Update repository to use modern Python packaging and development tooling

.github/workflows/ci.yml

@@ -15,13 +15,31 @@
   FORCE_COLOR: 3
 
 jobs:
+  pre-commit:
+    name: Pre-commit
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Run pre-commit hooks
+        run: uv run --locked --only-group dev pre-commit run --all-files
+
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
         runs-on: [ubuntu-latest]
 
     steps:
@@ -34,25 +52,23 @@
           python-version: ${{ matrix.python-version }}
           allow-prereleases: true
 
+      - uses: astral-sh/setup-uv@v7
+
       - name: Test regular installation
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install .
-          python -c "import hxntools; print(f'✓ hxntools imported successfully (editable): {hxntools.__file__}')"
-          python -c "from importlib.metadata import version; print(f'✓ Version: {version(\"hxntools\")}')"
-          python -m pip list | grep hxntools
-          python -m pip uninstall -y hxntools
+          uv sync --locked --no-dev --no-editable --python "${{ matrix.python-version }}"
+          uv run --no-sync python -c "import hxntools; print(f'✓ hxntools imported successfully (regular): {hxntools.__file__}')"
+          uv run --no-sync python -c "from importlib.metadata import version; print(f'✓ Version: {version(\"hxntools\")}')"
 
       - name: Test editable installation
         run: |
-          python -m pip install -e .
-          python -c "import hxntools; print(f'✓ hxntools imported successfully (editable): {hxntools.__file__}')"
-          python -c "from importlib.metadata import version; print(f'✓ Version: {version(\"hxntools\")} (editable)')"
-          python -m pip list | grep hxntools
+          uv sync --locked --no-dev --python "${{ matrix.python-version }}"
+          uv run --no-sync python -c "import hxntools; print(f'✓ hxntools imported successfully (editable): {hxntools.__file__}')"
+          uv run --no-sync python -c "from importlib.metadata import version; print(f'✓ Version: {version(\"hxntools\")} (editable)')"
 
       - name: Test package modules import
         run: |
-          python -c "
+          uv run --no-sync python -c "
           import hxntools
           import pkgutil
           modules = [name for _, name, _ in pkgutil.iter_modules(hxntools.__path__, hxntools.__name__ + '.')]

.github/workflows/python-publish.yml

@@ -29,7 +29,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: hynek/build-and-inspect-python-package@v2
+      - uses: hynek/build-and-inspect-python-package@v3.0.1
 
   publish:
     needs: [dist]

.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+.venv/
 env/
 bin/
 build/
@@ -94,5 +95,5 @@ __enamlcache__/
 # PyBuilder
 target/
 
-# setuptools_scm
+# Generated version metadata
 src/hxntools/_version.py

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.8
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format

README.md

@@ -1,3 +1,20 @@
 hxntools
 ========
 Python library of tools used at NSLS-II's Hard X-ray Nanoprobe (HXN, 03id) beamline
+
+Development
+-----------
+
+Install the repository hooks:
+
+```console
+uv run --locked --only-group dev pre-commit install
+```
+
+Run every hook without making a commit:
+
+```console
+uv run --locked --only-group dev pre-commit run --all-files
+```
+
+Ruff formatting runs on every commit. The legacy `src/` tree is temporarily excluded from both Ruff checks and formatting; narrow or remove that exclusion as files are adopted.

pyproject.toml

@@ -1,13 +1,13 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm[toml]>=7"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
 [project]
 name = "hxntools"
 dynamic = ["version"]
 description = "NSLS-II Hard X-ray Nanoprobe data acquisition tools"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = "BSD-3-Clause"
 authors = [
     {name = "Brookhaven National Laboratory", email = "DAMA@bnl.gov"}
@@ -21,7 +21,6 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
@@ -47,12 +46,23 @@ Homepage = "https://github.com/NSLS-II-HXN/hxntools"
 Discussions = "https://github.com/NSLS-II-HXN/hxntools/discussions"
 Changelog = "https://github.com/NSLS-II-HXN/hxntools/releases"
 
-[tool.setuptools]
-include-package-data = true
+[dependency-groups]
+dev = [
+    "pre-commit>=4.3",
+]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/hxntools"]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/hxntools/_version.py"
 
-[tool.setuptools.packages.find]
-where = ["src"]
-include = ["hxntools*"]
+[tool.ruff]
+target-version = "py311"
+extend-exclude = ["src"]
 
-[tool.setuptools_scm]
-write_to = "src/hxntools/_version.py"
+[tool.ruff.lint]
+select = ["F"]

src/hxntools/CompositeBroker.py

@@ -1,17 +1,10 @@
 from databroker.v0 import Broker
 from databroker.headersource.mongo import MDS
 from databroker.assets.mongo import Registry
-from databroker.headersource.core import doc_or_uid_to_uid
+from databroker.headersource.core import BAD_KEYS_FMT, doc_or_uid_to_uid
 from databroker.assets.handlers import HandlerBase
-from jsonschema import validate as js_validate
-from collections import deque
 
 import numpy as np
-import pandas as pd
-import warnings
-import uuid
-import certifi
-import os
 import six
 import pymongo
 import h5py
@@ -317,7 +310,6 @@ def insert(self, name, doc):
             if f_benchmark:
                 f_benchmark.write("\n scan_id: {} \n".format(doc['scan_id']))
                 f_benchmark.flush()
-            datum_counts = {}
 
         ts =  str(datetime.now().timestamp())
 
