From 35fb8ab8db2079fee8b0bd999e7dd9a8e5f92547 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Thu, 11 Sep 2025 14:50:44 -0400 Subject: [PATCH 01/42] add bare workflow to publish image to ghcr --- .github/workflows/publish-image.yml | 60 +++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 .github/workflows/publish-image.yml diff --git a/.github/workflows/publish-image.yml b/.github/workflows/publish-image.yml new file mode 100644 index 0000000..6fde597 --- /dev/null +++ b/.github/workflows/publish-image.yml @@ -0,0 +1,60 @@ +# +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: ['release'] + +# 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 + From f8d53b51253165aa660eabe1a1aa6fe39af77da7 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 16 Sep 2025 11:43:00 -0400 Subject: [PATCH 02/42] update branch to main, rename to same as other repos --- .github/workflows/{publish-image.yml => publish-ghcr.yml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename .github/workflows/{publish-image.yml => publish-ghcr.yml} (99%) diff --git a/.github/workflows/publish-image.yml b/.github/workflows/publish-ghcr.yml similarity index 99% rename from .github/workflows/publish-image.yml rename to .github/workflows/publish-ghcr.yml index 6fde597..263bdf8 100644 --- a/.github/workflows/publish-image.yml +++ b/.github/workflows/publish-ghcr.yml @@ -4,7 +4,7 @@ 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: ['release'] + 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: From b1f46ee1476ee8cf267a74f27663b2b274f8aaa0 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 17 Sep 2025 11:35:47 -0400 Subject: [PATCH 03/42] add Dockerfile, pixi files, prefect.yaml file * bring over from smi workflows --- Dockerfile | 29 + pixi.lock | 5173 ++++++++++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 11 + prefect.yaml | 32 + 4 files changed, 5245 insertions(+) create mode 100644 Dockerfile create mode 100644 pixi.lock create mode 100644 pixi.toml create mode 100644 prefect.yaml diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..211834c --- /dev/null +++ b/Dockerfile @@ -0,0 +1,29 @@ +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 +# either here or when docker run is done, make sure that the TILED_SITE_PROFILES directory on disk is mounted to the container. this will be necessary for data access. we will also need to allow outside network access from the container to get data from tiled + +COPY test.py . + +ENV TILED_API_KEY="" +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"] diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..5349689 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,5173 @@ +version: 6 +environments: + default: + channels: + - 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prefect.deployments.steps.git_clone: + repository: https://github.com/nsls2/tst-workflows.git + branch: main + +deployments: + - name: tst-end-of-run-workflow-docker + version: null + description: Deploy the updated Docker image + entrypoint: end_of_run_workflow.py:end_of_run_workflow + parameters: {} + schedule: {} + work_pool: + job_variables: + env: + TILED_SITE_PROFILES: /nsls2/software/etc/tiled/profiles + TILED_API_KEY: "{{ prefect.blocks.secret.tiled-tst-api-key }}" + image: ghcr.io/nsls2/tst-workflows:main + network_mode: slirp4netns + userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst + volumes: + - /nsls2/data/tst/proposals:/nsls2/data/tst/proposals + - /nsls2/software/etc/tiled:/nsls2/software/etc/tiled + auto_remove: true + name: tst-work-pool-docker From 3e6f5e3c81d82a9d5f6046a60debe71b95d78f3d Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 10:44:54 -0400 Subject: [PATCH 04/42] remove extra line --- .github/workflows/publish-ghcr.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/publish-ghcr.yml b/.github/workflows/publish-ghcr.yml index 263bdf8..8c677ba 100644 --- a/.github/workflows/publish-ghcr.yml +++ b/.github/workflows/publish-ghcr.yml @@ -57,4 +57,3 @@ jobs: subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}} subject-digest: ${{ steps.push.outputs.digest }} push-to-registry: true - From 4e80ae8c4caee6c0f027d04edaaf1a6c9cecdddd Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 10:45:07 -0400 Subject: [PATCH 05/42] use Secrets class for retrieving API key * inject into from_profile() client creation --- data_validation.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/data_validation.py b/data_validation.py index 1baeceb..12a5532 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,4 +1,5 @@ from prefect import task, flow, get_run_logger +from prefect.blocks.system import Secret import time as ttime from tiled.client import from_profile @@ -6,7 +7,8 @@ @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - tiled_client = from_profile("nsls2") + api_key = Secret.load("prefect.blocks.secret.tiled-tst-api-key") + 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() From b78e24480c179f58cc7d271d9743b0c28fcbbedb Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 10:46:58 -0400 Subject: [PATCH 06/42] remove ENV var to pass in API key * use Secrets to get value directly from Prefect in data_validation() instead --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 211834c..723dc62 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,6 @@ ENV PYTHONUNBUFFERED=1 COPY test.py . -ENV TILED_API_KEY="" RUN mkdir /etc/tiled RUN mkdir /.prefect -m 0777 RUN mkdir /repo -m 0777 From 960edf371766f6e89046ec5d4317c12ecd68f570 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 10:48:50 -0400 Subject: [PATCH 07/42] set version number, remove Tiled API key * do not use ENV to push Tiled API key into the workflow, use Prefect Secrets instead --- prefect.