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

.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/Dockerfile.example

@@ -8,7 +8,7 @@ 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 \
+    && unzip -p bcl2fastq2-v2-20-0-linux-x86-64.zip bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm \
     | tar xvz -C / usr/local/bin/bcl2fastq \
     && rm /tmp/bcl2fastq2*
 

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",