PyroLab 0.3.1__tar.gz → 0.4.0__tar.gz

pyrolab-0.4.0/MANIFEST.in

@@ -0,0 +1,4 @@
+include NOTICE.txt AUTHORS.txt 
+graft pyrolab/ 
+prune pyrolab/data/local/
+global-exclude *.py[cod]

{PyroLab-0.3.1 → pyrolab-0.4.0}/NOTICE.txt

@@ -31,7 +31,7 @@ PPCL55X
 The code found in the following files were included in Pyrolab with some
 modifications:
 
-pyrolab/drivers/lasers/pplaser.py
+pyrolab/drivers/lasers/ppcl55x.py
 
 The original source is available at 
 https://www.pure-photonics.com/s/ITLA_v3-CUSTOMER.PY

pyrolab-0.4.0/PKG-INFO

@@ -0,0 +1,299 @@
+Metadata-Version: 2.4
+Name: pyrolab
+Version: 0.4.0
+Summary: A framework for using remote lab instruments as local resources built on Pyro5.
+Author-email: Sequoia Ploeg <sequoiap4@gmail.com>, BYU CamachoLab <camacho@byu.edu>
+Maintainer-email: Sequoia Ploeg <sequoiap4@gmail.com>, BYU CamachoLab <camacho@byu.edu>
+License: GPL-3.0+
+Project-URL: Homepage, https://pyrolab.readthedocs.io/en/latest/
+Project-URL: Documentation, https://pyrolab.readthedocs.io/en/latest/
+Project-URL: Source, https://github.com/BYUCamachoLab/pyrolab
+Project-URL: Bug Reports, https://github.com/BYUCamachoLab/pyrolab/issues
+Project-URL: Research Group, https://camacholab.byu.edu/
+Keywords: PyroLab,Pyro5,Pyro,lab,instrument,remote,resources,framework,laboratory,instrumentation,hardware,science,remote,network,integration
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Scientific/Engineering
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE.txt
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: Pyro5
+Requires-Dist: pydantic<2.0.0,>=1.9.1
+Requires-Dist: pyyaml
+Requires-Dist: deprecation
+Requires-Dist: typer
+Requires-Dist: colorama
+Requires-Dist: tabulate
+Requires-Dist: requests
+Requires-Dist: packaging>=23.0
+Provides-Extra: tsl550
+Requires-Dist: pyserial; extra == "tsl550"
+Provides-Extra: ppcl55x
+Requires-Dist: pyserial; extra == "ppcl55x"
+Provides-Extra: rto
+Requires-Dist: pyvisa; extra == "rto"
+Requires-Dist: pyvisa-py; extra == "rto"
+Provides-Extra: arduino
+Requires-Dist: pyfirmata; extra == "arduino"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Provides-Extra: dev
+Requires-Dist: notebook; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8>=4.0.1; extra == "dev"
+Requires-Dist: isort>=5.10.1; extra == "dev"
+Requires-Dist: black>=22.1.0; extra == "dev"
+Requires-Dist: autopep8>=1.6.0; extra == "dev"
+Requires-Dist: twine>=4.0.0; extra == "dev"
+Requires-Dist: build>=0.10.0; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: bump2version~=1.0.1; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: jupyter-book==1.0.3; extra == "docs"
+Requires-Dist: numpydoc==1.5.0; extra == "docs"
+Dynamic: license-file
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/BYUCamachoLab/pyrolab/master/docs/_static/images/pyrolab_logo.svg" width="40%" alt="PyroLab">
+</p>
+
+---
+
+<p align="center">
+<img alt="Development version" src="https://img.shields.io/badge/master-v0.4.0-informational">
+<a href="https://pypi.python.org/pypi/pyrolab"><img alt="PyPI Version" src="https://img.shields.io/pypi/v/pyrolab.svg"></a>
+<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/pyrolab">
+<a href="https://pyrolab.readthedocs.io/"><img alt="Documentation Status" src="https://readthedocs.org/projects/pyrolab/badge/?version=latest"></a>
+<a href="https://pypi.python.org/pypi/pyrolab/"><img alt="License" src="https://img.shields.io/pypi/l/pyrolab.svg"></a>
+<a href="https://github.com/BYUCamachoLab/pyrolab/commits/master"><img alt="Latest Commit" src="https://img.shields.io/github/last-commit/BYUCamachoLab/pyrolab.svg"></a>
+</p>
+
+A framework for using remote lab instruments as local resources, built on Pyro5.
+
+Developed by Sequoia Ploeg (for [CamachoLab](https://camacholab.byu.edu/), 
+Brigham Young University).
+
+## About
+This project aims to allow all laboratory instruments to be accessed as
+local objects from a remote machine. Instruments that don't natively
+support such access, such as those required to be connected by a USB cable
+(or similar), are wrapped with a Pyro5 interface. However, this library may
+contain other instruments that are already internet-capable and don't rely
+on Pyro5. That's alright; we're just trying to create a minimal-dependency,
+one-stop-shop for laboratory instruments!
+
+**Note:** while the software says "OS Independent", some of the servers *are*
+OS-specific. For example, ThorLabs DLL's only work on Windows. However, you could
+use PyroLab to connect to those devices from any operating system.
+
+## Installation
+
+PyroLab is pip installable:
+
+```
+pip install pyrolab
+```
+
+PyroLab declares several "extras", depending on which instruments you need
+to support:
+
+```
+pip install pyrolab[tsl550, oscope]
+```
+
+The full list of supported extras is:
+- ``tsl550`` (Santec lasers)
+- ``ppcl55x`` (PurePhotonics lasers)
+- ``rto`` (Rohde & Schwarz oscilloscopes)
+- ``arduino`` (Arduino)
+- ``test`` (PyroLab unit testing)
+<!-- - ``thorlabs`` (ThorLabs motion controllers) -->
+<!-- - ``adiscovery`` (Analog Discovery boards from Digilent) -->
+<!-- - ``monitor`` (PyroMonitor web application) -->
+
+You can also clone the repository, navigate to the toplevel, and install in 
+editable mode (make sure you have pip >= 21.1):
+
+```
