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Simon Conseil saimn Gemini Observatory La Serena, Chile sconseil.fr

Piwigo/simple-theme-piwigo 14

simple theme for piwigo

ktsoto/zap 5

the Zurich Atmosphere Purge

saimn/color-theme-molokai 3

An Emacs port of the Vim port of the Monokai color scheme for TextMate.

saimn/doit-redis 2

Redis backend for doit

musevlt/muse-psfr 1

MUSE-PSFR - PSF reconstruction for MUSE WFM-AO

musevlt/origin 1

ORIGIN: detectiOn and extRactIon of Galaxy emIssion liNes

musevlt/mpdaf 0

MUSE Python Data Analysis Framework

saimn/aplpy 0

Astronomical Plotting Library in Python

saimn/archlinux-pkgbuilds 0

PKGBUILDs for archlinux

saimn/astropy 0

Main AstroPy repository

issue commentsaimn/sigal

Please list filenames of images with corrupt EXIF data

Hi, The warning comes from Pillow, but if you run sigal in verbose mode (-v) it would print the filenames.

LaurentBonnaud

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issue commentastropy/sphinx-astropy

Missing dependencies for astropy docs build

I tried replacing it with warnings.catch_warnings in astropy/astropy#10504 but it broke most spectacularly.

I had a look, and that's a nice can of worms ;D. Basically Astropy's catch_warnings is overwriting the warnings defined in setup.cfg for pytest, by calling treat_deprecations_as_exceptions in its __exit__ method. So the global error clause in pytest's config was ignored once Astropy's catch_warnings was called...

https://github.com/astropy/astropy/blob/49708febbdaa1d1bf53f96981bf1f1d71295d33d/setup.cfg#L102-L103

When using warnings.catch_warnings this does not happen, so the global error clause is there, and the checksum verification in io.fits is issuing warning when the checksum is wrong, which turns into errors, which break the code's logic... Not sure what's the best solution here.

taldcroft

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Tom Aldcroft

commit sha 3662b5a9a6d5bb690fa8ca5b6d2c9e415cdc4ba0

Allow zero-length table from names and structured-array dtype

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Tom Aldcroft

commit sha 583804f813ddd2f7ead9b0cb45ae980421dd4ad2

Allow using np.dtype with data arg as well

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Marten van Kerkwijk

commit sha 0c4ea2d81cd2a6333a24f47af4a99155e8984e80

Relax precision test for scale UTC

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Tom Aldcroft

commit sha 71f0a16ee2e6242346d7e8031b76cb6ecd706941

WIP FIX change me

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Tom Aldcroft

commit sha e3ac90025bd982a9165271ee36ac543668a727f7

Move test to more expected location

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Ed Slavich

commit sha 32c22a2d9a24cdf7b9b6e37313712a5548cc56be

Ignore deprecation warnings due to ASDF pytest plugin

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P. L. Lim

commit sha 65d987a098f71f9ac338f4e20f8afab11e59b19b

Merge pull request #10436 from eslavich/eslavich-ignore-asdf-pytest-warning Ignore pytest warnings due to asdf plugin

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Marten van Kerkwijk

commit sha 1da60c5449d381a8166ec58e68ca3ba338aebf78

Merge pull request #10419 from taldcroft/table-empty-names-dtype Allow zero-length table from names and structured-array dtype

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Tom Aldcroft

commit sha 7cc204fc187fdf0187ef7155ea79ecdf0fe53de5

Merge pull request #10428 from mhvk/time-hypothesis-relax-for-utc Relax precision test for scale UTC

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Pey Lian Lim

commit sha 164c1ba3e88c394aabf3759e8f6e9032b2b411a3

MNT: Replace catch_warnings in erfa tests

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Pey Lian Lim

commit sha 271891297be80190541eea492292940983103e5a

MNT: Replace catch_warnings in config tests

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Pey Lian Lim

commit sha 10391d28e7fc54c842fd8107b6b28a46cabbd399

MNT: Replace catch_warnings in coordinates tests. Apply coordinates comments from @mhvk. Fix regex for warning messages.

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Pey Lian Lim

commit sha faf20ec3ea643effdc4ff60947ff524d5cf799d9

MNT: Replace catch_warnings in io.ascii tests

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Pey Lian Lim

commit sha d3ae2df1828642ad1600d1fe44ed29db9b2b9991

MNT: Remove catch_warnings from test guide

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Pey Lian Lim

commit sha 3f1fc4864d7f0f10db7605d35ef4cebef2137f5f

MNT: Remove catch_warnings from units tests. Also fix pytest message caught in io.ascii test_ecsv.py and remove accidental blank line in test guide.

