Merge branch 'dev'

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 International Brain Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,26 +1,76 @@
-# PyBpod #
+# iblpybpod #
 
-**version:** 1.8.2a2
+**version:** 2.0.0
 
 iblpybpod is a GUI application that enables interaction with the Bpod device from [Sanworks](https://sanworks.io/). Much credit 
 and thanks go to the original creators of the [pybpod project](https://github.com/pybpod/pybpod).
 
-This project is has recently been adopted by the software development team at the International Brain Lab and is very much a 'work 
-in progress' at the moment.
+This project has recently been adopted by the software development team at the International Brain Lab to bring the code into 
+modernity.
 
-## Steps to install ##
+## Installation for use
+
+Currently, only Python v3.8 on Ubuntu 22.04 and Windows 10 is being tested.
+
+### Python venv commands for setup
+```bash
+python3.8 -m venv iblpybpod
+source iblpybpod/bin/activate
+python -m pip install --upgrade pip wheel
+python -m pip install iblpybpod
+start-pybpod
+```
+
+### Anaconda commands for setup
 ```bash
 conda create --name iblpybpod python=3.8
 conda activate iblpybpod
 pip install iblpybpod
 start-pybpod
 ```
 
-## Steps to setup development environment ##
+---
+
+## For developers
+This repository is adhering to the following conventions:
+* [semantic versioning](https://semver.org/) for consistent version numbering logic
+* [gitflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow) for managing branches 
+* [Flake8](https://flake8.pycqa.org/) for style guide enforcement 
+
+![](README_semver.png)
+![](README_gitflow_workflow.png)
+
+Please review these conventions to more easily contribute to the project.
+
+### New feature branches:
+- a `new_feature` branch is forked from the current `develop` branch
+- the `new_feature` branch is then merged back into the `develop` branch
+- the `new_feature` branch will eventually be deleted
+
+### Release candidate branches:
+- a release candidate, `rc` branch is a "pre-release" branch for beta testers on production rigs
+- the `rc` branch is forked from the `develop` branch
+- once the `rc` has been thoroughly tested, it will be merged into `master` and `develop`
+- the `rc` branch will eventually be deleted
+
+### Hotfix branches:
+- a `hotfix` or `maintenance` branch is forked from `master`
+- once the fix has been thoroughly tested, it will get merged back into `master` and `develop`
+- the `hotfix` branch will eventually be deleted
+
+### Python venv commands for setup
+```bash
+python3.8 -m venv iblpybpod-dev
+source iblpybpod-dev/bin/activate
+python -m pip install --upgrade pip wheel
+git clone https://github.com/int-brain-lab/iblpybpod
+python -m pip install --editable iblpybpod
+```
+
+### Anaconda commands for setup
 ```bash
 conda create --name iblpybpod-dev python=3.8
 conda activate iblpybpod-dev
 git clone https://github.com/int-brain-lab/iblpybpod
 pip install --editable iblpybpod
-start-pybpod
 ```

CHANGELOG.rst → release_notes.md

@@ -1,22 +1,28 @@
+# **Release Notes**
 
-Changelog
-=========
-v1.8.2 (2020/02/10)
--------------------
+## **v2.0.0 (2022-10-04)**
+- first IBL release
+- flattened git submodule structure to a single module
+- removed a multitude of abandoned packages
+- mogrified all png files
+- simplified logging
+- python v3.8 support
+- modern pandas python package support 
+- github actions automated pypi package publishing
+
+## v1.8.2 (2020/02/10)
 - pybpod-gui-plugin (v1.8.2)
     - Changed 'Skip all trials' button to 'Stop'
     - Changed 'Stop trial' button to 'Skip trial'
 - pybpod-gui-plugin-emulator (v0.1.5)
     - Update button names
 
-v1.8.1 (2019/12/09)
--------------------
+## v1.8.1 (2019/12/09)
 - pybpod-api (v1.8.1)
     - Fixed global_timer output actions for GlobalTimerTrig
     - Fixed default send_events value on set_global_timer to 1 (as expected in the Bpod firmware)
 
-v1.8.0 (2019/11/09)
--------------------
+## v1.8.0 (2019/11/09)
 - PyBpod's version number is now shared between the main packages of PyBpod
   (pybpod, pybpod-api, pybpod-gui-api and pybpod-gui-plugin).
 - pybpod-api (v1.8.0)
@@ -40,24 +46,20 @@ v1.8.0 (2019/11/09)
     - Added libusb backend support
     - Increased timeout duration on read
 
-v1.7.8 (2019/06/03)
--------------------
+## v1.7.8 (2019/06/03)
 - Fixed a problem with the setup requirements
 
-v1.7.7 (2019/06/03)
--------------------
+## v1.7.7 (2019/06/03)
 - Fixed a problem with pybpod-gui-plugin-waveplayer.
 
