PyTransit 2.6.0__tar.gz → 2.6.3__tar.gz

{PyTransit-2.6.0 → pytransit-2.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyTransit
-Version: 2.6.0
+Version: 2.6.3
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -30,6 +30,7 @@ Requires-Dist: deprecated
 Requires-Dist: uncertainties
 Requires-Dist: pyrr
 Requires-Dist: seaborn
+Requires-Dist: emcee
 
 PyTransit
 =========
@@ -40,14 +41,13 @@ PyTransit
 [![ASCL](https://img.shields.io/badge/ASCL-A1505.024-blue.svg?style=flat)](http://ascl.net/1505.024)
 [![DOI](https://zenodo.org/badge/5871/hpparvi/PyTransit.svg)](https://zenodo.org/badge/latestdoi/5871/hpparvi/PyTransit)
 
-Fast and easy-to-use tools for exoplanet transit light curve modelling with Python. PyTransit offers optimised CPU and 
-GPU implementations of popular exoplanet transit models with a unified interface, and thrives to be *the fastest and the 
-most versatile* tool for transit modelling in Python. 
+*PyTransit: fast and versatile exoplanet transit light curve modelling in Python.* PyTransit provides a set of optimised
+transit models with a unified API that makes modelling complex sets of heterogeneous light curve (nearly) as easy as 
+modelling individual transit light curves. 
+
+The package has been under continuous development since 2009, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
+[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract), and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract). 
 
-PyTransit makes transit model evaluation trivial whether modelling straightforward single-passband transit light curves or
-more complex science-cases, such as transmission spectroscopy. Further, the model can be evaluated for a large set of
-parameter sets simultaneously in parallel to optimize the evaluation speed with population-based MCMC samplers and 
-optimization methods, such as emcee and  DE-MCMC.
 
 ```Python
 from pytransit import RoadRunnerModel
@@ -57,9 +57,9 @@ tm.set_data(times)
 
 tm.evaluate(k=0.1, ldc=[0.2, 0.1], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1, 0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
+tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1], [0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
+tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
             t0=[0.0, 0.01], p=[1, 1], a=[3.0, 2.9], i=[.5*pi, .5*pi])
 ```
 
@@ -67,13 +67,15 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2,
 ![](doc/source/basic_example_2.svg)
 ![](doc/source/basic_example_3.svg)
 
-The package has been used in research since 2010, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
-[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract),
-and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract).
+
 
   
 ## Examples and tutorials
 
+### EMAC Workshop introduction video
+
+[![EMAC Workshop PyTransit introduction video](video1.png)](https://youtu.be/bLnxkFNrMDQ?si=OTjr4kUGK1kkhkLC)
+
 ### RoadRunner transit model
 
 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 
@@ -98,36 +100,6 @@ transmission spectrum light curves.
 
 Read the docs at [pytransit.readthedocs.io](https://pytransit.readthedocs.io).
 
-## News
-- **21.10.2020, version 2.5**
-    - Version 2.5 makes modelling of TTVs trivial with ``pytransit.RoadRunnerModel`` and ``pytransit.QuadraticModel``.
-    - See the [TTV modelling example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/ttv_model_example.ipynb) for an example of how to evaluate the models for a TTV analysis.
-
-- **14.10.2020, version 2.4**
-    - Version 2.4 adds ``pytransit.EclipseModel`` to model secondary eclipses with as little hassle as possible.
-    - See the [secondary eclipse model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/example_eclipse_model.ipynb)
-    for an example of how to use it.
-
-- **16.9.2020, Version 2.3** 
-    - Version 2.3 adds ``OblateStarModel`` to model transits over gravity-darkened rapidly rotating star as presented by Barnes (2009).
-    - See the [oblate star model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/osmodel_example_1.ipynb)
-    for an example of usage.
-
-- **13.9.2020, Version 2.2**
-    - Version 2.2 brings a significant speedup to the evaluation speed of all models. The normalised planet-star distances are
-    now calculated using a Taylor-series expansion of the planet's (x,y) sky-plane position. The method gives a 2-6 x speedup to the transit
-    model evaluation and is detailed in Parviainen & Korth (2020, submitted to MNRAS)
-
-- **7.7.2020, Version 2.1** 
-    - Version 2.1 introduces the *RoadRunner* transit model (Parviainen, submitted to MNRAS, 2020), 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.
-    - See the [basic example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb),
-   the [custom limb darkening notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb),
-   and the [LDTk limb darkening model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb).
-
-
-
 Installation
 ------------
 ### PyPI
@@ -142,7 +114,7 @@ Clone the repository from github and do the normal python package installation
 
     git clone https://github.com/hpparvi/PyTransit.git
     cd PyTransit
-    python setup.py install
+    pip install .
 
 
 Citing

{PyTransit-2.6.0 → pytransit-2.6.3}/PyTransit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PyTransit
-Version: 2.6.0
+Version: 2.6.3
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -30,6 +30,7 @@ Requires-Dist: deprecated
 Requires-Dist: uncertainties
 Requires-Dist: pyrr
 Requires-Dist: seaborn
+Requires-Dist: emcee
 
 PyTransit
 =========
@@ -40,14 +41,13 @@ PyTransit
 [![ASCL](https://img.shields.io/badge/ASCL-A1505.024-blue.svg?style=flat)](http://ascl.net/1505.024)
 [![DOI](https://zenodo.org/badge/5871/hpparvi/PyTransit.svg)](https://zenodo.org/badge/latestdoi/5871/hpparvi/PyTransit)
 
-Fast and easy-to-use tools for exoplanet transit light curve modelling with Python. PyTransit offers optimised CPU and 
-GPU implementations of popular exoplanet transit models with a unified interface, and thrives to be *the fastest and the 
-most versatile* tool for transit modelling in Python. 
+*PyTransit: fast and versatile exoplanet transit light curve modelling in Python.* PyTransit provides a set of optimised
+transit models with a unified API that makes modelling complex sets of heterogeneous light curve (nearly) as easy as 
+modelling individual transit light curves. 
+
+The package has been under continuous development since 2009, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
+[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract), and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract). 
 
-PyTransit makes transit model evaluation trivial whether modelling straightforward single-passband transit light curves or
-more complex science-cases, such as transmission spectroscopy. Further, the model can be evaluated for a large set of
-parameter sets simultaneously in parallel to optimize the evaluation speed with population-based MCMC samplers and 
-optimization methods, such as emcee and  DE-MCMC.
 
 ```Python
 from pytransit import RoadRunnerModel
@@ -57,9 +57,9 @@ tm.set_data(times)
 
 tm.evaluate(k=0.1, ldc=[0.2, 0.1], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1, 0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
+tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1], [0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
+tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
             t0=[0.0, 0.01], p=[1, 1], a=[3.0, 2.9], i=[.5*pi, .5*pi])
 ```
 
@@ -67,13 +67,15 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2,
 ![](doc/source/basic_example_2.svg)
 ![](doc/source/basic_example_3.svg)
 
-The package has been used in research since 2010, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
-[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract),
-and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract).
+
 
   
 ## Examples and tutorials
 
+### EMAC Workshop introduction video
+
+[![EMAC Workshop PyTransit introduction video](video1.png)](https://youtu.be/bLnxkFNrMDQ?si=OTjr4kUGK1kkhkLC)
+
 ### RoadRunner transit model
 
 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 
@@ -98,36 +100,6 @@ transmission spectrum light curves.
 
 Read the docs at [pytransit.readthedocs.io](https://pytransit.readthedocs.io).
 
