Merge pull request #545 from legend-exp/refactor

`math` refactor and `pargen` updates

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
   autoupdate_schedule: "quarterly"
   autofix_commit_msg: "style: pre-commit fixes"
 
-exclude: ^(attic|tutorials|src/pygama/math|src/pygama/flow/datagroup.py)
+exclude: ^(attic|src/pygama/flow/datagroup.py)
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: "v4.5.0"
@@ -17,7 +17,6 @@ repos:
   - id: check-json
   - id: check-toml
   - id: check-docstring-first
-    exclude: ^src/pygama/raw/(fc/fc_event_decoder.py|compass/compass_event_decoder.py)$
   - id: debug-statements
   - id: end-of-file-fixer
   - id: forbid-new-submodules
@@ -57,14 +56,12 @@ repos:
   rev: "v2.4.0"
   hooks:
   - id: pycln
-    exclude: ^src/pygama/pargen
     args: [--all]
 
 - repo: https://github.com/PyCQA/flake8
   rev: "7.0.0"
   hooks:
   - id: flake8
-    exclude: ^src/pygama/pargen
     additional_dependencies: [
       flake8-bugbear>=23.1.17,
       flake8-print,
@@ -89,6 +86,8 @@ repos:
   rev: "v2.2.6"
   hooks:
   - id: codespell
+    additional_dependencies:
+      - tomli
 
 - repo: https://github.com/shellcheck-py/shellcheck-py
   rev: "v0.10.0.1"

docs/source/index.rst

@@ -51,6 +51,11 @@ Next steps
 
    Package API reference <api/modules>
 
+.. toctree::
+   :maxdepth: 1
+
+   tutorials
+
 .. toctree::
    :maxdepth: 1
    :caption: Related projects