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Pey Lian Lim

commit sha d5504cca9cfbb3dd924ca85e1136ccfecc0022c2

MNT: Remove catch_warnings from wcsaxes tests

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Pey Lian Lim

commit sha 089626dd690da3bc1a10723f836188833aae8bec

MNT: Remove catch_warnings from utils iers and decorators

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Pey Lian Lim

commit sha 9748b1b6afb79e16107fa0dc0a6b3e2ecd2a61e0

MNT: Remove catch_warnings from utils data

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Pey Lian Lim

commit sha 51a59b41fc80bef1e53a966b44bcbab2ff5f4a45

Fix test failure seen in image-tests-mpl222

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Pey Lian Lim

commit sha 60146b5647e640a69ee1bacde5e38865194b6352

More fixes for coordinates, table, wcsapi

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pull request commentastropy/sphinx-astropy

Replace numpydoc with napoleon

Numpydoc is used by Numpy, Scipy, Matplotlib and probably many others, and is now well maintained (this was more a problem a few years ago), so what would be the gain of switching to napoleon which is less widely used and tested ?

pllim

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Pull request review commentastropy/astropy

MNT: Stop using our own catch_warnings and raises

 def test_file_output_overwrite_vs_clobber(self):         hb['C'] = 4         diffobj = HeaderDiff(ha, hb)         diffobj.report(fileobj=outpath)-        with catch_warnings(AstropyDeprecationWarning) as warning_lines:+        with pytest.warns(AstropyDeprecationWarning, match=r'"clobber" was '

I would vote to keep it forever ;)

pllim

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issue commentastropy/package-template

Coverage results not being sent to codecov/coveralls

Oh and probably this as well: https://github.com/astropy/astropy/blob/7cc204fc187fdf0187ef7155ea79ecdf0fe53de5/.travis.yml#L226-L228

dr-rodriguez

comment created time in 5 days

issue commentastropy/package-template

Coverage results not being sent to codecov/coveralls

Astropy is specifying the config path in the test command : --cov-config={toxinidir}/setup.cfg https://github.com/astropy/astropy/blob/master/tox.ini#L93 This way the coverage report works also when running tox manually. I found this while working on the coverage for astroscrappy recently, but forgot to report, sorry !

dr-rodriguez

comment created time in 5 days

issue closedsaimn/sigal

Skip video on conversion failure

Hi, I'm having a lot of trouble building my gallery with sigal because it gets errors in video conversion. While the conversion error isn't caused by sigal, the fact that it crashes the program is annoying (and it doesn't build the website).

Ideally, I think sigal shouldn't crash when a conversion fails but instead skip to the next file.

Otherwise, what would be the recommended way to turn off video conversion, give an empty list to video_extensions in the configuration file? It'd be a quick fix, but it's disappointing that it would ignore all videos instead of just the ones which failed.

Thanks!

P.S.: I could share more details on my video conversion errors, but I think fixing them is not relevant in this project (it's not sigal's problem; it's a ffmpeg problem on the Odroid XU4 with Ubuntu 18.04). Ultimately, multiprocessing crashes with the following output:

[h264_v4l2m2m @ 0x47dbc0] driver 'exynos-gsc' on card 'exynos-gsc gscaler'
    Last message repeated 1 times
[h264_v4l2m2m @ 0x47dbc0] driver 's5p-jpeg' on card 's5p-jpeg decoder'
[h264_v4l2m2m @ 0x47dbc0] driver 's5p-jpeg' on card 's5p-jpeg encoder'
[h264_v4l2m2m @ 0x47dbc0] driver 's5p-jpeg' on card 's5p-jpeg decoder'
[h264_v4l2m2m @ 0x47dbc0] driver 's5p-jpeg' on card 's5p-jpeg encoder'
[h264_v4l2m2m @ 0x47dbc0] Could not find a valid device
[h264_v4l2m2m @ 0x47dbc0] can't configure decoder
Stream mapping:
  Stream #0:0 -> #0:0 (h264 (h264_v4l2m2m) -> vp9 (libvpx-vp9))
  Stream #0:1 -> #0:1 (pcm_s16le (native) -> opus (libopus))
Error while opening decoder for input stream #0:0 : Invalid argument

DEBUG - Removing file /srv/sigal/Imprimante 3D/IMG_0007.webm
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/gallery.py", line 776, in worker
    return process_file(args)
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/gallery.py", line 768, in process_file
    ret = processor(*args[3:])
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/video.py", line 171, in process_video
    options=settings.get(video_format + '_options'))
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/video.py", line 127, in generate_video
    check_subprocess(cmd, source, outname)
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/video.py", line 59, in check_subprocess
    raise SubprocessException('Failed to process ' + source)
sigal.video.SubprocessException: Failed to process /mnt/Photos/Imprimante 3D/IMG_0005.MOV
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/sigal/app/bin/sigal", line 8, in <module>
    sys.exit(main())
  File "/home/sigal/app/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/sigal/app/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/sigal/app/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sigal/app/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/sigal/app/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/__init__.py", line 157, in build
    gal.build(force=force)
  File "/home/sigal/app/lib/python3.6/site-packages/sigal/gallery.py", line 689, in build
    for res in self.pool.imap_unordered(worker, media_list):
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 735, in next
    raise value
sigal.video.SubprocessException: Failed to process /mnt/Photos/Imprimante 3D/IMG_0005.MOV

P.P.S.: My user is sigal, the app is in /home/sigal/app, the shared gallery is in /mnt/Photos, the website build is set to /srv/sigal, and user sigal has all relevant accesses, including to these directories and groups video and audio.

closed time in 7 days

miek770

issue commentsaimn/sigal

Skip video on conversion failure

@miek770 - Yes this should be mentioned indeed. Fixed in 0e49dae02913495c0de69546c2725e180ecfede6.

miek770

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Simon Conseil

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Mention that --debug will raise exceptions

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Marten van Kerkwijk

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Add needs_array_function to broadcasting test of SkyCoord

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Marten van Kerkwijk

commit sha 96d721940bdc22fd2f80fce3a883463f3e487744

Ensure config tests do not change configuration.

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Marten van Kerkwijk

commit sha 1c877a39f16fe51913da9b240ac5fee542b163fa

Remove unnecessary remote_data in coordinates.

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Marten van Kerkwijk

commit sha 793c71120eaee51b134d540243f7980374793f15

Remove unnecessary remote_data in utils.iers.

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Marten van Kerkwijk

commit sha bb1368e36d7f25ac7647ec83e5a9f377a9c9c80b

Ensure set_temp_config restores old configuration. Here, it should not assume that the configuration is all stored in a file, but include any configuration done programmatically. This is particularly useful to keep utils.iers.conf.auto_download to any setting done in conftest.py.

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Marten van Kerkwijk

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Remove bad default configuration from travis setup

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Mihai Cara

commit sha 85e94975a656a5f2179608cd47bde25bbd3932a5

Add comments to SIP coefficients in WCS.to_header

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Simon Conseil

commit sha d151baf9e70cab8cd2174ef281011bc5fd9989f9

Avoid crash when table contains mixin info and yaml is missing Fix #7783

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Simon Conseil

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Run tests even if yaml is available

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Simon Conseil

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Avoid modifying .meta when serializing columns Fix #7364

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Simon Conseil

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Add changelog entries

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Simon Conseil

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Improve test to make sure meta's comments are preserved

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Inada Naoki

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Remove use of deprecated unicode APIs.

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Inada Naoki

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refactoring

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Inada Naoki

commit sha 7a3a85cea1a3bd066413120d9ec18ee0e758c08b

fix 32bit

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Inada Naoki

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Fix signed char overflow

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Inada Naoki

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fix typo

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Pey Lian Lim

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TST: Pin Sphinx so linkcheck works

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Pey Lian Lim

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DOC: Remove mention of author_lists.py [skip travis]

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P. L. Lim

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Merge pull request #10499 from pllim/doc-release-credits DOC: Remove mention of author_lists.py

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issue commentastropy/astropy

Pickling an astropy.io.fits.CompImageHDU fails

Indeed, it seems to be caused by #9229. But on the other hand it seems that HDU objects are not guaranteed to be pickable. It was working before #9229 if the HDU was instantiated manually, but it doesn't work if it is read from a file, because a file object is not pickable. Fixing only CompImageHeader should be easy, but making HDU objects always pickable would require a bit more work.

corbettht

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issue commentsaimn/sigal

Fully static-compatible theme (full-featured with shareable links not needing JS).

Thanks for the kind words :)

I did not notice the Wiki at first. Please consider linking to the wiki from the template configuration file, especially on the theme option documentation.

Yes, good idea.

