Merge pull request #29 from NSLS2/add-energy-fly-exporter

xanes fly exporter

Author: JunAishima

.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

.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: ["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

.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

README.md

@@ -1,3 +1,24 @@
 # SRX Workflows
 
 Repository of workflows for the SRX beamline.
+
+## Development
+
+### Pre-commit
+
+This project uses pre-commit to maintain code quality. To install and run
+pre-commit locally:
+
+```bash
+# Install pre-commit hooks
+pixi run pre-commit install
+
+# Run on all files
+pixi run pre-commit run --all-files
+
+# Run on staged files only
+pixi run pre-commit run
+
+# Run on files changed in your branch (compared to main)
+pixi run pre-commit run --from-ref main --to-ref HEAD
+```

data_validation.py

@@ -25,5 +25,4 @@ def read_all_streams(uid, beamline_acronym):
 
 @flow
 def data_validation(uid):
-    read_all_streams(uid, beamline_acronym='srx')
-
+    read_all_streams(uid, beamline_acronym="srx")

end_of_run_workflow.py

@@ -5,7 +5,6 @@
 from prefect.blocks.system import Secret
 from prefect.context import FlowRunContext
 
-from data_validation import data_validation
 from xanes_exporter import xanes_exporter
 from xrf_hdf5_exporter import xrf_hdf5_exporter
 from logscan import logscan
@@ -76,7 +75,6 @@ def log_completion():
 @flow
 @slack
 def end_of_run_workflow(stop_doc):
-
     uid = stop_doc["run_start"]
 
     # data_validation(uid, return_state=True)

logscan.py

@@ -67,7 +67,7 @@ def logscan_detailed(scanid):
             if "plan_name" in h.start:
                 out_str += f"\t{h.start['plan_name']}"
             else:
-                out_str += f"\tunknown scan"
+                out_str += "\tunknown scan"
         out_str += "\n"
 
         # Write to file