Address Deprecation Warnings (#201)

* Simplify 'pos()' in examples.
* Address deprecation warnings

empymod/transform.py

@@ -1213,7 +1213,7 @@ def get_dlf_points(filt, inp, nr_per_dec):
 
     # Get pts_per_dec and define number of out-values, depending on pts_per_dec
     if nr_per_dec < 0:  # Lagged Convolution DLF
-        pts_per_dec = 1/np.log(filt.factor)
+        pts_per_dec = 1/np.log(filt.factor.item())
 
         # Calculate number of output values
         nout = int(np.ceil(np.log(outmax/outmin)*pts_per_dec) + 1)

examples/reproducing/ward1988.py

@@ -129,18 +129,6 @@ def dhzdt(t, res, r, m=1.):
     return s
 
 
-###############################################################################
-
-def pos(data):
-    """Return positive data; set negative data to NaN."""
-    return np.array([x if x > 0 else np.nan for x in data])
-
-
-def neg(data):
-    """Return -negative data; set positive data to NaN."""
-    return np.array([-x if x < 0 else np.nan for x in data])
-
-
 ###############################################################################
 # Survey parameters
 # ~~~~~~~~~~~~~~~~~
@@ -174,17 +162,23 @@ def neg(data):
 # Plot the result
 # ~~~~~~~~~~~~~~~
 
+
+def pos(data):
+    """Return positive data; set negative data to NaN."""
+    return np.where(data > 0, data, np.nan)
+
+
 plt.figure(figsize=(5, 6))
 
 plt.plot(time*1e3, pos(dhz_ana), 'k-', lw=2, label='Ward & Hohmann')
-plt.plot(time*1e3, neg(dhz_ana), 'k--', lw=2)
+plt.plot(time*1e3, pos(-dhz_ana), 'k--', lw=2)
 plt.plot(time*1e3, pos(dhz_num), 'C1-', label='empymod; dHz/dt')
-plt.plot(time*1e3, neg(dhz_num), 'C1--')
+plt.plot(time*1e3, pos(-dhz_num), 'C1--')
 
 plt.plot(time*1e3, pos(hz_ana), 'k-', lw=2)
-plt.plot(time*1e3, neg(hz_ana), 'k--', lw=2)
+plt.plot(time*1e3, pos(-hz_ana), 'k--', lw=2)
 plt.plot(time*1e3, pos(hz_num), 'C0-', label='empymod; Hz')
-plt.plot(time*1e3, neg(hz_num), 'C0--')
+plt.plot(time*1e3, pos(-hz_num), 'C0--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -228,10 +222,10 @@ def neg(data):
 plt.figure(figsize=(5, 5))
 
 plt.plot(freq, pos(fhz_num.real), 'C0-', label='Real')
-plt.plot(freq, neg(fhz_num.real), 'C0--')
+plt.plot(freq, pos(-fhz_num.real), 'C0--')
 
 plt.plot(freq, pos(fhz_num.imag), 'C1-', label='Imaginary')
-plt.plot(freq, neg(fhz_num.imag), 'C1--')
+plt.plot(freq, pos(-fhz_num.imag), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -270,10 +264,10 @@ def neg(data):
 plt.figure(figsize=(5, 5))
 
 plt.plot(freq, pos(fhz_num.real), 'C0-', label='Real')
-plt.plot(freq, neg(fhz_num.real), 'C0--')
+plt.plot(freq, pos(-fhz_num.real), 'C0--')
 
 plt.plot(freq, pos(fhz_num.imag), 'C1-', label='Imaginary')
-plt.plot(freq, neg(fhz_num.imag), 'C1--')
+plt.plot(freq, pos(-fhz_num.imag), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -313,7 +307,7 @@ def neg(data):
 
 ax1 = plt.subplot(111)
 plt.plot(time*1e3, pos(fdhz_num), 'C0-', label='dHz/dt')
-plt.plot(time*1e3, neg(fdhz_num), 'C0--')
+plt.plot(time*1e3, pos(-fdhz_num), 'C0--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -327,7 +321,7 @@ def neg(data):
 ax2 = ax1.twinx()
 
 plt.plot(time*1e3, pos(fhz_num), 'C1-', label='Hz')
-plt.plot(time*1e3, neg(fhz_num), 'C1--')
+plt.plot(time*1e3, pos(-fhz_num), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -370,10 +364,10 @@ def neg(data):
 plt.figure(figsize=(5, 5))
 
 plt.plot(freq, pos(fhz_num.real), 'C0-', label='Real')
-plt.plot(freq, neg(fhz_num.real), 'C0--')
+plt.plot(freq, pos(-fhz_num.real), 'C0--')
 
 plt.plot(freq, pos(fhz_num.imag), 'C1-', label='Imaginary')
-plt.plot(freq, neg(fhz_num.imag), 'C1--')
+plt.plot(freq, pos(-fhz_num.imag), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -420,10 +414,10 @@ def neg(data):
 