Implementing a static theme would be very valuable for sure ! In that case we should probably consider including the possibility to generate per-image HTML in the core, instead of the media_page plugin. There is some room for improvements in the HTML writer, to have a more general way to render templates.

fidergo-stephane-gourichon

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startedguaix-ucm/megaradrp

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issue commentsaimn/sigal

standard config file lookup

like "no index.md file, will use directory name as album title"

There could be a logging message, indeed.

zip_gallery = 'Photo album {album.author} - {album.title}.zip'

That would be a good addition to the config file comment :+1: . Contributions are welcome ;)

anarcat

comment created time in 11 days

issue commentsaimn/sigal

Permanent description on a photo

I think it would need more than a CSS change.

sprnza

comment created time in 11 days

issue commentsaimn/sigal

Skip video on conversion failure

In debug mode (which you were using at least in the first example) it is expected to fail, as a help to debug issues, but it should not fail otherwise, and just report files for which there was a problem.

miek770

comment created time in 13 days

issue commentastropy/astropy

deprecate_renamed_argument doesn't pop removed arguments from kwargs

Trying to guess from the linked issue, this happens only when an argument is removed, not renamed, so when the "newname" is set to None, i.e. something like this:

In [18]: @deprecated_renamed_argument('foo', None, '1.0', arg_in_kwargs=True) 
    ...: def func(**kwargs): 
    ...:     print(kwargs) 

In [19]: func(foo=1)                                                                                     
WARNING: AstropyDeprecationWarning: "foo" was deprecated in version 1.0 and will be removed in a future version.  [warnings]
{'foo': 1}

In this case I think it makes sense to pass the old argument through kwargs. This is a deprecation warning, so the argument may still be used in the function while it is deprecated, and if it is not used then that should not be a problem ?

bsipocz

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Simon Conseil

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Simplify some HDU operations

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Simon Conseil

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Simplify some HDU operations

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James E.H. Turner

commit sha 540c6a104332adb6b2acf45d16413eb372a28263

Support serializing gWCS in AstroData for nddata.wcs (currently as a FITS ASCII table extension).

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James E.H. Turner

commit sha 495007eebe8d82d694491cee72732ebf7057bd98

Save WCS ASDF lines as separate FITS table rows, which is more navigable and avoids memory-related crashes in IRAF.

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James E.H. Turner

commit sha f5e0fdacee884dbde8d309322a6400f7606f9060

Allow reading gWCS from binary as well as ASCII tables, using the same conventions, because there's no real reason to disallow it, though currently AstroData is only writing ASCII.

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James E.H. Turner

commit sha b82bace49bc49f3604efecf4f996c5bcda46dba7

Decode/encode ASDF bytes to/from ASCII rather than UTF-8 because that's what ASDF is using and what (Bin)TableHDU is expecting for a character column.

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James E.H. Turner

commit sha 528a922a8025784c6b9ca26d19513d11a920f067

Fall back to dumping ASDF bytes to a binary table if they unexpectedly contain binary data so can't be encoded as ASCII (though I think this shouldn't happen). Read the table back in appropriately, according to its type.

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James E.H. Turner

commit sha 195b3ade9cc5eed1109022d50e0785804219c8c3

Only require asdf when actually reading/writing a gWCS serialization (but gwcs itself needs importing so we can check whether we actually have a gwcs object).

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James E.H. Turner

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Use the right type of error for the wrong type of value.

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James E.H. Turner

commit sha bae0ea14ba57c3c9183dceb402f05124fc43187f

Allow NDAstroData.wcs attribute to be None or astropy.wcs.WCS as well as gWCS. Simplify error formatting (so it doesn't say eg. '(NoneType, WCS, WCS)').

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James E.H. Turner

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Add a test for gWCS serialization in AstroData.

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James E.H. Turner

commit sha def228f59a159ada7ff5a72f5706ebd598f647f5

Merge branch 'master' into gwcs (resolving a conflict in astrodata/testing.py).

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James E.H. Turner

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Mark gWCS test xfail on astropy <4.0.1 due to incomplete model serialization.

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James E.H. Turner

commit sha e8fe03f41251752ecdbb9caee857e5f462a2f8e2

Compare gWCS co-ord frames (crudely) after serialization as well as transforms.

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James E.H. Turner

commit sha 225bc72b279fa922fa132386ad69b829702138af

Specify domain as a list rather than a tuple, as per the docs, otherwise its type currently changes after serialization (#9906).

