apsbits 1.0.1__tar.gz → 1.0.2__tar.gz

{apsbits-1.0.1 → apsbits-1.0.2}/.github/workflows/code.yml

@@ -104,7 +104,7 @@ jobs:
         shell: bash -l {0}
         run: |
           set -vxeuo pipefail
-          pip install -e .
+          pip install -e .[dev]
 
       - name: Run tests with pytest & coverage
         shell: bash -l {0}

{apsbits-1.0.1 → apsbits-1.0.2}/.github/workflows/docs.yml

@@ -43,6 +43,9 @@ jobs:
         sudo apt-get update
         sudo apt-get -y install pandoc
 
+    - name: Install graphviz
+      run: sudo apt install graphviz
+
     - name: Set time zone
       run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
 

{apsbits-1.0.1 → apsbits-1.0.2}/.gitignore

@@ -166,6 +166,7 @@ _version.py
 
 # Developer content
 dev_*
+.deleted/
 
 existing_plans_and_devices.yaml
 .vscode/

{apsbits-1.0.1 → apsbits-1.0.2}/.pre-commit-config.yaml

@@ -15,14 +15,9 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-case-conflict
-      # - id: check-json
-      # - id: check-symlinks
+      - id: check-json
+      - id: check-symlinks
       - id: check-executables-have-shebangs
-  # Don't strip output from jupyter notebooks ATM.
-  # - repo: https://github.com/kynan/nbstripout
-  #   rev: 0.7.1
-  #   hooks:
-  #     - id: nbstripout
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.4.8
     hooks:
@@ -30,3 +25,9 @@ repos:
         args:
           - --fix
       - id: ruff-format # replaces Black
+  - repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: v1.0.0
+    hooks:
+      - id: sphinx-lint
+        args:
+          - docs

apsbits-1.0.2/HISTORY.rst

@@ -0,0 +1,61 @@
+..
+  This file describes user-visible changes between the versions.
+  At this time, there is no automation to update this file.
+  Try to describe in human terms what is relevant for each release.
+
+  Revise this file before tagging a new release.
+
+  Subsections could include these headings (in this order), omit if no content.
+
+    Notice
+    Breaking Changes
+    New Features
+    Enhancements
+    Fixes
+    Maintenance
+    Deprecations
+    New Contributors
+
+.. _release_notes:
+
+========
+Releases
+========
+
+Brief notes describing each release and what's new.
+
+Project `milestones <https://github.com/prjemian/hklpy2/milestones>`_
+describe future plans.
+
+.. Coming release content can be gathered here.
+    Some people object to publishing unreleased changes.
+
+    1.0.2
+    #####
+
+    release expected 2025-Q2
+
+1.0.1
+#####
+
+released 2025-03-24
+
+Fixes
+-----
+
+* Calling RE(make_devices()) twice raises a lot of errors.
+* startup sequence needs revision
+* make_devices() needs a 'clear 'option
+* make_devices() is noisy
+* Why does make_devices() add all ophyd.sim simulator objects to ophyd registry?
+* First argument to logger.LEVEL() should not be an f-string
+* Adjust the order of steps when creating RE
+* bp.scan (& others) missing in queueserver
+* QS restart does not restart when QS was running
+
+1.0.0
+#####
+
+released 2025-03-21
+
+Initial public release.

{apsbits-1.0.1/apsbits.egg-info → apsbits-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.1
+Version: 1.0.2
 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>
@@ -42,6 +42,7 @@ Requires-Dist: isort; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Provides-Extra: doc
 Requires-Dist: babel; extra == "doc"
@@ -56,6 +57,8 @@ Requires-Dist: pygments; extra == "doc"
 Requires-Dist: sphinx-design; extra == "doc"
 Requires-Dist: sphinx-tabs; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: graphviz; extra == "doc"
+Requires-Dist: dot; extra == "doc"
 Provides-Extra: all
 Requires-Dist: apsbits[dev,doc]; extra == "all"
 Dynamic: license-file
@@ -76,16 +79,17 @@ queueserver.
 Please create a bits instrument using our template repository: https://github.com/BCDA-APS/DEMO-BITS
 
 
-## Installing the BITS Package for Development
+## Installing the BITS Package
 
 ```bash
-git clone github.com:BCDA-APS/BITS.git
-cd BITS
-conda create -y -n BITS_env python=3.11 pyepics
-conda activate BITS_env
-pip install -e ."[all]"
+export INSTALL_ENVIRONMENT_NAME=apsbits_env
+conda create -y -n "${INSTALL_ENVIRONMENT_NAME}" python=3.11 pyepics
+conda activate "${INSTALL_ENVIRONMENT_NAME}"
+pip install apsbits
 ```
 