+pip install -e .
+```
+
+## Web Monitor
+
+There's a web application that can monitor your PyroLab nameserver and 
+provide an easy-to-access status board. It's a Flask app that can be served
+using a production grade server. Install it using pip:
+
+```
+pip install pyromonitor
+```
+
+To run:
+
+```
+pyromonitor up
+```
+
+## Example
+
+### Local Instruments
+
+Locally available instruments just import drivers without using any of the 
+other features of PyroLab.
+
+```
+from pyrolab.drivers.lasers.tsl550 import TSL550
+
+laser = TSL550("COM4")
+laser.on()
+laser.power_dBm(12)
+laser.open_shutter()
+laser.sweep_set_mode(continuous=True, twoway=True, trigger=False, const_freq_step=False)
+```
+
+### Remote Instruments
+
+First, make sure all configurations on the nameserver computer, instrument 
+server computer, and client are correct (with the proper keys, if configured, 
+etc.).
+
+Run a nameserver:
+
+```python
+from pyrolab.api import start_ns_loop
+start_ns_loop()
+```
+
+Provide a service:
+
+```python
+from pyrolab.api import Daemon, locate_ns
+from pyrolab.drivers.sample import SampleService
+
+daemon = Daemon()
+ns = locate_ns(host="localhost")
+uri = daemon.register(SampleService)
+ns.register("test.SampleService", uri)
+
+try:
+    daemon.requestLoop()
+finally:
+    ns.remove("test.SampleService")
+```
+
+Connect using a remote client:
+
+```python
+from pyrolab.api import locate_ns, Proxy
+
+ns = locate_ns(host="localhost")
+uri = ns.lookup("test.SampleService")
+
+with Proxy(uri) as service:
+    resp = service.echo("Hello, server!")
+    print(type(resp), resp)
+```
+
+## Instrument Server Configuration
+
+PyroLab stores information about instruments and servers when it closes. This
+means that once PyroLab has been configured once, each time it is restarted,
+it will remember and reload the previous configuration. Hence, once a server
+is set up, unless the available instruments, nameserver, or other 
+configurations change, PyroLab will automatically work when started, every 
+time!
+
+For an example of how a new PyroLab instrument server should be configured the
+first time it's run, see ``examples/library-catalog/config.yaml``.
+
+## FAQ's
+1. **Another instrument library? What about all the others?**  
+    In our experience, many of the other libraries are buggy or have difficulty
+    with network connections. So, our approach was to rely on a well developed
+    and time-tested framework (Pyro) instead of worrying about developing and
+    supporting our own custom set of servers.
+
+2. **Is this a standalone software that automatically supports all the advertised 
+instruments?**  
+    No; many of these instruments depend on other software already being
+    installed. In particular, ThorLabs equipment depends on ThorLabs software
+    already being installed on the computer connected to the physical hardware
+    (but not on the remote computer!). As much as possible, though, we try to
+    make the drivers standalone capable.
+
+## For Developers
+
+Since the passing of data is, by definition, between hosts and over IP, PyroLab
+avoids the use of complex Python objects for return values that will be 
+transmitted to remote machines. Since serialization is complicated, and
+security is even harder, we resort to using only basic Python types when
+interfacing with hardware (i.e., Python lists, ints, tuples, and not NumPy 
+arrays, matplotlib plot objects, custom objects, etc.).
+
+## Releasing
+
+Make sure you have committed a changelog file under ``docs/changelog`` titled 
+``<major>.<minor>.<patch>-changelog.md`` before bumping version. Also, the git
+directory should be clean (no uncommitted changes).
+
+To bump version prior to a release, run one of the following commands:
+
+```
+bumpversion major
+bumpversion minor
+bumpversion patch
+```
+
+This will automatically create a git tag in the repository with the 
+corrresponding version number and commit the modified files (where version
+numbers were updated). Pushing the tags (a manual process) to the remote will 
+automatically create a new release. Releases are automatically published to 
+PyPI and GitHub when git tags matching the "v*" pattern are created 
+(e.g. "v0.4.0"), as bumpversion does.
+
+After bumping version, you can view the tags on the local machine by running 
+``git tag``. To push the tags to the remote server and trigger the release
+workflow, you can run ``git push origin <tagname>``.
+
+For code quality, please run isort and black before committing (note that the
+latest release of isort may not work through VSCode's integrated terminal, and
+it's safest to run it separately through another terminal).
+
+## Building the Docs
+
+Much of the API documentation is autogenerated from the source code. Gitignores
+are in place to prevent you from committing autogenerated pages.
+
+To build the docs, navigate to the ``docs/`` directory and run:
+
+```
+pip install -r requirements.txt
+make html
+```
+
+## Building the Package
+
+You can test the build and view the bundled artifacts using 
+[build](https://pypi.org/project/build/). It's recommended you build locally
+before pushing to PyPI. In particular, double check the included files and make
+sure only the required files are there by modifying MANIFEST.in as necessary.

