switch off a secrets file to using multiple hidden CI variables. Change name...

switch off a secrets file to using multiple hidden CI variables. Change name of image to match repo. Condense clone and prep_missing_tags jobs

.gitlab-ci.yml

 stages:
-  - clone
-  - find_tags
+  - prep_tags
   - build
 
 variables:
   GITHUB_URL: "github.com/google-deepmind/alphafold3.git"
   REGISTRY_URL: "${CI_REGISTRY_IMAGE}"
-  IMAGE_NAME: "alphafold"
+  IMAGE_NAME: "alphafold3"
   REPO_URL: "https://gitlab.rc.uab.edu/api/v4/projects/${CI_PROJECT_ID}/registry/repositories/"
   DOCKER_TLS_CERTDIR: "/certs"
 
-clone_repo:
-  image: alpine:latest
-  stage: clone
-  script:
-    - apk update && apk add curl bash git
-    - curl -s "https://gitlab.com/gitlab-org/incubation-engineering/mobile-devops/download-secure-files/-/raw/main/installer" | bash
-    - source .secure_files/github-key
-    - git clone https://${GITHUB_USER}:${GITHUB_TOKEN}@${GITHUB_URL}
-  artifacts:
-    paths: 
-      - alphafold3/
-    expire_in: 1 hour
+workflow:
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH # Only run on main
 
 prep_missing_tags:
   image: ubuntu:latest
-  stage: find_tags
+  stage: prep_tags
   script:
     - apt-get update && apt-get install -y curl git jq
+    - git clone https://${CI_GITHUB_USER}:${CI_GITHUB_TOKEN}@${GITHUB_URL}
     - cd alphafold3
     - git fetch --tags
     - 'REPO_ID=$(curl -s --header "PRIVATE-TOKEN: ${CI_PROJECT_ACCESS_TOKEN}" "${REPO_URL}" | jq ".[0].id")'
@@ -40,6 +31,7 @@ prep_missing_tags:
     - sed -e "s/REPLACE_HERE/${MISSING}/g" template-build-tags.yml > build-tags.yml
   artifacts:
     paths:
+      - alphafold3/
       - build-tags.yml
     expire_in: 1 hour