Updated python version + new builds

.github/workflows/build.yaml

@@ -0,0 +1,27 @@
+name: build
+on: [push, pull_request]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python3 -m venv venv
+          . venv/bin/activate
+          pip install setuptools wheel twine
+          pip install -r requirements.txt
+      - name: run tests
+        env: 
+          RETRY_ATTEMPTS: 1
+        run: |
+          . venv/bin/activate
+          pip install nose2
+          nose2

.github/workflows/package.yaml

@@ -0,0 +1,65 @@
+name: package
+on:
+  release:
+    types: [created]
+
+jobs:
+
+  version:
+    runs-on: ubuntu-latest
+    outputs:
+      app-version: ${{ steps.set-version.outputs.version }}
+    steps:
+    - uses: actions/checkout@v4
+    - run: echo "APP_VERSION=$(python setup.py --version)" >> $GITHUB_ENV
+    - run: echo app version is $APP_VERSION
+    - id: set-version
+      run: echo "::set-output name=version::$APP_VERSION"
+
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python3 -m venv venv
+        . venv/bin/activate
+        pip install setuptools wheel twine
+        pip install -r requirements.txt
+    - name: verify git tag vs. version
+      run: |
+        python3 -m venv venv
+        . venv/bin/activate
+        python setup.py verify        
+    - name: Build
+      run: |
+        . venv/bin/activate
+        python setup.py bdist_wheel --universal
+    - name: Publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_APIKEY }}
+      run: |
+        . venv/bin/activate
+        twine upload dist/*
+
+  container-build:
+    needs: version
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4   
+    - run: echo version ${{needs.version.outputs.app-version}}
+    - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+    - name: build & push image
+      run: |
+        IMAGE_ID=ghcr.io/duke-gcb/calrissian/calrissian
+        docker build . --file Dockerfile --tag calrissian
+        docker tag calrissian $IMAGE_ID:${{needs.version.outputs.app-version}}
+        docker push $IMAGE_ID:${{needs.version.outputs.app-version}}
+

.gitignore

@@ -9,3 +9,4 @@ tests/__pycache__/
 env37
 build
 *.egg
+env-calrissian*

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.7
+FROM python:3.10.0-slim-buster
 LABEL maintainer="dan.leehr@duke.edu"
 
 # cwltool requires nodejs

calrissian/job.py

@@ -67,8 +67,8 @@ def read_yaml(filename):
 
 
 def quoted_arg_list(arg_list):
-        shouldquote = needs_shell_quoting_re.search
-        return [shellescape.quote(arg) if shouldquote(arg) else arg for arg in arg_list]
+    shouldquote = needs_shell_quoting_re.search
+    return [shellescape.quote(arg) if shouldquote(arg) else arg for arg in arg_list]
 
 
 def total_size(outputs):

calrissian/k8s.py

@@ -1,7 +1,7 @@
 from typing import List, Union
 from kubernetes import client, config, watch
 from kubernetes.client.models import V1ContainerState, V1Container, V1ContainerStatus
-from kubernetes.client.api_client import ApiException
+from kubernetes.client.rest import ApiException
 from kubernetes.config.config_exception import ConfigException
 from calrissian.executor import IncompleteStatusException
 from calrissian.retry import retry_exponential_if_exception_type

requirements.in

@@ -0,0 +1,8 @@
+urllib3
+kubernetes
+cwltool
+tenacity
+importlib-metadata
+msgpack
+typing-extensions
+freezegun

requirements.txt

@@ -1,13 +1,147 @@
-cwltool==3.1.20230601100705
-freezegun==0.3.12
-kubernetes==10.0.1
-mypy-extensions==0.4.3
-nose2==0.9.1
-PyYAML==5.4
-requests==2.28.1
-scandir==1.10.0
-schema-salad>=8.2.20210914115719,<9
-shellescape>=3.4.1,<3.5
-tenacity==5.1.1
-typing-extensions==3.7.4
-msgpack==0.5.2
+#
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
+#
+#    pip-compile
+#
+argcomplete==3.1.6
+    # via cwltool
+cachecontrol[filecache]==0.13.1
+    # via schema-salad
+cachetools==5.3.2
+    # via google-auth
+certifi==2023.11.17
+    # via
+    #   kubernetes
+    #   requests
+charset-normalizer==3.3.2
+    # via requests
+coloredlogs==15.0.1
+    # via cwltool
+cwl-upgrader==1.2.10
+    # via cwl-utils
+cwl-utils==0.31
+    # via cwltool
+cwltool==3.1.20231114134824
+    # via -r requirements.in
+filelock==3.13.1
+    # via cachecontrol
+freezegun==1.2.2
+    # via -r requirements.in
+google-auth==2.23.4
+    # via kubernetes
+humanfriendly==10.0
+    # via coloredlogs
+idna==3.4
+    # via requests
+importlib-metadata==6.8.0
+    # via -r requirements.in
+importlib-resources==6.1.1
+    # via
+    #   cwltool
+    #   schema-salad
+isodate==0.6.1
+    # via rdflib
+kubernetes==28.1.0
+    # via -r requirements.in
+lxml==4.9.3
+    # via prov
+mistune==2.0.5
+    # via schema-salad
+msgpack==1.0.7
+    # via
+    #   -r requirements.in
+    #   cachecontrol
+mypy-extensions==1.0.0
+    # via
+    #   cwltool
+    #   schema-salad
+networkx==3.2.1
+    # via prov
+oauthlib==3.2.2
+    # via
+    #   kubernetes
+    #   requests-oauthlib
+packaging==23.2
+    # via cwl-utils
+prov==1.5.1
+    # via cwltool
+psutil==5.9.6
+    # via cwltool
+pyasn1==0.5.0
+    # via
+    #   pyasn1-modules
+    #   rsa
+pyasn1-modules==0.3.0
+    # via google-auth
+pydot==1.4.2
+    # via cwltool
+pyparsing==3.1.1
+    # via
+    #   cwltool
+    #   pydot
+    #   rdflib
+python-dateutil==2.8.2
+    # via
+    #   freezegun
+    #   kubernetes
+    #   prov
+pyyaml==6.0.1
+    # via kubernetes
+rdflib==7.0.0
+    # via
+    #   cwl-utils
+    #   cwltool
+    #   prov
+    #   schema-salad
+requests==2.31.0
+    # via
+    #   cachecontrol
+    #   cwl-utils
+    #   cwltool
+    #   kubernetes
+    #   requests-oauthlib
+    #   schema-salad
+requests-oauthlib==1.3.1
+    # via kubernetes
+rsa==4.9
+    # via google-auth
+ruamel-yaml==0.18.5
+    # via
+    #   cwl-upgrader
+    #   cwl-utils
+    #   cwltool
+    #   schema-salad
+ruamel-yaml-clib==0.2.8
+    # via ruamel-yaml
+schema-salad==8.4.20231117150958
+    # via
+    #   cwl-upgrader
+    #   cwl-utils
+    #   cwltool
+shellescape==3.4.1
+    # via cwltool
+six==1.16.0
+    # via
+    #   isodate
+    #   kubernetes
+    #   prov
+    #   python-dateutil
+tenacity==8.2.3
+    # via -r requirements.in
+typing-extensions==4.8.0
+    # via -r requirements.in
+urllib3==1.26.18
+    # via
+    #   -r requirements.in
+    #   kubernetes
+    #   requests
+websocket-client==1.6.4
+    # via kubernetes
+zipp==3.17.0
+    # via
+    #   importlib-metadata
+    #   importlib-resources
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools