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Home Page: https://ricemunk.github.io/omnifit/
This is a package for doing ice spectroscopy fitting of interstellar ices.
Home Page: https://ricemunk.github.io/omnifit/
Steps to reproduce:
convolve
Expected result:
y
of convolved spectrum should be of type astropy.units.Quantity
Actual result:
y
of convolved spectrum is of type numpy.ndarray
doing spec1.interpolate(spec2,clone=True)
throws a warning about no units given, and also breaks the units in the new spectrum.
Might be related to cloning or something with interpolate.
Currently you can do something like spectrum1.y -= spectrum2.y
to subtract one spectrum from another (assuming both have the same x), but this neither checks that the spectra are compatible, and it's also a bit clumsy.
It would be much nicer to be able to simply do spectrum1 -= spectrum2
to do the same thing, while also checking that it makes sense.
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While I see a .travis.yml
file, it seems that it has never run for this repository. While I acknowledge that you probably run the tests before releases, having a CI system that is integrated with GitHub can be extremely useful.
One common thing that is usually done with ice fitting results is being able to calculate the column density of the ice represented by the fit.
A few different ways of doing this currently exist:
Also stuff like CDE correction changes how these work, and has to be taken into account to get accurate results.
It would be very useful for Omnifit to be able to do this, instead of forcing the user to mess around with the exported fit results on their own.
When tox attempts to run python -m pip install setuptools setuptools_scm wheel extension-helpers oldest-supported-numpy cython==0.29.14
it creates a whole slew of errors which seems to revolve around ImportError: DLL load failed while importing _ctypes: The specified module could not be found
Running the example full fit (see example in documentation) seemingly does the fit successfully, but never modifies fit parameters from their original guesses. Figure of expected fit result as shown in example is not reproduced.
This seems to happen on fresh installs of Omnifit using the dependencies installed through PyPi, so it may be related to some change which has happened in newer version of the dependencies; probably in ones involving minimization.
Hello from Astropy Project!
The following updates to your package might be necessary to ensure compatibility with the latest stable version of Astropy:
ci-helpers
, packages expecting interactive plotting should override it in .travis.yml
sphinx-astropy
as a package dependency if you are using astropy-helpers
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that is bundled with Astropy, please consider using the standalone six
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This is an automated issue for packages that opted in for automated astropy-helpers update. If this is opened in error, please let @pllim know.
Python 3 is not yet supported.
Python 3 should be supported.
Currently the CDEspectrum
class makes use of complex refractive index values which are commonly calculated using the Kramers-Kronig (KK) relation equation. It is not a terribly complex calculation, yet it's not included as part of Omnifit.
An obvious improvement to Omnifit is to make it be included as part of the library, so CDEspectrum
can be initialised without outside help.
Currently Omnifit can export its fit results as a pair of CSV and XML files. While this way of doing things works, it's not necessarily very user-friendly.
A few alternative formats to export stuff in would be:
Either of these would probably be superior to the home-cooked format Omnifit currently uses, and thus it would make sense to include support for them.
Seems like one of the unit tests has started failing at some point. The following bit specifically seems to be raising an exception:
testfitter.add_analytical('gaussian',testpars,funcname='test gaussian') testfitter.perform_fit()
Fails with "fitting failed".
My guess: something has changed with lmfit which makes it not behave with omnifit. Should look into this when have time.
It seems like a lot of the omnifit functionality requires lmfit
. Should it be a requirement for installation?
This is an automated issue from Astropy. You might be using code removed in astropy v6.0.dev from astropy/astropy#14670 in the following files:
* omnifit/conftest.py
Please use https://docs.pytest.org/en/stable/how-to/capture-warnings.html instead.
If this issue is opened in error or irrelevant, feel free to close. We apologize for any inconvenience caused.
The https://ricemunk.github.io/omnifit/ home page is returning a 404
As recommended by the astropy folks and since it would be nice to reduce the number of dependencies, it might be a good idea to use astropy.modeling instead of lmfit as the fitting engine for omnifit.
To make me not forget to check whether or not this suits what omnifit needs to do, I'm creating this issue here to keep reminding me.
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