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/prefect.yaml b/prefect.yaml index 59b4dd7..6f46d34 100644 --- a/prefect.yaml +++ b/prefect.yaml @@ -12,7 +12,7 @@ pull: deployments: - name: tst-end-of-run-workflow-docker - version: null + version: 0.1.0 description: Deploy the updated Docker image entrypoint: end_of_run_workflow.py:end_of_run_workflow parameters: {} @@ -21,7 +21,6 @@ deployments: job_variables: env: TILED_SITE_PROFILES: /nsls2/software/etc/tiled/profiles - TILED_API_KEY: "{{ prefect.blocks.secret.tiled-tst-api-key }}" image: ghcr.io/nsls2/tst-workflows:main network_mode: slirp4netns userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst From 26cc1c38a1f4032b45a14d3d26c02aa8b0dbfcd4 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 11:29:10 -0400 Subject: [PATCH 08/42] use prefect3-pixi-upgrade for now * as with other beamlines, use this branch for the prefect3 upgrades * refactor from main for testing --- prefect.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/prefect.yaml b/prefect.yaml index 6f46d34..f5ee606 100644 --- a/prefect.yaml +++ b/prefect.yaml @@ -8,7 +8,7 @@ push: null pull: - prefect.deployments.steps.git_clone: repository: https://github.com/nsls2/tst-workflows.git - branch: main + branch: prefect3-pixi-upgrade deployments: - name: tst-end-of-run-workflow-docker @@ -21,7 +21,7 @@ deployments: job_variables: env: TILED_SITE_PROFILES: /nsls2/software/etc/tiled/profiles - image: ghcr.io/nsls2/tst-workflows:main + image: ghcr.io/nsls2/tst-workflows:prefect3-pixi-upgrade network_mode: slirp4netns userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst volumes: From 2bbf8dae1035c3f2ce3c0098d9a7ad29b211e6c9 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 11:36:02 -0400 Subject: [PATCH 09/42] rename build/push branch to current dev branch * want to be able to test with current branch for testing --- .github/workflows/publish-ghcr.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-ghcr.yml b/.github/workflows/publish-ghcr.yml index 8c677ba..3c59228 100644 --- a/.github/workflows/publish-ghcr.yml +++ b/.github/workflows/publish-ghcr.yml @@ -4,7 +4,7 @@ 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'] + branches: ['prefect3-pixi-upgrade'] # 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: From fc989c6f14f1734496f8869caf422b08fb88a401 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 1 Oct 2025 11:38:30 -0400 Subject: [PATCH 10/42] add missing file * used for doing something minimally useful when the image is run outside of Prefect --- test.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 test.py diff --git a/test.py b/test.py new file mode 100644 index 0000000..e54521c --- /dev/null +++ b/test.py @@ -0,0 +1,17 @@ +from __future__ import annotations + +import sys + + +def test(stuff=""): + if stuff: + print(f"test: {stuff}") # noqa: T201 + else: + print("test: EMPTY") # noqa: T201 + + +if __name__ == "__main__": + if len(sys.argv) > 1: + test(sys.argv[1]) + else: + test() From d81c14794860ed6a08b005102ea37805b4bf6525 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Thu, 2 Oct 2025 14:45:12 -0400 Subject: [PATCH 11/42] remove unnecessary line --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 723dc62..b4ac7e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,7 +13,6 @@ RUN pixi install --locked RUN pixi shell-hook -s bash > /shell-hook ENV PYTHONUNBUFFERED=1 -# either here or when docker run is done, make sure that the TILED_SITE_PROFILES directory on disk is mounted to the container. this will be necessary for data access. we will also need to allow outside network access from the container to get data from tiled COPY test.py . From a4c25de541375f61515d8102ca209d2e5279bf52 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 09:14:26 -0400 Subject: [PATCH 12/42] add script for testing beamline --- run-deployment.py | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 run-deployment.py diff --git a/run-deployment.py b/run-deployment.py new file mode 100644 index 0000000..8de6e5c --- /dev/null +++ b/run-deployment.py @@ -0,0 +1,9 @@ +from __future__ import annotations + +from prefect.deployments import run_deployment + +run_deployment( + name="end-of-run-workflow/hex-end-of-run-workflow-docker", + parameters={"stop_doc": {"run_start": ""}}, + timeout=15, # don't wait for the run to finish # edit to 15 sec +) From 2378fcc0b0178e28c65977625f7ed054bc92f9d9 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 09:29:49 -0400 Subject: [PATCH 13/42] remove posting message to Slack channel * this should be a test Slack channel, remove for now --- end_of_run_workflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index a0add6a..745441a 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -13,7 +13,7 @@ def log_completion(): @flow def end_of_run_workflow(stop_doc): uid = stop_doc["run_start"] - hello_world() + # hello_world() data_validation(uid, return_state=True) # long_flow(iterations=100, sleep_length=10) log_completion() From 5d0d1ea70d86f0a4ef5f54aa0c793efc359304a1 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 09:33:37 -0400 Subject: [PATCH 14/42] fix deployment to run to tst --- run-deployment.