apsbits 1.0.2__tar.gz → 1.0.3__tar.gz

{apsbits-1.0.2 → apsbits-1.0.3}/.github/workflows/code.yml

@@ -136,7 +136,7 @@ jobs:
         shell: bash -l {0}
         run: |
           set -vxeuo pipefail
-          ipython -c "from apsbits.demo_instrument.startup import *; RE(make_devices())"
+          ipython -c "from apsbits.demo_instrument.startup import *"
 
   # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
   coveralls:

{apsbits-1.0.2/apsbits.egg-info → apsbits-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.2
+Version: 1.0.3
 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>

{apsbits-1.0.2 → apsbits-1.0.3/apsbits.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.2
+Version: 1.0.3
 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>

{apsbits-1.0.2 → apsbits-1.0.3}/apsbits.egg-info/SOURCES.txt

@@ -80,9 +80,11 @@ src/apsbits/api/__init__.py
 src/apsbits/api/create_new_instrument.py
 src/apsbits/api/delete_instrument.py
 src/apsbits/api/run_instrument.py
+src/apsbits/configs/logging.yml
 src/apsbits/core/__init__.py
 src/apsbits/core/best_effort_init.py
 src/apsbits/core/catalog_init.py
+src/apsbits/core/instrument_init.py
 src/apsbits/core/run_engine_init.py
 src/apsbits/demo_instrument/README.md
 src/apsbits/demo_instrument/__init__.py
@@ -94,7 +96,6 @@ src/apsbits/demo_instrument/configs/__init__.py
 src/apsbits/demo_instrument/configs/devices.yml
 src/apsbits/demo_instrument/configs/devices_aps_only.yml
 src/apsbits/demo_instrument/configs/iconfig.yml
-src/apsbits/demo_instrument/configs/logging.yml
 src/apsbits/demo_instrument/devices/__init__.py
 src/apsbits/demo_instrument/plans/__init__.py
 src/apsbits/demo_instrument/plans/dm_plans.py
@@ -110,6 +111,7 @@ src/apsbits/tests/test_config.py
 src/apsbits/tests/test_delete_instrument.py
 src/apsbits/tests/test_device_factories.py
 src/apsbits/tests/test_general.py
+src/apsbits/tests/test_make_devices.py
 src/apsbits/tests/test_run_instrument.py
 src/apsbits/tests/test_stored_dict.py
 src/apsbits/utils/__init__.py
@@ -118,7 +120,6 @@ src/apsbits/utils/config_loaders.py
 src/apsbits/utils/controls_setup.py
 src/apsbits/utils/helper_functions.py
 src/apsbits/utils/logging_setup.py
-src/apsbits/utils/make_devices.py
 src/apsbits/utils/metadata.py
 src/apsbits/utils/sim_creator.py
 src/apsbits/utils/stored_dict.py

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.2'
-__version_tuple__ = version_tuple = (1, 0, 2)
+__version__ = version = '1.0.3'
+__version_tuple__ = version_tuple = (1, 0, 3)

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/api/run_instrument.py

@@ -16,7 +16,7 @@ from typing import Dict
 from typing import Optional
 from typing import Tuple
 
-from apsbits.utils.controls_setup import oregistry as Registry
+from apsbits.core.instrument_init import oregistry as Registry
 
 
 def run_instrument_startup(package_name: str) -> Tuple[bool, Optional[Dict[str, Any]]]:

{apsbits-1.0.2/src/apsbits/demo_instrument → apsbits-1.0.3/src/apsbits}/configs/logging.yml

@@ -37,5 +37,4 @@ modules:
   bluesky.RE: warning
   caproto: warning
   databroker: warning
-  instrument: bsdev
   ophyd: warning

apsbits-1.0.2/src/apsbits/utils/make_devices.py → apsbits-1.0.3/src/apsbits/core/instrument_init.py

@@ -21,10 +21,8 @@ from apstools.plans import run_blocking_function
 from apstools.utils import dynamic_import
 from bluesky import plan_stubs as bps
 
-from apsbits.utils.aps_functions import host_on_aps_subnet
 from apsbits.utils.config_loaders import get_config
 from apsbits.utils.config_loaders import load_config_yaml
-from apsbits.utils.controls_setup import oregistry  # noqa: F401
 
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)
@@ -32,27 +30,21 @@ logger.bsdev(__file__)
 MAIN_NAMESPACE = "__main__"
 
 
-def _get_make_devices_log_level() -> int:
-    """(internal) User choice for log level used in 'make_devices()'."""
-    level = get_config().get("MAKE_DEVICES", {}).get("LOG_LEVEL", "info")
-    if isinstance(level, str):
-        # Allow log level as str or int in iconfig.yml.
-        level = logging._nameToLevel[level.upper()]
-    return level
-
-
 def make_devices(
-    *, pause: float = 1, clear: bool = True, file: str | pathlib.Path | None = None
+    *,
+    pause: float = 1,
+    clear: bool = True,
+    file: str,
+    path: str | pathlib.Path | None = None,
 ):
     """
     (plan stub) Create the ophyd-style controls for this instrument.
 
-    Feel free to modify this plan to suit the needs of your instrument.
-
     EXAMPLE::
 
-        RE(make_devices())  # Use default iconfig.yml
-        RE(make_devices(file="custom_devices.yml"))  # Use custom devices file
+        RE(make_devices(file="custom_devices.yml"))  #Use custom devices file
+        RE(make_devices(path="custom_device_path",
+                        file="custom_devices.yml")) #Use custom path to find device file
 
     PARAMETERS
 
@@ -65,78 +57,54 @@ def make_devices(
         If provided, this file will be used instead of the default iconfig.yml.
         If None (default), uses the standard iconfig.yml configuration.
 
+    path: str | pathlib.Path | None
     """
+
     logger.debug("(Re)Loading local control objects.")
 
     if clear:
-        log_level = _get_make_devices_log_level()
-
         main_namespace = sys.modules[MAIN_NAMESPACE]
+
+        # Clear the oregistry and remove any devices registered previously.
         for dev_name in oregistry.device_names:
             # Remove from __main__ namespace any devices registered previously.
             if hasattr(main_namespace, dev_name):
-                logger.log(log_level, "Removing %r from %r", dev_name, MAIN_NAMESPACE)
+                logger.info("Removing %r from %r", dev_name, MAIN_NAMESPACE)
+
                 delattr(main_namespace, dev_name)
 
         oregistry.clear()
 
-    if file is not None:
-        # Use the provided file directly
-        device_path = pathlib.Path(file)
-        if not device_path.exists():
-            logger.error("Device file not found: %s", device_path)
-            return
-        logger.info("Loading device file: %s", device_path)
-        try:
-            yield from run_blocking_function(_loader, device_path, main=True)
-        except Exception as e:
-            logger.error("Error loading device file %s: %s", device_path, str(e))
-            return
+    if path is not None and file is None:
+        raise ValueError(
+            "When a custom path is provided, a specific device file must"
+            " also be provided"
+        )
+
+    if path is not None:
+        configs_path = pathlib.Path(path)
+        print(f"\n\nConfigs path: {configs_path}\n\n")
+
     else:
-        # Use standard iconfig.yml configuration
         iconfig = get_config()
-
         instrument_path = pathlib.Path(iconfig.get("INSTRUMENT_PATH")).parent
         configs_path = instrument_path / "configs"
 
-        # Get device files and ensure it's a list
-        device_files = iconfig.get("DEVICES_FILES", [])
-        if isinstance(device_files, str):
-            device_files = [device_files]
-        logger.debug("Loading device files: %r", device_files)
-
-        # Load each device file
-        for device_file in device_files:
-            device_path = configs_path / device_file
-            if not device_path.exists():
-                logger.error("Device file not found: %s", device_path)
-                continue
-            logger.info("Loading device file: %s", device_path)
-            try:
-                yield from run_blocking_function(_loader, device_path, main=True)
-            except Exception as e:
-                logger.error("Error loading device file %s: %s", device_path, str(e))
-                continue
-
-        # Handle APS-specific device files if on APS subnet
-        aps_control_devices_files = iconfig.get("APS_DEVICES_FILES", [])
-        if isinstance(aps_control_devices_files, str):
-            aps_control_devices_files = [aps_control_devices_files]
-
-        if aps_control_devices_files and host_on_aps_subnet():
-            for device_file in aps_control_devices_files:
-                device_path = configs_path / device_file
-                if not device_path.exists():
-                    logger.error("APS device file not found: %s", device_path)
-                    continue
-                logger.info("Loading APS device file: %s", device_path)
-                try:
-                    yield from run_blocking_function(_loader, device_path, main=True)
-                except Exception as e:
-                    logger.error(
-                        "Error loading APS device file %s: %s", device_path, str(e)
-                    )
-                    continue
+    device_file = file
+
+    logger.debug("Loading device files: %r", device_file)
+
+    # Load each device file
+    device_path = configs_path / device_file
+    if not device_path.exists():
+        logger.error("Device file not found: %s", device_path)
+
+    else:
+        logger.info("Loading device file: %s", device_path)
+        try:
+            yield from run_blocking_function(namespace_loader, device_path, main=True)
+        except Exception as e:
+            logger.error("Error loading device file %s: %s", device_path, str(e))
 
     if pause > 0:
         logger.debug(
@@ -145,12 +113,10 @@ def make_devices(
         )
         yield from bps.sleep(pause)
 
-    # Configure any of the controls here, or in plan stubs
-
 
-def _loader(yaml_device_file, main=True):
+def namespace_loader(yaml_device_file, main=True):
     """
-    Load our ophyd-style controls as described in a YAML file.
+    Load our ophyd-style controls as described in a YAML file into the main namespace.
 
