As of now I still have to manually update the submodule over in the main xgcm repo. Is there a way to do that automatically with a bot?

cc @rabernat

Currently we have too much whitespace in our thumbnail. I could just cut it (but that would contribute to the weird jagged layout of pangeo gallery. Not a priority, just pinning this here.

First of all, thanks for making these tutorials! They've really helped me master xgcm, which I use almost daily now.

I spotted a mistake in the MITgcm example. The computation of the divergence is incorrect. The right MITgcm discrete form is found here. The difference is that there should be no multiplication by ds.drF (which in the link you currently include is present to correctly represent the z-derivative of the vertical velocity in the continuity equation), and that there should be an additional division by ds.hFacC. This also means that you may want to rename u/v_transport, since you don't need the transport after all.

I figured it's easiest for me to open an issue over a PR, since I don't know your specific workflow/integration for getting these examples on the xgcm website.

Maybe mention that even if these are 2 different git repositories, they use the same conda environment, which instructions are found in the xgcm contributors guide.
That was this point that was not clear for me.

Originally posted by @rcaneill in #12 (comment)

I think it would be nice to give some more examples how to transform datasets between coordinates. Especially demonstrating this with gridded observational datasets seems to something people are interested in.

I'm trying to follow along from some of these sample notebooks but can't figure out the environment. I'm on sciserver. I have installed xgcm (it does appear in !conda list).
Can y'all help interpret this?

Traceback:

TypingErrorTraceback (most recent call last)
in
----> 1 from xgcm import Grid
2 from xgcm.autogenerate import generate_grid_ds

~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/init.py in
4 version = "unknown"
5
----> 6 from .autogenerate import generate_grid_ds
7 from .grid import Axis, Grid

~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/autogenerate.py in
1 import xarray as xr
2
----> 3 from xgcm.grid import Axis, raw_interp_function
4
5

~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/grid.py in
15 import numba
16
---> 17 from .transform import conservative_interpolation, linear_interpolation
18 except ImportError:
19 numba = None

~/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py in
17 ],
18 "(n),(n),(m),(),()->(m)",
---> 19 nopython=True,
20 )
21 def _interp_1d_linear(

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/decorators.py in wrap(func)
177 guvec = GUVectorize(func, signature, **kws)
178 for fty in ftylist:
--> 179 guvec.add(fty)
180 return guvec.build_ufunc()
181

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in add(self, sig)
194 targetoptions = self.nb_func.targetoptions
195 cres, args, return_type = _compile_element_wise_function(
--> 196 self.nb_func, targetoptions, sig)
197 sig = self._finalize_signature(cres, args, return_type)
198 self._sigs.append(sig)

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in _compile_element_wise_function(nb_func, targetoptions, sig)
128 # Do compilation
129 # Return CompileResult to test
--> 130 cres = nb_func.compile(sig, **targetoptions)
131 args, return_type = sigutils.normalize_signature(sig)
132 return cres, args, return_type

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in compile(self, sig, locals, **targetoptions)
77 flags.unset("enable_looplift")
78
---> 79 return self._compile_core(sig, flags, locals)
80
81 def _compile_core(self, sig, flags, locals):

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in _compile_core(self, sig, flags, locals)
112 self.py_func, args=args,
113 return_type=return_type,
--> 114 flags=flags, locals=locals)
115
116 # cache lookup failed before so safe to save

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
970 pipeline = pipeline_class(typingctx, targetctx, library,
971 args, return_type, flags, locals)
--> 972 return pipeline.compile_extra(func)
973
974

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in compile_extra(self, func)
388 self.lifted = ()
389 self.lifted_from = None
--> 390 return self._compile_bytecode()
391
392 def compile_ir(self, func_ir, lifted=(), lifted_from=None):

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in _compile_bytecode(self)
901 """
902 assert self.func_ir is None
--> 903 return self._compile_core()
904
905 def _compile_ir(self):

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in _compile_core(self)
888 self.define_pipelines(pm)
889 pm.finalize()
--> 890 res = pm.run(self.status)
891 if res is not None:
892 # Early pipeline completion

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler_lock.py in _acquire_compile_lock(*args, **kwargs)
30 def _acquire_compile_lock(*args, **kwargs):
31 with self:
---> 32 return func(*args, **kwargs)
33 return _acquire_compile_lock
34

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in run(self, status)
264 # No more fallback pipelines?
265 if is_final_pipeline:
--> 266 raise patched_exception
267 # Go to next fallback pipeline
268 else:

