geodels / gospl Goto Github PK

Global Scalable Paleo Landscape Evolution Model

License: GNU General Public License v3.0

Fortran 22.81% Python 76.70% Meson 0.49%

paleogeography sediment-transport paleoclimate landscape landscape-evolution-model basin-modeling sedimentation erosion-process lithology compaction

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kbarnhart rinzeschuurmans xinzhou1006 scottpham underworld-community qxzsilver1 utpal-singh lgtm-migrator blingwang1996 manish7sep richardscottoz

gospl's Issues

gospl package fails to install on Windows 10

Describe the bug
gospl package fails to install on Windows 10

To Reproduce
remove petsc4py from conda environment yml
try creating environment

Expected behavior
package installs

Desktop (please complete the following information):

OS:Windows 10
Additional context

Collecting gospl (from -r C:\Users\rscott\OneDrive - BHP\Exploration2024\condaenv.ofn7_qzu.requirements.txt (line 1))
  Downloading gospl-1.1.1.tar.gz (79.0 MB)
     ---------------------------------------- 79.0/79.0 MB 3.7 MB/s eta 0:00:00
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'

Pip subprocess error:
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
The system cannot find the path specified.
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [14 lines of output]
      + meson setup C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032 C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032\.mesonpy-kwr4rhds -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032\.mesonpy-kwr4rhds\meson-python-native-file.ini
      The Meson build system
      Version: 1.4.1
      Source dir: C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032
      Build dir: C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032\.mesonpy-kwr4rhds
      Build type: native build
      Project name: gospl
      Project version: 1.1.1

      ..\meson.build:1:0: ERROR: Unknown compiler(s): [['cl.exe']]
      The following exception(s) were encountered:
      Running `cl.exe /?` gave "[WinError 2] The system cannot find the file specified"

      A full log can be found at C:\Users\rscott\AppData\Local\Temp\pip-install-rtc58ov6\gospl_6e74fe112a1e455f925592173173b032\.mesonpy-kwr4rhds\meson-logs\meson-log.txt
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

failed

CondaEnvException: Pip failed

error running bfModel.ipynb within definegtin function

Hi @tristan-salles, I am testing your notebook example bfModel.ipynb as part of the review process for JOSS. I have installed gospl using mamba (its a wee bit faster, and developed locally here in Paris):

mamba env create -f conda-env.yml
mamba install jupyterlab

and then,

mamba install -c conda-forge pyvista
pip install stripy

The notebook however falls over with an error on the second cell:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-3-4e10a22dcc17> in <module>
     30 a = np.sort(Gmesh.idx_hierarchy.reshape(s[0], -1).T)
     31 Gmesh.edges = {"nodes": np.unique(a, axis=0)}
---> 32 ngbNbs, ngbID = definegtin(len(coords), Gmesh.cells['nodes'], 
     33                            Gmesh.edges['nodes'])
     34 

KeyError: 'nodes'

Do you have any ideas what is causing this error? I am probably missing a dependency, I guess.

bfModel hdf5

Describe the bug
non-existent flowAcc data

To Reproduce
run bfModel notebook udpated

Expected behavior
vtk output

Desktop (please complete the following information):

OS: WSL

Additional context

EDrate
elev
erodep
fillFA
hdisp
rain
sedLoad
waterFill
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[9], line 2
      1 # Reading the final output generated by gospl
----> 2 output = rout.readOutput(filename='forward.yml',step=15)
      4 # Exporting the final output as a VTK mesh
      5 output.exportVTK('step15.vtk')

File /mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/readOutput.py:33, in readOutput.__init__(self, filename, step)
     29 self._inputParser()
     31 self.nbCPUs = len(glob.glob1(self.outputDir + "/h5/", "topology.p*"))
---> 33 self._readElevationData(step)
     35 return

File /mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/readOutput.py:298, in readOutput._readElevationData(self, step)
    296 def _readElevationData(self, step):
--> 298     self._getCoordinates(step)
    300     return

