Add astroquery.linelists.exomol — ExoMol database query module by aditya-pandey-dev · Pull Request #3536 · astropy/astroquery

aditya-pandey-dev · 2026-02-21T18:51:04Z

Implements astroquery.linelists.exomol module for querying the
ExoMol molecular line list database (https://www.exomol.com).

Closes radis/radis#479
Related: radis/radis#925

Changes:-

ExoMolClass(BaseQuery) with 4 methods:
- query_lines() — fetch line lists as astropy.Table
- get_molecule_list() — list all 91+ molecules
- get_databases() — list databases per molecule
- get_partition_function() — fetch Q(T) data
broadening_species support (H2, He, air, CO2, H2O, self)
9/9 tests passing (5 mocked + 4 remote_data)
RST documentation added

Implements astroquery interface for ExoMol molecular line list database. Wraps RADIS ExoMol reader (radis.io.exomol) into BaseQuery pattern. Features: - query_lines() — fetch line lists as astropy.Table - get_molecule_list() — list all 91+ ExoMol molecules - get_databases() — list available databases per molecule - get_partition_function() — fetch Q(T) data - broadening_species support (H2, He, air, CO2, H2O, self) Tests: 9/9 passing (5 mocked + 4 remote_data) Related: radis/radis#925

codecov · 2026-02-22T17:58:57Z

Codecov Report

❌ Patch coverage is 46.26866% with 36 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.57%. Comparing base (12d9357) to head (5618a38).
⚠️ Report is 15 commits behind head on main.

Files with missing lines	Patch %	Lines
astroquery/linelists/exomol/core.py	43.75%	36 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3536      +/-   ##
==========================================
- Coverage   72.66%   72.57%   -0.09%     
==========================================
  Files         219      222       +3     
  Lines       20478    20547      +69     
==========================================
+ Hits        14880    14913      +33     
- Misses       5598     5634      +36

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keflavich

Thank you for this PR! I've wanted clean access to exomol for many years and never got around to writing it myself (...i think because the server wasn't mature yet?).

The implementation looks OK right now, but I have questions: Can this be refactored to avoid pandas and radis? Should it?

There are some minor code issues, and I haven't systematically reviewed the tests, but broadly it looks OK.

astroquery/linelists/exomol/tests/test_exomol.py

keflavich · 2026-02-22T18:34:16Z

astroquery/linelists/exomol/core.py

+        from radis.api.exomolapi import get_exomol_database_list
+        from radis.api.exomolapi import get_exomol_full_isotope_name


We're introducing a new dependency here, which I don't love doing - but if it's necessary, we'll allow it.

These methods look fairly simple and maybe safe to reimplement here, but if they're heavy methods in any way, it's OK to leave them in radis. I'll invite @bsipocz to comment on this too.

docs/linelists/exomol/exomol.rst

pyproject.toml

keflavich · 2026-02-22T18:36:16Z

pyproject.toml

 xfail_strict = true
 remote_data_strict = true
 addopts = ["--color=yes", "--doctest-rst", "--doctest-continue-on-failure"]
-timeout = 300


why is this removed?

keflavich · 2026-02-22T18:38:49Z

docs/linelists/exomol/exomol.rst

+        load_wavenum_min=2000,
+        load_wavenum_max=2100,
+    )
+    print(result)


the results should be shown here (and in the other doctest examples)

…re pytest-timeout, add dependency note to docs

aditya-pandey-dev · 2026-02-24T15:10:05Z

Hi @keflavich I've addressed all your review comments:

Removed pandas from tests (using pytest.importorskip only)
Restored pytest-timeout in pyproject.toml (lines 39 and 121)
Added radis + pandas dependency note clearly in docs
Added example output to all doctest examples in exomol.rst
Kept radis dependency for get_exomol_database_list and get_exomol_full_isotope_name as reimplementing would duplicate significant RADIS logic
All 9 CI checks are now passing (including Linux ARM ).

