make_paris_outputs fails for hfo1234yf

[joe-pitt]

Describe the bug
make_paris_outputs fails for inversion runs that used species-specific hfo1234yf fps. It works fine for hfo1234yf runs that used inert footprints, and it also works fine for runs using species-specific fps for hcfo1233zde. I have put the relevant runs on BP1 in the following directory: /group/chem/acrg/joe_hfo_output/24.06.1

To Reproduce
python ~/acrg/acrg/paris_formatting/make_paris_outputs.py \
-s hfo1234yf \
-r /group/chem/acrg/joe_hfo_output/24.06.1/pop_base \
-t RHIME_NAME_EUROPE_POPULATION_hfo1234yf_yearly \
-c /group/chem/acrg/PARIS_results_sharing/country_masks/country_EUROPE_EEZ_PARIS_gapfilled.nc \
-p "4h" \
-o /group/chem/acrg/joe_hfo_output/24.06.1 \
--pol-obs

Output
Traceback (most recent call last):
File "/user/home/zh21490/acrg/acrg/paris_formatting/make_paris_outputs.py", line 401, in
emissions, concentrations = main(
^^^^^
File "/user/home/zh21490/acrg/acrg/paris_formatting/make_paris_outputs.py", line 271, in main
country_output = make_country_output(species, inv_outs, countries, report_mode=report_em_mode)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/acrg/acrg/paris_formatting/make_paris_outputs.py", line 93, in make_country_output
countries.get_country_trace(species, inv_out).expand_dims({"time": [time_func(inv_out)]})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/acrg/acrg/paris_formatting/countries.py", line 140, in get_country_trace
x_to_country_mat = self.get_x_to_country_mat(inv_out)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/acrg/acrg/paris_formatting/countries.py", line 94, in get_x_to_country_mat
result = sparse_xr_dot(self.matrix, self.area_grid * inv_out.flux * inv_out.basis)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/_typed_ops.py", line 252, in mul
return self._binary_op(other, operator.mul)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/dataarray.py", line 4720, in _binary_op
self, other = align(self, other, join=align_type, copy=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 882, in align
aligner.align()
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 582, in align
self.reindex_all()
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 557, in reindex_all
self.results = tuple(
^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 558, in
self._reindex_one(obj, matching_indexes)
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 546, in _reindex_one
return obj._reindex_callback(
^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/dataarray.py", line 1890, in _reindex_callback
reindexed = ds._reindex_callback(
^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/dataset.py", line 3478, in _reindex_callback
reindexed_vars = alignment.reindex_variables(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/alignment.py", line 86, in reindex_variables
new_var = var[indxr]
~~~^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/variable.py", line 800, in getitem
data = indexing.apply_indexer(indexable, indexer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/indexing.py", line 1024, in apply_indexer
return indexable.oindex[indexer]
~~~~~~~~~~~~~~~~^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/indexing.py", line 366, in getitem
return self.getter(key)
^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/xarray/core/indexing.py", line 1501, in _oindex_get
return self.array[key]
~~~~~~~~~~^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/sparse/_coo/indexing.py", line 74, in getitem
mask, adv_idx = _mask(x.coords, index, x.shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/user/home/zh21490/.conda/envs/openghg_dev_env/lib/python3.12/site-packages/sparse/_coo/indexing.py", line 152, in _mask
raise IndexError("Only one-dimensional iterable indices supported.")
IndexError: Only one-dimensional iterable indices supported.

[joe-pitt]

From discussion with Brendan: basis functions in the inversion output are aligned with the footprint, whereas the flux is not. So we need to align the flux with the basis functions in make_paris_outputs before multiplying them