apsbits 1.0.6__tar.gz → 2.0.1__tar.gz

{apsbits-1.0.6 → apsbits-2.0.1}/.github/workflows/code.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - uses: actions/setup-python@v6
         with:
@@ -51,7 +51,7 @@ jobs:
       DISPLAY: ":99.0"
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: Install OS libraries to test Linux PyQt apps
         run: |

{apsbits-1.0.6 → apsbits-2.0.1}/.github/workflows/docs.yml

@@ -50,7 +50,7 @@ jobs:
       run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
 
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         fetch-depth: 0 # required for push to dest repo
 

{apsbits-1.0.6 → apsbits-2.0.1}/.github/workflows/pypi.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up Python
         uses: actions/setup-python@v6
         with:

{apsbits-1.0.6 → apsbits-2.0.1}/.gitignore

@@ -171,6 +171,7 @@ dev_*
 existing_plans_and_devices.yaml
 .vscode/
 .logs/
+.loglogin
 *.dat
 *.hdf
 

{apsbits-1.0.6 → apsbits-2.0.1}/HISTORY.rst

@@ -30,7 +30,7 @@ describe future plans.
 .. Coming release content can be gathered here.
     Some people object to publishing unreleased changes.
 
-    1.1.0
+    2.0.2
     #####
 
     release expected ?
@@ -46,6 +46,24 @@ describe future plans.
     * Bump iconfig version to 2.0.1 for the baseline addition.
     * Remove run_engine section from QS config.yml file and pin QS to 0.0.22+.
 
+2.0.1
+#####
+
+released 2026-01-13
+
+Enhancements
+------------
+
+* add support for TILED_PROFILE_NAME & TILED_PATH_NAME
+
+2.0.0 (PyPI) and 1.0.6 (repository)
+###################################
+
+released 2025-10-21
+
+Note that PyPI version (2.0.0) is different than repository (1.0.6).
+They share the same source code hash (``484b02f1537301``).
+
 1.0.4
 #####
 

{apsbits-1.0.6 → apsbits-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.6
+Version: 2.0.1
 Summary: Model of a Bluesky Data Acquisition Instrument in console, notebook, & queueserver.
 Author-email: Eric Codrea <ecodrea@anl.gov>, Pete Jemian <prjemian+instrument@gmail.com>, Rafael Vescovi <rvescovi@anl.gov>
 Maintainer-email: Eric Codrea <ecodrea@anl.gov>, Pete Jemian <prjemian+instrument@gmail.com>, Rafael Vescovi <rvescovi@anl.gov>
@@ -20,6 +20,7 @@ License-File: LICENSE
 Requires-Dist: apstools
 Requires-Dist: bluesky-queueserver>=0.0.22
 Requires-Dist: bluesky-queueserver-api
+Requires-Dist: bluesky-tiled-plugins
 Requires-Dist: bluesky-widgets
 Requires-Dist: bluesky
 Requires-Dist: caproto

{apsbits-1.0.6 → apsbits-2.0.1}/apsbits.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.6
+Version: 2.0.1
 Summary: Model of a Bluesky Data Acquisition Instrument in console, notebook, & queueserver.
 Author-email: Eric Codrea <ecodrea@anl.gov>, Pete Jemian <prjemian+instrument@gmail.com>, Rafael Vescovi <rvescovi@anl.gov>
 Maintainer-email: Eric Codrea <ecodrea@anl.gov>, Pete Jemian <prjemian+instrument@gmail.com>, Rafael Vescovi <rvescovi@anl.gov>
@@ -20,6 +20,7 @@ License-File: LICENSE
 Requires-Dist: apstools
 Requires-Dist: bluesky-queueserver>=0.0.22
 Requires-Dist: bluesky-queueserver-api
+Requires-Dist: bluesky-tiled-plugins
 Requires-Dist: bluesky-widgets
 Requires-Dist: bluesky
 Requires-Dist: caproto

{apsbits-1.0.6 → apsbits-2.0.1}/apsbits.egg-info/SOURCES.txt

@@ -109,7 +109,9 @@ src/apsbits/demo_instrument/utils/__init__.py
 src/apsbits/demo_scripts/qs_host.sh
 src/apsbits/tests/__init__.py
 src/apsbits/tests/conftest.py
+src/apsbits/tests/test_catalog_init.py
 src/apsbits/tests/test_config.py
+src/apsbits/tests/test_controls_setup.py
 src/apsbits/tests/test_delete_instrument.py
 src/apsbits/tests/test_device_factories.py
 src/apsbits/tests/test_general.py

