Various updates

.readthedocs.yaml

@@ -0,0 +1,34 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#     - requirements: docs/requirements.txt

docs/Makefile

@@ -0,0 +1,20 @@
+ # Minimal makefile for Sphinx documentation
+#
+
+# 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
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "eagle"
+copyright = "2025, eagle contributors "
+author = "eagle contributors"
+
+
+# -- General configuration ---------------------------------------------------
+# -- General configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+]
+
+intersphinx_mapping = {
+    "rtd": ("https://docs.readthedocs.io/en/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
+
+# 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"]
+
+# -- 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"
+
+# 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"]

docs/getting_started.rst

@@ -0,0 +1,18 @@
+=================
+Getting Started
+=================
+
+Learn how to use the full `ufs2arco + Anemoi + wxvx` pipeline.
+
+You will learn how to:
+
+1) Use `ufs2arco` to create training and validation datasets with NOAA Replay reanalysis
+2) Use `anemoi-core` modules to train a graph-based model
+3) Use `anemoi-inference` to run inference
+4) Use `wxvx` to verify a forecast
+
+-------------
+Ursa
+-------------
+
+Insert instructions for Ursa

docs/index.rst

@@ -0,0 +1,5 @@
+=================
+Welcome to Eagle!
+=================
+
+Enter overview of Eagle project....?

docs/inference.rst

@@ -0,0 +1,9 @@
+=================
+Inference
+=================
+
+We use the anemoi-inference package to create a forecast.
+
+Helpful quick tips for using anemoi-inference
+
+See `anemoi-inference documentation <https://anemoi.readthedocs.io/projects/inference/en/latest/>`_ documentation for further information:

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/nested-eagle.rst

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+=================
+Nested Eagle
+=================
+
+Overview of Nested-Eagle

docs/training.rst

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+=================
+Train a Graph-Based Model
+=================
+
+We use the anemoi-core modules to train a graph-based model.
+
+Helpful quick tips for using Anemoi
+
+See Anemoi documentation for further information:
+- `anemoi-graphs <https://anemoi.readthedocs.io/projects/graphs/en/latest/>`_
+- `anemoi-training <https://anemoi.readthedocs.io/projects/training/en/latest/>`_
+- `anemoi-models <https://anemoi.readthedocs.io/projects/models/en/latest/index.html>`_

docs/ufs2arco.rst

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+=================
+Create Training, Validation, and Test Datasets
+=================
+
+We use ufs2arco to generate our datasets.
+
+Helpful quick tips for ufs2arco
+
+See `ufs2arco <https://ufs2arco.readthedocs.io/en/latest/>`_  for further information.

docs/verification.rst

@@ -0,0 +1,9 @@
+=================
+Validation
+=================
+
+We use wxvx for forecast verification.
+
+Helpful quick tips for using wxvx.
+
+See `wxvx <https://github.com/maddenp-cu/wxvx>`_  for further information.

environment.yaml

@@ -0,0 +1,19 @@
+name: eagle
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - ufs2arco
+  - pip
+  - pip:
+      - torch<2.7
+      - anemoi-datasets==0.5.26
+      - anemoi-graphs==0.6.4
+      - anemoi-models==0.9.2
+      - anemoi-training==0.6.2
+      - anemoi-inference==0.7.1
+      - anemoi-utils==0.4.35
+      - anemoi-transform==0.1.16
+      - flash-attn<2.8 --no-build-isolation
+      - eagle-tools

nested_eagle/scientific_workflow/training/config.yaml

@@ -241,11 +241,9 @@ graph:
         _target_: anemoi.graphs.edges.attributes.EdgeDirection
         norm: unit-std
 
-    #post_processors:
-    #- _target_: anemoi.graphs.processors.SortEdgeIndexByTargetNodes
-    #  descending: True  # optional, defaults to true
-# commenting the post-processors out for right now because I think there may be a bug in Anemoi-Models
-# I'll circle back to this at some point.
+    post_processors:
+      - _target_: anemoi.graphs.processors.SortEdgeIndexByTargetNodes
+        descending: True # optional, defaults to true
 
 hardware:
   num_gpus_per_model: 1