4 add a jsonyaml config loader to specify port channels and params

.bumpversion.cfg

@@ -0,0 +1,32 @@
+[bumpversion]
+current_version = 0.0.2.dev0
+commit = True
+tag = True
+tag_name = {new_version}
+sign_tags = False
+message = "Upgrade: {current_version} → {new_version}"
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<build>\d+))?
+serialize =
+	{major}.{minor}.{patch}.{release}{build}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = rc
+first_value = dev
+values =
+	dev
+	rc
+
+[bumpversion:part:build]
+
+[bumpversion:file:setup.cfg]
+search = version = {current_version}
+replace = version = {new_version}
+
+[bumpversion:file:README.md]
+search = Version: "{current_version}"
+replace = Version: "{new_version}"
+
+[bumpversion:file:pypulsepal/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"

.pre-commit-config.yaml

@@ -11,9 +11,9 @@ repos:
     rev: v2.3.0
     hooks:
     - id: end-of-file-fixer
-      exclude: 'setup.cfg'
+      exclude: '.bumpversion.cfg'
     - id: trailing-whitespace
-      exclude: 'setup.cfg'
+      exclude: '.bumpversion.cfg'
     - id: check-case-conflict
     - id: check-merge-conflict
     - id: check-yaml

CONTRIBUTING.md

@@ -0,0 +1,7 @@
+## Contributing
+
+Contributions are absolutely encouraged, for bug fixes, new features, etc.
+
+If you are not sure where to start, check out the [issues](https://github.com/larsrollik/pypulsepal/issues).
+
+Please get in touch via [email](mailto:L.B.Rollik@protonmail.com) for other queries.

LICENSE

@@ -408,7 +408,7 @@ the above requirements apply either way.
 
   You may not propagate or modify a covered work except as expressly
 provided under this License.  Any attempt otherwise to propagate or
-modify it is void, and will automatically terminate your rights under
+modify it is void, and will automatically terminate_remote your rights under
 this License (including any patent licenses granted under the third
 paragraph of section 11).
 
@@ -426,7 +426,7 @@ received notice of violation of this License (for any work) from that
 copyright holder, and you cure the violation prior to 30 days after
 your receipt of the notice.
 
-  Termination of your rights under this section does not terminate the
+  Termination of your rights under this section does not terminate_remote the
 licenses of parties who have received copies or rights from you under
 this License.  If your rights have been terminated and not permanently
 reinstated, you do not qualify to receive new licenses for the same

README.md

@@ -1,15 +1,29 @@
+[//]: # (links)
+[Pulsepal]: https://github.com/sanworks/PulsePal
+[PyBpod]: https://github.com/pybpod/pybpod
+[PyBpod com ArCOM]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/arcom.py
+[PyBpod com protocol]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/bpod/bpod_com_protocol.py
+[PyBpod message headers]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/protocol/send_msg_headers.py
+[PulsePal Python 3 API]: https://github.com/sanworks/PulsePal/blob/develop/Python/Python3/PulsePal.py
+[PulsePal .ino file]: https://github.com/sanworks/PulsePal/blob/develop/Firmware/PulsePal_2_0_1/PulsePal_2_0_1.ino
+[PulsePal param definitions]: https://sites.google.com/site/pulsepalwiki/matlab-gnu-octave/functions/programpulsepalparam
+[PulsePal USB v2 opcode list]: https://sites.google.com/site/pulsepalwiki/usb-serial-interface/usb-interface-v2-x
+
+[//]: # (badges)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6379627.svg)](https://doi.org/10.5281/zenodo.6379627)
 [![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fgithub.com/larsrollik/pypulsepal)](https://github.com/larsrollik/pypulsepal)
 [![PyPI](https://img.shields.io/pypi/v/pypulsepal.svg)](https://pypi.org/project/pypulsepal)
 [![Wheel](https://img.shields.io/pypi/wheel/pypulsepal.svg)](https://pypi.org/project/pypulsepal)
+[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://github.com/larsrollik/pypulsepal/blob/main/CONTRIBUTING.md)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 
 
 # PyPulsePal
 Python API for the PulsePal open-source pulse train generator
 ---
 This package provides an API to the [PulsePal] hardware.
-This API is a re-implementation of the original [PulsePal Python 3 API] that draws from the `pybpod-api` communication protoool.
+It is an alternative implementation of the original [PulsePal Python 3 API]
+and draws from the [PyBpod com ArCOM] communication classes.
 
