PyTransit 2.6.8__tar.gz → 2.6.9__tar.gz

{pytransit-2.6.8 → pytransit-2.6.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyTransit
-Version: 2.6.8
+Version: 2.6.9
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -89,11 +89,11 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.
 RoadRunner [(Parviainen, 2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract) is a fast exoplanet transit model that can use any radially symmetric function to model stellar limb darkening 
 while still being faster to evaluate than the analytical transit model for quadratic limb darkening.
 
-- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb) 
+- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_1.ipynb) 
   shows how to use RoadRunner with the included limb darkening models.
-- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb)
+- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_2.ipynb)
   shows how to use RoadRunner with your own limb darkening model.
-- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb) 
+- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_3.ipynb) 
   shows how to use an LDTk-based limb darkening model LDTkM with RoadRunner.
 
 ### Transmission spectroscopy transit model

{pytransit-2.6.8 → pytransit-2.6.9}/PyTransit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyTransit
-Version: 2.6.8
+Version: 2.6.9
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -89,11 +89,11 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.
 RoadRunner [(Parviainen, 2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract) is a fast exoplanet transit model that can use any radially symmetric function to model stellar limb darkening 
 while still being faster to evaluate than the analytical transit model for quadratic limb darkening.
 
-- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb) 
+- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_1.ipynb) 
   shows how to use RoadRunner with the included limb darkening models.
-- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb)
+- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_2.ipynb)
   shows how to use RoadRunner with your own limb darkening model.
-- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb) 
+- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_3.ipynb) 
   shows how to use an LDTk-based limb darkening model LDTkM with RoadRunner.
 
 ### Transmission spectroscopy transit model

{pytransit-2.6.8 → pytransit-2.6.9}/PyTransit.egg-info/SOURCES.txt

@@ -10,7 +10,6 @@ PyTransit.egg-info/requires.txt
 PyTransit.egg-info/top_level.txt
 pytransit/__init__.py
 pytransit/limb_darkening.py
-pytransit/version.py
 pytransit/contamination/__init__.py
 pytransit/contamination/contamination.py
 pytransit/contamination/filter.py

{pytransit-2.6.8 → pytransit-2.6.9}/README.md

@@ -48,11 +48,11 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.
 RoadRunner [(Parviainen, 2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract) is a fast exoplanet transit model that can use any radially symmetric function to model stellar limb darkening 
 while still being faster to evaluate than the analytical transit model for quadratic limb darkening.
 
-- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb) 
+- [RRModel example 1](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_1.ipynb) 
   shows how to use RoadRunner with the included limb darkening models.
-- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb)
+- [RRModel example 2](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_2.ipynb)
   shows how to use RoadRunner with your own limb darkening model.
-- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb) 
+- [RRModel example 3](https://github.com/hpparvi/PyTransit/blob/dev/doc/source/notebooks/models/roadrunner/roadrunner_model_example_3.ipynb) 
   shows how to use an LDTk-based limb darkening model LDTkM with RoadRunner.
 
 ### Transmission spectroscopy transit model

{pytransit-2.6.8 → pytransit-2.6.9}/pyproject.toml

@@ -4,7 +4,6 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyTransit"
-version = "2.6.8"
 description = 'Fast and painless exoplanet transit light curve modelling.'
 authors=[{name='Hannu Parviainen', email='hpparvi@gmail.com'}]
 classifiers=[
@@ -21,13 +20,14 @@ keywords = ['astronomy',  'astrophysics',  'exoplanets']
 requires-python = ">= 3.8"
 readme = "README.md"
 license = {text = "GPLv2"}
-dynamic = ["dependencies"]
+dynamic = ["version", "dependencies"]
 
 [project.urls]
 homepage = 'https://github.com/hpparvi/PyTransit'
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
+version = {attr = "pytransit.__version__"}
 
