From ec28a1e69a8cedc0763888dae5d045d33dc73aea Mon Sep 17 00:00:00 2001 From: "Brett M. Morris" Date: Fri, 20 Mar 2026 11:41:39 -0400 Subject: [PATCH 1/3] prevent numpy deprecation warnings --- fleck/core.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/fleck/core.py b/fleck/core.py index 1482229..d4447a0 100644 --- a/fleck/core.py +++ b/fleck/core.py @@ -91,6 +91,13 @@ def ellipse(center, lengths, angle=0): """ ell = affinity.scale(Point(center).buffer(1), xfact=lengths[0], yfact=lengths[1]) + + # deprecations in numpy v1.25 drop support for vector + # `angle` in this shapely call. extract the first + # value in `angle` if it has ndim > 0 + if hasattr(angle, 'flat'): + angle = angle.flat[0] + ell_rotated = affinity.rotate(ell, angle=angle) return ell_rotated @@ -372,7 +379,7 @@ def spherical_to_cartesian(self, spot_lons, spot_lats, inc_stellar, # Generate array of rotation matrices to rotate the spots so that the # planet's orbit normal is tilted with respect to stellar spin - tilt = rotation_matrix(-lam, axis='x') + tilt = rotation_matrix(lam, axis='x') tilted_spots = inclined_spots.transform(tilt) return tilted_spots @@ -633,8 +640,9 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, spot_z = tilted_spots.z.value[0, i] # Compute the spot position and ellipsoidal shape - r_spot = np.hypot(spot_z, spot_y) - angle = np.arctan2(spot_z, spot_y) + r_spot = np.hypot(spot_z, spot_y)[0] + angle = np.arctan2(spot_z, spot_y)[0] + ellipse_centroid = np.array([ np.squeeze(spot_y), np.squeeze(spot_z) @@ -704,15 +712,15 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, # If pole is visible, mark it: if polar_spot.x > 0: - ax.scatter(-polar_spot.y, polar_spot.z, color='k', marker='x') + ax.scatter(polar_spot.y, polar_spot.z, color='k', marker='x') # Where equator is visible, mark it: equator_visible = equatorial_line.x > 0 - equator_xy = np.vstack([-equatorial_line.y[equator_visible], + equator_xy = np.vstack([equatorial_line.y[equator_visible], equatorial_line.z[equator_visible]]).T sort_equator = sort_plot_points(equator_xy, k0=np.argmax(equator_xy[:, 1])) - ax.plot(-equatorial_line.y[equator_visible][sort_equator], + ax.plot(equatorial_line.y[equator_visible][sort_equator], equatorial_line.z[equator_visible][sort_equator], ls=':', color='gray') From bf066de2df7c83b92b3f4312c040210e86b3ba25 Mon Sep 17 00:00:00 2001 From: "Brett M. Morris" Date: Tue, 24 Mar 2026 11:07:03 -0400 Subject: [PATCH 2/3] major refactor to correct projected spin-orbit angle --- fleck/core.py | 109 +-- fleck/data/README.rst | 7 - fleck/data/stsp_00.txt | 500 ++++++++++++++ fleck/data/stsp_01.txt | 500 ++++++++++++++ fleck/data/stsp_02.txt | 500 ++++++++++++++ fleck/data/stsp_03.txt | 500 ++++++++++++++ fleck/data/stsp_04.txt | 500 ++++++++++++++ fleck/data/stsp_05.txt | 500 ++++++++++++++ fleck/data/stsp_06.txt | 500 ++++++++++++++ fleck/data/stsp_07.txt | 500 ++++++++++++++ fleck/data/stsp_08.txt | 500 ++++++++++++++ fleck/data/stsp_09.txt | 500 ++++++++++++++ fleck/data/stsp_10.txt | 500 ++++++++++++++ fleck/data/stsp_11.txt | 500 ++++++++++++++ fleck/data/stsp_12.txt | 500 ++++++++++++++ fleck/data/stsp_13.txt | 500 ++++++++++++++ fleck/data/stsp_double_transit.txt | 1000 ---------------------------- fleck/data/stsp_rotation.txt | 1000 ---------------------------- fleck/data/stsp_single_transit.txt | 500 -------------- fleck/extern/__init__.py | 7 - fleck/tests/stsp.py | 201 ++++++ fleck/tests/test_core.py | 246 ++++--- fleck/utils/__init__.py | 4 - fleck/utils/tests/__init__.py | 0 pyproject.toml | 9 +- tox.ini | 7 +- 26 files changed, 7409 insertions(+), 2681 deletions(-) delete mode 100644 fleck/data/README.rst create mode 100644 fleck/data/stsp_00.txt create mode 100644 fleck/data/stsp_01.txt create mode 100644 fleck/data/stsp_02.txt create mode 100644 fleck/data/stsp_03.txt create mode 100644 fleck/data/stsp_04.txt create mode 100644 fleck/data/stsp_05.txt create mode 100644 fleck/data/stsp_06.txt create mode 100644 fleck/data/stsp_07.txt create mode 100644 fleck/data/stsp_08.txt create mode 100644 fleck/data/stsp_09.txt create mode 100644 fleck/data/stsp_10.txt create mode 100644 fleck/data/stsp_11.txt create mode 100644 fleck/data/stsp_12.txt create mode 100644 fleck/data/stsp_13.txt delete mode 100644 fleck/data/stsp_double_transit.txt delete mode 100644 fleck/data/stsp_rotation.txt delete mode 100644 fleck/data/stsp_single_transit.txt delete mode 100644 fleck/extern/__init__.py create mode 100644 fleck/tests/stsp.py delete mode 100644 fleck/utils/__init__.py delete mode 100644 fleck/utils/tests/__init__.py diff --git a/fleck/core.py b/fleck/core.py index d4447a0..89f237f 100644 --- a/fleck/core.py +++ b/fleck/core.py @@ -232,6 +232,12 @@ def light_curve(self, spot_lons, spot_lats, spot_radii, inc_stellar, Stellar light curves of shape ``(n_phases, len(inc_stellar))`` or ``(len(times), len(inc_stellar))`` """ + # in case these inputs are not 2D, make them so: + spot_lons, spot_lats, spot_radii = [ + np.atleast_2d(arr) + for arr in [spot_lons, spot_lats, spot_radii] + ] + if time_ref is None: if times is not None: time_ref = 0 @@ -266,7 +272,7 @@ def light_curve(self, spot_lons, spot_lats, spot_radii, inc_stellar, # Compute a transit model from batman import TransitModel - n_spots = len(spot_lons) + n_spots = spot_lons.shape[1] m = TransitModel(planet, times, **transit_model_kwargs) lambda_e = 1 - m.light_curve(planet)[:, np.newaxis] # Compute the true anomaly of the planet at each time, f: @@ -310,11 +316,11 @@ def light_curve(self, spot_lons, spot_lats, spot_radii, inc_stellar, # Return the flux missing from the star at each time due to spots # (f_spots/self.f0) and due to the transit (lambda_e): if return_spots_occulted: - return (1 - np.sum(f_spots.filled(0)/self.f0, axis=1) - lambda_e, + return (1 - np.sum(f_spots.filled(0)/self.f0, axis=2) - lambda_e, spots_occulted) else: - return 1 - np.sum(f_spots.filled(0)/self.f0, axis=1) - lambda_e + return 1 - np.sum(f_spots.filled(0)/self.f0, axis=2) - lambda_e def spherical_to_cartesian(self, spot_lons, spot_lats, inc_stellar, times=None, planet=None, time_ref=None): @@ -360,7 +366,7 @@ def spherical_to_cartesian(self, spot_lons, spot_lats, inc_stellar, else: if time_ref is None: time_ref = 0 - rotational_phase = 2 * np.pi * ((times - time_ref) / + rotational_phase = 2 * np.pi * ((time_ref - times) / self.rotation_period) * u.rad rotate = rotation_matrix(rotational_phase[:, np.newaxis, np.newaxis], axis='z') @@ -539,9 +545,9 @@ def _planet_spot_overlap_slow(self, planet, planet_disk, tilted_spots, for i in range(n_spots): # If the spot is visible (x > 0): - if tilted_spots.x.value[k, i] > 0: - spot_y = tilted_spots.y.value[k, i] - spot_z = tilted_spots.z.value[k, i] + if tilted_spots.x.value[k, 0, i] > 0: + spot_y = tilted_spots.y.value[k, 0, i] + spot_z = tilted_spots.z.value[k, 0, i] # Compute the spot position and ellipsoidal shape r_spot = np.hypot(spot_z, spot_y) @@ -552,11 +558,9 @@ def _planet_spot_overlap_slow(self, planet, planet_disk, tilted_spots, ]) ellipse_axes = np.array([ - np.squeeze(spot_radii[i, 0] * - np.sqrt(1 - r_spot ** 2)), - np.squeeze(spot_radii[i, 0]) + spot_radii[:, i] * np.sqrt(1 - r_spot ** 2), + spot_radii[:, i] ]) - spot = ellipse(ellipse_centroid, ellipse_axes, np.degrees(angle)) @@ -573,7 +577,6 @@ def _planet_spot_overlap_slow(self, planet, planet_disk, tilted_spots, # Compute