Switches to use version.py file for python package version.

Author: Robert Chu

.github/workflows/publish.yml

@@ -41,6 +41,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools pipenv
+          rm ./script_runner/version.py
       #     pipenv lock --dev --requirements > requirements.dev.txt
       #     pip install -r requirements.txt
       # - name: Lint with flake8
@@ -52,11 +53,16 @@ jobs:
       # - name: Test with pytest
       #   run: |
       #     pytest
+      - name: Inject package version
+        uses: nowactions/envsubst@v1
+        with:
+          input: ./script_runner/version.py.tmpl
+          output: ./script_runner/version.py
+        env:
+          SCRIPT_RUNNER_VERSION: ${{ steps.prep.outputs.version }}
       - name: Build python package
         run: |
           python setup.py sdist
-        env:
-          SCRIPT_RUNNER_VERSION: ${{ steps.prep.outputs.version }}
       - name: Deploy to PyPI
         if: success() && startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1
@@ -131,7 +137,7 @@ jobs:
   publish-docker-example:
     needs: publish-pypi
     if: startsWith(github.ref, 'refs/tags')
-    name: Build and push script-runner-server-example docker image
+    name: Publish script-runner-example to dockerhub
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
@@ -192,7 +198,7 @@ jobs:
   deploy-aws-example:
     needs: publish-docker-example
     if: startsWith(github.ref, 'refs/tags')
-    name: Deploy swabseq-analysis-example to AWS
+    name: Deploy script-runner-example to AWS
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
@@ -295,7 +301,7 @@ jobs:
   deploy-azure-example:
     needs: publish-docker-example
     if: startsWith(github.ref, 'refs/tags')
-    name: Deploy swabseq-analysis-example to Azure
+    name: Deploy script-runner-example to Azure
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo

docker-compose.yaml

@@ -3,8 +3,8 @@ services:
   server:
     image: labflow/script-runner-example:latest
     build:
-      dockerfile: ./docker/Dockerfile.example
-      context: .
+      dockerfile: ./Dockerfile.example
+      context: ./docker
       args:
         SERVER_VERSION: local+devcontainer
     command: "python3 -m flask run --host=0.0.0.0 --port=5000"
@@ -23,8 +23,8 @@ services:
   worker:
     image: labflow/script-runner-example:latest
     build:
-      context: .
-      dockerfile: ./docker/Dockerfile.example
+      dockerfile: ./Dockerfile.example
+      context: ./docker
       args:
         SERVER_VERSION: local+devcontainer
     command: "python3 -m celery -A script_runner.analysis worker"

docker/Dockerfile.example

@@ -4,14 +4,6 @@ ARG SCRIPT_RUNNER_VERSION=local+container
 # Start with rocker/tidyverse base image
 FROM rocker/verse:3.6.3
 
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# get and install bcl2fastq
-RUN cd /tmp \
-    && wget https://www.dropbox.com/s/idi0xfu0thurk7q/bcl2fastq2-v2-20-0-linux-x86-64.zip \
-    && unzip bcl2fastq2-v2-20-0-linux-x86-64.zip -p \
-    | tar xvz -C / usr/local/bin/bcl2fastq \
-    && rm /tmp/bcl2fastq2*
-
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # Install extra *nix utils
 # x11, mesa, glu1 are so we can install paletteer
@@ -27,6 +19,7 @@ RUN apt-get update \
     wget \
     parallel \
     python3-pip \
+    bsdtar \
     bzip2 \
     libcairo2-dev \
     libfontconfig1-dev \
@@ -35,6 +28,12 @@ RUN apt-get update \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# get and install bcl2fastq
+RUN wget -qO- https://www.dropbox.com/s/idi0xfu0thurk7q/bcl2fastq2-v2-20-0-linux-x86-64.zip \
+    | bsdtar -xOf - bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm \
+    | bsdtar -xf - -C / usr/local/bin/bcl2fastq
+
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # R Deps
 RUN install2.r --error \

script_runner/version.py

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+__all__ = ('__version__',)
+__version__ = "latest"

script_runner/version.py.tmpl

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+__all__ = ('__version__',)
+__version__ = "$SCRIPT_RUNNER_VERSION"

setup.py

@@ -1,14 +1,24 @@
 import os
 from distutils.core import setup
 
+def get_version():
+    """
+    Gets the latest version number out of the package,
+    saving us from maintaining it in multiple places.
+    """
+    local_results = {}
+    with open('script_runner/version.py') as version_file:
+        exec(version_file.read(), {}, local_results)
+    return local_results['__version__']
+
 setup(
     name="script-runner-api",
     packages=[
         "script_runner",
         "script_runner.api",
     ],
     scripts=["script_runner/main.py"],
-    version=os.environ.get("SCRIPT_RUNNER_VERSION", "latest"),
+    version=get_version(),
     license="MIT",
     description="Provides an API server + celery worker module for running arbitrary scripts.",
     author="Robert Chu",