Merge branch 'main' into rm-balsamic-qc

# Conflicts:
#	cg_hermes/config/balsamic_qc.py

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.1.0
+current_version = 5.1.2
 commit = True
 tag = True
 tag_name = {new_version}

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,31 +1,44 @@
 ## Description
-*This PR adds/fixes ...*
+
+### Added
+
+-
+
+### Changed
+
+-
+
+### Fixed
+
+-
+
+## Testing
 
 ### How to prepare for test
-- [ ] ssh to hasta.scilifelab.se
-- [ ] Use stage: `us`
-- [ ] Paxa the environment: `paxa`
-- [ ] Install on stage (example for hasta):
-`bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_hermes -t hermes -b [THIS-BRANCH-NAME]`
+
+- [ ] ssh to Hasta
+- [ ] Test your branch with
+
+```bash
+hermes-test-deploy <branch-name>
+hermes-test <command here>
+```
 
 ### How to test
-- [ ] Do ...
+- [ ] login to ...
+- [ ] do ...
 
-### Expected test outcome
-- [ ] Check that ...
+### Expected test result
+- [ ] check that ...
 - [ ] Take a screenshot and attach or copy/paste the output.
 
 ## Review
-- [ ] Tests executed by
+- [ ] code approved by
+- [ ] tests executed by
 - [ ] "Merge and deploy" approved by
 Thanks for filling in who performed the code review and the test!
 
-### This [version](https://semver.org/) is a
+This [version](https://semver.org/) is a:
 - [ ] **MAJOR** - when you make incompatible API changes
 - [ ] **MINOR** - when you add functionality in a backwards compatible manner
 - [ ] **PATCH** - when you make backwards compatible bug fixes or documentation/instructions
-
-## Implementation Plan
-- [ ] Document in ...
-- [ ] Deploy this branch
-- [ ] Inform to ...

.github/workflows/build_dockerfile_on_push.yml

@@ -0,0 +1,30 @@
+name: Build and publish docker image on push
+
+on: [push]
+
+jobs:
+  docker-image-push:
+    runs-on: ubuntu-latest
+    steps:
+     - name: Check out git repository
+       uses: actions/checkout@v4
+
+     - name: Extract branch name and remove illegal chars
+       id: get_branch_name
+       shell: bash
+       run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v3
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Build image
+       uses: docker/build-push-action@v6
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/hermes:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/hermes:latest"
+

.github/workflows/build_dockerfile_on_release.yml

@@ -0,0 +1,29 @@
+name: Build and publish image on new release event
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+  docker-image-release_push:
+    # Push to Docker Hub when a new release is created
+    runs-on: ubuntu-latest
+    steps:
+
+     - name: Check Out Repo
+       uses: actions/checkout@v4
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v3
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Build image
+       uses: docker/build-push-action@v6
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/hermes:${{github.event.release.tag_name}}, clinicalgenomics/hermes:latest"

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.8.0
+      rev: 24.10.0
       hooks:
           - id: black
             args: ["--line-length", "100"]
@@ -10,7 +10,7 @@ repos:
           - id: isort
             name: isort
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.6.2
+      rev: v0.8.0
       hooks:
           - id: ruff
 

DEPLOYMENT.md

@@ -1,52 +1,21 @@
-# Steps
+# Deployment guide
+This includes instructions for deploying Hermes in the Clinical Genomics :hospital: setting.
 
-When all tests done and successful and PR is approved by codeowners, follow these steps:
+## Steps
+When all tests are done and successful and the PR is approved by codeowners, follow these steps:
 
-1. Select "Squash and merge" to merge branch into default branch (master/main).
-
-
-2. A prompt for writing merge commit message will pop up.
-
-
-3. Find the title of the pull request already pre-filled in the merge commit title, or copy and paste 
-the title if not.
-
-
-4. Append version increment value `( major | minor | patch )` to specify what kind of release is to be created.
-
-
-5. Fill in markdown formatted changelog in merge commit comment details:
-
-` ### Added `
+### Deploy feature branch for testing
+To deploy your feature branch to test it, run
+1. `hermes-test-deploy <branch_name>`
+2. `hermes-test --help` or the command you want to test.
 
-` ### Changed `
+This will pull the latest image tagged with your branch from Dockerhub and make it available with `hermes-test`. Note that it is not necessary to paxa the environment to do this.
 
-` ### Fixed `
-
-6. Review the details once again and merge the branch into master.
-
-
-7. Wait for GitHub actions to process the event, bump version, create release, publish to Dockerhub and PyPi.
-
-
-8. Deploy master to stage:
-    1. Log in to appropriate server `ssh <server.scilifelab.se>`
-    2. `us`
-    3. Request stage environment `paxa` and follow instructions
-    4. ```shell
-       bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_hermes -t hermes -b main
-       ```
-    5. Make sure that installation was successful
-
-
-9. Deploy master to production
-     1. Log in to appropriate server `ssh <server.scilifelab.se>`
-     2. `up`
-     3. ```shell
-        bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_hermes -t hermes -b main
-        ```
-     4. Make sure that installation was successful
-
-
-11. Take a screenshot or copy log text and post as a comment on the PR. Screenshot should include environment and that it succeeded.
 
+### Deploy to stage and production
+1. Select "Squash and merge" to merge branch into default branch (master/main).
+2. Append version increment value `( major | minor | patch )` in the commit message to specify what kind of release is to be created.
+3. Review the details and merge the branch into master.
+4. Deploy the latest version to stage and production with `hermes-deploy`.
+5. Take a screenshot or copy log text and post as a comment on the PR. Screenshot should include environment and that it succeeded.
+6. Great job :whale2:

Dockerfile

@@ -0,0 +1,10 @@
+FROM docker.io/library/python:3.12-slim-bullseye
+
+WORKDIR /app
+COPY . /app/
+
+RUN pip install --no-cache-dir --ignore-installed poetry \
+    && poetry config virtualenvs.create false \
+    && poetry install --no-cache --only main
+
+ENTRYPOINT ["hermes"]