-## News
-- **21.10.2020, version 2.5**
-    - Version 2.5 makes modelling of TTVs trivial with ``pytransit.RoadRunnerModel`` and ``pytransit.QuadraticModel``.
-    - See the [TTV modelling example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/ttv_model_example.ipynb) for an example of how to evaluate the models for a TTV analysis.
-
-- **14.10.2020, version 2.4**
-    - Version 2.4 adds ``pytransit.EclipseModel`` to model secondary eclipses with as little hassle as possible.
-    - See the [secondary eclipse model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/example_eclipse_model.ipynb)
-    for an example of how to use it.
-
-- **16.9.2020, Version 2.3** 
-    - Version 2.3 adds ``OblateStarModel`` to model transits over gravity-darkened rapidly rotating star as presented by Barnes (2009).
-    - See the [oblate star model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/osmodel_example_1.ipynb)
-    for an example of usage.
-
-- **13.9.2020, Version 2.2**
-    - Version 2.2 brings a significant speedup to the evaluation speed of all models. The normalised planet-star distances are
-    now calculated using a Taylor-series expansion of the planet's (x,y) sky-plane position. The method gives a 2-6 x speedup to the transit
-    model evaluation and is detailed in Parviainen & Korth (2020, submitted to MNRAS)
-
-- **7.7.2020, Version 2.1** 
-    - Version 2.1 introduces the *RoadRunner* transit model (Parviainen, submitted to MNRAS, 2020), 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.
-    - See the [basic example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb),
-   the [custom limb darkening notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb),
-   and the [LDTk limb darkening model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb).
-
-
-
 Installation
 ------------
 ### PyPI
@@ -142,7 +114,7 @@ Clone the repository from github and do the normal python package installation
 
     git clone https://github.com/hpparvi/PyTransit.git
     cd PyTransit
-    python setup.py install
+    pip install .
 
 
 Citing

{PyTransit-2.6.0 → pytransit-2.6.3}/PyTransit.egg-info/requires.txt

@@ -12,3 +12,4 @@ deprecated
 uncertainties
 pyrr
 seaborn
+emcee

{PyTransit-2.6.0 → pytransit-2.6.3}/README.md

@@ -7,14 +7,13 @@ PyTransit
 [![ASCL](https://img.shields.io/badge/ASCL-A1505.024-blue.svg?style=flat)](http://ascl.net/1505.024)
 [![DOI](https://zenodo.org/badge/5871/hpparvi/PyTransit.svg)](https://zenodo.org/badge/latestdoi/5871/hpparvi/PyTransit)
 
-Fast and easy-to-use tools for exoplanet transit light curve modelling with Python. PyTransit offers optimised CPU and 
-GPU implementations of popular exoplanet transit models with a unified interface, and thrives to be *the fastest and the 
-most versatile* tool for transit modelling in Python. 
+*PyTransit: fast and versatile exoplanet transit light curve modelling in Python.* PyTransit provides a set of optimised
+transit models with a unified API that makes modelling complex sets of heterogeneous light curve (nearly) as easy as 
+modelling individual transit light curves. 
+
+The package has been under continuous development since 2009, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
+[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract), and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract). 
 
-PyTransit makes transit model evaluation trivial whether modelling straightforward single-passband transit light curves or
-more complex science-cases, such as transmission spectroscopy. Further, the model can be evaluated for a large set of
-parameter sets simultaneously in parallel to optimize the evaluation speed with population-based MCMC samplers and 
-optimization methods, such as emcee and  DE-MCMC.
 
 ```Python
 from pytransit import RoadRunnerModel
@@ -24,9 +23,9 @@ tm.set_data(times)
 
 tm.evaluate(k=0.1, ldc=[0.2, 0.1], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1, 0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
+tm.evaluate(k=[0.10, 0.12], ldc=[[0.2, 0.1], [0.5, 0.1]], t0=0.0, p=1.0, a=3.0, i=0.5*pi)
 
-tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
+tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1], [0.5, 0.1],[0.4, 0.2, 0.75, 0.1]],
             t0=[0.0, 0.01], p=[1, 1], a=[3.0, 2.9], i=[.5*pi, .5*pi])
 ```
 
@@ -34,13 +33,15 @@ tm.evaluate(k=[[0.10, 0.12], [0.11, 0.13]], ldc=[[0.2, 0.1, 0.5, 0.1],[0.4, 0.2,
 ![](doc/source/basic_example_2.svg)
 ![](doc/source/basic_example_3.svg)
 
