ENH: configurable dataset map for ZebraSaveIOC

.github/workflows/ci.yml

@@ -4,6 +4,8 @@ on:
   workflow_dispatch:
   pull_request:
   push:
+    branches:
+      - main
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -32,18 +34,13 @@ jobs:
           pipx run nox -s pylint
 
   checks:
-    # pull requests are a duplicate of a branch push if within the same repo.
-    if:
-      github.event_name != 'pull_request' ||
-      github.event.pull_request.head.repo.full_name != github.repository
-
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
     needs: [pre-commit]
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         # runs-on: [ubuntu-latest, macos-latest, windows-latest]
         runs-on: [ubuntu-latest]
 

.pre-commit-config.yaml

@@ -4,13 +4,13 @@ ci:
 
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
+    rev: "1.20.0"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v6.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -40,7 +40,7 @@ repos:
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.5"
+    rev: "v0.15.16"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -56,12 +56,13 @@ repos:
   #         - pytest
 
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.3.0"
+    rev: "v2.4.2"
     hooks:
       - id: codespell
+        args: ["--ignore-words-list=astroid"]
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.10.0.1"
+    rev: "v0.11.0.1"
     hooks:
       - id: shellcheck
 
@@ -74,13 +75,13 @@ repos:
         exclude: .pre-commit-config.yaml
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.18"
+    rev: "v0.25"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.28.4"
+    rev: "0.37.2"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling", "hatch-vcs", "setuptools>=61,<67"]
+requires = ["hatchling", "hatch-vcs", "setuptools>=61"]
 build-backend = "hatchling.build"
 
 
@@ -11,7 +11,7 @@ authors = [
 description = "Caproto IOCs for the NSLS-II SRX beamline"
 readme = "README.md"
 license.file = "LICENSE"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 classifiers = [
   "Development Status :: 1 - Planning",
   "Intended Audience :: Science/Research",
@@ -21,8 +21,6 @@ classifiers = [
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -44,6 +42,7 @@ dependencies = [
 test = [
   "pytest >=6",
   "pytest-cov >=3",
+  "pytest-timeout >=2",
 ]
 dev = [
   "ipython",
@@ -79,10 +78,11 @@ scripts.test = "pytest {args}"
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config", "--timeout=20"]
 xfail_strict = true
 filterwarnings = [
   "error",
+  "ignore:SelectableGroups dict interface is deprecated:DeprecationWarning",
 ]
 log_cli_level = "INFO"
 testpaths = [
@@ -104,7 +104,7 @@ report.exclude_also = [
 
 [tool.mypy]
 files = ["src", "tests"]
-python_version = "3.8"
+python_version = "3.10"
 warn_unused_configs = true
 strict = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
@@ -171,3 +171,32 @@ messages_control.disable = [
   "missing-module-docstring",
   "wrong-import-position",
 ]
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.feature.dev.pypi-dependencies]
+srx-caproto-iocs = { path = ".", editable = true }
+
+[tool.pixi.feature.test.pypi-dependencies]
+srx-caproto-iocs = { path = ".", editable = true, extras = ["test"] }
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+dev = { features = ["dev"], solve-group = "default" }
+docs = { features = ["docs"], solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+
+[tool.pixi.tasks]
+test = { cmd = "pytest", description = "Run the test suite" }
+
+[tool.pixi.dependencies]
+pip = ">=26.1.1,<27"
+
+[tool.pixi.feature.dev.dependencies]
+pre-commit = ">=4.6.0,<5"
+pytest = ">=9.0.3,<10"
+python = "3.12.*"
+nexpy = ">=2.0.1,<3"
+epics-base = ">=7.0.9.0,<8"

src/srx_caproto_iocs/base.py

@@ -214,7 +214,9 @@ def saver(request_queue, response_queue):
             data = received["data"]
             frame_number = received["frame_number"]
             try:
-                save_hdf5_nd(fname=filename, data=data, mode="x", group_path="enc1")
+                save_hdf5_nd(
+                    fname=filename, data=data, mode="a", group_path="data/data"
+                )
                 print(
                     f"{now()}: saved {frame_number=} {data.shape} data into:\n  {filename}"
                 )
@@ -272,13 +274,11 @@ def set(self, command):
         def cb(value, old_value, **kwargs):
             # pylint: disable=unused-argument
             # print(f"{now()}: {old_value} -> {value}")
-            if value == expected_new_value and old_value == expected_old_value:
-                return True
-            return False
+            return value == expected_new_value and old_value == expected_old_value
 
         st = SubscriptionStatus(obj, callback=cb, run=False)
         # print(f"{now()}: {cmd = }")
-        obj.put(cmd)
+        obj.put(cmd, timeout=10)
         return st
 
 

src/srx_caproto_iocs/zebra/caproto_ioc.py

@@ -1,6 +1,7 @@
 # pylint: disable=duplicate-code
 from __future__ import annotations
 
+import json
 import textwrap
 from enum import Enum
 
@@ -163,22 +164,53 @@ class ZebraSaveIOC(CaprotoSaveIOC):
     #     super().__init__(*args, **kwargs)
     #     self._external_pvs = external_pvs
 