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James E.H. Turner

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Clarify that NDData contains meta-data as well as pixel arrays.

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James E.H. Turner

commit sha f741b2fe5b5ac34ed384981883e6b4b9b6e33ad2

Document use of the NDData wcs attribute and serialization of gWCS.

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James E.H. Turner

commit sha 2ec355a0d7cdb1bae591529fd84f266607c72cfd

Replace vectorize(decode()) with np.char.decode as suggested by @saimn. It seems that vectorize isn't working properly with chararray anyway?

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James E.H. Turner

commit sha 66e18cff951907461bb8f36bcdcdd0cc90a6cb38

Get distortion correction working with gWCS in a preliminary fashion.

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James E.H. Turner

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Merge branch 'master' into gwcs.

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James E.H. Turner

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Merge branch 'gwcs' into gwcs2, resolving conflicts in primitives_spect.py.

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csimpson

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allow ext.nddata.wcs to be accessed directly as ext.wcs

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pull request commentastropy/astroscrappy

Cython coverage

Yep, it's good to go!

saimn

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pull request commentastropy/astroscrappy

Cython coverage

Happy to see this working, it will be useful for other projects :)

saimn

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Simon Conseil

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Need CYTHON_TRACE_NOGIL

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pull request commentastropy/astroscrappy

Cython coverage

Yes, it works (I was defining CFLAGS in two places, that wasn't good :)) https://codecov.io/gh/astropy/astroscrappy/tree/84c0e9e4ceb0028ab2437dfe34aa441eb06f5326/astroscrappy/utils

saimn

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Simon Conseil

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Try to get coverage for C files

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pull request commentastropy/astroscrappy

Cython coverage

In theory yes, with CFLAGS=--coverage, and codecov is running gcov by default, but I was getting a undefined symbol: __gcov_merge_add error. But now I think I know why, let's try it again.

saimn

comment created time in 17 days

pull request commentastropy/astroscrappy

Cython coverage

@cmccully - It works! See the coverage report here: https://codecov.io/gh/astropy/astroscrappy/tree/7ef27224f0ddcf3d63ddf04850222ce39dd42dbe/astroscrappy

saimn

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Simon Conseil

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Report results to codecov

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Simon Conseil

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Do not use tox for the coverage build

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Simon Conseil

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Do not use tox for the coverage build

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Simon Conseil

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Install deps manually

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Simon Conseil

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Remove --coverage for now

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Simon Conseil

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Remove --coverage for now

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PR opened astropy/astroscrappy

Cython coverage

Fix #30.

To get the Cython coverage, we need a "develop" build. Also I moved the linetrace and profile directives, as well as definition of CYTHON_TRACE=1, to be optional since it can have a performance impact for normal builds. So this is activated in the setup.py by setting the COVERAGE env var.

Refs: https://medium.com/@dfdeshom/better-test-coverage-workflow-for-cython-modules-631615eb197a http://blog.behnel.de/posts/coverage-analysis-for-cython-modules.html

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issue commentastropy/astropy

Meaning of empty string keywords in fits.Header

Yes indeed, it seems there are a few things to fix here :+1:

mcara

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issue commentastropy/astropy

Inconsistent representation of empty string values in repr(fits.Header)

Yes .value is stripping whitespaces, but there is a config item to deactivate this: conf.strip_header_whitespace.

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Pull request review commentGeminiDRSoftware/DRAGONS

Updated SkyCam AstroData implementation to latest underlying classes

 def _tag_site(self):      @astro_data_descriptor     def instrument(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('TELESCOP').strip('"')+        return self.phu['TELESCOP'].strip('"')      @astro_data_descriptor     def object(self):-        hdr = self.TABLE1.meta.get('header')         return 'ZENITH'      @astro_data_descriptor     def exposure_time(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('EXPTIME')+        return self.phu['EXPTIME']      @astro_data_descriptor     def ra(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('RA')+        return self.phu['RA']      @astro_data_descriptor     def dec(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('DEC')-    -    @astro_data_descriptor-    def ut_datetime(self):-        hdr = self.TABLE1.meta.get('header')-        return dateutil.parser.parse(hdr.get('DATE-OBS'))-        +        return self.phu['DEC']

Yes, out of curiosity ;)

olyoberdorf

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Pull request review commentGeminiDRSoftware/DRAGONS

Updated SkyCam AstroData implementation to latest underlying classes

 def _tag_site(self):      @astro_data_descriptor     def instrument(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('TELESCOP').strip('"')+        return self.phu['TELESCOP'].strip('"')      @astro_data_descriptor     def object(self):-        hdr = self.TABLE1.meta.get('header')         return 'ZENITH'      @astro_data_descriptor     def exposure_time(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('EXPTIME')+        return self.phu['EXPTIME']      @astro_data_descriptor     def ra(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('RA')+        return self.phu['RA']      @astro_data_descriptor     def dec(self):-        hdr = self.TABLE1.meta.get('header')-        return hdr.get('DEC')-    -    @astro_data_descriptor-    def ut_datetime(self):-        hdr = self.TABLE1.meta.get('header')-        return dateutil.parser.parse(hdr.get('DATE-OBS'))-        +        return self.phu['DEC']

Then there is probably no need to redefine those descriptors (ra, dec, exptime, ...) since the parent class is already getting those values from the primary header ?

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pull request commentastropy/astroscrappy

Follow up to the other PRs

There may still be updates from the template for affiliated packages, but I don't see much value in having a copy of the changelog here.

saimn

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PR opened astropy/astroscrappy

Follow up to the other PRs

Following #46 adn #47:

  • Replace coveralls badge with codecov
  • Using ccache on Travis should improve a bit compilation times
  • I removed the TEMPLATE_CHANGES file which was outdated, do you prefer to have a copy here ? The latest version is https://github.com/astropy/package-template/blob/cookiecutter/TEMPLATE_CHANGES.md I think.
+9 -157

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issue commentastropy/astroscrappy

Enable AppVeyor?

@cmccully - can be closed, the windows build is on Travis now.

astrofrog

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issue commentastropy/astroscrappy

Travis Fails to build Astroscrappy

I think this one was fixed by the latest release?

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pull request commentastropy/astroscrappy

Switch to codecov

It works! https://codecov.io/gh/astropy/astroscrappy/pull/47/tree

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PR opened astropy/astroscrappy

Switch to codecov

This is based on #46 but I wanted to test it separately.

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pull request commentastropy/astroscrappy

Remove astropy-helpers

It seems to be already activated: https://codecov.io/gh/astropy/astroscrappy So I think we just need to replace coveralls by codecov in the travis config.

saimn

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pull request commentastropy/astroscrappy

Remove astropy-helpers

For codecov you need to activate their app in the Github settings. I think it is already activated in the astropy org, and I'm sure if you need to activate it at the repo level as well.

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pull request commentastropy/astroscrappy

Remove astropy-helpers

I may have a solution for the coverage:

----------- coverage: platform linux, python 3.8.3-final-0 -----------
Name                                  Stmts   Miss  Cover
---------------------------------------------------------
astroscrappy/__init__.py                  5      0   100%
astroscrappy/astroscrappy.pyx           209     96    54%
astroscrappy/utils/__init__.py            4      0   100%
astroscrappy/utils/image_utils.pyx       62      6    90%
astroscrappy/utils/median_utils.pyx     106     16    85%
---------------------------------------------------------
TOTAL                                   386    118    69%

I need to check a few more things, and maybe I can put later in another PR (to avoid accumulating too many changes) ?

saimn

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pull request commentastropy/astroscrappy

Remove astropy-helpers

The c files were originally included because it was recommended by pypi. Is that no longer the case? This was also in response to #6, so we should make sure this fixes that issue as well.

Since it is now easier to have build dependencies (with the pyproject.toml file), it is recommended not to include the .c files generated by cython. This way, it would be easier to install from sources with a newer version of cython if needed (e.g. for newer versions of Python which sometimes require some changes on Cython side). For #6 I'm not sure what the problem was but yes I think this would be solved (it seems this was due to an issue in astropy-helpers).

Originally, in setup.py we tried to automatically detect if openmp was available on the system. I like having the option to compile with openmp, so can you comment on if this option is still available?

Yes, I just replaced your custom code by extension_helpers.add_openmp_flags_if_available which is doing the same: https://github.com/astropy/extension-helpers/blob/f5a3f6236796bc03349bb60ed5a5c419c66bdccd/extension_helpers/_openmp_helpers.py#L232

It's strange that the coverage report is not showing up here. Any ideas?

Is there a coverage report with coveralls ? Astropy and many projects switched to codecov, which has the reports and a nicer UI,.

We also originally had an issue that coveralls was not reporting the test coverage for the cython files (which is basically everything of use). Does this fix that as well?

