v0.1.7 Release (#35)

* Minor config change * Refactor into src layout * Update conf.py version * Minor update to configs * Minor update to configs 2 * Update docs config * Docs config update * Add citation.cff * Docs update * Fix doc errors * Change contents depth * Update rtd config * Update rtd * Fix rtd * Edit sphinx config * Depth 2 for docs contents * Remove module contents * Edit environment docs * Add docs contents * Depth 3 in docs * toctree depth 4 * index depth 2 * Update docs * Add environments to index * exclude all rtd * Test docs change * Names for openelm docs modules * Clearer section headers for docs * Test recursive rtd * Automatic docs version * Improve map-elites docstrings and doc config * Remove setup.py and change config
CarperAI · Dec 25, 2022 · ef40bc8 · ef40bc8
1 parent 85e7db8
commit ef40bc8
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -36,6 +36,6 @@ repos:
     -   id: pydocstyle
         args:
           - '--convention=google'
-          - '--add-ignore=D10'
+          - '--add-ignore=D10,D212'
           - '-v'
           - '--count'
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -7,7 +7,8 @@ version: 2
 
 # Remove report submodule from docs build
 submodules:
-  exclude: all
+  include: all
+  recursive: true
 
 build:
   os: ubuntu-20.04
@@ -26,3 +27,6 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
+   - method: pip
+     path: .
+   system_packages: True
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata from this file."
+authors:
+  - family-names: "Bradley"
+    given-names: "Herbie"
+    orcid: "https://orcid.org/0000-0001-5390-1257"
+  - family-names: "Fan"
+    given-names: "Honglu"
+  - family-names: "Carvalho"
+    given-names: "Francisco"
+  - family-names: "Fisher"
+    given-names: "Matthew"
+  - family-names: "Castricato"
+    given-names: "Louis"
+  - family-names: "reciprocated"
+  - family-names: "dmayhem93"
+title: "OpenELM"
+version: 0.1.7
+doi: 10.5281/zenodo.7361753
+date-released: 2022-12-25
+url: "https://github.com/CarperAI/OpenELM"
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -7,23 +7,30 @@
 # -- Path setup --------------------------------------------------------------
 
 import os
+import pathlib
 import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from importlib.metadata import version as importlib_version
+
 import sphinx_rtd_theme  # noqa: F401
 
-sys.path.insert(0, os.path.abspath(".."))
+if "READTHEDOCS" in os.environ:
+    src_folder = pathlib.Path(__file__).resolve().parent.parent.parent / "src"
+    sys.path.append(str(src_folder))
 
+    print("Detected running on ReadTheDocs")
+    print(f"Added {src_folder} to sys.path")
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "OpenELM"
 copyright = "2022, CarperAI"
 author = "CarperAI"
-release = "0.1.0"
+release = version = '.'.join(importlib_version('openelm').split('.')[:3])
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -35,6 +42,7 @@
 
 extensions = [
     "sphinx_rtd_theme",
+    "sphinx.ext.napoleon",
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.autodoc",
@@ -61,8 +69,6 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
-
 html_theme_options = {
     "logo_only": True,
     "display_version": True,

diff --git a/docs/source/openelm.codegen.rst b/docs/source/openelm.codegen.rst
diff --git a/docs/source/openelm.environments.rst b/docs/source/openelm.environments.rst
@@ -1,23 +1,11 @@
 openelm.environments package
 =============================
 
-Submodules
---------------------------------------
-
-openelm.environments.environments module
+OpenELM Environments module
 -------------------------------------------
 
 .. automodule:: openelm.environments.environments
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
-
-Module contents
---------------------------------------
-
-.. automodule:: openelm.environments
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :special-members: __init__
diff --git a/docs/source/openelm.rst b/docs/source/openelm.rst
@@ -5,15 +5,14 @@ Subpackages
 -----------
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    openelm.environments
-   openelm.codegen
 
 Submodules
 ----------
 
-openelm.elm module
+ELM
 -----------------------------------------
 
 .. automodule:: openelm.elm
@@ -22,7 +21,7 @@ openelm.elm module
    :show-inheritance:
    :special-members: __init__
 
-openelm.map_elites module
+MAP-Elites
 -----------------------------------------
 
