Merge pull request #1881 from pypeit/bump_to_313

Bump dependency restriction to enable use with python 3.13

.github/workflows/ci_cron.yml

@@ -15,8 +15,8 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: ['3.11', '3.12']
-        toxenv: [test-alldeps, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev]
+        python: ['3.11', '3.12', '3.13']
+        toxenv: [test, test-alldeps-cov, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev]
     steps:
     - name: Check out repository
       uses: actions/checkout@v3

.github/workflows/ci_tests.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: ['3.11', '3.12']
+        python: ['3.11', '3.12', '3.13']
         toxenv: [test, test-alldeps-cov, test-numpydev, test-linetoolsdev, test-gingadev, test-astropydev]
     steps:
     - name: Check out repository
@@ -48,7 +48,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macos-latest]
-        python: ['3.11', '3.12']
+        python: ['3.11', '3.12', '3.13']
         toxenv: [test-alldeps]
     steps:
     - name: Check out repository

deprecated/qa.py

@@ -213,3 +213,23 @@ def match_qa(arc_spec, tcent, line_list, IDs, scores, outfile = None, title=None
 
     plt.close()
     return
+
+
+def gen_timestamp():
+    """ Generate a simple time stamp including the current user
+
+    Returns
+    -------
+    timestamp : str
+      user_datetime
+    """
+    tstamp = datetime.datetime.today().strftime('%Y-%m-%d-T%Hh%Mm%Ss')
+    try:
+        import getpass
+        user = getpass.getuser()
+    except ModuleNotFoundError:
+        # there appears to be a bug in getpass in windows systems where the pwd module doesn't load
+        user = os.getlogin()
+    # Return
+    return '{:s}_{:s}'.format(user, tstamp)
+

doc/help/pypeit_chk_for_calibs.rst

@@ -12,7 +12,7 @@
     
     options:
       -h, --help            show this help message and exit
-      -s SPECTROGRAPH, --spectrograph SPECTROGRAPH
+      -s, --spectrograph SPECTROGRAPH
                             A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
@@ -34,7 +34,7 @@
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
                             vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
                             wht_isis_blue, wht_isis_red (default: None)
-      -e EXTENSION, --extension EXTENSION
+      -e, --extension EXTENSION
                             File extension to use. Must include the period (e.g.,
                             ".fits") and it must be one of the allowed extensions
                             for this spectrograph. If None, root directory will be

doc/help/pypeit_clean_cache.rst

@@ -8,13 +8,13 @@
     
     options:
       -h, --help            show this help message and exit
-      -p PATTERN [PATTERN ...], --pattern PATTERN [PATTERN ...]
+      -p, --pattern PATTERN [PATTERN ...]
                             Remove any files matching the provided pattern. If
                             combined with --version, this selects only files
                             downloaded from the identified GitHub versoin. If the
                             version is not specified, any file matching the provided
                             pattern(s) are removed. (default: None)
-      -v VERSION [VERSION ...], --version VERSION [VERSION ...]
+      -v, --version VERSION [VERSION ...]
                             Remove files associated one or more provided tags,
                             branches, or commit references on GitHub. These must be
                             an exact match to the relevant GitHub reference. If

doc/help/pypeit_coadd_1dspec.rst

@@ -107,7 +107,7 @@
       --show                show QA during coadding process
       --par_outfile PAR_OUTFILE
                             Output to save the parameters
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             coadd_1dspec_YYYYMMDD-HHMM.log

doc/help/pypeit_coadd_2dspec.rst

@@ -21,7 +21,7 @@
       --basename BASENAME   Basename of files to save the parameters, spec1d, and
                             spec2d (default: None)
       --debug               show debug plots? (default: False)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             coadd_2dspec_YYYYMMDD-HHMM.log (default: 1)

doc/help/pypeit_coadd_datacube.rst

@@ -13,7 +13,7 @@
       --det DET             Detector (default: 1)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             coadd_datacube_YYYYMMDD-HHMM.log (default: 1)

doc/help/pypeit_collate_1d.rst

@@ -94,7 +94,7 @@
                             to crash or lead to erroneous results. I.e., you really
                             need to know what you are doing if you set this to
                             False!
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             collate_1d_YYYYMMDD-HHMM.log

doc/help/pypeit_extract_datacube.rst

@@ -13,16 +13,16 @@
     
     options:
       -h, --help            show this help message and exit
-      -e EXT_FILE, --ext_file EXT_FILE
+      -e, --ext_file EXT_FILE
                             Configuration file with extraction parameters (default:
                             None)
-      -s SAVE, --save SAVE  Output spec1d filename (default: None)
+      -s, --save SAVE       Output spec1d filename (default: None)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
-      -b BOXCAR_RADIUS, --boxcar_radius BOXCAR_RADIUS
+      -b, --boxcar_radius BOXCAR_RADIUS
                             Radius of the circular boxcar (in arcseconds) to use for
                             the extraction. (default: None)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             extract_datacube_YYYYMMDD-HHMM.log (default: 1)