{apsbits-1.0.6 → apsbits-2.0.1}/apsbits.egg-info/requires.txt

@@ -1,6 +1,7 @@
 apstools
 bluesky-queueserver>=0.0.22
 bluesky-queueserver-api
+bluesky-tiled-plugins
 bluesky-widgets
 bluesky
 caproto

{apsbits-1.0.6 → apsbits-2.0.1}/docs/source/guides/startup.rst

@@ -70,7 +70,7 @@ Bluesky Initialization
 
     bec, peaks = init_bec_peaks(iconfig)
     cat = init_catalog(iconfig)
-    RE, sd = init_RE(iconfig, bec_instance=bec, cat_instance=cat)
+    RE, sd = init_RE(iconfig, subscribers=[bec, cat])
 
 This block initializes:
 * Best Effort Callback (BEC) and peak finding

{apsbits-1.0.6 → apsbits-2.0.1}/pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     "apstools",
     "bluesky-queueserver >=0.0.22",
     "bluesky-queueserver-api",
+    "bluesky-tiled-plugins",
     "bluesky-widgets",
     "bluesky",
     "caproto",

{apsbits-1.0.6 → apsbits-2.0.1}/src/apsbits/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.0.6'
-__version_tuple__ = version_tuple = (1, 0, 6)
+__version__ = version = '2.0.1'
+__version_tuple__ = version_tuple = (2, 0, 1)
 
-__commit_id__ = commit_id = 'g484b02f15'
+__commit_id__ = commit_id = 'ge2e0b30f3'

apsbits-2.0.1/src/apsbits/core/catalog_init.py

@@ -0,0 +1,143 @@
+"""
+Databroker catalog
+==================
+
+.. autosummary::
+    ~init_catalog
+"""
+
+import logging
+import weakref
+from typing import Any
+from typing import Union
+
+import databroker
+from bluesky_tiled_plugins.clients.catalog_of_bluesky_runs import CatalogOfBlueskyRuns
+from databroker._drivers.mongo_normalized import BlueskyMongoCatalog
+from databroker._drivers.msgpack import BlueskyMsgpackCatalog
+from tiled.client import from_profile
+from tiled.client import from_uri
+from tiled.client.container import Container
+from tiled.server import SimpleTiledServer
+
+logger = logging.getLogger(__name__)
+logger.bsdev(__file__)
+
+# The httpx (via tiled) logger is set too noisy.  Make it quieter.
+logging.getLogger("httpx").setLevel(logging.WARNING)
+
+DATABROKER_CATALOG_TYPE = Union[BlueskyMongoCatalog, BlueskyMsgpackCatalog]
+TILED_CATALOG_TYPE = Union[CatalogOfBlueskyRuns, Container]
+ANY_CATALOG_TYPE = Union[DATABROKER_CATALOG_TYPE, TILED_CATALOG_TYPE]
+
+
+def init_catalog(iconfig: dict[str, Any]) -> ANY_CATALOG_TYPE:
+    """
+    Setup for a catalog to record bluesky run documents.
+
+    Return only one catalog object, depending on the keys in 'iconfig'.
+    The object returned is the first successful match, in this order:
+
+    * tiled catalog: requires TILED_PROFILE_NAME and optional TILED_PATH_NAME
+    * databroker catalog: requires DATABROKER_CATALOG
+    * temporary databroker catalog: fallback is the above are not successful
+    * (TODO) temporary tiled catalog: replaces temporary databroker fallback
+    """
+    handlers = [  # try these, in order
+        _tiled_profile_client,
+        _databroker_named_catalog,
+        # fallbacks
+        _databroker_temporary_catalog,
+        # TODO: promote once `del client` is not needed for exit
+        _tiled_temporary_catalog,
+    ]
+    for handler in handlers:
+        try:
+            cat = handler(iconfig)
+            if cat is None:
+                continue
+            return cat
+        except Exception as exinfo:
+            logger.error(
+                "%s() Failed to create catalog: %s",
+                handler.__name__,
+                str(exinfo),
+            )
+    raise RuntimeError("Could not create a catalog for Bluesky run documents.")
+
+
+def _databroker_named_catalog(
+    iconfig: dict[str, Any],
+) -> Union[
+    DATABROKER_CATALOG_TYPE,
+    None,
+]:
+    """Connect with a named databroker catalog."""
+    cat = None
+    catalog_name = iconfig.get("DATABROKER_CATALOG")
+    if catalog_name is not None:
+        cat = databroker.catalog[catalog_name].v2
+    logger.debug("%s: cat=%s", type(cat).__name__, str(cat))
+    if cat is not None:
+        logger.info("Databroker catalog initialized: %s", cat.name)
+    return cat
+
+
+def _databroker_temporary_catalog(iconfig: dict[str, Any]) -> BlueskyMsgpackCatalog:
+    """Connect with a temporary databroker catalog."""
+    cat = databroker.temp().v2
+    logger.debug("%s: cat=%s", type(cat).__name__, str(cat))
+    logger.info("Databroker temporary catalog initialized")
+    return cat
+
+
+def _tiled_profile_client(iconfig: dict[str, Any]) -> Union[None, TILED_CATALOG_TYPE]:
+    """Connect with a tiled server using a profile."""
+    cat = None
+    profile = iconfig.get("TILED_PROFILE_NAME")
+    path = iconfig.get("TILED_PATH_NAME")
+    if profile is not None:
+        client = from_profile(profile)
+        cat = client if path is None else client[path]
+
+    logger.debug("%s: cat=%s", type(cat).__name__, str(cat))
+    if cat is not None:
+        logger.info(
+            "Tiled server (catalog) connected, profile=%r, path=%r",
+            profile,
+            path,
+        )
+
+    return cat
+
+
+def _tiled_temporary_catalog(iconfig: dict[str, Any]) -> Container:
+    """Connect with a temporary tiled catalog.
+
+    WARNING: The SimpleTiledServer creates background threads that may prevent
+    clean process exit. For interactive use, explicitly delete the returned
+    client when done: `del client`
+    """
+    save_path = iconfig.get("TILED_SAVE_PATH")  # testing only?
+    server = SimpleTiledServer(save_path)
+
+    try:
+        client = from_uri(server.uri)
+        logger.info("Tiled server (temporary catalog) connected")
+
+        # Store server reference for cleanup when client is deleted
+        client._tiled_server = server
+
+        # Cleanup when client is garbage collected
+        def cleanup():
+            try:
+                server.close()
+            except Exception:
+                pass
+
+        weakref.finalize(client, cleanup)
+
+        return client
+    except Exception:
+        server.close()
+        raise