 .. automodule:: openelm.map_elites
@@ -31,29 +30,11 @@ openelm.map_elites module
    :show-inheritance:
    :special-members: __init__
 
-openelm.diff_model module
+Diff Models
 -----------------------------------------
 
 .. automodule:: openelm.diff_model
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
-
-openelm.benchmarks module
------------------------------------------
-
-.. automodule:: openelm.benchmarks
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :special-members: __init__
-
-Module contents
------------------------------------------
-
-.. automodule:: openelm
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :special-members: __init__
diff --git a/openelm/__init__.py b/openelm/__init__.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -2,30 +2,35 @@
 profile = "black"
 
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=64", "setuptools_scm[toml]>=6.2", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
-packages = ["openelm"]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 
 [tool.setuptools_scm]
 
+
 [tool.pydocstyle]
 convention = "google"
-add-ignore = "D10"
+add-ignore = "D10, D212"
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-addopts = "-rA --doctest-modules" # --cov=openelm"  # Uncomment this for coverage by default
+addopts = "-rA --doctest-modules --color=yes" # --cov=openelm"  # Uncomment this for coverage by default
 testpaths = ["tests"]
 doctest_optionflags = ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
 
 [project]
 name = "OpenELM"
 description = "Evolution Through Large Models"
+authors = [{name = "CarperAI"}]
 readme = "README.md"
 requires-python = ">=3.9"
 license = {text = "MIT"}

diff --git a/setup.py b/setup.py
diff --git a/src/openelm/__init__.py b/src/openelm/__init__.py
@@ -0,0 +1,5 @@
+from importlib.metadata import version as importlib_version
+
+from openelm.elm import ELM
+
+__version__ = importlib_version("openelm")
diff --git a/openelm/benchmarks.py → src/openelm/benchmarks.py b/openelm/benchmarks.py → src/openelm/benchmarks.py
diff --git a/openelm/benchmarks_diff.py → src/openelm/benchmarks_diff.py b/openelm/benchmarks_diff.py → src/openelm/benchmarks_diff.py
diff --git a/openelm/benchmarks_tinygp.py → src/openelm/benchmarks_tinygp.py b/openelm/benchmarks_tinygp.py → src/openelm/benchmarks_tinygp.py
diff --git a/openelm/codegen/__init__.py → src/openelm/codegen/__init__.py b/openelm/codegen/__init__.py → src/openelm/codegen/__init__.py
diff --git a/openelm/codegen/codegen_utilities.py → src/openelm/codegen/codegen_utilities.py b/openelm/codegen/codegen_utilities.py → src/openelm/codegen/codegen_utilities.py
diff --git a/openelm/codegen/codex_execute.py → src/openelm/codegen/codex_execute.py b/openelm/codegen/codex_execute.py → src/openelm/codegen/codex_execute.py
diff --git a/openelm/codegen/configuration_codegen.py → src/openelm/codegen/configuration_codegen.py b/openelm/codegen/configuration_codegen.py → src/openelm/codegen/configuration_codegen.py
diff --git a/openelm/codegen/modelling_codegen.py → src/openelm/codegen/modelling_codegen.py b/openelm/codegen/modelling_codegen.py → src/openelm/codegen/modelling_codegen.py
diff --git a/openelm/config/__init__.py → src/openelm/config/__init__.py b/openelm/config/__init__.py → src/openelm/config/__init__.py
diff --git a/openelm/config/benchmark_cfg.yaml → src/openelm/config/benchmark_cfg.yaml b/openelm/config/benchmark_cfg.yaml → src/openelm/config/benchmark_cfg.yaml
diff --git a/openelm/config/benchmark_diff_cfg.yaml → src/openelm/config/benchmark_diff_cfg.yaml b/openelm/config/benchmark_diff_cfg.yaml → src/openelm/config/benchmark_diff_cfg.yaml
diff --git a/openelm/config/elm_config.py → src/openelm/config/elm_config.py b/openelm/config/elm_config.py → src/openelm/config/elm_config.py
diff --git a/openelm/config/elm_image_cfg.yaml → src/openelm/config/elm_image_cfg.yaml b/openelm/config/elm_image_cfg.yaml → src/openelm/config/elm_image_cfg.yaml
diff --git a/openelm/config/elm_sodarace_cfg.yaml → src/openelm/config/elm_sodarace_cfg.yaml b/openelm/config/elm_sodarace_cfg.yaml → src/openelm/config/elm_sodarace_cfg.yaml
diff --git a/openelm/constants.py → src/openelm/constants.py b/openelm/constants.py → src/openelm/constants.py
@@ -3,4 +3,4 @@
 # Note: constants should be UPPER_CASE
 constants_path = pathlib.Path(__file__)
 SRC_PATH = constants_path.parent
-PROJECT_PATH = SRC_PATH.parent
+PROJECT_PATH = SRC_PATH.parent.parent
diff --git a/openelm/diff_model.py → src/openelm/diff_model.py b/openelm/diff_model.py → src/openelm/diff_model.py
diff --git a/openelm/elm.py → src/openelm/elm.py b/openelm/elm.py → src/openelm/elm.py
diff --git a/openelm/environments/__init__.py → src/openelm/environments/__init__.py b/openelm/environments/__init__.py → src/openelm/environments/__init__.py
diff --git a/openelm/environments/environments.py → src/openelm/environments/environments.py b/openelm/environments/environments.py → src/openelm/environments/environments.py
@@ -332,6 +332,7 @@ def __init__(
     ) -> None:
         """
         Sodarace environment.
+
         Args:
             seed: the seed dict.
             config: the config file path or dict.

