Merge branch 'develop'

.gitignore

@@ -22,3 +22,6 @@ base/pybpod/dist/
 \.idea/
 
 \.vscode/
+
+.mypy_cache
+.pyre

CHANGELOG.rst

@@ -1,6 +1,31 @@
 
 Changelog
 =========
+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)
+    - Fixed several documentation related issues
+    - Updated documentation
+    - Add support to kill a task or skip all trials to run_state_machine
+- pybpod-gui-api (v1.8.0)
+    - Documentation fixes
+    - Add support to kill tasks
+- pybpod-gui-plugin (v1.8.0)
+    - Add support to kill tasks (updated Subject and Setup panels)
+    - Fixed bug where bpods that weren't connected were removed from the list when refreshed
+    - Fixed Task selection on setup panel being active while running a protocol
+    - Fixed issue#51 (Behaviour ports were being reset in every load)
+- pybpod-gui-plugin-emulator (v0.1.4)
+    - Add task kill button to UI
+    - Reordered the “Test Protocol IO” button in the UI
+- pybpod-gui-plugin-rotaryencoder (v0.1.4)
+    - Added support for enabling/disabling moduleOutputStream in the GUI
+- pybpod-gui-plugin-soundcard (v0.1.6)
+    - Added libusb backend support
+    - Increased timeout duration on read
+
 v1.7.8 (2019/06/03)
 -------------------
 - Fixed a problem with the setup requirements

README.md

@@ -1,64 +1,64 @@
 # PyBpod #
 
-**version:** 1.0.1
+**version:** 1.7.8
 
 PyBpod is a GUI application that enables interaction with the Bpod device from [Sanworks](https://sanworks.io/).
 
 This project is maintained by a team of SW developers at the Champalimaud Foundation.
 
-### Install PyBpod project ###
-
-1. Download & install [Anaconda](https://www.anaconda.com/download/) or [Miniconda](https://conda.io/miniconda.html) .
-2. Download the environment configuration file for your Operating System ( [Windows 10](https://bitbucket.org/fchampalimaud/pybpod/raw/e6c1c8da96c240ae638309359a97b28a2d36ca55/environment-windows-10.yml) ) and create a virtual environment with it by executing the following commands in the "Anaconda Prompt".
+## Install PyBpod ##
+1. Download & install [Anaconda](https://www.anaconda.com/download/) or [Miniconda](https://conda.io/miniconda.html) to your user.
+2. After the installation, open "Anaconda Prompt"
+3. Create a virtual environment for running PyBpod with Python 3.6
+```
+conda create -n pybpod-environment python=3.6
+```
+4. Activate the environment you just created
+```
+activate pybpod-environment
+```
+5. Install PyBpod through PyPI
 ```
-conda env create -f environment-windows-10.yml
+pip install pybpod
 ```
-**Notes:**
+6. Run the application.
+```
+start-pybpod
+```
+
+## Install PyBpod (for developers) ##
+
+1. Download & install [Anaconda](https://www.anaconda.com/download/) or [Miniconda](https://conda.io/miniconda.html) .
+
+**Note:**
 On windows if you install Anaconda/Miniconda for all the users, you should make sure you run the "Anaconda Prompt" as administrator.
 To avoid issues, make sure you install Anaconda/Miniconda only for your user.
 
+2. Create a virtual environment for running PyBpod with Python 3.6
+```
+conda create -n pybpod-environment python=3.6
+```
 3. Activate the environment you just created.
 ```
 activate pybpod-environment
 ```
-4. Clone the PyBpod repository.
+3. Clone the PyBpod repository.
 ```
-git clone https://UmSenhorQualquer@bitbucket.org/fchampalimaud/pybpod.git
+git clone https://github.com/pybpod/pybpod.git
 ```
 5. Access the created repository folder.
 ```
 cd pybpod
 ```
 6. Run the "install.py" script to install all necessary dependencies.
 ```
-python install.py
+python utils\install.py
 ```
 7. Run the PyBpod application.
 ```
-python -m pybpodgui_plugin
-```
-
-### Execute PyBpod GUI ###
-
-1. Open "Anaconda Prompt" and activate the "pybpod-environment".
-```
-activate pybpod-environment
-```
-2. Run the application.
+start-pybpod
 ```
-python -m pybpodgui_plugin
-```
-
-### Update PyBpod GUI ###
 
-1. Open the "Anaconda Prompt" and activate the "pybpod-environment".
-```
-activate pybpod-environment
-```
-2. Execute the script "update.py".
-```
-python update.py
-```
 
 #### Acknowledgments ####
 PyVmMonitor is being used to support the development of this open source software. For more information please see [PyVmMonitor's web site](http://pyvmmonitor.com)

base/pybpod/setup.py

@@ -1,42 +1,40 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
-import re, os
+import os
 from setuptools import setup
 
-with open(os.path.join('README.md'), 'r') as fd:
+with open(os.path.join("README.md"), "r") as fd:
     long_description = fd.read()
 
 setup(
-    name='pybpod',
-    version="1.7.8",
+    name="pybpod",
+    version="1.8.0",
     description="Pybpod is a behavioral experiments control system written in Python for Bpod",
-    author=['Ricardo Ribeiro', 'Luís Teixeira'],
-    author_email='ricardo.ribeiro@research.fchampalimaud.org, ricardojvr@gmail.com, micboucinha@gmail.com',
-    license='Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>',
-    url='https://pybpod.readthedocs.io',
+    author=["Ricardo Ribeiro", "Luís Teixeira"],
+    author_email="ricardo.ribeiro@research.fchampalimaud.org, ricardojvr@gmail.com, micboucinha@gmail.com",
+    license="MIT",
+    url="https://pybpod.readthedocs.io",
     include_package_data=True,
     packages=[],
-    long_description = long_description,
-    long_description_content_type = 'text/markdown',
-    install_requires = [
-        'pyforms-gui==4.901.2',
-        'pyforms_generic_editor==1.5.1',
-        'pybpod-api==1.6.4',
-        'pybpod-gui-api==1.2.2',
-        'pybpod-gui-plugin==1.6.2',
-        'pge-plugin-terminal==0.1',
-        'pybpod-gui-plugin-session-history==1.4.1',
-        'pybpod-gui-plugin-stmdiagram==1.0.0',
-        'pybpod-gui-plugin-timeline==1.0.1',
-        'pybpod-gui-plugin-trial-timeline==1.0.0',
-        'pybpod-gui-plugin-waveplayer==1.0',
-        'pybpod-gui-plugin-rotaryencoder==0.1.1',
-        'pybpod-gui-plugin-soundcard==0.1.5',
-        'pybpod-gui-plugin-emulator==0.1.3'
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    install_requires=[
+        "pyforms-gui==4.901.2",
+        "pyforms_generic_editor==1.5.1",
+        "pybpod-api==1.8.0",
+        "pybpod-gui-api==1.8.0",
+        "pybpod-gui-plugin==1.8.0",
+        "pge-plugin-terminal==0.1",
+        "pybpod-gui-plugin-session-history==1.4.2",
+        "pybpod-gui-plugin-stmdiagram==1.0.0",
+        "pybpod-gui-plugin-timeline==1.0.1",
+        "pybpod-gui-plugin-trial-timeline==1.0.0",
+        "pybpod-gui-plugin-waveplayer==1.0",
+        "pybpod-gui-plugin-rotaryencoder==0.1.4",
+        "pybpod-gui-plugin-soundcard==0.1.6",
+        "pybpod-gui-plugin-emulator==0.1.4",
     ],
     entry_points={
-        'console_scripts': [
-            'start-pybpod=pybpodgui_plugin.__main__:start',
-        ],
-    }
+        "console_scripts": ["start-pybpod=pybpodgui_plugin.__main__:start"],
+    },
 )

docs/environment.yml

@@ -11,5 +11,5 @@ dependencies:
     - sphinx-autobuild
     - sphinx-rtd-theme
     - pyqt5
-    - pyforms-gui
+    - pyforms-gui==4.901.2
     - pybpod

docs/source/about/about.rst

@@ -24,12 +24,12 @@ All examples and Bpod's state machine and communication logic were based on the
 
 License
 =======
-This is Open Source software. We use the `GNU General Public License version 3 <https://www.gnu.org/licenses/gpl.html>`_.
+This is Open Source software with a MIT license.
 
