Merge branch 'make-prerelease' into 'dev'

deploy from dev branch

See merge request epi2melabs/workflow-containers/wf-template!4

.gitlab-ci.yml

@@ -1,5 +1,7 @@
 stages:
-    - build_and_run
+    - test
+    - pre-release
+    - release-checks 
     - release
 
 image: ${IMAGE}
@@ -15,10 +17,31 @@ variables:
     source ./miniconda/bin/activate
     conda init
 
+# Insist a CHANGELOG entry has been made for tags
+.check-changelog: &check-changelog |
+    TAGVER=${CI_COMMIT_TAG}
+    MATCHES=$(grep -c "## \[${TAGVER}\]" CHANGELOG.md)
+    if [[ "${MATCHES}" != "1" ]] then;
+        echo "Expected one match to '${CI_COMMIT_TAG}' in CHANGELOG, found ${MATCHES}"
+        exit 1
+    else;
+        echo "Found CHANGELOG.md entry for tag"
+    fi
+
+# setup image for pushing to github
+.setup-gh-push: &setup-gh-push |
+    apt-get update -qq && apt-get install -y -qq
+    git python3-all-dev git-lfs python3-venv
+    mkdir ~/.ssh/
+    cp $LABS_BOT_GH_KEY ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
+    echo -e "Host github.com\n\tStrictHostKeyChecking no\n\tHostname ssh.github.com\n\tPort 443\n\n" > ~/.ssh/config
+    git config --global user.email "epi2melabs@nanoporetech.com"
+    git config --global user.name "epi2melabs-bot"
+
 
 conda-run:
     image: ubuntu:20.04
-    stage: build_and_run
+    stage: test
     before_script:
         - apt update && apt install -y wget default-jre
         - *install-nextflow
@@ -35,7 +58,7 @@ conda-run:
 
 
 build-image:
-    stage: build_and_run
+    stage: test
     before_script:
         - apk add wget openjdk11 bash
         - *install-nextflow
@@ -52,12 +75,15 @@ build-image:
               --wfversion latest
               --fastq test_data/reads.fq.gz 
               --out_dir ${OUTPUT}
-        # push
+        # push, to ont for later tagging, to dockerhub for release testing
         - if [[ ${CI_COMMIT_BRANCH} == 'dev' ]]; then
               SHATAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_SHORT_SHA};
-              echo "Pushing ${SHATAG}";
+              HUBTAG="${DOCKERHUB_NAMESPACE}/${CI_PROJECT_NAME}:${CI_COMMIT_SHORT_SHA}";
-              docker tag ${TAG} ${SHATAG};
+              for tag in SHATAG HUBTAG; do
-              docker push ${SHATAG};
+                  echo "Pushing ${tag}";
+                  docker tag ${TAG} ${tag};
+                  docker push ${tag};
+              done;
           fi;
     only:
         - branches
@@ -67,6 +93,30 @@ build-image:
             - ${CI_PROJECT_NAME}
         expire_in: 1 day
 
+###
+# Push dev branch to github for release testers
+release-dev:
+    stage: pre-release
+    image: $GH_PUSH_IMAGE
+    before_script:
+        - *setup-gh-push
+    script:
+        # Merge ont/dev into prerelease
+        - git remote add ont ${CI_REPOSITORY_URL} || true
+        - git remote add github git@github.com:epi2me-labs/${CI_PROJECT_NAME}.git || true
+        - git fetch ont dev
+        - git fetch github prerelease || echo "No 'prerelease' branch present on github"
+        - git checkout --track github/prerelease || git checkout prerelease
+        - git merge ont/dev
+        # Edit nextflow config to set wfversion
+        - grep 'wfversion = ".*"' nextflow.config || echo "Failed to replace wfversion" && exit 1
+        - git add nextflow.config
+        - git commit -m "Setting wfversion to:${CI_COMMIT_SHORT_SHA}"
+        - git push github prerelease
+    only:
+        - '/^dev$/'
+    except:
+        - tags
 
 ###
 # Retag the image for git tags (releases)
@@ -80,17 +130,6 @@ build-image:
     only:
         - tags
 
-# To ONT registry
-release-int:
-    stage: release
-    <<: *pull_tag
-    script:
-        - echo ${CI_BUILD_TOKEN} | docker login --username gitlab-ci-token --password-stdin ${CI_REGISTRY}
-        - RELTAG=${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_NAME}
-        - echo "Pushing ${TAG}"
-        - docker tag ${SHATAG} ${RELTAG}
-        - docker push ${RELTAG}
-
 # To dockerhub
 release-hub:
     stage: release
@@ -111,13 +150,7 @@ push-github:
     stage: release
     image: $GH_PUSH_IMAGE
     before_script:
-        - apt-get update -qq && apt-get install -y -qq
+        - *setup-gh-push
-          git python3-all-dev git-lfs python3-venv
-        - mkdir ~/.ssh/
-        - cp $LABS_BOT_GH_KEY ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
-        - echo -e "Host github.com\n\tStrictHostKeyChecking no\n\tHostname ssh.github.com\n\tPort 443\n\n" > ~/.ssh/config
-        - git config --global user.email "epi2melabs@nanoporetech.com"
-        - git config --global user.name "epi2melabs-bot"
     script:
         # Push master and tag to github
         - git remote add ont ${CI_REPOSITORY_URL} || true