Merge pull request #154 from cosimoNigro/mv_tests

Moved the tests in the respective submodule subdirectories

.github/workflows/test.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest pytest-cov
-        python -m pip install .
+        python -m pip install -e . --config-settings editable_mode=compat
         python -m pip install gammapy
         python -m pip install sherpa
     - name: Lint with flake8
@@ -37,7 +37,7 @@ jobs:
       run: |
         pytest -v --cov=./ --cov-report=xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml
         flags: unittests

agnpy/tests/test_absorption.py → agnpy/absorption/tests/test_absorption.py

@@ -11,7 +11,7 @@
 from agnpy.targets import PointSourceBehindJet, SSDisk, SphericalShellBLR, RingDustTorus
 from agnpy.absorption import Absorption, EBL
 from agnpy.utils.math import axes_reshaper
-from .utils import (
+from agnpy.utils.validation_utils import (
     make_comparison_plot,
     extract_columns_sample_file,
     check_deviation,
@@ -20,7 +20,7 @@
 
 mec2 = m_e.to("erg", equivalencies=u.mass_energy())
 
-agnpy_dir = Path(__file__).parent.parent
+agnpy_dir = Path(__file__).parent.parent.parent
 # where to read sampled files
 data_dir = agnpy_dir / "data"
 # where to save figures

agnpy/tests/test_compton.py → agnpy/compton/tests/test_compton.py

@@ -16,7 +16,7 @@
 )
 from agnpy.compton import SynchrotronSelfCompton, ExternalCompton
 from agnpy.utils.math import trapz_loglog
-from .utils import (
+from agnpy.utils.validation_utils import (
     make_comparison_plot,
     extract_columns_sample_file,
     check_deviation,
@@ -25,7 +25,7 @@
 
 agnpy_dir = Path(__file__).parent.parent.parent  # go to the agnpy root
 # where to read sampled files
-data_dir = agnpy_dir / "agnpy/data"
+data_dir = agnpy_dir / "data"
 # where to save figures, clean-up before making the new
 figures_dir_ssc = clean_and_make_dir(agnpy_dir, "crosschecks/figures/compton/ssc")
 figures_dir_ec_disk = clean_and_make_dir(
@@ -39,7 +39,7 @@
 # parameters of the Blob and EED used in Figure 7.4 of Dermer 2009
 # and for the EC scenario in Finke 2016
 R_b = 1e16 * u.cm
-V_b = 4 / 3 * np.pi * R_b ** 3
+V_b = 4 / 3 * np.pi * R_b**3
 W_e_ssc = 1e48 * u.Unit("erg")
 W_e_ec = 6e42 * u.Unit("erg")
 z_ssc = Distance(1e27, unit=u.cm).z

agnpy/constraints/tests/test_constraints.py

@@ -0,0 +1 @@
+# TODO: add some tests on the contraints class

agnpy/tests/test_emission_regions.py → agnpy/emission_regions/tests/test_emission_regions.py

@@ -42,7 +42,7 @@ def test_blob_properties(self):
         assert u.isclose(blob.d_L, 5.21497473e28 * u.cm, atol=0 * u.cm, rtol=1e-3)
         # - change cosmology
         blob = Blob(z=0.1, cosmology=Planck18)
-        d_L = 1.4682341e+27 * u.cm
+        d_L = 1.4682341e27 * u.cm
         assert u.isclose(blob.d_L, d_L, atol=0 * u.cm, rtol=1e-5)
 
     def test_particles_spectra(self):

agnpy/tests/test_fit.py → agnpy/fit/tests/test_fit.py

@@ -236,7 +236,12 @@ def test_pks_1510_fit(self):
         wrappers return the same results."""
         # electron energy distribution
         n_e = LogParabola(
-            k=1 * u.Unit("cm-3"), p=2.0, q=0.2, gamma_0=1e2, gamma_min=1, gamma_max=3e4,
+            k=1 * u.Unit("cm-3"),
+            p=2.0,
+            q=0.2,
+            gamma_0=1e2,
+            gamma_min=1,
+            gamma_max=3e4,
         )
 
         # initialise the wrappers
@@ -258,8 +263,8 @@ def test_pks_1510_fit(self):
         L_disk = 6.7e45 * u.Unit("erg s-1")  # disk luminosity
         M_BH = 5.71 * 1e7 * M_sun
         eta = 1 / 12
-        m_dot = (L_disk / (eta * c ** 2)).to("g s-1")
-        R_g = ((G * M_BH) / c ** 2).to("cm")
+        m_dot = (L_disk / (eta * c**2)).to("g s-1")
+        R_g = ((G * M_BH) / c**2).to("cm")
         R_in = 6 * R_g
         R_out = 3e4 * R_g
         xi_dt = 0.6

agnpy/tests/test_wrappers.py → agnpy/fit/tests/test_wrappers.py

@@ -19,10 +19,14 @@
 from agnpy.synchrotron import Synchrotron
 from agnpy.compton import SynchrotronSelfCompton, ExternalCompton
 from agnpy.fit import SynchrotronSelfComptonModel, ExternalComptonModel
-from .utils import make_comparison_plot, check_deviation, clean_and_make_dir
+from agnpy.utils.validation_utils import (
+    make_comparison_plot,
+    check_deviation,
+    clean_and_make_dir,
+)
 
 
-agnpy_dir = Path(__file__).parent.parent
+agnpy_dir = Path(__file__).parent.parent.parent
 # where to read sampled files
 data_dir = agnpy_dir / "data"
 # where to save figures, clean-up before making the new

agnpy/tests/test_spectra.py → agnpy/spectra/tests/test_spectra.py

@@ -18,7 +18,7 @@
 
 agnpy_dir = Path(__file__).parent.parent.parent  # go to the agnpy root
 # where to read sampled files
-data_dir = agnpy_dir / "agnpy/data"
+data_dir = agnpy_dir / "data"
 
 gamma_init_interp = np.logspace(2, 5)
 n_e_interp = 1e-3 * u.Unit("cm-3") * gamma_init_interp ** (-2.1)

agnpy/tests/test_proton_synchrotron.py → agnpy/synchrotron/tests/test_proton_synchrotron.py

@@ -10,7 +10,7 @@
 from agnpy.synchrotron import Synchrotron, nu_synch_peak
 from agnpy.synchrotron import ProtonSynchrotron
 from agnpy.utils.math import trapz_loglog
-from .utils import (
+from agnpy.utils.validation_utils import (
     make_comparison_plot,
     extract_columns_sample_file,
     check_deviation,
@@ -19,18 +19,18 @@
 
 agnpy_dir = Path(__file__).parent.parent.parent  # go to the agnpy root
 # where to read sampled files
-data_dir = agnpy_dir / "agnpy/data"
+data_dir = agnpy_dir / "data"
 # where to save figures, clean-up before making the new
 figures_dir = clean_and_make_dir(agnpy_dir, "crosschecks/figures/proton_synchrotron")
 
 
 # Define source parameters
 B = 10 * u.G
 redshift = 0.32
-distPKS = Distance(z=redshift) # Already inside blob definition
+distPKS = Distance(z=redshift)  # Already inside blob definition
 doppler_s = 30
 Gamma_bulk = 16
-R = 1e16 * u.cm #radius of the blob
+R = 1e16 * u.cm  # radius of the blob
 
 
 class TestProtonSynchrotron:
@@ -39,28 +39,31 @@ class TestProtonSynchrotron:
     def test_synch_reference_sed(self):
         """Test agnpy proton synchrotron SED against the SED produced by the same particle distribution from Matteo Cerruti's code."""
         # reference SED
-        lognu, lognuFnu = np.genfromtxt(f"{data_dir}/reference_seds/cerruti_psynch/test_pss.dat",  dtype = 'float', comments = '#', usecols = (0,4), unpack = True)
-        nu_ref = 10**lognu * u.Unit('Hz')
-        sed_ref = 10**lognuFnu *u.Unit("erg cm-2 s-1")
+        lognu, lognuFnu = np.genfromtxt(
+            f"{data_dir}/reference_seds/cerruti_psynch/test_pss.dat",
+            dtype="float",
+            comments="#",
+            usecols=(0, 4),
+            unpack=True,
+        )
+        nu_ref = 10**lognu * u.Unit("Hz")
+        sed_ref = 10**lognuFnu * u.Unit("erg cm-2 s-1")
 
