Merge branch 'develop' into Two_leaf_irradience_model

.pre-commit-config.yaml

@@ -1,35 +1,36 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.2
+    rev: v0.6.9
     hooks:
       # Run the linter.
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       # Run the formatter.
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.1"
+    rev: "v1.11.2"
     hooks:
       - id: mypy
         additional_dependencies: [numpy, types-tabulate, pandas-stubs]
         exclude: "pyrealm_build_data/splash/splash_py_version/.*\\.py"
         # https://stackoverflow.com/a/75447331/3401916
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.41.0
+    rev: v0.42.0
     hooks:
     - id: markdownlint
   - repo: https://github.com/mwouts/jupytext
-    rev: v1.16.3d
+    rev: v1.16.4b
     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

@@ -1,6 +1,7 @@
 root: index
 subtrees:
 
+
 - caption: Users
   entries: 
   - file: users/pmodel/module_overview.md
@@ -12,7 +13,8 @@ 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
@@ -26,7 +28,16 @@ subtrees:
               - file: users/pmodel/subdaily_details/worked_example.md
         - file: users/pmodel/c3c4model.md
         - file: users/pmodel/isotopic_discrimination.md
+  - file: users/demography/module_overview.md
+    subtrees:
+      - entries:
+        - file: users/demography/flora.md
+        - file: users/demography/t_model.md
+        - file: users/demography/crown.md
+        - file: users/demography/community.md
+        - file: users/demography/canopy.md
   - file: users/tmodel/tmodel.md
+  - file: users/tmodel/canopy.md
   - file: users/splash.md
   - file: users/constants.md
   - file: users/hygro.md 

docs/source/api/constants_api.md

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # The {mod}`~pyrealm.constants` module

docs/source/api/core_api.md

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # The {mod}`~pyrealm.core` module

docs/source/api/demography_api.md

@@ -0,0 +1,71 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.16.4
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
+---
+
+# The {mod}`~pyrealm.demography` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography
+    :autosummary:
+    :members:
+```
+
+## The {mod}`~pyrealm.demography.flora` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.flora
+    :autosummary:
+    :members:
+```
+
+## The {mod}`~pyrealm.demography.t_model_functions` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.t_model_functions
+    :autosummary:
+    :members:
+```
+
+## The {mod}`~pyrealm.demography.crown` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.crown
+    :autosummary:
+    :members:
+```
+
+## The {mod}`~pyrealm.demography.community` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.community
+    :autosummary:
+    :members:
+```
+
+## The {mod}`~pyrealm.demography.canopy` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.canopy
+    :autosummary:
+    :members:
+```

docs/source/api/pmodel_api.md

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # The {mod}`~pyrealm.pmodel` module
@@ -50,6 +60,14 @@ 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

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # The {mod}`~pyrealm.splash` module

docs/source/api/tmodel_api.md

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # The {mod}`~pyrealm.tmodel` module

docs/source/conf.py

@@ -12,13 +12,18 @@
 from dataclasses import dataclass, field
 from datetime import datetime
 
+# Import Matplotlib to avoid this message in notebooks:
+# "Matplotlib is building the font cache; this may take a moment."
+import matplotlib.pyplot  # noqa: F401
 import sphinxcontrib.bibtex.plugin
 from sphinxcontrib.bibtex.style.referencing import BracketStyle
 from sphinxcontrib.bibtex.style.referencing.author_year import AuthorYearReferenceStyle
 
 from pyrealm import __version__ as pyrealm_version
 
+# +
 sys.path.insert(0, os.path.abspath("../"))
+# -
 
 
 # -- Project information -----------------------------------------------------
@@ -55,7 +60,9 @@
 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 +89,7 @@ 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
@@ -92,6 +99,8 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "numpy._typing._array_like._ScalarType_co"),
     ("py:class", "numpy._typing._generic_alias.ScalarType"),
     ("py:class", "numpy.float32"),
+    ("py:class", "numpy.float64"),
+    ("py:class", "numpy.int64"),
     ("py:class", "numpy.timedelta64"),
     ("py:class", "numpy.bool_"),
     ("py:class", "numpy.ndarray"),
@@ -140,15 +149,20 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
             "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]"
         ),
     ),
+    ("py:class", "pandas.core.frame.DataFrame"),
 ]
 
+# +
 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),
+    "pandas": ("http://pandas.pydata.org/pandas-docs/dev/", None),
     "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
+    "marshmallow": ("https://marshmallow.readthedocs.io/en/stable/", None),
 }
+# -
 
 
 autodoc_default_flags = ["members"]
@@ -195,6 +209,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 # html_theme = 'sphinx_material'
 html_theme = "sphinx_rtd_theme"
 
+# +
 html_theme_options = {
     "logo_only": False,
     "display_version": True,
@@ -208,6 +223,7 @@ 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

@@ -5,11 +5,21 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.16.3
+    jupytext_version: 1.16.4
 kernelspec:
   display_name: Python 3
   language: python
   name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
 ---
 
 # Code quality and static typing