File /mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/readOutput.py:105, in readOutput._getCoordinates(self, step)
    103 erodep = np.array((df2["/erodep"]))
    104 sedLoad = np.array((df2["/sedLoad"]))
--> 105 flowAcc = np.array((df2["/flowAcc"]))
    106 uplift = np.array((df2["/uplift"]))
    107 hdisp = np.array((df2["/hdisp"]))

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File ~/miniconda3/envs/gospl-package/lib/python3.9/site-packages/h5py/_hl/group.py:357, in Group.__getitem__(self, name)
    355         raise ValueError("Invalid HDF5 object reference")
    356 elif isinstance(name, (bytes, str)):
--> 357     oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
    358 else:
    359     raise TypeError("Accessing a group is done with bytes or str, "
    360                     "not {}".format(type(name)))

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5o.pyx:241, in h5py.h5o.open()

KeyError: "Unable to synchronously open object (object 'flowAcc' doesn't exist)"

AttributeError: 'icosahedral_mesh' object has no attribute 'lpoints'

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Install an environment, try and run bfModel notebook

Expected behavior
runs

Desktop (please complete the following information):

OS: WSL

Additional context
Add any other context about the problem here.

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[2], line 18
     14     grid = stripy.spherical_meshes.octahedral_mesh(include_face_points=False, 
     15                                                    refinement_levels=ref_lvl)
     17 str_fmt = "{:25} {:9}"
---> 18 print(str_fmt.format('Number of points', grid.lpoints))
     19 print(str_fmt.format('Number of cells', grid.simplices.shape[0]))
     21 # Take the unit sphere mesh and assign the Earth radius to the coordinates

AttributeError: 'icosahedral_mesh' object has no attribute 'lpoints'

JOSS review: very minor points

This issue is part of my JOSS review: openjournals/joss-reviews#2804.

Hi @tristan-salles, congratulations on a really nice piece of software! I have used it through Docker and run the example notebooks without trouble (except for occasionally running out of memory on my machine, but that's my problem not yours).

I also find the technical guide very thorough after the changes suggested by John. I have just a couple of small reference additions to request for the paper (they may also be relevant to the technical guide). These are very minor:

Rivenaes (1992, Basin Research) should be cited for the two-fraction diffusion model.
Sclater and Christie (1980, JGR) should be cited for the compaction in addition to Yuan et al., since the latter is really presenting a clever shortcut to approximating the compaction law reported by the former.
Might you consider citing one of the foundational stream power papers given that you provide citations for the other process components? Howard et al (1994, JGR) would be one good option.

I wish I had more to offer in this review, but the software is working well and the technical guide is very thorough. gospl will be a big asset to the community.

AttributeError: 'Model' object has no attribute 'platedata' with no tectonic data inputted

Describe the bug
AttributeError: 'Model' object has no attribute 'platedata' despite not having inserted any plate or tectonic data into the model in the first place.

To Reproduce
Steps to reproduce the behavior:

Set up docker container with jupyter
Set up input.yml (without tectonic or precipitation data)
Run erosion.ipynb
See error relating to tectonic data (?)

Expected behavior
No error considering there is no tectonic data inputted

Screenshots
From input.yml:

From erosion.ipynb:

Desktop:

OS: Windows 11 WSL
Browser: Firefox
Version: gospl v1.1.2

Additional context
This is all from worldbuildingpasta's tutorial on the matter, in case reference is necessary.

vtk Ambigous data error

Describe the bug
need to pick activate scalrs

To Reproduce
run bfModel notebook

Expected behavior
countour chosen

Desktop (please complete the following information):

OS: WSL
Additional context

---------------------------------------------------------------------------
AmbiguousDataError                        Traceback (most recent call last)
Cell In[14], line 23
     21 mesh.points[:, 1] *= factor
     22 mesh.points[:, 2] *= factor
---> 23 contour = mesh.contour([0])
     24 plot = pv.PlotterITK()
     25 plot.add_mesh(mesh, scalars="vTec")

