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2 changes: 1 addition & 1 deletion CITATION.cff
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Expand Up @@ -17,7 +17,7 @@ doi: "10.1101/807693"
keywords:
license: "MPL-2.0"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/wehr-lab/autopilot"
repository-code: "https://github.com/auto-pi-lot/autopilot"
title: "Autopilot: Automating behavioral experiments with lots of Raspberry Pis"
version: "0.4.4"
...
22 changes: 11 additions & 11 deletions README.md
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Status:

[![Documentation Status](https://readthedocs.org/projects/auto-pi-lot/badge/?version=latest)](https://docs.auto-pi-lot.com/en/latest/?badge=latest)
[![Travis (.com) branch](https://img.shields.io/travis/com/wehr-lab/autopilot/main)](https://app.travis-ci.com/github/wehr-lab/autopilot/branches)
[![Coveralls branch](https://img.shields.io/coveralls/github/wehr-lab/autopilot/main)](https://coveralls.io/github/wehr-lab/autopilot)
[![Travis (.com) branch](https://img.shields.io/travis/com/auto-pi-lot/autopilot/main)](https://app.travis-ci.com/github/auto-pi-lot/autopilot/branches)
[![Coveralls branch](https://img.shields.io/coveralls/github/auto-pi-lot/autopilot/main)](https://coveralls.io/github/auto-pi-lot/autopilot)
![Jonny Status](https://img.shields.io/badge/jonny-dissertating-critical)


Expand All @@ -19,9 +19,9 @@ Status:

![Autopilot Banner Logo](docs/_images/autopilot_logo_banner.png)

| [Docs](https://docs.auto-pi-lot.com) | [Paper](https://www.biorxiv.org/content/10.1101/807693v1) | [Forum](https://github.com/wehr-lab/autopilot/discussions) | [Wiki](https://wiki.auto-pi-lot.com) |
| [Docs](https://docs.auto-pi-lot.com) | [Paper](https://www.biorxiv.org/content/10.1101/807693v1) | [Forum](https://github.com/auto-pi-lot/autopilot/discussions) | [Wiki](https://wiki.auto-pi-lot.com) |
| :-: | :-: | :-: | :-: |
| [![Read the Docs](docs/_images/docs_link.png)](https://docs.auto-pi-lot.com) | [![Paper](docs/_images/paper_link.png)](https://www.biorxiv.org/content/10.1101/807693v1) | [![Forum](docs/_images/discussion_link.png)](https://github.com/wehr-lab/autopilot/discussions) | [![Wiki](docs/_images/hardware_link.png)](https://wiki.auto-pi-lot.com)
| [![Read the Docs](docs/_images/docs_link.png)](https://docs.auto-pi-lot.com) | [![Paper](docs/_images/paper_link.png)](https://www.biorxiv.org/content/10.1101/807693v1) | [![Forum](docs/_images/discussion_link.png)](https://github.com/auto-pi-lot/autopilot/discussions) | [![Wiki](docs/_images/hardware_link.png)](https://wiki.auto-pi-lot.com)

Autopilot is a Python framework for performing complex, hardware-intensive behavioral experiments with swarms of networked Raspberry Pis.
As a tool, it provides researchers with a toolkit of flexible modules to design experiments without rigid programming & API limitations.
Expand Down Expand Up @@ -91,7 +91,7 @@ python3 -m autopilot.setup.setup
![Autopilot Setup Console](docs/_images/installer.png)

All of Autopilot is quite new, so bugs, incomplete documentation, missing features are very much expected! Don't be shy about
[raising issues](https://github.com/wehr-lab/autopilot/issues) or [asking questions in the forum](https://github.com/wehr-lab/autopilot/discussions).
[raising issues](https://github.com/auto-pi-lot/autopilot/issues) or [asking questions in the forum](https://github.com/auto-pi-lot/autopilot/discussions).


