Added back <=3.11 for tomli dependency. Removed black and isort from …

…format.sh script. Updated documentation to more modern format.

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
     rev: v4.6.0
     hooks:
       - id: check-yaml
+        exclude: mkdocs.yml
       - id: check-added-large-files
         args: ["--maxkb=250"]
   - repo: https://github.com/Yelp/detect-secrets

README.md

@@ -15,7 +15,7 @@
 
 ## The QC Suite of Programs
 
-- [qcio](https://github.com/coltonbh/qcio) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations.
+- [qcio](https://github.com/coltonbh/qcio) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcio.coltonhicks.com)
 - [qcparse](https://github.com/coltonbh/qcparse) - A library for efficient parsing of quantum chemistry data into structured `qcio` objects.
 - [qcop](https://github.com/coltonbh/qcop) - A package for operating quantum chemistry programs using `qcio` standardized data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC`, and many more, featuring seamless Jupyter Notebook visualizations.
 - [BigChem](https://github.com/mtzgroup/bigchem) - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program, featuring seamless Jupyter Notebook visualizations.

chemcloud/config.py

@@ -1,4 +1,4 @@
-from __future__ import annotations
+from __future__ import annotations  # Can remove once we drop Python 3.9 support
 
 from pathlib import Path
 from typing import Optional

docs/CHANGELOG.md

@@ -6,13 +6,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Changed
+
 - Removed `black` and `isort` in favor for `ruff`
 - Updated:
-    - `python` (`>3.8` -> `>3.9`)
-    - `tomli` (`^1.0` -> `^2.0`)
-    - `httpx` (`^0.23.1` -> `^0.27`)
-    - `ruff` (`^0.0287` -> `^0.5`)
-    - `pytest-httpx` (`<0.23.0` -> `>=0.23.0`)
+  - `python` (`>3.8` -> `>3.9`)
+  - `tomli` (`^1.0` -> `^2.0`)
+  - `httpx` (`^0.23.1` -> `^0.27`)
+  - `ruff` (`^0.0287` -> `^0.5`)
+  - `pytest-httpx` (`<0.23.0` -> `>=0.23.0`)
+- `format.sh` script dropped `black` and `isort`.
 
 ## [0.11.1] - 2024-07-19
 

docs/index.md

@@ -15,7 +15,7 @@
 
 ## The QC Suite of Programs
 
-- [qcio](https://github.com/coltonbh/qcio) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations.
+- [qcio](https://github.com/coltonbh/qcio) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcio.coltonhicks.com)
 - [qcparse](https://github.com/coltonbh/qcparse) - A library for efficient parsing of quantum chemistry data into structured `qcio` objects.
 - [qcop](https://github.com/coltonbh/qcop) - A package for operating quantum chemistry programs using `qcio` standardized data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC`, and many more, featuring seamless Jupyter Notebook visualizations.
 - [BigChem](https://github.com/mtzgroup/bigchem) - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program, featuring seamless Jupyter Notebook visualizations.

mkdocs.yml

@@ -3,14 +3,36 @@ site_url: https://mtzgroup.github.io/chemcloud-client/
 theme:
   name: material
   palette:
-    - scheme: default
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
       primary: teal
       accent: amber
+      toggle:
+        icon: material/lightbulb
+        name: Switch to dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: teal
+      accent: amber
+      toggle:
+        icon: material/lightbulb-outline
+        name: Switch to light mode
   features:
-    - search.suggest
-    - search.highlight
+    - content.tabs.link
+    - content.code.annotate
+    - content.code.copy
+    - announce.dismiss
+    - navigation.tabs
     - navigation.instant
-    - navigation.expand
+    - navigation.instant.prefetch
+    - navigation.instant.preview
+    - navigation.instant.progress
+    - navigation.path
+    - navigation.sections
+    - navigation.top
+    - navigation.tracking
+    - search.suggest
+    - toc.follow
   icon:
     repo: fontawesome/brands/github-alt
 
@@ -24,27 +46,46 @@ plugins:
   - mkdocstrings:
       handlers:
         python:
-          rendering:
-            show_root_heading: False
-            show_root_full_path: True
-            show_category_heading: True
-            show_signature_annotations: True
-            show_if_no_docstring: True
-            group_by_category: True
-            heading_level: 2
-          selection:
-            new_path_syntax: True
-            inherited_members: True
+          options:
+            members_order: source
+            separate_signature: true
+            show_bases: false
+            show_root_heading: true
+            show_symbol_type_heading: true
+            show_symbol_type_toc: true
+            merge_init_into_class: true
+            show_signature_annotations: true
+            signature_crossrefs: true
+            inherited_members: false
+            # Pretty sure I want this false.
+            show_if_no_docstring: false
+
+            docstring_options:
+              ignore_init_summary: true
+
             filters:
               - "!^_"
-              - "^__init__$"
+              - "!^model"
+              - "^__init__"
+
+          selection:
+            new_path_syntax: true
+
 markdown_extensions:
-  - pymdownx.highlight
-  - pymdownx.superfences
-  - pymdownx.details
-  - admonition
   - toc:
-      permalink: 🔗
+      permalink: true
+      title: Page contents
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.highlight:
+      pygments_lang_class: true
+  - pymdownx.extra
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - pymdownx.tabbed:
+      alternate_style: true
   - markdown_include.include:
       base_path: docs
 

pyproject.toml

@@ -27,7 +27,7 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-tomli = "^2.0"
+tomli = { version = "^2.0", python = "<3.11" }
 tomli-w = "^1.0.0"
 httpx = "^0.27"
 qcio = "^0.11.0"
@@ -63,9 +63,7 @@ target-version = "py39"
 
 [tool.ruff.lint]
 isort = { known-first-party = ["tests"] }
-select = [
-    "I"
-]
+select = ["I"]
 
 [tool.coverage.run]
 branch = true

scripts/format.sh

@@ -2,6 +2,4 @@
 
 set -x
 
-poetry run black .
-poetry run isort .
 poetry run ruff check --fix .