File ~/miniconda3/envs/gospl-package/lib/python3.9/site-packages/pyvista/core/filters/data_set.py:1860, in DataSetFilters.contour(self, isosurfaces, scalars, compute_normals, compute_gradients, compute_scalars, rng, preference, method, progress_bar)
   1858 # set the array to contour on
   1859 if scalars is None:
-> 1860     set_default_active_scalars(self)
   1861     field, scalars_name = self.active_scalars_info
   1862 else:

File ~/miniconda3/envs/gospl-package/lib/python3.9/site-packages/pyvista/core/utilities/arrays.py:748, in set_default_active_scalars(mesh)
    746     raise MissingDataError("No data available.")
    747 elif n_possible_scalars > 1:
--> 748     raise AmbiguousDataError(
    749         "Multiple data available\n"
    750         f"cell data: {possible_scalars_cell}.\n"
    751         f"point data: {possible_scalars_point}.\n"
    752         "Set one as active using DataSet.set_active_scalars(name, preference=type)"
    753     )

AmbiguousDataError: Multiple data available
cell data: [].
point data: ['Z', 'vTec'].
Set one as active using DataSet.set_active_scalars(name, preference=type)

conda has no win64 petsc4py

To Reproduce
Try installing environment yml in Windows 10

Expected behavior
Environment installed

Screenshots

PackagesNotFoundError: The following packages are not available from current channels:
  - petsc4py

Desktop (please complete the following information):

Windows 10

Additional context
Add any other context about the problem here.

e.g. why I asked re: WSL etc.

yaml load deprecation bfModel notebook

Describe the bug
yaml error in bfModel notebook

To Reproduce
run bfModel notebook

Expected behavior
it works

Desktop (please complete the following information):

Additional context

Traceback (most recent call last):
  File "/mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/runBF.py", line 23, in <module>
    merger.mergeBackModels(backin, backout)
  File "/mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/mergeBack.py", line 237, in mergeBackModels
    tStart, tEnd, tOut, outputDir, nbCPUs = readOutputs(inputs[k])
  File "/mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/mergeBack.py", line 43, in readOutputs
    input = yaml.load(finput, Loader=yaml.Loader)
  File "/home/richard/miniconda3/envs/gospl-package/lib/python3.9/site-packages/ruamel/yaml/main.py", line 1085, in load
    error_deprecation('load', 'load', arg=_error_dep_arg, comment=_error_dep_comment)
  File "/home/richard/miniconda3/envs/gospl-package/lib/python3.9/site-packages/ruamel/yaml/main.py", line 1037, in error_deprecation
    raise AttributeError(s)
AttributeError: 
"load()" has been removed, use

  yaml = YAML(typ='rt')
  yaml.load(...)

and register any classes that you use, or check the tag attribute on the loaded data,
instead of file "/mnt/c/users/rscott/OneDrive - BHP/exploration2024/gospl/notebooks/bfModel/scripts/mergeBack.py", line 43

        input = yaml.load(finput, Loader=yaml.Loader)```

technical guide : description of plate tectonics?

As part of the JOSS review (openjournals/joss-reviews#2804), I am thinking that a description of how plate tectonics is included might be a great addition to the page https://gospl.readthedocs.io/en/latest/tech_guide/index.html#tech-guide. The erosion, deposition, and compaction algorithms are described, but I don't see a description of the methods used to:

laterally move the surfaces (gplates?)
remesh if needed, as the grids get distorted
deal with the collision of sediments (I assume there is no actual compression of sediment and crust, but something must be done at the plate boundaries, right?)

Or if all of the above is wrong, then maybe some text explaining what is done, because it is possible I am assuming a complexity that does not exist.

Issue

When I follow your tutorial this command won't work. Am I doing something wrong?

