Setting standards & cleanup (#16)

* Rewrite genotypes to abstract base classes

* Remove test notebooks

* Fix three_channel_average

* Add pre-commit

* Add pyproject.toml and tox.ini

* Big refactor

* Revert "Big refactor"

This reverts commit c05abee.

* Big refactor (for real this time)

* Add pydocstyle config

* Improve hydra config and add type validation

* Fix diff model import

* Add github actions

* Add stats to flake8 precommit config

* Fix imports

* Fix diff model type hint

* Fix import bugs, make package

* Update pre-commit-config

* rewrite walk_creator w/dataclasses

* Fix serialization

* Add history to mapelites

* Fix map

* Add full history option to mapelites

* Fix mapelites history buffer

* Small refactor, add dev-reqs

* fix ghactions

* Linting fix

* Update config files

* change to requirements.txt

* Match the key of the new config file.

* Add pytest config

* Add contributing.md

Co-authored-by: Honglu Fan <[email protected]>

.github/workflows/build.yml

@@ -2,9 +2,11 @@ name: Build
 
 on:
   push:
-    branches: [ $default-branch ]
+    branches:
+      - main
   pull_request:
-    branches: [ $default-branch ]
+    branches:
+      - main
 
 jobs:
   build:

.gitignore

@@ -131,6 +131,7 @@ dmypy.json
 # Project dirs
 checkpoints/
 logs/
+archive/
 
 # generated dot files and tree graphs
 .gv

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+# This should be the _latest_ version of python supported by us
+default_language_version:
+  python: python3.9
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+        files: ^(elm|test|setup.py)/
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        name: isort (python)
+-   repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+      - id: flake8
+        args:
+          - '--ignore=E203,E501,W503,F811'
+          - '--max-line-length=88'
+          - '--statistics'
+          - '--count'
+          - '--show-source'
+-   repo: https://github.com/pycqa/pydocstyle
+    rev: 6.1.1
+    hooks:
+    -   id: pydocstyle
+        args:
+          - '--convention=google'
+          - '--add-ignore=D10'

CONTRIBUTING.md

@@ -0,0 +1,64 @@
+# Contributing to `OpenEvolve`
+
+Looking to improve `OpenEvolve`? Thanks for considering!
+
+There are many ways to contribute, from writing tutorials in [Colab notebooks](https://colab.research.google.com) to improving the project's documentation, submitting bug reports and feature requests, or implementing new features themselves. See the outstanding [issues](https://github.com/CarperAI/ELM/issues) for ideas on where to begin.
+
+Here are some guidelines to help you get started 🚀.
+
+## Submitting a bug report or a feature request¶
+
+To submit a bug report or a feature request, please open an [issue](https://github.com/CarperAI/ELM/issues) by clicking on the `New Issue` button and selecting the respective issue template. Make sure to fill out all the required information and provide as much detail as possible. For bug reports, this means including a minimal code example that reproduces the bug, and for feature requests, it means providing a clear and detailed description of the feature you would like to see implemented.
+
+## Submitting code
+
+> **Note**: Make sure to first search through the [issue tracker](https://github.com/CarperAI/ELM/issues) and [PR list](https://github.com/CarperAI/ELM/pulls) to avoid duplicating work. If you want to work on a non-trivial feature, we highly recommended that you first open an issue in the [issue tracker](https://github.com/CarperAI/ELM/issues) to get feedback from core developers.
+
+Follow these steps to start contributing code:
+
+1. Create your own [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo#forking-a-repository) of the repository and clone it to your local machine.
+    ```bash
+    git clone https://github.com/<YOUR-USERNAME>/OpenEvolve.git
+    cd OpenEvolve
+    git remote add upstream https://github.com/CarperAI/OpenEvolve.git
+    ```
+2. Create a new branch for your changes and give it a concise name that reflects your contribution.
+    ```bash
+    git checkout -b <BRANCH-NAME>
+    ```
+2. Install the development dependencies in a Python environment.
+    ```bash
+    pip install -e ".[dev]"
+    pre-commit install
+    ```
+4. Implement your changes. Make small, independent, and well documented commits along the way (check out [these](https://cbea.ms/git-commit/) tips).
+5. Add unit tests whenever appropriate and ensure that the tests pass. To run the entire test suite, use the following command from within the project root directory.
+    ```bash
+    pytest
+    ```
+    For changes with minimal project scope (e.g. a simple bug fix), you might want to run the unit tests for just a specific test file instead:
+    ```bash
+    pytest -vv -k "<TEST-FILE-NAME>"
+    ```
+5. Commit your final changes. Our `pre-commit` hooks will automatically run before each commit and will prevent you from committing code that does not pass our style and linter checks. They'll also automatically format your code! To run these manually, use the following command:
+    ```bash
+    pre-commit run --all-files
+    ```
+
+6. Push the changes to your fork.
+
+Finally ... 🥁 ... Create a [pull request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) to the `OpenEvolve` repository! Make sure to include a description of your changes and link to any relevant issues.
+
+## Asking questions
+
+Have a question? Rather than opening an issue, you can readily chat with the core team on our [Discord server](https://discord.gg/canadagoose).
+
+## Code of conduct
+
+This project adheres to the [Contributor Covenant Code of Conduct](https://github.com/CarperAI/ELM/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under its MIT License.
+
+# Thank you for your contribution 🐠!

README.md

@@ -13,10 +13,10 @@ For more details, see our full research proposal at https://carperai.notion.site
 
 Weekly meetings are in the EleutherAI discord at 20:00 UTC on Fridays.
 
-- [ ] Sodarace environment implemented
-- [ ] Stage 1: Diff Models & MAP-Elites
-  - [ ] Prompt Engineering on CodeGen
-  - [ ] Train diff model
-  - [ ] MAP-Elites implemented
+- [x] Sodarace environment implemented
+- [x] Stage 1: Diff Models & MAP-Elites
+  - [x] Prompt Engineering on CodeGen
+  - [x] Train diff model
+  - [x] MAP-Elites implemented
 - [ ] Stage 2: Train LLM on generated data
 - [ ] Stage 3: Conditional generation with PPO

elm/__init__.py

@@ -0,0 +1 @@
+from elm.elm import ELM