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run-deployment.py b/run-deployment.py index 8de6e5c..7729131 100644 --- a/run-deployment.py +++ b/run-deployment.py @@ -3,7 +3,7 @@ from prefect.deployments import run_deployment run_deployment( - name="end-of-run-workflow/hex-end-of-run-workflow-docker", + name="end-of-run-workflow/tst-end-of-run-workflow-docker", parameters={"stop_doc": {"run_start": ""}}, timeout=15, # don't wait for the run to finish # edit to 15 sec ) From afb2435b4b252b769b668638922ab26219406cdf Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 09:33:50 -0400 Subject: [PATCH 15/42] fix name of API key - do not add full prefix --- data_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data_validation.py b/data_validation.py index 12a5532..6cfd830 100644 --- a/data_validation.py +++ b/data_validation.py @@ -7,7 +7,7 @@ @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - api_key = Secret.load("prefect.blocks.secret.tiled-tst-api-key") + api_key = Secret.load("tiled-tst-api-key") tiled_client = from_profile("nsls2", api_key=api_key) run = tiled_client[beamline_acronym]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") From f0dcb043ff76420d4b8475bd48f1d2aeeaa564cf Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 09:58:47 -0400 Subject: [PATCH 16/42] put Tiled API key into environment variable * Tiled requires this for non-interactive uses --- data_validation.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/data_validation.py b/data_validation.py index 6cfd830..59e0d7c 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,14 +1,15 @@ from prefect import task, flow, get_run_logger from prefect.blocks.system import Secret import time as ttime -from tiled.client import from_profile - +from tiled.client import from_profile, Context +import os @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() api_key = Secret.load("tiled-tst-api-key") - tiled_client = from_profile("nsls2", api_key=api_key) + os.environ["TILED_API_KEY"] = api_key.get() + tiled_client = from_profile("nsls2") run = tiled_client[beamline_acronym]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() From 0897e364552d789123ec59fe3430ab7191eb4749 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 10:02:50 -0400 Subject: [PATCH 17/42] update dependencies * loosen prefect requirement * add databroker to get more familiar structure of returned objects --- pixi.lock | 1795 +++++++++++++++++++++++++++++++++++++++++++++++------ pixi.toml | 5 +- 2 files changed, 1620 insertions(+), 180 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5349689..e80ceeb 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,13 +11,20 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/_x86_64-microarch-level-1-2_x86_64.conda - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-48.0-unix_0.conda + - 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python-jose - python-multipart + - redis-py - sqlalchemy + - stamina - starlette - - tiled-base 0.1.0b28 pyhd8ed1ab_0 + - tiled-base 0.1.6 pyhd8ed1ab_0 - toolz - uvicorn - watchfiles @@ -5867,8 +6042,8 @@ packages: license: BSD-3-Clause license_family: BSD purls: [] - size: 8512 - timestamp: 1747870876207 + size: 8612 + timestamp: 1759181267058 - conda: https://conda.anaconda.org/conda-forge/linux-64/time-machine-2.16.0-py312h66e93f0_0.conda sha256: d5b2d33791dfe0ff6dee9a7f2f9f866b1e29611fa252a520cd85d8652b2b06db md5: d2bf5a1a6e2034b2e64729b474499a7c diff --git a/pixi.toml b/pixi.toml index fe961a2..d61358f 100644 --- a/pixi.toml +++ b/pixi.toml @@ -5,7 +5,7 @@ platforms = ["linux-64"] [dependencies] prefect = "3.*" -tiled-client = "0.1.*" +tiled-client = ">0.1.1" databroker = "*" [pypi-dependencies] From d6437d94071a93e3fe60fc61f807c57cbaf1271a Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 11:04:04 -0400 Subject: [PATCH 19/42] remove API key from environment * reduce chance of key getting hijacked --- data_validation.py | 1 + 1 file changed, 1 insertion(+) diff --git a/data_validation.py b/data_validation.py index 59e0d7c..511b74b 100644 --- a/data_validation.py +++ b/data_validation.py @@ -10,6 +10,7 @@ def read_all_streams(uid, beamline_acronym): api_key = Secret.load("tiled-tst-api-key") os.environ["TILED_API_KEY"] = api_key.get() tiled_client = from_profile("nsls2") + os.environ.pop("TILED_API_KEY") run = tiled_client[beamline_acronym]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() From 268b730430f15a20f7f9669ec0682ef3eb7cb70d Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 13:35:02 -0400 Subject: [PATCH 20/42] create utils to reduce number of Tiled clients * use in current workflow --- data_validation.py | 7 ++----- utils.py | 11 +++++++++++ 2 files changed, 13 insertions(+), 5 deletions(-) create mode 100644 utils.py diff --git a/data_validation.py b/data_validation.py index 511b74b..c2bd866 100644 --- a/data_validation.py +++ b/data_validation.py @@ -2,16 +2,13 @@ from prefect.blocks.system import Secret import time as ttime from tiled.client import from_profile, Context +from utils import get_tiled_client import os @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - api_key = Secret.load("tiled-tst-api-key") - os.environ["TILED_API_KEY"] = api_key.get() - tiled_client = from_profile("nsls2") - os.environ.pop("TILED_API_KEY") - run = tiled_client[beamline_acronym]["raw"][uid] + run = get_tiled_client()[beamline_acronym]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() for stream in run: diff --git a/utils.py b/utils.py new file mode 100644 index 0000000..852fea8 --- /dev/null +++ b/utils.py @@ -0,0 +1,11 @@ +from tiled.client import from_profile +from prefect.blocks.system import Secret + +import os + +os.environ["TILED_API_KEY"] = Secret("tiled-tst-api-key").get() +tiled_client = from_profile("nsls2") +os.environ.pop("TILED_API_KEY") + +def get_tiled_client(): + return tiled_client From 2fa63883da35c1973404515896eda3280327e2a6 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 15:48:58 -0400 Subject: [PATCH 21/42] fix parentheses --- utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils.py b/utils.py index 852fea8..d0db938 100644 --- a/utils.py +++ b/utils.py @@ -3,7 +3,7 @@ import os -os.environ["TILED_API_KEY"] = Secret("tiled-tst-api-key").get() +os.environ["TILED_API_KEY"] = (Secret("tiled-tst-api-key")).get() tiled_client = from_profile("nsls2") os.environ.pop("TILED_API_KEY") From ed6c13d324d4636706b5d1076661d28ed8eb09c2 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 15:52:31 -0400 Subject: [PATCH 22/42] use load function --- utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils.py b/utils.py index d0db938..346d9eb 100644 --- a/utils.py +++ b/utils.py @@ -3,7 +3,7 @@ import os -os.environ["TILED_API_KEY"] = (Secret("tiled-tst-api-key")).get() +os.environ["TILED_API_KEY"] = Secret.load("tiled-tst-api-key").get() tiled_client = from_profile("nsls2") os.environ.pop("TILED_API_KEY") From 1d302c12bc30a7af8a647ab759e6b3c3e1113f48 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 16:02:49 -0400 Subject: [PATCH 23/42] refactor to get beamline/endstation-specific Tiled client * make it slightly easier to configure with a single constant --- data_validation.py | 2 +- utils.