bugs found by @ykawashima for v1.4.1

[HajimeKawahara]

See #404, but I made a new issue for the record (with adding numbering).

• [x] 1. I would like to confirm whether the change of the file path in the retrieval tutorial (0af60abd305a04aed50889d158c9f9e77c337c70) is correct or not. I think it is more straightforward to mention the tutorial notebook itself. Or did you intend to mention this python file? (In the latter case, some parts need to be fixed to be compatible with the current version.)
• [x] 2. I got the following error for tests/integration/premodit/checindex.py due to the change of the input parameters of init_premodit.

  File "/home/kawashima/exojax/tests/integration/premodit/checkindex.py", line 28, in <module>
  ngamma_ref_grid_H2O, n_Texp_grid_H2O, R_H2O, pmarray_H2O = initspec.init_premodit(
  TypeError: init_premodit() got an unexpected keyword argument 'interval_contrast'

• [x] 3. I got the following error for tests/integration/premodit/line_strength_comparison_exomol.py due to the change of the input parameters of unbiased_ngamma_grid. Could you add Tref_broadening parameter? The same thing applies to tests/integration/premodit/line_strength_comparison_hitemp.py. Thank you.

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/premodit/line_strength_comparison_exomol.py", line 78, in <module>
  ngamma_grid = unbiased_ngamma_grid(Ttest, P, ngamma_ref_grid, n_Texp_grid,
  TypeError: unbiased_ngamma_grid() missing 1 required positional argument: 'Tref_broadening'

• [x] 4. I got the following errors for tests/integration/moldb/comparison_api.py and tests/integration/moldb/comparison_api_xs.py. I think these two tests are no more needed given that MdbExomol and MdbHit have been discarded in exojax.spec.moldb.

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/moldb/comparison_api.py", line 8, in <module>
  from exojax.spec.moldb import MdbExomol as MdbExomol_orig
  ImportError: cannot import name 'MdbExomol' from 'exojax.spec.moldb' (/home/kawashima/anaconda3/lib/python3.9/site-packages/ExoJAX-1.4-py3.9.egg/exojax/spec/moldb.py)

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/moldb/comparison_api_xs.py", line 28, in <module>
  mdbCO_moldb = moldb.MdbHit('~/exojax/data/CO/05_hit12.par', nus)
  AttributeError: module 'exojax.spec.moldb' has no attribute 'MdbHit'

• [x] 5. I got the following error for tests/integration/moldb/quantum_states_filter_exomol.py. Maybe v_u and v_l should be replaced by j_upper and j_lower?

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/moldb/quantum_states_filter_exomol.py", line 31, in <module>
  mask = mdb.df["v_u"] - mdb.df["v_l"] == dv
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/vaex/dataframe.py", line 5395, in __getitem__
  self.validate_expression(item)
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/vaex/dataframe.py", line 3446, in validate_expression
  raise NameError(str(e)) from None
  NameError: Column or variable 'v_u' does not exist. Did you mean: 'v_l'

• [x] 6. I got the following errors, saying that the lengeth of mdb.Sij0 is just 1, for tests/integration/moldb/quantum_states_filter_hitemp.py and tests/integration/moldb/quantum_states_filter_hitran_co.py. I cannot recognize the line where the line strength is assigned when the activate function is used. Or do I misunderstand?

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/moldb/quantum_states_filter_hitemp.py", line 32, in <module>
  plt.plot(1.e4 / mdb.nu_lines,
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/pyplot.py", line 2740, in plot
  return gca().plot(
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_axes.py", line 1662, in plot
  lines = [*self._get_lines(*args, data=data, **kwargs)]
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 311, in __call__
  yield from self._plot_args(
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 504, in _plot_args
  raise ValueError(f"x and y must have same first dimension, but "
  ValueError: x and y must have same first dimension, but have shapes (1300,) and (1,)

  Traceback (most recent call last):
  File "/home/kawashima/exojax/tests/integration/moldb/quantum_states_filter_hitran_co.py", line 28, in <module>
  plt.plot(1.e4 / mdb.nu_lines,
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/pyplot.py", line 2740, in plot
  return gca().plot(
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_axes.py", line 1662, in plot
  lines = [*self._get_lines(*args, data=data, **kwargs)]
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 311, in __call__
  yield from self._plot_args(
  File "/home/kawashima/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 504, in _plot_args
  raise ValueError(f"x and y must have same first dimension, but "
  ValueError: x and y must have same first dimension, but have shapes (634,) and (1,)

[HajimeKawahara]

5. It should have v_l and v_u. I found that radis develop branch is needed to load these quantities. I added Warning in doc: https://secondearths.sakura.ne.jp/exojax/userguide/api.html#quantum-states-filtering-exomol-hitemp Also, https://secondearths.sakura.ne.jp/exojax/tutorials/Fortrat.html

[HajimeKawahara]

6. Sij0 is now deprecated. Use line_strength_ref.

tests/integration/moldb/quantum_states_filter_hitran_co.py). requires develop branch of radis.

[HajimeKawahara]

1. Thanks. The former one is correct. I think all of the bugs have been fixed.