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

Author: herbiebradley

.pre-commit-config.yaml

@@ -36,6 +36,6 @@ repos:
     -   id: pydocstyle
         args:
           - '--convention=google'
-          - '--add-ignore=D10'
+          - '--add-ignore=D10,D212'
           - '-v'
           - '--count'

.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

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"

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,

docs/source/openelm.codegen.rst

@@ -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"}