update docs

.gitignore

@@ -62,3 +62,5 @@ target/
 
 #Ipython Notebook
 .ipynb_checkpoints
+
+.DS_Store

README.md

@@ -29,12 +29,6 @@ If you just want `reach`:
 pip install reach
 ```
 
-If you also want [`AutoReach`](#autoreach):
-
-```
-pip install reach[auto]
-```
-
 ## Example
 
 ```python

docs/Makefile

@@ -1,10 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = reach
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/conf.py

@@ -1,114 +1,37 @@
-# -*- coding: utf-8 -*-
-#
-# Configuration file for the Sphinx documentation builder.
-#
-# This file does only contain a selection of the most common options. For a
-# full list see the documentation:
-# http://www.sphinx-doc.org/en/master/config
-
-# -- Path setup --------------------------------------------------------------
-
-# 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.
-#
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../"))
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath(".."))
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "reach"
-copyright = "2023, Stéphan Tulkens"
+copyright = "2024, Stéphan Tulkens"
 author = "Stéphan Tulkens"
-
-# The short X.Y version
-version = "4.1.0"
-# The full version, including alpha/beta/rc tags
-release = "4.1.0"
-
+release = "5.0.0"
 
 # -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
-    "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
 ]
 
-# Add any paths that contain templates here, relative to this directory.
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
 templates_path = ["_templates"]
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
-
-# The master toctree document.
-master_doc = "index"
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = "en"
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path .
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
-
 
 # -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "sphinx_rtd_theme"
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# 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']
-
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# The default sidebars (for documents that don't match any pattern) are
-# defined by theme itself.  Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
-#
-# html_sidebars = {}
-
-
-# -- Options for HTMLHelp output ---------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = "reachdoc"
-
-# -- Extension configuration -------------------------------------------------
-
-# Napoleon settings
-# napoleon_include_init_with_doc = True
-
-# autodoc
-autodoc_member_order = "bysource"
+html_theme = "alabaster"
+html_static_path = ["_static"]

docs/index.rst

@@ -1,3 +1,8 @@
+.. reach documentation master file, created by
+   sphinx-quickstart on Sun Jul 14 20:50:46 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
 `reach <https://github.com/stephantul/reach>`_ documentation
 ===================================================================
 
@@ -26,15 +31,6 @@ If you just want reach:
     $ pip install reach
 
 
-
-If you also want AutoReach:
-
-
-::
-
-    $ pip install reach[auto]
-
-
 Contents
 --------
 

docs/source/api.rst

@@ -10,11 +10,3 @@ Reach
 .. autoclass:: reach.Reach
     :members:
     :undoc-members:
-
-
-AutoReach
--------------------------
-
-.. autoclass:: reach.AutoReach
-    :members:
-    :undoc-members:

reach/__init__.py

@@ -2,11 +2,5 @@
 
 from reach.reach import Reach, normalize
 
-try:
-    from reach.autoreach import AutoReach  # noqa
-
-    __all__ = ["Reach", "normalize", "AutoReach"]
-except ImportError:
-    __all__ = ["Reach", "normalize"]
-
+__all__ = ["Reach", "normalize"]
 __version__ = "4.1.1"

reach/reach.py

@@ -54,6 +54,7 @@ def __init__(
         vectors: Matrix,
         items: list[str],
         name: str = "",
+        metadata: dict[str, Any] | None = None,
     ) -> None:
         """Initialize a Reach instance with an array and list of items."""
         if len(items) != len(vectors):
@@ -75,6 +76,7 @@ def __init__(
         self.name = name
         self._unk_token: str | None = None
         self._unk_index: int | None = None
+        self.metadata = metadata or {}
 
     @property
     def unk_token(self) -> str | None:
@@ -972,7 +974,6 @@ def save_fast_format(
         self,
         path: PathLike,
         overwrite: bool = False,
-        additional_metadata: dict[str, str] | None = None,
     ) -> None:
         """
         Save a reach instance in a fast format.
@@ -1007,8 +1008,7 @@ def save_fast_format(
             "unk_token": self.unk_token,
             "name": self.name,
         }
-        if additional_metadata is not None:
-            metadata.update(additional_metadata)
+        metadata.update(self.metadata)
 
         items = self.sorted_items
         items_dict = {
@@ -1045,9 +1045,9 @@ def load_fast_format(
             data: dict[str, Any] = json.load(file_handle)
         items: list[str] = data["items"]
 
-        metadata: dict[str, Any] = data.get("metadata", {})
-        unk_token = metadata.get("unk_token")
-        name = metadata.get("name", "")
+        metadata: dict[str, Any] = data["metadata"]
+        unk_token = metadata.pop("unk_token")
+        name = metadata.pop("name")
         numpy_path = filename_path.parent / Path(data["vectors_path"])
 
         if not numpy_path.exists():
@@ -1056,7 +1056,7 @@ def load_fast_format(
         with open(numpy_path, "rb") as file_handle:
             vectors: npt.NDArray = np.load(file_handle)
         vectors = vectors.astype(desired_dtype)
-        instance = cls(vectors, items, name=name)
+        instance = cls(vectors, items, name=name, metadata=metadata)
         instance.unk_token = unk_token
 
         return instance