{PyroLab-0.3.1 → pyrolab-0.4.0}/README.md

@@ -5,7 +5,7 @@
 ---
 
 <p align="center">
-<img alt="Development version" src="https://img.shields.io/badge/master-v0.3.1-informational">
+<img alt="Development version" src="https://img.shields.io/badge/master-v0.4.0-informational">
 <a href="https://pypi.python.org/pypi/pyrolab"><img alt="PyPI Version" src="https://img.shields.io/pypi/v/pyrolab.svg"></a>
 <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/pyrolab">
 <a href="https://pyrolab.readthedocs.io/"><img alt="Documentation Status" src="https://readthedocs.org/projects/pyrolab/badge/?version=latest"></a>
@@ -47,10 +47,14 @@ pip install pyrolab[tsl550, oscope]
 ```
 
 The full list of supported extras is:
-- tsl550
-- oscope
-- arduino
-- monitor
+- ``tsl550`` (Santec lasers)
+- ``ppcl55x`` (PurePhotonics lasers)
+- ``rto`` (Rohde & Schwarz oscilloscopes)
+- ``arduino`` (Arduino)
+- ``test`` (PyroLab unit testing)
+<!-- - ``thorlabs`` (ThorLabs motion controllers) -->
+<!-- - ``adiscovery`` (Analog Discovery boards from Digilent) -->
+<!-- - ``monitor`` (PyroMonitor web application) -->
 
 You can also clone the repository, navigate to the toplevel, and install in 
 editable mode (make sure you have pip >= 21.1):
@@ -61,9 +65,15 @@ pip install -e .
 
 ## Web Monitor
 
-PyroLab comes with a web application that can monitor your nameserver and 
+There's a web application that can monitor your PyroLab nameserver and 
 provide an easy-to-access status board. It's a Flask app that can be served
-using a production grade server. To run:
+using a production grade server. Install it using pip:
+
+```
+pip install pyromonitor
+```
+
+To run:
 
 ```
 pyromonitor up
@@ -184,7 +194,7 @@ corrresponding version number and commit the modified files (where version
 numbers were updated). Pushing the tags (a manual process) to the remote will 
 automatically create a new release. Releases are automatically published to 
 PyPI and GitHub when git tags matching the "v*" pattern are created 
-(e.g. "v0.3.1"), as bumpversion does.
+(e.g. "v0.4.0"), as bumpversion does.
 
