apsbits 1.0.4__tar.gz → 2.0.0__tar.gz

{apsbits-1.0.4 → apsbits-2.0.0}/.github/workflows/code.yml

@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 
@@ -51,7 +51,7 @@ jobs:
       DISPLAY: ":99.0"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install OS libraries to test Linux PyQt apps
         run: |

{apsbits-1.0.4 → apsbits-2.0.0}/.github/workflows/docs.yml

@@ -50,11 +50,11 @@ jobs:
       run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
 
     - name: Checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         fetch-depth: 0 # required for push to dest repo
 
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
           python-version: "3.11"
 

{apsbits-1.0.4 → apsbits-2.0.0}/.github/workflows/pypi.yml

@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 

{apsbits-1.0.4 → apsbits-2.0.0}/.gitignore

@@ -176,3 +176,9 @@ existing_plans_and_devices.yaml
 
 # Local Run Engine metadata dictionary
 .re_md_dict.yml
+
+# Test/deleted artifacts
+.deleted/
+
+# Claude Code context files
+CLAUDE.md

{apsbits-1.0.4 → apsbits-2.0.0}/HISTORY.rst

@@ -30,11 +30,27 @@ describe future plans.
 .. Coming release content can be gathered here.
     Some people object to publishing unreleased changes.
 
-    1.0.4
+    1.1.0
     #####
 
     release expected ?
 
+    New Features
+    ---------------
+
+    * Hoist support to setup baseline stream using labels kwarg from USAXS.
+
+    Maintenance
+    ---------------
+
+    * 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+.
+
+1.0.4
+#####
+
+released 2025-05-14
+
 1.0.3
 #####
 
@@ -68,6 +84,31 @@ Maintenance
 * adding install docs given new workflow
 * Feature/API_functionalities and Makedevices
 
+    Breaking Changes
+    ----------------
+
+    * **Callback file renaming**: Demo callback files renamed to follow `_demo` naming convention:
+
+      * ``nexus_data_file_writer.py`` → ``demo_nexus_callback.py``
+      * ``spec_data_file_writer.py`` → ``demo_spec_callback.py``
+
+      Import paths updated in startup.py. Direct imports of these modules will need updating.
+
+    * **DM plans removed**: The ``dm_plans.py`` file has been removed to reduce apstools dependency.
+      DM configuration infrastructure remains in iconfig.yml and startup.py.
+
+    * **StoredDict implementation**: Now uses local implementation instead of ``apstools.utils.StoredDict``.
+      This reduces external dependencies while maintaining full compatibility.
+
+    Enhancements
+    ------------
+
+    * **Improved error handling**: Enhanced error messages with specific exception types and detailed context across core modules (device loading, configuration parsing, RunEngine initialization, databroker catalog setup).
+
+    * **Complete type annotations**: Added comprehensive type annotations to all public APIs for better IDE support and code maintainability.
+
+    * **Code quality improvements**: Added ``py.typed`` marker for mypy support and improved code formatting compliance.
+
 1.0.1
 #####
 

{apsbits-1.0.4/apsbits.egg-info → apsbits-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.4
+Version: 2.0.0
 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>
@@ -17,25 +17,27 @@ Classifier: Topic :: Utilities
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: apstools>=1.7.2
+Requires-Dist: apstools
+Requires-Dist: bluesky-queueserver>=0.0.22
 Requires-Dist: bluesky-queueserver-api
-Requires-Dist: bluesky-queueserver
 Requires-Dist: bluesky-widgets
 Requires-Dist: bluesky
 Requires-Dist: caproto
 Requires-Dist: databroker==1.2.5
-Requires-Dist: guarneri
+Requires-Dist: guarneri>=0.4.0
 Requires-Dist: ipython
 Requires-Dist: jupyterlab
+Requires-Dist: matplotlib
+Requires-Dist: ophyd-async
 Requires-Dist: ophyd-registry
 Requires-Dist: ophyd
 Requires-Dist: PyQt5>5.15
 Requires-Dist: pyRestTable
 Requires-Dist: pysumreg
 Requires-Dist: qtpy
-Requires-Dist: toml
-Requires-Dist: tomli
+Requires-Dist: tiled[all]
 Requires-Dist: tomli-w
+Requires-Dist: tomli
 Provides-Extra: dev
 Requires-Dist: build; extra == "dev"
 Requires-Dist: isort; extra == "dev"
@@ -59,6 +61,7 @@ Requires-Dist: sphinx-tabs; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: graphviz; extra == "doc"
 Requires-Dist: dot; extra == "doc"
+Requires-Dist: tomli-w; extra == "doc"
 Provides-Extra: all
 Requires-Dist: apsbits[dev,doc]; extra == "all"
 Dynamic: license-file

