Merge branch 'sim-dmgp' into wbfit

CHANGELOG-unreleased.md

@@ -22,18 +22,15 @@ the released changes.
 - `add_param` returns the name of the parameter (useful for numbered parameters)
 - `introduces_dm_errors` class attribute in `NoiseComponent`s to distinguish DM noise
 - Simulate correlated DM noise for wideband TOAs
-- Abstract base classes `WhiteNoiseComponent` and `CorrelatedNoiseComponent`
-- `get_dm_noise_basis` and `get_wideband_noise_basis` methods in `CorrelatedNoiseComponent`s
-- `scaled_wideband_uncertainty`, `noise_model_wideband_designmatrix`, `dm_designmatrix`, `wideband_designmatrix`,  `full_designmatrix`, and `full_basis_weight` methods in `TimingModel`
-- `get_wideband_errors` method in `TOAs`
-- `calc_combined_resids` method in `WidebandTOAResiduals`
 - Rerun intermittent failures in CI
 - micromamba CI environment for testing macOS-latest, without tox
+
 ### Fixed
 - Changed WAVE_OM units from 1/d to rad/d.
 - When EQUAD is created from TNEQ, has proper TCB->TDB conversion info
 - TOA selection masks will work when only TOA is the first one
 - Condense code in Glitch model and add test coverage.
+- `find_empty_masks` will now search through `CMX` parameters
+- Fixed some docstrings for binary models.
 ### Removed
 - macOS 12 CI 
-

src/pint/models/binary_bt.py

@@ -21,7 +21,7 @@
 class BinaryBT(PulsarBinary):
     """Blandford and Teukolsky binary model.
 
-    This binary model is described in Blandford and Teukolshy 1976. It is
+    This binary model is described in Blandford and Teukolsky (1976). It is
     a relatively simple parametrized post-Keplerian model that does not
     support Shapiro delay calculations.
 
@@ -36,12 +36,16 @@ class BinaryBT(PulsarBinary):
     Notes
     -----
     Because PINT's binary models all support specification of multiple orbital
-    frequency derivatives FBn, this is capable of behaving like the model called
-    BTX in tempo2. The model called BTX in tempo instead supports multiple
-    (non-interacting) companions, and that is not supported here. Neither can
-    PINT accept "BTX" as an alias for this model.
+    frequency derivatives ``FBn``, this is capable of behaving like the model called
+    ``BTX`` in ``tempo2``. The model called ``BTX`` in ``tempo`` instead supports multiple
+    (non-interacting) companions, and that is not supported here.
+
+    References
+    ----------
+    - Blandford & Teukolsky 1976, ApJ, 205, 580 [1]_
+
+    .. [1] https://ui.adsabs.harvard.edu/abs/1976ApJ...205..580B/abstract
 
-    See Blandford & Teukolsky 1976, ApJ, 205, 580.
     """
 
     register = True
@@ -82,16 +86,23 @@ def validate(self):
 
 
 class BinaryBTPiecewise(PulsarBinary):
-    """Model implementing the BT model with piecewise orbital parameters A1X and T0X. This model lets the user specify time ranges and fit for a different piecewise orbital parameter in each time range,
-    This is a PINT pulsar binary BTPiecewise model class, a subclass of PulsarBinary.
-    It is a wrapper for stand alone BTPiecewise class defined in
-    ./stand_alone_psr_binary/BT_piecewise.py
-    The aim for this class is to connect the stand alone binary model with the PINT platform.
-    BTpiecewise special parameters, where xxxx denotes the 4-digit index of the piece:
-    T0X_xxxx Piecewise T0 values for piece
-    A1X_xxxx Piecewise A1 values for piece
-    XR1_xxxx Lower time boundary of piece
-    XR2_xxxx Upper time boundary of piece
+    """BT model with piecewise orbital parameters ``A1X`` and ``T0X``. This model lets the user specify time ranges and fit for a different piecewise orbital parameter in each time range.
+
+    ``BTpiecewise`` special parameters, where xxxx denotes the 4-digit index of the piece:
+
+        - ``T0X_xxxx``: Piecewise ``T0`` values for piece
+        - ``A1X_xxxx``: Piecewise ``A1`` values for piece
+        - ``XR1_xxxx``: Lower time boundary of piece
+        - ``XR2_xxxx``: Upper time boundary of piece
+
+    The actual calculations for this are done in
+    :class:`pint.models.stand_alone_psr_binaries.BT_piecewise.BTpiecewise`
+
+    Parameters supported:
+
+    .. paramtable::
+        :class: pint.models.binary_bt.BinaryBTPiecewise
+
     """
 
