starfeeder 0.3.4

Install

From a command prompt:

sudo apt-get install python3 python3-pip  # install Python with pip
python3 -m virtualenv /PATH/TO/MY/NEW/VIRTUALENV  # make a virtualenv
source /PATH/TO/MY/NEW/VIRTUALENV/bin/activate  # activate the virtualenv

pip install starfeeder  # install from PyPI

Run

/PATH/TO/MY/NEW/VIRTUALENV/bin/starfeeder

Install

1. You need to have Python 3.5 installed (which will come with pip, pyvenv, and sometimes virtualenv). Obtain it from https://www.python.org/ and install it. We’ll suppose you’ve installed Python at C:\Python35.

2. On Windows 10, install a copy of cmake, because PySide wants it. Also Qt. Also Git if you want to work with repositories directly. Possibly other things. (I have this working on Windows XP but not Windows 10; PySide is not building itself happily.)

3. Then fire up a Command Prompt and do:

   C:\Python34\Tools\Scripts\pyvenv.py C:\PATH\TO\MY\NEW\VIRTUALENV
   
   C:\PATH\TO\MY\NEW\VIRTUALENV\Scripts\activate
   
   pip install starfeeder

Run

Run the starfeeder program from within your virtual environment.

Windows: just the GUI

For normal use:

C:\PATH\TO\MY\NEW\VIRTUALENV\Scripts\pythonw.exe C:\PATH\TO\MY\NEW\VIRTUALENV\Scripts\starfeeder-script.py

Windows: to see command-line output

Use this for database upgrades, command-line help, and to see debugging output:

C:\PATH\TO\MY\NEW\VIRTUALENV\Scripts\starfeeder

You can append -v for more verbose output, or --help for full details.

If you use this method to run the graphical user interface (GUI) application, do not close the console window (this will close the GUI app).

v0.1.2 (2015-12-23)

• Initial release.

• Hardware tested via Windows XP, Windows 10, and Ubuntu 14.04.

v0.1.3 (2015-12-26)

• Ugly moveToThread() hack fixed by declaring QTimer(self) rather than QTimer().

• More general updates to declare parents of QObject objects, except in GUI code where it just clutters things up needlessly. Note that QLayout.addWidget(), QLayout.addLayout(), and QWidget.setLayout() all take ownership.

• Bugfix related to using lambdas as slots (PySide causes a segmentation fault on exit; https://bugreports.qt.io/browse/PYSIDE-88).

• Launch PDF manual as help.

• Retested with hardware on Windows XP and Linux.

v0.1.4 (2015-12-26)

• callback_id set by GUI, not by derived classes of SerialOwner

v0.1.5 (2016-02-27)

• bugfix to BaseWindow.on_rfid_state()

v0.2.0 (2016-04-07)

• GUI log window, for PyInstaller environments.

• Uses Whisker Python library.

• Switch to Arrow datetimes internally.

• Bugfix in error handling when trying to open non-existent serial ports.

v0.2.3 (2016-04-19)

v0.2.4 (2016-04-19)

• Bugfix.

v0.2.5

• Internal changes only?

v0.2.6 (2016-11-24)

• Python type hints.

• NOTE that to install Python 3.4 (required for this version of PySide) under Ubuntu 16.10, you need to: - download Python 3.4.4 source, then:

  $ tar xvf Python-3.4.4.tgz
  $ cd Python-3.4.4
  $ configure --enable-shared
  $ make
  $ sudo make install
  
      # now unbreak wrong symlink and replace with old:
  $ sudo rm /usr/bin/python3  # "make install" made this point to python3.4
  $ sudo ln -s /usr/bin/python3.5 /usr/bin/python3
  
      # now set up library links
  $ sudo ln -s /usr/local/lib/libpython3.4m.so.1.0 /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
  
      # this should now work:
  $ python3.4

• Upgraded from pyserial 3.0.1 to 3.2.1 … also allows the use of Linux pseudoterminals for testing; http://stackoverflow.com/questions/34831131

• Passwords obscured in debug-level database URLs.

• Top-level exception tracebacks go to log (like all others), not to print() using traceback.print_exc().

• BalanceController could send ‘ICRNone’, which is wrong; the frequency 10 Hz was offered in the dialogue, but should have been 12. Validity check added.

• Bug workaround:

  • PROBLEM

    • sometimes, WeightWhiskerTask.on_mass() received something that was not a MassEvent. Not sure why (it doesn’t look like anything else is ever sent); could this be a PySide signals bug?