-The package has been used in research since 2010, and is described in [Parviainen (2015)](http://arxiv.org/abs/1504.07433), 
-[Parviainen (2020a)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.1633P/abstract),
-and [Parviainen (2020b)](https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3356P/abstract).
+
 
   
 ## Examples and tutorials
 
+### EMAC Workshop introduction video
+
+[![EMAC Workshop PyTransit introduction video](video1.png)](https://youtu.be/bLnxkFNrMDQ?si=OTjr4kUGK1kkhkLC)
+
 ### RoadRunner transit model
 
 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 
@@ -65,36 +66,6 @@ transmission spectrum light curves.
 
 Read the docs at [pytransit.readthedocs.io](https://pytransit.readthedocs.io).
 
-## News
-- **21.10.2020, version 2.5**
-    - Version 2.5 makes modelling of TTVs trivial with ``pytransit.RoadRunnerModel`` and ``pytransit.QuadraticModel``.
-    - See the [TTV modelling example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/ttv_model_example.ipynb) for an example of how to evaluate the models for a TTV analysis.
-
-- **14.10.2020, version 2.4**
-    - Version 2.4 adds ``pytransit.EclipseModel`` to model secondary eclipses with as little hassle as possible.
-    - See the [secondary eclipse model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/example_eclipse_model.ipynb)
-    for an example of how to use it.
-
-- **16.9.2020, Version 2.3** 
-    - Version 2.3 adds ``OblateStarModel`` to model transits over gravity-darkened rapidly rotating star as presented by Barnes (2009).
-    - See the [oblate star model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/osmodel_example_1.ipynb)
-    for an example of usage.
-
-- **13.9.2020, Version 2.2**
-    - Version 2.2 brings a significant speedup to the evaluation speed of all models. The normalised planet-star distances are
-    now calculated using a Taylor-series expansion of the planet's (x,y) sky-plane position. The method gives a 2-6 x speedup to the transit
-    model evaluation and is detailed in Parviainen & Korth (2020, submitted to MNRAS)
-
-- **7.7.2020, Version 2.1** 
-    - Version 2.1 introduces the *RoadRunner* transit model (Parviainen, submitted to MNRAS, 2020), 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.
-    - See the [basic example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_1.ipynb),
-   the [custom limb darkening notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_2.ipynb),
-   and the [LDTk limb darkening model example notebook](https://github.com/hpparvi/PyTransit/blob/master/notebooks/roadrunner/roadrunner_model_example_3.ipynb).
-
-
-
 Installation
 ------------
 ### PyPI
@@ -109,7 +80,7 @@ Clone the repository from github and do the normal python package installation
 
     git clone https://github.com/hpparvi/PyTransit.git
     cd PyTransit
-    python setup.py install
+    pip install .
 
 
 Citing

{PyTransit-2.6.0 → pytransit-2.6.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "PyTransit"
-version = "2.6.0"
+version = "2.6.3"
 description = 'Fast and painless exoplanet transit light curve modelling.'
 authors=[{name='Hannu Parviainen', email='hpparvi@gmail.com'}]
 classifiers=[
@@ -14,7 +14,7 @@ classifiers=[
 ]
 keywords = ['astronomy',  'astrophysics',  'exoplanets']
 dependencies = ["numpy", "numba", "scipy", "pandas", "xarray", "tables", "meepmeep", "pyopencl", "ldtk",
-                "semantic_version", "deprecated", "uncertainties", "pyrr", "seaborn"]
+                "semantic_version", "deprecated", "uncertainties", "pyrr", "seaborn", "emcee"]
 requires-python = ">= 3.8"
 readme = "README.md"
 license = {text = "GPLv2"}
@@ -32,7 +32,3 @@ include-package-data = true
 [tool.setuptools.packages.find]
 include = ["pytransit"]
 namespaces = true
-
-#[tool.setuptools.package-data]
-#"pytransit.contamination.data" = ["*.nc"]
-#"pytransit" = ["*.fits", "*.txt", "*.csv", "*.h5", "*.nc", "*.cl"]

