[pre-commit.ci] pre-commit autoupdate (#248)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 21.12b0 → 22.1.0](psf/black@21.12b0...22.1.0)
- [github.com/dfm/black_nbconvert: v0.3.0 → v0.4.0](dfm/black_nbconvert@v0.3.0...v0.4.0)
- [github.com/mwouts/jupytext: v1.13.6 → v1.13.7](mwouts/jupytext@v1.13.6...v1.13.7)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -22,17 +22,17 @@ repos:
     exclude: docs/tutorials
 
 - repo: https://github.com/psf/black
-  rev: "21.12b0"
+  rev: "22.1.0"
   hooks:
   - id: black
 
 - repo: https://github.com/dfm/black_nbconvert
-  rev: v0.3.0
+  rev: v0.4.0
   hooks:
   - id: black_nbconvert
 
 - repo: https://github.com/mwouts/jupytext
-  rev: v1.13.6
+  rev: v1.13.7
   hooks:
   - id: jupytext
     files: |

docs/tutorials/about.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

docs/tutorials/autodiff.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

docs/tutorials/citation.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

docs/tutorials/data-and-models.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python
@@ -236,7 +236,7 @@ t_plot = np.linspace(0, 50, 500)
 t = np.sort(random.uniform(0, 50, 20))
 rv_err = 0.5 + np.zeros_like(t)
 rv_obs = 5.0 * np.sin(2 * np.pi * t / 10.0) + np.sqrt(
-    0.05 ** 2 + rv_err ** 2
+    0.05**2 + rv_err**2
 ) * random.normal(size=len(t))
 
 with pm.Model():
@@ -277,7 +277,7 @@ with pm.Model():
     rv_model = zero_point + orbit.get_radial_velocity(t, K=semiamp)
 
     # Finally add in the observation model
-    err = tt.sqrt(rv_err ** 2 + tt.exp(2 * log_jitter))
+    err = tt.sqrt(rv_err**2 + tt.exp(2 * log_jitter))
     pm.Normal("obs", mu=rv_model, sigma=rv_err, observed=rv_obs)
 
     # We'll also track the model just for plotting purposes

docs/tutorials/intro-to-pymc3.md

@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

docs/tutorials/light-delay.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

docs/tutorials/reparameterization.md

@@ -4,7 +4,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.6
+    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3
   language: python

src/exoplanet/distributions/transforms.py

@@ -26,12 +26,12 @@ def backward(self, y):
 
     def forward(self, x):
         usum = tt.sum(x, axis=0)
-        q = tt.stack([usum ** 2, 0.5 * x[0] / usum])
+        q = tt.stack([usum**2, 0.5 * x[0] / usum])
         return tt.log(q) - tt.log(1 - q)
 
     def forward_val(self, x, point=None):
         usum = np.sum(x, axis=0)
-        q = np.array([usum ** 2, 0.5 * x[0] / usum])
+        q = np.array([usum**2, 0.5 * x[0] / usum])
         return np.log(q) - np.log(1 - q)
 
     def jacobian_det(self, y):

src/exoplanet/estimators.py

@@ -68,7 +68,7 @@ def estimate_semi_amplitude(periods, x, y, yerr=None, t0s=None):
     if yerr is None:
         ivar = np.ones_like(y)
     else:
-        ivar = 1.0 / yerr ** 2
+        ivar = 1.0 / yerr**2
 
     periods = u.Quantity(np.atleast_1d(periods), unit=u.day)
     if t0s is not None:
@@ -149,9 +149,9 @@ def find_peaks(freq, power, max_peaks=0):
         peaks.append(
             dict(
                 index=i + 1,
-                log_power=w[2] + 0.5 * freq0 ** 2 / sigma2,
+                log_power=w[2] + 0.5 * freq0**2 / sigma2,
                 period=1.0 / freq0,
-                period_uncert=np.sqrt(sigma2 / freq0 ** 4),
+                period_uncert=np.sqrt(sigma2 / freq0**4),
             )
         )
     if max_peaks:

src/exoplanet/light_curves/interpolated.py

@@ -35,7 +35,7 @@ def interp(n, x, xmin, xmax, dx, func):
 
