Merge 211be0e into 9095618

.readthedocs.yml

@@ -19,6 +19,9 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
-    - requirements: requirements/requirements_docs.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

.travis.yml

@@ -38,13 +38,8 @@ env:
   - DISPLAY=":99.0" QT_DEBUG_PLUGINS=1  # https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html?highlight=travis#xvfb-assertionerror-timeouterror-when-using-waituntil-waitexposed-and-ui-events
 
 install:
-  - pip install -U pip
-  - pip install -U pytest
-  - pip install -U pytest-cov
-  - pip install -U pylint
-  - pip install -U coveralls
-  - pip install -U pytest-qt~=3.3.0
-  - pip install -e .
+  - pip install --upgrade setuptools importlib_metadata
+  - pip install .[tests]
   - "/sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX +render -noreset"
   - sleep 3
 
@@ -63,17 +58,14 @@ after_script:
   - coverage combine --append
   - coveralls
 
-before_deploy:
-  - pip install scikit-build
-
 deploy:
   provider: pypi
   username: __token__
   pasword:
     secure: 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
   on:
     tags: true
-    branch: master
+    branch: main
     condition: "$TRAVIS_PYTHON_VERSION = 3.9"
   distributions: "sdist"
 

CITATION.cff

@@ -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"
 ...

README.md

@@ -9,8 +9,8 @@
 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)
 
 
@@ -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. 
@@ -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
@@ -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
 

autopilot/__init__.py

@@ -1,5 +1,20 @@
 __author__  = 'Jonny Saunders <j@nny.fyi>'
-__version__ = '0.4.4'
+
+import sys
+if sys.version_info < (3,8):
+    from importlib_metadata import version
+    # monkeypatch typing
+    import typing
+    from typing_extensions import Literal
+    typing.Literal = Literal
+else:
+    from importlib.metadata import version
+
+
+__version__ = version("auto-pi-lot")
+
+from autopilot.root import Autopilot_Type, Autopilot_Pref
+
 
 from autopilot.setup import setup_autopilot
 from autopilot.utils.registry import get, get_task, get_hardware, get_names

autopilot/agents/base.py

@@ -0,0 +1,28 @@
+"""
+Base Agent class.
+
+Currently a stub just to get them in the object hierarchy
+"""
+
+from autopilot.root import Autopilot_Object
+
+
+class Agent(Autopilot_Object):
+    """
+    Metaclass for agent types.
+
+    Currently a stub, but will provide hooks for basic lifecycle methods of agents:
+
+    * ``pre_init`` - to be run before any other standard initialization
+    * ``init`` - main initialization hook
+    * ``init_external`` - initialize external processes
+    * ``post_init`` - to be run after other initialization
+    * ... to be continued
+
+    And core class and instance attributes:
+
+    * ``prefs`` - prefs that are needed to configure this agent
+    * ``processes`` - processes spawned by this agent
+    * ``listens`` - methods to handle messages sent to this agent
+    * ``dependencies`` - additional optional python packages or system configurations that this agent depends on.
+    """