Merge pull request #1773 from pypeit/hotfix_cube_sig

Hotfix : Correct handling of error cube generation
pypeit · Feb 24, 2024 · 137644a · 137644a
2 parents 7dc5307 + 27ebb93
commit 137644a
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diff --git a/doc/api/pypeit.astrometry.rst b/doc/api/pypeit.astrometry.rst
@@ -0,0 +1,8 @@
+pypeit.astrometry module
+========================
+
+.. automodule:: pypeit.astrometry
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst
@@ -27,6 +27,7 @@ Submodules
 
    pypeit.alignframe
    pypeit.archive
+   pypeit.astrometry
    pypeit.bitmask
    pypeit.calibframe
    pypeit.calibrations

diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst
@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.14.1.dev729+g948bfc229.d20240202[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.15.1.dev38+g075fdecaa.d20240212[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

diff --git a/doc/include/dev_suite_readme.rst b/doc/include/dev_suite_readme.rst
@@ -419,6 +419,21 @@ To monitor a test in Nautilus as it is running, the logs can be tailed:
 
 Additionally they can be monitored with the `Nautilus Grafana page <https://grafana.nrp-nautilus.io/?orgId=1>`__.
 
+By default ``gen_kube_devsuite`` creates a job using a default container with PypeIt 
+pre-installed. It also supports running with different python versions by
+selecting a different container. For example:
+
+.. code-block:: console
+
+    $ ./gen_kube_devsuite devsuite-python3.11-job devsuite-python3.11-job.yml --container python3.11
+
+Any of the standard python images in docker hub can be used. To use a different container the full 
+download path must be given. For example:
+
+.. code-block:: console
+
+    $ ./gen_kube_devsuite devsuite-ubuntu-job devsuite-ubuntu-job.yml --container docker.io/library/ubuntu:22.04
+
 
 Additional Options
 ------------------

diff --git a/doc/include/gemini_gnirs_echelle_A.pypeit.rst b/doc/include/gemini_gnirs_echelle_A.pypeit.rst
@@ -17,7 +17,7 @@
     
     # Data block 
     data read
-     path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/gemini_gnirs_echelle/32_SB_SXD
+     path /Users/rcooke/Software/PypeIt-development-suite/RAW_DATA/gemini_gnirs_echelle/32_SB_SXD
                 filename |         frametype |           ra |         dec |   target |      dispname |           decker | binning |              mjd | airmass | exptime | dispangle |           dithoff | calib | comb_id | bkg_id
     cN20170331S0216.fits |  arc,science,tilt | 205.53380833 |  9.47733611 |    pisco | 32/mmSB_G5533 | 0.68arcsec_G5530 |     1,1 | 57843.3709743134 |   1.077 |   300.0 |    6.1887 | -0.34225501721318 |     0 |       5 |     -1
     cN20170331S0217.fits |  arc,science,tilt | 205.53380833 |  9.47733611 |    pisco | 32/mmSB_G5533 | 0.68arcsec_G5530 |     1,1 | 57843.3746886267 |   1.068 |   300.0 |    6.1887 |  2.65774498278682 |     0 |       6 |     -1

diff --git a/doc/include/keck_deimos.sorted.rst b/doc/include/keck_deimos.sorted.rst
@@ -10,14 +10,14 @@
           filter1: OG550
     #---------------------------------------------------------
                   filename |                 frametype |                 ra |                dec |     target | dispname |   decker | binning |          mjd |    airmass | exptime |     dispangle |      amp | filter1 |  lampstat01 |    dateobs |         utc | frameno | calib
-        d0527_0030.fits.gz |                  arc,tilt |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.077631 | 1.41291034 |     1.0 | 8099.98291016 | SINGLE:B |   OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 |      30 |     0
     DE.20170527.06713.fits |                  arc,tilt |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.077631 | 1.41291034 |     1.0 | 8099.98291016 | SINGLE:B |   OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 |      30 |     0
-    DE.20170527.06790.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 |  57900.07851 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:53:10.93 |      31 |     0
+        d0527_0030.fits.gz |                  arc,tilt |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.077631 | 1.41291034 |     1.0 | 8099.98291016 | SINGLE:B |   OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 |      30 |     0
         d0527_0031.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 |  57900.07851 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:53:10.93 |      31 |     0
+    DE.20170527.06790.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 |  57900.07851 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:53:10.93 |      31 |     0
         d0527_0032.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.079356 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:54:24.03 |      32 |     0
     DE.20170527.06864.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.079356 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:54:24.03 |      32 |     0
-        d0527_0033.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
     DE.20170527.06936.fits | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
+        d0527_0033.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | DOME PHLAT |     830G | LongMirr |     1,1 | 57900.080211 | 1.41291034 |     4.0 | 8099.98291016 | SINGLE:B |   OG550 |          Qz | 2017-05-27 | 01:55:36.93 |      33 |     0
     DE.20170527.37601.fits |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.435131 | 1.03078874 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:26:41.61 |      80 |     0
     DE.20170527.38872.fits |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.449842 | 1.01267696 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:47:52.92 |      81 |     0
         d0527_0081.fits.gz |                   science |  261.0363749999999 | 19.028166666666667 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.449842 | 1.01267696 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 10:47:52.92 |      81 |     0

