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Fix issue3296: prevent writing when running tests in CDMS #3297

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Merged
bsipocz merged 4 commits into from
Apr 21, 2025
Merged

Fix issue3296: prevent writing when running tests in CDMS #3297

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cdc13c0
fix issue3296: prevent writing when running tests
keflavich Apr 19, 2025
868772e
add another write=False that's redundant but helpfully explicit [skip…
keflavich Apr 19, 2025
650e2eb
improve behavior, make more clear keyword, fix incorrect documentatio…
keflavich Apr 21, 2025
213a0cd
the warning approach didn't really make sense, it was just 'extra sec…
keflavich Apr 21, 2025
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15 changes: 12 additions & 3 deletions astroquery/linelists/cdms/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -294,7 +294,8 @@ def _parse_result(self, response, *, verbose=False):

def get_species_table(self, *, catfile='partfunc.cat', use_cached=True,
catfile_url=conf.catfile_url,
catfile2='catdir.cat', catfile_url2=conf.catfile_url2):
catfile2='catdir.cat', catfile_url2=conf.catfile_url2,
write=True):
"""
A directory of the catalog is found in a file called 'catdir.cat.'

Expand All @@ -304,6 +305,13 @@ def get_species_table(self, *, catfile='partfunc.cat', use_cached=True,
----------
catfile : str, name of file, default 'catdir.cat'
The catalog file, installed locally along with the package
use_cached : bool, optional
If True, use the cached file if it exists. If False, download the
file from the CDMS server and save it to the cache (if ``write`` is set).
write : bool, optional

@bsipocz bsipocz Apr 21, 2025

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A more verbose arg would be nice, maybe call this write_cached or refresh_cashed?

@keflavich keflavich Apr 21, 2025

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I'll be more verbose, but I think a different keyword is warranted... write_new_cache, probably.

@bsipocz bsipocz Apr 21, 2025

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Sure. Anything more that just write is an improvement, and write_new_cache is quite good. Though maybe it will need a switch in logic, e.g. if it's set then ignore whatever is in use_cache rather than the other way around.

If True, and if ``use_cached`` is set, write the file to the cache. Use this
option if you need to update the index from CDMS; this should be set to False
for testing.

Returns
-------
Expand Down Expand Up @@ -332,8 +340,9 @@ def get_species_table(self, *, catfile='partfunc.cat', use_cached=True,
else:
result = retrieve_catfile(catfile_url)
result2 = retrieve_catfile2(catfile_url2)
result.write(data_path(catfile), format='ascii.fixed_width', delimiter='|', overwrite=True)
result2.write(data_path(catfile2), format='ascii.fixed_width', delimiter='|', overwrite=True)
if write:
result.write(data_path(catfile), format='ascii.fixed_width', delimiter='|', overwrite=True)
result2.write(data_path(catfile2), format='ascii.fixed_width', delimiter='|', overwrite=True)

merged = table.join(result, result2, keys=['tag'])
if not all(merged['#lines'] == merged['# lines']):
Expand Down
4 changes: 2 additions & 2 deletions astroquery/linelists/cdms/tests/test_cdms_remote.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ def test_complex_molecule_remote():

@pytest.mark.remote_data
def test_retrieve_species_table():
species_table = CDMS.get_species_table(use_cached=False)
species_table = CDMS.get_species_table(use_cached=False, write=False)
# as of 2025/01/16
assert len(species_table) >= 1293
assert 'int' in species_table['tag'].dtype.name
Expand All @@ -127,7 +127,7 @@ def test_regression_allcats():
"""
Expensive test - try all the molecules
"""
species_table = CDMS.get_species_table()
species_table = CDMS.get_species_table(write=False)
for row in species_table:
tag = f"{row['tag']:06d}"
result = CDMS.get_molecule(tag)
Expand Down