+For development please reference our documentation
+
 ## Testing the apsbits base installation
 
 On an ipython console
@@ -97,48 +101,3 @@ RE(sim_print_plan())
 RE(sim_count_plan())
 RE(sim_rel_scan_plan())
 ```
-
-## Testing
-
-Use this command to run the test suite locally:
-
-```bash
-pytest -vvv --lf ./src
-```
-
-## Documentation
-
-<details>
-<summary>prerequisite</summary>
-
-To build the documentation locally, install [`pandoc`](https://pandoc.org/) in
-your conda environment:
-
-```bash
-conda install conda-forge::pandoc
-```
-
-</details>
-
-Use this command to build the documentation locally:
-
-```bash
-make -C docs clean html
-```
-
-Once the documentation builds, view the HTML pages using your web browser:
-
-```bash
-BROWSER ./docs/build/html/index.html &
-```
-
-### Adding to the documentation source
-
-The documentation source is located in files and directories under
-`./docs/source`.  Various examples are provided.
-
-Documentation can be added in these formats:
-[`.rst`](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)
-(reStructured text), [`.md`](https://en.wikipedia.org/wiki/Markdown) (markdown),
-and [`.ipynb`](https://jupyter.org/) (Jupyter notebook). For more information,
-see the [Sphinx](https://www.sphinx-doc.org/) documentation.

apsbits-1.0.2/README.md

@@ -0,0 +1,38 @@
+# APSBITS: Template Package for Bluesky Instruments
+
+| PyPI | Coverage |
+| --- | --- |
+[![PyPi](https://img.shields.io/pypi/v/apsbits.svg)](https://pypi.python.org/pypi/apsbits) | [![Coverage Status](https://coveralls.io/repos/github/BCDA-APS/BITS/badge.svg?branch=main)](https://coveralls.io/github/BCDA-APS/BITS?branch=main) |
+
+BITS: **B**luesky **I**nstrument **T**emplate **S**tructure
+
+Template of a Bluesky Data Acquisition Instrument in console, notebook, &
+queueserver.
+
+## Production use of BITS
+
+Please create a bits instrument using our template repository: https://github.com/BCDA-APS/DEMO-BITS
+
+
+## Installing the BITS Package
+
+```bash
+export INSTALL_ENVIRONMENT_NAME=apsbits_env
+conda create -y -n "${INSTALL_ENVIRONMENT_NAME}" python=3.11 pyepics
+conda activate "${INSTALL_ENVIRONMENT_NAME}"
+pip install apsbits
+```
+
+For development please reference our documentation
+
+## Testing the apsbits base installation
+
+On an ipython console
+
+```py
+from apsbits.demo_instrument.startup import *
+listobjects()
+RE(sim_print_plan())
+RE(sim_count_plan())
+RE(sim_rel_scan_plan())
+```

{apsbits-1.0.1 → apsbits-1.0.2/apsbits.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: apsbits
-Version: 1.0.1
+Version: 1.0.2
 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>
@@ -42,6 +42,7 @@ Requires-Dist: isort; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Provides-Extra: doc
 Requires-Dist: babel; extra == "doc"
@@ -56,6 +57,8 @@ Requires-Dist: pygments; extra == "doc"
 Requires-Dist: sphinx-design; extra == "doc"
 Requires-Dist: sphinx-tabs; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: graphviz; extra == "doc"
+Requires-Dist: dot; extra == "doc"
 Provides-Extra: all
 Requires-Dist: apsbits[dev,doc]; extra == "all"
 Dynamic: license-file
@@ -76,16 +79,17 @@ queueserver.
 Please create a bits instrument using our template repository: https://github.com/BCDA-APS/DEMO-BITS
 
 
-## Installing the BITS Package for Development
+## Installing the BITS Package
 
