apsbits 1.0.0rc2__py3-none-any.whl

apsbits/utils/stored_dict.py

@@ -0,0 +1,192 @@
+"""
+Storage-backed Dictionary
+=========================
+
+A dictionary that writes its contents to YAML file.
+
+Replaces ``bluesky.utils.PersistentDict``.
+
+* Contents must be JSON serializable.
+* Contents stored in a single human-readable YAML file.
+* Sync to disk shortly after dictionary is updated.
+
+.. autosummary::
+
+    ~StoredDict
+"""
+
+__all__ = ["StoredDict"]
+
+import collections.abc
+import datetime
+import inspect
+import json
+import logging
+import pathlib
+import threading
+import time
+
+import yaml
+
+logger = logging.getLogger(__name__)
+logger.bsdev(__file__)
+
+
+class StoredDict(collections.abc.MutableMapping):
+    """
+    Dictionary that syncs to storage.
+
+    .. autosummary::
+
+        ~flush
+        ~popitem
+        ~reload
+
+    .. rubric:: Static methods
+
+    All support for the YAML format is implemented in the static methods.
+
+    .. autosummary::
+
+        ~dump
+        ~load
+
+    ----
+    """
+
+    def __init__(self, file, delay=5, title=None, serializable=True):
+        """
+        StoredDict : Dictionary that syncs to storage
+
+        PARAMETERS
+
+        file : str or pathlib.Path
+            Name of file to store dictionary contents.
+        delay : number
+            Time delay (s) since last dictionary update to write to storage.
+            Default: 5 seconds.
+        title : str or None
+            Comment to write at top of file.
+            Default: "Written by StoredDict."
+        serializable : bool
+            If True, validate new dictionary entries are JSON serializable.
+        """
+        self._file = pathlib.Path(file)
+        self._delay = max(0, delay)
+        self._title = title or f"Written by {self.__class__.__name__}."
+        self.test_serializable = serializable
+
+        self.sync_in_progress = False
+        self._sync_deadline = time.time()
+        self._sync_key = f"sync_agent_{id(self):x}"
+        self._sync_loop_period = 0.005
+
+        self._cache = {}
+        self.reload()
+
+    def __delitem__(self, key):
+        """Delete dictionary value by key."""
+        del self._cache[key]
+
+    def __getitem__(self, key):
+        """Get dictionary value by key."""
+        return self._cache[key]
+
+    def __iter__(self):
+        """Iterate over the dictionary keys."""
+        yield from self._cache
+
+    def __len__(self):
+        """Number of keys in the dictionary."""
+        return len(self._cache)
+
+    def __repr__(self):
+        """representation of this object."""
+        return f"<{self.__class__.__name__} {dict(self)!r}>"
+
+    def __setitem__(self, key, value):
+        """Write to the dictionary."""
+        outermost_frame = inspect.getouterframes(inspect.currentframe())[-1]
+        if "sphinx-build" in outermost_frame.filename:
+            # Seems that Sphinx is building the documentation.
+            # Ignore all the objects it tries to add.
+            return
+
+        if self.test_serializable:
+            json.dumps({key: value})
+
+        self._cache[key] = value  # Store the new (or revised) content.
+
+        # Reset the deadline.
+        self._sync_deadline = time.time() + self._delay
+        logger.debug("new sync deadline in %f s.", self._delay)
+
+        if not self.sync_in_progress:
+            # Start the sync_agent (thread).
+            self._delayed_sync_to_storage()
+
+    def _delayed_sync_to_storage(self):
+        """
+        Sync the metadata to storage.
+
+        Start a time-delay thread.  New writes to the metadata dictionary will
+        extend the deadline.  Sync once the deadline is reached.
+        """
+
+        def sync_agent():
+            """Threaded task."""
+            logger.debug("Starting sync_agent...")
+            self.sync_in_progress = True
+            while time.time() < self._sync_deadline:
+                time.sleep(self._sync_loop_period)
+            logger.debug("Sync waiting period ended")
+            self.sync_in_progress = False
+
+            StoredDict.dump(self._file, self._cache, title=self._title)
+
+        thred = threading.Thread(target=sync_agent)
+        thred.start()
+
+    def flush(self):
+        """Force a write of the dictionary to disk"""
+        logger.debug("flush()")
+        if not self.sync_in_progress:
+            StoredDict.dump(self._file, self._cache, title=self._title)
+        self._sync_deadline = time.time()
+        self.sync_in_progress = False
+
+    def popitem(self):
+        """
+        Remove and return a (key, value) pair as a 2-tuple.
+
+        Pairs are returned in LIFO (last-in, first-out) order.
+        Raises KeyError if the dict is empty.
+        """
+        return self._cache.popitem()
+
+    def reload(self):
+        """Read dictionary from storage."""
+        logger.debug("reload()")
+        self._cache = StoredDict.load(self._file)
+
+    @staticmethod
+    def dump(file, contents, title=None):
+        """Write dictionary to YAML file."""
+        logger.debug("_dump(): file='%s', contents=%r, title=%r", file, contents, title)
+        with open(file, "w") as f:
+            if isinstance(title, str) and len(title) > 0:
+                f.write(f"# {title}\n")
+            f.write(f"# Dictionary contents written: {datetime.datetime.now()}\n\n")
+            f.write(yaml.dump(contents, indent=2))
+
+    @staticmethod
+    def load(file):
+        """Read dictionary from YAML file."""
+        from .config_loaders import load_config_yaml
+
+        file = pathlib.Path(file)
+        logger.debug("_load('%s')", file)
+        md = None
+        if file.exists():
+            md = load_config_yaml(file)
+        return md or {}  # In case file is empty.

