From e4740940fd2c2bb839c36b9cee9c47ea13de57b4 Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Mon, 7 Oct 2024 10:55:52 +0200
Subject: [PATCH 1/9] compare_parfiles

---
 src/pint/scripts/compare_parfiles.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/pint/scripts/compare_parfiles.py b/src/pint/scripts/compare_parfiles.py
index 0c4ca5da2..87eb005a0 100644
--- a/src/pint/scripts/compare_parfiles.py
+++ b/src/pint/scripts/compare_parfiles.py
@@ -89,8 +89,9 @@ def main(argv=None):
         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=True, allow_tcb=True)
+    m2 = get_model(args.input2, allow_T2=True, allow_tcb=True)
+
     print(
         m1.compare(
             m2,

From 5f7bc2dd431a0209bc29d41fc5f238f9cda11d5d Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Mon, 7 Oct 2024 10:56:50 +0200
Subject: [PATCH 2/9] convert_parfile

---
 src/pint/scripts/convert_parfile.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/pint/scripts/convert_parfile.py b/src/pint/scripts/convert_parfile.py
index 55b45415b..0612a46a8 100644
--- a/src/pint/scripts/convert_parfile.py
+++ b/src/pint/scripts/convert_parfile.py
@@ -83,7 +83,9 @@ def main(argv=None):
         return
 
     log.info(f"Reading '{args.input}'")
-    model = get_model(args.input)
+
+    model = get_model(args.input, allow_T2=True, allow_tcb=True)
+
     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":

From f2abeb723c588d6d00333ed8430b541d78295359 Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Mon, 7 Oct 2024 11:01:53 +0200
Subject: [PATCH 3/9] scripts

---
 src/pint/pintk/pulsar.py                      | 8 ++++++--
 src/pint/scripts/event_optimize.py            | 2 +-
 src/pint/scripts/event_optimize_MCMCFitter.py | 2 +-
 src/pint/scripts/event_optimize_multiple.py   | 2 +-
 src/pint/scripts/fermiphase.py                | 3 ++-
 src/pint/scripts/photonphase.py               | 3 ++-
 src/pint/scripts/pintbary.py                  | 2 +-
 src/pint/scripts/pintempo.py                  | 2 +-
 src/pint/scripts/pintpublish.py               | 2 +-
 src/pint/scripts/tcb2tdb.py                   | 2 +-
 src/pint/scripts/zima.py                      | 2 +-
 11 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/src/pint/pintk/pulsar.py b/src/pint/pintk/pulsar.py
index 65d8048df..ce6aa8560 100644
--- a/src/pint/pintk/pulsar.py
+++ b/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
diff --git a/src/pint/scripts/event_optimize.py b/src/pint/scripts/event_optimize.py
index e4c9dd4ff..b79fb1c20 100755
--- a/src/pint/scripts/event_optimize.py
+++ b/src/pint/scripts/event_optimize.py
@@ -719,7 +719,7 @@ 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=True, allow_tcb=True)
 
     # File name setup and clobber file check
     filepath = args.filepath or os.getcwd()
diff --git a/src/pint/scripts/event_optimize_MCMCFitter.py b/src/pint/scripts/event_optimize_MCMCFitter.py
index bbab8ccee..43bc89858 100755
--- a/src/pint/scripts/event_optimize_MCMCFitter.py
+++ b/src/pint/scripts/event_optimize_MCMCFitter.py
@@ -164,7 +164,7 @@ 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=True, allow_tcb=True)
 
     # The custom_timing version below is to manually construct the TimingModel
     # class, which allows it to be pickled. This is needed for parallelizing
diff --git a/src/pint/scripts/event_optimize_multiple.py b/src/pint/scripts/event_optimize_multiple.py
index 41316a000..daa40a9e9 100755
--- a/src/pint/scripts/event_optimize_multiple.py
+++ b/src/pint/scripts/event_optimize_multiple.py
@@ -261,7 +261,7 @@ 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=True, allow_tcb=True)
 
     # Set the target coords for automatic weighting if necessary
     if "ELONG" in modelin.params:
diff --git a/src/pint/scripts/fermiphase.py b/src/pint/scripts/fermiphase.py
index b1427e61f..6785bc156 100755
--- a/src/pint/scripts/fermiphase.py
+++ b/src/pint/scripts/fermiphase.py
@@ -88,7 +88,8 @@ 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=True, allow_tcb=True)
+
     if "ELONG" in modelin.params:
         tc = SkyCoord(
             modelin.ELONG.quantity,
diff --git a/src/pint/scripts/photonphase.py b/src/pint/scripts/photonphase.py
index 7d72eec18..38505c629 100755
--- a/src/pint/scripts/photonphase.py
+++ b/src/pint/scripts/photonphase.py
@@ -153,7 +153,8 @@ 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=True, allow_tcb=True)
+
     use_planets = False
     if "PLANET_SHAPIRO" in modelin.params:
         if modelin.PLANET_SHAPIRO.value:
diff --git a/src/pint/scripts/pintbary.py b/src/pint/scripts/pintbary.py
index 4876474d8..c29d42fbb 100755
--- a/src/pint/scripts/pintbary.py
+++ b/src/pint/scripts/pintbary.py
@@ -105,7 +105,7 @@ 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=True, allow_tcb=True)
     else:
         # Construct model by hand
         m = pint.models.StandardTimingModel
diff --git a/src/pint/scripts/pintempo.py b/src/pint/scripts/pintempo.py
index d99c772ba..36e8ca509 100755
--- a/src/pint/scripts/pintempo.py
+++ b/src/pint/scripts/pintempo.py
@@ -69,7 +69,7 @@ def main(argv=None):
     )
 
     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=True, allow_tcb=True)
 
     log.warning(m.params)
 
diff --git a/src/pint/scripts/pintpublish.py b/src/pint/scripts/pintpublish.py
index 6d5b0142f..36cc5786e 100644
--- a/src/pint/scripts/pintpublish.py
+++ b/src/pint/scripts/pintpublish.py
@@ -62,7 +62,7 @@ def main(argv=None):
 
     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=True)
 
     output = publish(
         model,
diff --git a/src/pint/scripts/tcb2tdb.py b/src/pint/scripts/tcb2tdb.py
index 4c427d21a..5b15d56ae 100644
--- a/src/pint/scripts/tcb2tdb.py
+++ b/src/pint/scripts/tcb2tdb.py
@@ -34,7 +34,7 @@ def main(argv=None):
     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=True)
     model.write_parfile(args.output_par)
 
     log.info(f"Output written to {args.output_par}.")
diff --git a/src/pint/scripts/zima.py b/src/pint/scripts/zima.py
index 3305129f7..3485c6c5b 100755
--- a/src/pint/scripts/zima.py
+++ b/src/pint/scripts/zima.py
@@ -122,7 +122,7 @@ def main(argv=None):
     )
 
     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=True, allow_tcb=True)
 
     out_format = args.format
     error = args.error * u.microsecond

From f8bbeae61c7651341e82168b4f7cc9e075ac4c6d Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Mon, 7 Oct 2024 11:03:13 +0200
Subject: [PATCH 4/9] CHANGELOG

---
 CHANGELOG-unreleased.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG-unreleased.md b/CHANGELOG-unreleased.md
index 2c7ea6521..2d433bfab 100644
--- a/CHANGELOG-unreleased.md
+++ b/CHANGELOG-unreleased.md
@@ -14,6 +14,7 @@ the released changes.
 - `maskParameter.__repr__()` output now includes the frozen attribute.
 - Changed default value of `FDJUMPLOG` to `Y`
 - Bumped `black` version to 24.x
+- Command line scripts now automatically do `allow_tcb` and `allow_T2` while reading par files.
 ### Added
 - arXiv link of PINT noise paper in README
 - Type hints in `pint.derived_quantities`, `pint.modelutils`, `pint.binaryconvert`, `pint.config`, 

From a88f15ade5bd19549d26034f17ade32c6a2557aa Mon Sep 17 00:00:00 2001
From: Matthew Kerr <matthew.kerr@nrl.navy.mil>
Date: Wed, 6 Nov 2024 12:51:04 -0500
Subject: [PATCH 5/9] Provide physical formulas for magnetic field
 calculations.

