Merge pull request #157 from LSSTDESC/156-switch-nose-to-pytest

156 switch nose to pytest

config/auxtel.ini

@@ -20,7 +20,7 @@ SPECTRACTOR_FIT_TIMEOUT_PER_ITER = 1200
 # maximum time per gradient descent before TimeoutError in seconds
 SPECTRACTOR_FIT_TIMEOUT = 7200
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
-SPECTRACTOR_ATMOSPHERE_SIM = getobstamo
+SPECTRACTOR_ATMOSPHERE_SIM = getobsatmo
 
 [instrument]
 # instrument name

config/stardice.ini

@@ -18,7 +18,7 @@ SPECTRACTOR_DECONVOLUTION_FFM = False
 # value of sigma clip parameter for the spectractor deconvolution process PSF2D and FFM
 SPECTRACTOR_DECONVOLUTION_SIGMA_CLIP = 100
 # library to compute atmospheric transmission: none, libradtran, getobsatmo
-SPECTRACTOR_ATMOSPHERE_SIM = getobstamo
+SPECTRACTOR_ATMOSPHERE_SIM = getobsatmo
 
 [instrument]
 # instrument name

requirements.txt

@@ -18,7 +18,7 @@ configparser
 coveralls
 deprecated
 pyyaml
-pytest<8.1
+pytest
 pytest-cov
 getCalspec>=2.0.0
 lsst_utils

setup.cfg

@@ -1,5 +1,5 @@
 [tool:pytest]
-exclude=test_(extractor_ctio_planetary_nebula|astrometry|mcmc|multispectra)
+addopts = --ignore=tests/test_astrometry.py --ignore=tests/test_mcmc.py --ignore=tests/test_extractor_ctio_planetary_nebula.py
 
 [coverage:run]
 omit=spectractor/fit/mcmc.py

setup.py

@@ -30,8 +30,6 @@
     version=current_version,
     packages=['spectractor', 'spectractor.extractor', 'spectractor.simulation', 'spectractor.fit'],
     install_requires=reqs,
-    test_suite='nose.collector',
-    tests_require=['nose'],
     package_dir={'spectractor': './spectractor'},
     package_data={'spectractor': ['../config/*.ini'],
                   'spectractor.extractor': ['dispersers/HoloPhAg/*.txt', 'dispersers/HoloPhP/*.txt',

spectractor/extractor/spectrum.py

@@ -1787,8 +1787,8 @@ def detect_lines(lines, lambdas, spec, spec_err=None, cov_matrix=None, fwhm_func
             Y = -Gauss / Continuum
             Ydata = 1 - spectr_data / Continuum
 
-            line.fit_eqwidth_mod = integrate.simps(Y, x_int)  # sol1
-            line.fit_eqwidth_data = integrate.simps(Ydata, x_int)  # sol2
+            line.fit_eqwidth_mod = integrate.simpson(Y, x=x_int)  # sol1
+            line.fit_eqwidth_data = integrate.simpson(Ydata, x=x_int)  # sol2
 
             line.fit_popt = popt
             line.fit_pcov = pcov

tests/test_simulator.py

@@ -30,9 +30,9 @@ def test_atmosphere():
                        ozone_grid=[400, 400, 1], aerosol_grid=[0.0, 0.1, 2])
     atmospheric_grid = a.compute()
     assert np.sum(atmospheric_grid) > 0
-    assert np.all(np.isclose(a.atmgrid[0, a.index_atm_data:], parameters.LAMBDAS))
-    assert not np.any(np.isclose(a.atmgrid[1, a.index_atm_data:], np.zeros_like(parameters.LAMBDAS), rtol=1e-6))
-    assert a.atmgrid.shape == (3, a.index_atm_data + len(parameters.LAMBDAS))
+    assert np.all(np.isclose(a.atmgrid[0, a.index_atm_data:], a.lambdas))
+    assert not np.any(np.isclose(a.atmgrid[1, a.index_atm_data:], np.zeros_like(a.lambdas), rtol=1e-6))
+    assert a.atmgrid.shape == (3, a.index_atm_data + len(a.lambdas))
     a.save_file(a.image_filename.replace('.fits', '_atmsim.fits'))
     assert os.path.isfile('tests/data/reduc_20170605_028_atmsim.fits')
     a.load_file(a.image_filename.replace('.fits', '_atmsim.fits'))