 Maintenance team
 ================
 
-The current and past members of the **pybpod-api** team.
+The current and past members of the **pybpod** team.
 
 * `@cajomferro <https://github.com/cajomferro/>`_ Carlos Mão de Ferro
 * `@JBauto <https://github.com/JBauto>`_ João Baúto
@@ -38,4 +38,4 @@ The current and past members of the **pybpod-api** team.
 
 Questions?
 ==========
-If you have any questions or want to report a problem with this library please fill a issue `here <https://bitbucket.org/fchampalimaud/pybpod-api/issues>`_.
+If you have any questions or want to report a problem with this library please fill a issue `here <https://github.com/pybpod/pybpod/issues>`_.

docs/source/conf.py

@@ -28,7 +28,7 @@
 copyright = '2018, Ricardo Ribeiro'
 author = 'Ricardo Ribeiro'
 
-version = release = '1.7.8'
+version = release = '1.8.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/developers/developing_plugins.rst

@@ -23,7 +23,7 @@ Session history plugin, an example
 
 This plugin allows you to display session data in a table view and you can order events by column.
 
-https://bitbucket.org/fchampalimaud/pybpod-gui-plugin-session-history
+https://github.com/pybpod/pybpod-gui-plugin-session-history
 
 .. image:: /_images/basic-usage/session_history.png
     :scale: 100 %

docs/source/getting-started/install.rst

@@ -54,19 +54,19 @@ ___________________________
 2. Download the environment configuration file for your Operating System and create a virtual environment with it by
 executing the following commands in the "Anaconda Prompt".
 
-   Windows 10: `environment-windows-10.yml <https://bitbucket.org/fchampalimaud/pybpod/raw/248b05a43c2d6059187fa33b609e425e0ef76026/utils/environment-windows-10.yml>`_ (right click->Save Link as):
+   Windows 10: `environment-windows-10.yml <https://raw.githubusercontent.com/pybpod/pybpod/master/utils/environment-windows-10.yml>`_ (right click->Save Link as):
 
    .. code::
 
       conda env create -f utils/environment-windows-10.yml
 
-   Ubuntu 17.10 and up: `environment-ubuntu-17.10.yml <https://bitbucket.org/fchampalimaud/pybpod/raw/248b05a43c2d6059187fa33b609e425e0ef76026/utils/environment-ubuntu-17.10.yml>`_ (right click->Save Link as):
+   Ubuntu 17.10 and up: `environment-ubuntu-17.10.yml <https://raw.githubusercontent.com/pybpod/pybpod/master/utils/environment-ubuntu-17.10.yml>`_ (right click->Save Link as):
 
    .. code::
 
       conda env create -f utils/environment-ubuntu-17.10.yml
 
-   Mac OSx: `environment-macOSx.yml <https://bitbucket.org/fchampalimaud/pybpod/raw/248b05a43c2d6059187fa33b609e425e0ef76026/utils/environment-macOSx.yml>`_ (right click->Save Link as):
+   Mac OSx: `environment-macOSx.yml <https://raw.githubusercontent.com/pybpod/pybpod/master/utils/environment-macOSx.yml>`_ (right click->Save Link as):
 
    .. code::
 
@@ -82,7 +82,7 @@ executing the following commands in the "Anaconda Prompt".
 
 .. code::
 
-  git clone https://bitbucket.org/fchampalimaud/pybpod.git
+  git clone https://github.com/pybpod/pybpod.git
   git submodule update --init
   
 5. Access the created repository folder.

docs/source/getting-started/plugins.rst

@@ -14,6 +14,38 @@ You can use plugins for:
 
 For detailed information on how to develop plugins please see :ref:`Developing PyBpod GUI plugins <developing_plugins-label>`.
 