{apsbits-1.0.4 → apsbits-2.0.0/apsbits.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.4
+Version: 2.0.0
 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>
@@ -17,25 +17,27 @@ Classifier: Topic :: Utilities
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: apstools>=1.7.2
+Requires-Dist: apstools
+Requires-Dist: bluesky-queueserver>=0.0.22
 Requires-Dist: bluesky-queueserver-api
-Requires-Dist: bluesky-queueserver
 Requires-Dist: bluesky-widgets
 Requires-Dist: bluesky
 Requires-Dist: caproto
 Requires-Dist: databroker==1.2.5
-Requires-Dist: guarneri
+Requires-Dist: guarneri>=0.4.0
 Requires-Dist: ipython
 Requires-Dist: jupyterlab
+Requires-Dist: matplotlib
+Requires-Dist: ophyd-async
 Requires-Dist: ophyd-registry
 Requires-Dist: ophyd
 Requires-Dist: PyQt5>5.15
 Requires-Dist: pyRestTable
 Requires-Dist: pysumreg
 Requires-Dist: qtpy
-Requires-Dist: toml
-Requires-Dist: tomli
+Requires-Dist: tiled[all]
 Requires-Dist: tomli-w
+Requires-Dist: tomli
 Provides-Extra: dev
 Requires-Dist: build; extra == "dev"
 Requires-Dist: isort; extra == "dev"
@@ -59,6 +61,7 @@ Requires-Dist: sphinx-tabs; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: graphviz; extra == "doc"
 Requires-Dist: dot; extra == "doc"
+Requires-Dist: tomli-w; extra == "doc"
 Provides-Extra: all
 Requires-Dist: apsbits[dev,doc]; extra == "all"
 Dynamic: license-file