 ## Example usage
 
@@ -143,13 +157,5 @@ For changes from the original implementation, see the git history since [commit
   - to make overwrites on channels to get from value-based logic to channel parameter sets
   - add write function to save all settings to json for documentation
 
-[//]: # (links)
-[Pulsepal]: https://github.com/sanworks/PulsePal
-[PyBpod]: https://github.com/pybpod/pybpod
-[PyBpod com ArCOM]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/arcom.py
-[PyBpod com protocol]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/bpod/bpod_com_protocol.py
-[PyBpod message headers]: https://github.com/pybpod/pybpod-api/blob/master/pybpodapi/com/protocol/send_msg_headers.py
-[PulsePal Python 3 API]: https://github.com/sanworks/PulsePal/blob/develop/Python/Python3/PulsePal.py
-[PulsePal .ino file]: https://github.com/sanworks/PulsePal/blob/develop/Firmware/PulsePal_2_0_1/PulsePal_2_0_1.ino
-[PulsePal param definitions]: https://sites.google.com/site/pulsepalwiki/matlab-gnu-octave/functions/programpulsepalparam
-[PulsePal USB v2 opcode list]: https://sites.google.com/site/pulsepalwiki/usb-serial-interface/usb-interface-v2-x
+---
+Version: "0.0.2.dev0"

examples/config_handler.py

@@ -0,0 +1,26 @@
+from pathlib import Path
+
+from configobj import ConfigObj
+from validate import Validator
+
+
+def run_example(
+    config_path="pypulsepal.config.test",
+    config_spec_path="pypulsepal.config.spec",
+):
+    config = ConfigObj(
+        infile=str(config_path),
+        configspec=str(config_spec_path),
+        unrepr=True,
+        list_values=True,
+    )
+    v = Validator()
+    validation_success = config.validate(v, copy=True)
+    print(config.dict(), validation_success)
+
+    c2 = ConfigObj(configspec=config_spec_path)
+    c2.validate(Validator(), copy=True)
+
+
+if __name__ == "__main__":
+    run_example()

examples/pypulsepal.config.spec

@@ -0,0 +1,42 @@
+serial_port = string(default="")
+baudrate = integer(default=115200)
+cycle_frequency = integer(default=20000)
+nr_output_channels = integer(default=4)
+nr_trigger_channels = integer(default=2)
+firmware_opcode = integer(default=213)
+
+# https://sites.google.com/site/pulsepalwiki/matlab-gnu-octave/functions/programpulsepalparam
+
+custom_pulse_train_1 = float_list(default=list())
+custom_pulse_train_2 = float_list(default=list())
+
+[channels]
+    [[ __many__]]
+        # channel ID
+        channel = integer(default=0, min=0, max=3)
+
+        # channel params
+        isBiphasic = boolean(default=False)
+        phase1Voltage = float(default=5, min=-10, max=10)
+        phase2Voltage = float(default=-5, min=-10, max=10)
+
+        phase1Duration = float(default=0.001, min=0.001, max=3600)
+        interPhaseInterval = float(default=0.001)
+        phase2Duration = float(default=0.001)
+        interPulseInterval = float(default=0.01)
+        burstDuration = float(default=0)
+
+        interBurstInterval = float(default=0)
+        pulseTrainDuration = float(default=1)
+        pulseTrainDelay = float(default=0)
+
+        linkTriggerChannel1 = integer(default=1, min=0, max=1)
+        linkTriggerChannel2 = integer(default=0, min=0, max=1)
+        customTrainID = integer(default=0, min=0, max=2)
+        customTrainTarget = integer(default=0, min=0, max=1)
+        restingVoltage = integer(default=0, min=-10, max=10)
+
+
+[triggers]
+    [[__many__]]
+        triggerMode = integer(default=0, min=0, max=2)

examples/pypulsepal.config.test

@@ -0,0 +1,9 @@
+nr_trigger_channels = 14
+
+[channels]
+    [[0]]
+        isBiphasic = True
+        phase1Voltage = 6
+
+    [[1]]
+        phase1Voltage = 4

examples/run_ppp_with_config.py

@@ -0,0 +1,17 @@
+from pathlib import Path
+
+from pypulsepal import PulsePal
+
+
+def run_example():
+    config_path = "pypulsepal.config.test"
+    serial_port = "/dev/ttyACM0"
+
+    p = PulsePal(serial_port=serial_port)
+    p.load_from_config(config_path=config_path)
+
+    print(p)
+
+
+if __name__ == "__main__":
+    run_example()

.toml → pyproject.toml

@@ -18,3 +18,7 @@ exclude = '''
   | dist
 )/
 '''
+
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"

pypulsepal/__init__.py

@@ -2,3 +2,9 @@
 __version__ = "0.0.2.dev0"
 
 from pypulsepal.pulsepal import PulsePal
+
+
+def run():
+    raise NotImplementedError(
+        "placeholder for commandline interface to program from given config file"
+    )