 [tool.setuptools]
 include-package-data = true

pytransit-2.6.9/pytransit/__init__.py

@@ -0,0 +1,93 @@
+#  PyTransit: fast and easy exoplanet transit modelling in Python.
+#  Copyright (C) 2010-2020  Hannu Parviainen
+#
+#  This program is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+#  This program is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+
+"""PyTransit: fast and easy exoplanet transit modelling in Python
+
+This package offers Python interfaces for a set of exoplanet transit light curve
+models implemented in Python (with Numba acceleration) and OpenCL.
+
+Author
+  Hannu Parviainen  <hannu@iac.es>
+
+Date
+  06.08.2024
+
+"""
+
+__version__ = '2.6.9'
+
+# Generic
+# -------
+from .models.transitmodel import TransitModel
+from .contamination.filter import DeltaFilter, BoxcarFilter, TabulatedFilter, sdss_g, sdss_r, sdss_i, sdss_z
+
+# Numba models
+# ------------
+from .models.qpower2 import QPower2Model
+from .models.ma_quadratic import QuadraticModel
+from .models.ma_uniform import UniformModel
+from .models.eclipse_model import EclipseModel
+from .models.ma_chromosphere import ChromosphereModel
+from .models.general import GeneralModel
+from .models.osmodel import OblateStarModel
+from .models.gdmodel import GravityDarkenedModel
+
+from .models import RoadRunnerModel, OblatePlanetModel, TransmissionSpectroscopyModel
+
+TSModel = TransmissionSpectroscopyModel
+OPModel = OblatePlanetModel
+RRModel = RoadRunnerModel
+
+# OpenCL models
+# -------------
+from .models.qpower2_cl import QPower2ModelCL
+from .models.ma_quadratic_cl import QuadraticModelCL
+from .models.ma_uniform_cl import UniformModelCL
+
+# LDTk limb darkening for the Swift model
+# ---------------------------------------
+
+from .models.ldtkldm import LDTkLDModel #, LDTkLD
+from .models.ldtkldm import LDTkLD
+
+# Log posterior functions
+# -----------------------
+from .lpf.lpf import BaseLPF
+from .lpf.transitlpf import TransitLPF
+from .lpf.cntlpf import PhysContLPF
+from .lpf.baselines.legendrebaseline import LegendreBaseline
+from .lpf.baselines.linearbaseline import LinearModelBaseline
+from .lpf.transitanalysis import TransitAnalysis
+
+# Utilities
+# ---------
+from .param.parameter import UniformPrior, NormalPrior
+from .utils import md_rs_from_rho
+from .utils.mocklc import create_mock_light_curve

{pytransit-2.6.8 → pytransit-2.6.9}/pytransit/lpf/logposteriorfunction.py

@@ -136,11 +136,12 @@ class LogPosteriorFunction:
 
     def optimize_global(self, niter=200, npop=50, population=None, pool=None, lnpost=None, vectorize=True,
                         label='Global optimisation', leave=False, plot_convergence: bool = True, use_tqdm: bool = True,
-                        plot_parameters: tuple = (0, 2, 3, 4)):
+                        plot_parameters: tuple = (0, 2, 3, 4), min_ptp: float = 1e-2):
 
         lnpost = lnpost or self.lnposterior
         if self.de is None:
-            self.de = DiffEvol(lnpost, clip(self.ps.bounds, -1, 1), npop, maximize=True, vectorize=vectorize, pool=pool)
+            self.de = DiffEvol(lnpost, clip(self.ps.bounds, -1, 1), npop, maximize=True, vectorize=vectorize,
+                               pool=pool, min_ptp=min_ptp)
             if population is None:
                 self.de._population[:, :] = self.create_pv_population(npop)
             else:
@@ -179,24 +180,28 @@ class LogPosteriorFunction:
             raise ValueError('The MCMC sampler is set to save the results, but the result directory is not set.')
 
         lnpost = lnpost or self.lnposterior
-        if self.sampler is None:
-            if population is not None:
-                pop0 = population
-            elif hasattr(self, '_local_minimization') and self._local_minimization is not None:
-                pop0 = multivariate_normal(self._local_minimization.x, diag(full(len(self.ps), 0.001 ** 2)), size=npop)
-            elif self.de is not None:
-                pop0 = self.de.population.copy()
+        if population is not None:
+            pop0 = population
+        else:
+            if self.sampler is None:
+                if hasattr(self, '_local_minimization') and self._local_minimization is not None:
+                    pop0 = multivariate_normal(self._local_minimization.x, diag(full(len(self.ps), 0.001 ** 2)), size=npop)
+                elif self.de is not None:
+                    pop0 = self.de.population.copy()
+                else:
+                    raise ValueError('Sample MCMC needs an initial population.')
             else:
-                raise ValueError('Sample MCMC needs an initial population.')
+                pop0 = self.sampler.chain[:, -1, :].copy()
+
+        if self.sampler is None:
             self.sampler = EnsembleSampler(pop0.shape[0], pop0.shape[1], lnpost, vectorize=vectorize, pool=pool)
-        else:
-            pop0 = self.sampler.chain[:, -1, :].copy()
 
