add flake8

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 89
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "mesonbuild.configureOnOpen": true,
+    "C_Cpp.default.compileCommands": "/Users/galois/codes/gospl/builddir/compile_commands.json",
+    "C_Cpp.default.configurationProvider": "mesonbuild.mesonbuild"
+}

docs/api_ref/flow_ref.rst

@@ -19,17 +19,14 @@ Class FAMesh
 
       ~FAMesh.flowAccumulation
       ~FAMesh.matrixFlow
-      ~FAMesh.riverIncision
 
    .. rubric:: Private Methods
 
    .. autosummary::
 
       ~FAMesh._buildFlowDirection
-      ~FAMesh._distanceCoasts
       ~FAMesh._distributeDownstream
-      ~FAMesh._getErosionRate
-      ~FAMesh._globalCoastsTree
+      ~FAMesh._getEroDepRatex
       ~FAMesh._matrix_build
       ~FAMesh._matrix_build_diag
       ~FAMesh._solve_KSP
@@ -39,17 +36,14 @@ Public functions
 
 .. automethod:: flow.flowplex.FAMesh.flowAccumulation
 .. automethod:: flow.flowplex.FAMesh.matrixFlow
-.. automethod:: flow.flowplex.FAMesh.riverIncision
 
 
 Private functions
 ---------------------
 
 .. automethod:: flow.flowplex.FAMesh._buildFlowDirection
-.. automethod:: flow.flowplex.FAMesh._distanceCoasts
 .. automethod:: flow.flowplex.FAMesh._distributeDownstream
-.. automethod:: flow.flowplex.FAMesh._getErosionRate
-.. automethod:: flow.flowplex.FAMesh._globalCoastsTree
+.. automethod:: flow.flowplex.FAMesh._getEroDepRate
 .. automethod:: flow.flowplex.FAMesh._matrix_build
 .. automethod:: flow.flowplex.FAMesh._matrix_build_diag
 .. automethod:: flow.flowplex.FAMesh._solve_KSP

docs/api_ref/in_ref.rst

@@ -20,7 +20,6 @@ Class ReadYaml
       ~ReadYaml._addTime
       ~ReadYaml._defineRain
       ~ReadYaml._defineTectonic
-      ~ReadYaml._extraCompaction
       ~ReadYaml._extraDomain
       ~ReadYaml._readCompaction
       ~ReadYaml._readDomain
@@ -40,7 +39,6 @@ Private functions
 .. automethod:: tools.inputparser.ReadYaml._addTime
 .. automethod:: tools.inputparser.ReadYaml._defineRain
 .. automethod:: tools.inputparser.ReadYaml._defineTectonic
-.. automethod:: tools.inputparser.ReadYaml._extraCompaction
 .. automethod:: tools.inputparser.ReadYaml._extraDomain
 .. automethod:: tools.inputparser.ReadYaml._readCompaction
 .. automethod:: tools.inputparser.ReadYaml._readDomain

docs/api_ref/sea_ref.rst

@@ -23,14 +23,8 @@ Class SEAMesh
 
    .. autosummary::
 
-      ~SEAMesh._diffuseOcean
       ~SEAMesh._distanceCoasts
-      ~SEAMesh._distOcean
-      ~SEAMesh._evalFunction
-      ~SEAMesh._evalJacobian
-      ~SEAMesh._getSeaVol
       ~SEAMesh._globalCoastsTree
-      ~SEAMesh._matOcean
 
 Public functions
 ---------------------
@@ -41,11 +35,5 @@ Public functions
 Private functions
 ---------------------
 
-.. automethod:: sed.seaplex.SEAMesh._diffuseOcean
 .. automethod:: sed.seaplex.SEAMesh._distanceCoasts
-.. automethod:: sed.seaplex.SEAMesh._distOcean
-.. automethod:: sed.seaplex.SEAMesh._evalFunction
-.. automethod:: sed.seaplex.SEAMesh._evalJacobian
-.. automethod:: sed.seaplex.SEAMesh._getSeaVol
 .. automethod:: sed.seaplex.SEAMesh._globalCoastsTree
-.. automethod:: sed.seaplex.SEAMesh._matOcean

docs/api_ref/sed_ref.rst

@@ -26,7 +26,6 @@ Class SEDMesh
    .. autosummary::
 
       ~SEDMesh._distributeSediment
-      ~SEDMesh._getSedVol
       ~SEDMesh._hillSlope
       ~SEDMesh._moveDownstream
       ~SEDMesh._updateSinks
@@ -43,7 +42,6 @@ Private functions
 ---------------------
 
 .. automethod:: sed.sedplex.SEDMesh._distributeSediment
-.. automethod:: sed.sedplex.SEDMesh._getSedVol
 .. automethod:: sed.sedplex.SEDMesh._hillSlope
 .. automethod:: sed.sedplex.SEDMesh._moveDownstream
 .. automethod:: sed.sedplex.SEDMesh._updateSinks

docs/conf.py

@@ -308,6 +308,8 @@ def __getattr__(cls, name):
     "scipy.interpolate",
     "vtk",
     "vtk.util",
+    "gflex",
+    "xarray",
 ]
 
 for m in MOCK_MODULES:

docs/index.rst

@@ -17,7 +17,7 @@ goSPL documentation
 `Source Repository <https://github.com/Geodels/gospl>`__ |
 `Issues & Ideas <https://github.com/Geodels/gospl/issues>`__ 
 
-**goSLP** (short for ``Global Scalable Paleo Landscape Evolution`` and pronounced: **/ˈɡospel/**, **[ˈɡo̞s̠pe̞l]**) is an open source, GPL-licensed library providing a scalable parallelised Python-based numerical model to simulate landscapes and basins reconstruction at global scale. goSPL is developed by the `EarthCodeLab Group <https://earthcolab.org>`_ at the University of Sydney.
+**goSPL** (short for ``Global Scalable Paleo Landscape Evolution``) is an open source, GPL-licensed library providing a scalable parallelised Python-based numerical model to simulate landscapes and basins reconstruction at global scale. goSPL is developed by the `EarthCodeLab Group <https://earthcolab.org>`_ at the University of Sydney.
 
 
 Statement of need

gospl/tools/cgflex.py

@@ -7,13 +7,14 @@
 import petsc4py
 import numpy as np
 
-# import rioxarray
 import xarray as xr
 from mpi4py import MPI
 from pathlib import Path
-from gflex.f2d import F2D
 from time import process_time
 
+if "READTHEDOCS" not in os.environ:
+    from gflex.f2d import F2D
+
 petsc4py.init(sys.argv)
 MPIrank = petsc4py.PETSc.COMM_WORLD.Get_rank()
 MPIsize = petsc4py.PETSc.COMM_WORLD.Get_size()

gospl/tools/inputparser.py

@@ -3,10 +3,12 @@
 import petsc4py
 import numpy as np
 import pandas as pd
-from ruamel.yaml import YAML
 
 from operator import itemgetter
-from scipy.interpolate import interp1d
+
+if "READTHEDOCS" not in os.environ:
+    from ruamel.yaml import YAML
+    from scipy.interpolate import interp1d
 
 petsc4py.init(sys.argv)
 MPIrank = petsc4py.PETSc.COMM_WORLD.Get_rank()