+    "T10", # flake8-debugger
+    # "DJ", # flake8-django
+    "EM", # flake8-errmsg
+    "EXE", # flake8-executable
+    "FA", # flake8-future-annotations
+    "ISC", # flake8-implicit-str-concat
+    "ICN", # flake8-import-conventions
+    "G", # flake8-logging-format
+    "INP", # flake8-no-pep420
+    "PIE", # flake8-pie
+    "T20", # flake8-print
+    "PYI", # flake8-pyi
+    "PT", # flake8-pytest-style
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "SLF", # flake8-self
+    # "SLOT", # flake8-slots
+    "SIM", # flake8-simplify
+    "TID", # flake8-tidy-imports
+    "TCH", # flake8-type-checking
+    "INT", # flake8-gettext
+    "ARG", # flake8-unused-arguments
+    "PTH", # flake8-use-pathlib
+    "TD", # flake8-todos
+    "FIX", # flake8-fixme
+    "ERA", # eradicate
+    # "PD", # pandas-vet
+    "PGH", # pygrep-hooks
+    "PL", # Pylint
+    "TRY", # tryceratops
+    "FLY", # flynt
+    # "NPY", # NumPy-specific rules
+    "AIR", # Airflow
+    "PERF", # Perflint
+    "FURB", # refurb
+    "LOG", # flake8-logging
+    "RUF", # Ruff-specific rules
+]
+
+# E203: whitespace before ‘,’, ‘;’, or ‘:’
+# E501: line length
+# ISC001: conflicts with Ruff's formatter
+# W503: line break after binary operator
+ignore = [
+    "E203",
+    "E501",
+    "ISC001",
+    "S101",
+]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    "__pypackages__",
+    "_build",
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git-rewrite",
+    ".git",
+    ".github",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "*.pyc",
+    "buck-out",
+    "build",
+    "deps",
+    "dist",
+    "node_modules",
+    "other_schema",
+    "python-coverage",
+    "sample_data",
+    "venv",
+]
+per-file-ignores = {}
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"