 After bumping version, you can view the tags on the local machine by running 
 ``git tag``. To push the tags to the remote server and trigger the release

{PyroLab-0.3.1 → pyrolab-0.4.0}/pyproject.toml

@@ -1,10 +1,10 @@
 [project]
-name = "PyroLab"
-version = "0.3.1"
-description = "A framework for using remote lab instruments as local resources built on Pyro5"
+name = "pyrolab"
+version = "0.4.0"
+description = "A framework for using remote lab instruments as local resources built on Pyro5."
 readme = "README.md"
-requires-python = ">=3.7"
-license = {file = "LICENSE"}
+requires-python = ">=3.9"
+license = {text = "GPL-3.0+"}
 keywords = [
   "PyroLab", 
   "Pyro5", 
@@ -47,11 +47,11 @@ classifiers = [
   "Topic :: Scientific/Engineering",
   "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.7",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3 :: Only",
   "Operating System :: MacOS",
   "Operating System :: Microsoft :: Windows",
@@ -63,7 +63,7 @@ dependencies = [
   "numpy",
   "scipy",
   "Pyro5",
-  "pydantic",
+  "pydantic >= 1.9.1, < 2.0.0",
   "pyyaml",
   "deprecation",
   "typer",
@@ -81,10 +81,34 @@ dependencies = [
 [project.optional-dependencies]
 tsl550 = ["pyserial"]
 ppcl55x = ["pyserial"]
+# thorlabs = ["thorlabs_kinesis@git+https://github.com/BYUCamachoLab/thorlabs-kinesis"]
 rto = ["pyvisa", "pyvisa-py"]
 arduino = ["pyfirmata"]
-monitor = ["flask", "omegaconf", "waitress"]
+# adiscovery = ["WF_SDK@git+https://github.com/Digilent/WaveForms-SDK-Getting-Started-PY#egg=WF_SDK"]
+# monitor = ["pyromonitor@git+https://github.com/BYUCamachoLab/pyromonitor"]
 test = ["pytest", "coverage"]
+dev = [
+  "notebook",
+  "pytest",
+  "mypy",
+  "coverage",
+  "flake8 >= 4.0.1",
+  "isort >= 5.10.1",
+  "black >= 22.1.0",
+  "autopep8 >= 1.6.0",
+  "twine >= 4.0.0",
+  "build >= 0.10.0",
+  "pre-commit",
+  "bump2version ~= 1.0.1",
+]
+docs = [
+  "jupyter-book == 1.0.3",
+  "numpydoc==1.5.0",
+]
+
+[tool.setuptools.packages.find]
+include = ["pyrolab"]
+namespaces = false
 
 [project.urls]
 "Homepage" = "https://pyrolab.readthedocs.io/en/latest/"
@@ -95,11 +119,6 @@ test = ["pytest", "coverage"]
 
 [project.scripts]
 pyrolab = "pyrolab.cli:app"
-pyromonitor = "pyromonitor.cli:app"
-
-[tool.setuptools.packages.find]
-where = ["src"]
-include = ["pyrolab", "pyromonitor"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"

{PyroLab-0.3.1/src → pyrolab-0.4.0}/pyrolab/__init__.py

@@ -27,6 +27,12 @@ import os
 import pathlib
 import platform
 import sys
+import atexit
+import fileinput
+import re
+from typing import Callable, Iterable
+from time import strptime
+from pathlib import Path
 
 # Check if Python version is supported
 pyversion = sys.version_info
@@ -42,11 +48,11 @@ if pyversion < (3, 7, 0):
 __name__ = "PyroLab"
 __author__ = "CamachoLab"
 __copyright__ = "Copyright 2020, The PyroLab Project"
-__version__ = "0.3.1"
+__version__ = "0.4.0"
 __license__ = "GPLv3+"
 __maintainer__ = "Sequoia Ploeg"
 __maintainer_email__ = "sequoia.ploeg@byu.edu"
-__status__ = "Development" # "Production"
+__status__ = "Development"  # "Production"
 __project_url__ = "https://github.com/sequoiap/pyrolab"
 __forum_url__ = "https://github.com/sequoiap/pyrolab/issues"
 __website_url__ = "https://camacholab.byu.edu/"
@@ -66,6 +72,7 @@ if pyversion < (3, 9, 0):
     base_path = pathlib.Path(__file__).resolve().parent
 else:
     from importlib.resources import files
+
     base_path = files("pyrolab")
 base_path = base_path / "data" / "local"
 
@@ -78,6 +85,7 @@ NAMESERVER_STORAGE.mkdir(parents=True, exist_ok=True)
 