---
 src/pint/derived_quantities.py   | 70 +++++++++++++++++++++-----------
 tests/test_derived_quantities.py |  4 +-
 2 files changed, 49 insertions(+), 25 deletions(-)

diff --git a/src/pint/derived_quantities.py b/src/pint/derived_quantities.py
index d5852ae4b..6cae3c39a 100644
--- a/src/pint/derived_quantities.py
+++ b/src/pint/derived_quantities.py
@@ -130,12 +130,22 @@ def pferrs(
         return [1.0 / porf, porferr / porf**2.0]
     forperr = porferr / porf**2.0
     fdorpderr = np.sqrt(
-        (4.0 * pdorfd**2.0 * porferr**2.0) / porf**6.0 + pdorfderr**2.0 / porf**4.0
+        (4.0 * pdorfd**2.0 * porferr**2.0) / porf**6.0
+        + pdorfderr**2.0 / porf**4.0
     )
     [forp, fdorpd] = p_to_f(porf, pdorfd)
     return (forp, forperr, fdorpd, fdorpderr)
 
 
+def _to_gauss(B: u.Quantity) -> u.G:
+    """Convert quantity with mass, length, and time units to Gauss.
+
+    In cgs units, magnetic field is has units (mass/length)^(1/2) / time.
+    """
+    eq = [u.Gauss, u.Hz * (u.g / u.cm) ** (1 / 2), lambda x: x, lambda x: x]
+    return B.to(u.Gauss, equivalencies=[eq])
+
+
 @u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, fo=u.Hz)
 def pulsar_age(
     f: u.Quantity, fdot: u.Quantity, n: int = 3, fo: u.Quantity = 1e99 * u.Hz
@@ -219,12 +229,16 @@ def pulsar_edot(
     return (-4.0 * np.pi**2 * I * f * fdot).to(u.erg / u.s)
 
 
-@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s)
-def pulsar_B(f: u.Quantity, fdot: u.Quantity) -> u.G:
+@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, I=u.g * u.cm**2, R=u.km)
+def pulsar_B(
+    f: u.Quantity,
+    fdot: u.Quantity,
+    I: u.Quantity = 1.0e45 * u.g * u.cm**2,
+    R: u.Quantity = 10 * u.km,
+) -> u.G:
     r"""Compute pulsar surface magnetic field
 
-    Return the estimated pulsar surface magnetic field strength
-    given the spin frequency and frequency derivative.
+    Return the pulsar surface magnetic field strength given the spin frequency `f` and frequency derivative `fdot`.
 
     Parameters
     ----------
@@ -232,6 +246,10 @@ def pulsar_B(f: u.Quantity, fdot: u.Quantity) -> u.G:
         pulsar frequency
     fdot : astropy.units.Quantity
         frequency derivative :math:`\dot f`
+    I : astropy.units.Quantity, optional
+        pulsar moment of inertia, default of 1e45 g*cm**2
+    R : astropy.units.Quantity, optional
+        pulsar radius, default of 10 km
 
     Returns
     -------
@@ -247,15 +265,19 @@ def pulsar_B(f: u.Quantity, fdot: u.Quantity) -> u.G:
 
     Notes
     -----
-    Calculates :math:`B=3.2\times 10^{19}\,{\rm  G}\sqrt{ f \dot f^{-3}}`
+    Calculates :math:`B=\sqrt{\frac{3\,I\,c^3}{8\pi^2\,R^6}\times\frac{-\dot{f}}{f^3}}`
     """
-    # This is a hack to use the traditional formula by stripping the units.
-    # It would be nice to improve this to a  proper formula with units
-    return 3.2e19 * u.G * np.sqrt(-fdot.to_value(u.Hz / u.s) / f.to_value(u.Hz) ** 3.0)
+    factor = (3.0 * I * const.c**3) / (8.0 * np.pi**2 * R**6)
+    return _to_gauss((factor * (-fdot) / f**3) ** 0.5)
 
 
-@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s)
-def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
+@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, I=u.g * u.cm**2, R=u.km)
+def pulsar_B_lightcyl(
+    f: u.Quantity,
+    fdot: u.Quantity,
+    I: u.Quantity = 1.0e45 * u.g * u.cm**2,
+    R=10 * u.km,
+) -> u.G:
     r"""Compute pulsar magnetic field at the light cylinder
 
     Return the estimated pulsar magnetic field strength at the
@@ -268,6 +290,10 @@ def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
         pulsar frequency
     fdot : astropy.units.Quantity
         frequency derivative :math:`\dot f`
+    I : astropy.units.Quantity, optional
+        pulsar moment of inertia, default of 1e45 g*cm**2
+    R : astropy.units.Quantity, optional
+        pulsar radius, default of 10 km
 
     Returns
     -------
@@ -283,17 +309,10 @@ def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
 