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/data_validation.py b/data_validation.py index c2bd866..8e69459 100644 --- a/data_validation.py +++ b/data_validation.py @@ -8,7 +8,7 @@ @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - run = get_tiled_client()[beamline_acronym]["raw"][uid] + run = get_tiled_client()[uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() for stream in run: diff --git a/utils.py b/utils.py index 346d9eb..f20f329 100644 --- a/utils.py +++ b/utils.py @@ -3,8 +3,10 @@ import os -os.environ["TILED_API_KEY"] = Secret.load("tiled-tst-api-key").get() -tiled_client = from_profile("nsls2") +LOCATION="tst" + +os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key").get() +tiled_client = from_profile("nsls2")[LOCATION]["raw"] os.environ.pop("TILED_API_KEY") def get_tiled_client(): From 1d2dba69f20bec92e9485d6261ad7c495b767d28 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 16:06:52 -0400 Subject: [PATCH 24/42] create another task to test getting the client from utils --- end_of_run_workflow.py | 2 ++ test_extra_client.py | 7 +++++++ 2 files changed, 9 insertions(+) create mode 100644 test_extra_client.py diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index 745441a..c47898b 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -1,6 +1,7 @@ from prefect import task, flow, get_run_logger from data_validation import data_validation from prefect2_test_flow import hello_world +from test_extra_client import get_other_docs # from long_flow import long_flow @@ -15,6 +16,7 @@ def end_of_run_workflow(stop_doc): uid = stop_doc["run_start"] # hello_world() data_validation(uid, return_state=True) + get_other_docs(uid) # long_flow(iterations=100, sleep_length=10) log_completion() diff --git a/test_extra_client.py b/test_extra_client.py new file mode 100644 index 0000000..212ef4d --- /dev/null +++ b/test_extra_client.py @@ -0,0 +1,7 @@ +from utils import get_tiled_client + +@task +def get_other_docs(uid): + result = get_tiled_client()[uid] + for name, doc in result.documents(): + print(name, doc) From dbd40eeeb27962a0038080e52577b4676a883852 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 16:09:45 -0400 Subject: [PATCH 25/42] missing import, use run logging --- test_extra_client.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/test_extra_client.py b/test_extra_client.py index 212ef4d..aa839b6 100644 --- a/test_extra_client.py +++ b/test_extra_client.py @@ -1,7 +1,9 @@ +from prefect import task, get_run_logger from utils import get_tiled_client @task def get_other_docs(uid): + logger = get_run_logger() result = get_tiled_client()[uid] for name, doc in result.documents(): - print(name, doc) + logger.info(f"name: {name}, doc: {doc}") From 0811677494db765a44d64cd967fb620456766eee Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Fri, 3 Oct 2025 17:11:45 -0400 Subject: [PATCH 26/42] make new clients each time get_tiled_client() is called * the underlying object is not async-compatible so make a new client every time one is requested instead of sharing --- utils.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/utils.py b/utils.py index f20f329..d572594 100644 --- a/utils.py +++ b/utils.py @@ -5,9 +5,8 @@ LOCATION="tst" -os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key").get() -tiled_client = from_profile("nsls2")[LOCATION]["raw"] -os.environ.pop("TILED_API_KEY") - def get_tiled_client(): + os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key").get() + tiled_client = from_profile("nsls2")[LOCATION]["raw"] + os.environ.pop("TILED_API_KEY") return tiled_client From 9c01be5fa4bd111cd8a2cdf2279e7de28f7e7825 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Sun, 5 Oct 2025 21:28:44 -0400 Subject: [PATCH 27/42] refactor to remove raw from get_tiled_client() * enable use of different selections * remove imports that are no longer used --- data_validation.py | 3 +-- test_extra_client.py | 2 +- utils.py | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/data_validation.py b/data_validation.py index 8e69459..3a19aef 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,14 +1,13 @@ from prefect import task, flow, get_run_logger from prefect.blocks.system import Secret import time as ttime -from tiled.client import from_profile, Context from utils import get_tiled_client import os @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - run = get_tiled_client()[uid] + run = get_tiled_client()["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() for stream in run: diff --git a/test_extra_client.py b/test_extra_client.py index aa839b6..2b8084f 100644 --- a/test_extra_client.py +++ b/test_extra_client.py @@ -4,6 +4,6 @@ @task def get_other_docs(uid): logger = get_run_logger() - result = get_tiled_client()[uid] + result = get_tiled_client()["raw"][uid] for name, doc in result.documents(): logger.info(f"name: {name}, doc: {doc}") diff --git a/utils.py b/utils.py index d572594..3529898 100644 --- a/utils.py +++ b/utils.py @@ -7,6 +7,6 @@ def get_tiled_client(): os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key").get() - tiled_client = from_profile("nsls2")[LOCATION]["raw"] + tiled_client = from_profile("nsls2")[LOCATION] os.environ.pop("TILED_API_KEY") return tiled_client From a573d8d296f99e978e20fa7651fcc42ca3ce8605 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 7 Oct 2025 10:54:46 -0400 Subject: [PATCH 28/42] go back to using from_profile(..., api_key=api_key) --- data_validation.