# Development Status
Expand All @@ -102,17 +102,17 @@ Jonny is trying to graduate! Autopilot will be slow and maybe a little chaotic u

We're working on a formal contribution system, pardon the mess! Until we get that and our CI coverage up, `main` will lag a bit behind the development branches:

* [`dev`](https://github.com/wehr-lab/autopilot/tree/dev) - main development branch that collects hotfixes, PRs, etc. Unstable but usually has lots of extra goodies
* [`hotfix`](https://github.com/wehr-lab/autopilot/tree/hotfix) - branches from `dev` for building and testing hotfixes, PRs back to `dev`.
* [`lab`](https://github.com/wehr-lab/autopilot/tree/lab) - branches from `dev` but doesn't necessarily PR back, the local branch used in the maintaining ([Wehr](http://uoneuro.uoregon.edu/wehr/)) lab
* [`parallax`](https://github.com/wehr-lab/autopilot/tree/parallax) - experimental departure from `dev` to implement a particular experiment and rebuild a lot of components along the way, will eventually return to `dev` <3
* [`dev`](https://github.com/auto-pi-lot/autopilot/tree/dev) - main development branch that collects hotfixes, PRs, etc. Unstable but usually has lots of extra goodies
* [`hotfix`](https://github.com/auto-pi-lot/autopilot/tree/hotfix) - branches from `dev` for building and testing hotfixes, PRs back to `dev`.
* [`lab`](https://github.com/auto-pi-lot/autopilot/tree/lab) - branches from `dev` but doesn't necessarily PR back, the local branch used in the maintaining ([Wehr](http://uoneuro.uoregon.edu/wehr/)) lab
* [`parallax`](https://github.com/auto-pi-lot/autopilot/tree/parallax) - experimental departure from `dev` to implement a particular experiment and rebuild a lot of components along the way, will eventually return to `dev` <3

## Short-Term

See the short-term development goals in our version milestones:

* [`v0.4.0`](https://github.com/wehr-lab/autopilot/milestone/1) - Implement registries to separate user code extensions like tasks and local hardware devices in a user directory, preserve source code in produced data so local development isn't lost.
* [`v0.5.0`](https://github.com/wehr-lab/autopilot/milestone/2) - Make a unitary inheritance structure from a root Autopilot object such that a) common operations like logging and networking are implemented only once, b) the plugin system for `v0.4.0` can not only add new objects, but replace core objects while maintaining provenance (ie. no monkey patching needed), c) object behavior that requires coordination across multiple instances gets much easier, making some magical things like self-healing self-discovering networking possible. This will also include a major refactoring of the code structure, finally breaking up some of the truly monstrous thousand-line modules in `core` into an actually modular system we can build from <3
* [`v0.4.0`](https://github.com/auto-pi-lot/autopilot/milestone/1) - Implement registries to separate user code extensions like tasks and local hardware devices in a user directory, preserve source code in produced data so local development isn't lost.
* [`v0.5.0`](https://github.com/auto-pi-lot/autopilot/milestone/2) - Make a unitary inheritance structure from a root Autopilot object such that a) common operations like logging and networking are implemented only once, b) the plugin system for `v0.4.0` can not only add new objects, but replace core objects while maintaining provenance (ie. no monkey patching needed), c) object behavior that requires coordination across multiple instances gets much easier, making some magical things like self-healing self-discovering networking possible. This will also include a major refactoring of the code structure, finally breaking up some of the truly monstrous thousand-line modules in `core` into an actually modular system we can build from <3

## Long-Term

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Changelog
*********

For full details, see commit logs and issues at http://github.com/wehr-lab/autpilot
For full details, see commit logs and issues at http://github.com/auto-pi-lot/autpilot

Version 0.4
-----------
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Expand Up @@ -18,29 +18,29 @@ v0.3.4 (December 13, 2020)