doc/help/pypeit_flux_calib.rst

@@ -50,7 +50,7 @@
     options:
       -h, --help            show this help message and exit
       --par_outfile         Output to save the parameters
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             flux_calib_YYYYMMDD-HHMM.log

doc/help/pypeit_identify.rst

@@ -41,7 +41,7 @@
       --force_save          Save the solutions, despite the RMS (default: False)
       --rescale_resid       Rescale the residual plot to include all points?
                             (default: False)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename identify_YYYYMMDD-
                             HHMM.log (default: 1)

doc/help/pypeit_obslog.rst

@@ -34,7 +34,7 @@
     
     options:
       -h, --help            show this help message and exit
-      -r ROOT, --root ROOT  Root to search for data files. You can provide the top-
+      -r, --root ROOT       Root to search for data files. You can provide the top-
                             level directory (e.g., /data/Kast) or the search string
                             up through the wildcard (.e.g, /data/Kast/b). Use the
                             --extension option to set the types of files to search
@@ -44,7 +44,7 @@
                             associated header cards. Metadata keys with header cards
                             that are None have no simple mapping between keyword and
                             header card. (default: False)
-      -c COLUMNS, --columns COLUMNS
+      -c, --columns COLUMNS
                             A comma-separated list of columns to include in the
                             output table. Each column must be a valid pypeit
                             metadata keyword specific to this spectrograph (run
@@ -57,7 +57,7 @@
                             (default: pypeit)
       -b, --bad_frames      Clean the output of bad frames that cannot be reduced by
                             pypeit. (default: False)
-      -t BAD_TYPES, --bad_types BAD_TYPES
+      -t, --bad_types BAD_TYPES
                             Dictates how frames that could not be given a valid type
                             should be treated. Options are: "keep" to include them
                             in the output, "rm" to remove them from the output,
@@ -72,20 +72,20 @@
                             IPython session that you can use to interact with the
                             table (an Astropy.Table called fitstbl) directly.
                             (default: False)
-      -s SORT, --sort SORT  Metadata keyword (pypeit-specific) to use to sort the
+      -s, --sort SORT       Metadata keyword (pypeit-specific) to use to sort the
                             output table. (default: mjd)
-      -e EXTENSION, --extension EXTENSION
+      -e, --extension EXTENSION
                             File extension to use. Must include the period (e.g.,
                             ".fits") and it must be one of the allowed extensions
                             for this spectrograph. If None, root directory will be
                             searched for all files with any of the allowed
                             extensions. (default: None)
-      -d OUTPUT_PATH, --output_path OUTPUT_PATH
+      -d, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default: current
                             working directory)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
-      -f FILE, --file FILE  Name for the ascii output file. Any leading directory
+      -f, --file FILE       Name for the ascii output file. Any leading directory
                             path is stripped; use -d to set the output directory. If
                             None, the table is just printed to stdout. If set to
                             'default', the file is set to [spectrograph].obslog.

doc/help/pypeit_sensfunc.rst

@@ -55,7 +55,7 @@
                                 [sensfunc]
                                     multi_spec_det = 3,7
                              
-      -o OUTFILE, --outfile OUTFILE
+      -o, --outfile OUTFILE
                             Output file for sensitivity function. If not specified,
                             the sensitivity function will be written out to a
                             standard filename in the current working directory, i.e.
@@ -69,7 +69,7 @@
                             same extensions for QA and throughput will be used if
                             outfile is provided but with .fits trimmed off if it is
                             in the filename.
-      -s SENS_FILE, --sens_file SENS_FILE
+      -s, --sens_file SENS_FILE
                             Configuration file with sensitivity function parameters
       -f, --use_flat        Use the extracted spectrum of the flatfield calibration
                             to estimate the blaze function when generating the
@@ -89,7 +89,7 @@
       --par_outfile PAR_OUTFILE
                             Name of output file to save the parameters used by the
                             fit
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename sensfunc_YYYYMMDD-
                             HHMM.log

doc/help/pypeit_setup.rst

@@ -10,7 +10,7 @@
     
     options:
       -h, --help            show this help message and exit
-      -s SPECTROGRAPH, --spectrograph SPECTROGRAPH
+      -s, --spectrograph SPECTROGRAPH
                             A valid spectrograph identifier: aat_uhrf, bok_bc,
                             gemini_flamingos1, gemini_flamingos2,
                             gemini_gmos_north_e2v, gemini_gmos_north_ham,
@@ -32,24 +32,24 @@
                             soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
                             vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
                             wht_isis_blue, wht_isis_red (default: None)
-      -r ROOT [ROOT ...], --root ROOT [ROOT ...]
+      -r, --root ROOT [ROOT ...]
                             Root to search for data files. You can provide the top-
                             level directory (e.g., /data/Kast) or the search string
                             up through the wildcard (.e.g, /data/Kast/b). Use the
                             --extension option to set the types of files to search
                             for. (default: current working directory)
-      -e EXTENSION, --extension EXTENSION
+      -e, --extension EXTENSION
                             File extension to use. Must include the period (e.g.,
                             ".fits") and it must be one of the allowed extensions
                             for this spectrograph. If None, root directory will be
                             searched for all files with any of the allowed
                             extensions. (default: None)
-      -d OUTPUT_PATH, --output_path OUTPUT_PATH
+      -d, --output_path OUTPUT_PATH
                             Path to top-level output directory. (default: current
                             working directory)
       -o, --overwrite       Overwrite any existing files/directories (default:
                             False)
-      -c CFG_SPLIT, --cfg_split CFG_SPLIT
+      -c, --cfg_split CFG_SPLIT
                             Generate the PypeIt files and folders by input
                             configuration. To write all unique configurations
                             identifed, use 'all', otherwise provide the list of
@@ -62,7 +62,7 @@
       -m, --manual_extraction
                             Include the manual extraction column for the user to
                             edit (default: False)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename setup_YYYYMMDD-
                             HHMM.log (default: 1)