the overlap between each spot and the # planet using shapely's `intersection` method spot_planet_overlap = planet_disk_i.intersection(spots[j]).area - intersections[j] = ((1 - self.spot_contrast) / spot_ld_factors[j] * spot_planet_overlap / @@ -626,22 +629,26 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, ax : `~matplotlib.pyplot.Axes` Axis object. """ + # in case these inputs are not 2D, make them so: + spot_lons, spot_lats, spot_radii = [ + np.atleast_2d(arr) + for arr in [spot_lons, spot_lats, spot_radii] + ] tilted_spots = self.spherical_to_cartesian(spot_lons, spot_lats, inc_stellar, times=np.array([time]), planet=planet, time_ref=time_ref) spots = [] - - for i in range(len(spot_lons)): + for i in range(spot_lons.shape[1]): # If the spot is visible (x > 0): - if tilted_spots.x.value[0, i] > 0: - spot_y = tilted_spots.y.value[0, i] - spot_z = tilted_spots.z.value[0, i] + if tilted_spots.x.value[0, 0, i] > 0: + spot_y = tilted_spots.y.value[0, 0, i] + spot_z = tilted_spots.z.value[0, 0, i] # Compute the spot position and ellipsoidal shape - r_spot = np.hypot(spot_z, spot_y)[0] - angle = np.arctan2(spot_z, spot_y)[0] + r_spot = np.hypot(spot_z, spot_y) + angle = np.arctan2(spot_z, spot_y) ellipse_centroid = np.array([ np.squeeze(spot_y), @@ -649,9 +656,9 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, ]) ellipse_axes = np.array([ - np.squeeze(spot_radii[i, 0] * + np.squeeze(spot_radii[0, i] * np.sqrt(1 - r_spot ** 2)), - np.squeeze(spot_radii[i, 0]) + np.squeeze(spot_radii[0, i]) ]) spot = ellipse(ellipse_centroid, ellipse_axes, @@ -676,8 +683,8 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, planet_lower_extent = -b-p.rp planet_upper_extent = -b+p.rp - ax.axhline(planet_lower_extent, color=color, ls='--') - ax.axhline(planet_upper_extent, color=color, ls='--') + ax.axhline(planet_lower_extent, color=color, ls='--', lw=0.75) + ax.axhline(planet_upper_extent, color=color, ls='--', lw=0.75) elif hasattr(planet, 'a'): # Calculate impact parameter b = (planet.a * np.cos(np.radians(planet.inc)) * (1 - planet.ecc**2) / @@ -688,17 +695,29 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, planet_lower_extent = -b-planet.rp planet_upper_extent = -b+planet.rp - ax.axhline(planet_lower_extent, color='gray', ls='--') - ax.axhline(planet_upper_extent, color='gray', ls='--') + ax.axhline(planet_lower_extent, color='gray', ls='--', lw=0.75) + ax.axhline(planet_upper_extent, color='gray', ls='--', lw=0.75) # Compute the position of the rotational pole of the star - pole_lat, pole_lon = np.array([90])*u.deg, np.array([0])*u.deg - polar_spot = self.spherical_to_cartesian(pole_lon, pole_lat, - inc_stellar, - times=np.array([0]), - planet=planet) - - equator_lon = np.linspace(0, 2*np.pi, 50) * u.rad + north_pole_lon, north_pole_lat = np.array([0])*u.deg, np.array([90])*u.deg + north_polar_spot = self.spherical_to_cartesian( + north_pole_lon, + north_pole_lat, + inc_stellar, + times=np.array([0]), + planet=planet + ) + + south_pole_lon, south_pole_lat = np.array([0])*u.deg, np.array([-90])*u.deg + south_polar_spot = self.spherical_to_cartesian( + south_pole_lon, + south_pole_lat, + inc_stellar, + times=np.array([0]), + planet=planet + ) + + equator_lon = np.linspace(0, 2*np.pi, 100) * u.rad equator_lat = np.zeros(len(equator_lon)) * u.rad equatorial_line = self.spherical_to_cartesian(equator_lon, equator_lat, inc_stellar, @@ -710,19 +729,21 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, ax.plot(x, np.sqrt(1-x**2), color='k') ax.plot(x, -np.sqrt(1-x**2), color='k') - # If pole is visible, mark it: - if polar_spot.x > 0: - ax.scatter(polar_spot.y, polar_spot.z, color='k', marker='x') + # If