No sadly, I saw the issues related to this, but last time I tried with another project I never managed to get coverage report for Cython files. Astropy used to have coverage for c files (not cython), but that seems broken.

saimn

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issue commentastropy/astropy

Meaning of empty string keywords in fits.Header

With an empty string this is a "blank" keyword, which is just a special kind of comment keyword. image

And h[''] returns the list of blank cards, same as h['COMMENT'] or h['HISTORY'] for comment and history cards. In your case hdr[''] crashes because values are int, and should be strings instead. And for hdr[' '] (with a space) I don't know what that means yet ;).

mcara

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issue commentastropy/astropy

Inconsistent representation of empty string values in repr(fits.Header)

This behavior is defined in the FITS standard:

image

image

And the code doing this is here:

https://github.com/astropy/astropy/blob/3b0c42f1c4e0352f76f55d98aaad9f2006376fa7/astropy/io/fits/card.py#L1207-L1241

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Fix issues with mixins serialization and FITS

 def _encode_mixins(tbl):     if encode_tbl is tbl and not info_lost:         return tbl +    # Copy the meta dict if it was not copied by represent_mixins_as_columns+    if encode_tbl is tbl:+        meta_copy = deepcopy(tbl.meta)

Good points, thanks, I did the changes.

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Fix issues with mixins serialization and FITS io.fits table

Fix #7783 and #7364.

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Fix issue when setting a keyword ending with space Bug io.fits

Fix #10479.

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issue closedastropy/astropy

Keywords' values are not replaced in fits.Header when keywords end in space

Description

Normally, when a keyword in astropy.io.fits.Header is set twice second value replaces previous value of the same keyword. This does not happen when keywords end in space (' ')

Expected behavior

I would expect that setting a keyword value of a keyword like 'KEY ' to 1 (first time) and to 2 (second time), the second value would replace the first value.

Actual behavior

When setting a keyword value of a keyword like 'KEY ' to 1 (first time) and to 2 (second time), the second value does not replace the first value. Instead the header has two cards with the same keyword with two different values (1 and 2 in this case).

Steps to Reproduce

In [1]: from astropy.io import fits
   ...: print("--- FIRST iteration ---")
   ...: hdr = fits.Header()
   ...: hdr['KEY1'] = 1
   ...: hdr['KEY2 '] = 2
   ...: print(repr(hdr))
   ...: hdr['KEY1'] = 3
   ...: hdr['KEY2 '] = 4
   ...: print("--- SECOND iteration ---")
   ...: print(repr(hdr))
   ...: print("value of 'KEY2 ' is: {}".format(hdr['KEY2 ']))
--- FIRST iteration ---
KEY1    =                    1
KEY2    =                    2
--- SECOND iteration ---
KEY1    =                    3
KEY2    =                    2
KEY2    =                    4
value of 'KEY2 ' is: 2

I would expect the value of 'KEY2 ' to be 4 and that there were just one entry for this keyword in the header.

If space character is supported in keyword names (i.e., if it is simply ignored, like strip()), then the behavior should be as expected by me. If space at the end is not supported, then I would expect to see a warning like in the following situation:

In [2]: hdr['a#'] = 9
WARNING: VerifyWarning: Keyword name 'a#' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]

In [3]: hdr['a '] = 9  # No warning!

In [4]:

System Details

Darwin-17.7.0-x86_64-i386-64bit
Python 3.7.6 (default, Jan  8 2020, 13:42:34)
[Clang 4.0.1 (tags/RELEASE_401/final)]
Numpy 1.18.0
astropy 4.2.dev167+g8bdd24b04
Scipy 1.3.2
Matplotlib 3.2.0

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mcara

pull request commentastropy/astropy

Fix issue when setting a keyword ending with space

Thanks @mcara and @pllim :), merging.

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Pull request review commentastropy/astropy

Fix Table.read/write.help when reader/writer has no docstring

 def test_ccddata_read_help_fits():     assert "CCDData.read(format='fits') documentation" in doc     assert "Generate a CCDData object from a FITS file" in doc     assert "hdu_uncertainty : str or None, optional" in doc+++def test_table_write_help_jsviewer():+    """+    Test dynamically created documentation help via the I/O registry for+    'jsviewer'.+    """+    out = StringIO()+    Table.write.help('jsviewer', out)+    doc = out.getvalue()++    # Check a smattering of expected content+    assert "Table.write general documentation" not in doc+    assert "The available built-in formats" not in doc+    assert "Table.write(format='jsviewer') documentation" in doc+++def test_table_read_no_help():+    try:+        io_registry.register_reader('test1', Table, empty_reader)

Ok, I removed the tests and added the changelog entry. And squashed and rebased to get the fix for the docs build.

