From 917d9c9beda69b0ba648f470cc0c87ca6a49dcc7 Mon Sep 17 00:00:00 2001
From: Chris Rosenthal <crosenth@uw.edu>
Date: Mon, 1 Jul 2024 15:36:19 -0700
Subject: [PATCH] Workflow update (#78)

* added pip install --requirement since it is was removed from bin/bootstrap.sh

* need to build image on latest Dockerfile before running tests

* need to build image on latest Dockerfile before running tests

* need github sha like this

* trying to reorder to see if I can access git

* just going to cut the sha manually using cut

* loading version from file before install

* version file will not be there if run as Github Action

* Updating actions versions
---
 .github/workflows/docker-publish.yml |  6 ++---
 .github/workflows/tests.yml          | 38 ++++++++++++++++++++++------
 Dockerfile                           |  3 ++-
 setup.py                             | 10 +++++---
 4 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
index 5bc33c2..e50c863 100644
--- a/.github/workflows/docker-publish.yml
+++ b/.github/workflows/docker-publish.yml
@@ -14,17 +14,17 @@ jobs:
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
       -
         name: Build and push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6
         with:
           push: true
           tags: |
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 4f8b930..91ac9b0 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,18 +1,40 @@
 name: Run deenurp tests on deenurp image
 
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+on: push
 
 jobs:
-  build:
+  dev_image:
+    environment: docker_build
+    runs-on: ubuntu-latest
+    outputs:
+      sha_short: ${{ env.sha_short }}
+    steps:
+      -
+        name: Set env
+        run: echo "sha_short=`echo ${GITHUB_SHA} | cut -c1-7`" >> $GITHUB_ENV
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: ghcr.io/fhcrc/deenurp:${{ env.sha_short }}
+  test:
+    needs: [dev_image]
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/fhcrc/deenurp:latest
+      image: ghcr.io/fhcrc/deenurp:${{ needs.dev_image.outputs.sha_short }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: |
         python3 -m deenurp.test
         tests/run.sh
diff --git a/Dockerfile b/Dockerfile
index 24b7b1c..7b3e03a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,7 +17,8 @@ COPY deenurp.py setup.py requirements.txt /usr/local/share/deenurp/
 RUN cd /usr/local/share/deenurp/ && \
     PYTHON=/usr/local/bin/python3 \
     DEENURP=/usr/local/share/deenurp/ \
-    bin/bootstrap.sh /usr/local/
+    bin/bootstrap.sh /usr/local/ \
+    pip install --upgrade --requirement requirements.txt
 
 # clean up sources apt packages
 RUN rm -rf /var/lib/apt/lists/* && \
diff --git a/setup.py b/setup.py
index 06016e2..18a76ce 100644
--- a/setup.py
+++ b/setup.py
@@ -14,8 +14,12 @@
      f'|| rm -f {version_file}.tmp'),
     shell=True, stderr=open(os.devnull, "w"))
 
-# import must follow 'git describe' command above to update version
-from deenurp import __version__
+try:
+    with open(version_file) as f:
+        version = f.read().strip().lstrip('v').replace(
+            '-', '+', 1).replace('-', '.')
+except Exception as e:
+    version = ''
 
 
 class CheckVersion(Command):
@@ -77,7 +81,7 @@ def run(self):
 
 setup(
     name='deenurp',
-    version=__version__,
+    version=version,
     package_data={'deenurp': ['data/*', 'test/data/*']},
     entry_points={
         'console_scripts': {'deenurp = deenurp:main'}},