north pole is visible, mark it: + if north_polar_spot.x > 0: + ax.scatter(north_polar_spot.y, north_polar_spot.z, color='k', marker='x') + + # If south pole is visible, mark it: + if south_polar_spot.x > 0: + ax.scatter(south_polar_spot.y, south_polar_spot.z, color='dodgerblue', marker='+') # Where equator is visible, mark it: - equator_visible = equatorial_line.x > 0 - equator_xy = np.vstack([equatorial_line.y[equator_visible], - equatorial_line.z[equator_visible]]).T - sort_equator = sort_plot_points(equator_xy, - k0=np.argmax(equator_xy[:, 1])) - ax.plot(equatorial_line.y[equator_visible][sort_equator], - equatorial_line.z[equator_visible][sort_equator], - ls=':', color='gray') + equator_visible = equatorial_line.x >= 0 + ax.scatter( + equatorial_line.y[equator_visible], + equatorial_line.z[equator_visible], + marker='s', color='gray', s=1, zorder=-10 + ) ax.set(ylim=[-1.01, 1.01], xlim=[-1.01, 1.01], aspect=1) @@ -731,7 +752,7 @@ def plot(self, spot_lons, spot_lats, spot_radii, inc_stellar, time=None, spot_x, spot_y = [np.array(j.tolist()) for j in spots[i].exterior.xy] ax.fill(spot_x, spot_y, alpha=1-self.spot_contrast, - color='k') + color='k', zorder=10) return ax diff --git a/fleck/data/README.rst b/fleck/data/README.rst deleted file mode 100644 index 9cc3b1a..0000000 --- a/fleck/data/README.rst +++ /dev/null @@ -1,7 +0,0 @@ -Data directory -============== - -This directory contains data files included with the package source -code distribution. Note that this is intended only for relatively small files -- large files should be externally hosted and downloaded as needed. - diff --git a/fleck/data/stsp_00.txt b/fleck/data/stsp_00.txt new file mode 100644 index 0000000..560bfbc --- /dev/null +++ b/fleck/data/stsp_00.txt @@ -0,0 +1,500 @@ +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979259999999999797e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 +9.979249999999999510e-01 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deleted file mode 100644 index d0c13ab..0000000 --- a/fleck/extern/__init__.py +++ /dev/null @@ -1,7 +0,0 @@ -# Licensed under a 3-clause BSD style license - see LICENSE.rst -""" -This packages contains python packages that are bundled with the package but -are external to it, and hence are developed in a separate source tree. Note -that this package is distinct from the /cextern directory of the source code -distribution, as that directory only contains C extension code. -""" diff --git a/fleck/tests/stsp.py b/fleck/tests/stsp.py new file mode 100644 index 0000000..fa7536a --- /dev/null +++ b/fleck/tests/stsp.py @@ -0,0 +1,201 @@ +# Licensed under the MIT License - see LICENSE.rst +import tempfile +import os +import subprocess + +import numpy as np + +from astropy.table import Table +import astropy.units as u +from astropy.constants import G, M_sun, R_sun + + +# path to STSP executable: +stsp_executable = os.getenv('STSP_PATH') + +infile_template_l = ("""#PLANET PROPERTIES +1 ; Number of planets +{t0:2.10f} ; T0, epoch (middle of first transit) in days. +{period:2.10f} ; Planet Period (days) +{depth:2.10f} ; (Rp/Rs)^2 (Rplanet / Rstar )^ 2 +{duration:2.10f} ; Duration (days) (physical duration of transit, not used) +{b:2.10f} ; Impact parameter (0= planet cross over equator) +{inclination:2.10f} ; Inclination angle of orbit (90 deg = transit equator) +{lam:2.10f} ; Lambda of orbit (0 deg = orbital axis along z-axis) +{ecosw:2.10f} ; ecosw +{esinw:2.10f} ; esinw +#STAR PROPERTIES +{rho_s:2.10f} ; Mean Stellar density (Msun/Rsun^3) +{per_rot:2.10f} ; Stellar Rotation period (days) +4780 ; Stellar Temperature +0.31 ; Stellar metallicity +{tilt_from_z:2.10f} ; Tilt of stellar rotation axis down from z-axis (deg) +{nonlinear_ld} ; Limb darkening (4 coefficients) +{n_ld_rings:d} ; number of rings for limb darkening appoximation +#SPOT PROPERTIES +{n_spots} ; number of spots +{contrast} ; fractional lightness of spots (0.0=total dark, 1.0=no contrast) +#LIGHT CURVE +{model_path} ; lightcurve input data file +{start_time:2.10f} ; start time to start fitting the light curve +{lc_duration:2.10f} ; duration of light curve to fit (days) +{real_max:2.10f} ; real max of LC, 0 -> use downfrommax +0 ; is light curve flattened (to zero) outside of transits? +#ACTION +l ; l= generate light curve from parameters +{spot_params} +1.00 +""") + +spot_params_template = """{spot_radius:2.10f} ; spot radius +{spot_theta:2.10f} ; theta +{spot_phi:2.10f} ; phi +""" + + +def quadratic_to_nonlinear(u1, u2): + a1 = a3 = 0 + a2 = u1 + 2*u2 + a4 = -u2 + return (a1, a2, a3, a4) + + +def rho_star(transit_params): + aRs = transit_params.a + + rho_s = 3*np.pi/(G*(transit_params.per*u.day)**2) * aRs**3 + rho_s = rho_s.to(M_sun/(4./3 * np.pi * R_sun**3)) + return rho_s.value + + +class STSP(object): + def __init__(self, lc, transit_params, spot_params, outdir=None): + """ + Parameters + ---------- + lc : `LightCurve` + Light curve object + transit_params : `batman.TransitParams` + Parameters for planet and star + spot_params : `numpy.ndarray` + [r, theta, phi] for each spot to model with STSP + outdir : str + Directory to write temporary outputs into + """ + self.lc = lc + self.transit_params = transit_params + self.spot_params = np.atleast_2d(spot_params) + + def stsp_lc( + self, + contrast=0.7, + n_ld_rings=100, + real_max=1, + verbose=False, + stsp_exec=None): + + if stsp_exec is None: + stsp_exec = stsp_executable + + with tempfile.TemporaryDirectory() as tmp_dir: + times = self.lc.times.jd + fluxes = np.ones_like(times) + model_path = os.path.join(tmp_dir, 'model_lc.dat') + np.savetxt(model_path, + np.vstack([times, fluxes, + 0 * fluxes]).T, + fmt='%1.10f', delimiter='\t', header='stspinputs') + + # Calculate parameters for STSP: + eccentricity = self.transit_params.ecc + omega = self.transit_params.w + ecosw = eccentricity * np.cos(np.radians(omega)) + esinw = eccentricity * np.sin(np.radians(omega)) + start_time = times[0] + lc_duration = times[-1] - times[0] + nonlinear_ld = quadratic_to_nonlinear(*self.transit_params.u) + nonlinear_ld_string = ' '.join(map("{0:.5f}".format, nonlinear_ld)) + + # get spot parameters sorted out + spot_params_str = spot_params_to_string(self.spot_params) + + # Stick those values into the template file + b = ( + self.transit_params.a * + np.cos(np.radians(self.transit_params.inc)) + ) + duration = duration_t14(self.transit_params) + in_file_text = infile_template_l.format( + contrast=contrast, + period=self.transit_params.per, + ecosw=ecosw, + esinw=esinw, + lam=self.transit_params.lam, + tilt_from_z=90-self.transit_params.inc_stellar, + start_time=start_time, + lc_duration=lc_duration, + real_max=real_max, + per_rot=self.transit_params.per_rot, + rho_s=rho_star(self.transit_params), + depth=self.transit_params.rp**2, + duration=duration, + t0=self.transit_params.t0, + b=b, + inclination=self.transit_params.inc, + nonlinear_ld=nonlinear_ld_string, + n_ld_rings=n_ld_rings, + spot_params=spot_params_str[:-1], + n_spots=self.spot_params.shape[0], + model_path=os.path.basename(model_path) + ) + + # Write out the `.in` file + with open(os.path.join(tmp_dir, 'test.in'), 'w') as in_file: + in_file.write(in_file_text) + + # Run STSP + old_cwd = os.getcwd() + os.chdir(tmp_dir) + completed = subprocess.run( + [stsp_exec, 'test.in'], + capture_output=True + ) + if verbose: + print(completed.stdout) + os.chdir(old_cwd) + + # Read the outputs + lc_out = os.path.join(tmp_dir, 'test_lcout.txt') + tbl = Table.read(lc_out, format='ascii') + # tbl.write('~/Desktop/tmp.csv', overwrite=True) + stsp_times = np.array(tbl[tbl.colnames[0]]) + stsp_fluxes = np.array(tbl[tbl.colnames[3]]) + return stsp_times, stsp_fluxes + + +def spot_params_to_string(spot_params): + spot_params_str = "" + spot_params = np.atleast_2d(spot_params) + for param_set in spot_params: + spot_params_str += spot_params_template.format( + spot_radius=param_set[0], + spot_theta=param_set[1], + spot_phi=param_set[2] + ) + return spot_params_str + + +def duration_t14(transit_params): + """transit 1-4 contact duration""" + inc = np.radians(transit_params.inc) + b = transit_params.a * np.cos(inc) + return ( + transit_params.per / np.pi * + np.arcsin( + np.sqrt((1 - transit_params.rp)**2 - b**2) / + (transit_params.a * np.sin(inc)) + ) * + (1 - transit_params.ecc**2) ** 0.5 / + (1 - transit_params.ecc * + np.sin(np.radians(transit_params.w))) + ) diff --git a/fleck/tests/test_core.py b/fleck/tests/test_core.py index 081a79a..e2eb29e 100644 --- a/fleck/tests/test_core.py +++ b/fleck/tests/test_core.py @@ -1,117 +1,132 @@ -import numpy as np import os -import astropy.units as u import pytest +from collections import namedtuple -from ..core import Star - - -@pytest.mark.parametrize("fast,", [ - ("True", ), - ("False", ), -]) -def test_stsp_rotational_modulation(fast): - """ - Compare fleck results to STSP results - """ - stsp_lc = np.loadtxt(os.path.join(os.path.dirname(__file__), os.pardir, - 'data', 'stsp_rotation.txt')) - - n_phases = 1000 - spot_contrast = 0.7 - u_ld = [0.5079, 0.2239] - inc_stellar = 90 - - lat1, lon1, rad1 = 10, 0, 0.1 - lat2, lon2, rad2 = 75, 180, 0.1 - - lats = np.array([lat1, lat2])[:, np.newaxis] - lons = np.array([lon1, lon2])[:, np.newaxis] - rads = np.array([rad1, rad2])[:, np.newaxis] - - star = Star(spot_contrast, u_ld, n_phases=n_phases) - fleck_lc = star.light_curve(lons * u.deg, lats * u.deg, rads, - inc_stellar * u.deg, fast=fast) - - # Assert matches STSP results to within 100 ppm: - np.testing.assert_allclose(fleck_lc[:, 0], stsp_lc, atol=100e-6) - - -@pytest.mark.parametrize("fast,", [ - ("True", ), - ("False", ), -]) -def test_stsp_transit(fast): - from batman import TransitParams - - planet = TransitParams() - planet.per = 88 - planet.a = float(0.387*u.AU / u.R_sun) - planet.rp = 0.1 - planet.w = 90 - planet.ecc = 0 - planet.inc = 90 - planet.t0 = 0 - planet.limb_dark = 'quadratic' - planet.u = [0.5079, 0.2239] - - stsp_lc = np.loadtxt(os.path.join(os.path.dirname(__file__), os.pardir, - 'data', 'stsp_single_transit.txt')) - - inc_stellar = 90 * u.deg - spot_radii = np.array([[0.1], [0.1]]) - spot_lats = np.array([[0], [0]]) * u.deg - spot_lons = np.array([[360-30], [30]]) * u.deg - - times = np.linspace(-0.5, 0.5, 500) - - star = Star(spot_contrast=0.7, u_ld=planet.u, rotation_period=100) - - fleck_lc = star.light_curve(spot_lons, spot_lats, spot_radii, - inc_stellar, planet=planet, times=times, - fast=fast, time_ref=0) - - # Assert matches STSP results to within 350 ppm: - np.testing.assert_allclose(fleck_lc[:, 0], stsp_lc, atol=350e-6) - - -@pytest.mark.parametrize("fast,", [ - ("True", ), - ("False", ), -]) -def test_stsp_double_transit(fast): - from batman import TransitParams - - planet = TransitParams() - planet.per = 88 - planet.a = float(0.387*u.AU / u.R_sun) - planet.rp = 0.1 - planet.w = 90 - planet.ecc = 0 - planet.inc = 90 - planet.t0 = 0 - planet.limb_dark = 'quadratic' - planet.u = [0.5079, 0.2239] - - stsp_lc = np.loadtxt(os.path.join(os.path.dirname(__file__), os.pardir, - 'data', 