     register = True

src/pint/models/dispersion_model.py

@@ -627,6 +627,10 @@ def validate(self):
                 r2[j] = getattr(self, f"DMXR2_{index:04d}").quantity.mjd
                 indices[j] = index
         for j, index in enumerate(DMXR1_mapping):
+            if (r1[j] == r2[j]) and (r1[j] > 0):
+                log.warning(
+                    f"Start of DMX_{index:04d} ({r1[j]}) equal to end of DMX_{index:04d} ({r2[j]})"
+                )
             if np.any((r1[j] > r1) & (r1[j] < r2)):
                 k = np.where((r1[j] > r1) & (r1[j] < r2))[0]
                 for kk in k.flatten():
@@ -639,6 +643,8 @@ def validate(self):
                     log.warning(
                         f"End of DMX_{index:04d} ({r1[j]}-{r2[j]}) overlaps with DMX_{indices[kk]:04d} ({r1[kk]}-{r2[kk]})"
                     )
+        if not hasattr(self, "dmx_toas_selector"):
+            self.dmx_toas_selector = TOASelect(is_range=True)
 
     def validate_toas(self, toas):
         DMX_mapping = self.get_prefix_mapping_component("DMX_")
@@ -651,7 +657,7 @@ def validate_toas(self, toas):
             b = self._parent[DMXR1_mapping[k]].quantity.mjd * u.d
             e = self._parent[DMXR2_mapping[k]].quantity.mjd * u.d
             mjds = toas.get_mjds()
-            n = np.sum((b <= mjds) & (mjds < e))
+            n = np.sum((b <= mjds) & (mjds <= e))
             if n == 0:
                 bad_parameters.append(DMX_mapping[k])
         if bad_parameters:

src/pint/models/model_builder.py

@@ -251,6 +251,10 @@ def __call__(
         if not hasattr(tm, "NoiseComponent_list"):
             setattr(tm, "NoiseComponent_list", [])
 
+        tm.meta["allow_tcb"] = allow_tcb_
+        tm.meta["convert_tcb"] = convert_tcb
+        tm.meta["allow_T2"] = allow_T2
+
         return tm
 
     def _validate_components(self):
@@ -851,6 +855,7 @@ def get_model(
         **kwargs,
     )
     model.name = parfile
+    model.meta["original_name"] = parfile
 
     return model
 

src/pint/models/noise_model.py

@@ -499,9 +499,11 @@ class PLDMNoise(CorrelatedNoiseComponent):
     .. paramtable::
         :class: pint.models.noise_model.PLDMNoise
 
-    Note
-    ----
-    Ref: Lentati et al. 2014, MNRAS 437(3), 3004-3023
+    References
+    ----------
+    - Lentati et al. 2014, MNRAS 437(3), 3004-3023 [1]_
+
+    .. [1] https://ui.adsabs.harvard.edu/abs/2014MNRAS.437.3004L/abstract
 
     """
 
@@ -619,9 +621,11 @@ class PLChromNoise(CorrelatedNoiseComponent):
     .. paramtable::
         :class: pint.models.noise_model.PLChromNoise
 
-    Note
-    ----
-    Ref: Lentati et al. 2014, MNRAS 437(3), 3004-3023
+    References
+    ----------
+    - Lentati et al. 2014, MNRAS 437(3), 3004-3023 [1]_
+
+    .. [1] https://ui.adsabs.harvard.edu/abs/2014MNRAS.437.3004L/abstract
     """
 
     register = True
@@ -731,10 +735,11 @@ class PLRedNoise(CorrelatedNoiseComponent):
     .. paramtable::
         :class: pint.models.noise_model.PLRedNoise
 
-    Note
-    ----
-    Ref: Lentati et al. 2014, MNRAS 437(3), 3004-3023
+    References
+    ----------
+    - Lentati et al. 2014, MNRAS 437(3), 3004-3023 [1]_
 
+    .. [1] https://ui.adsabs.harvard.edu/abs/2014MNRAS.437.3004L/abstract
     """
 
     register = True

src/pint/models/timing_model.py

@@ -29,6 +29,7 @@
 
 import abc
 import copy
+import datetime
 import inspect
 import contextlib
 from collections import OrderedDict, defaultdict
@@ -109,6 +110,9 @@
 
