Publication output

CHANGELOG-unreleased.md

@@ -19,6 +19,7 @@ the released changes.
 - `pint.print_info()` function for bug reporting
 - Added an autocorrelation function to check for chain convergence in `event_optimize`
 - Minor doc updates to explain default NHARMS and missing derivative functions
+- `pint.output.publish` module and `pintpublish` script for generating publication (LaTeX) output.
 ### Fixed
 - Deleting JUMP1 from flag tables will not prevent fitting
 - Simulating TOAs from tim file when PLANET_SHAPIRO is true now works

setup.cfg

@@ -61,6 +61,7 @@ console_scripts =
     convert_parfile = pint.scripts.convert_parfile:main
     compare_parfiles = pint.scripts.compare_parfiles:main
     tcb2tdb = pint.scripts.tcb2tdb:main
+    pintpublish = pint.scripts.pintpublish:main
 
 
 # See the docstring in versioneer.py for instructions. Note that you must

src/pint/models/absolute_phase.py

@@ -30,19 +30,21 @@ def __init__(self):
         super().__init__()
         self.add_param(
             MJDParameter(
-                name="TZRMJD", description="Epoch of the zero phase.", time_scale="utc"
+                name="TZRMJD",
+                description="Epoch of the zero phase TOA.",
+                time_scale="utc",
             )
         )
         self.add_param(
             strParameter(
-                name="TZRSITE", description="Observatory of the zero phase measured."
+                name="TZRSITE", description="Observatory of the zero phase TOA."
             )
         )
         self.add_param(
             floatParameter(
                 name="TZRFRQ",
                 units=u.MHz,
-                description="The frequency of the zero phase measured.",
+                description="The frequency of the zero phase TOA.",
             )
         )
         self.tz_cache = None

src/pint/models/binary_ell1.py

@@ -117,7 +117,7 @@ def __init__(self):
             floatParameter(
                 name="EPS1",
                 units="",
-                description="First Laplace-Lagrange parameter, ECC x sin(OM) for ELL1 model",
+                description="First Laplace-Lagrange parameter",
                 long_double=True,
             )
         )
@@ -126,7 +126,7 @@ def __init__(self):
             floatParameter(
                 name="EPS2",
                 units="",
-                description="Second Laplace-Lagrange parameter, ECC x cos(OM) for ELL1 model",
+                description="Second Laplace-Lagrange parameter",
                 long_double=True,
             )
         )

src/pint/models/frequency_dependent.py

@@ -36,7 +36,7 @@ def __init__(self):
                 name="FD1",
                 units="second",
                 value=0.0,
-                description="Coefficient of delay as a polynomial function of log-frequency",
+                description="Coefficient of frequency-dependent delay",
                 # descriptionTplt=lambda x: (
                 #    "%d term of frequency" " dependent  coefficients" % x
                 # ),

src/pint/models/jump.py

@@ -93,7 +93,7 @@ def __init__(self):
             maskParameter(
                 name="JUMP",
                 units="second",
-                description="Amount to jump the selected TOAs by.",
+                description="Phase jump for selection.",
             )
         )
         self.phase_funcs_component += [self.jump_phase]

src/pint/models/noise_model.py

@@ -58,8 +58,7 @@ def __init__(
                 name="EFAC",
                 units="",
                 aliases=["T2EFAC", "TNEF"],
-                description="A multiplication factor on"
-                " the measured TOA uncertainties,",
+                description="A multiplication factor for the measured TOA uncertainties,",
             )
         )
 