     inds = tt.cast(tt.floor((x - xmin) / dx), "int64")
     x0 = (x - xp[inds + 1]) / dx
-    return a0[inds] + a1[inds] * x0 + a2[inds] * x0 ** 2 + a3[inds] * x0 ** 3
+    return a0[inds] + a1[inds] * x0 + a2[inds] * x0**2 + a3[inds] * x0**3
 
 
 class InterpolatedLightCurve:

src/exoplanet/light_curves/limb_dark.py

@@ -90,8 +90,8 @@ def get_ror_from_approx_transit_depth(self, delta, b, jac=False):
         b = as_tensor_variable(b)
         delta = as_tensor_variable(delta)
         f0 = 1 - 2 * self.u1 / 6.0 - 2 * self.u2 / 12.0
-        arg = 1 - tt.sqrt(1 - b ** 2)
-        f = 1 - self.u1 * arg - self.u2 * arg ** 2
+        arg = 1 - tt.sqrt(1 - b**2)
+        f = 1 - self.u1 * arg - self.u2 * arg**2
         factor = f0 / f
         ror = tt.sqrt(delta * factor)
         if not jac:

src/exoplanet/light_curves/secondary_eclipse.py

@@ -67,6 +67,6 @@ def get_light_curve(
         )
 
         k = r / orbit.r_star
-        flux_ratio = self.surface_brightness_ratio * k ** 2
+        flux_ratio = self.surface_brightness_ratio * k**2
 
         return (lc1 + flux_ratio * lc2) / (1 + flux_ratio)

src/exoplanet/orbits/constants.py

@@ -15,16 +15,16 @@
 import numpy as np
 
 try:
-    G_grav = c.G.to(u.R_sun ** 3 / u.M_sun / u.day ** 2).value
-    gcc_per_sun = (u.M_sun / u.R_sun ** 3).to(u.g / u.cm ** 3)
+    G_grav = c.G.to(u.R_sun**3 / u.M_sun / u.day**2).value
+    gcc_per_sun = (u.M_sun / u.R_sun**3).to(u.g / u.cm**3)
     au_per_R_sun = u.R_sun.to(u.au)
     c_light = c.c.to(u.R_sun / u.day).value
 
     day_per_yr_over_2pi = (
         (1.0 * u.au) ** (3 / 2)
         / (
             np.sqrt(
-                c.G.to(u.au ** 3 / (u.M_sun * u.day ** 2)) * (1.0 * u.M_sun)
+                c.G.to(u.au**3 / (u.M_sun * u.day**2)) * (1.0 * u.M_sun)
             )
         )
     ).value

src/exoplanet/orbits/dur_to_ecc.py

@@ -37,17 +37,17 @@ def duration_to_eccentricity(
     a, period, rho_star, r_star, m_star, m_planet = inputs
     b = kwargs.get("b", 0.0)
     s = tt.sin(kwargs["omega"])
-    umax_inv = tt.switch(tt.lt(s, 0), tt.sqrt(1 - s ** 2), 1.0)
+    umax_inv = tt.switch(tt.lt(s, 0), tt.sqrt(1 - s**2), 1.0)
 
     const = (
-        period * tt.shape_padright(r_star) * tt.sqrt((1 + ror) ** 2 - b ** 2)
+        period * tt.shape_padright(r_star) * tt.sqrt((1 + ror) ** 2 - b**2)
     )
     const /= np.pi * a
 
     u = duration / const
 
-    e1 = -s * u ** 2 / ((s * u) ** 2 + 1)
-    e2 = tt.sqrt((s ** 2 - 1) * u ** 2 + 1) / ((s * u) ** 2 + 1)
+    e1 = -s * u**2 / ((s * u) ** 2 + 1)
+    e2 = tt.sqrt((s**2 - 1) * u**2 + 1) / ((s * u) ** 2 + 1)
 
     models = []
     logjacs = []
@@ -63,7 +63,7 @@ def duration_to_eccentricity(
         logjac = tt.switch(
             tt.all(valid_ecc),
             tt.sum(
-                0.5 * tt.log(1 - ecc ** 2)
+                0.5 * tt.log(1 - ecc**2)
                 + 2 * tt.log(s * ecc + 1)
                 - tt.log(tt.abs_(s + ecc))
                 - tt.log(const)

src/exoplanet/orbits/keplerian.py

@@ -164,7 +164,7 @@ def __init__(
                 * (self.a / self.r_star) ** 2
                 * daordtau
                 * gcc_per_sun
-                / (G_grav * self.period ** 2)
+                / (G_grav * self.period**2)
             )
 
         self.K0 = self.n * self.a / self.m_total
@@ -207,7 +207,7 @@ def __init__(
             )
             self.M0 = E0 - self.ecc * tt.sin(E0)
 
-            ome2 = 1 - self.ecc ** 2
+            ome2 = 1 - self.ecc**2
             self.K0 /= tt.sqrt(ome2)
             incl_factor = (1 + self.ecc * self.sin_omega) / ome2
 
@@ -243,17 +243,17 @@ def __init__(
             aor = self.a_planet / self.r_star
             esinw = self.ecc * self.sin_omega
             self.b = tt.sqrt(
-                (aor ** 2 * c2 - 1)
+                (aor**2 * c2 - 1)
                 / (
-                    c2 * esinw ** 2
+                    c2 * esinw**2
                     + 2 * c2 * esinw
                     + c2
-                    - self.ecc ** 4
-                    + 2 * self.ecc ** 2
+                    - self.ecc**4
+                    + 2 * self.ecc**2
                     - 1
                 )
             )
-            self.b *= 1 - self.ecc ** 2
+            self.b *= 1 - self.ecc**2
             self.cos_incl = self.dcosidb * self.b
             self.incl = tt.arccos(self.cos_incl)
         else:
@@ -338,7 +338,7 @@ def _get_position_and_velocity(self, t, parallax=None):
             r = 1.0
             vx, vy, vz = self._rotate_vector(-self.K0 * sinf, self.K0 * cosf)
         else:
-            r = (1.0 - self.ecc ** 2) / (1 + self.ecc * cosf)
+            r = (1.0 - self.ecc**2) / (1 + self.ecc * cosf)
             vx, vy, vz = self._rotate_vector(
                 -self.K0 * sinf, self.K0 * (cosf + self.ecc)
             )
@@ -398,7 +398,7 @@ def _get_position(self, a, t, parallax=None, light_delay=False, _pad=True):
         if self.ecc is None:
             r = a
         else:
-            r = a * (1.0 - self.ecc ** 2) / (1 + self.ecc * cosf)
+            r = a * (1.0 - self.ecc**2) / (1 + self.ecc * cosf)
 
         if parallax is not None:
             # convert r into arcseconds
@@ -432,16 +432,16 @@ def _get_retarded_position(self, a, t, parallax=None, z0=0.0, _pad=True):
             vamp = angvel * a
             vz = vamp * self.sin_incl * cosf
         else:
-            r = a * (1.0 - self.ecc ** 2) / (1 + self.ecc * cosf)
-            vamp = angvel * a / tt.sqrt(1 - self.ecc ** 2)
+            r = a * (1.0 - self.ecc**2) / (1 + self.ecc * cosf)
+            vamp = angvel * a / tt.sqrt(1 - self.ecc**2)
             cwf = self.cos_omega * cosf - self.sin_omega * sinf
             vz = vamp * self.sin_incl * (self.ecc * self.cos_omega + cwf)
 
         # True position of the body
         x, y, z = self._rotate_vector(r * cosf, r * sinf)
 
         # Component of the acceleration in the z direction
-        az = -(angvel ** 2) * (a / r) ** 3 * z
+        az = -(angvel**2) * (a / r) ** 3 * z
 
         # Compute the time delay at the **retarded** position, accounting
         # for the instantaneous velocity and acceleration of the body.
@@ -454,7 +454,7 @@ def _get_retarded_position(self, a, t, parallax=None, z0=0.0, _pad=True):
                 (1 + vz / c_light)
                 - tt.sqrt(
                     (1 + vz / c_light) * (1 + vz / c_light)
-                    - 2 * az * (z0 - z) / c_light ** 2
+                    - 2 * az * (z0 - z) / c_light**2
                 )
             ),
         )
@@ -562,7 +562,7 @@ def get_relative_angles(self, t, parallax=None, light_delay=False):
         )
 
         # calculate rho and theta
-        rho = tt.squeeze(tt.sqrt(X ** 2 + Y ** 2))  # arcsec
+        rho = tt.squeeze(tt.sqrt(X**2 + Y**2))  # arcsec
         theta = tt.squeeze(tt.arctan2(Y, X))  # radians between [-pi, pi]
 
         return (rho, theta)
@@ -678,10 +678,10 @@ def _get_acceleration(self, a, m, t):
         sinf, cosf = self._get_true_anomaly(t)
         K = self.K0 * m
         if self.ecc is None:
-            factor = -(K ** 2) / a
+            factor = -(K**2) / a
         else:
             factor = (
-                K ** 2 * (self.ecc * cosf + 1) ** 2 / (a * (self.ecc ** 2 - 1))
+                K**2 * (self.ecc * cosf + 1) ** 2 / (a * (self.ecc**2 - 1))
             )
         return self._rotate_vector(factor * cosf, factor * sinf)
 
@@ -833,14 +833,14 @@ def get_aor_from_transit_duration(duration, period, b, ror=None):
     """
     if ror is None:
         ror = as_tensor_variable(0.0)
-    b2 = b ** 2
+    b2 = b**2
     opk2 = (1 + ror) ** 2
     phi = np.pi * duration / period
     sinp = tt.sin(phi)
     cosp = tt.cos(phi)
-    num = tt.sqrt(opk2 - b2 * cosp ** 2)
+    num = tt.sqrt(opk2 - b2 * cosp**2)
     aor = num / sinp
-    grad = np.pi * cosp * (b2 - opk2) / (num * period * sinp ** 2)
+    grad = np.pi * cosp * (b2 - opk2) / (num * period * sinp**2)
     return aor, grad
 
 
@@ -878,11 +878,11 @@ def _get_consistent_inputs(a, period, rho_star, r_star, m_star, m_planet):
             r_star = as_tensor_variable(to_unit(r_star, u.R_sun))
 
         # Compute the implied mass via Kepler's 3rd law
-        m_tot = 4 * np.pi * np.pi * a ** 3 / (G_grav * period ** 2)
+        m_tot = 4 * np.pi * np.pi * a**3 / (G_grav * period**2)
 
         # Compute the implied density
         m_star = m_tot - m_planet
-        vol_star = 4 * np.pi * r_star ** 3 / 3.0
+        vol_star = 4 * np.pi * r_star**3 / 3.0
         rho_star = m_star / vol_star
         implied_rho_star = True
 
@@ -902,7 +902,7 @@ def _get_consistent_inputs(a, period, rho_star, r_star, m_star, m_planet):
     if rho_star is not None and not implied_rho_star:
         if has_unit(rho_star):
             rho_star = as_tensor_variable(
-                to_unit(rho_star, u.M_sun / u.R_sun ** 3)
+                to_unit(rho_star, u.M_sun / u.R_sun**3)
             )
         else:
             rho_star = as_tensor_variable(rho_star) / gcc_per_sun
@@ -913,16 +913,16 @@ def _get_consistent_inputs(a, period, rho_star, r_star, m_star, m_planet):
 
     # Work out the stellar parameters
     if rho_star is None:
-        rho_star = 3 * m_star / (4 * np.pi * r_star ** 3)
+        rho_star = 3 * m_star / (4 * np.pi * r_star**3)
     elif r_star is None:
         r_star = (3 * m_star / (4 * np.pi * rho_star)) ** (1 / 3)
     elif m_star is None:
-        m_star = 4 * np.pi * r_star ** 3 * rho_star / 3.0
+        m_star = 4 * np.pi * r_star**3 * rho_star / 3.0
 
     # Work out the planet parameters
     if a is None:
         a = (
-            G_grav * (m_star + m_planet) * period ** 2 / (4 * np.pi ** 2)
+            G_grav * (m_star + m_planet) * period**2 / (4 * np.pi**2)
         ) ** (1.0 / 3)
     elif period is None:
         period = (