         for i in tqdm(range(repeats), desc=label, disable=(not use_tqdm), leave=leave):
-            if reset or i > 0:
+            if (self.sampler is not None and reset) or i > 0:
                 self.sampler.reset()
-            for _ in tqdm(self.sampler.sample(pop0, iterations=niter, thin=thin), total=niter,
-                          desc='Run {:d}/{:d}'.format(i + 1, repeats), leave=False, disable=(not use_tqdm)):
+            for _ in tqdm(self.sampler.sample(pop0, iterations=niter, thin=thin, skip_initial_state_check=False),
+                          total=niter, desc='Run {:d}/{:d}'.format(i + 1, repeats), leave=False,
+                          disable=(not use_tqdm)):
                 pass
             if save:
                 self.save(self.result_dir)

{pytransit-2.6.8 → pytransit-2.6.9}/pytransit/models/roadrunner/ecintersection.py

@@ -4,9 +4,93 @@ from numpy import ndarray, fabs, pi, full, arange
 from numba import njit
 
 @njit
-def create_ellipse(ny: int, k: float, f: float, a: float) -> (ndarray, ndarray):
+def rotated_ellipse_bbox(a: float, f: float):
+    """
+    Parameters
+    ----------
+    a : float
+        The angle (in radians) by which the ellipse is rotated.
+    f : float
+        The eccentricity of the ellipse, with a value between 0 and 1.
+
+    Returns
+    -------
+    hw : float
+        The half-width of the bounding box of the rotated ellipse.
+    hh : float
+        The half-height of the bounding box of the rotated ellipse.
+
+    """
+    r1, r2 = 1.0, 1.0-f
+    ux = r1 * cos(a)
+    uy = r1 * sin(a)
+    vx = r2 * cos(a + pi/2)
+    vy = r2 * sin(a + pi/2)
+    hw = sqrt(ux*ux + vx*vx)
+    hh = sqrt(uy*uy + vy*vy)
+    return hw, hh
+
+@njit
+def rotated_ellipse_x(y: float, a: float, f: float) -> tuple[float, float]:
+    """Calculate the x coordinates for a rotated ellipse given the y coordinate and the flattening factor.
+
+    Parameters
+    ----------
+    y
+        The y-coordinate of the point on the ellipse.
+    a
+        The angle (in radians) of rotation for the ellipse.
+    f
+        The flattening parameter of the ellipse.
+
+    Returns
+    -------
+    tuple[float, float]
+        The ellipse x-coordinates for the given y coordinate.
+    """
+    ca, sa = cos(a), sin(a)
+    b = 1.0 - f
+    d = b**2*ca**2 - y**2*sa**4 - 2*y**2*sa**2*ca**2 - y**2*ca**4 + sa**2
+    if d >= 0.0:
+        xl = (y*(-sa*ca + sa*ca/b**2) - sqrt(d)/b) / (ca**2 + sa**2/b**2)
+        xr = (y*(-sa*ca + sa*ca/b**2) + sqrt(d)/b) / (ca**2 + sa**2/b**2)
+        return xl, xr
+    else:
+        return nan, nan
+
+
+@njit
+def rotated_ellipse_dxdy(y: float, a: float, f: float) -> tuple[float, float]:
+    """Calculate dx/dy for a rotated ellipse given the y coordinate and the flattening factor.
+
+    Parameters
+    ----------
+    y
+        The y-coordinate of the point on the ellipse.
+    a
+        The angle, in radians, of rotation of the ellipse.
+    f
+        The flattening parameter of the ellipse.
+
+    Returns
+    -------
+    tuple[float, float]
+        The ellipse derivatives (dx/dy) for the given y coordinate.
     """
-    Create the coordinates for a rotated ellipse.
+    ca, sa = cos(a), sin(a)
+    b = 1.0 - f
+    d = b**2*ca**2 - y**2*sa**4 - 2*y**2*sa**2*ca**2 - y**2*ca**4 + sa**2
+    if d >= 0.0:
+        dxl = (-sa*ca - (-y*sa**4 - 2*y*sa**2*ca**2 - y*ca**4)/(b*sqrt(d)) + sa*ca/b**2)/(ca**2 + sa**2/b**2)
+        dxr = (-sa*ca + (-y*sa**4 - 2*y*sa**2*ca**2 - y*ca**4)/(b*sqrt(d)) + sa*ca/b**2)/(ca**2 + sa**2/b**2)
+        return dxl, dxr
+    else:
+        return nan, nan
+
+
+@njit
+def create_ellipse(ny: int, k: float, f: float, a: float) -> (ndarray, ndarray):
+    """Create the coordinates for a rotated ellipse.
 