     PARAMETERS
 
@@ -162,15 +128,15 @@ def _loader(yaml_device_file, main=True):
     """
     logger.debug("Devices file %r.", str(yaml_device_file))
     t0 = time.time()
-    _instr.load(yaml_device_file)
-    logger.info("Devices loaded in %.3f s.", time.time() - t0)
 
-    if main:
-        log_level = _get_make_devices_log_level()
+    instrument.load(yaml_device_file)
 
+    logger.info("Devices loaded in %.3f s.", time.time() - t0)
+    if main:
         main_namespace = sys.modules[MAIN_NAMESPACE]
         for label in oregistry.device_names:
-            logger.log(log_level, "Adding ophyd device %r to main namespace", label)
+            logger.info("Adding ophyd device %r to main namespace", label)
+
             setattr(main_namespace, label, oregistry[label])
 
 
@@ -208,4 +174,6 @@ class Instrument(guarneri.Instrument):
         return devices
 
 
-_instr = Instrument({}, registry=oregistry)  # singleton
+instrument = Instrument({})  # singleton
+oregistry = instrument.devices
+"""Registry of all ophyd-style Devices and Signals."""

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/core/run_engine_init.py

@@ -34,6 +34,7 @@ def init_RE(
     iconfig: Dict[str, Any],
     bec_instance: Optional[Any] = None,
     cat_instance: Optional[Any] = None,
+    **kwargs: Any,
 ) -> Tuple[bluesky.RunEngine, bluesky.SupplementalData]:
     """
     Initialize and configure a Bluesky RunEngine instance.
@@ -55,6 +56,8 @@ def init_RE(
             to the RunEngine. Defaults to None.
         cat_instance (Optional[Any]): Instance of a databroker catalog for subscribing
             to the RunEngine. Defaults to None.
+        **kwargs: Additional keyword arguments passed to the RunEngine constructor.
+            For example, run_returns_result=True.
 
     Returns:
         Tuple[bluesky.RunEngine, bluesky.SupplementalData]: A tuple containing the
@@ -75,7 +78,7 @@ def init_RE(
     set_control_layer(control_layer=control_layer)
     set_timeouts(timeouts=iconfig.get("OPHYD", {}).get("TIMEOUTS", {}))
 
-    RE = bluesky.RunEngine()
+    RE = bluesky.RunEngine(**kwargs)
     """The Bluesky RunEngine object."""
 
     sd = bluesky.SupplementalData()

apsbits-1.0.3/src/apsbits/demo_instrument/__init__.py

@@ -0,0 +1,9 @@
+"""
+Demo instrument package.
+
+This package provides a demo instrument implementation for testing and development.
+"""
+
+from apsbits.utils.logging_setup import configure_logging
+
+configure_logging()

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/demo_instrument/configs/iconfig.yml

@@ -29,9 +29,6 @@ RUN_ENGINE:
     ### Default: False
     USE_PROGRESS_BAR: false
 
-# Command-line tools, such as %wa, %ct, ...
-USE_BLUESKY_MAGICS: true
-
 ### Best Effort Callback Configurations
 ### Defaults: all true
 ### except no plots in queueserver
@@ -56,16 +53,6 @@ SPEC_DATA_FILES:
 ### Use bash shell, deactivate all conda environments, source this file:
 DM_SETUP_FILE: "/home/dm/etc/dm.setup.sh"
 
-### Local OPHYD Device Control Yaml
-DEVICES_FILES:
-- devices.yml
-APS_DEVICES_FILES:
-- devices_aps_only.yml
-
-# Log when devices are added to console (__main__ namespace)
-MAKE_DEVICES:
-    LOG_LEVEL: info
-
 # ----------------------------------
 
 OPHYD:
@@ -80,6 +67,4 @@ OPHYD:
         PV_WRITE: *TIMEOUT
         PV_CONNECTION: *TIMEOUT
 
-# Control detail of exception traces in IPython (console and notebook).
-# Options are: 'Plain', 'Context', 'Verbose', 'Minimal', 'Docs'
 XMODE_DEBUG_LEVEL: Plain

