Initial draft of new quantum yield module

.pre-commit-config.yaml

@@ -29,7 +29,8 @@ repos:
     hooks:
     - id: jupytext
       args: [--pipe, black]
-      files: docs/source 
+      files: docs/source
+      exclude: docs/source/conf.py
       additional_dependencies:
         - black==24.4.2 # Matches hook
 

docs/source/_toc.yml

@@ -12,7 +12,8 @@ subtrees:
               - file: users/pmodel/pmodel_details/worked_examples.md
               - file: users/pmodel/pmodel_details/photosynthetic_environment.md
               - file: users/pmodel/pmodel_details/optimal_chi.md
-              - file: users/pmodel/pmodel_details/lue_limitation.md
+              - file: users/pmodel/pmodel_details/quantum_yield.md
+              - file: users/pmodel/pmodel_details/jmax_limitation.md
               - file: users/pmodel/pmodel_details/envt_variation_outputs.md
               - file: users/pmodel/pmodel_details/soil_moisture.md
               - file: users/pmodel/pmodel_details/extreme_values.md

docs/source/api/constants_api.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/api/core_api.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/api/pmodel_api.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
@@ -50,6 +49,14 @@ kernelspec:
     :members:
 ```
 
+## The {mod}`~pyrealm.pmodel.quantum_yield` submodule
+
+```{eval-rst}
+.. automodule:: pyrealm.pmodel.quantum_yield
+    :autosummary:
+    :members:
+```
+
 ## The {mod}`~pyrealm.pmodel.functions` submodule
 
 ```{eval-rst}

docs/source/api/splash_api.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/api/tmodel_api.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/conf.py

@@ -18,7 +18,9 @@
 
 from pyrealm import __version__ as pyrealm_version
 
+# +
 sys.path.insert(0, os.path.abspath("../"))
+# -
 
 
 # -- Project information -----------------------------------------------------
@@ -55,7 +57,9 @@
 external_toc_path = "_toc.yml"  # optional, default: _toc.yml
 external_toc_exclude_missing = False  # optional, default: False
 
+# + [markdown]
 # Citation styling
+# -
 
 
 def bracket_style() -> BracketStyle:
@@ -82,7 +86,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 )
 
 bibtex_reference_style = "author_year_round"
-
+bibtex_default_style = "plain"
 
 # Cross-reference checking
 # TODO - find some better solution than this to all of these bizarre cross reference
@@ -142,13 +146,15 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ),
 ]
 
+# +
 intersphinx_mapping = {
     "pytest": ("https://docs.pytest.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "python": ("https://docs.python.org/3/", None),
     "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
 }
+# -
 
 
 autodoc_default_flags = ["members"]
@@ -195,6 +201,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 # html_theme = 'sphinx_material'
 html_theme = "sphinx_rtd_theme"
 
+# +
 html_theme_options = {
     "logo_only": False,
     "display_version": True,
@@ -208,6 +215,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     "includehidden": True,
     "titles_only": False,
 }
+# -
 
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/source/development/code_qa_and_typing.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/code_testing.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/documentation.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
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docs/source/development/github_actions.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/overview.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/profiling_and_benchmarking.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/pyrealm_build_data.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/development/release_process.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python

docs/source/index.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python