     Parameters
     ----------
@@ -54,8 +138,7 @@ def create_ellipse(ny: int, k: float, f: float, a: float) -> (ndarray, ndarray):
 
 @njit
 def ellipse_circle_intersection_area(cx: float, cy: float, z: float, k: float, f: float, xs: ndarray, ys: ndarray) -> float:
-    """
-     Calculate the intersection area between a rotated ellipse and a circle using a scanline fill approach.
+    """Calculate the intersection area between a rotated ellipse and a circle using a scanline fill approach.
 
    Parameters
     ----------

pytransit-2.6.8/pytransit/__init__.py

@@ -1,101 +0,0 @@
-#  PyTransit: fast and easy exoplanet transit modelling in Python.
-#  Copyright (C) 2010-2020  Hannu Parviainen
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation, either version 3 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation, either version 3 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-
-"""PyTransit: fast and easy exoplanet transit modelling in Python
-
-This package offers Python interfaces for a set of exoplanet transit light curve
-models implemented in Python (with Numba acceleration) and OpenCL.
-
-Author
-  Hannu Parviainen  <hannu@iac.es>
-
-Date
-  31.01.2024
-
-"""
-
-import warnings
-from numba import NumbaDeprecationWarning
-
-#TODO: Find where we're using generated_jit and fix it...
-
-with warnings.catch_warnings():
-    warnings.simplefilter('ignore', NumbaDeprecationWarning)
-
-    from .version import __version__
-
-    # Generic
-    # -------
-    from .models.transitmodel import TransitModel
-    from .contamination.filter import DeltaFilter, BoxcarFilter, TabulatedFilter, sdss_g, sdss_r, sdss_i, sdss_z
-
-    # Numba models
-    # ------------
-    from .models.qpower2 import QPower2Model
-    from .models.ma_quadratic import QuadraticModel
-    from .models.ma_uniform import UniformModel
-    from .models.eclipse_model import EclipseModel
-    from .models.ma_chromosphere import ChromosphereModel
-    from .models.general import GeneralModel
-    from .models.osmodel import OblateStarModel
-    from .models.gdmodel import GravityDarkenedModel
-
-    from .models import RoadRunnerModel, OblatePlanetModel, TransmissionSpectroscopyModel
-
-    TSModel = TransmissionSpectroscopyModel
-    OPModel = OblatePlanetModel
-    RRModel = RoadRunnerModel
-
-    # OpenCL models
-    # -------------
-    from .models.qpower2_cl import QPower2ModelCL
-    from .models.ma_quadratic_cl import QuadraticModelCL
-    from .models.ma_uniform_cl import UniformModelCL
-
-    # LDTk limb darkening for the Swift model
-    # ---------------------------------------
-
-    from .models.ldtkldm import LDTkLDModel #, LDTkLD
-    from .models.ldtkldm import LDTkLD
-
-    # Log posterior functions
-    # -----------------------
-    from .lpf.lpf import BaseLPF
-    from .lpf.transitlpf import TransitLPF
-    from .lpf.cntlpf import PhysContLPF
-    from .lpf.baselines.legendrebaseline import LegendreBaseline
-    from .lpf.baselines.linearbaseline import LinearModelBaseline
-    from .lpf.transitanalysis import TransitAnalysis
-
-    # Utilities
-    # ---------
-    from .param.parameter import UniformPrior, NormalPrior
-    from .utils import md_rs_from_rho
-    from .utils.mocklc import create_mock_light_curve

pytransit-2.6.8/pytransit/version.py

@@ -1,19 +0,0 @@
-#  PyTransit: fast and easy exoplanet transit modelling in Python.
-#  Copyright (C) 2010-2019  Hannu Parviainen
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation, either version 3 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-from semantic_version import Version
-
-__version__ = Version('2.6.8')