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/data_validation.py b/data_validation.py index 3a19aef..7e2b63d 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,13 +1,15 @@ from prefect import task, flow, get_run_logger from prefect.blocks.system import Secret import time as ttime -from utils import get_tiled_client +from tiled.client import get_profile import os @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() - run = get_tiled_client()["raw"][uid] + api_key = Secret.load("tiled-tst-api-key").get() + cl = get_profile("nsls2", api_key=api_key) + run = cl["tst"]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() for stream in run: From 7a40d29250abc9258755261ecec04fc630e788b5 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 7 Oct 2025 10:57:46 -0400 Subject: [PATCH 29/42] fix bad import --- data_validation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data_validation.py b/data_validation.py index 7e2b63d..112ac2c 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,14 +1,14 @@ from prefect import task, flow, get_run_logger from prefect.blocks.system import Secret import time as ttime -from tiled.client import get_profile +from tiled.client import from_profile import os @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): logger = get_run_logger() api_key = Secret.load("tiled-tst-api-key").get() - cl = get_profile("nsls2", api_key=api_key) + cl = from_profile("nsls2", api_key=api_key) run = cl["tst"]["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = ttime.monotonic() From cf9ba093bb872c4da408e3cabede26742629d302 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 8 Oct 2025 10:28:24 -0400 Subject: [PATCH 30/42] add improt --- run-deployment.py | 1 + 1 file changed, 1 insertion(+) diff --git a/run-deployment.py b/run-deployment.py index 7729131..1dd798a 100644 --- a/run-deployment.py +++ b/run-deployment.py @@ -1,6 +1,7 @@ from __future__ import annotations from prefect.deployments import run_deployment +from datetime import datetime run_deployment( name="end-of-run-workflow/tst-end-of-run-workflow-docker", From 772daf3c41e26dbb3eb61f8fdaef9b9101e432c4 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 8 Oct 2025 10:28:33 -0400 Subject: [PATCH 31/42] give a dummy uid --- run-deployment.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run-deployment.py b/run-deployment.py index 1dd798a..206ab7f 100644 --- a/run-deployment.py +++ b/run-deployment.py @@ -5,6 +5,6 @@ run_deployment( name="end-of-run-workflow/tst-end-of-run-workflow-docker", - parameters={"stop_doc": {"run_start": ""}}, + parameters={"stop_doc": {"run_start": "adfwerwerwerw"}}, timeout=15, # don't wait for the run to finish # edit to 15 sec ) From 8d41d1607844ac62f97e2878bb8c8435494f8fa7 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Thu, 9 Oct 2025 13:59:17 -0400 Subject: [PATCH 32/42] update to add tzdata to honor timezone --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b4ac7e4..ea94aca 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,8 @@ FROM ghcr.io/prefix-dev/pixi:latest ENV TZ="America/New_York" RUN apt-get -y update && \ - apt-get -y install git + apt-get -y install git \ + apt-get -y install tzdata COPY pixi.toml . COPY pixi.lock . From acd6d163cfd19d390dc37e73b4953044e429e415 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Thu, 9 Oct 2025 14:01:06 -0400 Subject: [PATCH 33/42] fix punctuation --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ea94aca..a7777d4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ FROM ghcr.io/prefix-dev/pixi:latest ENV TZ="America/New_York" RUN apt-get -y update && \ - apt-get -y install git \ + apt-get -y install git && \ apt-get -y install tzdata COPY pixi.toml . From a950aea1e760ceea95942bec48fb9efb6f59d063 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Thu, 9 Oct 2025 14:06:18 -0400 Subject: [PATCH 34/42] clean up syntax - no extra call to apt-get --- Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a7777d4..5f49c36 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,8 +3,7 @@ FROM ghcr.io/prefix-dev/pixi:latest ENV TZ="America/New_York" RUN apt-get -y update && \ - apt-get -y install git && \ - apt-get -y install tzdata + apt-get -y install git tzdata COPY pixi.toml . COPY pixi.lock . From 033dd70ce6c1e9044f21ad4a36a780107c6cf636 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 13 Jan 2026 11:22:55 -0500 Subject: [PATCH 35/42] fix pixi version in Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5f49c36..690b7a3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/prefix-dev/pixi:latest +FROM ghcr.io/prefix-dev/pixi:0.57.0 ENV TZ="America/New_York" From 14c41e196f02dbd875ecd167cba1b2ebcdf0afad Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 13 Jan 2026 11:23:51 -0500 Subject: [PATCH 36/42] fix to publish on main, remove extra spaces * changes to match ucal-workflows's version of the file --- .github/workflows/publish-ghcr.