Galaxy (#40)

* fix

* make galaxy tools prototype

* galaxy tool PR; container 4 galaxy mode

* allow clean settings (no components)

* no pr if exist

* fix str + bytes

* PR name

* move logger.info components

* galaxy requirements already merged

* betetr naming

* fix

* version from master

* fix tool id not allowed symbols

* write last commit even if not changed

* cleanup before generation

* .shed.yml generation

* fix typo

* continue next repo if exception

* shed repo name is tool_id

* gitlab commit link in comment

* fix filenotfound on new tool cleanup

* reduce long lines and duplication

* main nb2workflow in Dockerfile_galaxy

* build galaxy bot action

* branch name in tag for pr in action

* action triggers

* proper if in action

.github/workflows/docker-image-galaxy.yml

@@ -0,0 +1,55 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image for Galaxy bot
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    types:
+      - labeled
+      - opened
+      - synchronize
+      - reopened
+
+
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    if: contains( github.event.pull_request.labels.*.name, 'galaxy')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: odahub/odabot-galaxy
+          tags: |
+            type=raw,value={{sha}}-{{date 'YYMMDDHHmmss'}}-${{ github.head_ref || github.ref_name }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./Dockerfile_galaxy
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -2,7 +2,7 @@ FROM python:3.9
 
 COPY . /source
 
-RUN pip install -r /source/requirements.txt && pip install /source && rm -r /source
+RUN pip install -r /source/requirements.txt && pip install /source[k8sdeploy] && rm -r /source
 
 RUN curl -LO "https://dl.k8s.io/release/$(curl -L -s https://dl.k8s.io/release/stable.txt)/bin/linux/amd64/kubectl" &&\
     install -o root -g root -m 0755 kubectl /usr/local/bin/kubectl && rm ./kubectl

Dockerfile_galaxy

@@ -0,0 +1,14 @@
+FROM python:3.9
+
+COPY . /source
+
+# RUN pip install git+https://github.com/oda-hub/nb2workflow@master#egg=nb2workflow[galaxy]
+RUN pip install /source[galaxy] && rm -r /source
+
+# Add Tini
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+ENTRYPOINT ["/tini", "--"]
+
+CMD ["odabot", "--settings", "/settings.toml", "make-galaxy-tools", "--loop", "10"]