doc update

pypeit · Jul 11, 2022 · 9b3d222 · 9b3d222
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,5 +1,5 @@
-1.9.2dev
---------
+1.10.0 (11 July 2022)
+---------------------
 
 - Modify tweak_standard for Mosfire/J2
 - Apply find_min_max when clipping the image for object finding

diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst
@@ -31,7 +31,6 @@ Submodules
    pypeit.coadd1d
    pypeit.coadd2d
    pypeit.compiler_version
-   pypeit.compiler_version
    pypeit.datamodel
    pypeit.edgetrace
    pypeit.extraction

diff --git a/doc/help/pypeit_install_ql_masters.rst b/doc/help/pypeit_install_ql_masters.rst
@@ -14,6 +14,6 @@
                          directory. (default: None)
       --odir ODIR        The directory in which to extract the zip file. Ignored if
                          a direct path is provided using --ql_path. (default:
-                         /Users/dpelliccia/PypeIt/PypeIt/doc)
+                         /Users/westfall/Work/packages/pypeit/doc)
       --rmzip            Remove the downloaded zip file (default: False)
     
diff --git a/doc/help/pypeit_obslog.rst b/doc/help/pypeit_obslog.rst
@@ -35,7 +35,7 @@
                             up through the wildcard (.e.g, /data/Kast/b). Use the
                             --extension option to set the types of files to search
                             for. Default is the current working directory. (default:
-                            /Users/dpelliccia/PypeIt/PypeIt/doc)
+                            /Users/westfall/Work/packages/pypeit/doc)
       -k, --keys            Do not produce the log; simply list the pypeit-specific
                             metadata keys available for this spectrograph and their
                             associated header cards. Metadata keys with header cards
@@ -76,7 +76,7 @@
                             required. (default: .fits)
       -d OUTPUT_PATH, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default:
-                            /Users/dpelliccia/PypeIt/PypeIt/doc)
+                            /Users/westfall/Work/packages/pypeit/doc)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
       -f FILE, --file FILE  Name for the ascii output file. Any leading directory

diff --git a/doc/help/pypeit_ql_keck_deimos.rst b/doc/help/pypeit_ql_keck_deimos.rst
@@ -1,8 +1,11 @@
 .. code-block:: console
 
     $ pypeit_ql_keck_deimos -h
-    usage: pypeit_ql_keck_deimos [-h] [--redux_path REDUX_PATH] [--root ROOT] [--calibs_only] [--science SCIENCE] [-b BOX_RADIUS] [-d DET] [--ignore_headers] [--user_pixflat USER_PIXFLAT]
-                                 [--maskID MASKID] [--slit_spat SLIT_SPAT]
+    usage: pypeit_ql_keck_deimos [-h] [--redux_path REDUX_PATH] [--root ROOT]
+                                 [--calibs_only] [--science SCIENCE]
+                                 [-b BOX_RADIUS] [-d DET] [--ignore_headers]
+                                 [--user_pixflat USER_PIXFLAT] [--maskID MASKID]
+                                 [--slit_spat SLIT_SPAT]
                                  full_rawpath
     
     Script to run PypeIt in QuickLook on a set of Keck/DEIMOS files
@@ -18,12 +21,17 @@
       --calibs_only         Run on calibs only (default: False)
       --science SCIENCE     Science frame filename (default: None)
       -b BOX_RADIUS, --box_radius BOX_RADIUS
-                            Set the radius for the boxcar extraction (arcsec) (default: None)
-      -d DET, --det DET     Detector number. Cannot use with --slit_spat (default: 0)
+                            Set the radius for the boxcar extraction (arcsec)
+                            (default: None)
+      -d DET, --det DET     Detector number. Cannot use with --slit_spat (default:
+                            0)
       --ignore_headers      Ignore bad headers? (default: False)
       --user_pixflat USER_PIXFLAT
-                            Use a user-supplied pixel flat (e.g. keck_lris_blue) (default: None)
-      --maskID MASKID       Reduce this slit as specified by the maskID value (default: None)
+                            Use a user-supplied pixel flat (e.g. keck_lris_blue)
+                            (default: None)
+      --maskID MASKID       Reduce this slit as specified by the maskID value
+                            (default: None)
       --slit_spat SLIT_SPAT
-                            Reduce only this slit on this detector DET:SPAT_ID, e.g. 0:175 (default: None)
+                            Reduce only this slit on this detector DET:SPAT_ID,
+                            e.g. 0:175 (default: None)
     
