ExoIris 0.23.0__tar.gz → 0.23.2__tar.gz

{exoiris-0.23.0 → exoiris-0.23.2}/CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to ExoIris will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.23.1] - 2025-12-18
+
+### Fixed
+- Fixed least-squares baseline fitting for transit models with NaNs.
+- Added "bspline-cubic" interpolation option as an alias for "bspline". The "bspline" option will be removed in a future 
+  release.
+
 ## [0.23.0] - 2025-12-16
 
 ### Changed

{exoiris-0.23.0 → exoiris-0.23.2}/ExoIris.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ExoIris
-Version: 0.23.0
+Version: 0.23.2
 Summary: Easy and robust exoplanet transmission spectroscopy.
 Author-email: Hannu Parviainen <hannu@iac.es>
 License: GPLv3

{exoiris-0.23.0 → exoiris-0.23.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ExoIris
-Version: 0.23.0
+Version: 0.23.2
 Summary: Easy and robust exoplanet transmission spectroscopy.
 Author-email: Hannu Parviainen <hannu@iac.es>
 License: GPLv3

{exoiris-0.23.0 → exoiris-0.23.2}/exoiris/exoiris.py

@@ -163,7 +163,7 @@ class ExoIris:
 
     def __init__(self, name: str, ldmodel, data: TSDataGroup | TSData, nk: int = 50, nldc: int = 10, nthreads: int = 1,
                  tmpars: dict | None = None, noise_model: Literal["white", "fixed_gp", "free_gp"] = 'white',
-                 interpolation: Literal['nearest', 'linear', 'pchip', 'makima', 'bspline', 'bspline-quadratic'] = 'makima'):
+                 interpolation: Literal['nearest', 'linear', 'pchip', 'makima', 'bspline', 'bspline-quadratic', 'bspline-cubic'] = 'linear'):
         """
         Parameters
         ----------
@@ -529,6 +529,16 @@ class ExoIris:
         """
         self._tsa.set_k_knots(knot_wavelengths)
 
+    def free_radius_ratio_knot_locations(self, knot_ids: list[int] | ndarray) -> None:
+        """Add the wavelength locations of chosen radius ratio knots to the model as free parameters.
+
+        Parameters
+        ----------
+        knot_ids
+            List of radius ratio knot indices to be made free parameters.
+        """
+        self._tsa.free_k_knot_locations(knot_ids)
+
     def create_dense_radius_ratio_block(self, wlmin: float, wlmax: float) -> None:
         """Create a block of radius ratio knots using the full data resolution.
 

{exoiris-0.23.0 → exoiris-0.23.2}/exoiris/tslpf.py

@@ -40,8 +40,9 @@ from numpy import (
     dstack,
     diff,
     ascontiguousarray,
+    nan,
 )
-from numpy.linalg import lstsq
+from numpy.linalg import lstsq, LinAlgError
 from numpy.random import default_rng
 from pytransit.lpf.logposteriorfunction import LogPosteriorFunction
 from pytransit.orbits import as_from_rhop, i_from_ba
@@ -133,11 +134,11 @@ def add_knots(x_new, x_old):
     return sort(concatenate([x_new, x_old]))
 
 
-interpolator_choices = ("bspline", "pchip", "makima", "nearest", "linear", "bspline-quadratic")
+interpolator_choices = ("bspline", "pchip", "makima", "nearest", "linear", "bspline-quadratic", "bspline-cubic")
 
 
-interpolators = {'bspline': ip_bspline, 'bspline-quadratic': ip_bspline_quadratic, 'pchip': ip_pchip,
-                 'makima': ip_makima, 'nearest': ip_nearest, 'linear': ip_linear}
+interpolators = {'bspline': ip_bspline, 'bspline-cubic': ip_bspline, 'bspline-quadratic': ip_bspline_quadratic,
+                 'pchip': ip_pchip, 'makima': ip_makima, 'nearest': ip_nearest, 'linear': ip_linear}
 
 
 def clean_knots(knots, min_distance, lmin=0, lmax=inf):
@@ -181,7 +182,7 @@ def clean_knots(knots, min_distance, lmin=0, lmax=inf):
 class TSLPF(LogPosteriorFunction):
     def __init__(self, runner, name: str, ldmodel, data: TSDataGroup, nk: int = 50, nldc: int = 10, nthreads: int = 1,
                  tmpars = None, noise_model: Literal["white", "fixed_gp", "free_gp"] = 'white',
-                 interpolation: Literal['nearest', 'linear', 'pchip', 'makima', 'bspline', 'bspline-quadratic'] = 'makima'):
+                 interpolation: Literal['nearest', 'linear', 'pchip', 'makima', 'bspline', 'bspline-quadratic', 'bspline-cubic'] = 'linear'):
         super().__init__(name)
         self._runner = runner
         self._original_data: TSDataGroup | None = None
@@ -549,7 +550,14 @@ class TSLPF(LogPosteriorFunction):
             self._mc_chains = fmcn.reshape([mco.shape[0], mco.shape[1], ndn])
             self.sampler = None
 
-    def set_free_k_knots(self, ids):
+    def set_free_k_knots(self, ids: list[int] | ndarray) -> None:
+        """Add the wavelength locations of chosen radius ratio knots as free model parameters.
+
+        Parameters
+        ----------
+        ids : list of int
+            List of radius ratio knot indices to be made free parameters.
+        """
         self.free_k_knot_ids = ids
 
         # Remove existing parameter block if one exists
@@ -749,8 +757,11 @@ class TSLPF(LogPosteriorFunction):
         for i, d in enumerate(self.data):
             for ipv in range(npv):
                 res = d.fluxes / mtransit[i][ipv]
-                coeffs = nlstsq(d.covs, res, d.mask, d._wlmask, d._wls_with_nan)
-                self._baseline_models[i][ipv, :, :] = (d.covs @ coeffs).T
+                try:
+                    coeffs = nlstsq(d.covs, res, d.mask, d._wlmask, d._wls_with_nan)
+                    self._baseline_models[i][ipv, :, :] = (d.covs @ coeffs).T
+                except LinAlgError:
+                    self._baseline_models[i][ipv, :, :] = nan
         return self._baseline_models
 
     def flux_model(self, pv):

{exoiris-0.23.0 → exoiris-0.23.2}/exoiris/wlpf.py

@@ -128,7 +128,7 @@ class WhiteLPF(BaseLPF):
         pv = self._local_minimization.x
         a = as_from_rhop(pv[1], pv[0])
         i = i_from_ba(pv[2], a)
-        t14 = d_from_pkaiews(pv[0], sqrt(pv[4]), a, i, 0., 0., 1, 14)
+        t14 = d_from_pkaiews(pv[0], sqrt(pv[self._start_k2]), a, i, 0., 0., 1, 14)
         return t14
 
     def plot(self, axs=None, figsize=None, ncols=2) -> Figure: