Merge branch 'v1.5.0' into v1.4.0

pybpod · Nov 3, 2017 · c1e2011 · c1e2011
2 parents 10a5712 + b8850ab
commit c1e2011
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Showing 70 changed files with 977 additions and 1,214 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,9 +8,6 @@
 org.eclipse.core.resources.prefs
 
 # APP USER SETTINGS
-user_settings.py
-user_settings.*.py
-user_settings*.py
 pyforms_generic_editor_user_settings.py
 
 # PIP
@@ -43,4 +40,8 @@ uninstall-requirements-dev-*.txt
 **/*.propsfile
 
 # Node JS (for documentation)
-**/node_modules/*
+**/node_modules/*
+
+examples/BPOD-WORKSPACE/
+
+
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,13 @@
-## v.1.4.0.beta ()
-VERSION IN DEVELOPMENT
+## v.1.5.3
+Bpod modules functionalities are now configured dynamically
+
+## v.1.5.0
+Update session logs format file.
+Added ports enabled variable to the settings.
+Fixed some bugs.
+
+## v.1.4.0
+Added compatibility with the bpod firmware v17.
 
 ## v.1.3.0 (2017/06/21)
 Fixes Issue #9 - Cannot run several consecutive trials without a timer between them

diff --git a/docs/source/api_reference/pybpodapi/bpod_modules/index.rst b/docs/source/api_reference/pybpodapi/bpod_modules/index.rst
@@ -3,15 +3,18 @@
 **************************************
 
 .. module:: pybpodapi.bpod_modules
-   :synopsis: bpod modules
-
-|
-|
-
+   :synopsis: structure to manage the bpod modules
+
+structure to manage the bpod modules
 
 .. toctree::
    :titlesonly:
-
 
    bpod_module
    bpod_modules
+
+
+.. module:: pybpodapi.bpod_modules.modules
+   :synopsis: Implementation of specific modules
+
+
diff --git a/docs/source/api_reference/pybpodapi/event_occurrence.rst b/docs/source/api_reference/pybpodapi/event_occurrence.rst
diff --git a/docs/source/api_reference/pybpodapi/index.rst b/docs/source/api_reference/pybpodapi/index.rst
@@ -9,13 +9,8 @@
    :titlesonly:
 
    bpod/index
-   plugins/index
    bpod_modules/index
    exceptions/index
    state_machine/index
    session
-   event_occurrence
-   state_occurrences
-   trial
-   event_occurrence
-
+
diff --git a/docs/source/api_reference/pybpodapi/plugins/index.rst b/docs/source/api_reference/pybpodapi/plugins/index.rst
diff --git a/docs/source/api_reference/pybpodapi/plugins/session_data_csv_exporter.rst b/docs/source/api_reference/pybpodapi/plugins/session_data_csv_exporter.rst
diff --git a/docs/source/api_reference/pybpodapi/plugins/session_data_json_exporter.rst b/docs/source/api_reference/pybpodapi/plugins/session_data_json_exporter.rst
diff --git a/docs/source/api_reference/pybpodapi/state_machine/index.rst b/docs/source/api_reference/pybpodapi/state_machine/index.rst
@@ -13,7 +13,6 @@
    state_machine
    builder
    runner
-   raw_data
 
 Overview
 --------

diff --git a/docs/source/api_reference/pybpodapi/state_machine/raw_data.rst b/docs/source/api_reference/pybpodapi/state_machine/raw_data.rst
diff --git a/docs/source/api_reference/pybpodapi/state_machine/state_machine.rst b/docs/source/api_reference/pybpodapi/state_machine/state_machine.rst
@@ -12,10 +12,6 @@ Implementation
     :members:
     :private-members:
 
-.. automodule:: pybpodapi.state_machine.raw_data
-    :members:
-    :private-members:
-
 .. automodule:: pybpodapi.state_machine.global_counters
     :members:
     :private-members:

diff --git a/docs/source/api_reference/pybpodapi/state_occurrences.rst b/docs/source/api_reference/pybpodapi/state_occurrences.rst
diff --git a/docs/source/api_reference/pybpodapi/trial.rst b/docs/source/api_reference/pybpodapi/trial.rst
diff --git a/docs/source/getting_started/exporting.rst b/docs/source/getting_started/exporting.rst
diff --git a/docs/source/getting_started/installing.rst b/docs/source/getting_started/installing.rst
@@ -37,4 +37,35 @@ On the project root folder (where *'setup.py'* is located) run the following com
 ::
 
