Merge pull request #1047 from pypeit/staged

Merges develop into master (1.2.0 tag)
pypeit · Oct 16, 2020 · 0c3f22b · 0c3f22b
2 parents d34dcf6 + ce7eea9
commit 0c3f22b
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Showing 250 changed files with 19,010 additions and 16,306 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.1
+current_version = 1.2.0
 commit = False
 tag = False
 tag_name = {new_version}
@@ -20,3 +20,5 @@ values =
 
 [bumpversion:file:doc/conf.py]
 
+[bumpversion:file:doc/index.rst]
+
diff --git a/.gitignore b/.gitignore
@@ -13,8 +13,11 @@ dist/*
 *.exe
 *.o
 *.so
+*.pyd
 *.pyc
 *_rjc*
+*.nbi
+*.nbc
 
 # Packages #
 ############

diff --git a/.travis.yml b/.travis.yml
@@ -34,7 +34,7 @@ env:
         - SKLEARN_VERSION=stable
         - MAIN_CMD='python setup.py'
         - SETUP_CMD='test'
-        - CONDA_DEPENDENCIES='scipy pyyaml matplotlib future numba scikit-learn configobj IPython'
+        - CONDA_DEPENDENCIES='scipy pyyaml matplotlib future numba scikit-learn configobj IPython pytest'
         - PIP_DEPENDENCIES='extension_helpers ginga linetools'
         - EVENT_TYPE='pull_request push'
         - TASK='test'
@@ -115,13 +115,13 @@ matrix:
 
         # Do a PEP8 test with pycodestyle
         - os: linux
-          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
+          env: MAIN_CMD='pycodestyle pypeit --count' SETUP_CMD=''
 
     allow_failures:
         # Do a PEP8 test with pycodestyle
         # (allow to fail unless your code completely compliant)
         - os: linux
-          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
+          env: MAIN_CMD='pycodestyle pypeit --count' SETUP_CMD=''
 
 install:
 

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,4 +1,26 @@
 
+1.2.0 (15 Oct 2020)
+-------------------
+
+- Frame-typing tweaks for DEIMOS
+    - Exposure-time ranges removed
+    - All frame types now key off OBSTYPE
+- Added more detail on citation policy to main page on readthedocs
+- Added docs for BitMasks
+- Altered scripts interface to allow for dynamically making the help
+  doc files
+- full spatial/spectral flexure and heliocentric corrections implemented for IFU reductions
+- optimal weights in datacube generation
+- Docs for skysub, extraction, flat fielding
+- New skysub options for masking and suppressing local
+- Added `pypeit/core/convert_DEIMOSsavfiles.py` to convert .sav files into fits files
+- Added "amap" and "bmap" fits files in `pypeit/data/static_calibs/keck_deimos/` for DEIMOS
+   optical model
+- Added `pypeit/core/slitdesign_matching.py` and `maskdesign_matching` to `EdgeTraceSet`
+- Added ParSet for switching ON the slit-mask design matching. Default is ON for `keck_deimos`
+- Pypeit registers `maskdef_id` in SlitTraceSet if instrument is `keck_deimos`
+- Fix assignment bug in fitting bspline
+
 1.1.1 (10 Sep 2020)
 -------------------
 
@@ -53,7 +75,7 @@
 - Correct det bug in keck_lris
 - Modifications to allow for flailing LRISr detector
 - Modifications for parse LRIS LAMPS prior to 2010 upgrade
-- Add P200/TripleSpec
+- Added support for P200/DBSP and P200/TripleSpec
 
 1.0.6 (22 Jul 2020)
 -------------------

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,5 @@
 include README.md
+include LICENSE.rst
 #include CHANGES.rst
 
 include setup.cfg

diff --git a/README.md b/README.md
@@ -41,7 +41,8 @@ Conduct](https://pypeit.readthedocs.io/en/latest/codeconduct.html).
 * MMT/MMIRS (HK_zJ, J_zJ, and K_K tested)
 * MDM/OSMOS
 * Keck/DEIMOS (600ZD, 830G, 1200G)
-* Keck/LRIS 
+* Keck/KCWI (BM, BH2)
+* Keck/LRIS
 * Keck/MOSFIRE  (J and Y gratings tested)
 * Keck/NIRES
 * Keck/NIRSPEC (low-dispersion)

diff --git a/bin/pypeit_arcid_plot b/bin/pypeit_arcid_plot
@@ -8,8 +8,8 @@
 This script generates an ArcID plot from a Master WaveSoln file
 """
 