@@ -335,7 +327,7 @@ def insert(self, name, doc):
 logger = logging.getLogger(__name__)
 
 FMT_ROI_KEY = 'entry/instrument/detector/NDAttributes/CHAN{}ROI{}'
-from databroker.assets.handlers import HandlerBase, ImageStack
+from databroker.assets.handlers import ImageStack
 
 
 class HDF5DatasetSliceHandler(HandlerBase):
@@ -378,7 +370,6 @@ def __call__(self, point_number):
         return self._data_objects[point_number]
 
     def open(self):
-        import h5py
         if self._file:
             return
 

src/hxntools/detectors/__init__.py

@@ -5,3 +5,15 @@
 from .trigger_mixins import (HxnModalBase, )
 from .mercury import (HxnMercuryDetector, )
 from .dexela import (HxnDexelaDetector, )
+
+__all__ = [
+    "TimepixDetector",
+    "HxnTimepixDetector",
+    "HxnZebra",
+    "Zebra",
+    "HxnMerlinDetector",
+    "BeamStatusDetector",
+    "HxnModalBase",
+    "HxnMercuryDetector",
+    "HxnDexelaDetector",
+]

src/hxntools/detectors/dexela.py

@@ -1,5 +1,4 @@
 from __future__ import print_function
-import itertools
 import logging
 
 from ophyd import (AreaDetector, CamBase, TIFFPlugin, Component as Cpt,
@@ -10,10 +9,9 @@
 from ophyd.areadetector.filestore_mixins import (FileStoreTIFF,
                                                  FileStorePluginBase)
 
-from .utils import (makedirs, make_filename_add_subdirectory)
+from .utils import (makedirs)
 from .trigger_mixins import (HxnModalTrigger, FileStoreBulkReadable)
 
-from pathlib import PurePath
 
 logger = logging.getLogger(__name__)
 

src/hxntools/detectors/hxn_xspress3.py

@@ -1,6 +1,4 @@
 from collections import OrderedDict, namedtuple
-import uuid
-import itertools
 import logging
 import time
 import numpy as np
@@ -10,8 +8,8 @@
 from ophyd.status import DeviceStatus
 from ophyd.device import (BlueskyInterface, Staged)
 
-from nslsii.detectors.xspress3 import (XspressTrigger, Xspress3Detector,
-                                       Xspress3FileStore, Xspress3ROI)
+from nslsii.detectors.xspress3 import (Xspress3Detector,
+                                       Xspress3FileStore)
 from .trigger_mixins import HxnModalBase
 
 import pandas as pd

src/hxntools/detectors/merlin.py

@@ -1,6 +1,5 @@
 from __future__ import print_function
 import logging
-from pathlib import PurePath
 from ophyd import (AreaDetector, CamBase, TIFFPlugin, Component as Cpt,
                    HDF5Plugin, Device, StatsPlugin, ProcessPlugin,
                    ROIPlugin, TransformPlugin, EpicsSignal)

src/hxntools/detectors/utils.py

@@ -1,6 +1,5 @@
 from __future__ import print_function
 import os
-from ophyd import Signal
 
 
 def makedirs(path, mode=0o777):

src/hxntools/detectors/zebra.py

@@ -328,7 +328,6 @@ class HxnZebra(Zebra):
     def mode_internal(self):
         super().mode_internal()
 
-        scan_type = self.mode_settings.scan_type.get()
         # no concept of internal triggering for now
         # raise ValueError('Unknown scan type for internal triggering: '
         #                  '{}'.format(scan_type))

src/hxntools/handlers/__init__.py

@@ -3,6 +3,8 @@
 # imports to expose out to world
 from .timepix import TimepixHDF5Handler
 
+__all__ = ["TimepixHDF5Handler"]
+
 
 def register(db):
     from .xspress3 import register

src/hxntools/handlers/bulkdata.py

@@ -1,6 +1,4 @@
 from .hxn_handler import HXNHandlerBase
-from databroker.assets.handlers import HandlerBase
-import h5py
 
 
 class BulkMerlin(HXNHandlerBase):

src/hxntools/handlers/rasmi2.py

@@ -1,6 +1,4 @@
 from .hxn_handler import HXNHandlerBase
-from databroker.assets.handlers import HandlerBase
-import h5py
 
 class SISHDF5Handler(HXNHandlerBase):
     HANDLER_NAME = "SIS_HDF51_FLY_STREAM_V1"

src/hxntools/scans.py

@@ -1,4 +1,3 @@
-import asyncio
 import functools
 import logging