Enable allow_tcb and allow_T2 by default in command line scripts

CHANGELOG-unreleased.md

@@ -9,6 +9,7 @@ the released changes.
 
 ## Unreleased
 ### Changed
+- Command line scripts now automatically do `allow_tcb` and `allow_T2` while reading par files.
 - Updated the `plot_chains` function in `event_optimize` so that the subplots are a fixed size to prevent the subplots from being condensed in the case of many fit parameters.
 ### Added
 - Added an option `linearize_model` to speed up the photon phases calculation within `event_optimize` through the designmatrix.

src/pint/pintk/pulsar.py

@@ -151,7 +151,9 @@ def __contains__(self, key):
         return key in self.prefit_model.params
 
     def reset_model(self):
-        self.prefit_model = pint.models.get_model(self.parfile)
+        self.prefit_model = pint.models.get_model(
+            self.parfile, allow_T2=True, allow_tcb=True
+        )
         self.add_model_params()
         self.postfit_model = None
         self.postfit_resids = None
@@ -172,7 +174,9 @@ def reset_TOAs(self):
         self.update_resids()
 
     def resetAll(self):
-        self.prefit_model = pint.models.get_model(self.parfile)
+        self.prefit_model = pint.models.get_model(
+            self.parfile, allow_T2=True, allow_tcb=True
+        )
         self.postfit_model = None
         self.postfit_resids = None
         self.fitted = False

src/pint/scripts/compare_parfiles.py

@@ -83,14 +83,25 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
         level=pint.logging.get_level(args.loglevel, args.verbosity, args.quiet)
     )
 
-    m1 = get_model(args.input1)
-    m2 = get_model(args.input2)
+    m1 = get_model(args.input1, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+    m2 = get_model(args.input2, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+
     print(
         m1.compare(
             m2,

src/pint/scripts/convert_parfile.py

@@ -73,6 +73,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -83,7 +93,9 @@ def main(argv=None):
         return
 
     log.info(f"Reading '{args.input}'")
-    model = get_model(args.input)
+
+    model = get_model(args.input, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+
     if hasattr(model, "BINARY") and args.binary is not None:
         log.info(f"Converting from {model.BINARY.value} to {args.binary}")
         if args.binary == "ELL1H":

src/pint/scripts/event_optimize.py

@@ -706,6 +706,16 @@ def main(argv=None):
         action="store_true",
         dest="linearize_model",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -739,7 +749,9 @@ def main(argv=None):
     ncores = args.ncores
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # File name setup and clobber file check
     filepath = args.filepath or os.getcwd()

src/pint/scripts/event_optimize_MCMCFitter.py

@@ -128,6 +128,17 @@ def main(argv=None):
         help="Logging level",
         dest="loglevel",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
+
     global nwalkers, nsteps, ftr
 
     args = parser.parse_args(argv)
@@ -164,7 +175,9 @@ def main(argv=None):
     wgtexp = args.wgtexp
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # The custom_timing version below is to manually construct the TimingModel
     # class, which allows it to be pickled. This is needed for parallelizing

src/pint/scripts/event_optimize_multiple.py

@@ -228,6 +228,16 @@ def main(argv=None):
         help="Logging level",
         dest="loglevel",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     global nwalkers, nsteps, ftr
 
@@ -261,7 +271,9 @@ def main(argv=None):
     wgtexp = args.wgtexp
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # Set the target coords for automatic weighting if necessary
     if "ELONG" in modelin.params:

src/pint/scripts/fermiphase.py

@@ -77,6 +77,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -88,7 +98,10 @@ def main(argv=None):
         args.addphase = True
 
     # Read in model
-    modelin = pint.models.get_model(args.parfile)
+    modelin = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
+
     if "ELONG" in modelin.params:
         tc = SkyCoord(
             modelin.ELONG.quantity,

src/pint/scripts/photonphase.py

@@ -112,6 +112,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -153,7 +163,10 @@ def main(argv=None):
                 "Please barycenter the event file using the official mission tools before processing with PINT"
             )
     # Read in model
-    modelin = pint.models.get_model(args.parfile)
+    modelin = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
+
     use_planets = False
     if "PLANET_SHAPIRO" in modelin.params:
         if modelin.PLANET_SHAPIRO.value:

src/pint/scripts/pintbary.py

@@ -74,6 +74,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -105,7 +115,9 @@ def main(argv=None):
     )
 
     if args.parfile is not None:
-        m = pint.models.get_model(args.parfile)
+        m = pint.models.get_model(
+            args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+        )
     else:
         # Construct model by hand
         m = pint.models.StandardTimingModel

src/pint/scripts/pintempo.py

@@ -62,14 +62,26 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
         level=pint.logging.get_level(args.loglevel, args.verbosity, args.quiet)
     )
 
     log.info("Reading model from {0}".format(args.parfile))
-    m = pint.models.get_model(args.parfile)
+    m = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     log.warning(m.params)
 

src/pint/scripts/pintpublish.py

@@ -59,10 +59,22 @@ def main(argv=None):
         action="store_true",
         default=False,
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
 
-    model, toas = get_model_and_toas(args.parfile, args.timfile)
+    model, toas = get_model_and_toas(
+        args.parfile, args.timfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     output = publish(
         model,

src/pint/scripts/t2binary2pint.py

@@ -45,12 +45,17 @@ def main(argv=None):
         default=True,
         help="Whether to drop SINI if the model is DDK (True)",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
 
     args = parser.parse_args(argv)
 
     mb = ModelBuilder()
 
-    model = mb(args.input_par, allow_T2=True, allow_tcb=True)
+    model = mb(args.input_par, allow_T2=True, allow_tcb=args.allow_tcb)
     model.write_parfile(args.output_par)
     print(f"Output written to {args.output_par}")
 

src/pint/scripts/tcb2tdb.py

@@ -30,11 +30,16 @@ def main(argv=None):
     )
     parser.add_argument("input_par", help="Input par file name (TCB)")
     parser.add_argument("output_par", help="Output par file name (TDB)")
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
 
     mb = ModelBuilder()
-    model = mb(args.input_par, allow_tcb=True)
+    model = mb(args.input_par, allow_tcb=True, allow_T2=args.allow_T2)
     model.write_parfile(args.output_par)
 
     log.info(f"Output written to {args.output_par}.")

src/pint/scripts/zima.py

@@ -115,14 +115,26 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
         level=pint.logging.get_level(args.loglevel, args.verbosity, args.quiet)
     )
 
     log.info("Reading model from {0}".format(args.parfile))
-    m = pint.models.get_model(args.parfile)
+    m = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     out_format = args.format
     error = args.error * u.microsecond