Could you please re-review

keflavich · 2026-02-24T23:22:23Z

Could you say what it would take to remove RADIS as a dependency? Adding it as a dependency creates a circular dependency (https://github.com/radis/radis/blob/be14d4b101b9f068ea0ee04b4e902d57049ea813/environment.yml#L17), so it would be better if astroquery could stand alone.

aditya-pandey-dev · 2026-02-25T06:22:02Z

Hi @keflavich I go through what it would take to remove RADIS as a dependency:

It is comparatively easy to reimplement without radis:

get_exomol_database_list — simple BeautifulSoup HTML scraper (30 lines)
get_exomol_full_isotope_name — static isotope lookup dict (5 lines)

Very complex to reimplement:

fetch_exomol (352 lines) — handles HDF5 file download, caching, line intensity calculations, isotopologue filtering, and broadening parameters. Reimplementing this would essentially duplicate a major portion of RADIS.

I can remove the two helper functions from RADIS and reimplement them natively. But for fetch_exomol, the options are:

a) Keep RADIS as optional dependency (skip tests if unavailable)
b) Reimplement fetch_exomol from scratch — significant effort but removes circular dependency completely
c) Drop query_lines() / get_partition_function() for now and only expose get_molecule_list() and get_databases() without RADIS

What would you prefer?

keflavich · 2026-02-25T12:19:39Z

Thanks @aditya-pandey-dev . I think the former functions, including the bs4 scraper, belong here.

for fetch_exomol, that sounds like a more involved calculation - @bsipocz I'm loosely inclined to allow this function to use exomol. It's not purely database work, I think, but a little calculation on top. Are you OK with including radis only as a dependency for this function - i.e., import within the function?

keflavich · 2026-02-26T15:42:56Z

astroquery/linelists/exomol/core.py

+    Query CO lines between 2000-2100 cm^-1::
+
+        from astroquery.linelists.exomol import ExoMol
+        result = ExoMol.query_lines('CO',
+                                    load_wavenum_min=2000,
+                                    load_wavenum_max=2100)


To follow the astroquery standard for APIs, these should be specified with units - so load_wavenum_min=2000*u.cm**-1, for example. Also, the keyword name should be wavenum_min - load doesn't fit here, afaict.

keflavich · 2026-02-26T15:43:17Z

astroquery/linelists/exomol/core.py

+        load_wavenum_min=None,
+        load_wavenum_max=None,


see above

Suggested change

load_wavenum_min=None,

load_wavenum_max=None,

wavenum_min=None,

wavenum_max=None,

keflavich · 2026-02-26T15:43:37Z

astroquery/linelists/exomol/core.py

+            Minimum wavenumber in cm^-1.
+        load_wavenum_max : float, optional
+            Maximum wavenumber in cm^-1.
+        broadening_species : str or list of str, optional


these should be Quantitys

keflavich · 2026-02-26T15:45:21Z

pyproject.toml

   "pytest>=7.4",
   "pytest-doctestplus>=1.4",
-   "pytest-timeout",
+    "pytest-timeout",


… lazy RADIS import

…DIS dependency, fix pyproject.toml whitespace

aditya-pandey-dev · 2026-02-28T11:24:39Z

Hi @keflavich all your review comments have been addressed:

Renamed load_wavenum_min/max → wavenum_min/max with ~astropy.units.Quantity support
get_databases() reimplemented natively with BeautifulSoup4 scraper — no RADIS dependency
RADIS lazy-imported only inside query_lines() and get_partition_function()
pyproject.toml whitespace fixed, timeout = 300 restored

Could you please re-review?

keflavich

There are a few more things to clean up in tests now

keflavich · 2026-02-28T13:30:55Z

astroquery/linelists/exomol/tests/test_exomol.py

+try:
+    import radis  # noqa: F401
+except ImportError as e:
+    pytest.skip(f"radis required for exomol tests: {e}",
+                allow_module_level=True)


radis is no longer required for most tests, so let's switch this global skip to skipif RADEX_NOT_AVAILABLE down below

keflavich · 2026-02-28T13:33:24Z

astroquery/linelists/exomol/tests/test_exomol.py

+    monkeypatch.setattr(
+        "radis.io.exomol.fetch_exomol", lambda *a, **kw: fake_linelist_df
+    )
+    result = ExoMol.query_lines("CO", wavenum_min=2000, wavenum_max=2100)


these should now require Quantities (and this test should not be skipped)

ah, actually, this test should be skipped if radis is unavailable, sorry - but still, these should be quantities