Improvements
~~~~~~~~~~~~
* Unify the creation of loggers!!!! See the docs ;) :mod:`autopilot.core.loggers` : https://github.com/wehr-lab/autopilot/pull/52/commits/d55638f985ab38044fc95ffeff5945021c2e198e https://github.com/wehr-lab/autopilot/issues/38
* Unify prefs, including sensible defaults, refactoring of scripts into a reasonable format, multiprocess-safety, and just generally a big weight off my mind. Note that this is a **breaking change** to the way prefs are accessed. Previously one would do `prefs.PREF_NAME`, but that made it very difficult to provide default values or handle missing prefs. the new syntax is `prefs.get('PREF_NAME')` which returns defaults with a warning and `None` if the pref is not set: https://github.com/wehr-lab/autopilot/pull/52/commits/c40a212bcaf5f184f2a6a606027fe15b1b4df59c https://github.com/wehr-lab/autopilot/issues/38
* Unify the creation of loggers!!!! See the docs ;) :mod:`autopilot.core.loggers` : https://github.com/auto-pi-lot/autopilot/pull/52/commits/d55638f985ab38044fc95ffeff5945021c2e198e https://github.com/auto-pi-lot/autopilot/issues/38
* Unify prefs, including sensible defaults, refactoring of scripts into a reasonable format, multiprocess-safety, and just generally a big weight off my mind. Note that this is a **breaking change** to the way prefs are accessed. Previously one would do `prefs.PREF_NAME`, but that made it very difficult to provide default values or handle missing prefs. the new syntax is `prefs.get('PREF_NAME')` which returns defaults with a warning and `None` if the pref is not set: https://github.com/auto-pi-lot/autopilot/pull/52/commits/c40a212bcaf5f184f2a6a606027fe15b1b4df59c https://github.com/auto-pi-lot/autopilot/issues/38
* completely clean up scripts, and together that opened the path to clean up setup as well. so all things configuration got a major promotion
* We're on the board with CI and automated testing with a positively massive 3% code coverage!!! https://github.com/wehr-lab/autopilot/pull/52/commits/743bb8fe67a69fcc556fa76e81f72f97f510dff7
* new scripts to eg. create autopilot alias: https://github.com/wehr-lab/autopilot/pull/52/commits/211919b05922e18a85d8ef6216973f4000fd32c5
* We're on the board with CI and automated testing with a positively massive 3% code coverage!!! https://github.com/auto-pi-lot/autopilot/pull/52/commits/743bb8fe67a69fcc556fa76e81f72f97f510dff7
* new scripts to eg. create autopilot alias: https://github.com/auto-pi-lot/autopilot/pull/52/commits/211919b05922e18a85d8ef6216973f4000fd32c5

Bugfixes
~~~~~~~~~
* cleanup scripts on object deletion: https://github.com/wehr-lab/autopilot/pull/52/commits/e8218304bd7ef2e13d2adfc236f3e781abea5f78 https://github.com/wehr-lab/autopilot/issues/41
* don't drop 'floats' from gui when we say we can use them...: https://github.com/wehr-lab/autopilot/pull/52/commits/743bb8fe67a69fcc556fa76e81f72f97f510dff7
* pigpio scripts dont like floats: https://github.com/wehr-lab/autopilot/pull/52/commits/9f939cd78a5296db3bf318115bee0213bcd1afc0
* cleanup scripts on object deletion: https://github.com/auto-pi-lot/autopilot/pull/52/commits/e8218304bd7ef2e13d2adfc236f3e781abea5f78 https://github.com/auto-pi-lot/autopilot/issues/41
* don't drop 'floats' from gui when we say we can use them...: https://github.com/auto-pi-lot/autopilot/pull/52/commits/743bb8fe67a69fcc556fa76e81f72f97f510dff7
* pigpio scripts dont like floats: https://github.com/auto-pi-lot/autopilot/pull/52/commits/9f939cd78a5296db3bf318115bee0213bcd1afc0

Docs
~~~~
* Clarification of supported systems: https://github.com/wehr-lab/autopilot/pull/52/commits/ce0ddf78b7f59f5487fec2ca7e8fb3c0ad162051
* Solved an ancient sphinx riddle of how to get data objects/constants to pretty-print: https://github.com/wehr-lab/autopilot/pull/52/commits/ec6d5a75dada05688b6bd3c1a53b3d9e5923870f
* Clarify hardware prefs https://github.com/wehr-lab/autopilot/pull/52/commits/f3a7609995c84848004891a0f41c7847cb754aae
* what numbering system do we use: https://github.com/wehr-lab/autopilot/pull/52/commits/64267249d7b1ec1040b522308cd60f928f2b2ee6
* Clarification of supported systems: https://github.com/auto-pi-lot/autopilot/pull/52/commits/ce0ddf78b7f59f5487fec2ca7e8fb3c0ad162051
* Solved an ancient sphinx riddle of how to get data objects/constants to pretty-print: https://github.com/auto-pi-lot/autopilot/pull/52/commits/ec6d5a75dada05688b6bd3c1a53b3d9e5923870f
* Clarify hardware prefs https://github.com/auto-pi-lot/autopilot/pull/52/commits/f3a7609995c84848004891a0f41c7847cb754aae
* what numbering system do we use: https://github.com/auto-pi-lot/autopilot/pull/52/commits/64267249d7b1ec1040b522308cd60f928f2b2ee6

Logging
~~~~~~~
* catch pigpio script init exception: https://github.com/wehr-lab/autopilot/pull/52/commits/3743f8abde7bbd3ed7766bdd75aee52afedf47e2
* more of it idk https://github.com/wehr-lab/autopilot/pull/52/commits/b682d088dbad0f206c3630543e96a5a00ceabe25
* catch pigpio script init exception: https://github.com/auto-pi-lot/autopilot/pull/52/commits/3743f8abde7bbd3ed7766bdd75aee52afedf47e2
* more of it idk https://github.com/auto-pi-lot/autopilot/pull/52/commits/b682d088dbad0f206c3630543e96a5a00ceabe25


