From 464c314403d691d6d0e5cc7cfc09781867b4277c Mon Sep 17 00:00:00 2001
From: Logan Drescher <drescher@uchc.edu>
Date: Sun, 22 Sep 2024 12:36:13 -0400
Subject: [PATCH] Added replacement for pyproject.toml

---
 .github/workflows/ci.yml | 54 ++++++++++++++++++++++++----------------
 1 file changed, 32 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3fa7ad0..9f2c3b3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -153,6 +153,21 @@ jobs:
                 if: steps.check-new-release.outputs.needDeploy == 'true'
                 run: echo 'Beginning Deploy Steps'
 
+            #############################################
+            ## Form-fill the versions to the container and to `pyproject.toml`
+            #############################################
+            - name: Update versioning in "Dockerfile" and "pyproject.toml"
+              if: steps.check-new-release.outputs.needDeploy == 'true'
+              run: |
+                  copasiVersion=${{ steps.check-new-release.outputs.copasiVersion }}
+                  bioSimVersion=${{ steps.check-new-release.outputs.bioSimVersion }}
+
+                  sed -i -E "s/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" Dockerfile
+                  sed -i -E "s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" Dockerfile
+
+                  sed -i -E "s/^version\s+=\s+(\".*?\")/version = \"${bioSimVersion}\"/mg" pyproject.toml
+                  poetry update
+
             #############################################
             # Create PyPI release
             #############################################
@@ -180,28 +195,6 @@ jobs:
                     poetry build
                     poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI
 
-            #############################################
-            ## Form-fill the versions to the container and to `biosimulators.json`
-            #############################################
-            - name: Update versioning in "Dockerfile" and "biosimulators.json"
-              if: steps.check-new-release.outputs.needDeploy == 'true'
-              run: |
-                  containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
-                  docker pull $containerLabel
-                  imageId=docker image ls | grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \
-                    grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | awk '{ print $3; ]'
-                  
-                  
-                  dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2
-                  copasiVersion=${{ steps.check-new-release.outputs.copasiVersion }}
-                  bioSimVersion=${{ steps.check-new-release.outputs.bioSimVersion }}
-                  
-                  sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json
-                  sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json
-                  
-                  sed -i -E "s/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" Dockerfile
-                  sed -i -E "s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" Dockerfile
-
             #############################################
             ## Build and Push Docker image
             #############################################
@@ -251,6 +244,23 @@ jobs:
                       docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
                     fi
 
+            #############################################
+            ## Form-fill the versions to "biosimulators.json"
+            #############################################
+            - name: Update versioning in "biosimulators.json"
+              if: steps.check-new-release.outputs.needDeploy == 'true'
+              run: |
+                  containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
+                  docker pull $containerLabel
+                  imageId=docker image ls | grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \
+                    grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | awk '{ print $3; ]'
+                  
+                  dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2
+                  copasiVersion=${{ steps.check-new-release.outputs.copasiVersion }}
+                  
+                  sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json
+                  sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json
+
             #############################################
             # Submit to BioSimulators registry
             #############################################