Make Vaex the default HDF5 engine, add Exomol hdf5 support, add fetch_hitran()

[erwanp]

Description

• can read & parse multiple .h5 files directly to vaex-hdf5 (creating temp batch files & combining them). @gagan-aryan this is finally working ;)
• ⭐ make vaex the default memory-mapping-engine for radis
• add config key for default MEMORY_MAPPING_ENGINE (vaex, pytables) so users can change it
• add warning if using Spyder and Vaex. See Vaex process stuck in the Spyder IPython console (only) spyder-ide/spyder#16183. Same for Partition function calculation stuck in Spyder with "tabulation" mode (vaex) #338
• use hjson to parse default_radis.json, allows to add explicit comments in default_radis.json . Fixes config file with comments #328 for the moment
• add HDF5 (vaex) support for exomol files. make files more up to date with Exojax parsers
• re-add broadening for ExoMol molecules. Should fix Broadening of ExoMol molecules #372

And 2nd batch of changes

• ⭐ add fetch_hitran() which downloads all lines/isotopes of HITRAN database (Vaex compatible)

from radis.io.hitran import fetch_hitran
df = fetch_hitran("CO")

• eventually, keep the choice between 2 HITRAN retrieval modes: 'full' (new, new default) and 'range' (old, download only required range)

calc_spectrum(..., databank=("hitran", "full"))   # predownload full database & isotopes (once for all)
calc_spectrum(..., databank=("hitran", "range"))   # download only the required the range & isotope

• ⭐ only load required columns by default (makes it 8-10x faster to load databases)

Ex : Load full CO2 HITEMP database

from radis import calc_spectrum
s = calc_spectrum(1, 26777,         # cm-1           # <<< full spectral range!
                  molecule='CO2',
                  isotope='1,2,3',
                  pressure=760 * u.torr,
                  Tgas=700,           # K
                  mole_fraction=1,
                  wstep=0.01,
                  databank='hitemp',
                  verbose=3,
                  cutoff=0,

                  )
s.print_perf_profile()
s.plot(yscale='log')

Before (Pandas's Pytables) : ~ 85s
With Vaex : ~ 30s
With Vaex + load only required columns: ~4.5 s

So about ~8x faster than with all columns, 20x faster than initally, and of course reduces memory usage.

[lgtm-com]

This pull request introduces 3 alerts when merging 96125b7 into 01a6544 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Wrong number of arguments in a call

[lgtm-com]

This pull request introduces 5 alerts when merging 267ebdb into 01a6544 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 2 for Module is imported with 'import' and 'import from'
• 1 for Wrong number of arguments in a call

[lgtm-com]

This pull request introduces 5 alerts when merging 7978226 into 01a6544 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 2 for Module is imported with 'import' and 'import from'
• 1 for Wrong number of arguments in a call

[codecov-commenter]

Codecov Report

Merging #398 (9a7b598) into develop (eb9258b) will decrease coverage by 0.25%.
The diff coverage is 67.93%.

@@             Coverage Diff             @@
##           develop     #398      +/-   ##
===========================================
- Coverage    75.38%   75.12%   -0.26%     
===========================================
  Files          156      157       +1     
  Lines        17673    18097     +424     
===========================================
+ Hits         13323    13596     +273     
- Misses        4350     4501     +151     

[lgtm-com]

This pull request introduces 4 alerts and fixes 2 when merging 9a7b598 into 01a6544 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Module is imported with 'import' and 'import from'
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Module is imported more than once
• 1 for Missing named arguments in formatting call

[lgtm-com]

This pull request introduces 4 alerts and fixes 2 when merging 93bbce7 into 92aae0d - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Module is imported with 'import' and 'import from'
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Module is imported more than once
• 1 for Missing named arguments in formatting call

[lgtm-com]

This pull request introduces 4 alerts and fixes 2 when merging 1cc2d82 into 92aae0d - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Module is imported with 'import' and 'import from'
• 1 for Wrong number of arguments in a call

fixed alerts:

• 1 for Module is imported more than once
• 1 for Missing named arguments in formatting call