v0.3.3 (October 25, 2020)
Expand All @@ -64,7 +64,7 @@ Improvements
* Better internal handling of pigpiod -- you're now able to import and use hardware modules without needing to explicitly start pigpiod!!
* Hopefully better killing of processes on exit, though still should work into unified process manager so don't need to reimplement everything (eg. as is done with launching pigpiod and jackd)
* Environment scripts have been split out into ``setup/scripts.py`` and you can now run them with ``python -m autopilot.setup.run_script`` (use ``--help`` to see how!)
* Informative error when setup is run with too narrow terminal: https://github.com/wehr-lab/autopilot/issues/23
* Informative error when setup is run with too narrow terminal: https://github.com/auto-pi-lot/autopilot/issues/23
* More loggers, but increased need to unify logger creation!!!


Expand All @@ -84,8 +84,8 @@ v0.3.2 (September 28, 2020)
Bugfixes
~~~~~~~~

* https://github.com/wehr-lab/autopilot/issues/19 - previously, I attempted to package binaries for the lightly modified pigpio and for jackd (the apt binary used to not work), but after realizing that was the worst possible way of going about it I changed install strategies, but didn't entirely remove the vestiges of the prior attempt. The installation expected certain directories to exist (in autopilot/external) that didn't, which crashed and choked install. Still need to formalize a configuration and plugin system, but getting there.
* https://github.com/wehr-lab/autopilot/issues/20 - the jackd binary in the apt repos for the raspi used to not work, so i was in the habit of compiling jackd audio from source. I had build that into the install routine, but something about that now causes the JACK-Client python interface to throw segfaults. Somewhere along the line someone fixed the apt repo version of jackd so we use that now.
* https://github.com/auto-pi-lot/autopilot/issues/19 - previously, I attempted to package binaries for the lightly modified pigpio and for jackd (the apt binary used to not work), but after realizing that was the worst possible way of going about it I changed install strategies, but didn't entirely remove the vestiges of the prior attempt. The installation expected certain directories to exist (in autopilot/external) that didn't, which crashed and choked install. Still need to formalize a configuration and plugin system, but getting there.
* https://github.com/auto-pi-lot/autopilot/issues/20 - the jackd binary in the apt repos for the raspi used to not work, so i was in the habit of compiling jackd audio from source. I had build that into the install routine, but something about that now causes the JACK-Client python interface to throw segfaults. Somewhere along the line someone fixed the apt repo version of jackd so we use that now.
* previously I had only tested in a virtual environment, but now the installation routine properly handles not being in a venv.

Cleanup
Expand Down Expand Up @@ -337,12 +337,12 @@ Regressions


.. _whitepaper: https://www.biorxiv.org/content/10.1101/807693v1
.. _plaintext: https://github.com/wehr-lab/autopilot/blob/master/notes/todo
.. _plaintext: https://github.com/auto-pi-lot/autopilot/blob/master/notes/todo
.. _sphinx-autobuild: https://github.com/GaretJax/sphinx-autobuild
.. _altair: https://altair-viz.github.io/
.. _blosc: http://python-blosc.blosc.org/
.. _Spinnaker: https://www.flir.com/products/spinnaker-sdk/
.. _LSM9DS1: https://www.sparkfun.com/products/13944
.. _MLX90640: https://www.melexis.com/en/product/MLX90640/Far-Infrared-Thermal-Sensor-Array
.. _DeepLabCut-live: https://github.com/DeepLabCut/DeepLabCut-live/
.. _dlclive_example: https://github.com/wehr-lab/autopilot/blob/2to3/examples/example_transformation_dlc.ipynb
.. _dlclive_example: https://github.com/auto-pi-lot/autopilot/blob/2to3/examples/example_transformation_dlc.ipynb
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