apsbits-1.0.0rc2.dist-info/LICENSE

@@ -0,0 +1,48 @@
+Copyright (c) 2023-2025, UChicago Argonne, LLC
+
+All Rights Reserved
+
+BITS
+
+BCDA, Advanced Photon Source, Argonne National Laboratory
+
+
+OPEN SOURCE LICENSE
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.  Software changes,
+   modifications, or derivative works, should be noted with comments and
+   the author and organization's name.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+   nor the names of its contributors may be used to endorse or promote
+   products derived from this software without specific prior written
+   permission.
+
+4. The software and the end-user documentation included with the
+   redistribution, if any, must include the following acknowledgment:
+
+   "This product includes software produced by UChicago Argonne, LLC
+   under Contract No. DE-AC02-06CH11357 with the Department of Energy."
+
+****************************************************************************
+
+DISCLAIMER
+
+THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT WARRANTY OF ANY KIND.
+
+Neither the United States GOVERNMENT, nor the United States Department
+of Energy, NOR uchicago argonne, LLC, nor any of their employees, makes
+any warranty, express or implied, or assumes any legal liability or
+responsibility for the accuracy, completeness, or usefulness of any
+information, data, apparatus, product, or process disclosed, or
+represents that its use would not infringe privately owned rights.
+
+****************************************************************************