 PYROLAB_LOGDIR = PYROLAB_DATA_DIR / "logs"
 PYROLAB_LOGDIR.mkdir(parents=True, exist_ok=True)
+PYROLAB_MASTERLOG = PYROLAB_LOGDIR / "pyrolab.log"
 
 LOCKFILE = PYROLAB_DATA_DIR / "pyrolabd.lock"
 USER_CONFIG_FILE = PYROLAB_DATA_DIR / "user_configuration.yaml"
@@ -98,11 +106,14 @@ def get_loglevel() -> int:
     return loglevel
 
 
-if len(logging.root.handlers) == 0:    
+if len(logging.root.handlers) == 0:
     logfile = PYROLAB_LOGDIR / f"pyrolab_{os.getpid()}.log"
     root = logging.getLogger()
-    h = logging.handlers.RotatingFileHandler(logfile, 'a', 30000, 10)
-    f = logging.Formatter('[%(asctime)s.%(msecs)03d] %(process)-5s %(processName)-10s %(name)-12s %(levelname)-8s %(message)s', datefmt="%Y-%m-%d %H:%M:%S")
+    h = logging.handlers.RotatingFileHandler(logfile, "a", 30000, 10)
+    f = logging.Formatter(
+        "[%(asctime)s.%(msecs)03d] %(levelname)-8s %(process)-5s %(processName)-16s %(name)-20s %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
     h.setFormatter(f)
     root.addHandler(h)
     root.setLevel(get_loglevel())
@@ -124,10 +135,10 @@ try:
 
     url = "https://pypi.org/pypi/pyrolab/json"
     with requests.Session() as s:
-        s.mount('https://pypi.org', HTTPAdapter(max_retries=3))
+        s.mount("https://pypi.org", HTTPAdapter(max_retries=3))
         resp = s.get(url).text
 
-    v = json.loads(resp)['info']['version']
+    v = json.loads(resp)["info"]["version"]
     curver = parse(__version__)
     latest = parse(v)
 
@@ -139,3 +150,41 @@ try:
         log.info(message)
 except:
     pass
+
+
+def try_itr(func: Callable, itr: Iterable, *exceptions, **kwargs):
+    """
+    Tests a function on an iterable, yields iterable if no exception is raised.
+    """
+    for elem in itr:
+        try:
+            func(elem, **kwargs)
+            yield elem
+        except exceptions:
+            pass
+
+
+# @atexit.register
+# def condense_logs():
+#     """
+#     Cleans up the logfile directory every once in a while.
+
+#     Runs at exit or when "pyrolab down" is called. Condenses all process log
+#     files into a single logfile that is sorted by timestamp.
+#     """
+#     f_names = list(PYROLAB_LOGDIR.glob("*.*"))
+#     lines = list(fileinput.input(f_names))
+#     t_fmt = "%Y-%m-%d %H:%M:%S.%f"  # format of time stamps
+#     t_pat = re.compile(r"\[(.+?)\]")  # pattern to extract timestamp
+#     lines = list(
+#         try_itr(
+#             lambda l: strptime(t_pat.search(l).group(1), t_fmt), lines, AttributeError
+#         )
+#     )
+#     with PYROLAB_MASTERLOG.open(mode="w") as f:
+#         for l in sorted(lines, key=lambda l: strptime(t_pat.search(l).group(1), t_fmt)):
+#             f.write(l)
+#     if PYROLAB_MASTERLOG in f_names:
+#         f_names.remove(PYROLAB_MASTERLOG)
+#     for f in f_names:
+#         f.unlink()

{PyroLab-0.3.1/src → pyrolab-0.4.0}/pyrolab/api.py

@@ -14,11 +14,11 @@ from Pyro5.core import locate_ns
 from Pyro5.server import behavior, expose, oneway, serve
 from pyrolab import USER_CONFIG_FILE
 from pyrolab.configure import (
-    PyroLabConfiguration, 
-    NameServerConfiguration, 
-    DaemonConfiguration, 
-    ServiceConfiguration, 
-    reset_config, 
+    PyroLabConfiguration,
+    NameServerConfiguration,
+    DaemonConfiguration,
+    ServiceConfiguration,
+    reset_config,
     update_config,
 )
 from pyrolab.server import Daemon, LockableDaemon
@@ -47,7 +47,7 @@ __all__ = [
 ]
 
 # If a user config file exists, load the first listed nameserver by default,
-# so that locate_ns "just works." 
+# so that locate_ns "just works."
 if USER_CONFIG_FILE.exists():
     cfg = PyroLabConfiguration.from_file(USER_CONFIG_FILE)
     nscfg = next(iter(cfg.nameservers.values()))