 ```bash
-git clone github.com:BCDA-APS/BITS.git
-cd BITS
-conda create -y -n BITS_env python=3.11 pyepics
-conda activate BITS_env
-pip install -e ."[all]"
+export INSTALL_ENVIRONMENT_NAME=apsbits_env
+conda create -y -n "${INSTALL_ENVIRONMENT_NAME}" python=3.11 pyepics
+conda activate "${INSTALL_ENVIRONMENT_NAME}"
+pip install apsbits
 ```
 
+For development please reference our documentation
+
 ## Testing the apsbits base installation
 
 On an ipython console
@@ -97,48 +101,3 @@ RE(sim_print_plan())
 RE(sim_count_plan())
 RE(sim_rel_scan_plan())
 ```
-
-## Testing
-
-Use this command to run the test suite locally:
-
-```bash
-pytest -vvv --lf ./src
-```
-
-## Documentation
-
-<details>
-<summary>prerequisite</summary>
-
-To build the documentation locally, install [`pandoc`](https://pandoc.org/) in
-your conda environment:
-
-```bash
-conda install conda-forge::pandoc
-```
-
-</details>
-
-Use this command to build the documentation locally:
-
-```bash
-make -C docs clean html
-```
-
-Once the documentation builds, view the HTML pages using your web browser:
-
-```bash
-BROWSER ./docs/build/html/index.html &
-```
-
-### Adding to the documentation source
-
-The documentation source is located in files and directories under
-`./docs/source`.  Various examples are provided.
-
-Documentation can be added in these formats:
-[`.rst`](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)
-(reStructured text), [`.md`](https://en.wikipedia.org/wiki/Markdown) (markdown),
-and [`.ipynb`](https://jupyter.org/) (Jupyter notebook). For more information,
-see the [Sphinx](https://www.sphinx-doc.org/) documentation.

{apsbits-1.0.1 → apsbits-1.0.2}/apsbits.egg-info/SOURCES.txt

@@ -1,5 +1,6 @@
 .gitignore
 .pre-commit-config.yaml
+HISTORY.rst
 LICENSE
 README.md
 pyproject.toml
@@ -21,35 +22,64 @@ apsbits.egg-info/requires.txt
 apsbits.egg-info/top_level.txt
 docs/Makefile
 docs/make.bat
-docs/template_creation.md
 docs/resources/create-repository-name.webp
 docs/resources/create-repository-owner.webp
+docs/resources/demo.ipynb
 docs/resources/use-this-template-button.webp
+docs/source/bits_overview.rst
 docs/source/conf.py
-docs/source/console.rst
-docs/source/demo.ipynb
+docs/source/history.rst
 docs/source/index.rst
 docs/source/install.rst
 docs/source/license.rst
-docs/source/logging_config.rst
-docs/source/notebook.rst
-docs/source/qserver.rst
-docs/source/script.rst
-docs/source/sessions.rst
 docs/source/_static/.gitkeep
-docs/source/api/callbacks.rst
-docs/source/api/configs.rst
+docs/source/api/api.rst
 docs/source/api/core.rst
-docs/source/api/devices.rst
+docs/source/api/demo_instrument.rst
+docs/source/api/demo_qserver.rst
 docs/source/api/index.rst
-docs/source/api/plans.rst
-docs/source/api/startup.rst
 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.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
+docs/source/api/generated/apsbits.utils.logging_setup.rst
+docs/source/api/generated/apsbits.utils.metadata.rst
+docs/source/api/generated/apsbits.utils.stored_dict.rst
+docs/source/deprecated/console.rst
+docs/source/deprecated/logging_config.rst
+docs/source/deprecated/notebook.rst
+docs/source/deprecated/script.rst
+docs/source/guides/creating_devices.rst
+docs/source/guides/creating_instrument.rst
+docs/source/guides/developing_bits.rst
 docs/source/guides/dm.md
 docs/source/guides/index.rst
-docs/source/guides/template_sync.rst
+docs/source/guides/qserver.rst
+docs/source/guides/qserver_service.rst
+docs/source/guides/sessions.rst
+docs/source/guides/setting_iconfig.rst
+docs/source/guides/template_creation.rst
 src/apsbits/__init__.py
 src/apsbits/_version.py
+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/core/__init__.py
 src/apsbits/core/best_effort_init.py
 src/apsbits/core/catalog_init.py
@@ -69,20 +99,23 @@ 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/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/tests/__init__.py
 src/apsbits/tests/conftest.py
 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_run_instrument.py
 src/apsbits/tests/test_stored_dict.py
 src/apsbits/utils/__init__.py
 src/apsbits/utils/aps_functions.py
 src/apsbits/utils/config_loaders.py
 src/apsbits/utils/controls_setup.py
-src/apsbits/utils/create_new_instrument.py
 src/apsbits/utils/helper_functions.py
 src/apsbits/utils/logging_setup.py
 src/apsbits/utils/make_devices.py

apsbits-1.0.2/apsbits.egg-info/entry_points.txt

@@ -0,0 +1,5 @@
+[console_scripts]
+bits-create = apsbits.api.create_new_instrument:main
+bits-delete = apsbits.api.delete_instrument:main
+bits-run = apsbits.api.run_instrument:main
+create-bits = apsbits.api.create_new_instrument:main