-import pypeit.scripts.arcid_plot as arcid_plot
+from pypeit.scripts import arcid_plot
 
 if __name__ == '__main__':
-    args = arcid_plot.parser()
-    arcid_plot.main(args)
+    arcid_plot.main(arcid_plot.parse_args())
+
diff --git a/bin/pypeit_chk_2dslits b/bin/pypeit_chk_2dslits
@@ -4,6 +4,6 @@
 Print slit info summary to the screen for a given spec2D file
 """
 
-from pypeit.scripts import chk_spec2d_slits
+from pypeit.scripts import chk_2dslits
 if __name__ == '__main__':
-    chk_spec2d_slits.main(chk_spec2d_slits.parser())
+    chk_2dslits.main(chk_2dslits.parse_args())
diff --git a/bin/pypeit_chk_alignments b/bin/pypeit_chk_alignments
@@ -6,4 +6,4 @@ Show the alignments in a Ginga window
 
 from pypeit.scripts import chk_alignments
 if __name__ == '__main__':
-    chk_alignments.main(chk_alignments.parser())
+    chk_alignments.main(chk_alignments.parse_args())
diff --git a/bin/pypeit_chk_edges b/bin/pypeit_chk_edges
@@ -7,6 +7,5 @@ Show the trace image in a Ginga window with edges
 from pypeit.scripts import chk_edges
 
 if __name__ == '__main__':
-    args = chk_edges.parser()
-    chk_edges.main(args)
+    chk_edges.main(chk_edges.parse_args())
 
diff --git a/bin/pypeit_chk_flats b/bin/pypeit_chk_flats
@@ -6,4 +6,4 @@ Show the trace image in a Ginga window with edges
 
 from pypeit.scripts import chk_flats
 if __name__ == '__main__':
-    chk_flats.main(chk_flats.parser())
+    chk_flats.main(chk_flats.parse_args())
diff --git a/bin/pypeit_chk_for_calibs b/bin/pypeit_chk_for_calibs
@@ -10,8 +10,7 @@ This script examines a set of files and figures
 out which have sufficient calibrations and which do not!
 """
 
-import pypeit.scripts.chk_calibs as chk_calibs
+from pypeit.scripts import chk_for_calibs
 
 if __name__ == '__main__':
-    args = chk_calibs.parser()
-    chk_calibs.main(args)
+    chk_for_calibs.main(chk_for_calibs.parse_args())
diff --git a/bin/pypeit_chk_tilts b/bin/pypeit_chk_tilts
@@ -4,8 +4,8 @@
 Show the arc image in a Ginga window with tilts
 """
 
-import pypeit.scripts.chk_tilts as chk_tilts
+from pypeit.scripts import chk_tilts
 
 if __name__ == '__main__':
-    args = chk_tilts.parser()
-    chk_tilts.main(args)
+    chk_tilts.main(chk_tilts.parse_args())
+
diff --git a/bin/pypeit_coadd_1dspec b/bin/pypeit_coadd_1dspec
@@ -4,8 +4,8 @@
 Plot a spectrum with an interactive QT GUI
 """
 
-import pypeit.scripts.coadd_1dspec as coadd_1dspec
+from pypeit.scripts import coadd_1dspec
 
 if __name__ == '__main__':
-    args = coadd_1dspec.parser()
-    coadd_1dspec.main(args)
+    coadd_1dspec.main(coadd_1dspec.parse_args())
+
diff --git a/bin/pypeit_coadd_2dspec b/bin/pypeit_coadd_2dspec
@@ -4,8 +4,8 @@
 Perform 2d coadds of PypeIt spectra.
 """
 
-import pypeit.scripts.coadd_2dspec as coadd_2dspec
+from pypeit.scripts import coadd_2dspec
 
 if __name__ == '__main__':
-    args = coadd_2dspec.parser()
-    coadd_2dspec.main(args)
+    coadd_2dspec.main(coadd_2dspec.parse_args())
+
diff --git a/bin/pypeit_coadd_datacube b/bin/pypeit_coadd_datacube
@@ -4,8 +4,8 @@
 Perform datacube coadds of PypeIt 2D spectra.
 """
 
