Merge pull request #9 from JunAishima/prefect3-pixi-upgrade

add pixi and Dockerfile-related files

Author: AbbyGi

.github/workflows/publish-ghcr.yml

@@ -0,0 +1,59 @@
+#
+name: Create and publish a Docker image
+
+# Configures this workflow to run every time a change is pushed to the branch called `release`.
+on:
+  push:
+    branches: ['main']
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      #
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see [Usage](https://github.com/docker/build-push-action#usage) in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+      
+      # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see [Using artifact attestations to establish provenance for builds](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds).
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

Dockerfile

@@ -0,0 +1,27 @@
+FROM ghcr.io/prefix-dev/pixi:latest
+
+ENV TZ="America/New_York"
+
+RUN apt-get -y update && \
+    apt-get -y install git
+
+COPY pixi.toml .
+COPY pixi.lock .
+# use `--locked` to ensure the lockfile is up to date with pixi.toml
+RUN pixi install --locked
+# create the shell-hook bash script to activate the environment
+RUN pixi shell-hook -s bash > /shell-hook
+
+ENV PYTHONUNBUFFERED=1
+
+COPY test.py .
+
+RUN mkdir /etc/tiled
+RUN mkdir /.prefect -m 0777
+RUN mkdir /repo -m 0777
+
+RUN /bin/bash /shell-hook
+
+#now reapply deployment to push the image that is being created
+ENTRYPOINT ["pixi", "run"]
+CMD ["python", "-m", "test", "arg"]

analysis.py

@@ -11,14 +11,16 @@
 
 import numpy as np
 from prefect import flow, get_run_logger, task
+from prefect.blocks.system import Secret
 from tiled.client import from_profile
 
 from ophyd.utils.epics_pvs import data_shape, data_type
 from event_model import compose_run
 from typing import Iterable, TypedDict
 
 
-tiled_client = from_profile("nsls2")["cms"]
+api_key = Secret.load("tiled-cms-api-key", _sync=True).get()
+tiled_client = from_profile("nsls2", api_key=api_key)["cms"]
 tiled_client_raw = tiled_client["raw"]
 # tiled_client_processed = tiled_client["sandbox"]
 cms_sandbox_tiled_client = tiled_client["bluesky_sandbox"]

data_validation.py

@@ -1,13 +1,15 @@
 import time as ttime
 
 from prefect import flow, get_run_logger, task
+from prefect.blocks.system import Secret
 from tiled.client import from_profile
 
 
 @task(retries=2, retry_delay_seconds=10)
 def read_all_streams(beamline_acronym, uid):
     logger = get_run_logger()
-    tiled_client = from_profile("nsls2")
+    api_key = Secret.load("tiled-cms-api-key", _sync=True).get()
+    tiled_client = from_profile("nsls2", api_key=api_key)
     run = tiled_client[beamline_acronym]["raw"][uid]
     logger.info(f"Validating uid {run.start['uid']}")
     start_time = ttime.monotonic()

linker.py

@@ -1,11 +1,13 @@
 from prefect import task, get_run_logger
+from prefect.blocks.system import Secret
 from pathlib import Path
 from tiled.client import from_profile
 import os
 import glob
 
 #tiled_client = from_uri('https://tiled.nsls2.bnl.gov')
-tiled_client = from_profile("nsls2")['cms']
+api_key = Secret.load("tiled-cms-api-key", _sync=True).get()
+tiled_client = from_profile("nsls2", api_key=api_key)['cms']
 tiled_client_raw = tiled_client["raw"]
 
 #logger = logging.getLogger()