'stsp_double_transit.txt')) - - inc_stellar = 90 * u.deg - spot_radii = np.array([[0.05], [0.05]]) - spot_lats = np.array([[0], [0]]) * u.deg - spot_lons = np.array([[360-30], [30]]) * u.deg - - times = np.concatenate([np.linspace(-0.5, 0.5, 500), - np.linspace(87.5, 88.5, 500)]) - - star = Star(spot_contrast=0.7, u_ld=planet.u, rotation_period=10) - - fleck_lc = star.light_curve(spot_lons, spot_lats, spot_radii, - inc_stellar, planet=planet, times=times, - fast=fast, time_ref=0) +from batman import TransitParams +import numpy as np +import astropy.units as u - # Assert matches STSP results to within 1 ppt: - np.testing.assert_allclose(fleck_lc[:, 0], stsp_lc, atol=1e-3) +from fleck.core import Star +from fleck.tests.stsp import STSP + + +p = TransitParams() +p.per = 1.5 +p.a = 15 +p.t0 = 0 +p.rp = 0.05 +p.u = [0.1, 0.05] +p.limb_dark = 'quadratic' +p.w = 90 +p.ecc = 0 + +# stellar params: +p.per_rot = 5 +contrast = 0.2 + +test_times = np.linspace(-0.05, 0.05, 500) + +# spot_params order: [r, theta, phi] +system_configurations = [ + + # columns: i_s, i_orb, lambda, OOT max, and + # spot [r, theta, phi] int STSP coord convention: + + # with stellar inclination 85 deg, b=0: + # vary projected spin-orbit angle and spot positions + (85, 90, 0, 1, [0.05, np.pi/2, 0]), + (85, 90, 30, 1, [0.05, 1.15 * np.pi/2, 2 * np.pi - 0.5]), + (85, 90, 30, 1, [0.05, 0.8 * np.pi/2, 0.5 + 0.03]), + (85, 90, 90, 1, [0.05, np.pi/4, 0]), + (85, 90, 270, 1, [0.05, 3 * np.pi/4, 0]), + + # with stellar inclination 120 deg, b=0.4: + # vary projected spin-orbit angle and spot positions + (120, 88.5, -30, 1, [0.03, 0.55 * np.pi, 2*np.pi - 1.1]), + (200, 88.5, 200, 1, [0.05, 0.55 * np.pi, 2*np.pi - 0.45]), + + # with stellar inclination {0, 180} deg, b=0.1, check that STSP's + # "real maximum" parameter brings the STSP model into + # agreement with fleck's default output. + (0, 89.6, 0, 0.9992497284217082, [0.03, 0.05, 0.05]), + (180, 89.6, 45, 0.9992497284217082, [0.03, np.pi - 0.05, 0.9 * np.pi]), + + # with stellar inclination {0, 180} deg, b={0.1, 0.4}: + # vary projected spin-orbit angle and spot positions + (0, 89.6, 0, 0.9992497284217082, [0.03, 0.05, 0.05]), + (180, 89.6, 45, 0.9939219210476027, + [[0.04, 0.7 * np.pi, 0.3 * np.pi], [0.08, np.pi - 0.06, 2.5]]), + (180, 89.6, 90, 0.9939219210476027, + [[0.04, 0.7 * np.pi, 3.03], [0.08, np.pi - 0.06, 2.5]]), + (0, 89.6, 90, 0.9939219210476027, + [[0.04, 0.3 * np.pi, 3.03], [0.08, 0.06, 2.5]]), + (0, 88.5, 100, 0.998567636449246, + [[0.04, 0.3 * np.pi, 0.2 * np.pi], [0.03, 0.4, 0.4 * np.pi]]), +] + + +def generate_stsp_light_curves(): + # run this manually to recreate the test light curve files + LightCurve = namedtuple('LightCurve', 'times') + JD = namedtuple('JD', 'jd') + + for i, config in enumerate(system_configurations): + inc_stellar, inc, lam, real_max, spot_params = config + p.lam = lam + p.inc_stellar = inc_stellar + p.inc = inc + lc = LightCurve(times=JD(test_times)) + sim = STSP(lc, transit_params=p, spot_params=spot_params) + _, flux_stsp = sim.stsp_lc( + contrast=contrast, + n_ld_rings=100, + real_max=real_max, + verbose=False + ) + path = os.path.join( + os.path.dirname(__file__), + os.pardir, + 'data', + f'stsp_{i:02d}.txt' + ) + np.savetxt(path, flux_stsp) + + +@pytest.mark.parametrize( + "i, config,", + enumerate(system_configurations) +) +def test_fleck_against_stsp(i, config): + inc_stellar, inc, lam, _, spot_params = config + p.lam = lam + p.inc_stellar = inc_stellar + p.inc = inc + star = Star(contrast, p.u, rotation_period=p.per_rot) + spot_params = np.atleast_2d(spot_params) + fleck_lon, fleck_lat, fleck_rad = [ + spot_params[:, 2] * u.rad, + # convert colatitude to latitude: + (np.pi/2 - spot_params[:, 1]) * u.rad, + spot_params[:, 0] + ] + flux_fleck = star.light_curve( + fleck_lon, fleck_lat, fleck_rad, + inc_stellar=p.inc_stellar * u.deg, + times=test_times, + planet=p, + time_ref=0.0 + ).ravel() + + path = os.path.join( + os.path.dirname(__file__), + os.pardir, + 'data', + f'stsp_{i:02d}.txt' + ) + flux_stsp = np.loadtxt(path) + + # absolute agreement of 80 ppm + np.testing.assert_allclose(flux_fleck, flux_stsp, atol=80e-6) def test_flux_decrement(): @@ -138,3 +153,14 @@ def test_flux_decrement(): # Ensure that the maximum flux is unity: assert fleck_lc.max() == 1.0 + + +if __name__ == '__main__': + """ + To re-generate STSP light curves for the tests, clone + https://github.com/lesliehebb/STSP and compile the executable. + Then add an env var $STSP_PATH to your .bashrc which points to the + executable, and run this python script by calling: + python fleck/tests/test_core.py + """ + generate_stsp_light_curves() diff --git a/fleck/utils/__init__.py b/fleck/utils/__init__.py deleted file mode 100644 index d3f4517..0000000 --- a/fleck/utils/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -# Licensed under a 3-clause BSD style license - see LICENSE.rst - -# This sub-module is destined for common non-package specific utility -# functions. diff --git a/fleck/utils/tests/__init__.py b/fleck/utils/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/pyproject.toml b/pyproject.toml index 1e752d4..b24e451 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,10 +7,9 @@ license = { file = "LICENSE", content-type = "text/plain" } authors = [ { name = "Brett Morris", email = "morrisbrettm@gmail.com" }, ] -# require numpy < 2 until batman supports 2.x+ dependencies = [ "astropy", - "numpy<2", + "numpy", "scipy", "shapely", "matplotlib" @@ -22,7 +21,8 @@ test = [ "pytest-doctestplus", 'pytest >=4.6.0', 'pytest-astropy', - "batman-package" + 'batman-package', + 'setuptools' ] docs = [ "sphinx", @@ -40,8 +40,9 @@ docs = [ "corner", ] jax = [ - "jaxoplanet == 0.0.4", + "jaxoplanet", "specutils", + "equinox" ] [project.urls] diff --git a/tox.ini b/tox.ini index 7b8da8e..0ce7307 100644 --- a/tox.ini +++ b/tox.ini @@ -2,7 +2,6 @@ env_list = check-style test{-oldestdeps,-pyargs,-jaxdeps} - test-xdist build-{dist,docs} isolated_build = true # This is included for testing of the template. You can remove it safely. @@ -29,7 +28,6 @@ commands = description = run tests oldestdeps: with the oldest supported version of key dependencies - xdist: in parallel jax: tests which depend on jax use_develop = true @@ -44,9 +42,8 @@ set_env = deps = oldestdeps: minimum_dependencies - xdist: pytest-xdist jaxdeps: - jaxoplanet == 0.0.4 + jaxoplanet specutils # The following indicates which extras_require from setup.cfg will be installed @@ -60,7 +57,7 @@ commands_pre = commands = pip freeze - test: pytest --pyargs fleck {toxinidir}/docs {posargs} + test: pytest --pyargs --ignore=fleck/jax.py --ignore=fleck/test_jax.py fleck {toxinidir}/docs {posargs} [testenv:check-build] description = check PEP517 package build From e42045f4a259230b5f9f6f5271dc8a37a655c7d2 Mon Sep 17 00:00:00 2001 From: "Brett M. Morris" Date: Tue, 24 Mar 2026 11:11:27 -0400 Subject: [PATCH 3/3] tmp: ignore jax tests --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index 0ce7307..625c569 100644 --- a/tox.ini +++ b/tox.ini @@ -57,7 +57,7 @@ commands_pre = commands = pip freeze - test: pytest --pyargs --ignore=fleck/jax.py --ignore=fleck/test_jax.py fleck {toxinidir}/docs {posargs} + test: pytest --pyargs --ignore=fleck/jax.py --ignore=fleck/tests/test_jax.py fleck {toxinidir}/docs {posargs} [testenv:check-build] description = check PEP517 package build