Windows 10 pip install petsc4py install fails

Describe the bug
petsc4py installation fails

To Reproduce

pip install petsc4py

Expected behavior
package installs

Desktop (please complete the following information):

Windows 10
Browser [e.g. chrome, safari]
Version [e.g. 22]

Smartphone (please complete the following information):

Device: [e.g. iPhone6]
OS: [e.g. iOS8.1]
Browser [e.g. stock browser, safari]
Version [e.g. 22]

Additional context

>pip install petsc4py
Collecting petsc4py
  Downloading petsc4py-3.21.2.tar.gz (420 kB)
     ---------------------------------------- 420.2/420.2 kB 1.9 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... error
  error: subprocess-exited-with-error

  × pip subprocess to install backend dependencies did not run successfully.
  │ exit code: 1
  ╰─> [85 lines of output]
      Collecting petsc<3.22,>=3.21
        Downloading petsc-3.21.2.tar.gz (17.3 MB)
           ---------------------------------------- 17.3/17.3 MB 4.0 MB/s eta 0:00:00
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting wheel
        Using cached wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
      Using cached wheel-0.43.0-py3-none-any.whl (65 kB)
      Building wheels for collected packages: petsc
        Building wheel for petsc (pyproject.toml): started
        Building wheel for petsc (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error

        Building wheel for petsc (pyproject.toml) did not run successfully.
        exit code: 1

        [58 lines of output]
        running bdist_wheel
        running build
        running build_py
        creating build
        creating build\lib
        creating build\lib\petsc
        copying config\pypi\__init__.py -> build\lib\petsc
        copying config\pypi\__main__.py -> build\lib\petsc
        installing to build\bdist.win-amd64\wheel
        running install
        PETSc: configure
        configure options:
            --prefix=C:\Users\rscott\AppData\Local\Temp\pip-install-dm5mv7gc\petsc_0c2c11fd351d45a899e55d6d6eaccad5\build\bdist.win-amd64\wheel\petsc
            PETSC_ARCH=arch-python
            --with-shared-libraries=1
            --with-debugging=0
            --with-c2html=0
            --with-mpi=0
        ===============================================================================
         *** Windows python detected. Please rerun ./configure with cygwin-python. ***
        ===============================================================================
        Traceback (most recent call last):
          File "C:\Users\rscott\AppData\Local\miniconda3\envs\gospl-package\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
            main()
          File "C:\Users\rscott\AppData\Local\miniconda3\envs\gospl-package\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
            json_out['return_val'] = hook(**hook_input['kwargs'])
          File "C:\Users\rscott\AppData\Local\miniconda3\envs\gospl-package\Lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 251, in build_wheel
            return _build_backend().build_wheel(wheel_directory, config_settings,
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\build_meta.py", line 410, in build_wheel
            return self._build_with_temp_dir(
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\build_meta.py", line 395, in _build_with_temp_dir
            self.run_setup()
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
            exec(code, locals())
          File "<string>", line 363, in <module>
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\__init__.py", line 103, in setup
            return distutils.core.setup(**attrs)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 184, in setup
            return run_commands(dist)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 200, in run_commands
            dist.run_commands()
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 969, in run_commands
            self.run_command(cmd)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\dist.py", line 968, in run_command
            super().run_command(command)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
            cmd_obj.run()
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\wheel\bdist_wheel.py", line 403, in run
            self.run_command("install")
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 316, in run_command
            self.distribution.run_command(command)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\dist.py", line 968, in run_command
            super().run_command(command)
          File "C:\Users\rscott\AppData\Local\Temp\pip-build-env-ct0yw5my\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
            cmd_obj.run()
          File "<string>", line 286, in run
          File "<string>", line 189, in config
        RuntimeError: 3
        [end of output]

        note: This error originates from a subprocess, and is likely not a problem with pip.
        ERROR: Failed building wheel for petsc
      Failed to build petsc
      ERROR: Could not build wheels for petsc, which is required to install pyproject.toml-based projects
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

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