Python 2 will not be maintained past Jan 1, 2020 (see https://pythonclock.org/). Please remove all Python 2 compatibility and move this package to Python 3 only.

For conda recipe (including astroconda-contrib), please include the following to prevent packaging it for Python 2 (https://conda.io/docs/user-guide/tasks/build-packages/define-metadata.html?preprocessing-selectors#skipping-builds):

build: 
  skip: true  # [py2k] 

Please close this issue if it is irrelevant to your repository. This is an automated issue. If this is opened in error, please let pllim know!

🔥

To close out INC0152118

Q: There is a way to obtain the value of the different DQ flag contained only in the postage stamp?

>>> from astropy.io import fits
>>> from reftools.interpretdq import DQParser, ImageDQ
>>> dqdata = fits.getdata('jbt7a3k7q_flc.fits', 3)  # DQ, 1
>>> dqparser = DQParser.from_instrument('ACS')
>>> acsdq = ImageDQ(dqdata[:100, :100], dqparser=dqparser)
>>> acsdq.interpret_all()                                                                       
Parsing DQ flag(s)...
Done!
Run time: 0.006 s
N_FLAGGED: 366/10000 (3.660%)
FLAG=1    : 0 (0.000%)
FLAG=2    : 0 (0.000%)
FLAG=4    : 0 (0.000%)
FLAG=8    : 0 (0.000%)
FLAG=16   : 111 (1.110%)
FLAG=32   : 21 (0.210%)
FLAG=64   : 115 (1.150%)
FLAG=128  : 0 (0.000%)
FLAG=256  : 0 (0.000%)
FLAG=512  : 100 (1.000%)
FLAG=1024 : 0 (0.000%)
FLAG=2048 : 0 (0.000%)
FLAG=4096 : 49 (0.490%)
FLAG=8192 : 0 (0.000%)
FLAG=16384: 0 (0.000%)
FLAG=32768: 0 (0.000%)
>>> acsdq.data
array([[ 512,  512,  512, ...,  512,  512,  512],
       [   0,    0,    0, ..., 4144,    0,    0],
       [   0,    0,    0, ...,    0,    0,    0],
       ...,
       [   0,    0,    0, ...,    0,    0,    0],
       [   0,    0,    0, ...,    0,    0,    0],
       [   0,    0,    0, ...,    0,    0,    0]], dtype=int16)
>>> acsdq.data.shape
(100, 100)

Ref: INC0152118

https://pypi.org/project/setuptools-scm/

Some issues with existing tests in reftools/tests:

• I can only get nosetests *py to run in the source build directory (not the actual source) because it cannot find the C-extension import (*.so) otherwise. So, I think the solution here is to convert the tests to use pytest. EDIT: Check if aae6e21 fixed this issue.
• Do the tests even matter anymore? Do some of the modules even matter anymore? I have no idea what half of them are supposed to be used for, or who actually find them useful. If they are not used anymore, why waste resources maintaining or testing them?
• Fix some tests in test_getphotpars that are currently marked as "expected failures" due to ValueError: new type not compatible with array. If it even matters, that is.

astropy.extern.six is gone. Among other things.

Currently, it fails with this with "fail on warnings" turned on:

Warning, treated as error:
autodoc: failed to import module 'getphotpars' from module 'reftools'; the following exception was raised:
.../reftools/_computephotpars.cpython-37m-x86_64-linux-gnu.so: undefined symbol: PyInt_AsLong

And also results in getphotpars page being empty.

The following flags have changed:

32 - No longer CTE trails, now indicates unstable pixel using method in ACS ISR 2017-05
64 - Warm pixel (no more date dependence)

Example log: https://github.com/spacetelescope/reftools/actions/runs/7606682322/job/20712860995

        # Find all the possible DQ flags
        else:
>           idx = (dqval & self._valid_flags) != 0
E           DeprecationWarning: __array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0)

reftools/interpretdq.py:329: DeprecationWarning

I think @mcara originally wrote this.

Caused by:

• numpy/numpy#25409

Say, @sean-lockwood , would you be interested in this while you're doing the whole acceptance testing stuff with STIS?