@@ -68,20 +67,15 @@ def __init__(
                 name="EQUAD",
                 units="us",
                 aliases=["T2EQUAD"],
-                description="An error term added in "
-                "quadrature to the scaled (by"
-                " EFAC) TOA uncertainty.",
+                description="An error term added in quadrature to the TOA uncertainty.",
             )
         )
 
         self.add_param(
             maskParameter(
                 name="TNEQ",
                 units=u.LogUnit(physical_unit=u.second),
-                description="An error term added in "
-                "quadrature to the scaled (by"
-                " EFAC) TOA uncertainty in "
-                " the unit of log10(second).",
+                description="A log10-scale error term added in quadrature to the TOA uncertainty",
             )
         )
         self.covariance_matrix_funcs += [self.sigma_scaled_cov_matrix]
@@ -307,9 +301,7 @@ def __init__(
                 name="ECORR",
                 units="us",
                 aliases=["TNECORR"],
-                description="An error term added that"
-                " correlated all TOAs in an"
-                " observing epoch.",
+                description="An error term that correlates all TOAs in an observing epoch.",
             )
         )
 

src/pint/models/parameter.py

@@ -1163,6 +1163,18 @@ def as_ufloats(self):
         error = self.uncertainty.to_value(u.d) if self.uncertainty is not None else 0
         return ufloat(value1, 0), ufloat(value2, error)
 
+    def as_ufloat(self):
+        """Return the parameter as a :class:`uncertainties.ufloat`
+        value.
+
+        If the uncertainty is not set will be returned as 0
+
+        Returns
+        -------
+        uncertainties.ufloat
+        """
+        return ufloat(self.value, self.uncertainty_value)
+
 
 class AngleParameter(Parameter):
     """Parameter in angle units.
@@ -1297,6 +1309,32 @@ def _print_uncertainty(self, unc):
             angle_arcsec /= 15.0
         return angle_arcsec.to_string(decimal=True, precision=20)
 
+    def as_ufloat(self, units=None):
+        """Return the parameter as a :class:`uncertainties.ufloat`
+
+        Will cast to the specified units, or the default
+        If the uncertainty is not set will be returned as 0
+
+        Parameters
+        ----------
+        units : astropy.units.core.Unit, optional
+            Units to cast the value
+
+        Returns
+        -------
+        uncertainties.ufloat
+
+        Notes
+        -----
+        Currently :class:`~uncertainties.ufloat` does not support double precision values,
+        so some precision may be lost.
+        """
+        if units is None:
+            units = self.units
+        value = self.quantity.to_value(units) if self.quantity is not None else 0
+        error = self.uncertainty.to_value(units) if self.uncertainty is not None else 0
+        return ufloat(value, error)
+
 
 class prefixParameter:
     """Families of parameters identified by a prefix like ``DMX_0123``.

src/pint/models/pulsar_binary.py

@@ -102,7 +102,9 @@ def __init__(self):
         )
         self.add_param(
             floatParameter(
-                name="A1", units=ls, description="Projected semi-major axis, a*sin(i)"
+                name="A1",
+                units=ls,
+                description="Projected semi-major axis of pulsar orbit",
             )
         )
         # NOTE: the DOT here takes the value and times 1e-12, tempo/tempo2 can
@@ -158,7 +160,7 @@ def __init__(self):
             floatParameter(
                 name="M2",
                 units=u.M_sun,
-                description="Mass of companion in the unit Sun mass",
+                description="Companion mass",
             )
         )
         self.add_param(

src/pint/models/spindown.py

@@ -108,7 +108,7 @@ def F_terms(self):
 
     def F_description(self, n):
         """Template function for description"""
-        return "Spin-frequency %d derivative" % n  # if n else "Spin-frequency"
+        return "Spin-frequency derivative %d" % n if n > 0 else "Spin-frequency"
 
     def F_unit(self, n):
         """Template function for unit"""

src/pint/models/timing_model.py

@@ -308,7 +308,7 @@ def __init__(self, name="", components=[]):
         self.add_param_from_top(
             strParameter(
                 name="BINARY",
-                description="The Pulsar System/Binary model to use.",
+                description="Pulsar System/Binary model",
                 value=None,
             ),
             "",
@@ -2909,6 +2909,9 @@ def add_param(self, param, deriv_func=None, setup=False):
             param.name = prefix + str(idx)
             param.index = idx
 
+            if hasattr(self, f"{prefix}1"):
+                param.description = getattr(self, f"{prefix}1").description
+
         # A more general check
         if param.name in self.params:
             exist_par = getattr(self, param.name)