apsbits-1.0.0rc2.dist-info/METADATA

@@ -0,0 +1,349 @@
+Metadata-Version: 2.2
+Name: apsbits
+Version: 1.0.0rc2
+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>
+License: Copyright (c) 2023-2025, UChicago Argonne, LLC
+        
+        All Rights Reserved
+        
+        BITS
+        
+        BCDA, Advanced Photon Source, Argonne National Laboratory
+        
+        
+        OPEN SOURCE LICENSE
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice,
+           this list of conditions and the following disclaimer.  Software changes,
+           modifications, or derivative works, should be noted with comments and
+           the author and organization's name.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+           nor the names of its contributors may be used to endorse or promote
+           products derived from this software without specific prior written
+           permission.
+        
+        4. The software and the end-user documentation included with the
+           redistribution, if any, must include the following acknowledgment:
+        
+           "This product includes software produced by UChicago Argonne, LLC
+           under Contract No. DE-AC02-06CH11357 with the Department of Energy."
+        
+        ****************************************************************************
+        
+        DISCLAIMER
+        
+        THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT WARRANTY OF ANY KIND.
+        
+        Neither the United States GOVERNMENT, nor the United States Department
+        of Energy, NOR uchicago argonne, LLC, nor any of their employees, makes
+        any warranty, express or implied, or assumes any legal liability or
+        responsibility for the accuracy, completeness, or usefulness of any
+        information, data, apparatus, product, or process disclosed, or
+        represents that its use would not infringe privately owned rights.
+        
+        ****************************************************************************
+        
+Project-URL: Homepage, https://BCDA-APS.github.io/APSBITS/
+Project-URL: Bug Tracker, https://github.com/BCDA-APS/APSBITS/issues
+Keywords: bluesky,queueserver
+Classifier: Development Status :: 6 - Mature
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
+Classifier: License :: Freely Distributable
+Classifier: License :: Public Domain
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Utilities
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: apstools>=1.7.2
+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: ipython
+Requires-Dist: jupyterlab
+Requires-Dist: ophyd-registry
+Requires-Dist: ophyd
+Requires-Dist: PyQt5>5.15
+Requires-Dist: pyRestTable
+Requires-Dist: pysumreg
+Requires-Dist: qtpy
+Requires-Dist: toml
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: babel; extra == "doc"
+Requires-Dist: ipykernel; extra == "doc"
+Requires-Dist: jinja2; extra == "doc"
+Requires-Dist: markupsafe; extra == "doc"
+Requires-Dist: myst_parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Requires-Dist: pygments-ipython-console; extra == "doc"
+Requires-Dist: pygments; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinx-tabs; extra == "doc"
+Requires-Dist: sphinx; extra == "doc"
+Provides-Extra: all
+Requires-Dist: apsbits[dev,doc]; extra == "all"
+
+# 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)](https://coveralls.io/github/BCDA-APS/BITS) |
+
+BITS: **B**luesky **I**nstrument **T**emplate**S**
+
+Template of a Bluesky Data Acquisition Instrument in console, notebook, &
+queueserver.
+
+## Create repository from this template.
+
+
+
+https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template
+
+Creating a repository from a template
+On GitHub, navigate to the main page of the repository.
+
+Above the file list, click Use this template.
+
+Select Create a new repository.
+
+![Screenshot of the "Use this template" button and the dropdown menu expanded to show the "Open in a codespace" option.
+](docs/resources/use-this-template-button.webp)
+
+Alternatively, you can open the template in a codespace and publish your work to a new repository later. For more information, see Creating a codespace from a template.
+
+Use the Owner dropdown menu to select the account you want to own the repository.
+
+Screenshot of the owner menu for a new GitHub repository. The menu shows two options, octocat and github.
+Type a name for your repository, and an optional description.
+
+![Image 2](docs/resources/create-repo-from-template.webp)
+
+
+Screenshot of a the first step in creating a repository. The "Repository name" field contains the text "hello-world" and is outlined in orange.
+Choose a repository visibility. For more information, see About repositories.
+
+![Image 3](docs/resources/create-repository-owner.webp)
+
+Optionally, to include the directory structure and files from all branches in the template, and not just the default branch, select Include all branches.
+
+Optionally, if the personal account or organization in which you're creating uses any GitHub Apps from GitHub Marketplace, select any apps you'd like to use in the repository.
+
+Click Create repository from template.
+
+## Installing your own BITS instrument
+
+```bash
+export ENV_NAME=BITS_env
+
+conda create -y -n $ENV_NAME python=3.11 pyepics