         # agnpy
-        n_p = ExpCutoffPowerLaw(k=12e4 / u.Unit('cm3'), #12e3 / u.Unit('cm3'),
-            p = 2.2 ,
-            gamma_c= 2.5e9,
-            gamma_min= 1,
+        n_p = ExpCutoffPowerLaw(
+            k=12e4 / u.Unit("cm3"),  # 12e3 / u.Unit('cm3'),
+            p=2.2,
+            gamma_c=2.5e9,
+            gamma_min=1,
             gamma_max=1e20,
-            mass=m_p
+            mass=m_p,
         )
 
-        blob = Blob(R_b=R,
-                z=redshift,
-                delta_D=doppler_s,
-                Gamma=Gamma_bulk,
-                B=B,
-                n_p=n_p
+        blob = Blob(
+            R_b=R, z=redshift, delta_D=doppler_s, Gamma=Gamma_bulk, B=B, n_p=n_p
         )
 
-        psynch = ProtonSynchrotron(blob)#, ssa = True)
+        psynch = ProtonSynchrotron(blob)  # , ssa = True)
         sed_agnpy = psynch.sed_flux(nu_ref)
 
         # sed comparison plot
@@ -80,26 +83,22 @@ def test_synch_reference_sed(self):
         # requires that the SED points deviate less than 25% from the figure
         assert check_deviation(nu_ref, sed_agnpy, sed_ref, 0.25, nu_range)
 
-
     def test_sed_integration_methods(self):
         """
         Test different integration methods against each other:
         simple trapezoidal rule vs trapezoidal rule in log-log space.
         """
-        n_p = ExpCutoffPowerLaw(k=12e4 / u.Unit('cm3'), #12e3 / u.Unit('cm3'),
-            p = 2.2 ,
-            gamma_c= 2.5e9,
-            gamma_min= 1,
+        n_p = ExpCutoffPowerLaw(
+            k=12e4 / u.Unit("cm3"),  # 12e3 / u.Unit('cm3'),
+            p=2.2,
+            gamma_c=2.5e9,
+            gamma_min=1,
             gamma_max=1e20,
-            mass=m_p
+            mass=m_p,
         )
 
-        blob = Blob(R_b=R,
-                z=redshift,
-                delta_D=doppler_s,
-                Gamma=Gamma_bulk,
-                B=B,
-                n_p=n_p
+        blob = Blob(
+            R_b=R, z=redshift, delta_D=doppler_s, Gamma=Gamma_bulk, B=B, n_p=n_p
         )
 
         psynch = ProtonSynchrotron(blob)
@@ -136,5 +135,5 @@ def test_sed_integration_methods(self):
     def test_nu_synch_peak(self):
         """Test peak synchrotron frequency for a given magnetic field and Lorentz factor."""
         gamma = 100
-        nu_synch = nu_synch_peak(1 * u.G, gamma, mass = m_p).to_value("Hz")
+        nu_synch = nu_synch_peak(1 * u.G, gamma, mass=m_p).to_value("Hz")
         assert np.isclose(nu_synch, 15245186.451944835, atol=0)

agnpy/tests/test_synchrotron.py → agnpy/synchrotron/tests/test_synchrotron.py

@@ -10,7 +10,7 @@
 from agnpy.synchrotron import Synchrotron, nu_synch_peak
 from agnpy.utils.math import trapz_loglog
 
-from .utils import (
+from agnpy.utils.validation_utils import (
     make_comparison_plot,
     extract_columns_sample_file,
     check_deviation,
@@ -19,15 +19,15 @@
 
 agnpy_dir = Path(__file__).parent.parent.parent  # go to the agnpy root
 # where to read sampled files
-data_dir = agnpy_dir / "agnpy/data"
+data_dir = agnpy_dir / "data"
 # where to save figures, clean-up before making the new
 figures_dir = clean_and_make_dir(agnpy_dir, "crosschecks/figures/synchrotron")
 