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/__init__.py

@@ -64,12 +64,13 @@ with warnings.catch_warnings():
     from .models.eclipse_model import EclipseModel
     from .models.ma_chromosphere import ChromosphereModel
     from .models.general import GeneralModel
-    from .models.roadrunner.rrmodel import RoadRunnerModel
-    from .models.roadrunner.tsmodel import TransmissionSpectroscopyModel
     from .models.osmodel import OblateStarModel
     from .models.gdmodel import GravityDarkenedModel
 
+    from .models import RoadRunnerModel, OblatePlanetModel, TransmissionSpectroscopyModel
+
     TSModel = TransmissionSpectroscopyModel
+    OPModel = OblatePlanetModel
     RRModel = RoadRunnerModel
 
     # OpenCL models

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/models/__init__.py

@@ -14,4 +14,11 @@
 #  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 .transitmodel import TransitModel
+from .transitmodel import TransitModel
+from .roadrunner.rrmodel import RoadRunnerModel
+from .roadrunner.opmodel import OblatePlanetModel
+from .roadrunner.tsmodel import TransmissionSpectroscopyModel
+
+RRModel = RoadRunnerModel
+OPModel = OblatePlanetModel
+TSModel = TransmissionSpectroscopyModel

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/models/ldtkldm.py

@@ -22,6 +22,7 @@ from numpy import zeros, interp, pi, ndarray, linspace, meshgrid, transpose
 from scipy.interpolate import interpn, interpnd, RegularGridInterpolator as RGI
 
 from .ldmodel import LDModel
+from .numba.ldtkldm import trilinear_interpolation_set, integrate_profiles_set
 
 try:
     from ldtk import LDPSetCreator
@@ -53,33 +54,31 @@ class LDTkLDModel(LDModel):
         self.profiles = None
         self.rgi = None
 
-    def _init_interpolation(self, mu, nteff, nlogg, nz):
+    def _init_interpolation(self, mu):
         self.mu = mu
         self.nmu = mu.size
         c = self.sc.client
 
-        teffs = linspace(*c.teffl, nteff)
-        loggs = linspace(*c.loggl, nlogg)
-        zs = linspace(*c.zl, nz)
+        teffs = linspace(*c.teffl, self.sc.client.nteff)
+        loggs = linspace(*c.loggl, self.sc.client.nlogg)
+        zs = linspace(*c.zl, self.sc.client.nz)
         teffg, loggg, zg = meshgrid(teffs, loggs, zs)
+        self.teff0, self.dteff, self.nteff = teffs[0], teffs[1]-teffs[0], self.sc.client.nteff
+        self.logg0, self.dlogg, self.nlogg = loggs[0], loggs[1]-loggs[0], self.sc.client.nlogg
+        self.metal0, self.dmetal, self.nmetal = zs[0], zs[1]-zs[0], self.sc.client.nz
 
         self.ps = self.sc.create_profiles(teff=teffg.ravel(), logg=loggg.ravel(), metal=zg.ravel())
         self.ps.resample(mu=self.mu)
-        self.profiles = transpose(self.ps._ldps.copy(), axes=(1, 0, 2)).reshape((nteff, nlogg, nz, self.npb, self.nmu))
-        self.rgi = RGI((teffs, loggs, zs), self.profiles)
+        self.profiles = transpose(self.ps._ldps.copy(), axes=(1, 0, 2)).reshape((self.nteff, self.nlogg, self.nmetal, self.npb, self.nmu))
 
     def __call__(self, mu: ndarray, x: ndarray) -> Tuple[ndarray, ndarray]:
         if self.mu is None or id(mu) != id(self.mu):
-            self._init_interpolation(mu, 5, 3, 3)
-
-        npv = x.shape[0]
-        z = self.ps._z
-        ldp = zeros((npv, self.npb, self.nmu))
-        ldi = zeros((npv, self.npb))
-        for ipv in range(npv):
-            ldp[ipv] = self.rgi(x[ipv])
-            for ipb in range(self.npb):
-                ldi[ipv, ipb] = 2 * pi * ntrapz(z, z * ldp[ipv, ipb, :])
+            self._init_interpolation(mu)
+        ldp = trilinear_interpolation_set(self.profiles, x[:, 0, 0], x[:, 0, 1], x[:, 0, 2],
+                                          self.teff0, self.dteff, self.nteff,
+                                          self.logg0, self.dlogg, self.nlogg,
+                                          self.metal0, self.dmetal, self.nmetal)
+        ldi = integrate_profiles_set(self.mu, ldp)
         return ldp, ldi
 
     def _evaluate(self, mu: ndarray, x: ndarray) -> ndarray:

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/models/roadrunner/model_trspec.py

@@ -83,3 +83,79 @@ def tsmodel_serial(times: ndarray,
                         flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * aplanet * afac[ipb]) / istar[ipv, ipb]
                 flux[ipv, :, ipt] /= nsamples[0]
     return flux
+
+
+@njit(parallel=True, fastmath=False)
+def tsmodel_parallel(times: ndarray,
+                   k: ndarray, t0: ndarray, p: ndarray, a: ndarray, i: ndarray, e: ndarray, w: ndarray,
+                   nsamples: ndarray, exptimes: ndarray, ldp: ndarray, istar: ndarray,
+                   weights: ndarray, dk: float, kmin: float, kmax: float, dg: float, z_edges: ndarray) -> ndarray:
+    if k.ndim != 2:
+        raise ValueError(" The radius ratios must be given as a 2D array with shape (npv, npb)")
+
+    if ldp.ndim != 3:
+        raise ValueError("The limb darkening profiles must be given as a 3D array with shape (npv, npb, nmu)")
+
+    if k.shape[1] != ldp.shape[1]:
+        raise ValueError("The transmission spectrum transit model requires that the number or radius ratios and the number of passbands match.")
+
+    npt = times.size
+    npv = k.shape[0]
+    npb = k.shape[1]
+    ng = weights.shape[1]
+
+    flux = zeros((npv, npb, npt))  # Model flux
+    ldm = zeros((npb, ng))         # Limb darkening means
+    xyc = zeros((2, 5))            # Taylor series coefficients for the (x, y) position
+
+    for ipv in prange(npv):
+        if isnan(a[ipv]) or (a[ipv] <= 1.0) or (e[ipv] < 0.0):
+            flux[ipv, :, :] = nan
+            continue
+
+        kmean = mean(k[ipv])
+        afac = k[ipv] ** 2 / kmean ** 2
+
+        # -----------------------------------#
+        # Calculate the limb darkening means #
+        # -----------------------------------#
+        if kmin <= kmean <= kmax:
+            ik = int(floor((kmean - kmin) / dk))
+            ak = (kmean - kmin - ik * dk) / dk
+            for ipb in range(npb):
+                ldm[ipb, :] = (1.0 - ak) * dot(weights[ik], ldp[ipv, ipb, :]) + ak * dot(weights[ik + 1],
+                                                                                         ldp[ipv, ipb, :])
+        else:
+            _, _, wg = calculate_weights_2d(kmean, z_edges, ng)
+            for ipb in range(npb):
+                ldm[ipb, :] = dot(wg, ldp[ipv, ipb, :])
+
+        # -----------------------------------------------------#
+        # Calculate the Taylor series expansions for the orbit #
+        # -----------------------------------------------------#
+        xyc[:, :] = solve_xy_p5s(0.0, p[ipv], a[ipv], i[ipv], e[ipv], w[ipv])
+
+        # --------------------------------#
+        # Calculate the half-window width #
+        # --------------------------------#
+        hww = 0.5 * d_from_pkaiews(p[ipv], kmean, a[ipv], i[ipv], e[ipv], w[ipv], 1, 14)
+        hww = 0.0015 + exptimes[0] + hww
+
+        # --------------------------#
+        # Calculate the light curve #
+        # --------------------------#
+        for ipt in range(npt):
+            epoch = floor((times[ipt] - t0[ipv] + 0.5 * p[ipv]) / p[ipv])
+            tc = times[ipt] - (t0[ipv] + epoch * p[ipv])
+            if fabs(tc) > hww:
+                flux[ipv, :, ipt] = 1.0
+            else:
+                for isample in range(1, nsamples[0] + 1):
+                    time_offset = exptimes[0] * ((isample - 0.5) / nsamples[0] - 0.5)
+                    z = pd_t15sc(tc + time_offset, xyc)
+                    aplanet = ccia(1.0, kmean, z)[0]
+                    for ipb in range(npb):
+                        iplanet = interpolate_mean_limb_darkening_s(z / (1.0 + kmean), dg, ldm[ipb])
+                        flux[ipv, ipb, ipt] += (istar[ipv, ipb] - iplanet * aplanet * afac[ipb]) / istar[ipv, ipb]
+                flux[ipv, :, ipt] /= nsamples[0]
+    return flux