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/publish-ghcr.yml b/.github/workflows/publish-ghcr.yml index 3c59228..45e4f05 100644 --- a/.github/workflows/publish-ghcr.yml +++ b/.github/workflows/publish-ghcr.yml @@ -4,7 +4,7 @@ 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: ['prefect3-pixi-upgrade'] + 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: @@ -49,7 +49,7 @@ jobs: 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 From 17a0c17b895c0bfbc6edd1aba079639283561fa9 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 13 Jan 2026 11:26:48 -0500 Subject: [PATCH 37/42] update pixi dependencies, store pixi.lock, update prefect.yaml * update pixi dependencies to match other beamlines' workflows * pixi update and store resulting pixi.lock file * update prefect version in prefect.yaml --- pixi.lock | 7050 ++++++++++++++++++++++---------------------------- pixi.toml | 5 +- prefect.yaml | 2 +- 3 files changed, 3030 insertions(+), 4027 deletions(-) diff --git a/pixi.lock b/pixi.lock index b5d2ce9..983a60f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -9,450 +9,381 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - 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__glibc >=2.17,<3.0.a0 - - libgcc >=13 - - libstdcxx >=13 - libzlib >=1.3.1,<2.0a0 license: BSD-3-Clause license_family: BSD purls: [] - size: 567578 - timestamp: 1742433379869 + size: 601375 + timestamp: 1764777111296 diff --git a/pixi.toml b/pixi.toml index d61358f..50e3351 100644 --- a/pixi.toml +++ b/pixi.toml @@ -5,8 +5,9 @@ platforms = ["linux-64"] [dependencies] prefect = "3.*" -tiled-client = ">0.1.1" -databroker = "*" +python = "<3.14" +tiled-client = ">=0.2.3" +bluesky-tiled-plugins = ">=2" [pypi-dependencies] lixtools = "==2023.1.23.0" diff --git a/prefect.yaml b/prefect.yaml index f5ee606..a3b5048 100644 --- a/prefect.yaml +++ b/prefect.yaml @@ -1,5 +1,5 @@ name: prefect-docker-pixi-tiled -prefect-version: 3.6.0 +prefect-version: 3.6.10 build: null From 1a6432a94f131e8335ed38c919bed5737ef1e306 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 13 Jan 2026 11:28:53 -0500 Subject: [PATCH 38/42] update test.py to default.py, update Dockerfile * update to the same default.py module used with other workflow repos * update Dockerfile to use default.py instead of test.py --- Dockerfile | 4 ++-- default.py | 28 ++++++++++++++++++++++++++++ test.py | 17 ----------------- 3 files changed, 30 insertions(+), 19 deletions(-) create mode 100644 default.py delete mode 100644 test.py diff --git a/Dockerfile b/Dockerfile index 690b7a3..f7fa067 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN pixi shell-hook -s bash > /shell-hook ENV PYTHONUNBUFFERED=1 -COPY test.py . +COPY default.py . RUN mkdir /etc/tiled RUN mkdir /.prefect -m 0777 @@ -24,4 +24,4 @@ RUN /bin/bash /shell-hook #now reapply deployment to push the image that is being created ENTRYPOINT ["pixi", "run"] -CMD ["python", "-m", "test", "arg"] +CMD ["python", "-m", "default", "arg"] diff --git a/default.py b/default.py new file mode 100644 index 0000000..c69fc15 --- /dev/null +++ b/default.py @@ -0,0 +1,28 @@ +from __future__ import annotations + +import prefect +import subprocess +import sys +import tiled + + +def print_argument(argument_to_print=""): + if argument_to_print: + print(f"argument to print: {argument_to_print}") # noqa: T201 + else: + print("argument to print: EMPTY") # noqa: T201 + + +def info(): + print(f"Prefect info: {prefect.__version_info__}") + print(f"Tiled info: {tiled.__version__}") + output = subprocess.check_output(["pixi", "--version"]) + print(f"Pixi info: {output.decode().strip()}") + + +if __name__ == "__main__": + info() + if len(sys.argv) > 1: + print_argument(sys.argv[1]) + else: + print_argument() diff --git a/test.py b/test.py deleted file mode 100644 index e54521c..0000000 --- a/test.py +++ /dev/null @@ -1,17 +0,0 @@ -from __future__ import annotations - -import sys - - -def test(stuff=""): - if stuff: - print(f"test: {stuff}") # noqa: T201 - else: - print("test: EMPTY") # noqa: T201 - - -if __name__ == "__main__": - if len(sys.argv) > 1: - test(sys.argv[1]) - else: - test() From 5f94bab3f6d26208e5d4aa5bf642e2b29a7ead19 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 4 Feb 2026 14:11:23 -0500 Subject: [PATCH 39/42] update deployment file to match others --- prefect.yaml | 12 +++++++++--- run-deployment.py | 10 ---------- 2 files changed, 9 insertions(+), 13 deletions(-) delete mode 100644 run-deployment.py diff --git a/prefect.yaml b/prefect.yaml index a3b5048..7bf4575 100644 --- a/prefect.yaml +++ b/prefect.yaml @@ -6,13 +6,18 @@ build: null push: null pull: + - prefect.deployments.steps.set_working_directory: + directory: /repo - prefect.deployments.steps.git_clone: repository: https://github.com/nsls2/tst-workflows.git - branch: prefect3-pixi-upgrade + branch: main deployments: - name: tst-end-of-run-workflow-docker - version: 0.1.0 + version: 0.1.1 + tags: + - tst + - main description: Deploy the updated Docker image entrypoint: end_of_run_workflow.py:end_of_run_workflow parameters: {} @@ -21,7 +26,8 @@ deployments: job_variables: env: TILED_SITE_PROFILES: /nsls2/software/etc/tiled/profiles - image: ghcr.io/nsls2/tst-workflows:prefect3-pixi-upgrade + image: ghcr.io/nsls2/tst-workflows:main + image_pull_policy: Always network_mode: slirp4netns userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst volumes: diff --git a/run-deployment.py b/run-deployment.py deleted file mode 100644 index 206ab7f..0000000 --- a/run-deployment.py +++ /dev/null @@ -1,10 +0,0 @@ -from __future__ import annotations - -from prefect.deployments import run_deployment -from datetime import datetime - -run_deployment( - name="end-of-run-workflow/tst-end-of-run-workflow-docker", - parameters={"stop_doc": {"run_start": "adfwerwerwerw"}}, - timeout=15, # don't wait for the run to finish # edit to 15 sec -) From 27f09b801f988d72076be5c8c624b0afba1250c3 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 4 Feb 2026 14:16:01 -0500 Subject: [PATCH 40/42] add linting and pre-commit files --- .github/workflows/linting.yml | 14 ++++++ .pre-commit-config.yaml | 92 +++++++++++++++++++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 .github/workflows/linting.yml create mode 100644 .pre-commit-config.yaml diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 0000000..6e3d4d6 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,14 @@ +name: pre-commit + +on: + pull_request: + push: + branches: [main] + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.3.0 + - uses: actions/setup-python@v5.6.0 + - uses: pre-commit/action@v3.0.1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..7949fff --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,92 @@ +ci: + autoupdate_commit_msg: "chore: update pre-commit hooks" + autofix_commit_msg: "style: pre-commit fixes" + +exclude: ^.cruft.json|.copier-answers.yml$ + +repos: + - repo: https://github.com/adamchainz/blacken-docs + rev: "1.19.1" + hooks: + - id: blacken-docs + additional_dependencies: [black==24.*] + + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: "v5.0.0" + hooks: + - id: check-added-large-files + - id: check-case-conflict + - id: check-merge-conflict + - id: check-symlinks + - id: check-yaml + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + - id: name-tests-test + args: ["--pytest-test-first"] + - id: requirements-txt-fixer + - id: trailing-whitespace + + - repo: https://github.com/pre-commit/pygrep-hooks + rev: "v1.10.0" + hooks: + - id: rst-backticks + - id: rst-directive-colons + - id: rst-inline-touching-normal + + - repo: https://github.com/rbubley/mirrors-prettier + rev: "v3.5.3" + hooks: + - id: prettier + types_or: [yaml, markdown, html, css, scss, javascript, json] + args: [--prose-wrap=always] + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.11.11" + hooks: + - id: ruff + args: ["--fix", "--show-fixes"] + - id: ruff-format + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: "v1.15.0" + hooks: + - id: mypy + files: src|tests + args: [] + additional_dependencies: + - pytest + + - repo: https://github.com/codespell-project/codespell + rev: "v2.4.1" + hooks: + - id: codespell + additional_dependencies: + - tomli; python_version<'3.11' + exclude: "pixi.*" + + - repo: https://github.com/shellcheck-py/shellcheck-py + rev: "v0.10.0.1" + hooks: + - id: shellcheck + + - repo: local + hooks: + - id: disallow-caps + name: Disallow improper capitalization + language: pygrep + entry: PyBind|Numpy|Cmake|CCache|Github|PyTest + exclude: .pre-commit-config.yaml + + - repo: https://github.com/abravalheri/validate-pyproject + rev: "v0.24.1" + hooks: + - id: validate-pyproject + additional_dependencies: ["validate-pyproject-schema-store[all]"] + + - repo: https://github.com/python-jsonschema/check-jsonschema + rev: "0.33.0" + hooks: + - id: check-dependabot + - id: check-github-workflows + - id: check-readthedocs From 3602d366e61a25ceff06149485b43502a40996f8 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 4 Feb 2026 14:17:53 -0500 Subject: [PATCH 41/42] LINT: linting fixes --- .gitignore | 1 - LICENSE | 1 - README.md | 1 - data_validation.py | 2 +- end_of_run_workflow.py | 2 -- long_flow.py | 1 - prefect.yaml | 2 +- prefect2_test_flow.py | 7 ++---- pyhyper.py | 51 +++++++++++++++++++++++------------------- test-flow.py | 5 ++++- test_extra_client.py | 1 + utils.py | 3 ++- 12 files changed, 39 insertions(+), 38 deletions(-) diff --git a/.gitignore b/.gitignore index 4b247eb..abd84a5 100644 --- a/.gitignore +++ b/.gitignore @@ -80,4 +80,3 @@ target/ #Ipython Notebook .ipynb_checkpoints - diff --git a/LICENSE b/LICENSE index a6393ed..3c99b84 100644 --- a/LICENSE +++ b/LICENSE @@ -27,4 +27,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/README.md b/README.md index d02a468..c05f7e5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ # Workflows Repository of workflows for the TST beamline. - diff --git a/data_validation.py b/data_validation.py index 112ac2c..60ad578 100644 --- a/data_validation.py +++ b/data_validation.py @@ -2,7 +2,7 @@ from prefect.blocks.system import Secret import time as ttime from tiled.client import from_profile -import os + @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym): diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index c47898b..f56291b 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -1,6 +1,5 @@ from prefect import task, flow, get_run_logger from data_validation import data_validation -from prefect2_test_flow import hello_world from test_extra_client import get_other_docs # from long_flow import long_flow @@ -19,4 +18,3 @@ def end_of_run_workflow(stop_doc): get_other_docs(uid) # long_flow(iterations=100, sleep_length=10) log_completion() - diff --git a/long_flow.py b/long_flow.py index 7866900..ca48572 100644 --- a/long_flow.py +++ b/long_flow.py @@ -1,4 +1,3 @@ -import numpy as np from prefect import task, flow import time as ttime diff --git a/prefect.yaml b/prefect.yaml index 7bf4575..065a601 100644 --- a/prefect.yaml +++ b/prefect.yaml @@ -29,7 +29,7 @@ deployments: image: ghcr.io/nsls2/tst-workflows:main image_pull_policy: Always network_mode: slirp4netns - userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst + userns: "keep-id:uid=402974,gid=402974" # workflow-tst:workflow-tst volumes: - /nsls2/data/tst/proposals:/nsls2/data/tst/proposals - /nsls2/software/etc/tiled:/nsls2/software/etc/tiled diff --git a/prefect2_test_flow.py b/prefect2_test_flow.py index 7cabe94..2b5911f 100644 --- a/prefect2_test_flow.py +++ b/prefect2_test_flow.py @@ -1,4 +1,3 @@ -import os import traceback from prefect import flow, task, get_run_logger @@ -26,9 +25,7 @@ def wrapper(*args, **kwargs): return result except Exception as e: tb = traceback.format_exception_only(e) - slack_webhook.notify( - f":bangbang: Flow-run failed. (*{flow_run_name}*)" - ) + slack_webhook.notify(f":bangbang: Flow-run failed. (*{flow_run_name}*)") raise return wrapper @@ -41,7 +38,7 @@ def hello_world(): logger.info("Starting flow") print_task() test_dict = dict() - #test_dict["key"] # Trying to create a key error here. + # test_dict["key"] # Trying to create a key error here. if __name__ == "__main__": diff --git a/pyhyper.py b/pyhyper.py index 71fb366..1da7ab5 100644 --- a/pyhyper.py +++ b/pyhyper.py @@ -1,47 +1,53 @@ import prefect from prefect import task, Flow, Parameter -from prefect.tasks.prefect import create_flow_run from prefect.triggers import all_finished from tiled.client import from_profile -import matplotlib.pyplot as plt -from matplotlib.colors import LogNorm import PyHyperScattering -print(f'{PyHyperScattering.