{apsbits-1.0.4 → apsbits-2.0.0}/apsbits.egg-info/SOURCES.txt

@@ -42,18 +42,16 @@ docs/source/api/utils.rst
 docs/source/api/generated/apsbits.core.best_effort_init.rst
 docs/source/api/generated/apsbits.core.catalog_init.rst
 docs/source/api/generated/apsbits.core.run_engine_init.rst
-docs/source/api/generated/apsbits.demo_instrument.callbacks.nexus_data_file_writer.rst
+docs/source/api/generated/apsbits.demo_instrument.callbacks.demo_nexus_callback.rst
+docs/source/api/generated/apsbits.demo_instrument.callbacks.demo_spec_callback.rst
 docs/source/api/generated/apsbits.demo_instrument.callbacks.rst
-docs/source/api/generated/apsbits.demo_instrument.callbacks.spec_data_file_writer.rst
 docs/source/api/generated/apsbits.demo_instrument.configs.rst
 docs/source/api/generated/apsbits.demo_instrument.devices.rst
-docs/source/api/generated/apsbits.demo_instrument.plans.dm_plans.rst
 docs/source/api/generated/apsbits.demo_instrument.plans.rst
 docs/source/api/generated/apsbits.demo_instrument.plans.sim_plans.rst
 docs/source/api/generated/apsbits.demo_instrument.rst
 docs/source/api/generated/apsbits.demo_instrument.startup.rst
 docs/source/api/generated/apsbits.demo_qserver.rst
-docs/source/api/generated/apsbits.utils.aps_functions.rst
 docs/source/api/generated/apsbits.utils.config_loaders.rst
 docs/source/api/generated/apsbits.utils.controls_setup.rst
 docs/source/api/generated/apsbits.utils.helper_functions.rst
@@ -79,6 +77,7 @@ docs/source/guides/startup.rst
 docs/source/guides/template_creation.rst
 src/apsbits/__init__.py
 src/apsbits/_version.py
+src/apsbits/py.typed
 src/apsbits/api/__init__.py
 src/apsbits/api/create_new_instrument.py
 src/apsbits/api/delete_instrument.py
@@ -93,8 +92,8 @@ src/apsbits/demo_instrument/README.md
 src/apsbits/demo_instrument/__init__.py
 src/apsbits/demo_instrument/startup.py
 src/apsbits/demo_instrument/callbacks/__init__.py
-src/apsbits/demo_instrument/callbacks/nexus_data_file_writer.py
-src/apsbits/demo_instrument/callbacks/spec_data_file_writer.py
+src/apsbits/demo_instrument/callbacks/demo_nexus_callback.py
+src/apsbits/demo_instrument/callbacks/demo_spec_callback.py
 src/apsbits/demo_instrument/configs/__init__.py
 src/apsbits/demo_instrument/configs/devices.yml
 src/apsbits/demo_instrument/configs/devices_aps_only.yml
@@ -102,13 +101,12 @@ src/apsbits/demo_instrument/configs/extra_logging.yml
 src/apsbits/demo_instrument/configs/iconfig.yml
 src/apsbits/demo_instrument/devices/__init__.py
 src/apsbits/demo_instrument/plans/__init__.py
-src/apsbits/demo_instrument/plans/dm_plans.py
 src/apsbits/demo_instrument/plans/sim_plans.py
+src/apsbits/demo_instrument/qserver/qs-config.yml
+src/apsbits/demo_instrument/qserver/user_group_permissions.yaml
 src/apsbits/demo_instrument/suspenders/__init__.py
 src/apsbits/demo_instrument/utils/__init__.py
-src/apsbits/demo_qserver/qs-config.yml
-src/apsbits/demo_qserver/qs_host.sh
-src/apsbits/demo_qserver/user_group_permissions.yaml
+src/apsbits/demo_scripts/qs_host.sh
 src/apsbits/tests/__init__.py
 src/apsbits/tests/conftest.py
 src/apsbits/tests/test_config.py
@@ -120,6 +118,7 @@ src/apsbits/tests/test_run_instrument.py
 src/apsbits/tests/test_stored_dict.py
 src/apsbits/utils/__init__.py
 src/apsbits/utils/aps_functions.py
+src/apsbits/utils/baseline_setup.py
 src/apsbits/utils/config_loaders.py
 src/apsbits/utils/controls_setup.py
 src/apsbits/utils/helper_functions.py

{apsbits-1.0.4 → apsbits-2.0.0}/apsbits.egg-info/requires.txt

@@ -1,22 +1,24 @@
-apstools>=1.7.2
+apstools
+bluesky-queueserver>=0.0.22
 bluesky-queueserver-api
-bluesky-queueserver
 bluesky-widgets
 bluesky
 caproto
 databroker==1.2.5
-guarneri
+guarneri>=0.4.0
 ipython
 jupyterlab
+matplotlib
+ophyd-async
 ophyd-registry
 ophyd
 PyQt5>5.15
 pyRestTable
 pysumreg
 qtpy
-toml
-tomli
+tiled[all]
 tomli-w
+tomli
 
 [all]
 apsbits[dev,doc]
@@ -45,3 +47,4 @@ sphinx-tabs
 sphinx
 graphviz
 dot
+tomli-w

apsbits-2.0.0/docs/source/api/generated/apsbits.demo_instrument.callbacks.demo_nexus_callback.rst

@@ -0,0 +1,17 @@
+apsbits.demo\_instrument.callbacks.demo\_nexus\_callback
+======================================================
+
+.. automodule:: apsbits.demo_instrument.callbacks.demo_nexus_callback
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      nxwriter_init
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      MyNXWriter

apsbits-2.0.0/docs/source/api/generated/apsbits.demo_instrument.callbacks.demo_spec_callback.rst

@@ -0,0 +1,13 @@
+apsbits.demo\_instrument.callbacks.demo\_spec\_callback
+=====================================================
+
+.. automodule:: apsbits.demo_instrument.callbacks.demo_spec_callback
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      spec_comment
+      newSpecFile
+      init_specwriter_with_RE