     Notes
     -----
-    Calculates :math:`B_{LC} = 2.9\times 10^8\,{\rm G} P^{-5/2} \dot P^{1/2}`
+    Calculates :math:`B_{LC} = \sqrt{\frac{-24\pi^4\,I}{c^3}\dot{f}f^3}`
     """
-    p, pd = p_to_f(f, fdot)
-    # This is a hack to use the traditional formula by stripping the units.
-    # It would be nice to improve this to a  proper formula with units
-    return (
-        2.9e8
-        * u.G
-        * p.to_value(u.s) ** (-5.0 / 2.0)
-        * np.sqrt(pd.to(u.dimensionless_unscaled).value)
-    )
+    factor = 24.0 * np.pi**4.0 * I / const.c**3.0
+    return _to_gauss((factor * (-fdot) * f**3.0) ** 0.5)
 
 
 @u.quantity_input(pb=u.d, x=u.cm)
@@ -533,12 +552,17 @@ def companion_mass(
     # delta1 is always <0
     # delta1 = 2 * b ** 3 - 9 * a * b * c + 27 * a ** 2 * d
     delta1 = (
-        -2 * massfunct**3 - 18 * a * mp * massfunct**2 - 27 * a**2 * massfunct * mp**2
+        -2 * massfunct**3
+        - 18 * a * mp * massfunct**2
+        - 27 * a**2 * massfunct * mp**2
     )
     # Q**2 is always > 0, so this is never a problem
     # in terms of complex numbers
     # Q = np.sqrt(delta1**2 - 4*delta0**3)
-    Q = np.sqrt(108 * a**3 * mp**3 * massfunct**3 + 729 * a**4 * mp**4 * massfunct**2)
+    Q = np.sqrt(
+        108 * a**3 * mp**3 * massfunct**3
+        + 729 * a**4 * mp**4 * massfunct**2
+    )
     # this could be + or - Q
     # pick the - branch since delta1 is <0 so that delta1 - Q is never near 0
     Ccubed = 0.5 * (delta1 + Q)
diff --git a/tests/test_derived_quantities.py b/tests/test_derived_quantities.py
index cf5e845b0..833e98a86 100644
--- a/tests/test_derived_quantities.py
+++ b/tests/test_derived_quantities.py
@@ -67,7 +67,7 @@ def test_Edot():
 def test_Bfield():
     # B
     assert np.isclose(
-        pulsar_B(0.033 * u.Hz, -2.0e-15 * u.Hz / u.s), 238722891596281.66 * u.G
+        pulsar_B(0.033 * u.Hz, -2.0e-15 * u.Hz / u.s), 238693670891966.22 * u.G
     )
 
 
@@ -75,7 +75,7 @@ def test_Blc():
     # B_lc
     assert np.isclose(
         pulsar_B_lightcyl(0.033 * u.Hz, -2.0e-15 * u.Hz / u.s),
-        0.07774704753236616 * u.G,
+        0.07896965114785195 * u.G,
     )
 
 

From 53ae031e946af0e75c27ecdbbec8f0411487f0df Mon Sep 17 00:00:00 2001
From: Matthew Kerr <matthew.kerr@nrl.navy.mil>
Date: Thu, 14 Nov 2024 12:45:51 -0500
Subject: [PATCH 6/9] Re-black with v24.

---
 src/pint/derived_quantities.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/src/pint/derived_quantities.py b/src/pint/derived_quantities.py
index 6cae3c39a..8f3373cf6 100644
--- a/src/pint/derived_quantities.py
+++ b/src/pint/derived_quantities.py
@@ -130,8 +130,7 @@ def pferrs(
         return [1.0 / porf, porferr / porf**2.0]
     forperr = porferr / porf**2.0
     fdorpderr = np.sqrt(
-        (4.0 * pdorfd**2.0 * porferr**2.0) / porf**6.0
-        + pdorfderr**2.0 / porf**4.0
+        (4.0 * pdorfd**2.0 * porferr**2.0) / porf**6.0 + pdorfderr**2.0 / porf**4.0
     )
     [forp, fdorpd] = p_to_f(porf, pdorfd)
     return (forp, forperr, fdorpd, fdorpderr)
@@ -552,17 +551,12 @@ def companion_mass(
     # delta1 is always <0
     # delta1 = 2 * b ** 3 - 9 * a * b * c + 27 * a ** 2 * d
     delta1 = (
-        -2 * massfunct**3
-        - 18 * a * mp * massfunct**2
-        - 27 * a**2 * massfunct * mp**2
+        -2 * massfunct**3 - 18 * a * mp * massfunct**2 - 27 * a**2 * massfunct * mp**2
     )
     # Q**2 is always > 0, so this is never a problem
     # in terms of complex numbers
     # Q = np.sqrt(delta1**2 - 4*delta0**3)
-    Q = np.sqrt(
-        108 * a**3 * mp**3 * massfunct**3
-        + 729 * a**4 * mp**4 * massfunct**2
-    )
+    Q = np.sqrt(108 * a**3 * mp**3 * massfunct**3 + 729 * a**4 * mp**4 * massfunct**2)
     # this could be + or - Q
     # pick the - branch since delta1 is <0 so that delta1 - Q is never near 0
     Ccubed = 0.5 * (delta1 + Q)