{apsbits-1.0.1 → apsbits-1.0.2}/apsbits.egg-info/requires.txt

@@ -27,6 +27,7 @@ isort
 mypy
 pre-commit
 pytest
+pytest-mock
 ruff
 
 [doc]
@@ -42,3 +43,5 @@ pygments
 sphinx-design
 sphinx-tabs
 sphinx
+graphviz
+dot

apsbits-1.0.2/docs/source/api/api.rst

@@ -0,0 +1,49 @@
+.. _api.api:
+
+API
+===
+
+The API module provides command-line interfaces for instrument management:
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   apsbits.api.create_new_instrument
+   apsbits.api.delete_instrument
+   apsbits.api.run_instrument
+
+These command-line tools help with:
+
+1. Creating new instruments from templates
+2. Deleting instruments and their associated qserver configurations
+3. Running instruments and retrieving their ophyd registry information
+
+Example Usage
+-------------
+
+Create a new instrument:
+
+.. code-block:: bash
+
+   create-bits --name my_instrument --path /path/to/instrument
+
+Delete an instrument:
+
+.. code-block:: bash
+
+   delete-bits --name my_instrument --path /path/to/instrument
+
+Run an instrument:
+
+.. code-block:: bash
+
+   run-bits --name my_instrument --path /path/to/instrument
+
+API Reference
+-------------
+
+.. automodule:: apsbits.api
+   :members:
+   :undoc-members:
+   :show-inheritance:

apsbits-1.0.2/docs/source/api/core.rst

@@ -0,0 +1,49 @@
+.. _api.core:
+
+Core Components
+===============
+
+The core module provides fundamental components for building a Bluesky data acquisition system.
+
+.. currentmodule:: apsbits.core
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   best_effort_init
+   catalog_init
+   run_engine_init
+
+These components are used to:
+
+1. Initialize the Run Engine
+2. Set up data catalogs
+3. Configure best-effort callbacks
+4. Establish baseline configurations
+
+Example Usage
+-------------
+
+Here's how to initialize the Run Engine, set up data catalogs, and configure best-effort callbacks:
+
+.. code-block:: python
+
+    from apsbits.core import run_engine_init, catalog_init, best_effort_init
+
+    # Initialize the Run Engine
+    RE = run_engine_init()
+
+    # Set up data catalogs
+    cat = catalog_init()
+
+    # Configure best-effort callbacks
+    bec = best_effort_init(RE)
+
+API Reference
+-------------
+
+.. automodule:: apsbits.core
+   :members:
+   :undoc-members:
+   :show-inheritance:

apsbits-1.0.2/docs/source/api/demo_instrument.rst

@@ -0,0 +1,55 @@
+.. _api.demo_instrument:
+
+Demo Instrument
+===============
+
+.. currentmodule:: apsbits.demo_instrument
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   startup
+   callbacks
+   devices
+   plans
+
+Example Usage
+-------------
+
+.. code-block:: py
+
+    from apsbits.demo_instrument.startup import *
+
+Components
+----------
+
+The demo instrument is organized into several components:
+
+callbacks
+~~~~~~~~~
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   callbacks.nexus_data_file_writer
+   callbacks.spec_data_file_writer
+
+devices
+~~~~~~~
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+
+plans
+~~~~~
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   plans.dm_plans
+   plans.sim_plans

apsbits-1.0.2/docs/source/api/demo_qserver.rst

@@ -0,0 +1,30 @@
+.. _api.demo_qserver:
+
+Demo Queue Server
+=================
+
+.. currentmodule:: apsbits.demo_qserver
+
+
+
+Starting the Server
+===================
+
+.. code-block:: bash
+
+    ./qs_host.sh
+
+Configuration
+-------------
+
+.. code-block:: yaml
+
+    # qs-config.yml
+    host: localhost
+    port: 8080
+    name: demo_qserver
+    log_level: INFO
+
+The demo queue server provides an example implementation of a Bluesky Queue Server using APSBITS.
+
+For more details on using the Queue Server, see :doc:`../guides/qserver_service`.

apsbits-1.0.2/docs/source/api/generated/apsbits.core.best_effort_init.rst

@@ -0,0 +1,11 @@
+apsbits.core.best\_effort\_init
+===============================
+
+.. automodule:: apsbits.core.best_effort_init
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      init_bec_peaks

apsbits-1.0.2/docs/source/api/generated/apsbits.core.catalog_init.rst

@@ -0,0 +1,11 @@
+apsbits.core.catalog\_init
+==========================
+
+.. automodule:: apsbits.core.catalog_init
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      init_catalog