-import pypeit.scripts.coadd_datacube as coadd_datacube
+from pypeit.scripts import coadd_datacube
 
 if __name__ == '__main__':
-    args = coadd_datacube.parser()
-    coadd_datacube.main(args)
+    coadd_datacube.main(coadd_datacube.parse_args())
+
diff --git a/bin/pypeit_compare_sky b/bin/pypeit_compare_sky
@@ -1,67 +1,12 @@
 #!/usr/bin/env python
+#
+# See top-level LICENSE file for Copyright information
+#
+# -*- coding: utf-8 -*-
 
-"""
-Plots an extracted sky spectrum with an archived one
-  Probably most useful for exploring sky spectra in the blue
-"""
-import pdb
-import sys, os
+from pypeit.scripts import compare_sky
 
-this_file = os.path.realpath(__file__)
-#sky_path = this_file[:this_file.rfind('/')]+'/../data/sky_spec/'
-sky_path ='/{0}/pypeit/data/sky_spec/'.format(this_file.strip('bin/pypeit_compare_sky'))
-#sys.path.append(os.path.abspath(this_path+'/../src'))
-
-from linetools.spectra.io import readspec
-
-try:
-    from xastropy.xutils import xdebug as debugger
-except:
-    import pdb as debugger
-
-# Script to run XSpec from the command line or ipython
-def main(*args, **kwargs):
-    """ Runs the XSpecGui on an input file
-    """
-    import argparse
-
-    parser = argparse.ArgumentParser(description='Parse')
-    parser.add_argument("file", type=str, help="Spectral file")
-    parser.add_argument("skyfile", type=str, help="Archived PypeIt sky file (e.g. paranal_sky.fits")
-    parser.add_argument("--exten", type=int, help="FITS extension")
-    parser.add_argument("--optimal", default=False,
-                        help="Show Optimal? Default is boxcar", action="store_true")
-    parser.add_argument("--scale_user", default=1., type=float, help="Scale user spectrum by a factor")
-
-    pargs = parser.parse_args()
-    from matplotlib import pyplot as plt
-
-    # Extension
-    exten = (pargs.exten if hasattr(pargs, 'exten') else 0)
-    #scale = (pargs.scale_user if hasattr(pargs, 'scale_user') else 1.)
-
-    # Read spec keywords
-    ikwargs = {}
-    if pargs.optimal:
-        ikwargs['wave_tag'] = 'opt_wave'
-        ikwargs['flux_tag'] = 'opt_sky'
-    else:
-        ikwargs['wave_tag'] = 'box_wave'
-        ikwargs['flux_tag'] = 'box_sky'
-
-    # Load user file
-    user_sky = readspec(pargs.file, exten=exten, **ikwargs)
-    # Load sky spec
-    arx_sky = readspec(sky_path+pargs.skyfile)
-
-    # Plot
-    plt.clf()
-    plt.plot(user_sky.wavelength, user_sky.flux*pargs.scale_user, 'k-', label='user')
-    plt.plot(arx_sky.wavelength, arx_sky.flux, 'b-', label='archive')
-    legend = plt.legend(loc='upper left', scatterpoints=1, borderpad=0.3,
-                        handletextpad=0.3, fontsize='small', numpoints=1)
-    plt.show()
+if __name__ == '__main__':
+    compare_sky.main(compare_sky.parse_args())
 
 
-if __name__ == '__main__':
-    main()
diff --git a/bin/pypeit_find_objects b/bin/pypeit_find_objects
@@ -8,8 +8,9 @@
 This script opens the interactive object finding/tracing
 """
 
-import pypeit.scripts.object_finding as object_finding
+from pypeit.scripts import find_objects
 
 if __name__ == '__main__':
-    args = object_finding.parser()
-    object_finding.main(args)
+    find_objects.main(find_objects.parse_args())
+
+
diff --git a/bin/pypeit_flux_calib b/bin/pypeit_flux_calib
@@ -4,8 +4,8 @@
 Flux the spectra and/or generate a sensitity function
 """
 