+conda activate $ENV_NAME
+pip install -e ."[all]"
+```
+
+
+## Edit your instrument
+
+
+
+## IPython console Start
+
+To start the bluesky instrument session in a ipython execute the next command in a terminal:
+
+```bash
+ipython
+```
+
+## Jupyter Notebook Start
+Start JupyterLab, a Jupyter notebook server, or a notebook, VSCode.
+
+## Starting the BITS Package
+
+```py
+from instrument.startup import *
+RE(make_devices())  # create all the ophyd-style control devices
+```
+
+## Run Sim Plan Demo
+
+To run some simulated plans that ensure the installation worked as expected
+please run the next commands inside an ipython session or a jupyter notebook
+after starting the data acquisition:
+
+```py
+RE(sim_print_plan())
+RE(sim_count_plan())
+RE(sim_rel_scan_plan())
+```
+
+See this [example](./docs/source/demo.ipynb).
+
+## Configuration files
+
+The files that can be configured to adhere to your preferences are:
+
+- `configs/iconfig.yml` - configuration for data collection
+- `configs/logging.yml` - configuration for session logging to console and/or files
+- `qserver/qs-config.yml`    - contains all configuration of the QS host process. See the [documentation](https://blueskyproject.io/bluesky-queueserver/manager_config.html) for more details of the configuration.
+
+## queueserver
+
+The queueserver has a host process that manages a RunEngine. Client sessions
+will interact with that host process.
+
+### Run a queueserver host process
+
+Use the queueserver host management script to start the QS host process.  The
+`restart` option stops the server (if it is running) and then starts it.  This is
+the usual way to (re)start the QS host process. Using `restart`, the process
+runs in the background.
+
+```bash
+./qserver/qs_host.sh restart
+```
+
+### Run a queueserver client GUI
+
+To run the gui client for the queueserver you can use the next command inside the terminal:
+
+```bash
+queue-monitor &
+```
+
+### Shell script explained
+
+A [shell script](./qserver/qs_host.sh) is used to start the QS host process. Below
+are all the command options, and what they do.
+
+```bash
+(bstest) $ ./qserver/qs_host.sh help
+Usage: qs_host.sh {start|stop|restart|status|checkup|console|run} [NAME]
+
+    COMMANDS
+        console   attach to process console if process is running in screen
+        checkup   check that process is running, restart if not
+        restart   restart process
+        run       run process in console (not screen)
+        start     start process
+        status    report if process is running
+        stop      stop process
+
+    OPTIONAL TERMS
+        NAME      name of process (default: bluesky_queueserver-)
+```
+
+Alternatively, run the QS host's startup command directly within the `./qserver/`
+subdirectory.
+
+```bash
+cd ./qserver
+start-re-manager --config=./qs-config.yml
+```
+
+## 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.
+
+## Warnings
+
+### Bluesky Queueserver
+
+The QS host process writes files into the `qserver/` directory. This directory can be
+relocated. However, it should not be moved into the instrument package since
+that might be installed into a read-only directory.
+
+## How-To Guides
+### How to use the template
+
+Consider renaming this `instrument` package to be more clear that is specific to *this*
+instrument.  This will be the name by which it is `pip` installed and also used with
+`import`.  Let's use an example instrument package name `my_instrument` below to show which parts are edited.
+
+1) Click on use as template button
+2) Adjust the following parameters in the following files:
+    - `pyproject.toml`
+        - `[project]` `name =` *example: `my_instrument`*
+        - `[project.urls]`  *change URLs for your repo*
+        - `[tool.setuptools]` `package-dir = {"instrument" = "src/instrument"}` *example: `{"my_instrument" = "src/instrument"}`*
+    - `src/instrument/init.py`
+        - `__package__ = "instrument"` *example: `"my_instrument"`*
+    - `src/instrument/configs/iconfig.yml`
+        - `DATABROKER_CATALOG:` *change from `temp` to your catalog's name*
+        - `beamline_id:` *one word beamline name (such as known by APS scheduling system)*
+        - `instrument_name:` *descriptive name of your beamline*
+        - `DM_SETUP_FILE:` *Path to DM bash setup file, comment out if you do not have*
+        - `BEC:` *adjust for your preferences*
+    - `qserver/qs-config.yml`
+        - `startup_module: instrument.startup` *example: `my_instrument.startup`*
+    - `docs/source/conf.py`
+        - `import instrument` *example `import my_instrument`*
+        - `project = "instrument"` *example: `"my_instrument"`*
+        - `version = instrument.__version__` *example: `my_instrument.__version__`*
+
+- [APS Data Management Plans](./docs/source/guides/dm.md)

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+apsbits-1.0.0rc2.dist-info/METADATA,sha256=KxfP9_A5b3mCZfs5-602bYJYbztrnJz3M_Sa-u7G3dQ,12544
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+apsbits-1.0.0rc2.dist-info/RECORD,,

apsbits-1.0.0rc2.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (76.1.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

apsbits-1.0.0rc2.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+create-bits = apsbits.utils.create_new_instrument:main

apsbits-1.0.0rc2.dist-info/top_level.txt

@@ -0,0 +1 @@
+apsbits