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in run(self, status)
255 try:
256 event("-- %s" % stage_name)
--> 257 stage()
258 except _EarlyPipelineCompletion as e:
259 return e.result

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in stage_nopython_frontend(self)
513 self.args,
514 self.return_type,
--> 515 self.locals)
516 self.typemap = typemap
517 self.return_type = return_type

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/compiler.py in type_inference_stage(typingctx, interp, args, return_type, locals)
1122
1123 infer.build_constraint()
-> 1124 infer.propagate()
1125 typemap, restype, calltypes = infer.unify()
1126

~/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py in propagate(self, raise_errors)
925 if errors:
926 if raise_errors:
--> 927 raise errors[0]
928 else:
929 return errors

TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Invalid use of Function(<function interp at 0x7f44f9406cb0>) with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A))

• parameterized
  In definition 0:
  TypingError: Failed in nopython mode pipeline (step: nopython frontend)
  Invalid use of Function(<function np_interp_impl_inner_factory..impl at 0x7f44f60215f0>) with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A), dtype(float64))
• parameterized
  In definition 0:
  TypingError: Failed in nopython mode pipeline (step: nopython frontend)
  Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120:
def impl(x, xp, fp, dtype):

if lenxp <= lenx:
slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1])
^

[1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122:
def impl(x, xp, fp, dtype):

else:
slopes = np.empty(0, dtype=dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

In definition 1:
TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120:
def impl(x, xp, fp, dtype):

if lenxp <= lenx:
slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1])
^

[1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122:
def impl(x, xp, fp, dtype):

else:
slopes = np.empty(0, dtype=dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

This error is usually caused by passing an argument of a type that is unsupported by the named function.
[1] During: resolving callee type: Function(<function np_interp_impl_inner_factory..impl at 0x7f44f60215f0>)
[2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2237)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2237:
def np_interp_impl(x, xp, fp):
return inner(x, xp, fp, dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

In definition 1:
TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Invalid use of Function(<function np_interp_impl_inner_factory..impl at 0x7f44f60215f0>) with argument(s) of type(s): (array(float32, 1d, A), array(float32, 1d, A), array(float32, 1d, A), dtype(float64))

• parameterized
  In definition 0:
  TypingError: Failed in nopython mode pipeline (step: nopython frontend)
  Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120:
def impl(x, xp, fp, dtype):

if lenxp <= lenx:
slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1])
^

[1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122:
def impl(x, xp, fp, dtype):

else:
slopes = np.empty(0, dtype=dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

In definition 1:
TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Cannot unify array(float32, 1d, C) and array(float64, 1d, C) for 'slopes', defined at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2120)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2120:
def impl(x, xp, fp, dtype):

if lenxp <= lenx:
slopes = (dy[1:] - dy[:-1]) / (dx[1:] - dx[:-1])
^

[1] During: typing of assignment at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2122)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2122:
def impl(x, xp, fp, dtype):

else:
slopes = np.empty(0, dtype=dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

This error is usually caused by passing an argument of a type that is unsupported by the named function.
[1] During: resolving callee type: Function(<function np_interp_impl_inner_factory..impl at 0x7f44f60215f0>)
[2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py (2237)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/numba/targets/arraymath.py", line 2237:
def np_interp_impl(x, xp, fp):
return inner(x, xp, fp, dtype)
^

raised from /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/numba/typeinfer.py:927

This error is usually caused by passing an argument of a type that is unsupported by the named function.
[1] During: resolving callee type: Function(<function interp at 0x7f44f9406cb0>)
[2] During: typing of call at /home/idies/miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py (31)

File "../../../../miniconda3/envs/py37/lib/python3.7/site-packages/xgcm/transform.py", line 31:
def _interp_1d_linear(

output[:] = np.interp(target_theta_levels, theta, phi)
^

I wanted to rework the NEMO example (fix the typos, and reshape some stuff now that I am more confident with xgcm) and I am wondering, what environment should I use? Previously I used the environment.yml provided in xgcm (for readthedocs), is it still the same case now?
I feel lost between all the environments + the pangeo gallery.
Thanks!

I don't think this will work with binderbot because you are not pointing to a proper binder repo here:

Can you try using the default binder?

https://github.com/pangeo-gallery/example-gallery/blob/315eb264ebfb94651ee336ea1e7babe48b22fd1c/binder-gallery.yaml#L8-L9

That will also fix your build, because the image is already built.

Reminder from xgcm/xgcm#166 (comment)

The mitgcm and MOM6 examples are both producing errors. Could the authors check on those?