Merge pull request #1621 from abhisrkckl/publish

Publication output

.gitignore

@@ -119,4 +119,10 @@ docs/examples/*.ipynb
 docs/examples-rendered/*.py
 
 # VSCode wants to put virtualenvs here
-.env
+.env
+
+# pintpublish output
+*.tex
+*.aux
+*.log
+*.pdf

.readthedocs.yml

@@ -17,7 +17,8 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  builder: html
+  configuration: docs/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 formats:
@@ -29,4 +30,4 @@ python:
     - requirements: requirements_dev.txt
     - requirements: requirements.txt
     - method: pip
-      path: .
+      path: .

CHANGELOG-unreleased.md

@@ -13,7 +13,9 @@ the released changes.
 - Moved design matrix normalization code from `pint.fitter` to the new `pint.utils.normalize_designmatrix()` function.
 - Made `Residuals` independent of `GLSFitter` (GLS chi2 is now computed using the new function `Residuals._calc_gls_chi2()`).
 ### Added
-- Added WaveX model as DelayComponent with wave amplitudes as fitted parameters
+- Added `WaveX` model as a `DelayComponent` with Fourier amplitudes as fitted parameters
+- `Parameter.as_latex` method for latex representation of a parameter.
+- `pint.output.publish` module and `pintpublish` script for generating publication (LaTeX) output.
 - Added radial velocity methods for binary models
 ### Fixed
 - Wave model `validate()` can correctly use PEPOCH to assign WAVEEPOCH parameter

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, ECC*sin(OM)",
                 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, ECC*cos(OM)",
                 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="Polynomial coefficient of log-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 is correlated among all TOAs in an observing epoch.",
             )
         )
 

src/pint/models/parameter.py

@@ -571,6 +571,26 @@ def from_parfile_line(self, line):
             self.uncertainty = self._set_uncertainty(ucty)
         return True
 
+    def value_as_latex(self):
+        return f"${self.as_ufloat():.1uSL}$" if not self.frozen else f"{self.value:f}"
+
+    def as_latex(self):
+        try:
+            unit_latex = (
+                ""
+                if self.units == "" or self.units is None
+                else f" ({self.units.to_string(format='latex', fraction=False)})"
+            )
+        except TypeError:
+            # to deal with old astropy
+            unit_latex = (
+                ""
+                if self.units == "" or self.units is None
+                else f" ({self.units.to_string(format='latex')})"
+            )
+        value_latex = self.value_as_latex()
+        return f"{self.name}, {self.description}{unit_latex}", value_latex
+
     def add_alias(self, alias):
         """Add a name to the list of aliases for this parameter."""
         self.aliases.append(alias)
@@ -868,6 +888,9 @@ def _set_quantity(self, val):
         """Convert to string."""
         return str(val)
 
+    def value_as_latex(self):
+        return self.value
+
 
 class boolParameter(Parameter):
     """Boolean-valued parameter.
@@ -935,6 +958,9 @@ def _set_quantity(self, val):
             return bool(float(val))
         return bool(val)
 
+    def value_as_latex(self):
+        return "Y" if self.value else "N"
+
 
 class intParameter(Parameter):
     """Integer parameter values.
@@ -1003,6 +1029,9 @@ def _set_quantity(self, val):
 
         return ival
 
+    def value_as_latex(self):
+        return str(self.value)
+
 
 class MJDParameter(Parameter):
     """Parameters for MJD quantities.
@@ -1166,6 +1195,18 @@ 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.
@@ -1300,6 +1341,32 @@ 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``.
@@ -1547,6 +1614,9 @@ def name_matches(self, name):
     def as_parfile_line(self, format="pint"):
         return self.param_comp.as_parfile_line(format=format)
 
+    def as_latex(self):
+        return self.param_comp.as_latex()
+
     def help_line(self):
         return self.param_comp.help_line()
 
@@ -1892,6 +1962,25 @@ def as_parfile_line(self, format="pint"):
             line += " 1"
         return line + "\n"
 
+    def as_latex(self):
+        try:
+            unit_latex = (
+                ""
+                if self.units == "" or self.units is None
+                else f" ({self.units.to_string(format='latex', fraction=False)})"
+            )
+        except TypeError:
+            # `fraction` option is not available in old astropy versions.
+            unit_latex = (
+                ""
+                if self.units == "" or self.units is None
+                else f" ({self.units.to_string(format='latex')})"
+            )
+        return (
+            f"{self.prefix} {self.key} {' '.join(self.key_value)}, {self.description}{unit_latex}",
+            self.value_as_latex(),
+        )
+
     def new_param(self, index, copy_all=False):
         """Create a new but same style mask parameter"""
         return (

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, ap*sin(i)",
             )
         )
         # NOTE: the DOT here takes the value and times 1e-12, tempo/tempo2 can
@@ -112,7 +114,7 @@ def __init__(self):
                 name="A1DOT",
                 aliases=["XDOT"],
                 units=ls / u.s,
-                description="Derivative of projected semi-major axis, da*sin(i)/dt",
+                description="Derivative of projected semi-major axis, d[ap*sin(i)]/dt",
                 unit_scale=True,
                 scale_factor=1e-12,
                 scale_threshold=1e-7,
@@ -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

@@ -309,7 +309,7 @@ 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,
             ),
             "",
@@ -3003,6 +3003,9 @@ 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)