add missing functions in the API doc

Geodels · Jun 24, 2024 · deef2f0 · deef2f0
1 parent 931e7d0
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,5 +1,6 @@
 {
     "mesonbuild.configureOnOpen": true,
     "C_Cpp.default.compileCommands": "/Users/galois/codes/gospl/builddir/compile_commands.json",
-    "C_Cpp.default.configurationProvider": "mesonbuild.mesonbuild"
+    "C_Cpp.default.configurationProvider": "mesonbuild.mesonbuild",
+    "fortran.fortls.disabled": true
 }
diff --git a/docs/_static/version_switch.json b/docs/_static/version_switch.json
@@ -9,10 +9,5 @@
         "version":"1.1.1",
         "preferred": true,
         "url": "https://gospl.readthedocs.io"
-    },
-    {
-        "name": "0.2.10 (stable)",
-        "version":"0.2.10-stable",
-        "url": "https://gospl.readthedocs.io/en/stable/"
     }
 ]
diff --git a/docs/api_ref/flow_ref.rst b/docs/api_ref/flow_ref.rst
@@ -17,6 +17,7 @@ Class FAMesh
 
    .. autosummary::
 
+      ~FAMesh.erodepSPL
       ~FAMesh.flowAccumulation
       ~FAMesh.matrixFlow
 
@@ -26,14 +27,17 @@ Class FAMesh
 
       ~FAMesh._buildFlowDirection
       ~FAMesh._distributeDownstream
-      ~FAMesh._getEroDepRatex
+      ~FAMesh._getEroDepRate
+      ~FAMesh._iceFlow
       ~FAMesh._matrix_build
       ~FAMesh._matrix_build_diag
       ~FAMesh._solve_KSP
+      ~FAMesh._upstreamDeposition
 
 Public functions
 ---------------------
 
+.. automethod:: flow.flowplex.FAMesh.erodepSPL
 .. automethod:: flow.flowplex.FAMesh.flowAccumulation
 .. automethod:: flow.flowplex.FAMesh.matrixFlow
 
@@ -44,6 +48,8 @@ Private functions
 .. automethod:: flow.flowplex.FAMesh._buildFlowDirection
 .. automethod:: flow.flowplex.FAMesh._distributeDownstream
 .. automethod:: flow.flowplex.FAMesh._getEroDepRate
+.. automethod:: flow.flowplex.FAMesh._iceFlow
 .. automethod:: flow.flowplex.FAMesh._matrix_build
 .. automethod:: flow.flowplex.FAMesh._matrix_build_diag
 .. automethod:: flow.flowplex.FAMesh._solve_KSP
+.. automethod:: flow.flowplex.FAMesh._upstreamDeposition
diff --git a/docs/api_ref/gflex_ref.rst b/docs/api_ref/gflex_ref.rst
@@ -0,0 +1,51 @@
+.. _grid_ref:
+
+
+=================
+Class GlobalFlex
+=================
+
+.. autoclass:: tools.cgflex.GlobalFlex
+
+   .. rubric:: Initialise
+
+   .. autosummary::
+
+      ~GlobalFlex.__init__
+
+   .. rubric:: Public Methods
+
+   .. autosummary::
+
+      ~GlobalFlex.globalFlexIso
+
+   .. rubric:: Private Methods
+
+   .. autosummary::
+
+      ~GlobalFlex._cmptFlex
+      ~GlobalFlex._getFlex
+      ~GlobalFlex._getNorthPole
+      ~GlobalFlex._getSouthPole
+      ~GlobalFlex._getTiles
+      ~GlobalFlex._flexTiles
+      ~GlobalFlex._mergeTile
+      ~GlobalFlex._runFlexure
+
+Public functions
+---------------------
+
+.. automethod:: tools.cgflex.GlobalFlex.globalFlexIso
+
+
+Private functions
+---------------------
+
+.. automethod:: tools.cgflex.GlobalFlex._cmptFlex
+.. automethod:: tools.cgflex.GlobalFlex._getFlex
+.. automethod:: tools.cgflex.GlobalFlex._getNorthPole
+.. automethod:: tools.cgflex.GlobalFlex._getSouthPole
+.. automethod:: tools.cgflex.GlobalFlex._getTiles
+.. automethod:: tools.cgflex.GlobalFlex._flexTiles
+.. automethod:: tools.cgflex.GlobalFlex._mergeTile
+.. automethod:: tools.cgflex.GlobalFlex._runFlexure
diff --git a/docs/api_ref/grid_ref.rst b/docs/api_ref/grid_ref.rst
@@ -0,0 +1,39 @@
+.. _grid_ref:
+
+
+=================
+Class GridProcess
+=================
+
+.. autoclass:: tools.addprocess.GridProcess
+
+   .. rubric:: Initialise
+
+   .. autosummary::
+
+      ~GridProcess.__init__
+
+   .. rubric:: Public Methods
+
+   .. autosummary::
+
+      ~GridProcess.applyFlexure
+      ~GridProcess.cptOrography
+
+   .. rubric:: Private Methods
+
+   .. autosummary::
+
+      ~GridProcess._buildRegGrid
+
+Public functions
+---------------------
+
+.. automethod:: tools.addprocess.GridProcess.applyFlexure
+.. automethod:: tools.addprocess.GridProcess.cptOrography
+
+
+Private functions
+---------------------
+
+.. automethod:: tools.addprocess.GridProcess._buildRegGrid
diff --git a/docs/api_ref/in_ref.rst b/docs/api_ref/in_ref.rst
@@ -18,35 +18,57 @@ Class ReadYaml
    .. autosummary::
 