-v1.7.6 (2019/06/03)
--------------------
+## v1.7.6 (2019/06/03)
 - Requirements for PyBpod now point to specific package versions to ease upgrades
 - pybpod-api (updated to v1.6.4)
     - Fixed problem with bad indexing when accessing modules in _bpodcom_module_write
 - pybpod-gui-plugin-waveplayer (v1.0)
     - Corrected version number in the package and PyPi
 
-v1.7.5 (2019/05/15)
--------------------
+## v1.7.5 (2019/05/15)
 - pybpod-gui-plugin (updated to v1.6.2)
     - Fixed png that was creating a warning on PyBpod initialization
     - Now it points correctly to the master branch
@@ -73,16 +75,13 @@ v1.7.5 (2019/05/15)
 - pybpod-soundcard-module (v0.1.5)
     - Added bumpversion support to this module
 
-v1.7.4 (2019/05/08)
--------------------
+## v1.7.4 (2019/05/08)
 - The pybpodgui_plugin_session_history is now pointing to the master branch as it should (v1.4.1)
 
-v1.7.3 (2019/05/08)
--------------------
+## v1.7.3 (2019/05/08)
 - Fixed problem with wrong pybpod-alyx-module version (now it is v1.1)
 
-v1.7.2 (2019/05/03)
--------------------
+## v1.7.2 (2019/05/03)
 - Python base version changed to v3.6.6
 - Conda environment files are now more coherent between Windows and Linux
 - pybpod-api (updated to v1.6.3)

requirements.txt

@@ -4,11 +4,8 @@ confapp
 markdown2
 matplotlib
 numpy
-# ONE-api
-# opencv-python
 opencv-python==4.3.0.36  # locking down may just be necessary on dev box
 pandas
-# pydot
 PyOpenGL
 PyQt5
 PyQtWebEngine

setup.py

@@ -3,7 +3,7 @@
 
 from setuptools import setup, find_packages
 
-IBLPYBPOD_CURRENT_VERSION = "1.8.2a3"
+IBLPYBPOD_CURRENT_VERSION = "2.0.0"
 CURRENT_DIRECTORY = Path(__file__).parent
 CURRENT_PYTHON_VERSION = sys.version_info[:2]
 REQUIRED_PYTHON_VERSION = (3, 8)
@@ -26,7 +26,6 @@
 
 setup(
     name='iblpybpod',
-    # version=get_version(Path("iblpybpod").joinpath("__init__.py")),
     version=IBLPYBPOD_CURRENT_VERSION,
     python_requires='>={}.{}'.format(*REQUIRED_PYTHON_VERSION),
     description='IBL implementation of pybpod software',

tests/test_iblrig_params.py

@@ -1,5 +1,3 @@
-# Entry point for iblpybpod
-# /home/michele/Documents/repos/iblpybpod/src/pybpodgui_plugin/__main__.py
 import os
 import shutil
 from pathlib import Path
@@ -12,21 +10,17 @@ def create_setup(exp, setup_name: str, board: str, subj: object, task: str = Non
     # task name is defined as the experiment_name + '_' + setup_name
     # Create or get preexisting setup
     setup = exp.create_setup()
-
     setup.name = setup_name
     setup.task = task if isinstance(task, str) else exp.name + "_" + setup_name
     setup.board = board
     setup += subj
     setup.detached = True
-
     return setup
 
 
-def setup_iblpybpod_for_iblrig_params():
+def setup_iblpybpod_for_iblrig_params(iblrig_path: Path, iblrig_params_path: Path):
     # Set path vars
-    iblrig_path = Path("/home/michele/Documents/repos/iblrig")
     iblrig_tasks_path = iblrig_path / "tasks"
-    iblrig_params_path = Path("/home/michele/Documents/iblrig_params")  # IBLRIG_FOLDER.parent / "iblrig_params"
     iblrig_params_plugins_path = iblrig_params_path / "plugins"
     iblrig_params_project_path = iblrig_params_path / "IBL"
     iblrig_params_project_tasks_path = iblrig_params_project_path / "tasks"
@@ -80,7 +74,19 @@ def setup_iblpybpod_for_iblrig_params():
     # create ibl tasks
     task_names = [
         "_iblrig_calibration_screen",
-        "_iblrig_calibration_water"
+        "_iblrig_calibration_water",
+        "_iblrig_calibration_input_listner",
+        "_iblrig_calibration_frame2TTL",
+        "_iblrig_misc_flush_water",
+        "_iblrig_misc_bpod_ttl_test",
+        "_iblrig_misc_frame2TTL_freq_test",
+        "_iblrig_tasks_biasedChoiceWorld",
+        "_iblrig_tasks_habituationChoiceWorld",
+        "_iblrig_tasks_trainingChoiceWorld",
+        "_iblrig_tasks_ephysChoiceWorld",
+        "_iblrig_tasks_ephys_certification",
+        "_iblrig_tasks_passiveChoiceWorld",
+        "_iblrig_tasks_passiveChoiceWorldIndependent"
     ]
     for task_name in task_names:
         # create task
@@ -94,8 +100,6 @@ def setup_iblpybpod_for_iblrig_params():
         p.load(iblrig_params_project_path)
         task = p.find_task(task_name)
         task._commands = []
-        if task.name == "_iblrig_calibration_screen":
-            print("configuring task")
         p.save(str(iblrig_params_project_path))
 
     # create ibl experiments
@@ -169,6 +173,8 @@ def setup_iblpybpod_for_iblrig_params():
 
 
 if __name__ == "__main__":
-    setup_iblpybpod_for_iblrig_params()
-    os.chdir("/home/michele/Documents/iblrig_params/")
-    pybpod_start()
+    iblrig_path = Path.home() / "Documents" / "repos" / "iblrig"
+    iblrig_params_path = Path.home() / "Documents" / "iblrig_params"
+    setup_iblpybpod_for_iblrig_params(iblrig_path, iblrig_params_path)
+    os.chdir(iblrig_params_path)
+    pybpod_start()