Merge branch 'main' into saanika/changes

sblunt · Jun 30, 2023 · 8f0f17f · 8f0f17f
2 parents 62d86a3 + 3eefbce
commit 8f0f17f
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diff --git a/docs/index.rst b/docs/index.rst
@@ -54,6 +54,14 @@ User Guide:
 Changelog:
 ++++++++++
 
+**2.2.2 (2023-06-30)**
+
+- tests now overwrite any generated text files (@sblunt)
+
+**2.2.1 (2023-06-28)**
+
+- tau_to_tp function now accepts array of after_date (@tomasstolker/@semaphoreP)
+
 **2.2.0 (2023-06-21)**
 
 - set up new CI system using GH actions (@sblunt)

diff --git a/orbitize/__init__.py b/orbitize/__init__.py
@@ -1,6 +1,6 @@
 import os
 
-__version__ = "2.2.0"
+__version__ = "2.2.2"
 
 # set Python env variable to keep track of example data dir
 orbitize_dir = os.path.dirname(__file__)

diff --git a/orbitize/basis.py b/orbitize/basis.py
@@ -1140,7 +1140,7 @@ def tau_to_tp(tau, ref_epoch, period, after_date=None):
         tau (float or np.array): value of tau to convert
         ref_epoch (float or np.array): date (in days, typically MJD) that tau is defined relative to
         period (float or np.array): period (in years) that tau is noralized with
-        after_date (float): tp will be the first periastron after this date. If None, use ref_epoch.
+        after_date (float or np.array): tp will be the first periastron after this date. If None, use ref_epoch.
 
     Returns:
         float or np.array: corresponding t_p of the taus
@@ -1151,7 +1151,7 @@ def tau_to_tp(tau, ref_epoch, period, after_date=None):
 
     if after_date is not None:
         num_periods = (after_date - tp)/period_days
-        num_periods = int(np.ceil(num_periods))
+        num_periods = np.ceil(num_periods).astype(int)
 
         tp += num_periods * period_days
 

diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 import re
 
 USE_C_KEPLER_MODULE = 1
-if ("--disable-cython" in sys.argv):
+if "--disable-cython" in sys.argv:
     sys.argv.remove("--disable-cython")
     USE_C_KEPLER_MODULE = 0
 else:
@@ -13,44 +13,58 @@
         print("Error: Importing cython build environment failed")
         USE_C_KEPLER_MODULE = 0
 
+
 # auto-updating version code stolen from RadVel
 def get_property(prop, project):
-    result = re.search(r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
-                       open(project + '/__init__.py').read())
+    result = re.search(
+        r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
+        open(project + "/__init__.py").read(),
+    )
     return result.group(1)
 
+
 def get_requires():
     reqs = []
-    for line in open('requirements.txt', 'r').readlines():
+    for line in open("requirements.txt", "r").readlines():
         reqs.append(line)
     return reqs
 
+
 def get_extensions():
     extensions = []
-    if(USE_C_KEPLER_MODULE):
-        extensions = cythonize([Extension("orbitize._kepler", ["orbitize/_kepler.pyx"], include_dirs=[numpy.get_include()])])
+    if USE_C_KEPLER_MODULE:
+        extensions = cythonize(
+            [
+                Extension(
+                    "orbitize._kepler",
+                    ["orbitize/_kepler.pyx"],
+                    include_dirs=[numpy.get_include()],
+                )
+            ]
+        )
     return extensions
 
+
 setup(
-    name='orbitize',
-    version=get_property('__version__', 'orbitize'),
-    description='orbitize! Turns imaging data into orbits',
-    url='https://github.com/sblunt/orbitize',
-    author='',
-    author_email='',
-    license='BSD',
+    name="orbitize",
+    version=get_property("__version__", "orbitize"),
+    description="orbitize! Turns imaging data into orbits",
+    url="https://github.com/sblunt/orbitize",
+    author="",
+    author_email="",
+    license="BSD",
     packages=find_packages(),
-    package_data={"":["kernels/*.cu"]},
+    package_data={"": ["kernels/*.cu"]},
     ext_modules=get_extensions(),
     include_dirs=[numpy.get_include()],
-    include_package_data = True,
+    include_package_data=True,
     zip_safe=False,
     classifiers=[
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Astronomy',
-        'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python :: 3.6',
-        ],
-    keywords='Orbits Astronomy Astrometry',
-    install_requires=get_requires()
-    )
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Astronomy",
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python :: 3.6",
+    ],
+    keywords="Orbits Astronomy Astrometry",
+    install_requires=get_requires(),
+)
diff --git a/tests/test_abs_astrometry.py b/tests/test_abs_astrometry.py
@@ -6,6 +6,7 @@
 import orbitize
 from orbitize import kepler, read_input, system
 
+
 def test_1planet():
     """
     Check that for the 2-body case, the primary orbit around the barycenter
@@ -26,51 +27,50 @@ def test_1planet():
     mass_b = 100 * mjup
     mtot = mass_b + m0
 
-    epochs = np.linspace(0, 300, 100) + tau_ref_epoch # nearly the full period, MJD
+    epochs = np.linspace(0, 300, 100) + tau_ref_epoch  # nearly the full period, MJD
 
     ra_model, dec_model, _ = kepler.calc_orbit(
-        epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, 
-        tau_ref_epoch=tau_ref_epoch
+        epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, tau_ref_epoch=tau_ref_epoch
     )
 
