Merge pull request #7 from JuliaGeodynamics/nr-vtk-python2julia

Replace python with julia

Project.toml

@@ -7,16 +7,14 @@ version = "0.1.6"
 GeophysicalModelGenerator = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 LaMEM_jll = "15d6fa20-f789-5486-b71b-22b4ac8eb1c1"
-MicroMamba = "0b3b1443-0f03-428d-bdfb-f27f9c1191ea"
-PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+ReadVTK = "dc215faf-f008-4882-a9f7-a79a826fadc3"
 
 [compat]
 GeophysicalModelGenerator = "0.4"
 Glob = "1"
-LaMEM_jll = "1.2"
-MicroMamba = "0.1.9 - 0.1.9"        # MicroMamba 0.1.10 appears to be broken
-PythonCall = "0.9"
+LaMEM_jll = "1.2.3"
 julia = "1.6"
+ReadVTK = "0.1.5"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/IO.jl

@@ -0,0 +1,11 @@
+module IO
+# this contains I/O routines of LaMEM, which don't require LaMEM_jll
+
+include("read_timestep.jl")
+export Read_LaMEM_PVTR_File, Read_LaMEM_PVTS_File, field_names, readPVD, Read_LaMEM_PVTU_File
+
+include("utils_IO.jl")
+export clean_directory, changefolder
+
+
+end

src/LaMEM.jl

@@ -1,40 +1,16 @@
 module LaMEM
-using LaMEM_jll
-using PythonCall
-using Glob
 
-ENV["JULIA_CONDAPKG_BACKEND"] = "MicroMamba"
-
-# load the correct MPI
-const mpiexec = if isdefined(LaMEM_jll,:MPICH_jll)
-    LaMEM_jll.MPICH_jll.mpiexec()
-elseif isdefined(LaMEM_jll,:MicrosoftMPI_jll) 
-    LaMEM_jll.MicrosoftMPI_jll.mpiexec()
-else
-    nothing
-end
-
-# Reading files back into julia
-const pyvtk = PythonCall.pynew()
-
-function __init__()
-
-    println("Adding PythonCall dependencies to read LaMEM timesteps")
-    pth = (@__DIR__)*"/python"        # Path where the python routines are
-    pyimport("sys").path.append(pth)  # append path
-
-    # link vtk. Note that all python dependencies are listed in PythonCallDeps.toml
-    PythonCall.pycopy!(pyvtk, pyimport("vtk"))            # used to read VTK files
-end
-
-
-include("run_lamem.jl")
-include("run_lamem_save_grid.jl")
-include("read_timestep.jl")
-include("utils.jl")
-
-export run_lamem
-export run_lamem_save_grid
-export pyvtk
+# Functions to read LaMEM output
+include("IO.jl")
+using .IO
+export Read_LaMEM_PVTR_File, Read_LaMEM_PVTS_File, Read_LaMEM_PVTU_File
+export Read_LaMEM_simulation, Read_LaMEM_timestep, Read_LaMEM_fieldnames
+export clean_directory, changefolder
+
+# Functions 
+include("Run.jl")
+using .Run
+export run_lamem, run_lamem_save_grid, mpiexec
+export remove_popup_messages_mac, show_paths_LaMEM
 
 end # module

src/Run.jl

@@ -0,0 +1,22 @@
+module Run
+# module to run LaMEM_jll
+using LaMEM_jll,Glob
+
+export run_lamem, run_lamem_save_grid, mpiexec
+export remove_popup_messages_mac, show_paths_LaMEM
+
+include("run_lamem.jl")
+include("run_lamem_save_grid.jl")
+include("utils_Run.jl")
+
+# load the correct MPI
+const mpiexec = if isdefined(LaMEM_jll,:MPICH_jll)
+    LaMEM_jll.MPICH_jll.mpiexec()
+elseif isdefined(LaMEM_jll,:MicrosoftMPI_jll) 
+    LaMEM_jll.MicrosoftMPI_jll.mpiexec()
+else
+    nothing
+end
+
+
+end