{apsbits-1.0.6 → apsbits-2.0.1}/src/apsbits/core/run_engine_init.py

@@ -19,8 +19,8 @@ import bluesky
 import databroker._drivers.mongo_normalized
 import databroker._drivers.msgpack
 import tiled
-from bluesky.callbacks.tiled_writer import TiledWriter
 from bluesky.utils import ProgressBarManager
+from bluesky_tiled_plugins import TiledWriter
 
 from apsbits.utils.controls_setup import connect_scan_id_pv
 from apsbits.utils.controls_setup import set_control_layer
@@ -36,7 +36,6 @@ logger.bsdev(__file__)
 def init_RE(
     iconfig: collections.abc.Mapping[str, Any],
     subscribers: Optional[list[Any]] = None,
-    oregistry: Optional[Any] = None,
     **kwargs: Any,
 ) -> tuple[bluesky.RunEngine, bluesky.SupplementalData]:
     """
@@ -66,9 +65,6 @@ def init_RE(
               documentation.
             Order in the list does not matter.
 
-        oregistry : Optional[Any], default=None
-            Registry instance for scan ID PV connection.
-
         **kwargs: Additional keyword arguments passed to the RunEngine constructor.
             For example, run_returns_result=True.
 
@@ -130,7 +126,7 @@ def init_RE(
             # Check if it's a tiled client
             if isinstance(instance, tiled.client.container.Container):
                 try:
-                    tiled_writer = TiledWriter(instance)
+                    tiled_writer = TiledWriter(instance, batch_size=1)
                     RE.subscribe(tiled_writer)
                 except Exception:
                     logger.exception(
@@ -172,7 +168,7 @@ def init_RE(
                     raise
 
     scan_id_pv = iconfig.get("RUN_ENGINE", {}).get("SCAN_ID_PV")
-    connect_scan_id_pv(RE, pv=scan_id_pv, oregistry=oregistry)
+    connect_scan_id_pv(RE, pv=scan_id_pv)
 
     if re_config.get("USE_PROGRESS_BAR", True):
         # Add a progress bar.