diff --git a/doc/help/pypeit_setup.rst b/doc/help/pypeit_setup.rst
@@ -33,13 +33,13 @@
                             up through the wildcard (.e.g, /data/Kast/b). Use the
                             --extension option to set the types of files to search
                             for. Default is the current working directory. (default:
-                            /Users/dpelliccia/PypeIt/PypeIt/doc)
+                            /Users/westfall/Work/packages/pypeit/doc)
       -e EXTENSION, --extension EXTENSION
                             File extension; compression indicators (e.g. .gz) not
                             required. (default: .fits)
       -d OUTPUT_PATH, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default:
-                            /Users/dpelliccia/PypeIt/PypeIt/doc)
+                            /Users/westfall/Work/packages/pypeit/doc)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
       -c CFG_SPLIT, --cfg_split CFG_SPLIT

diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst
@@ -5,7 +5,7 @@
                       [-d DETECTOR] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.9.2.dev322+gbe682ddb1[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.8.2.dev482+gf1da42021.d20220523[0m
     ##  
     ##  Available spectrographs include:
     ##   bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v,

diff --git a/doc/include/keck_deimos.sorted.rst b/doc/include/keck_deimos.sorted.rst
@@ -10,8 +10,8 @@
           filter1: OG550
     #---------------------------------------------------------
                   filename |                 frametype |                 ra |                dec |     target | dispname |   decker | binning |          mjd |    airmass | exptime |     dispangle |      amp | filter1 |  lampstat01 |    dateobs |         utc | frameno
-        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
     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
+        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
         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
     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
         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
@@ -21,8 +21,8 @@
     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
         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
     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
-        d0527_0083.fits.gz |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.483427 | 1.00093023 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:36:15.35 |      83
     DE.20170527.41775.fits |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.483427 | 1.00093023 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:36:15.35 |      83
+        d0527_0083.fits.gz |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.483427 | 1.00093023 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:36:15.35 |      83
     DE.20170527.43045.fits |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.498135 | 1.00838805 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 11:57:25.35 |      84
     DE.20170527.44316.fits |                   science |  261.0362916666666 | 19.028888888888886 |   P261_OFF |     830G | LongMirr |     1,1 | 57900.512854 | 1.02377681 |  1200.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 12:18:36.71 |      85
     DE.20170527.53184.fits |                   science | 349.99316666666664 |           -5.16575 |  Feige 110 |     830G | LongMirr |     1,1 | 57900.615484 | 1.42505162 |    45.0 | 8099.98291016 | SINGLE:B |   OG550 |         Off | 2017-05-27 | 14:46:24.88 |      93

diff --git a/doc/include/shane_kast_blue_A.pypeit.rst b/doc/include/shane_kast_blue_A.pypeit.rst
@@ -1,7 +1,7 @@
 .. code-block:: console
 
-    # Auto-generated PypeIt input file using PypeIt version: 1.9.2.dev322+gbe682ddb1
-    # UTC 2022-07-09T01:15:05.545
+    # Auto-generated PypeIt input file using PypeIt version: 1.8.2.dev482+gf1da42021.d20220523
+    # UTC 2022-07-11T17:05:23.772
     
     # User-defined execution parameters
     [rdx]
@@ -16,7 +16,7 @@
     
     # Data block 
     data read
-     path /Users/dpelliccia/Pypeit/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55
+     path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55
        filename |                 frametype |                 ra |                dec |     target | dispname |     decker | binning |                mjd |        airmass | exptime | dichroic
      b1.fits.gz |                  arc,tilt | 140.44166666666663 |  37.43222222222222 |       Arcs | 600/4310 | 0.5 arcsec |     1,1 |  57162.06664467593 |            1.0 |    30.0 |      d55
     b14.fits.gz |                      bias | 172.34291666666664 |  36.86833333333333 |       Bias | 600/4310 | 2.0 arcsec |     1,1 |  57162.15420034722 |            1.0 |     0.0 |      d55