     pip3 install -r requirements.txt --upgrade # installs dependencies
-    pip3 install . # installs this API
+    pip3 install . --upgrade # installs this API
+
+
+Settings file
+=============
+
+::
+
+	# list of python libraries to interfaces bpod modules. 
+	PYBPOD_API_MODULES = [
+		'pybpod_rotaryencoder_module'
+	]
+
+	# folder where the bpod output files are be saved
+	WORKSPACE_PATH 	= 'BPOD-WORKSPACE'
+
+	# name of the session file
+	PROTOCOL_NAME	= now()  
+
+	# serial port settings
+	BAUDRATE 		= 1312500
+	SYNC_CHANNEL	= 255
+	SYNC_MODE		= 1
+	SERIAL_PORT = '/dev/ttyACM0'
+
+	# enable or disable bpod ports
+	BPOD_BNC_PORTS_ENABLED 		= [True, True]
+	BPOD_WIRED_PORTS_ENABLED 	= [True, True]
+	BPOD_BEHAVIOR_PORTS_ENABLED	= [True, True, True, True, True, True, True, True]
+
+
+
diff --git a/docs/source/getting_started/running.rst b/docs/source/getting_started/running.rst
@@ -13,7 +13,7 @@ Running examples
 Configure settings
 ==================
 
-In order to run protocols you need to specify bpod serial port on the file *'examples/user_settings.py'*.
+In order to run protocols you need to specify bpod *'user_settings.py'* file that should be located at the execution directory.
 
 Example of  *'examples/user_settings.py'*  file:
 
@@ -24,7 +24,10 @@ Example of  *'examples/user_settings.py'*  file:
 	PYBPOD_API_LOG_LEVEL = None
 	
 	WORKSPACE_PATH  = 'BPOD-WORKSPACE'
-	PROTOCOL_NAME   = 'PROTOCOL-NAME'
+
+	# if you do not define the next variable, the PROTOCOL_NAME 
+	# will assume the current datetime value.
+	PROTOCOL_NAME   = 'PROTOCOL-NAME' 
 
 	SERIAL_PORT   = '/dev/ttyACM0'
 

diff --git a/docs/source/getting_started/writing_protocols.rst b/docs/source/getting_started/writing_protocols.rst
@@ -40,7 +40,7 @@ Initialize Bpod and provide serial connection.
 
 	my_bpod = Bpod(serial_port='/dev/ttyACM0')
 
-Instead of hard coding the serial port in your script you can configure it using the **user_settings.py** file.
+Instead of hard coding the serial port in your scripts you can configure it using the **user_settings.py** file.
 
 Create the files \_\_init\_\_.py and user_settings.py in the running directory (check the examples folder on pybpod source code).
 Now you can instantiate Bpod() without having to pass the serial port as parameter.
@@ -132,7 +132,7 @@ On run completion, we can print the data available for the current trial includi
 
 		my_bpod.run_state_machine(sma)  # Run state machine
 
-		print("Current trial info: ", my_bpod.session.current_trial())
+		print("Current trial info: ", my_bpod.session.current_trial)
 
 
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -57,7 +57,6 @@ If you have any questions or want to report a problem with this library please f
    getting_started/installing
    getting_started/running
    getting_started/writing_protocols
-   getting_started/exporting
    getting_started/manual_interaction
    getting_started/firmware_update
    getting_started/output_action_codes

diff --git a/examples/function_examples/add_trial_events.py b/examples/function_examples/add_trial_events.py
@@ -72,7 +72,7 @@
 
 	my_bpod.run_state_machine(sma)  # Run state machine
 
-	print("Current trial info: {0}".format(my_bpod.session.current_trial()))
+	print("Current trial info: {0}".format(my_bpod.session.current_trial))
 
 my_bpod.stop()  # Disconnect Bpod
 
diff --git a/examples/function_examples/add_trial_events2.py b/examples/function_examples/add_trial_events2.py
@@ -99,6 +99,6 @@
 
 	my_bpod.run_state_machine(sma)  # Run state machine
 
-	print("Current trial info: {0}".format(my_bpod.session.current_trial()))
+	print("Current trial info: {0}".format(my_bpod.session.current_trial))
 
 my_bpod.stop()  # Disconnect Bpod
diff --git a/examples/function_examples/test_soft_codes.py b/examples/function_examples/test_soft_codes.py
@@ -85,7 +85,7 @@ def my_softcode_handler(data):
 
 	my_bpod.run_state_machine(sma)  # Run state machine
 
-	print("Current trial info: {0}".format(my_bpod.session.current_trial()))
+	print("Current trial info: {0}".format(my_bpod.session.current_trial))
 
 my_bpod.stop()  # Disconnect Bpod