Limit dependencies to strictly necessary packages.

[mkelley]

Make scipy, ads, astroquery, and synphot optional packages, limiting the required packages to numpy and astropy.

• Add new functions and decorators in utils to facilitate testing for optional packages, and raising errors when they are needed.
• Skip tests that require the above packages when they are not available.

To do:

• Verify that tests are working when the above packages are installed (i.e., alldeps).
• Update documentation so that it can be built without optional packages?

Addresses #382

[codecov]

Codecov Report

Attention: 17 lines in your changes are missing coverage. Please review.

Comparison is base (ca24266) 76.84% compared to head (e342b89) 77.52%.

Files	Patch %	Lines
sbpy/data/tests/test_orbit_remote.py	20.00%	4 Missing ⚠️
sbpy/activity/gas/tests/test_prodrate_remote.py	25.00%	3 Missing ⚠️
sbpy/calib/tests/test_sun.py	80.00%	3 Missing ⚠️
sbpy/calib/tests/test_core.py	98.13%	2 Missing ⚠️
sbpy/photometry/tests/test_iau.py	75.00%	2 Missing ⚠️
sbpy/activity/gas/productionrate.py	93.33%	1 Missing ⚠️
sbpy/data/tests/test_ephem_remote.py	50.00%	1 Missing ⚠️
sbpy/utils/tests/test_decorators.py	93.75%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #383      +/-   ##
==========================================
+ Coverage   76.84%   77.52%   +0.67%     
==========================================
  Files          78       81       +3     
  Lines        6974     7096     +122     
==========================================
+ Hits         5359     5501     +142     
+ Misses       1615     1595      -20     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[mkelley]

Cannot build the docs. Sphinx crashes with the traceback:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/cmd/build.py", line 298, in build_main
    app.build(args.force_all, args.filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/application.py", line 355, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 313, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 420, in read
    self._read_serial(docnames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 441, in _read_serial
    self.read_doc(docname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 498, in read_doc
    publisher.publish()
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/core.py", line 234, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/io.py", line 105, in read
    self.parse()
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/readers/__init__.py", line 76, in parse
    self.parser.parse(self.input, document)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/sphinx/parsers.py", line 81, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 169, in run
    results = StateMachineWS.run(self, input_lines, input_offset,
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2785, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 325, in section
    self.new_subsection(title, lineno, messages)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 391, in new_subsection
    newabsoffset = self.nested_parse(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2785, in underline
    self.section(title, source, style, lineno - 1, messages)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 325, in section
    self.new_subsection(title, lineno, messages)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 391, in new_subsection
    newabsoffset = self.nested_parse(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 279, in nested_parse
    state_machine.run(block, input_offset, memo=self.memo,
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 195, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 233, in run
    context, next_state, result = self.check_line(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 445, in check_line
    return method(match, context, next_state)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2355, in explicit_markup
    nodelist, blank_finish = self.explicit_construct(match)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2367, in explicit_construct
    return method(self, expmatch)
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2104, in directive
    return self.run_directive(
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/parsers/rst/states.py", line 2154, in run_directive
    result = directive_instance.run()
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/pytest_doctestplus/sphinx/doctestplus.py", line 23, in run
    if re.match('win32', self.content[0]):
  File "/home/docs/checkouts/readthedocs.org/user_builds/sbpy/envs/383/lib/python3.10/site-packages/docutils/statemachine.py", line 1136, in __getitem__
    return self.data[i]
IndexError: list index out of range

which doesn't mean anything to me. I can build ffa5115, so it is definitely something I changed with sbpy. I will look into this some more. Meanwhile, the rest of the checks are good.

[mkelley]

Resolving the documentation build error is pending some more information on the problem via scientific-python/pytest-doctestplus#219

[mkelley]

@jianyangli Remote tests are also passing locally with and without alldeps. Ready for a re-review.

[jianyangli]

Have a general question about how to set up the test in the case when the functions being called inside a function depend on an optional package.

For example, function a doesn't directly uses synphot, but a calls function b, and b uses synphot. Should we leave everything (check the availability of a module, test) about optional packages to the functions that directly use the module, and don't do this check for higher level functions or classes?

[mkelley]

I guess just consider the user experience for each? But also consider what happens if function b is later revised and no longer needs synphot. I guess then the requirement on a will be obsolete and might be difficult to find. So, best to leave it to the point the package is actually used?

[jianyangli]

I agree.

[jianyangli]

I don't see any obvious problems or questions now. I think it's ready to deploy.

[mkelley]

Thanks, @jianyangli !