     # generate some fake measurements to feed into system.py to test bookkeeping
     t = table.Table(
         [
-            epochs, 
-            np.ones(epochs.shape, dtype=int), 
-            ra_model, 
-            np.zeros(ra_model.shape), 
-            dec_model, 
-            np.zeros(dec_model.shape)
-        ], 
-        names=["epoch", "object" ,"raoff", "raoff_err","decoff","decoff_err"]
+            epochs,
+            np.ones(epochs.shape, dtype=int),
+            ra_model,
+            np.zeros(ra_model.shape),
+            dec_model,
+            np.zeros(dec_model.shape),
+        ],
+        names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_1planet.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # create the orbitize system and generate model predictions using ground truth
     astrom_dat = read_input.read_file(filename)
 
     sys = system.System(
-        1, astrom_dat, m0, plx, tau_ref_epoch=tau_ref_epoch, 
-        fit_secondary_mass=True
+        1, astrom_dat, m0, plx, tau_ref_epoch=tau_ref_epoch, fit_secondary_mass=True
     )
     sys.track_planet_perturbs = True
 
     params = np.array([sma, ecc, inc, aop, pan, tau, plx, mass_b, m0])
     ra, dec, _ = sys.compute_all_orbits(params)
 
     # the planet and stellar orbit should just be scaled versions of one another
-    planet_ra = ra[:,1,:]
-    planet_dec = dec[:,1,:]
-    star_ra = ra[:,0,:]
-    star_dec = dec[:,0,:]
+    planet_ra = ra[:, 1, :]
+    planet_dec = dec[:, 1, :]
+    star_ra = ra[:, 0, :]
+    star_dec = dec[:, 0, :]
 
     assert np.all(np.abs(star_ra + (mass_b / mtot) * planet_ra) < 1e-16)
     assert np.all(np.abs(star_dec + (mass_b / mtot) * planet_dec) < 1e-16)
 
     # remove the created csv file to clean up
-    os.system('rm {}'.format(filename))
+    os.system("rm {}".format(filename))
+
 
-if __name__ == '__main__':
-    test_1planet()
+if __name__ == "__main__":
+    test_1planet()
diff --git a/tests/test_conversions.py b/tests/test_conversions.py
@@ -22,6 +22,10 @@ def test_tau_tp_conversion():
     tp = basis.tau_to_tp(tau, ref_epoch, period, after_date=47000)
     assert tp == pytest.approx(51000 - 9 * 365.25, rel=1e-7)
 
+    tps = basis.tau_to_tp(tau, ref_epoch, period, after_date=np.array([47000, 51000]))
+    assert tps[0] == pytest.approx(51000 - 9 * 365.25, rel=1e-7)
+    assert tps[1] == pytest.approx(51000 + 365.25, rel=1e-7)
+
     tau3 = basis.tp_to_tau(tp, ref_epoch, period)
     assert tau == pytest.approx(tau3, rel=1e-7)
 

diff --git a/tests/test_multiplanet_rebound.py b/tests/test_multiplanet_rebound.py
@@ -60,7 +60,7 @@ def test_1planet():
         names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_1planet.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # create the orbitize system and generate model predictions using the ground truth
     astrom_dat = read_input.read_file(filename)
@@ -112,7 +112,7 @@ def test_1planet():
     assert np.all(np.abs(diff_dec) < 1e-9)
 
     # clean up
-    os.system("rm {}".format(filename))
+    # os.system("rm {}".format(filename))
 
 
 def test_2planet_massive():
@@ -200,7 +200,7 @@ def test_2planet_massive():
         names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_2planet_outer.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # TEST THE OUTER PLANET
 
@@ -292,7 +292,7 @@ def test_2planet_massive():
     assert np.all(np.abs(diff_dec) / (params[0]) < 1e-3)
 
     # clean up
-    os.system("rm {}".format(filename))
+    # os.system("rm {}".format(filename))
 
     # NOW TEST THE INNER PLANET
 
@@ -310,7 +310,7 @@ def test_2planet_massive():
         names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_2planet_inner.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # create the orbitize system and generate model predictions using the ground truth
     astrom_dat = read_input.read_file(filename)
@@ -385,7 +385,7 @@ def test_2planet_massive():
     assert np.all(np.abs(diff_dec) / (params[0]) < 3e-3)
 
     # clean up
-    os.system("rm {}".format(filename))
+    # os.system("rm {}".format(filename))
 
 
 def test_2planet_massive_reverse_order():
@@ -454,7 +454,7 @@ def test_2planet_massive_reverse_order():
         names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_2planet_swapped_outer.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # TEST THE OUTER PLANET ####
 
@@ -543,7 +543,7 @@ def test_2planet_massive_reverse_order():
     assert np.all(np.abs(diff_dec) / (params[6]) < 1e-3)
 
     # clean up
-    os.system("rm {}".format(filename))
+    # os.system("rm {}".format(filename))
 
 
 def test_2planet_nomass():
@@ -611,7 +611,7 @@ def test_2planet_nomass():
         names=["epoch", "object", "raoff", "raoff_err", "decoff", "decoff_err"],
     )
     filename = os.path.join(orbitize.DATADIR, "rebound_2planet.csv")
-    t.write(filename)
+    t.write(filename, overwrite=True)
 
     # create the orbitize system and generate model predictions using the ground truth
     astrom_dat = read_input.read_file(filename)
@@ -693,7 +693,7 @@ def test_2planet_nomass():
     assert np.all(np.abs(diff_dec) / (params[0] * params[6 * 2]) < 1e-9)
 
     # clean up
-    os.system("rm {}".format(filename))
+    # os.system("rm {}".format(filename))
 
 
 if __name__ == "__main__":