-import pypeit.scripts.flux_calib as flux_calib
+from pypeit.scripts import flux_calib
 
 if __name__ == '__main__':
-    args = flux_calib.parser()
-    flux_calib.main(args)
+    flux_calib.main(flux_calib.parse_args())
+
diff --git a/bin/pypeit_flux_setup b/bin/pypeit_flux_setup
@@ -4,8 +4,8 @@
 Generate pypeit files for fluxing, coadd1d and telluric fitting.
 """
 
-import pypeit.scripts.flux_setup as flux_setup
+from pypeit.scripts import flux_setup
 
 if __name__ == '__main__':
-    args = flux_setup.parser()
-    flux_setup.main(args)
+    flux_setup.main(flux_setup.parse_args())
+
diff --git a/bin/pypeit_identify b/bin/pypeit_identify
@@ -4,8 +4,8 @@
 Launch the identify GUI tool
 """
 
-from pypeit.scripts import launch_identify
+from pypeit.scripts import identify
 
 if __name__ == '__main__':
-    args = launch_identify.parser()
-    launch_identify.main(args)
+    identify.main(identify.parse_args())
+
diff --git a/bin/pypeit_lowrdx_pixflat b/bin/pypeit_lowrdx_pixflat
@@ -8,9 +8,8 @@
 This script pushes a FITS file to ginga
 """
 
-import pypeit.scripts.lowrdx_pixflat as lowrdx_pixflat
+from pypeit.scripts import lowrdx_pixflat
 
 if __name__ == '__main__':
-    args = lowrdx_pixflat.parser()
-    lowrdx_pixflat.main(args)
+    lowrdx_pixflat.main(lowrdx_pixflat.parse_args())
 
diff --git a/bin/pypeit_lowrdx_skyspec b/bin/pypeit_lowrdx_skyspec
@@ -8,9 +8,8 @@
 This script generates a sky spectrum from a LowRedux IDL save file
 """
 
-import pypeit.scripts.lowrdx_skyspec as lowrdx_skyspec
+from pypeit.scripts import lowrdx_skyspec
 
 if __name__ == '__main__':
-    args = lowrdx_skyspec.parser()
-    lowrdx_skyspec.main(args)
+    lowrdx_skyspec.main(lowrdx_skyspec.parse_args())
 
diff --git a/bin/pypeit_qa_html b/bin/pypeit_qa_html
@@ -4,8 +4,8 @@
 Build the HTML files for QA
 """
 
-import pypeit.scripts.qa_html as qa_html
+from pypeit.scripts import qa_html
 
 if __name__ == '__main__':
-    args = qa_html.parser()
-    qa_html.main(args)
+    qa_html.main(qa_html.parse_args())
+
diff --git a/bin/pypeit_ql_keck_mosfire b/bin/pypeit_ql_keck_mosfire
@@ -13,6 +13,5 @@ from pypeit.scripts import ql_keck_mosfire
 import sys
 
 if __name__ == '__main__':
-    args = ql_keck_mosfire.parser()
-    rtval = ql_keck_mosfire.main(args)
-    sys.exit(rtval)
+    sys.exit(ql_keck_mosfire.main(ql_keck_mosfire.parse_args()))
+
diff --git a/bin/pypeit_ql_keck_nires b/bin/pypeit_ql_keck_nires
@@ -13,7 +13,5 @@ from pypeit.scripts import ql_keck_nires
 import sys
 
 if __name__ == '__main__':
-    args = ql_keck_nires.parser()
-    rtval = ql_keck_nires.main(args)
-    sys.exit(rtval)
+    sys.exit(ql_keck_nires.main(ql_keck_nires.parse_args()))
 
diff --git a/bin/pypeit_ql_mos b/bin/pypeit_ql_mos
@@ -7,5 +7,5 @@ Run QL on MOS
 from pypeit.scripts import  ql_mos
 
 if __name__ == '__main__':
-    args = ql_mos.parser()
-    ql_mos.main(args)
+    ql_mos.main(ql_mos.parse_args())
+
diff --git a/bin/pypeit_sensfunc b/bin/pypeit_sensfunc
@@ -4,8 +4,8 @@
 Computes sensitivity function
 """
 
-import pypeit.scripts.sensfunc as sensfunc
+from pypeit.scripts import sensfunc
 
 if __name__ == '__main__':
-    args = sensfunc.parser()
-    sensfunc.main(args)
+    sensfunc.main(sensfunc.parse_args())
+