+=================
+Available Plugins
+=================
+
+PyBpod has several plugins and modules for different purposes.
+The ones developed by our team are:
+
+* Session history (`GitHub <https://github.com/pybpod/pybpod-gui-plugin-session-history>`_)
+* Trial timeline (`GitHub <https://github.com/pybpod/pybpod-gui-plugin-trial-timeline>`_)
+* Wave player (`GitHub <https://github.com/pybpod/pybpod-gui-plugin-waveplayer>`_)
+* Alyx module (`GitHub <https://github.com/pybpod/pybpod-gui-plugin-alyx>`_)
+* Rotary encoder module (`Documentation <https://pybpod-api-rotary-encoder-module.readthedocs.io/>`_, `GitHub <https://github.com/pybpod/pybpod-gui-plugin-rotaryencoder>`_)
+* Harp Sound card module (`Documentation <https://pybpod-soundcard-module.readthedocs.io/>`_, `GitHub <https://github.com/pybpod/pybpod-gui-plugin-soundcard>`_)
+* Emulator module (`Documentation <https://pybpod-gui-plugin-emulator.readthedocs.io/>`_, `GitHub <https://github.com/pybpod/pybpod-gui-plugin-emulator>`_)
+
+More information can be found at the PyBpod's page in GitHub `here <https://github.com/pybpod>`_.
+
+Community made plugins
+----------------------
+
+There are also some plugins developed by the PyBpod's community.
+The following plugins were developed by the *de la Rocha* lab:
+
+* Water calibration (`BitBucket <https://bitbucket.org/delaRochaLab/water-calibration-plugin/>`_)
+* Graphics Trend plugin for 2FC tasks (`BitBucket <https://bitbucket.org/delaRochaLab/trend-2fc-plugin/src/master-3A/>`_)
+* Raster plot visualization of live or recorded sessions (`BitBucket <https://bitbucket.org/delaRochaLab/raster-plugin/>`_)
+* Sound calibration (`BitBucket <https://bitbucket.org/delaRochaLab/sound-calibration-plugin/src/master-3A/>`_)
+
+.. warning::
+    These plugins might not work with the latest PyBpod version. Please check their respective documentation to confirm for which PyBpod version they were developed.
+
+
 ======================
 How to install plugins
 ======================
@@ -48,7 +80,7 @@ Session history
 
 This plugin allows you to display session data in a table view and you can order events by column.
 
-https://bitbucket.org/fchampalimaud/pybpod-gui-plugin-session-history
+https://github.com/pybpod/pybpod-gui-plugin-session-history
 
 .. image:: /_images/basic-usage/session_history.png
     :scale: 100 %
@@ -59,7 +91,7 @@ Session timeline
 
 This plugin displays trial states in a bar plot.
 
-https://bitbucket.org/fchampalimaud/pybpod-gui-plugin-timeline
+https://github.com/pybpod/pybpod-gui-plugin-timeline
 
 .. image:: /_images/basic-usage/session_timeline.png
     :scale: 100 %

docs/source/index.rst

@@ -46,7 +46,7 @@ Python is one of the most popular programming languages today `[1] <https://pypl
 
 Questions?
 ==========
-If you have any questions or want to report a problem with this library please fill in an issue `here <https://bitbucket.org/fchampalimaud/pybpod-api/issues>`_.
+If you have any questions or want to report a problem with this library please fill in an issue `here <https://github.com/pybpod/pybpod/issues>`_.
 
 Contents
 ========
@@ -81,7 +81,8 @@ Contents
    :caption: API reference
 
    PyBpod API <https://pybpod-api.readthedocs.io/>
-
+   PyBpod GUI API <https://pybpod-gui-api.readthedocs.io/>
+
 .. toctree::
    :maxdepth: 4
    :includehidden: