Merge pull request #272 from sblunt/deprecation

Remove deprecated functions

orbitize/basis.py

@@ -1110,20 +1110,6 @@ def verify_params(self):
             if (max_index - best_epoch_loc < 2):
                 raise Exception("For now, the epoch with the lowest sepparation error should not be one of the last two entries for body{}".format(body_num))
 
-# Other conversions
-def tau_to_t0(tau, ref_epoch, period, after_date=None):
-    """
-    DEPRECATING!! Replaced by tau_to_tp
-    """
-    warnings.warn('DEPRECATION: tau_to_t0 is being deprecated in the next orbitize! release. Please use tau_to_tp instead!', FutureWarning)
-    return tau_to_tp(tau, ref_epoch, period, after_date=after_date)
-
-def t0_to_tau(tp, ref_epoch, period):
-    """
-    DEPRECATING!! Replaced by tp_to_tau
-    """
-    warnings.warn('DEPRECATION: t0_to_tau is being deprecated in the next orbitize! release. Please use t0_to_tau instead!', FutureWarning)
-    return tp_to_tau(tp, ref_epoch, period)
 
 def tau_to_tp(tau, ref_epoch, period, after_date=None):
     """

orbitize/kepler.py

@@ -44,7 +44,7 @@ def tau_to_manom(date, sma, mtot, tau, tau_ref_epoch):
     return mean_anom
 
 
-def calc_orbit(epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, mass_for_Kamp=None, tau_ref_epoch=58849, tolerance=1e-9, max_iter=100, tau_warning=True):
+def calc_orbit(epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, mass_for_Kamp=None, tau_ref_epoch=58849, tolerance=1e-9, max_iter=100):
     """
     Returns the separation and radial velocity of the body given array of
     orbital parameters (size n_orbs) at given epochs (array of size n_dates)
@@ -68,9 +68,6 @@ def calc_orbit(epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, mass_for_Kamp=No
         tau_ref_epoch (float, optional): reference date that tau is defined with respect to (i.e., tau=0)
         tolerance (float, optional): absolute tolerance of iterative computation. Defaults to 1e-9.
         max_iter (int, optional): maximum number of iterations before switching. Defaults to 100.
-        tau_warning (bool, optional, depricating): temporary argument to warn users about tau_ref_epoch default value change. 
-            Users that are calling this function themsleves should receive a warning since default is True. 
-            To be removed when tau_ref_epoch change is fully propogated to users. Users can turn it off to stop getting the warning.
 
     Return:
         3-tuple:
@@ -85,11 +82,6 @@ def calc_orbit(epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, mass_for_Kamp=No
 
     Written: Jason Wang, Henry Ngo, 2018
     """
-    if tau_warning:
-        warnings.warn("tau_ref_epoch default for kepler.calc_orbit is 58849 now instead of 0 MJD. "
-                      "Please check that this does not break your code. You can turn off this warning by setting "
-                      "tau_warning=False when you call kepler.calc_orbit.")
-
     n_orbs = np.size(sma)  # num sets of input orbital parameters
     n_dates = np.size(epochs)  # number of dates to compute offsets and vz
 
@@ -245,7 +237,7 @@ def _newton_solver(manom, ecc, tolerance=1e-9, max_iter=100, eanom0=None):
 
     if niter >= max_iter:
         print(manom[ind], eanom[ind], diff[ind], ecc[ind], '> {} iter.'.format(max_iter))
-        eanom[ind] = _mikkola_solver_wrapper(manom[ind], ecc[ind], use_c) # Send remaining orbits to the analytical version, this has not happened yet...
+        eanom[ind] = _mikkola_solver_wrapper(manom[ind], ecc[ind], cext) # Send remaining orbits to the analytical version, this has not happened yet...
 
     return eanom
 

orbitize/read_input.py

@@ -2,7 +2,6 @@
 Module to read user input from files and create standardized input for orbitize
 """
 
-import deprecation
 import numpy as np
 import orbitize
 from astropy.table import Table
@@ -314,19 +313,6 @@ def read_file(filename):
     return output_table
 
 
-@deprecation.deprecated(deprecated_in="1.0.2", removed_in="2.0",
-                        current_version=orbitize.__version__,
-                        details="Use read_file() instead. v1.0.2 replaces read_formatted_file and read_orbitize_input with read_file(). For now, this will be a wrapper for read_file and will be removed in the v2.0 release.")
-def read_formatted_file(filename):
-    """
-    Version 1.0.2 replaces this function with `read_file`.
-    Currently exists as a wrapper for `read_file` and will be removed in v2.0
-
-    Written: Henry Ngo, 2018
-    """
-
-    return read_file(filename)
-
 
 def write_orbitize_input(table, output_filename, file_type='csv'):
     """ Writes orbitize-readable input as an ASCII file
@@ -353,14 +339,3 @@ def write_orbitize_input(table, output_filename, file_type='csv'):
     write(table, output=output_filename, format=file_type)
 
 
-@deprecation.deprecated(deprecated_in="1.0.2", removed_in="2.0",
-                        current_version=orbitize.__version__,
-                        details="Use read_file() instead. v1.0.2 replaces read_orbitize_input and read_formatted_file with read_file(). For now, this will be a wrapper for read_file and will be removed in the v2.0 release.")
-def read_orbitize_input(filename):
-    """
-    Version 1.0.2 replaces this function with `read_file`.
-    Currently exists as a wrapper for `read_file` and will be removed in v2.0
-
-    Written: Henry Ngo, 2018
-    """
-    return read_file(filename)

orbitize/results.py

@@ -568,7 +568,7 @@ def plot_orbits(self, object_to_plot=1, start_mjd=51544.,
                 # Calculate ra/dec offsets for all epochs of this orbit
                 raoff0, deoff0, _ = kepler.calc_orbit(
                     epochs[i, :], sma[i], ecc[i], inc[i], aop[i], pan[i],
-                    tau[i], plx[i], mtot[i], tau_ref_epoch=self.tau_ref_epoch, tau_warning=False
+                    tau[i], plx[i], mtot[i], tau_ref_epoch=self.tau_ref_epoch
                 )
 
                 raoff[i, :] = raoff0
@@ -739,15 +739,15 @@ def plot_orbits(self, object_to_plot=1, start_mjd=51544.,
                     raoff0, deoff0, _ = kepler.calc_orbit(
                         epochs_seppa[i, :], sma[i], ecc[i], inc[i], aop[i], pan[i],
                         tau[i], plx[i], mtot[i], tau_ref_epoch=self.tau_ref_epoch,
-                        mass_for_Kamp=m0[i], tau_warning=False
+                        mass_for_Kamp=m0[i]
                     )
 
                     raoff[i, :] = raoff0
                     deoff[i, :] = deoff0
                 else:
                     raoff0, deoff0, _ = kepler.calc_orbit(
                         epochs_seppa[i, :], sma[i], ecc[i], inc[i], aop[i], pan[i],
-                        tau[i], plx[i], mtot[i], tau_ref_epoch=self.tau_ref_epoch, tau_warning=False
+                        tau[i], plx[i], mtot[i], tau_ref_epoch=self.tau_ref_epoch
                     )
 
                     raoff[i, :] = raoff0

orbitize/sampler.py

@@ -269,7 +269,7 @@ def prepare_samples(self, num_samples):
             # compute sep/PA of generated orbits
             ra, dec, _ = orbitize.kepler.calc_orbit(
                 self.epochs[min_epoch], sma, ecc, inc, argp, lan, tau, plx, mtot, 
-                tau_ref_epoch=0, mass_for_Kamp=m1, tau_warning=False
+                tau_ref_epoch=0, mass_for_Kamp=m1
             )
             sep, pa = orbitize.system.radec2seppa(ra, dec) # sep[mas], PA[deg]
 

orbitize/system.py

@@ -347,8 +347,7 @@ def compute_all_orbits(self, params_arr, epochs=None, comp_rebound=False):
                     # solve Kepler's equation
                     raoff, decoff, vz_i = kepler.calc_orbit(
                         epochs, sma, ecc, inc, argp, lan, tau, plx, mtot,
-                        mass_for_Kamp=m0, tau_ref_epoch=self.tau_ref_epoch, 
-                        tau_warning=False
+                        mass_for_Kamp=m0, tau_ref_epoch=self.tau_ref_epoch
                     )
 
                     # raoff, decoff, vz are scalers if the length of epochs is 1

tests/test_OFTI.py

@@ -30,8 +30,7 @@ def test_scale_and_rotate():
     sma, ecc, inc, argp, lan, tau, plx, mtot = [samp for samp in samples]
 
     ra, dec, vc = orbitize.kepler.calc_orbit(
-        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0,
-        tau_warning=False
+        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0
     )
     sep, pa = orbitize.system.radec2seppa(ra, dec)
     sep_sar, pa_sar = np.median(sep[s.epoch_idx]), np.median(pa[s.epoch_idx])
@@ -58,8 +57,7 @@ def test_scale_and_rotate():
     mtot = samples[:, 7]
 
     ra, dec, vc = orbitize.kepler.calc_orbit(
-        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0,
-        tau_warning=False
+        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0
     )
     assert np.max(lan) > np.pi
     sep, pa = orbitize.system.radec2seppa(ra, dec)
@@ -81,8 +79,7 @@ def test_scale_and_rotate():
     assert np.max(argp) > np.pi and np.max(argp) < 2 * np.pi
 
     ra, dec, vc = orbitize.kepler.calc_orbit(
-        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0,
-        tau_warning=False
+        s.epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0
     )
     sep, pa = orbitize.system.radec2seppa(ra, dec)
     sep_sar, pa_sar = np.median(sep[s.epoch_idx]), np.median(pa[s.epoch_idx])

tests/test_abs_astrometry.py

@@ -30,7 +30,7 @@ def test_1planet():
 
     ra_model, dec_model, _ = kepler.calc_orbit(
         epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, 
-        tau_ref_epoch=tau_ref_epoch, tau_warning=False
+        tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements to feed into system.py to test bookkeeping

tests/test_kepler_solver.py

@@ -60,7 +60,7 @@ def test_orbit_e03():
     raoffs, deoffs, vzs = kepler.calc_orbit(
         epochs, orbital_params[0], orbital_params[1], orbital_params[2], 
         orbital_params[3], orbital_params[4], orbital_params[5], 
-        orbital_params[6], orbital_params[7], tau_ref_epoch=0, tau_warning=False
+        orbital_params[6], orbital_params[7], tau_ref_epoch=0
     )
 
     true_raoff = [152.86786,  180.39408] #mas
@@ -89,8 +89,7 @@ def test_orbit_e03_array():
     mtot = np.array([1.5,1.5,1.5])
     epochs = np.array([1000, 1101.4])
     raoffs, deoffs, vzs = kepler.calc_orbit(
-        epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0,
-        tau_warning=False
+        epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0
     )
 
     true_raoff = np.array([[ 152.86786, 152.86786, 152.86786],
@@ -119,8 +118,7 @@ def test_orbit_e99():
     raoffs, deoffs, vzs = kepler.calc_orbit(
         epochs, orbital_params[0], orbital_params[1], orbital_params[2], 
         orbital_params[3], orbital_params[4], orbital_params[5], 
-        orbital_params[6], orbital_params[7], tau_ref_epoch=0,
-        tau_warning=False
+        orbital_params[6], orbital_params[7], tau_ref_epoch=0
     )
 
     true_raoff = [-589.45575, -571.48432]
@@ -148,7 +146,7 @@ def test_orbit_with_mass():
         epochs, orbital_params[0], orbital_params[1], orbital_params[2], 
         orbital_params[3], orbital_params[4], orbital_params[5], 
         orbital_params[6], orbital_params[7], mass_for_Kamp=orbital_params[7]/2, 
-        tau_ref_epoch=0, tau_warning=False
+        tau_ref_epoch=0
     )
 
     true_raoff = [-589.45575, -571.48432]
@@ -179,7 +177,7 @@ def test_orbit_with_mass_array():
     mass = mtot/2
     raoffs, deoffs, vzs = kepler.calc_orbit(
         epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, mass_for_Kamp=mass, 
-        tau_ref_epoch=0, tau_warning=False
+        tau_ref_epoch=0
     )
 
 
@@ -212,8 +210,7 @@ def test_orbit_scalar():
     mtot = 1.5
     epochs = 1000
     raoffs, deoffs, vzs = kepler.calc_orbit(
-        epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0,
-        tau_warning=False
+        epochs, sma, ecc, inc, argp, lan, tau, plx, mtot, tau_ref_epoch=0
     )
 
     true_raoff = 152.86786

tests/test_multiplanet.py

@@ -36,7 +36,7 @@ def test_compute_model():
 
     ra_model, dec_model, vz_model = kepler.calc_orbit(
         epochs, b_params[0], b_params[1], b_params[2], b_params[3], b_params[4], 
-        b_params[5], plx, mtot, tau_ref_epoch=tau_ref_epoch, tau_warning=False
+        b_params[5], plx, mtot, tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements just to feed into system.py to test bookkeeping
@@ -105,15 +105,13 @@ def test_fit_selfconsist():
     # comptue Keplerian orbit of b
     ra_model_b, dec_model_b, vz_model = kepler.calc_orbit(
         epochs, b_params[0], b_params[1], b_params[2], b_params[3], b_params[4], 
-        b_params[5], plx, mtot_b, mass_for_Kamp=m0, tau_ref_epoch=tau_ref_epoch,
-        tau_warning=False
+        b_params[5], plx, mtot_b, mass_for_Kamp=m0, tau_ref_epoch=tau_ref_epoch
     )
 
     # comptue Keplerian orbit of c
     ra_model_c, dec_model_c, vz_model_c = kepler.calc_orbit(
         epochs, c_params[0], c_params[1], c_params[2], c_params[3], c_params[4], 
-        c_params[5], plx, mtot_c, tau_ref_epoch=tau_ref_epoch, 
-        tau_warning=False
+        c_params[5], plx, mtot_c, tau_ref_epoch=tau_ref_epoch
     )
 
     # perturb b due to c

tests/test_multiplanet_rebound.py

@@ -43,7 +43,7 @@ def test_1planet():
 
     ra_model, dec_model, vz_model = kepler.calc_orbit(
         epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, 
-        tau_ref_epoch=tau_ref_epoch, tau_warning=False
+        tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements just to feed into system.py to test bookkeeping
@@ -130,7 +130,7 @@ def test_2planet_massive():
     # just want to generate some measurements of plaent b to test compute model
     b_ra_model, b_dec_model, b_vz_model = kepler.calc_orbit(
         epochs, params[0], params[1], params[2], params[3], params[4], params[5], 
-        params[-2], params[-1], tau_ref_epoch=tau_ref_epoch, tau_warning=False
+        params[-2], params[-1], tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements of planet b, just to feed into system.py to test bookkeeping
@@ -284,8 +284,7 @@ def test_2planet_massive_reverse_order():
     # just want to generate some measurements of plaent b to test compute model
     b_ra_model, b_dec_model, b_vz_model = kepler.calc_orbit(
         epochs, params[6+0], params[6+1], params[6+2], params[6+3], params[6+4], 
-        params[6+5], params[-2], params[-1], tau_ref_epoch=tau_ref_epoch,
-        tau_warning=False
+        params[6+5], params[-2], params[-1], tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements of planet b, just to feed into system.py to test bookkeeping
@@ -373,7 +372,7 @@ def test_2planet_nomass():
     # just want to generate some measurements of plaent b to test compute model
     b_ra_model, b_dec_model, b_vz_model = kepler.calc_orbit(
         epochs, params[0], params[1], params[2], params[3], params[4], params[5], 
-        params[-2], params[-1], tau_ref_epoch=tau_ref_epoch, tau_warning=False
+        params[-2], params[-1], tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements of planet b, just to feed into system.py to test bookkeeping

tests/test_read_input.py

@@ -1,9 +1,8 @@
 import pytest
-import deprecation
 import numpy as np
 import os
 import orbitize
-from orbitize.read_input import read_file, write_orbitize_input, read_formatted_file, read_orbitize_input
+from orbitize.read_input import read_file, write_orbitize_input
 
 
 def _compare_table(input_table):
@@ -70,21 +69,6 @@ def test_read_file():
     read_file(input_file_radec)
 
 
-@deprecation.fail_if_not_removed
-def test_read_formatted_file():
-    """
-    Tests the read_formatted_file function using the test_val.csv file and test_val_radec.csv
-
-    This test exists with the fail_if_not_removed decorator as a reminder to remove in v2.0
-    """
-    # Check that main test input is read in with correct values
-    input_file = os.path.join(orbitize.DATADIR, 'test_val.csv')
-    _compare_table(read_formatted_file(input_file))
-    # Check that an input value with all valid entries and only ra/dec columns can be read
-    input_file_radec = os.path.join(orbitize.DATADIR, 'test_val_radec.csv')
-    read_file(input_file_radec)
-
-
 def test_write_orbitize_input():
     """
     Test the write_orbitize_input and the read_file functions
@@ -107,30 +91,6 @@ def test_write_orbitize_input():
         os.remove(output_file)
 
 
-@deprecation.fail_if_not_removed
-def test_write_orbitize_input_2():
-    """
-    Test the write_orbitize_input and the read_orbitize_input functions
-
-    This test exists with the fail_if_not_removed decorator as a reminder to remove in v2.0
-    """
-    input_file = os.path.join(orbitize.DATADIR, 'test_val.csv')
-    test_table = read_file(input_file)
-    output_file = os.path.join(orbitize.DATADIR, 'temp_test_orbitize_input.csv')
-    # If temp output file already exists, delete it
-    if os.path.isfile(output_file):
-        os.remove(output_file)
-    try:  # Catch these tests so that we remove temporary file
-        # Test that we were able to write the table
-        write_orbitize_input(test_table, output_file)
-        assert os.path.isfile(output_file)
-        # Test that we can read the table and check if it's correct
-        test_table_2 = read_orbitize_input(output_file)
-        _compare_table(test_table_2)
-    finally:
-        # Remove temporary file
-        os.remove(output_file)
-
 def test_cov_input():
     """
     Test including radec and seppa covariances/correlations.
@@ -173,8 +133,6 @@ def test_read_old_orbitize_format():
 
 if __name__ == "__main__":
     test_read_file()
-    test_read_formatted_file()
     test_write_orbitize_input()
-    test_write_orbitize_input_2()
     test_cov_input()
     test_read_old_orbitize_format()