  • ATTEMPT 1

    • Workaround is to verify type on receipt (and complain loudly if wrong but ignore/continue).

    • … no; irremediable bug in PySide (see development notes); it fails to keep references to signal parameters, so sometimes they go AWOL.

  • ATTEMPT 2

    • Switched from PySide to PyQt5, and thus GPLv3 licensing.

    • Generally, this seems much better.

    • Even then, apparent corruption in “bytes” object passed from

    SerialController.process_data()
    -> SerialController.line_received
    -> [change thread]
    -> RfidController.on_receive

    • Sometimes the received bytes object is b’’, not what was sent. PyQt does some sort of autoconversion to C++ objects; see http://pyqt.sourceforge.net/Docs/PyQt5/signals_slots.html ; and the problem appears to go away by using an encapsulating Python object… Not ideal! Does it also affect str? No, str seems OK. BUG REPRODUCED RELIABLY in pyqt5_signal_with_bytes.py. Reported to PyQt mailing list on 2016-12-01. SO FOR NOW: AVOID bytes OBJECTS IN PyQt5 SIGNALS.

v0.3.0 (2017-06-22 to 2017-06-25)

Bug fixes / performance improvements:

• Attempts to find/fix crash relating to very heavy multiple serial port use, likely relating to hardware serial overflow as devices are not properly buffered/flow-controlled.

• Changes to package structure so that it installs cleanly via “pip install starfeeder”, under Python 3.5 (PyQt5 not happy with Python 3.4, or at least its dependency “sip” isn’t).

• Extra-space-typo instant-crash bug fixed (introduced since 2.6!).

• Bugfix: SerialController.__init__(): wasn’t stashing self.output_encoding; not relevant in actual use as this value was only read by send_bytes(), which is in use only for debugging.

• Bugfix: mis-indexing of the RFID/balance display lines on the main GUI page. (Was only relevant when a device, e.g. RFID, is present and disabled.)

• Remove requirement for “twisted” in “whisker” package, so we can install without compilers under Windows.

• Pin all package version numbers exactly, for consistency. [Note pyserial now 3.3 (was 3.2.1).]

• Fixed a bug in Whisker package: things got stuck when trying to shut down, as the immediate socket was waiting for a reply with an EOL in it despite being closed (in WhiskerController.getline_immsock).

• Added two indexes on RfidEventRecord for speed.

• Moved to a single connection for the Task.

• Reduce database thrashing substantially by keeping RFID events in Python primarily, with checks there, and occasional flushes.

• Reworked balance reset code to make it more reliable.

• Trapped CTRL-C and CTRL-BREAK, so it’s safe to run from the command line.

New features:

• Tare balance via command from another Whisker client. Use “Tare BALANCE_NAME” as the client message; so, in full, send to Whisker “SendToClient CLIENTNUM Tare BALANCENAME” where CLIENTNUM is the client number of Starfeeder (or -1 if you’re very lazy and want to broadcast).

• Record perch duration. For this, “arrival” is a mass-lock event, and “departure” is a mass-unlock event. Two options: (a) separate table; (b) extend mass_event table. It’s a pretty clear choice to extend the mass_event table; half of the information is identical, and one would want arrival/departure in the same row to make it easy to calculate duration; arrival and departure times have an obligatory pairing in the way the balance operates. So we’ll add “unlocked_at”.

  • rename MassEvent.locked to MassEvent.locked_now

  • add MassEvent.unlocked_now

  • rework WeightWhiskerTask.on_mass

  • add MassEventRecord.unlocked_at

  Perch duration is then given by an SQL expression such as

  TIMEDIFF(mass_event.unlocked_at, mass_event.at)

  There’s a new Whisker broadcast event: BALANCE_UNLOCK_EVENT.

v0.3.2 (2017-08)

• updated for cardinal_pythonlib 1.0.0

• faulthandler added to debug segfaults

• removed “default=arrow.now” from MassEventRecord fields “at” and “unlocked_at”, and RfidEventRecord fields “first_detected_at”, “last_detected_at”, and “n_events”. These are mostly changes of no functional consequence, but MassEventRecord.unlocked_at may be relevant; we were getting occasional warnings of “Mass unlock event without a matching lock event” that might be relatd to unlocked_at being filled in inappropriately, which might have been triggered by flush_mass_records().

v0.3.4 (2017-09-07)

• make SQLAlchemy session use new “pool_pre_ping” feature, to avoid problems with MySQL timing out