New hyperleda service 298 #2023

iskren-y-g · 2021-03-22T17:23:28Z

Hi all,

I am not sure if there has been any interest/progress on this, but since I already worked on this for my own projects, I decided to prepare a new class to query from HyperLEDA in relation to [#298].

I have followed closely the astropy's guidelines as well as the astroquery's template module to prepare the module and simple tests to match the astroquery API. I also placed a doc example in astroquery/docs/hyperleda/

All tests passed here, so, I hope it is in a decent shape for a review.

pep8speaks · 2021-03-22T17:23:34Z

Hello @iskren-y-g! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-03-22 17:44:46 UTC

codecov · 2021-03-22T17:50:48Z

Codecov Report

Merging #2023 (3ac1663) into master (c4dde9d) will increase coverage by 2.58%.
The diff coverage is 73.09%.

@@            Coverage Diff             @@
##           master    #2023      +/-   ##
==========================================
+ Coverage   64.45%   67.03%   +2.58%     
==========================================
  Files         200      416     +216     
  Lines       15930    27300   +11370     
==========================================
+ Hits        10267    18300    +8033     
- Misses       5663     9000    +3337

Impacted Files	Coverage Δ
astroquery/hyperleda/tests/setup_package.py	`50.00% <50.00%> (ø)`
...stroquery/hyperleda/tests/test_hyperleda_remote.py	`50.00% <50.00%> (ø)`
astroquery/hyperleda/core.py	`57.69% <57.69%> (ø)`
astroquery/splatalogue/load_species_table.py	`89.47% <66.66%> (ø)`
astroquery/hyperleda/tests/test_hyperleda.py	`93.75% <93.75%> (ø)`
astroquery/simbad/core.py	`89.66% <95.00%> (+0.23%)`	⬆️
astroquery/hyperleda/__init__.py	`100.00% <100.00%> (ø)`
astroquery/sdss/core.py	`86.33% <100.00%> (ø)`
astroquery/sdss/tests/test_sdss.py	`94.57% <100.00%> (ø)`
astroquery/sha/core.py	`70.58% <100.00%> (ø)`
... and 262 more

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keflavich · 2021-03-22T18:01:43Z

Thanks for the contribution!

@low-sky, since you requested this long long ago, are you interested in reviewing this PR (or at least testing it out)?

keflavich

This is a great contribution, thanks! And, sorry there was a bit of delay in reviewing - I'm always backlogged.

I've left several style and cleanup requests. I believe this is actually in working order and can be merged after a bit of cleanup though. Nice work!

keflavich · 2021-10-22T10:01:33Z

astroquery/hyperleda/core.py

+
+# Based on: https://astroquery.readthedocs.io/en/latest/template.html
+
+# Imports organized as shown below


Could you remove these various comments that are part of the template/tutorial?

keflavich · 2021-10-22T10:02:39Z

astroquery/hyperleda/core.py

+
+        param_str = str(param_lst)
+        param_str = param_str[2:param_str.rfind('\'')]
+        param_str = param_str.replace('\', \'', ',')


this might be more readable as:

Suggested change

param_str = param_str.replace('\', \'', ',')

param_str = param_str.replace("', '", ',')

keflavich · 2021-10-22T10:02:50Z

astroquery/hyperleda/core.py

+                param_lst.remove(param)
+
+        param_str = str(param_lst)
+        param_str = param_str[2:param_str.rfind('\'')]


Suggested change

param_str = param_str[2:param_str.rfind('\'')]

param_str = param_str[2:param_str.rfind("'")]

keflavich · 2021-10-22T10:03:30Z

astroquery/hyperleda/core.py

+        >>> result_table = hyperleda.query_object(obj_name = 'UGC12591',
+                                           properties = 'objname,type,logr25,
+                                           btc,v,modbest,al2000,de2000,
+                                           celposJ(pgc)')


Minor whitespace suggestion:

Suggested change

>>> result_table = hyperleda.query_object(obj_name = 'UGC12591',

properties = 'objname,type,logr25,

btc,v,modbest,al2000,de2000,

celposJ(pgc)')