 
 # parameters of the Blob and EED in Figure 7.4 Dermer and Menon 2009
 W_e = 1e48 * u.Unit("erg")
 R_b = 1e16 * u.cm
-V_b = 4 / 3 * np.pi * R_b ** 3
+V_b = 4 / 3 * np.pi * R_b**3
 z = Distance(1e27, unit=u.cm).z
 
 
@@ -116,7 +116,11 @@ def test_synch_reference_sed(self, gamma_max, nu_range_max):
         ],
     )
     def test_ssa_reference_sed(
-        self, file_ref, n_e, figure_title, figure_path,
+        self,
+        file_ref,
+        n_e,
+        figure_title,
+        figure_path,
     ):
         """Test SSA SED generated by a given electron distribution against the
         ones generated with jetset version 1.1.2, via jetset_ssa_sed.py script."""

agnpy/tests/test_targets.py → agnpy/targets/tests/test_targets.py

@@ -112,7 +112,10 @@ def test_m_dot(self):
 
     @pytest.mark.parametrize(
         "R_in, R_out, R_g_units",
-        [(R_in_tilde_test, R_out_tilde_test, False), (R_in_test, R_out_test, True),],
+        [
+            (R_in_tilde_test, R_out_tilde_test, False),
+            (R_in_test, R_out_test, True),
+        ],
     )
     def test_R_in_R_out_units(self, R_in, R_out, R_g_units):
         """check if a TypeError is raised when passing R_in and R_out with

agnpy/tests/test_utils.py → agnpy/utils/tests/test_utils.py

@@ -6,14 +6,13 @@
 import agnpy.utils.math as math
 import agnpy.utils.geometry as geom
 from agnpy.utils.plot import load_mpl_rc, plot_sed
-from .utils import clean_and_make_dir
 
 twopi = 2 * np.pi
 
 
 def line_loglog(x, m, n):
     """a straight line in loglog-space"""
-    return x ** m * np.exp(n)
+    return x**m * np.exp(n)
 
 
 def integral_line_loglog(x_min, x_max, m, n):
@@ -62,7 +61,7 @@ def test_x_re_ring_mu_s_perp(self, R_re, r, uu, phi_re):
         mu_s = 0.01
         x1 = geom.x_re_ring_mu_s(R_re, r, phi_re, uu, mu_s)
         x2 = np.sqrt(
-            r ** 2 + (uu - R_re * np.cos(phi_re)) ** 2 + (R_re * np.sin(phi_re)) ** 2
+            r**2 + (uu - R_re * np.cos(phi_re)) ** 2 + (R_re * np.sin(phi_re)) ** 2
         )
         assert np.isclose(x1, x2, atol=0, rtol=0.01)
 
@@ -146,7 +145,7 @@ def test_x_re_shell_mu_s(self, phi_re):
         uu = 5e17 * u.cm
         mu_re = 0.999
         mu_s = 0.001
-        x_true = np.sqrt((r - R_re) ** 2 + uu ** 2)
+        x_true = np.sqrt((r - R_re) ** 2 + uu**2)
         x_shell = geom.x_re_shell_mu_s(R_re, r, phi_re, mu_re, uu, mu_s)
         assert np.isclose(x_shell, x_true, atol=0, rtol=0.01)
 
@@ -177,9 +176,9 @@ def test_phi_mu_re_shell(self, R_re, r, phi_re, uu, mu_s):
         mu_re = 0.99999
         phi_shell, mu_shell = geom.phi_mu_re_shell(R_re, r, phi_re, mu_re, uu, mu_s)
         phi_true = 0  # unless mu_s = 1 in which case phi_true can be whatever
-        dx = uu * np.sqrt(1 - mu_s ** 2)
+        dx = uu * np.sqrt(1 - mu_s**2)
         dz = r - R_re + uu * mu_s
-        mu_true = dz / np.sqrt(dx ** 2 + dz ** 2)
+        mu_true = dz / np.sqrt(dx**2 + dz**2)
         assert np.isclose(mu_shell, mu_true, atol=0.01, rtol=0)
         print(phi_true, phi_shell, R_re, r, phi_re, uu, mu_s)