From 3ad5f9b39f0e81f5c7e7e67f879bea35b5d82092 Mon Sep 17 00:00:00 2001
From: Matthew Kerr <matthew.kerr@nrl.navy.mil>
Date: Thu, 14 Nov 2024 13:28:31 -0500
Subject: [PATCH 7/9] Move gauss equivalency to pint __init__ file.

---
 src/pint/__init__.py           | 3 +++
 src/pint/derived_quantities.py | 3 +--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/pint/__init__.py b/src/pint/__init__.py
index 5706dff7e..7906be01f 100644
--- a/src/pint/__init__.py
+++ b/src/pint/__init__.py
@@ -105,6 +105,9 @@
     "hourangle_second": hourangle_second,
 }
 
+# define a units equivalency for gauss in cgs
+gauss_equiv = [u.Gauss, u.Hz * (u.g / u.cm) ** (1 / 2), lambda x: x, lambda x: x]
+
 import astropy.version
 
 if astropy.version.major < 4:
diff --git a/src/pint/derived_quantities.py b/src/pint/derived_quantities.py
index 8f3373cf6..24dcb1934 100644
--- a/src/pint/derived_quantities.py
+++ b/src/pint/derived_quantities.py
@@ -141,8 +141,7 @@ def _to_gauss(B: u.Quantity) -> u.G:
 
     In cgs units, magnetic field is has units (mass/length)^(1/2) / time.
     """
-    eq = [u.Gauss, u.Hz * (u.g / u.cm) ** (1 / 2), lambda x: x, lambda x: x]
-    return B.to(u.Gauss, equivalencies=[eq])
+    return B.to(u.Gauss, equivalencies=[pint.gauss_equiv])
 
 
 @u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, fo=u.Hz)

From cbf1e57f8cb5ef5d96092cc8e14df280ea6dd2e9 Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Wed, 20 Nov 2024 09:36:09 +0100
Subject: [PATCH 8/9] allow_tcb and allow_T2 are false by default

---
 src/pint/scripts/compare_parfiles.py          | 14 ++++++++++++--
 src/pint/scripts/convert_parfile.py           | 12 +++++++++++-
 src/pint/scripts/event_optimize.py            | 14 +++++++++++++-
 src/pint/scripts/event_optimize_MCMCFitter.py | 15 ++++++++++++++-
 src/pint/scripts/event_optimize_multiple.py   | 14 +++++++++++++-
 src/pint/scripts/fermiphase.py                | 14 +++++++++++++-
 6 files changed, 76 insertions(+), 7 deletions(-)

diff --git a/src/pint/scripts/compare_parfiles.py b/src/pint/scripts/compare_parfiles.py
index 87eb005a0..d65785041 100644
--- a/src/pint/scripts/compare_parfiles.py
+++ b/src/pint/scripts/compare_parfiles.py
@@ -83,14 +83,24 @@ 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, allow_T2=True, allow_tcb=True)
-    m2 = get_model(args.input2, allow_T2=True, allow_tcb=True)
+    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(
diff --git a/src/pint/scripts/convert_parfile.py b/src/pint/scripts/convert_parfile.py
index 0612a46a8..2975d5acc 100644
--- a/src/pint/scripts/convert_parfile.py
+++ b/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(
@@ -84,7 +94,7 @@ def main(argv=None):
 
     log.info(f"Reading '{args.input}'")
 