{apsbits-1.0.6 → apsbits-2.0.1}/src/apsbits/demo_instrument/configs/iconfig.yml

@@ -5,8 +5,12 @@ ICONFIG_VERSION: 2.0.1
 
 # Add additional configuration for use with your instrument.
 
-### The short name for the databroker catalog.
+### The databroker catalog name. (legacy use only)
 DATABROKER_CATALOG: temp
+### Tiled server profile and path name: (overrides DATABROKER_CATALOG key)
+#TILED_PROFILE_NAME: raw
+# Use TILED_PATH_NAME according to local tiled server configuration
+#TILED_PATH_NAME: /raw
 
 ### RunEngine configuration
 RUN_ENGINE:

apsbits-2.0.1/src/apsbits/tests/conftest.py

@@ -0,0 +1,124 @@
+"""
+Pytest fixtures for instrument tests.
+
+This module provides fixtures for initializing the RunEngine with devices,
+allowing tests to operate with device-dependent configurations without relying
+on the production startup logic.
+
+Fixtures:
+    runengine_with_devices: A RunEngine object in a session with devices configured.
+"""
+
+import time
+from pathlib import Path
+from typing import Any
+
+import pytest
+
+from apsbits.demo_instrument.startup import RE
+from apsbits.demo_instrument.startup import make_devices
+from apsbits.utils.config_loaders import load_config
+
+
+@pytest.fixture(scope="session")
+def runengine_with_devices() -> Any:
+    """
+    Initialize the RunEngine with devices for testing.
+
+    This fixture calls RE with the `make_devices()` plan stub to mimic
+    the behavior previously performed in the startup module.
+
+    Returns:
+        Any: An instance of the RunEngine with devices configured.
+    """
+    # Load the configuration before testing
+    instrument_path = Path(__file__).parent.parent / "demo_instrument"
+    iconfig_path = instrument_path / "configs" / "iconfig.yml"
+    load_config(iconfig_path)
+
+    # Initialize instrument and make devices
+    from apsbits.core.instrument_init import init_instrument
+
+    instrument, oregistry = init_instrument("guarneri")
+    make_devices(file="devices.yml", device_manager=instrument)
+
+    return RE
+
+
+@pytest.fixture(scope="session")
+def ioc():
+    """Run a softIoc in a subprocess.
+
+    Create a temporary EPICS database file that defines a long integer
+    record at "test:scan_id", start softIoc in a subprocess and yield
+    connection info for tests. Teardown stops the subprocess and
+    removes the temporary file.
+    """
+    import os
+    import subprocess
+    import tempfile
+
+    # Minimal EPICS DB defining a longout record for 'test:scan_id'.
+    db_text = "\n".join(
+        [
+            'record(longout, "test:scan_id") {',
+            # .
+            '   field(DESC, "scan id")',
+            "   field(VAL, -10)",
+            "}",
+        ]
+    )
+
+    # Write DB to a temporary file that persists until teardown.
+    tf = tempfile.NamedTemporaryFile(mode="w", suffix=".db", delete=False)
+    try:
+        tf.write(db_text)
+        tf.flush()
+        tf.close()
+
+        # Start softIoc. Capture output so if it fails immediately we can
+        # surface useful error messages.
+        proc = subprocess.Popen(
+            [
+                "softIoc",
+                "-S",
+                "-d",
+                tf.name,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        # Wait briefly for the process to initialize. If it exits early,
+        # collect stdout/stderr and raise.
+        timeout = 5.0
+        poll = 0.0
+        interval = 0.05
+        while poll < timeout and proc.poll() is None:
+            time.sleep(interval)
+            poll += interval
+
+        if proc.poll() is not None:
+            out, err = proc.communicate(timeout=1)
+            raise RuntimeError(
+                "softIoc terminated unexpectedly. stdout: %r stderr: %r"
+                % (out.decode(errors="ignore"), err.decode(errors="ignore"))
+            )
+
+        # Provide connection info for tests.
+        yield dict(prefix="test1:", host="127.0.0.1", pv="test:scan_id")
+
+    finally:
+        # Teardown: terminate the softIoc subprocess and remove the DB file.
+        try:
+            proc.terminate()
+            proc.wait(timeout=2)
+        except Exception:
+            try:
+                proc.kill()
+            except Exception:
+                pass
+        try:
+            os.remove(tf.name)
+        except Exception:
+            pass