doc/help/pypeit_setup_coadd2d.rst

@@ -1,10 +1,9 @@
 .. code-block:: console
 
     $ pypeit_setup_coadd2d -h
-    usage: pypeit_setup_coadd2d [-h]
-                                (-f PYPEIT_FILE | -d SCIENCE_DIR [SCIENCE_DIR ...])
-                                [--keep_par] [--obj OBJ [OBJ ...]]
-                                [--det DET [DET ...]]
+    usage: pypeit_setup_coadd2d [-h] (-f PYPEIT_FILE |
+                                -d SCIENCE_DIR [SCIENCE_DIR ...]) [--keep_par]
+                                [--obj OBJ [OBJ ...]] [--det DET [DET ...]]
                                 [--only_slits ONLY_SLITS [ONLY_SLITS ...]]
                                 [--exclude_slits EXCLUDE_SLITS [EXCLUDE_SLITS ...]]
                                 [--spat_toler SPAT_TOLER] [--offsets OFFSETS]
@@ -16,9 +15,9 @@
     
     options:
       -h, --help            show this help message and exit
-      -f PYPEIT_FILE, --pypeit_file PYPEIT_FILE
+      -f, --pypeit_file PYPEIT_FILE
                             PypeIt reduction file (default: None)
-      -d SCIENCE_DIR [SCIENCE_DIR ...], --science_dir SCIENCE_DIR [SCIENCE_DIR ...]
+      -d, --science_dir SCIENCE_DIR [SCIENCE_DIR ...]
                             One or more directories with spec2d files to stack (use
                             wildcard to specify multiple directories). (default:
                             None)

doc/help/pypeit_show_2dspec.rst

@@ -45,7 +45,7 @@
       --prefix PREFIX       Channel name prefix [lets you display more than one set]
                             (default: )
       --no_clear            Do *not* clear all existing tabs (default: True)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all] (default:
                             1)
       --try_old             Attempt to load old datamodel versions. A crash may

doc/help/pypeit_skysub_regions.rst

@@ -19,7 +19,7 @@
       -i, --initial         Use initial slit edges? (default: False)
       -f, --flexure         Use flexure corrected slit edges? (default: False)
       -s, --standard        List standard stars as well? (default: False)
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename
                             skysub_regions_YYYYMMDD-HHMM.log (default: 1)

doc/help/pypeit_tellfit.rst

@@ -28,23 +28,23 @@
                             poly = For other type object, You might need to set
                             fit_wv_min_max, and norder in the tell_file.
                              
-      -r REDSHIFT, --redshift REDSHIFT
+      -r, --redshift REDSHIFT
                             Specify redshift. Used with the --objmodel qso option
                             above.
-      -g TELL_GRID, --tell_grid TELL_GRID
+      -g, --tell_grid TELL_GRID
                             Telluric grid. You should download the giant grid file
                             to the pypeit/data/telluric folder. It should only be
                             passed if you want to overwrite the default tell_grid
                             that is set via each spectrograph file.
-      -p PCA_FILE, --pca_file PCA_FILE
+      -p, --pca_file PCA_FILE
                             Quasar PCA fits file with full path. The default file
                             (qso_pca_1200_3100.fits) is stored in the
                             pypeit/data/telluric folder. If you change the fits
                             file, make sure to set the pca_lower and pca_upper in
                             the tell_file to specify the wavelength coverage of your
                             model. The defaults are pca_lower=1220. and
                             pca_upper=3100.
-      -t TELL_FILE, --tell_file TELL_FILE
+      -t, --tell_file TELL_FILE
                             Configuration file to change default telluric
                             parameters.  Note that the parameters in this file will
                             be overwritten if you set argument in your terminal.
@@ -71,7 +71,7 @@
       --par_outfile PAR_OUTFILE
                             Name of output file to save the parameters used by the
                             fit
-      -v VERBOSITY, --verbosity VERBOSITY
+      -v, --verbosity VERBOSITY
                             Verbosity level between 0 [none] and 2 [all]. Default:
                             1. Level 2 writes a log with filename tellfit_YYYYMMDD-
                             HHMM.log