 ignore_prefix = {"DMXF1_", "DMXF2_", "DMXEP_"}
 
+# prefixes of parameters that may need to be checked for empty ranges
+prefixes = ["DM", "SW", "CM"]
+
 DEFAULT_ORDER = [
     "astrometry",
     "jump_delay",
@@ -225,6 +229,8 @@ class TimingModel:
     ----------
     name : str
         The name of the timing model
+    meta : dict
+        A dictionary of metadata
     component_types : list
         A list of the distinct categories of component. For example,
         delay components will be register as 'DelayComponent'.
@@ -239,6 +245,9 @@ def __init__(self, name="", components=[]):
                 "First parameter should be the model name, was {!r}".format(name)
             )
         self.name = name
+        self.meta = {
+            "read_time": f"{datetime.datetime.now().isoformat()}",
+        }
         self.component_types = []
         self.top_level_params = []
         self.add_param_from_top(
@@ -2870,6 +2879,7 @@ def as_parfile(
         if include_info:
             info_string = pint.utils.info_string(prefix_string="# ", comment=comment)
             info_string += f"\n# Format: {format.lower()}"
+            info_string += "".join([f"\n# {x}: {self.meta[x]}" for x in self.meta])
             result_begin = info_string + "\n"
         else:
             result_begin = ""
@@ -3008,7 +3018,7 @@ def find_empty_masks(self, toas, freeze=False):
                 if freeze:
                     log.info(f"'{maskpar}' has no TOAs so freezing")
                     getattr(self, maskpar).frozen = True
-        for prefix in ["DM", "SW"]:
+        for prefix in prefixes:
             mapping = pint.utils.xxxselections(self, toas, prefix=prefix)
             for k in mapping:
                 if len(mapping[k]) == 0:

src/pint/models/wavex.py

@@ -12,9 +12,7 @@
 
 class WaveX(DelayComponent):
     """
-    Implementation of the wave model as a delay correction
-
-    Delays are expressed as a sum of sinusoids.
+    Implementation of the wave model as a delay correction, with delays are expressed as a sum of sinusoids.
 
     Used for decomposition of timing noise into a series of sine/cosine components with the amplitudes as fitted parameters.
 
@@ -23,25 +21,34 @@ class WaveX(DelayComponent):
     .. paramtable::
         :class: pint.models.wavex.WaveX
 
-    This is an extension of the L13 method described in Lentati et al., 2013 doi: 10.1103/PhysRevD.87.104021
-    This model is similar to the TEMPO2 WAVE model parameters and users can convert a `TimingModel` with a Wave model
-    to a WaveX model and produce the same results. The main differences are that the WaveX frequencies are explicitly stated,
+    This is an extension of the method described in Lentati et al. (2013).
+    This model is similar to the TEMPO2 WAVE model parameters and users can convert a :class:`~pint.models/timing_model.TimingModel`
+    with a :class:`~pint.models.wave.Wave` model to a ``WaveX`` model and produce the same results.
+    The main differences are that the ``WaveX`` frequencies are explicitly stated,
     they do not necessarily need to be harmonics of some base frequency, the wave amplitudes are fittable parameters, and the
-    sine and cosine amplutides are reported as separate `prefixParameter`s rather than as a single `pairParameter`.
+    sine and cosine amplutides are reported as separate :class:`~pint.models.parameter.prefixParameter` rather than as a
+    single :class:`pint.models.parameter.pairParameter`.
 
     Analogous parameters in both models have the same units:
-    WAVEEPOCH is the same as WXEPOCH
-    WAVEOM and WXFREQ_000N have units of 1/d
-    WAVEN and WXSIN_000N/WXCOS_000N have units of seconds
 
-    The `pint.utils` functions `translate_wave_to_wavex()` and `translate_wavex_to_wave()` can be used to go back and forth between
-    two model.
+        - ``WAVEEPOCH`` is the same as ``WXEPOCH``
+        - ``WAVEOM`` and ``WXFREQ_000N`` have units of 1/d
+        - ``WAVEN`` and ``WXSIN_000N/WXCOS_000N`` have units of seconds
+
+    The :mod:`pint.utils` functions :func:`~pint.utils.translate_wave_to_wavex` and :func:`~pint.utils.translate_wavex_to_wave`
+    can be used to go back and forth between two model.
+
+    WARNING: If the choice of ``WaveX`` frequencies in a :class:`~pint.models/timing_model.TimingModel` doesn't correspond to harmonics of some base
+    freqeuncy, it will not be possible to convert it to a :class:`~pint.models.wave.Wave` model.
+
+    To set up a ``WaveX`` model, users can use the :mod:`pint.utils` function :func:`~pint.utils.wavex_setup` with either a list of frequencies or a choice
+    of harmonics of a base frequency determined by ``2 * pi /Timespan``
 
-    WARNING: If the choice of WaveX frequencies in a `TimingModel` doesn't correspond to harmonics of some base
-    freqeuncy, it will not be possible to convert it to a Wave model.
+    References
+    ----------
+    - Lentati et al. (2013), PRD, 87, 104021 [1]_
 
-    To set up a WaveX model, users can use the `pint.utils` function `wavex_setup()` with either a list of frequencies or a choice
-    of harmonics of a base frequency determined by 2 * pi /Timespan
+    .. [1] https://ui.adsabs.harvard.edu/abs/2013PhRvD..87j4021L/abstract
     """
 
     register = True