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/demo_instrument/plans/sim_plans.py

@@ -15,7 +15,7 @@ import logging
 from bluesky import plan_stubs as bps
 from bluesky import plans as bp
 
-from apsbits.utils.controls_setup import oregistry
+from apsbits.core.instrument_init import oregistry
 
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/demo_instrument/startup.py

@@ -10,32 +10,45 @@ Includes:
 """
 
 import logging
+from pathlib import Path
 
 from apsbits.core.best_effort_init import init_bec_peaks
 from apsbits.core.catalog_init import init_catalog
+from apsbits.core.instrument_init import make_devices
+from apsbits.core.instrument_init import oregistry
 from apsbits.core.run_engine_init import init_RE
 from apsbits.utils.aps_functions import aps_dm_setup
+from apsbits.utils.aps_functions import host_on_aps_subnet
 from apsbits.utils.config_loaders import get_config
-from apsbits.utils.controls_setup import oregistry
+from apsbits.utils.config_loaders import load_config
 from apsbits.utils.helper_functions import register_bluesky_magics
 from apsbits.utils.helper_functions import running_in_queueserver
-from apsbits.utils.make_devices import make_devices
 
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)
 
-oregistry.clear()  # Discard oregistry items loaded above.
+# Get the path to the instrument package
+instrument_path = Path(__file__).parent
+
+# Load configuration to be used by the instrument.
+iconfig_path = instrument_path / "configs" / "iconfig.yml"
+load_config(iconfig_path)
 
 # Get the configuration
 iconfig = get_config()
 
+logger.info("Starting Instrument with iconfig: %s", iconfig_path)
+
+# Discard oregistry items loaded above.
+oregistry.clear()
+
 # Configure the session with callbacks, devices, and plans.
 aps_dm_setup(iconfig.get("DM_SETUP_FILE"))
 
-if iconfig.get("USE_BLUESKY_MAGICS", False):
-    register_bluesky_magics()
+# Command-line tools, such as %wa, %ct, ...
+register_bluesky_magics()
 
-# Initialize core components
+# Initialize core bluesky components
 bec, peaks = init_bec_peaks(iconfig)
 cat = init_catalog(iconfig)
 RE, sd = init_RE(iconfig, bec_instance=bec, cat_instance=cat)
@@ -54,9 +67,6 @@ if iconfig.get("SPEC_DATA_FILES", {}).get("ENABLE", False):
 
     init_specwriter_with_RE(RE)
 
-# Import all plans
-from .plans import *  # noqa
-
 # These imports must come after the above setup.
 if running_in_queueserver():
     ### To make all the standard plans available in QS, import by '*', otherwise import
@@ -72,5 +82,7 @@ else:
     from bluesky import plan_stubs as bps  # noqa: F401
     from bluesky import plans as bp  # noqa: F401
 
+RE(make_devices(clear=False, file="devices.yml"))  # Create the devices.
 
-RE(make_devices(clear=False))
+if host_on_aps_subnet():
+    RE(make_devices(clear=False, file="device_aps_only.yml"))

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/tests/conftest.py

@@ -35,5 +35,5 @@ def runengine_with_devices() -> Any:
     iconfig_path = instrument_path / "configs" / "iconfig.yml"
     load_config(iconfig_path)
 
-    RE(make_devices())
+    RE(make_devices(file="devices.yml"))
     return RE

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/tests/test_delete_instrument.py

@@ -351,7 +351,7 @@ def test_copy_instrument(tmp_path: Path, mock_demo_dirs: tuple[Path, Path]) -> N
     content = startup_file.read_text()
     assert "Start Bluesky Data Acquisition sessions of all kinds." in content
     assert "from apsbits.core.best_effort_init import init_bec_peaks" in content
-    assert "RE(make_devices(clear=False))" in content
+    assert 'RE(make_devices(clear=False, file="devices.yml"))' in content
 
 
 def test_create_qserver(tmp_path: Path, mock_demo_dirs: tuple[Path, Path]) -> None:

apsbits-1.0.3/src/apsbits/tests/test_make_devices.py

@@ -0,0 +1,28 @@
+"""
+Test to check if the make_devices function works as expected.
+"""
+
+import logging
+
+from apsbits.demo_instrument.startup import RE
+from apsbits.demo_instrument.startup import make_devices
+
+
+def test_make_devices_file_name(caplog):
+    """
+    Test to check if the make_devices function works as expected.
+    """
+
+    # Set the log level to capture INFO messages
+    caplog.set_level(logging.INFO)
+
+    # Run your function
+    RE(make_devices(file="devices.yml"))
+
+    # Expected device names
+    expected_devices = ["sim_motor", "shutter", "sim_det"]
+
+    # Check if all expected device messages are in the log output
+    for device in expected_devices:
+        expected_message = f"Adding ophyd device '{device}' to main namespace"
+        assert any(expected_message in record.message for record in caplog.records)