-    model = get_model(args.input, allow_T2=True, allow_tcb=True)
+    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}")
diff --git a/src/pint/scripts/event_optimize.py b/src/pint/scripts/event_optimize.py
index b91c30a04..6e26ba784 100755
--- a/src/pint/scripts/event_optimize.py
+++ b/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, allow_T2=True, allow_tcb=True)
+    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()
diff --git a/src/pint/scripts/event_optimize_MCMCFitter.py b/src/pint/scripts/event_optimize_MCMCFitter.py
index 43bc89858..7357b1028 100755
--- a/src/pint/scripts/event_optimize_MCMCFitter.py
+++ b/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, allow_T2=True, allow_tcb=True)
+    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
diff --git a/src/pint/scripts/event_optimize_multiple.py b/src/pint/scripts/event_optimize_multiple.py
index daa40a9e9..0a3dc7336 100755
--- a/src/pint/scripts/event_optimize_multiple.py
+++ b/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, allow_T2=True, allow_tcb=True)
+    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:
diff --git a/src/pint/scripts/fermiphase.py b/src/pint/scripts/fermiphase.py
index 6785bc156..c5e43bb93 100755
--- a/src/pint/scripts/fermiphase.py
+++ b/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 +98,9 @@ def main(argv=None):
         args.addphase = True
 
     # Read in model
-    modelin = pint.models.get_model(args.parfile, allow_T2=True, allow_tcb=True)
+    modelin = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     if "ELONG" in modelin.params:
         tc = SkyCoord(

From 706f041098be6b14f862d7c0d569de4ffb7daf2d Mon Sep 17 00:00:00 2001
From: Abhimanyu Susobhanan <abhisrkckl@gmail.com>
Date: Wed, 20 Nov 2024 09:55:25 +0100
Subject: [PATCH 9/9] no default tcb t2

---
 src/pint/scripts/photonphase.py   | 14 +++++++++++++-
 src/pint/scripts/pintbary.py      | 14 +++++++++++++-
 src/pint/scripts/pintempo.py      | 14 +++++++++++++-
 src/pint/scripts/pintpublish.py   | 14 +++++++++++++-
 src/pint/scripts/t2binary2pint.py |  7 ++++++-
 src/pint/scripts/tcb2tdb.py       |  7 ++++++-
 src/pint/scripts/zima.py          | 14 +++++++++++++-
 7 files changed, 77 insertions(+), 7 deletions(-)

diff --git a/src/pint/scripts/photonphase.py b/src/pint/scripts/photonphase.py
index 38505c629..85a80907f 100755
--- a/src/pint/scripts/photonphase.py
+++ b/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 +163,9 @@ 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, allow_T2=True, allow_tcb=True)
+    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:
diff --git a/src/pint/scripts/pintbary.py b/src/pint/scripts/pintbary.py
index c29d42fbb..61cdcd0a0 100755
--- a/src/pint/scripts/pintbary.py
+++ b/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, allow_T2=True, allow_tcb=True)
+        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
diff --git a/src/pint/scripts/pintempo.py b/src/pint/scripts/pintempo.py
index 36e8ca509..ac9099008 100755
--- a/src/pint/scripts/pintempo.py
+++ b/src/pint/scripts/pintempo.py
@@ -62,6 +62,16 @@ 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(
@@ -69,7 +79,9 @@ def main(argv=None):
     )
 
     log.info("Reading model from {0}".format(args.parfile))
-    m = pint.models.get_model(args.parfile, allow_T2=True, allow_tcb=True)
+    m = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     log.warning(m.params)
 
diff --git a/src/pint/scripts/pintpublish.py b/src/pint/scripts/pintpublish.py
index 36cc5786e..1828a05c6 100644
--- a/src/pint/scripts/pintpublish.py
+++ b/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, allow_T2=True)
+    model, toas = get_model_and_toas(
+        args.parfile, args.timfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     output = publish(
         model,
diff --git a/src/pint/scripts/t2binary2pint.py b/src/pint/scripts/t2binary2pint.py
index 42d70f89a..bab43eef4 100644
--- a/src/pint/scripts/t2binary2pint.py
+++ b/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}")
 
diff --git a/src/pint/scripts/tcb2tdb.py b/src/pint/scripts/tcb2tdb.py
index 5b15d56ae..02a485d3c 100644
--- a/src/pint/scripts/tcb2tdb.py
+++ b/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, allow_T2=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}.")
diff --git a/src/pint/scripts/zima.py b/src/pint/scripts/zima.py
index 3485c6c5b..29b3e354c 100755
--- a/src/pint/scripts/zima.py
+++ b/src/pint/scripts/zima.py
@@ -115,6 +115,16 @@ 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(
@@ -122,7 +132,9 @@ def main(argv=None):
     )
 
     log.info("Reading model from {0}".format(args.parfile))
-    m = pint.models.get_model(args.parfile, allow_T2=True, allow_tcb=True)
+    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