Updated CI and added basic API docs.

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      # Check for updates once a week
+      interval: 'weekly'
+    groups:
+      actions:
+        patterns:
+          - "*"
+    cooldown:
+      default-days: 7

.github/workflows/python-package-conda.yml

@@ -12,7 +12,7 @@ jobs:
         shell: bash -l {0}
     steps:
     - uses: actions/checkout@v4
-    - uses: conda-incubator/setup-miniconda@v3
+    - uses: conda-incubator/setup-miniconda@v4.0.1
       with:
         miniforge-version: latest
         channel-priority: true

.github/workflows/python-publish.yml

@@ -1,4 +1,4 @@
-# This workflow will upload a Python Package using Twine when a release is created
+# This workflow will upload a Python Package to PyPI when a release is created
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
 
 # This workflow uses actions that are not certified by GitHub.
@@ -16,24 +16,61 @@ permissions:
   contents: read
 
 jobs:
-  deploy:
+  release-build:
+    name: Build and upload distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
+      - name: Setup Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: "3.11"
 
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    name: Upload to PyPI
     runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+        with:
+          packages-dir: dist/

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+echo/_version.py
 build/
 develop-eggs/
 dist/

.readthedocs.yml

@@ -0,0 +1,37 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# 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-22.04
+  tools:
+    python: "3.12"
+
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# 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:
+    - method: "pip"
+      path: "."
+      extra_requirements:
+        - docs

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     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+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/source/conf.py

@@ -0,0 +1,28 @@
+# 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 = 'ECHO'
+copyright = '2026, University Corporation for Atmospheric Research'
+author = 'John Schreck'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.napoleon", "autoapi.extension"]
+
+templates_path = ['_templates']
+exclude_patterns = []
+autoapi_dirs = ["../../echo/"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+html_logo = "_static/echo_logo.png"

docs/source/index.rst

@@ -0,0 +1,16 @@
+.. ECHO documentation master file, created by
+   sphinx-quickstart on Wed May  6 11:25:55 2026.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+ECHO documentation
+==================
+
+ECHO is a package for distributed hyperparameter optimization on HPC systems built on optuna. 
+The package provides both a way to generate lots of hyperparameter combos, track them, and
+analyze the importance of different hyperparameter choices.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+

environment.yml

@@ -1,23 +1,17 @@
 name: echo
 channels:
  - conda-forge
- - pytorch
 dependencies:
   - python=3.12
   - sphinx
   - pytest
   - setuptools
-  - optuna<4.0
+  - optuna>=3.0
   - numpy
   - scipy
   - matplotlib
   - scikit-learn
-  - jupyter
-  - jupyterlab
-  - jupyter_server
-  - distributed
   - pip
   - pyarrow
-  - xgboost
   - pip:
     - .

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -35,6 +35,8 @@ dependencies = [
     "scikit-learn",
     "pyarrow",
     "pyyaml",
+    "setuptools",
+    "setuptools_scm"
 ]
 
 [project.urls]
@@ -52,5 +54,5 @@ include-package-data = true
 [tool.setuptools.packages.find]
 include = ["echo", "echo.src"]
 
-[tool.setuptools.dynamic]
-version = {file = "echo/VERSION"}
+[tool.setuptools_scm]
+version_file = "echo/_version.py"

requirements.txt

@@ -4,6 +4,7 @@ matplotlib
 pandas
 optuna>=3.0
 setuptools
+setuptools_scm
 pyyaml
 scikit-learn
 pyarrow