apsbits-2.0.1/src/apsbits/tests/test_catalog_init.py

@@ -0,0 +1,121 @@
+"""Test the catalog_init module."""
+
+from contextlib import nullcontext as does_not_raise
+from unittest.mock import patch
+
+import pytest
+from tiled.profiles import ProfileNotFound
+
+# Run these tests without running startup.py.
+with patch("logging.Logger.bsdev"):
+    from apsbits.core.catalog_init import _databroker_named_catalog
+    from apsbits.core.catalog_init import _databroker_temporary_catalog
+    from apsbits.core.catalog_init import _tiled_profile_client
+    from apsbits.core.catalog_init import _tiled_temporary_catalog
+    from apsbits.core.catalog_init import init_catalog
+
+
+@pytest.mark.parametrize(
+    "iconfig, handler, cat_type, context",
+    [
+        pytest.param(
+            {},
+            _databroker_temporary_catalog,
+            "BlueskyMsgpackCatalog",
+            does_not_raise(),
+            id="temporary databroker catalog",
+        ),
+        pytest.param(
+            {},
+            init_catalog,
+            "BlueskyMsgpackCatalog",
+            does_not_raise(),
+            id="default to temporary databroker catalog",
+        ),
+        pytest.param(
+            dict(
+                DATABROKER_CATALOG="no_such_catalog",
+                TILED_PROFILE_NAME="no_such_profile",
+            ),
+            init_catalog,
+            "BlueskyMsgpackCatalog",
+            does_not_raise(),
+            id="invalid catalog & profile: fallback to temporary catalog",
+        ),
+        pytest.param(
+            {},
+            _databroker_named_catalog,
+            "NoneType",
+            does_not_raise(),
+            id="no databroker catalog name",
+        ),
+        pytest.param(
+            dict(DATABROKER_CATALOG="no_such_catalog"),
+            _databroker_named_catalog,
+            "ignored",
+            pytest.raises(KeyError, match="'no_such_catalog'"),
+            id="no such databroker catalog name",
+        ),
+        pytest.param(
+            {},
+            _tiled_profile_client,
+            "NoneType",
+            does_not_raise(),
+            id="no tiled profile name",
+        ),
+        pytest.param(
+            dict(TILED_PROFILE_NAME="no_such_profile"),
+            _tiled_profile_client,
+            "ignored",
+            pytest.raises(
+                ProfileNotFound,
+                match="Profile 'no_such_profile' not found.",
+            ),
+            id="no such tiled profile name",
+        ),
+        # TODO: _tiled_profile_client with:
+        #    valid TILED_PROFILE_NAME
+        #    valid TILED_PROFILE_NAME & valid TILED_PATH_NAME
+        #    valid TILED_PROFILE_NAME & invalid TILED_PATH_NAME
+        pytest.param(
+            {},
+            _tiled_temporary_catalog,
+            "Container",
+            does_not_raise(),
+            id="temporary tiled catalog",
+        ),
+        # TODO: _tiled_temporary_catalog & valid TILED_SAVE_PATH
+        # TODO: _tiled_temporary_catalog & invalid TILED_SAVE_PATH
+    ],
+)
+def test_handlers(iconfig, handler, cat_type, context):
+    """Test the handlers that create 'cat' objects."""
+    with context:
+        cat = handler(iconfig)
+        assert type(cat).__name__ == cat_type
+
+
+def test_use_temporary_tiled_catalog():
+    """Typical use of the tiled temporary catalog."""
+    import bluesky
+    from bluesky_tiled_plugins import TiledWriter
+    from ophyd.sim import noisy_det
+
+    cat = _tiled_temporary_catalog({})
+    tw = TiledWriter(cat, batch_size=1)
+    RE = bluesky.RunEngine()
+    RE.subscribe(tw)
+
+    delay = 0.1
+    npts = 15
+    nruns = len(cat)
+    (uid,) = RE(bluesky.plans.count([noisy_det], num=npts, delay=delay))
+    assert isinstance(uid, str)
+    assert len(cat) == 1 + nruns
+    run = cat[uid]
+    assert run.stop["num_events"]["primary"] == npts
+    assert (run.stop["time"] - run.start["time"]) >= delay * npts
+
+    data = run.primary.read()
+    assert "noisy_det" in data
+    assert len(data["noisy_det"]) == npts