Merge pull request #17 from kbaseapps/PUBLIC-2591_python_312_update

PUBLIC-2591: Python 3.12 update

.github/workflows/kb_sdk_test.yaml

@@ -18,7 +18,6 @@ jobs:
                     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
 

Dockerfile

@@ -1,25 +1,25 @@
-FROM kbase/sdkpython:3.8.10
+FROM python:3.12-bookworm
 LABEL maintainer="KBase Developers [[email protected]]"
 
 WORKDIR /kb/module
-# Update
 RUN apt-get update \
     && apt-get upgrade -y && \
     update-ca-certificates && \
     apt-get -y install xvfb curl && \
+    # these are all needed by PyQt5
+    apt-get -y install libdbus-1-3 libxcb-keysyms1 libxcb-image0 libxkbcommon-x11-0 libxkbcommon0 libxcb-icccm4 libxcb-image0 libxcb-render-util0 libxcb-shape0 libxcb-xinerama0 && \
+    apt-get clean && \
     # 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 && \
-    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
+    pip install --upgrade pip
 
 COPY ./ /kb/module
-
-RUN mkdir -p /kb/module/work && \
+# install the python requirements
+RUN pip install -r requirements.txt && \
+    mkdir -p /kb/module/work && \
     chmod -R a+rw /kb/module && \
     mv /kb/module/compile_report.json /kb/module/work/compile_report.json
 

requirements.txt

@@ -0,0 +1,14 @@
+coverage==7.6.1
+ete3==3.1.3
+jinja2==3.1.4
+jsonrpcbase==0.2.0
+numpy==2.0.1
+PyQt5==5.15.11
+pytest==8.3.2
+pytest-cov==5.0.0
+pytest-recording==0.13.2
+requests==2.32.3
+ruff==0.5.7
+six==1.16.0
+vcrpy==6.0.1
+uwsgi==2.0.26

scripts/entrypoint.sh

@@ -1,7 +1,5 @@
 #!/bin/bash
 
-. /kb/deployment/user-env.sh
-
 python ./scripts/prepare_deploy_cfg.py ./deploy.cfg ./work/config.properties
 
 if [ -f ./work/token ] ; then
@@ -16,13 +14,11 @@ elif [ "${1}" = "test" ] ; then
 elif [ "${1}" = "async" ] ; then
 #  sh ./scripts/run_async.sh
   xvfb-run bash ./scripts/run_async.sh
-elif [ "${1}" = "init" ] ; then
-  echo "Initialize module"
 elif [ "${1}" = "bash" ] ; then
   bash
 elif [ "${1}" = "report" ] ; then
   export KB_SDK_COMPILE_REPORT_FILE=./work/compile_report.json
   echo The compile report is available at /kb/module/work/compile_report.json
 else
-  echo Unknown
+  echo Unknown command
 fi

scripts/prepare_deploy_cfg.py

@@ -1,21 +1,44 @@
+"""Generate the deployment config file."""
+
+import os
+import os.path
 import sys
+from configparser import ConfigParser
+
 from jinja2 import Template
-from configparser import ConfigParser  # py3
 
 if __name__ == "__main__":
-    if len(sys.argv) != 3:
-        print("Usage: <program> <deploy_cfg_template_file> <file_with_properties>")
-        print("Properties from <file_with_properties> will be applied to <deploy_cfg_template_file>")
-        print("template which will be overwritten with .orig copy saved in the same folder first.")
+    if len(sys.argv) < 2 or len(sys.argv) > 3:
+        print("Usage:\nprepare_deploy_config.py <deploy_cfg_template_file> <file_with_properties>\nor:")  # noqa: T201
+        print("KBASE_ENDPOINT=https://kbase.endpoint.url prepare_deploy_config.py <deploy_cfg_template_file>")  # noqa: T201
+        print(  # noqa: T201
+            "Properties from <file_with_properties> or the KBASE_ENDPOINT env var will be applied to <deploy_cfg_template_file>"
+        )
+        print("template which will be overwritten with .orig copy saved in the same folder first.")  # noqa: T201
         sys.exit(1)
-    file = open(sys.argv[1], 'r')
-    text = file.read()
+
+    with open(sys.argv[1]) as file:
+        text = file.read()
     t = Template(text)
     config = ConfigParser()
-    config.read(sys.argv[2])
+
+    if os.path.isfile(sys.argv[2]):
+        config.read(sys.argv[2])
+    elif "KBASE_ENDPOINT" in os.environ:
+        kbase_endpoint = os.environ.get("KBASE_ENDPOINT")
+        props = f"[global]\nkbase_endpoint = {kbase_endpoint}\n"
+        for key in os.environ:
+            if key.startswith("KBASE_SECURE_CONFIG_PARAM_"):
+                param_name = key[len("KBASE_SECURE_CONFIG_PARAM_") :]
+                props += f"{param_name} = {os.environ.get(key)}\n"
+        config.read_string(props)
+    else:
+        err_msg = f"Neither {sys.argv[2]} file nor KBASE_ENDPOINT env var found"
+        raise ValueError(err_msg)
+
     props = dict(config.items("global"))
     output = t.render(props)
-    with open(sys.argv[1] + ".orig", 'w') as f:
+    with open(sys.argv[1] + ".orig", "w") as f:
         f.write(text)
-    with open(sys.argv[1], 'w') as f:
+    with open(sys.argv[1], "w") as f:
         f.write(output)

test/run_tests.sh

@@ -10,11 +10,9 @@ export PYTHONPATH=$PYTHON_LIB_DIR:$PYTHONPATH
 
 # collect coverage data
 pytest \
-    -vv
-    --cov=$PYTHON_LIB_DIR \
     --cov-config=.coveragerc \
     --cov-report=html \
     --cov-report=xml \
+    --cov=/kb/module/lib \
+    -vv \
     test
-
-echo "Finished tests!"