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/models/roadrunner/tsmodel.py

@@ -36,7 +36,7 @@ from ..ldmodel import LDModel
 from ..numba.ldmodels import *
 from .rrmodel import RoadRunnerModel
 
-from .model_trspec import tsmodel_serial
+from .model_trspec import tsmodel_serial, tsmodel_parallel
 
 __all__ = ['TransmissionSpectroscopyModel']
 
@@ -46,7 +46,7 @@ class TransmissionSpectroscopyModel(RoadRunnerModel):
     def evaluate(self, k: Union[float, ndarray], ldc: Union[ndarray, List],
                  t0: Union[float, ndarray], p: Union[float, ndarray], a: Union[float, ndarray],
                  i: Union[float, ndarray], e: Union[float, ndarray] = 0.0, w: Union[float, ndarray] = 0.0,
-                 copy: bool = True) -> ndarray:
+                 copy: bool = True, parallel: bool = False) -> ndarray:
         """Evaluate the transit model for a set of scalar or vector parameters.
 
         Parameters
@@ -115,8 +115,13 @@ class TransmissionSpectroscopyModel(RoadRunnerModel):
                         istar[ipv, ipb] = 2 * pi * trapz(self._ldz * ldpi[ipv, ipb], self._ldz)
 
         dk, dg, weights = calculate_weights_3d(self.nk, self.klims[0], self.klims[1], self.ze, self.ng)
-        flux = tsmodel_serial(self.time, k, t0, p, a, i, e, w, self.nsamples, self.exptimes,
-                              ldp, istar, weights, dk, self.klims[0], self.klims[1], dg, self.ze)
+
+        if parallel:
+            flux = tsmodel_parallel(self.time, k, t0, p, a, i, e, w, self.nsamples, self.exptimes,
+                                  ldp, istar, weights, dk, self.klims[0], self.klims[1], dg, self.ze)
+        else:
+            flux = tsmodel_serial(self.time, k, t0, p, a, i, e, w, self.nsamples, self.exptimes,
+                                  ldp, istar, weights, dk, self.klims[0], self.klims[1], dg, self.ze)
 
         return flux.squeeze()
 

{PyTransit-2.6.0 → pytransit-2.6.3}/pytransit/utils/keplerlc.py

@@ -79,7 +79,7 @@ class KeplerLC(object):
 
         # Remove orbits with too big ptp range
         # ------------------------------------
-        msk_inc = ones(self.npt, np.bool)
+        msk_inc = ones(self.npt, bool)
         for tid,ptp in enumerate(list(map(np.ptp, self.normalized_flux_per_transit))):
             if ptp > self.max_ptp:
                 msk_inc[self.tidarr==tid] = 0
@@ -116,7 +116,7 @@ class KeplerLC(object):
 
     def remove_common_orbits(self, lc2):
         is_unique = ~np.in1d(self.orbit_n, lc2.orbit_n)
-        mask = np.ones(self.npt, np.bool)
+        mask = np.ones(self.npt, bool)
         for tid,include in enumerate(is_unique):
             mask[self.tslices[tid]] = include
         self._compress_data(mask)