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Pull request review commentastropy/astropy

Fix Table.read/write.help when reader/writer has no docstring

 def test_ccddata_read_help_fits():     assert "CCDData.read(format='fits') documentation" in doc     assert "Generate a CCDData object from a FITS file" in doc     assert "hdu_uncertainty : str or None, optional" in doc+++def test_table_write_help_jsviewer():+    """+    Test dynamically created documentation help via the I/O registry for+    'jsviewer'.+    """+    out = StringIO()+    Table.write.help('jsviewer', out)+    doc = out.getvalue()++    # Check a smattering of expected content+    assert "Table.write general documentation" not in doc+    assert "The available built-in formats" not in doc+    assert "Table.write(format='jsviewer') documentation" in doc+++def test_table_read_no_help():+    try:+        io_registry.register_reader('test1', Table, empty_reader)

Yes agreed :smile:, but if I or someone else update the jsviewer docstring in the future it may lead to an inconsistent test/docstring, so I didn't want to rely on the jsviewer test for this. As you prefer, I'm happy to remove the two extra tests if using the registry like this is overkill.

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Pull request review commentastropy/astropy

Fix issue when setting a keyword ending with space

 def test_header_fromstring_bytes(self):         assert pri_hdr == pri_hdr_from_bytes         assert pri_hdr.tostring() == pri_hdr_from_bytes.tostring() +    def test_set_keyword_with_space(self):+        """+        Regression test for https://github.com/astropy/astropy/issues/10479+        """+        hdr = fits.Header()+        hdr['KEY2 '] = 2+        hdr['KEY2 '] = 4+        assert len(hdr) == 1+        assert hdr['KEY2 '] == 4

Good ideas, thanks, I updated the test.

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issue commentastropy/astropy

Keywords' values are not replaced in fits.Header when keywords end in space

@mcara : Indeed, the keyword is not normalized before checking its existence, which I think is a bug. Proposed fix in #10482.

mcara

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PR opened astropy/astropy

Fix issue when setting a keyword ending with space io.fits

Fix #10479.

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Do not allow panda to crash the build

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P. L. Lim

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Merge pull request #10452 from mhvk/travis-cron-tests-with-apt Fix travis cron tests with apt

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Pey Lian Lim

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Remove PY2 compat for urlparse import

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Marten van Kerkwijk

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Merge pull request #10472 from pllim/py3-urlparse MNT: Remove PY2 compat for urlparse import

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Pey Lian Lim

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Fix Sphinx warning for test runner [skip travis]

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Marten van Kerkwijk

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Merge pull request #10477 from pllim/fix-doc-build TST: Fix Sphinx warning for test runner

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Marten van Kerkwijk

commit sha 1b0fc5eb7e55ace801e1eae32537b3b39e1af9d9

Ensure we catch all exceptions when trying to set shape. The check was only for AttributeError, but a ValueError is possible too. Since we will want to undo any half-processed shape change regardless of the exception, we just catch them all (they will be re-raised anyway).

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Marten van Kerkwijk

commit sha e5c1d56e59a9d052c1d0f9e1d6c83751cce6c29b

Merge pull request #10431 from mhvk/shape-setting-exceptions Ensure we catch all exceptions when trying to set shape.

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Marten van Kerkwijk

commit sha c803a94ea6584daffebd93d41c085fca5374d853

Merge pull request #10424 from mhvk/earth-fix-broadcast-issue Fix broadcasting issue between EarthLocation and obstime in get_gcrs.

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Use debug instead of plot for debugging plot

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Simon Conseil

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Improve test and remove the other one

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Specify matplotlib's backend in the Jenkinsfile This is to allow showing plot when running tests manually.

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Add basic primitive flagging cosmics with astroscrappy

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Simon Conseil

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Add test

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Simon Conseil

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Add parameters

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Simon Conseil

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Use gain and read_noise from the ad object

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Add docstring

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Add astroscrappy to requirements

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Move primitive to Spect

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Simon Conseil

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Add background fitting From https://github.com/jehturner/ndmapper/blob/master/ndmapper/lib/cosmetics.py#L184-L327

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Simon Conseil

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Replace iters with maxiters for sigma_clip

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Simon Conseil

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Add test with GMOS LS data

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Simon Conseil

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Fix issue with fitter args and add debug plot

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Simon Conseil

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Update test

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Fix coverage reporting

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