keflavich · 2026-02-28T13:40:53Z

astroquery/linelists/exomol/tests/test_exomol.py

+    monkeypatch.setattr(
+        "radis.io.exomol.fetch_exomol", lambda *a, **kw: fake_linelist_df
+    )
+    result = ExoMol.query_lines("CO", wavenum_min=2000, wavenum_max=2100)


keflavich · 2026-02-28T13:41:06Z

astroquery/linelists/exomol/tests/test_exomol.py

+        wavenum_min=1000,
+        wavenum_max=1100,


keflavich · 2026-02-28T13:41:24Z

astroquery/linelists/exomol/tests/test_exomol.py

+            wavenum_min=2000,
+            wavenum_max=2100,


keflavich · 2026-02-28T13:41:36Z

astroquery/linelists/exomol/tests/test_exomol.py

+            wavenum_min=2000,
+            wavenum_max=2050,


keflavich · 2026-02-28T13:42:42Z

astroquery/linelists/exomol/tests/test_exomol.py

+# ===========================================================
+
+
+@pytest.mark.remote_data


all the remote_data-flagged tests should go into test_exomol_remote - it makes debugging and testing a lot easier when the non-remote tests and remote-requiring tests are separated

… tests to test_exomol_remote.py

aditya-pandey-dev · 2026-03-01T05:28:15Z

Hi @keflavich I've addressed all the review comments:

Replaced global pytest.skip with RADEX_NOT_AVAILABLE flag + @pytest.mark.skipif on each test
Added u.cm**-1 Quantities to all wavenum_min/wavenum_max args
Moved all @pytest.mark.remote_data tests to test_exomol_remote.py
6/6 tests passing locally

Could you please re-review?

aditya-pandey-dev added 5 commits February 22, 2026 00:08

Add exomol entry to CHANGES.rst

64a7d7b

Apply ruff formatting to exomol module

f8445f9

Fix pandas import using pytest.importorskip for CI compatibility

02165e2

Fix doctest example in core.py to use code block instead

7b4f4e3

Add exomol docs to toctree and fix automodapi

c6fb117

keflavich requested changes Feb 22, 2026

View reviewed changes

aditya-pandey-dev added 7 commits February 23, 2026 11:33

Address review: remove pandas from tests, fix Table conversion, resto…

abb9bef

…re pytest-timeout, add dependency note to docs

Add radis to tox deps and skip tests if radis unavailable

6af1b54

Add radis to MOCK_MODULES in conf.py and optional deps for RTD build

1e6d2fb

Fix importorskip exc_type and toctree indentation for exomol

0ba56e8

Revert exc_type: not supported in older pytest versions

abd6b2d

Remove unused sys import from test_exomol.py

c7a0d69

Add exc_type=ImportError to importorskip for NumPy 2.5 compat

d10be96

bsipocz added the New Service label Feb 23, 2026

aditya-pandey-dev added 5 commits February 23, 2026 23:13

Fix RTD toctree indent and radis skip for all pytest versions

6b37d59

Fix radis skip: add noqa F401 and allow_module_level=True

9db0db6

Fix RTD toctree: match exomol indentation with other entries

2b044be

Add example output to doctest examples in exomol.rst

892567a

Trigger CI re-run

062e043

keflavich requested changes Feb 26, 2026

View reviewed changes

aditya-pandey-dev added 4 commits February 28, 2026 12:50

Address review: rename load_wavenum to wavenum with Quantity support,…

55e715c

… lazy RADIS import

Address review: reimplement get_databases with bs4 scraper, remove RA…

bbd89ee

…DIS dependency, fix pyproject.toml whitespace

Add test for get_databases bs4 scraper to improve coverage

121df8e

Fix flake8: remove unused bs4 import from test

9312afd

aditya-pandey-dev added 3 commits February 28, 2026 15:04

Fix flake8 E302/E306: correct blank lines in test_get_databases

99c856a

Fix flake8: rewrite test_get_databases with correct formatting

974a1aa

Fix E303: remove extra blank line before test_get_databases

b0d1a6c

keflavich requested changes Feb 28, 2026

View reviewed changes

Tests: use skipif RADEX_NOT_AVAILABLE, add Quantity args, move remote…

5618a38

… tests to test_exomol_remote.py

		from radis.api.exomolapi import get_exomol_database_list
		from radis.api.exomolapi import get_exomol_full_isotope_name

		# ===========================================================


		@pytest.mark.remote_data

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