diff --git a/doc/include/keck_deimos_A.pypeit.rst b/doc/include/keck_deimos_A.pypeit.rst
@@ -20,7 +20,7 @@
     
     # Data block 
     data read
-     path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/keck_deimos/1200G_M_7750
+     path /Users/rcooke/Software/PypeIt-development-suite/RAW_DATA/keck_deimos/1200G_M_7750
                      filename |                 frametype |                 ra |                dec |  target | dispname | decker | binning |          mjd |    airmass | exptime |     dispangle |      amp | filter1 |  lampstat01 |    dateobs |         utc | frameno | calib
     DE.20170425.09554.fits.gz |                  arc,tilt |  57.99999999999999 |               45.0 | unknown |    1200G |  dra11 |     1,1 | 57868.110529 | 1.41291034 |     1.0 | 7699.95654297 | SINGLE:B |   OG550 | Kr Xe Ar Ne | 2017-04-25 | 02:39:14.41 |      49 |     0
     DE.20170425.09632.fits.gz | pixelflat,illumflat,trace |  57.99999999999999 |               45.0 | unknown |    1200G |  dra11 |     1,1 | 57868.111418 | 1.41291034 |    12.0 | 7699.95654297 | SINGLE:B |   OG550 |          Qz | 2017-04-25 | 02:40:32.06 |      50 |     0

diff --git a/doc/include/keck_nires_A.pypeit.rst b/doc/include/keck_nires_A.pypeit.rst
@@ -15,7 +15,7 @@
     
     # Data block 
     data read
-     path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/keck_nires/ABBA_wstandard
+     path /Users/rcooke/Software/PypeIt-development-suite/RAW_DATA/keck_nires/ABBA_wstandard
              filename |        frametype |               ra |              dec |     target | dispname |    decker | binning |              mjd |          airmass | exptime | dithpat | dithpos | dithoff | frameno | calib | comb_id | bkg_id
     s190519_0059.fits | arc,science,tilt | 194.259151362434 | 22.0313494322493 |      GD153 |     spec | 0.55 slit |     1,1 | 58622.3598610573 | 1.03675819208546 |   200.0 |    ABBA |       A |     2.0 |      59 |     0 |       1 |      2
     s190519_0060.fits | arc,science,tilt | 194.260349844733 | 22.0313316699865 |      GD153 |     spec | 0.55 slit |     1,1 |  58622.362605849 | 1.04142552296712 |   200.0 |    ABBA |       B |    -2.0 |      60 |     0 |       2 |      1

diff --git a/doc/include/shane_kast_blue_A.pypeit.rst b/doc/include/shane_kast_blue_A.pypeit.rst
@@ -16,7 +16,7 @@
     
     # Data block 
     data read
-     path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55
+     path /Users/rcooke/Software/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55
        filename |                 frametype |                 ra |                dec |     target | dispname |     decker | binning |                mjd |        airmass | exptime | dichroic | calib
      b1.fits.gz |                  arc,tilt | 140.44166666666663 |  37.43222222222222 |       Arcs | 600/4310 | 0.5 arcsec |     1,1 |  57162.06664467593 |            1.0 |    30.0 |      d55 |     0
     b14.fits.gz |                      bias | 172.34291666666664 |  36.86833333333333 |       Bias | 600/4310 | 2.0 arcsec |     1,1 |  57162.15420034722 |            1.0 |     0.0 |      d55 |     0