Merge branch 'main' into dev

Author: sgbaird

.github/workflows/ci.yml

@@ -52,6 +52,10 @@ jobs:
 
   test:
     needs: prepare
+    if: >
+      github.event_name == 'pull_request' ||
+      (github.event_name == 'push' &&
+      contains(github.event.head_commit.modified, '.py'))
     strategy:
       fail-fast: false
       matrix:

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -43,14 +43,14 @@ repos:
   - id: isort
 
 - repo: https://github.com/psf/black
-  rev: 24.2.0
+  rev: 24.4.0
   hooks:
   - id: black
     exclude: ^tests/generated_scripts/
     language_version: python3
 
 - repo: https://github.com/psf/black
-  rev: 24.2.0
+  rev: 24.4.0
   hooks:
   - id: black
     exclude: ^(?!tests/generated_scripts/).* # any string that does not start with tests/generated_scripts/

AUTHORS.md

@@ -1,3 +1,4 @@
 # Contributors
 
-* sgbaird [sterling.baird@utah.edu](mailto:sterling.baird@utah.edu)
+* Sterling Baird ([@sgbaird](https://github.com/sgbaird)) [sterling.baird@utoronto.ca](mailto:sterling.baird@utoronto.ca)
+* Andrew Falkowski ([@AndrewFalkowski](https://github.com/AndrewFalkowski))

README.md

@@ -17,15 +17,17 @@
 
 ![honegumi-logo](reports/figures/honegumi-logo.png)
 
-> Honegumi (骨組み, pronounced "ho neh goo mee"), which means "skeletal framework" in Japanese, is a package for
+> Honegumi ("ho-nay-goo-mee"), which means "skeletal framework" in Japanese, is a package for
 > interactively creating API tutorials with a focus on optimization packages such as Meta's Ax
-> Platform. We are [looking for contributors](https://github.com/sgbaird/honegumi/blob/main/CONTRIBUTING.md)!
+> Platform
 
 <!-- > Unlock the power of advanced optimization in materials science with Honegumi (骨組み,
 > pronounced "ho-neh-goo-mee"), our interactive "skeleton code" generator. -->
 
 <!-- TODO: refactor this paragraph to emphasize general API tutorial creation, and then focus in on materials science as one example that I'll be focusing on here -->
 
+# Honegumi
+
 Real-world materials science optimization tasks are complex! To cite a few examples:
 
 | Topic           | Description |

docs/conf.py

@@ -45,7 +45,10 @@
 try:
     import sphinx
 
-    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
+    # https://stackoverflow.com/questions/71343831/sphinx-ignores-py-file-starting-with-a-in-filename
+    cmd_line = (
+        f"sphinx-apidoc --implicit-namespaces --private -f -o {output_dir} {module_dir}"
+    )
 
     args = cmd_line.split(" ")
     if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
@@ -75,6 +78,8 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
+    "nbsphinx",
     # "sphinx_rtd_dark_mode", # Honegumi table looks strange with dark mode due to custom html
 ]
 
@@ -142,7 +147,13 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    ".venv",
+    "generated_notebooks/ax",
+]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 # default_role = None

docs/development.md

@@ -0,0 +1,11 @@
+# Development
+
+Find here additional information pertinent to developers.
+
+```{toctree}
+Contributions & Help <contributing>
+License <license>
+Authors <authors>
+Changelog <changelog>
+Module Reference <api/modules>
+```

docs/docs.md

@@ -0,0 +1,6 @@
+# Docs
+
+```{toctree}
+tutorials/sobo-vs-mobo/sobo-vs-mobo.md
+tutorials/freq-vs-bayes/freq-vs-bayes.md
+```