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/api/generated/apsbits.demo_instrument.callbacks.rst

@@ -10,5 +10,5 @@ apsbits.demo\_instrument.callbacks
    :toctree:
    :recursive:
 
-   nexus_data_file_writer
-   spec_data_file_writer
+   demo_nexus_callback
+   demo_spec_callback

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/api/generated/apsbits.demo_instrument.plans.rst

@@ -10,5 +10,4 @@ apsbits.demo\_instrument.plans
    :toctree:
    :recursive:
 
-   dm_plans
    sim_plans

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/api/index.rst

@@ -72,7 +72,6 @@ The utilities module provides helper functions and tools:
    :toctree: generated
    :recursive:
 
-   apsbits.utils.aps_functions
    apsbits.utils.config_loaders
    apsbits.utils.controls_setup
    apsbits.utils.helper_functions

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/api/utils.rst

@@ -11,7 +11,6 @@ The utilities module provides helper functions and tools for working with Bluesk
    :toctree: generated
    :recursive:
 
-   aps_functions
    config_loaders
    controls_setup
    helper_functions

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/guides/creating_devices.rst

@@ -46,32 +46,24 @@ You can also add a device from an external package to the ``devices.yml`` file.
        prefix: ioc:Slit1
        labels: ["slits"]
 
-2. Make sure all your device files are loaded on the ``iconfig.yml`` file.
-
-.. code-block:: yaml
-
-      DEVICES_FILES:
-        - devices.yml
-      APS_DEVICES_FILES:
-        - devices_aps_only.yml
-
-Note that the ``devices.yml`` file is loaded by default and the ``devices_aps_only.yml`` file is only loaded if the device is on the APS network.
 
 .. tip::
-    All kwargs of your device can be specified in the yaml file making it easy to resuse classes.
+    `APSTOOLS <https://github.com/BCDA-APS/apstools/tree/main/apstools>`_ has a lot of devices commonly used at the APS. Consider first checking the package and overwriting the device class to fit your needs before creating a new device.
 
 .. tip::
-   You can add any number of device files inside the iconfig file used by your instrument ``startup.py`` file. Just add another entry to the list.
+    You can add the `label: baseline` to any device in your configuration to automatically track its state during scans. This is particularly useful for monitoring environmental conditions or instrument parameters. For example:
 
-   .. code-block:: yaml
+    .. code-block:: yaml
 
-      ### Local OPHYD Device Control Yaml
-      DEVICES_FILES:
-        - devices.yml ## standard device file
-        - devices_2.yml ## another device file
-      APS_DEVICES_FILES:
-        - devices_aps_only.yml ## APS only device file
-        - devices_aps_only_2.yml ## another APS only device file
+        apstools.devices.ApsMachineParametersDevice:
+        - name: aps
+          labels:
+          - baseline
 
-.. tip::
-    `APSTOOLS <https://github.com/BCDA-APS/apstools/tree/main/apstools>`_ has a lot of devices commonly used at the APS. Consider first checking the package and overwriting the device class to fit your needs before creating a new device.
+        ophyd.EpicsSignalRO:
+        - name: temperature_monitor
+          prefix: "IOC:TEMP"
+          labels:
+          - baseline
+
+    Baseline devices will be automatically included in the metadata of each scan, making it easy to track changes in environmental conditions or instrument parameters over time.

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/guides/sessions.rst

@@ -35,4 +35,26 @@ When ready to load the bluesky data acquisition for use, type this command. For
 
 .. code-block:: bash
 
+    from demo_instrument.startup import *
+
+.. note::
+Change the demo_instrument to your instrument installed package name.
+
+Adding BITS to ipython profile
+----------------------------------
+
+To add BITS to your ipython profile, first create a new profile:
+
+.. code-block:: bash
+
+    ipython profile create bits-xx
+
+Then, add the following to your startup file:
+
+.. code-block:: bash
+
+    cat > ~/.ipython/profile_bits-xx/startup/00-start-bits.py  << EOF
     from new_instrument.startup import *
+    EOF
+
+For more detailed guidance on creating and configuring an ipython profile, see the `bluesky training documentation <https://github.com/BCDA-APS/bluesky_training/blob/304b8d02503044932afa5657cb43afd1f6be2f40/docs/source/instrument/_create_bluesky_ipython_profile.rst#L2>`_.

