Add pygmt

[weiji14]

Description

Placeholder for adding PyGMT (a library for processing geospatial data and making maps) to Pyodide.

TODO, include 2 runtime C dependencies, xref https://github.com/conda-forge/pygmt-feedstock/blob/b7ecf50df60e8e15cbf5d47122a7beb4ce349d9c/recipe/meta.yaml#L24-L31:

• gmt (https://github.com/GenericMappingTools/gmt)
• netCDF4, xref include netcdf4 and h5py #1582

Other Python dependencies:

• numpy >=1.19
• packaging
• pandas
• xarray (Add xarray #2538)

Notes on testing this branch

1. Follow https://pyodide.org/en/latest/development/new-packages.html, get pyodide development environment set-up
2. git clone this branch
3. cd packages/pygmt/
4. python -m pyodide_build buildpkg meta.yaml
5. cd ../../
6. PYODIDE_PACKAGES="pygmt" make

• May need to do sudo apt install gfortran f2c ccache build-essential and so on, ref https://pyodide.org/en/latest/development/building-from-sources.html#partial-builds

7. ...

Checklists

• Add a CHANGELOG entry
• Add / update tests
• Add new / update outdated documentation

[weiji14]

Note to self, get libgmt packaged, and update/patch code on PyGMT to fix this error https://app.circleci.com/pipelines/github/pyodide/pyodide/4095/workflows/6cd9a4d7-2f51-4f0b-ae57-15cd7be70b42/jobs/45300?invite=true#step-102-701:

----------------------------- Captured stdout call -----------------------------
JavascriptException message:  Traceback (most recent call last):
  File "/lib/python3.10/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/lib/python3.10/asyncio/tasks.py", line 232, in __step
    result = coro.send(None)
  File "/lib/python3.10/site-packages/_pyodide/_base.py", line 500, in eval_code_async
    await CodeRunner(
  File "/lib/python3.10/site-packages/_pyodide/_base.py", line 351, in run_async
    coroutine = eval(self.code, globals, locals)
  File "<exec>", line 1, in <module>
  File "/lib/python3.10/site-packages/pygmt/__init__.py", line 71, in <module>
    _begin()
  File "/lib/python3.10/site-packages/pygmt/session_management.py", line 16, in begin
    with Session() as lib:
  File "/lib/python3.10/site-packages/pygmt/clib/session.py", line 183, in __enter__
    self.create("pygmt-session")
  File "/lib/python3.10/site-packages/pygmt/clib/session.py", line 330, in create
    c_create_session = self.get_libgmt_func(
  File "/lib/python3.10/site-packages/pygmt/clib/session.py", line 282, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/lib/python3.10/site-packages/pygmt/clib/loading.py", line 47, in load_libgmt
    for libname in lib_fullnames:
  File "/lib/python3.10/site-packages/pygmt/clib/loading.py", line 107, in clib_full_names
    libnames = clib_names(os_name=sys.platform)  # e.g. libgmt.so, libgmt.dylib, gmt.dll
  File "/lib/python3.10/site-packages/pygmt/clib/loading.py", line 85, in clib_names
    raise GMTOSError(f"Operating system '{os_name}' not supported.")
pygmt.exceptions.GMTOSError: Operating system 'emscripten' not supported.

[leouieda]

@weiji14 this would be awesome! The major challenge will likely be getting GMT in first and all its dependencies. From the pyodide contributing docs it seems that C dependencies should be added separately and then included as dependencies here. So the way forward is probably to try to get all of the GMT dependencies in first: https://github.com/conda-forge/gmt-feedstock/blob/main/recipe/meta.yaml The ones that usually cause problems are GDAL and ghostscript.

[weiji14]

@weiji14 this would be awesome!

Yes, the goal is to have an in-browser version of https://github.com/GenericMappingTools/try-gmt. No install needed to try out PyGMT 😄

The major challenge will likely be getting GMT in first and all its dependencies. From the pyodide contributing docs it seems that C dependencies should be added separately and then included as dependencies here. So the way forward is probably to try to get all of the GMT dependencies in first: https://github.com/conda-forge/gmt-feedstock/blob/main/recipe/meta.yaml The ones that usually cause problems are GDAL and ghostscript.

No kidding, this definitely won't be easy, but let's take it one step at a time. There should be some smart people working on the GDAL port (e.g. the geopandas folks at #1569) since that's the basis of most geo-libraries. Ghostscript might be a tougher sell to port to WebAssembly, but hopefully doable (fingers crossed that PyQT doesn't creep in).

I don't have much dedicated time to push this forward, so if anyone wants to build on this, let me know and I can give you access to the branch at https://github.com/weiji14/pyodide/tree/pygmt to work on this (or you can fork a copy and work on it independently).

[agriyakhetarpal]

Hi @weiji14 and @leouieda, I'm trying to triage older PRs that have been inactive for a while; could you please investigate if running pygmt in the browser is still of interest to you? NetCDF4 has been available for some time now, and it would be okay to add the GMT library within the same PR.

[weiji14]

Hi @agriyakhetarpal, oh nice, good to know that netcdf4 is available now (though we are thinking of making it an optional dependency in GenericMappingTools/pygmt#3643).

I'm on holiday break and probably won't have much bandwidth to get to this PR anytime soon. Please feel free to close this PR, I can always reopen it or start a new one later.

[agriyakhetarpal]

Thank you for the response! I'll close this then – wishing you happy holidays and new year :D