Merge pull request #101 from kelle/fix-more-tests

Fix one tests and warnings

sedkit/catalog.py

@@ -10,7 +10,7 @@
 import dill
 import pickle
 from copy import copy
-from pkg_resources import resource_filename
+import importlib_resources
 import shutil
 
 from astropy.io import ascii
@@ -983,5 +983,5 @@ def __init__(self, **kwargs):
         super().__init__(name='M Dwarf Catalog', **kwargs)
 
         # Read the names from the file
-        file = resource_filename('sedkit', 'data/sources.txt')
+        file = importlib_resources.files('sedkit')/ 'data/sources.txt'
         self.from_file(file, run_methods=['find_SDSS', 'find_2MASS', 'find_WISE'])

sedkit/modelgrid.py

@@ -12,10 +12,10 @@
 import glob
 import itertools
 import pickle
-from copy import copy
 from functools import partial
 from multiprocessing import Pool
-from pkg_resources import resource_filename
+import importlib_resources
+from pathlib import Path
 
 import astropy.units as q
 import astropy.io.votable as vo
@@ -24,8 +24,8 @@
 from scipy.interpolate import RegularGridInterpolator
 from svo_filters import svo
 
-from . import utilities as u
-from .spectrum import Spectrum
+from sedkit import utilities as u
+from sedkit.spectrum import Spectrum
 
 
 def interp_flux(flux, params, values):
@@ -478,7 +478,7 @@ def load(self, dirname, **kwargs):
         self.index_path = os.path.join(dirname, 'index.p')
 
         if not os.path.isfile(self.index_path):
-            os.system("touch {}".format(self.index_path))
+            Path(self.index_path).touch()
 
             # Index the models
             self.index_models(parameters=self.parameters, **kwargs)
@@ -732,7 +732,8 @@ def save(self, file):
 
             # Make the file if necessary
             if not os.path.isfile(file):
-                os.system('touch {}'.format(file))
+                Path(file).touch()
+
 
             # Write the file
             f = open(file, 'wb')
@@ -762,7 +763,7 @@ def __init__(self, root=None, **kwargs):
 
         # Load the model grid
         modeldir = 'data/models/atmospheric/btsettl'
-        root = root or resource_filename('sedkit', modeldir)
+        root = root or importlib_resources.files('sedkit')/ modeldir
         self.load(root)
 
 
@@ -778,7 +779,7 @@ def __init__(self):
 
         # Load the model grid
         model_path = 'data/models/atmospheric/spexprismlibrary'
-        root = resource_filename('sedkit', model_path)
+        root = importlib_resources.files('sedkit')/ model_path
         self.load(root)
 
         # Add numeric spectral type

sedkit/spectrum.py

@@ -602,7 +602,7 @@ def integrate(self, units=None, n_samples=10):
         spec = u.scrub(self.data)
 
         # Integrate the spectrum
-        val = (np.trapz(spec[1], x=spec[0]) * m).to(units)
+        val = (np.trapezoid(spec[1], x=spec[0]) * m).to(units)
 
         if self.unc is None:
             vunc = None
@@ -615,7 +615,7 @@ def integrate(self, units=None, n_samples=10):
             uvals = []
             for n in range(n_samples):
                 usamp = np.random.normal(spec[1], spec[2])
-                err = (np.trapz(usamp, x=spec[0]) * m).to(units)
+                err = (np.trapezoid(usamp, x=spec[0]) * m).to(units)
                 uvals.append(abs(err.value - val.value))
 
             # Get 1-sigma of distribution
@@ -1153,7 +1153,7 @@ def synthetic_flux(self, bandpass, force=False, plot=False):
             idx = np.where([not np.isnan(i) for i in f])[0]
 
             # Calculate the flux
-            flx = (np.trapz(f[idx] * rsr[0][idx], x=wav[idx]) / np.trapz(rsr[0][idx], x=wav[idx])).to(self.flux_units)
+            flx = (np.trapezoid(f[idx] * rsr[0][idx], x=wav[idx]) / np.trapezoid(rsr[0][idx], x=wav[idx])).to(self.flux_units)
 
             # Calculate uncertainty
             if self.unc is not None:

sedkit/tests/test_catalog.py

@@ -1,11 +1,9 @@
 """A suite of tests for the catalog.py module"""
 import unittest
 import copy
-import os
-from pkg_resources import resource_filename
 
-from .. import sed
-from .. import catalog
+from sedkit import sed
+from sedkit import catalog
 
 
 class TestCatalog(unittest.TestCase):

sedkit/tests/test_helpers.py

@@ -1,16 +1,16 @@
 """A suite of tests for the helpers.py module"""
 import os
-from pkg_resources import resource_filename
+import importlib_resources
 
 from sedkit import helpers as help
 
 
 def test_process_dmestar():
     """Test the process_dmestar function"""
     # Process DMEStar files
-    dir = resource_filename('sedkit', 'data/models/evolutionary/DMESTAR/')
+    dir = importlib_resources.files('sedkit')/ 'data/models/evolutionary/DMESTAR/'
     help.process_dmestar(dir=dir, filename='dmestar_test.txt')
 
     # Delete temporary file
-    path = resource_filename('sedkit', 'data/models/evolutionary/dmestar_test.txt')
-    os.system('rm {}'.format(path))
+    temp_file = importlib_resources.files('sedkit')/ 'data/models/evolutionary/dmestar_test.txt'
+    os.remove(temp_file)

sedkit/tests/test_modelgrid.py

@@ -4,8 +4,8 @@
 
 import astropy.units as q
 
-from .. import modelgrid as mg
-from .. import utilities as u
+from sedkit import modelgrid as mg
+from sedkit import utilities as u
 
 
 class TestModelGrid(unittest.TestCase):
@@ -18,7 +18,7 @@ def setUp(self):
         path = resource_filename('sedkit', 'data/models/atmospheric/spexprismlibrary')
 
         # Delete the pickle so the models need to be indexed
-        os.system('rm {}'.format(os.path.join(path, 'index.p')))
+        os.remove(os.path.join(path, 'index.p'))
 
         # Load the model grid
         grid.load(path)
@@ -82,11 +82,11 @@ def test_load_model():
 def test_load_ModelGrid():
     """Test the load_ModelGrid function"""
     grid = mg.BTSettl()
-    path = './test.p'
-    grid.save(path)
-    lmg = mg.load_ModelGrid(path)
+    test_p = './test.p'
+    grid.save(test_p)
+    lmg = mg.load_ModelGrid(test_p)
     assert isinstance(lmg, mg.ModelGrid)
-    os.system('rm test.p')
+    os.remove(test_p)
 
 
 def test_BTSettl():