+    #: Default dataset mappings keyed by dev_type. Keys are PV attribute names;
+    #: values are the corresponding HDF5 dataset names written to file.
+    _DEFAULT_DATASET_MAPS: dict[str, dict[str, str]] = {
+        DevTypes.ZEBRA.value: {
+            "enc1": "enc1",
+            "enc2": "enc2",
+            "enc3": "enc3",
+            "zebra_time": "zebra_time",
+        },
+        DevTypes.SCALER.value: {
+            "i0": "i0",
+            "im": "im",
+            "it": "it",
+            "sis_time": "sis_time",
+        },
+    }
+
+    def __init__(
+        self,
+        *args,
+        dataset_map: dict[str, str] | None = None,
+        **kwargs,
+    ):
+        """Init method.
+
+        Parameters
+        ----------
+        dataset_map : dict, optional
+            Mapping of PV attribute names to HDF5 dataset names, e.g.
+            ``{"enc1": "x_pos", "enc2": "y_pos"}``.  When *None* (default)
+            the mapping is chosen automatically based on the ``dev_type`` PV.
+        """
+        self._dataset_map = dataset_map
+        super().__init__(*args, **kwargs)
+
     async def _get_current_dataset(self, *args, **kwargs):  # pylint: disable=unused-argument
-        # , frame, external_pv="enc1"):
-        # client_context = Context()
-        # (pvobject,) = await client_context.get_pvs(self._external_pvs[external_pv])
-        # print(f"{pvobject = }")
-        # # pvobject = pvobjects[0]
-        # ret = await pvobject.read()
-
-        if self.dev_type.value == DevTypes.ZEBRA.value:
-            pvnames = ["enc1", "enc2", "enc3", "zebra_time"]
+        if self._dataset_map is not None:
+            mapping = self._dataset_map
+        elif self.dev_type.value == DevTypes.ZEBRA.value:
+            mapping = self._DEFAULT_DATASET_MAPS[DevTypes.ZEBRA.value]
         else:
-            pvnames = ["i0", "im", "it", "sis_time"]
+            mapping = self._DEFAULT_DATASET_MAPS[DevTypes.SCALER.value]
 
-        dataset = {}
-        for pvname in pvnames:
-            dataset[pvname] = getattr(self, pvname).value
+        dataset = {
+            hdf5_name: getattr(self, pv_attr).value
+            for pv_attr, hdf5_name in mapping.items()
+        }
 
         print(f"{now()}:\n{dataset}")
 
@@ -193,7 +225,7 @@ def saver(request_queue, response_queue):
             data = received["data"]
             # 'frame_number' is not used for this exporter.
             try:
-                save_hdf5_zebra(fname=filename, data=data, mode="x")
+                save_hdf5_zebra(fname=filename, data=data, mode="a")
                 print(f"{now()}: saved data into:\n  {filename}")
 
                 success = True
@@ -213,22 +245,21 @@ def saver(request_queue, response_queue):
     parser, split_args = template_arg_parser(
         default_prefix="", desc=textwrap.dedent(ZebraSaveIOC.__doc__)
     )
+
+    parser.add_argument(
+        "--dataset-map",
+        help=(
+            "JSON mapping of PV attribute names to HDF5 dataset names, "
+            'e.g. \'{"enc1": "x_pos", "enc2": "y_pos"}\'. '
+            "When omitted, the mapping is chosen from the built-in SRX defaults "
+            "based on the dev_type PV (zebra or scaler)."
+        ),
+        type=json.loads,
+        default=None,
+    )
+
     ioc_options, run_options = check_args(parser, split_args)
+    dataset_map_arg = parser.parse_args().dataset_map
 
-    # external_pv_prefix = (
-    #     ioc_options["prefix"].replace("{{", "{").replace("}}", "}")
-    # )  # "XF:05IDD-ES:1{Dev:Zebra2}:"
-
-    # external_pvs = {
-    #     "pulse_step": external_pv_prefix + "PC_PULSE_STEP",
-    #     "data_in_progress": external_pv_prefix + "ARRAY_ACQ",
-    #     "enc1": external_pv_prefix + "PC_ENC1",
-    #     "enc2": external_pv_prefix + "PC_ENC2",
-    #     "enc3": external_pv_prefix + "PC_ENC3",
-    #     "enc4": external_pv_prefix + "PC_ENC4",
-    #     "time": external_pv_prefix + "PC_TIME",
-    # }
-
-    # ioc = ZebraSaveIOC(external_pvs=external_pvs, **ioc_options)
-    ioc = ZebraSaveIOC(**ioc_options)
+    ioc = ZebraSaveIOC(dataset_map=dataset_map_arg, **ioc_options)
     run(ioc.pvdb, **run_options)

src/srx_caproto_iocs/zebra/ophyd.py

@@ -1,7 +1,25 @@
 from __future__ import annotations
 
+from ophyd import Component as Cpt
+from ophyd import EpicsSignal, EpicsSignalRO
+
 from ..base import OphydDeviceWithCaprotoIOC
 
 
 class ZebraWithCaprotoIOC(OphydDeviceWithCaprotoIOC):
     """An ophyd Device which works with the Zebra caproto extension IOC."""
+
+    # Device-type selector (zebra / scaler)
+    dev_type = Cpt(EpicsSignal, "dev_type", string=True)
+
+    # Zebra position-capture channels
+    enc1 = Cpt(EpicsSignalRO, "enc1", auto_monitor=False)
+    enc2 = Cpt(EpicsSignalRO, "enc2", auto_monitor=False)
+    enc3 = Cpt(EpicsSignalRO, "enc3", auto_monitor=False)
+    zebra_time = Cpt(EpicsSignalRO, "zebra_time", auto_monitor=False)
+
+    # Scaler channels
+    i0 = Cpt(EpicsSignalRO, "i0", auto_monitor=False)
+    im = Cpt(EpicsSignalRO, "im", auto_monitor=False)
+    it = Cpt(EpicsSignalRO, "it", auto_monitor=False)
+    sis_time = Cpt(EpicsSignalRO, "sis_time", auto_monitor=False)