>>> result_table = hyperleda.query_object(obj_name='UGC12591',

properties='objname,type,logr25,

btc, v, modbest, al2000, de2000,

celposJ(pgc)')

keflavich · 2021-10-22T10:05:57Z

astroquery/hyperleda/core.py

+        request_payload = dict(n='meandata', c='o', of='1,leda,simbad',
+                               nra='l', nakd='1',
+                               d='{:}'.format(param_str),
+                               sql='{:}'.format(ls_SQL_search), ob='',
+                               a='csv[|]')
+        response = self._request("GET", url_http_request,
+                                 params=request_payload)
+        sql_result_tbl = Table.read(response.url, format='ascii', delimiter='|')


this code looks like it repeats query_sql below. Why not just return self.query_sql(search=ls_SQL_search, properties=properties)?

keflavich · 2021-10-22T10:06:40Z

astroquery/hyperleda/core.py

+# the default tool for users to interact with is an instance of the Class
+hyperleda = HyperLEDAClass()
+
+# once your class is done, tests should be written
+# See ./tests for examples on this
+
+# Next you should write the docs in astroquery/docs/module_name
+# using Sphinx.


remove the comments, and the capitalization should match that used in other modules (e.g., from astroquery.vizier import Vizier)

Suggested change

# the default tool for users to interact with is an instance of the Class

hyperleda = HyperLEDAClass()

# once your class is done, tests should be written

# See ./tests for examples on this

# Next you should write the docs in astroquery/docs/module_name

# using Sphinx.

HyperLEDA = HyperLEDAClass()

keflavich · 2021-10-22T10:07:55Z

docs/hyperleda/hyperleda.rst

+---------------
+
+This module can be used to query from the HyperLEDA web service. The
+queries will return the resultsin an astropy Table. Below are two


Suggested change

queries will return the resultsin an astropy Table. Below are two

queries will return the results in an astropy Table. Below are two

keflavich · 2021-10-22T10:08:05Z

docs/hyperleda/hyperleda.rst

+object,or using an SQL query request to the HyperLEDA SQL data access
+service.
+
+--------------


Suggested change

--------------

keflavich · 2021-10-22T10:08:31Z

docs/hyperleda/hyperleda.rst

+
+Query the object by name. For instance if you want to query UGC 1259
+
+.. code:: ipython3


I think this is generic python and therefore should be just python

Suggested change

.. code:: ipython3

.. code:: python

keflavich · 2021-10-22T10:09:04Z

docs/hyperleda/hyperleda.rst

+     celposJ(pgc) string              --         Return the J2000 celestial position of object "pgc" in sexagesimal format
+
+
+--------------


I don't think these -----'s separating sections are allowed? I'm not actually sure; how are they supposed to render?

keflavich · 2021-10-22T10:11:09Z

Also, could you add a changelog entry?

iskren-y-g added 3 commits December 12, 2020 18:15

Added hyperleda

b5b9808

New service to access HyperLEDA [astropy#298]

14e6a49

New service to access HyperLEDA [astropy#298]

daaaee8

iskren-y-g added 3 commits March 22, 2021 18:37

cleared pep8 style issues

3a4c017

cleared pep8 style issues

5db66e8

cleared pep8 style issues

3ac1663

bsipocz added this to the v0.4.3 milestone Apr 20, 2021

bsipocz added the New Service label Apr 20, 2021

bsipocz modified the milestones: v0.4.3, v0.4.4 Jul 7, 2021

keflavich requested changes Oct 22, 2021

View reviewed changes

bsipocz removed this from the v0.4.4 milestone Nov 13, 2021

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New hyperleda service 298 #2023

New hyperleda service 298 #2023

iskren-y-g commented Mar 22, 2021

pep8speaks commented Mar 22, 2021 •

edited

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keflavich commented Oct 22, 2021


		# Based on: https://astroquery.readthedocs.io/en/latest/template.html

		# Imports organized as shown below

	param_str = param_str.replace('\', \'', ',')
	param_str = param_str.replace("', '", ',')

	param_str = param_str[2:param_str.rfind('\'')]
	param_str = param_str[2:param_str.rfind("'")]

	queries will return the resultsin an astropy Table. Below are two
	queries will return the results in an astropy Table. Below are two


		Query the object by name. For instance if you want to query UGC 1259

		.. code:: ipython3

		celposJ(pgc) string -- Return the J2000 celestial position of object "pgc" in sexagesimal format


		--------------

New hyperleda service 298 #2023

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New hyperleda service 298 #2023

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iskren-y-g commented Mar 22, 2021

pep8speaks commented Mar 22, 2021 • edited

Comment last updated at 2021-03-22 17:44:46 UTC

codecov bot commented Mar 22, 2021

Codecov Report

keflavich commented Mar 22, 2021

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keflavich commented Oct 22, 2021

pep8speaks commented Mar 22, 2021 •

edited