The wfc3 PCTETAB and IMPHTTAB are different from the ACS tables and require special code. This should be added to this package. Perhaps something to make a sink pixel reference file as well.

There are three such warnings:

WARNING: AstropyDeprecationWarning: The new_table function is deprecated and may be removed in a future version.
        Use :meth:`BinTableHDU.from_columns` for new BINARY tables or :meth:`TableHDU.from_columns` for new ASCII tables instead. [reftools.mkimphttab]

when the following command is used:

>>> from reftools import mkimphttab
>>> mkimphttab.create_table('acs_wfc1','acs,wfc1','WFC1','Mar 01 2002 00:00:00')

As requested by @tddesjardins , it would be nice for interpretdq to accept Python's 0-indexed indices. Currently, the interface only supports 1-indexed IRAF pixel locations. Perhaps this behavior can be toggled using origin keyword.

• origin=0 (Python)
• origin=1 (IRAF)

This causes errors: TypeError: iter() returned non-iterator of type 'dict_values'

Should it be this instead?:
for edge in node.edges.values():

cc: @tonysohn

new_table() function has been removed from astropy.io.fits starting with version 1.3 (see commit astropy/astropy@1c3e876). The code in reftools needs to be updated to accommodate above mentioned changes.

I disabled "fail on warnings" for RTD in #58. If you want to enable it again, you have to fix the warnings. The CI had not run for 7 months before I touched it so no idea what happened and I don't have time to follow up on this.

reftools/getphotpars.py:docstring of reftools.getphotpars.GetPhotPars:40: WARNING: autosummary: stub file not found 'reftools.getphotpars.GetPhotPars.close'. Check your autosummary_generate setting.
reftools/getphotpars.py:docstring of reftools.getphotpars.GetPhotPars:40: WARNING: autosummary: stub file not found 'reftools.getphotpars.GetPhotPars.get_phot_pars'. Check your autosummary_generate setting.
reftools/imphtcomp.py:docstring of reftools.imphtcomp.ImphttabComp:68: WARNING: autosummary: stub file not found 'reftools.imphtcomp.ImphttabComp.make_plot'. Check your autosummary_generate setting.
reftools/imphtcomp.py:docstring of reftools.imphtcomp.ImphttabComp:68: WARNING: autosummary: stub file not found 'reftools.imphtcomp.ImphttabComp.print_diffs'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.DQParser:55: WARNING: autosummary: stub file not found 'reftools.interpretdq.DQParser.from_instrument'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.DQParser:55: WARNING: autosummary: stub file not found 'reftools.interpretdq.DQParser.interpret_array'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.DQParser:55: WARNING: autosummary: stub file not found 'reftools.interpretdq.DQParser.interpret_dqval'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.ImageDQ:38: WARNING: autosummary: stub file not found 'reftools.interpretdq.ImageDQ.dq_mask'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.ImageDQ:38: WARNING: autosummary: stub file not found 'reftools.interpretdq.ImageDQ.from_fits'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.ImageDQ:38: WARNING: autosummary: stub file not found 'reftools.interpretdq.ImageDQ.interpret_all'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.ImageDQ:38: WARNING: autosummary: stub file not found 'reftools.interpretdq.ImageDQ.interpret_pixel'. Check your autosummary_generate setting.
reftools/interpretdq.py:docstring of reftools.interpretdq.ImageDQ:38: WARNING: autosummary: stub file not found 'reftools.interpretdq.ImageDQ.pixlist'. Check your autosummary_generate setting.

Tyler Desjardins mentions that we should consider moving emails from help[at]stsci.edu to point to the web portal where possible and appropriate. For HST (or any non-JWST), it is https://hsthelp.stsci.edu . For JWST, it is https://jwsthelp.stsci.edu . Please update info in setup.py, setup.cfg, documentation, etc as appropriate.

Please close this issue if it is irrelevant to your repository. This is an automated issue. If this is opened in error, please let pllim know!

xref spacetelescope/hstcal#317