       ~ReadYaml._addTime
+      ~ReadYaml._defineErofactor
+      ~ReadYaml._definePlate
       ~ReadYaml._defineRain
       ~ReadYaml._defineTectonic
       ~ReadYaml._extraDomain
+      ~ReadYaml._extraHillslope
+      ~ReadYaml._extraOrography
       ~ReadYaml._readCompaction
       ~ReadYaml._readDomain
+      ~ReadYaml._readErofactor
+      ~ReadYaml._readFlex
+      ~ReadYaml._readGFlex
       ~ReadYaml._readHillslope
+      ~ReadYaml._readIce
+      ~ReadYaml._readOrography
       ~ReadYaml._readOut
+      ~ReadYaml._readPlate
       ~ReadYaml._readRain
       ~ReadYaml._readSPL
       ~ReadYaml._readSealevel
       ~ReadYaml._readTectonic
       ~ReadYaml._readTime
+      ~ReadYaml._storePlate
       ~ReadYaml._storeTectonic
 
 
 Private functions
 ---------------------
 
 .. automethod:: tools.inputparser.ReadYaml._addTime
+.. automethod:: tools.inputparser.ReadYaml._defineErofactor
+.. automethod:: tools.inputparser.ReadYaml._definePlate
 .. automethod:: tools.inputparser.ReadYaml._defineRain
 .. automethod:: tools.inputparser.ReadYaml._defineTectonic
 .. automethod:: tools.inputparser.ReadYaml._extraDomain
+.. automethod:: tools.inputparser.ReadYaml._extraHillslope
+.. automethod:: tools.inputparser.ReadYaml._extraOrography
 .. automethod:: tools.inputparser.ReadYaml._readCompaction
 .. automethod:: tools.inputparser.ReadYaml._readDomain
+.. automethod:: tools.inputparser.ReadYaml._readErofactor
+.. automethod:: tools.inputparser.ReadYaml._readFlex
+.. automethod:: tools.inputparser.ReadYaml._readGFlex
 .. automethod:: tools.inputparser.ReadYaml._readHillslope
+.. automethod:: tools.inputparser.ReadYaml._readIce
+.. automethod:: tools.inputparser.ReadYaml._readOrography
 .. automethod:: tools.inputparser.ReadYaml._readOut
+.. automethod:: tools.inputparser.ReadYaml._readPlate
 .. automethod:: tools.inputparser.ReadYaml._readRain
 .. automethod:: tools.inputparser.ReadYaml._readSPL
 .. automethod:: tools.inputparser.ReadYaml._readSealevel
 .. automethod:: tools.inputparser.ReadYaml._readTectonic
 .. automethod:: tools.inputparser.ReadYaml._readTime
+.. automethod:: tools.inputparser.ReadYaml._storePlate
 .. automethod:: tools.inputparser.ReadYaml._storeTectonic
diff --git a/docs/api_ref/index.rst b/docs/api_ref/index.rst
@@ -7,7 +7,7 @@ API reference
 
 .. note::
 
-    This section provides an overview of main goSPL objects, functions and methods.
+    This section provides an overview of goSPL main objects, functions and methods.
 