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/guides/startup.rst

@@ -52,7 +52,6 @@ Tips:
 * Create an extra_logging.yml file if you need custom logging configuration
 * The default logging setup from apsbits will be used if no extra configuration is provided
 
-
 Data Management Setup
 ~~~~~~~~~~~~~~~~~~~
 
@@ -129,10 +128,51 @@ Device Loading
     if host_on_aps_subnet():
         RE(make_devices(clear=False, file="device_aps_only.yml"))
 
+This block:
+* Loads the main device configuration from devices.yml
+* Optionally loads APS-specific devices from devices_aps_only.yml if running on APS subnet
+* Uses clear=False to preserve existing devices
+
 Tips:
 * Create a devices.yml file with your instrument's device configurations
 * Optionally create device_aps_only.yml for APS-specific devices
-* Set clear=False to preserve existing devices
+* The make_devices function will automatically register devices with the ophyd registry
+
+Baseline Device Setup
+~~~~~~~~~~~~~~~~~~~
+
+The baseline device setup allows you to track and record the state of specific devices during each scan. This is particularly useful for monitoring environmental conditions or instrument parameters that might affect your measurements.
+
+To configure baseline devices:
+
+1. In your devices.yml file, add a `label: baseline` to any device you want to track:
+
+   .. code-block:: yaml
+
+       apstools.devices.ApsMachineParametersDevice:
+       - name: aps
+         labels:
+         - baseline
+
+       ophyd.EpicsSignalRO:
+       - name: temperature_monitor
+         prefix: "IOC:TEMP"
+         labels:
+         - baseline
+
+2. The baseline devices will be automatically included in the metadata of each scan through the setup_baseline_stream function:
+
+   .. code-block:: python
+
+       setup_baseline_stream(sd, oregistry, connect=False)
+
+3. You can access baseline device values in your analysis using the scan metadata.
+
+Tips:
+* Use baseline devices for monitoring critical environmental parameters
+* Consider including timestamps, temperature, pressure, or other relevant measurements
+* Baseline devices should be read-only to avoid accidental modifications
+* Keep the number of baseline devices reasonable to avoid excessive data collection
 
 Configuration Tips
 ----------------

{apsbits-1.0.4 → apsbits-2.0.0}/docs/source/license.rst

@@ -6,7 +6,7 @@ Software License
 ================
 
 License
-=======
+-------
 
 The project is licensed under the following terms:
 

{apsbits-1.0.4 → apsbits-2.0.0}/pyproject.toml

@@ -33,25 +33,27 @@ classifiers = [
     "Topic :: Utilities",
 ]
 dependencies = [
-    "apstools >= 1.7.2",
+    "apstools",
+    "bluesky-queueserver >=0.0.22",
     "bluesky-queueserver-api",
-    "bluesky-queueserver",
     "bluesky-widgets",
     "bluesky",
     "caproto",
-    "databroker ==1.2.5",
-    "guarneri",
+    "databroker==1.2.5",
+    "guarneri>=0.4.0",
     "ipython",
     "jupyterlab",
+    "matplotlib",
+    "ophyd-async",
     "ophyd-registry",
     "ophyd",
     "PyQt5>5.15",
     "pyRestTable",
     "pysumreg",
     "qtpy",
-    "toml",
-    "tomli",
+    "tiled[all]",
     "tomli-w",
+    "tomli",
 ]
 
 [project.optional-dependencies]
@@ -73,6 +75,7 @@ doc = [
     "sphinx",
     "graphviz",
     "dot",
+    "tomli-w",
 ]
 
 all = ["apsbits[dev,doc]"]

{apsbits-1.0.4 → apsbits-2.0.0}/src/apsbits/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '1.0.4'
-__version_tuple__ = version_tuple = (1, 0, 4)
+__version__ = version = '2.0.0'
+__version_tuple__ = version_tuple = (2, 0, 0)
+
+__commit_id__ = commit_id = 'g484b02f15'