__version__}') +print(f"{PyHyperScattering.__version__}") RUN_TO_PLOT = 36106 -PATH = f"/nsls2/data/tst/proposals/2022-2/prefect-test/" +PATH = "/nsls2/data/tst/proposals/2022-2/prefect-test/" + @task def write_run_artifacts(RUN_TO_PLOT): - ''' + """ Example live-analysis function Parameters: run_to_plot (int): the local scan id from DataBroker - ''' + """ # Prefect logger logger = prefect.context.get("logger") - c = from_profile('nsls2') - rsoxsload = PyHyperScattering.load.SST1RSoXSDB(corr_mode='none', catalog=c["rsoxs"]) - itp = rsoxsload.loadRun(c["rsoxs"][RUN_TO_PLOT],dims=['energy']) + c = from_profile("nsls2") + rsoxsload = PyHyperScattering.load.SST1RSoXSDB(corr_mode="none", catalog=c["rsoxs"]) + itp = rsoxsload.loadRun(c["rsoxs"][RUN_TO_PLOT], dims=["energy"]) - if itp.rsoxs_config == 'waxs': - maskmethod = 'nika' - mask = '/nsls2/data/sst/legacy/RSoXS/analysis/SST1_WAXS_mask.hdf' - elif itp.rsoxs_config == 'saxs': - maskmethod = 'nika' - mask = '/nsls2/data/sst/legacy/RSoXS/analysis/SST1-SAXS_mask.hdf' + if itp.rsoxs_config == "waxs": + maskmethod = "nika" + mask = "/nsls2/data/sst/legacy/RSoXS/analysis/SST1_WAXS_mask.hdf" + elif itp.rsoxs_config == "saxs": + maskmethod = "nika" + mask = "/nsls2/data/sst/legacy/RSoXS/analysis/SST1-SAXS_mask.hdf" else: - maskmethod = 'none' - warnings.warn(f'Bad rsoxs_config, expected saxs or waxs but found {itp.rsoxs_config}. This will disable masking and certainly cause issues later.',stacklevel=2) - - - integ = PyHyperScattering.integrate.PFEnergySeriesIntegrator(maskmethod=maskmethod,maskpath=mask,geomethod='template_xr',template_xr=itp,integration_method='csr_ocl') + maskmethod = "none" + warnings.warn( + f"Bad rsoxs_config, expected saxs or waxs but found {itp.rsoxs_config}. This will disable masking and certainly cause issues later.", + stacklevel=2, + ) + + integ = PyHyperScattering.integrate.PFEnergySeriesIntegrator( + maskmethod=maskmethod, + maskpath=mask, + geomethod="template_xr", + template_xr=itp, + integration_method="csr_ocl", + ) name = itp.attrs["sample_name"] @@ -50,7 +56,7 @@ def write_run_artifacts(RUN_TO_PLOT): # print(integratedimages) try: - integratedimages.fileio.saveNexus(f'{PATH}reduced_{RUN_TO_PLOT}_{name}.nxs') + integratedimages.fileio.saveNexus(f"{PATH}reduced_{RUN_TO_PLOT}_{name}.nxs") except Exception: logger.warning("Couldn't save as NeXus file.") @@ -71,4 +77,3 @@ def log_status(trigger=all_finished): # log_task = log_status() # log_task.set_upstream(da) log_status(upstream_tasks=[da]) - diff --git a/test-flow.py b/test-flow.py index d6c4a34..da1823f 100644 --- a/test-flow.py +++ b/test-flow.py @@ -1,14 +1,15 @@ -import prefect import time as ttime from prefect import task, flow, get_run_logger + @task def print_task(): logger = get_run_logger() logger.info("Agent connection testing") # print("Agent connection testing") + @task def simple_task(): logger = get_run_logger() @@ -16,6 +17,7 @@ def simple_task(): with open("/nsls2/data/dssi/scratch/prefect-outputs/tst/test-data.txt", "w") as f: f.write(f"Flow test - {ttime.ctime()}") + @flow def test_flow(): logger = get_run_logger() @@ -23,5 +25,6 @@ def test_flow(): print_task() simple_task() + if __name__ == "__main__": test_flow() diff --git a/test_extra_client.py b/test_extra_client.py index 2b8084f..30d0b88 100644 --- a/test_extra_client.py +++ b/test_extra_client.py @@ -1,6 +1,7 @@ from prefect import task, get_run_logger from utils import get_tiled_client + @task def get_other_docs(uid): logger = get_run_logger() diff --git a/utils.py b/utils.py index 3529898..1cd0072 100644 --- a/utils.py +++ b/utils.py @@ -3,7 +3,8 @@ import os -LOCATION="tst" +LOCATION = "tst" + def get_tiled_client(): os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key").get() From c260efc6efa526ebcfcc993afe3e537f6fb00cd0 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 4 Feb 2026 14:22:05 -0500 Subject: [PATCH 42/42] LINT: fix more issues --- prefect2_test_flow.py | 6 +----- pyhyper.py | 1 + 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/prefect2_test_flow.py b/prefect2_test_flow.py index 2b5911f..5253a47 100644 --- a/prefect2_test_flow.py +++ b/prefect2_test_flow.py @@ -1,5 +1,3 @@ -import traceback - from prefect import flow, task, get_run_logger from prefect.blocks.notifications import SlackWebhook from prefect.context import FlowRunContext @@ -23,8 +21,7 @@ def wrapper(*args, **kwargs): f":white_check_mark: Flow-run successful. (*{flow_run_name}*)" ) return result - except Exception as e: - tb = traceback.format_exception_only(e) + except Exception: slack_webhook.notify(f":bangbang: Flow-run failed. (*{flow_run_name}*)") raise @@ -37,7 +34,6 @@ def hello_world(): logger = get_run_logger() logger.info("Starting flow") print_task() - test_dict = dict() # test_dict["key"] # Trying to create a key error here. diff --git a/pyhyper.py b/pyhyper.py index 1da7ab5..07318f8 100644 --- a/pyhyper.py +++ b/pyhyper.py @@ -1,6 +1,7 @@ import prefect from prefect import task, Flow, Parameter from prefect.triggers import all_finished +import warnings from tiled.client import from_profile