diff --git a/openelm/environments/sodaracer/README.md → src/openelm/environments/sodaracer/README.md b/openelm/environments/sodaracer/README.md → src/openelm/environments/sodaracer/README.md
diff --git a/openelm/environments/sodaracer/__init__.py → ...penelm/environments/sodaracer/__init__.py b/openelm/environments/sodaracer/__init__.py → ...penelm/environments/sodaracer/__init__.py
diff --git a/...ronments/sodaracer/framework_simulator.py → ...ronments/sodaracer/framework_simulator.py b/...ronments/sodaracer/framework_simulator.py → ...ronments/sodaracer/framework_simulator.py
diff --git a/openelm/environments/sodaracer/helpers.py → ...openelm/environments/sodaracer/helpers.py b/openelm/environments/sodaracer/helpers.py → ...openelm/environments/sodaracer/helpers.py
diff --git a/openelm/environments/sodaracer/simulator.py → ...enelm/environments/sodaracer/simulator.py b/openelm/environments/sodaracer/simulator.py → ...enelm/environments/sodaracer/simulator.py
diff --git a/...vironments/sodaracer/walker/CPPN_fixed.py → ...vironments/sodaracer/walker/CPPN_fixed.py b/...vironments/sodaracer/walker/CPPN_fixed.py → ...vironments/sodaracer/walker/CPPN_fixed.py
diff --git a/...ronments/sodaracer/walker/CPPN_mutable.py → ...ronments/sodaracer/walker/CPPN_mutable.py b/...ronments/sodaracer/walker/CPPN_mutable.py → ...ronments/sodaracer/walker/CPPN_mutable.py
diff --git a/...m/environments/sodaracer/walker/README.md → ...m/environments/sodaracer/walker/README.md b/...m/environments/sodaracer/walker/README.md → ...m/environments/sodaracer/walker/README.md
diff --git a/...environments/sodaracer/walker/__init__.py → ...environments/sodaracer/walker/__init__.py b/...environments/sodaracer/walker/__init__.py → ...environments/sodaracer/walker/__init__.py
diff --git a/...m/environments/sodaracer/walker/radial.py → ...m/environments/sodaracer/walker/radial.py b/...m/environments/sodaracer/walker/radial.py → ...m/environments/sodaracer/walker/radial.py
diff --git a/...m/environments/sodaracer/walker/square.py → ...m/environments/sodaracer/walker/square.py b/...m/environments/sodaracer/walker/square.py → ...m/environments/sodaracer/walker/square.py
diff --git a/...ronments/sodaracer/walker/walk_creator.py → ...ronments/sodaracer/walker/walk_creator.py b/...ronments/sodaracer/walker/walk_creator.py → ...ronments/sodaracer/walker/walk_creator.py