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/utils/controls_setup.py

@@ -15,7 +15,8 @@ from typing import Optional
 
 import ophyd
 from ophyd.signal import EpicsSignalBase
-from ophydregistry import Registry
+
+from apsbits.core.instrument_init import oregistry
 
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)
@@ -101,8 +102,3 @@ def set_timeouts(timeouts):
             write_timeout=timeouts.get("PV_WRITE", DEFAULT_TIMEOUT),
             connection_timeout=timeouts.get("PV_CONNECTION", DEFAULT_TIMEOUT),
         )
-
-
-oregistry = Registry(auto_register=True)
-"""Registry of all ophyd-style Devices and Signals."""
-oregistry.warn_duplicates = False

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/utils/logging_setup.py

@@ -26,9 +26,7 @@ MB = 1024 * kB
 
 BRIEF_DATE = "%a-%H:%M:%S"
 BRIEF_FORMAT = "%(levelname)-.1s %(asctime)s.%(msecs)03d: %(message)s"
-DEFAULT_CONFIG_FILE = (
-    pathlib.Path(__file__).parent.parent / "demo_instrument" / "configs" / "logging.yml"
-)
+DEFAULT_CONFIG_FILE = pathlib.Path(__file__).parent.parent / "configs" / "logging.yml"
 
 
 # Add your custom logging level at the top-level, before configure_logging()
@@ -86,7 +84,7 @@ def addLoggingLevel(levelName, levelNum, methodName=None):
 addLoggingLevel("BSDEV", logging.INFO - 5)
 
 
-def configure_logging():
+def configure_logging(extra_logging_configs_path=None):
     """Configure logging as described in file."""
     from apsbits.utils.config_loaders import load_config_yaml
 
@@ -94,13 +92,10 @@ def configure_logging():
     logger = logging.getLogger(__name__).root
     logger.debug("logger=%r", logger)
 
-    config_file = os.environ.get("BLUESKY_INSTRUMENT_CONFIG_FILE")
-    if config_file is None:
-        config_file = DEFAULT_CONFIG_FILE
-    else:
-        config_file = pathlib.Path(config_file)
+    config_file = DEFAULT_CONFIG_FILE
 
     logging_configuration = load_config_yaml(config_file)
+
     for part, cfg in logging_configuration.items():
         logging.debug("%r - %s", part, cfg)
 
@@ -116,6 +111,24 @@ def configure_logging():
         elif part == "modules":
             _setup_module_logging(cfg)
 
+    if extra_logging_configs_path is not None:
+        logging_configuration = load_config_yaml(extra_logging_configs_path)
+
+        for part, cfg in logging_configuration.items():
+            logging.debug("%r - %s", part, cfg)
+
+            if part == "console_logs":
+                _setup_console_logger(logger, cfg)
+
+            elif part == "file_logs":
+                _setup_file_logger(logger, cfg)
+
+            elif part == "ipython_logs":
+                _setup_ipython_logger(logger, cfg)
+
+            elif part == "modules":
+                _setup_module_logging(cfg)
+
 
 def _setup_console_logger(logger, cfg):
     """

{apsbits-1.0.2 → apsbits-1.0.3}/src/apsbits/utils/sim_creator.py

@@ -21,8 +21,6 @@ import logging
 
 from apstools.utils import dynamic_import
 
-from apsbits.utils.controls_setup import oregistry
-
 logger = logging.getLogger(__name__)
 logger.bsdev(__file__)
 
@@ -53,7 +51,6 @@ def predefined_device(*, name="", creator=""):
     if name != "":
         device.name = name
     logger.debug(device)
-    oregistry.register(device)
     yield device
 
 

apsbits-1.0.2/src/apsbits/demo_instrument/__init__.py

@@ -1,22 +0,0 @@
-"""
-Demo instrument package.
-
-This package provides a demo instrument implementation for testing and development.
-"""
-
-import logging
-from pathlib import Path
-
-from apsbits.utils.config_loaders import load_config
-
-logger = logging.getLogger(__name__)
-logger.bsdev(__file__)
-
-# Get the path to the instrument package
-instrument_path = Path(__file__).parent
-
-# Load configuration
-iconfig_path = instrument_path / "configs" / "iconfig.yml"
-load_config(iconfig_path)
-
-logger.info("Starting Instrument with iconfig: %s", iconfig_path)