 .. grid:: 1
     :padding: 5
@@ -112,7 +112,21 @@ API reference
 
             See functions and source code.
 
+    .. grid-item-card::
+        :text-align: center
+
+        **Class Earth Plates**
+        ^^^
+
+        Functions to evaluate horizontal interpolation when considering tectonic plate reconstruction.
 
+        +++
+
+        .. button-ref:: plate_ref
+            :color: secondary
+            :click-parent:
+
+            See functions and source code.
 
     .. grid-item-card::
         :text-align: center
@@ -146,6 +160,39 @@ API reference
 
             See functions and source code.
 
+
+    .. grid-item-card::
+        :text-align: center
+
+        **Class Grid Processes**
+        ^^^
+
+        Functions related to additional processes performed on a regular grid.
+
+        +++
+
+        .. button-ref:: grid_ref
+            :color: secondary
+            :click-parent:
+
+            See functions and source code.
+
+    .. grid-item-card::
+        :text-align: center
+
+        **Class Global Flexure**
+        ^^^
+
+        This class solves flexural isostasy at global scale.
+
+        +++
+
+        .. button-ref:: gflex_ref
+            :color: secondary
+            :click-parent:
+
+            See functions and source code.
+
     .. grid-item-card::
         :text-align: center
 
@@ -173,5 +220,8 @@ API reference
     sed_ref
     sea_ref
     stra_ref
+    plate_ref
     in_ref
+    grid_ref
+    gflex_ref
     out_ref
diff --git a/docs/api_ref/plate_ref.rst b/docs/api_ref/plate_ref.rst
@@ -0,0 +1,47 @@
+.. _plate_ref:
+
+
+=================
+Class EarthPlate
+=================
+
+.. autoclass:: mesher.earthplates.EarthPlate
+
+   .. rubric:: Initialise
+
+   .. autosummary::
+
+      ~EarthPlate.__init__
+
+   .. rubric:: Public Methods
+
+   .. autosummary::
+
+      ~EarthPlate.advectPlates
+
+   .. rubric:: Private Methods
+
+   .. autosummary::
+
+      ~EarthPlate._advectStrata
+      ~EarthPlate._getPaleoInfo
+      ~EarthPlate._readAdvectionData
+      ~EarthPlate._stratPlates
+      ~EarthPlate._updatePaleoElev
+      ~EarthPlate._updateStrataVars
+
+Public functions
+---------------------
+
+.. automethod:: mesher.earthplates.EarthPlate.advectPlates
+
+
+Private functions
+---------------------
+
+.. automethod:: mesher.earthplates.EarthPlate._advectStrata
+.. automethod:: mesher.earthplates.EarthPlate._getPaleoInfo
+.. automethod:: mesher.earthplates.EarthPlate._readAdvectionData
+.. automethod:: mesher.earthplates.EarthPlate._stratPlates
+.. automethod:: mesher.earthplates.EarthPlate._updatePaleoElev
+.. automethod:: mesher.earthplates.EarthPlate._updateStrataVars
diff --git a/docs/api_ref/sea_ref.rst b/docs/api_ref/sea_ref.rst
@@ -25,6 +25,7 @@ Class SEAMesh
 
       ~SEAMesh._distanceCoasts
       ~SEAMesh._globalCoastsTree
+      ~SEAMesh._marineFluxes
 
 Public functions
 ---------------------
@@ -37,3 +38,4 @@ Private functions
 
 .. automethod:: sed.seaplex.SEAMesh._distanceCoasts
 .. automethod:: sed.seaplex.SEAMesh._globalCoastsTree
+.. automethod:: sed.seaplex.SEAMesh._marineFluxes
diff --git a/docs/tech_guide/index.rst b/docs/tech_guide/index.rst
@@ -18,7 +18,7 @@ Further information on any specific methods can be obtained in the :ref:`api_ref
         **Short Description**
         ^^^
 
-        The code is primarily a **parallel global scale landscape evolution model**, built to simulate **topography and basins** dynamics. It has the ability to track **two types of clastic sediment size**. The following processes are considered:
+        The code is primarily a **parallel global scale landscape evolution model**, built to simulate **topography and basins** dynamics. The following processes are considered:
 
         - **river incision** and **deposition** using stream power law,
         - continental **deposition** in depressions,