 ax1 = plt.subplot(111)
 plt.plot(time*1e3, pos(fdhz_num), 'C0-', label=r'dhz/dt (A/m-s)')
-plt.plot(time*1e3, neg(fdhz_num), 'C0--')
+plt.plot(time*1e3, pos(-fdhz_num), 'C0--')
 
 plt.plot(time*1e3, pos(fhz_num), 'C1-', label='hz (A/m)')
-plt.plot(time*1e3, neg(fhz_num), 'C1--')
+plt.plot(time*1e3, pos(-fhz_num), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -462,10 +456,10 @@ def neg(data):
 plt.figure(figsize=(5, 5))
 
 plt.plot(freq, pos(fhz_num.real), 'C0-', label='Real')
-plt.plot(freq, neg(fhz_num.real), 'C0--')
+plt.plot(freq, pos(-fhz_num.real), 'C0--')
 
 plt.plot(freq, pos(fhz_num.imag), 'C1-', label='Imaginary')
-plt.plot(freq, neg(fhz_num.imag), 'C1--')
+plt.plot(freq, pos(-fhz_num.imag), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -504,10 +498,10 @@ def neg(data):
 plt.figure(figsize=(5, 5))
 
 plt.plot(freq, pos(fhz_num.real), 'C0-', label='Real')
-plt.plot(freq, neg(fhz_num.real), 'C0--')
+plt.plot(freq, pos(-fhz_num.real), 'C0--')
 
 plt.plot(freq, pos(fhz_num.imag), 'C1-', label='Imaginary')
-plt.plot(freq, neg(fhz_num.imag), 'C1--')
+plt.plot(freq, pos(-fhz_num.imag), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -548,7 +542,7 @@ def neg(data):
 ax1 = plt.subplot(111)
 
 plt.plot(time*1e3, pos(fdhz_num), 'C0-', label='dHz/dt')
-plt.plot(time*1e3, neg(fdhz_num), 'C0--')
+plt.plot(time*1e3, pos(-fdhz_num), 'C0--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -562,7 +556,7 @@ def neg(data):
 ax2 = ax1.twinx()
 
 plt.plot(time*1e3, pos(fhz_num), 'C1-', label='Hz')
-plt.plot(time*1e3, neg(fhz_num), 'C1--')
+plt.plot(time*1e3, pos(-fhz_num), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -603,7 +597,7 @@ def neg(data):
 ax1 = plt.subplot(111)
 
 plt.plot(time*1e3, pos(fdhz_num), 'C0-', label='dHz/dt')
-plt.plot(time*1e3, neg(fdhz_num), 'C0--')
+plt.plot(time*1e3, pos(-fdhz_num), 'C0--')
 
 plt.xscale('log')
 plt.yscale('log')
@@ -617,7 +611,7 @@ def neg(data):
 ax2 = ax1.twinx()
 
 plt.plot(time*1e3, pos(fhz_num), 'C1-', label='Hz')
-plt.plot(time*1e3, neg(fhz_num), 'C1--')
+plt.plot(time*1e3, pos(-fhz_num), 'C1--')
 
 plt.xscale('log')
 plt.yscale('log')

examples/time_domain/cole_cole_ip.py

@@ -57,16 +57,6 @@
 plt.style.use('ggplot')
 
 
-def pos(data):
-    """Return positive data; set negative data to NaN."""
-    return np.array([x if x > 0 else np.nan for x in data])
-
-
-def neg(data):
-    """Return -negative data; set positive data to NaN."""
-    return np.array([-x if x < 0 else np.nan for x in data])
-
-
 ###############################################################################
 # Use empymod with user-def. func. to adjust :math:`\eta` and :math:`\zeta`
 # -------------------------------------------------------------------------
@@ -258,21 +248,29 @@ def cole_perm(inp, p_dict):
 out_cole_perm = empymod.bipole(res=cole_perm_model, **model)
 out_pelton = empymod.bipole(res=pelton_model, **model)
 
+
 # Plot
+
+
+def pos(data):
+    """Return positive data; set negative data to NaN."""
+    return np.where(data > 0, data, np.nan)
+
+
 plt.figure()
 plt.title('Switch-off')
 plt.plot(times, pos(out_bipole), '-', label='Regular Bipole')
-plt.plot(times, neg(out_bipole), '--', label='')
+plt.plot(times, pos(-out_bipole), '--', label='')
 
 plt.plot(times, pos(out_cole), '-', label='Cole and Cole (1941) Conductivity')
-plt.plot(times, neg(out_cole), '--', label='')
+plt.plot(times, pos(-out_cole), '--', label='')
 
 plt.plot(times, pos(out_cole_perm), '-',
          label='Cole and Cole (1941) Permittivity')
-plt.plot(times, neg(out_cole_perm), '--', label='')
+plt.plot(times, pos(-out_cole_perm), '--', label='')
 
 plt.plot(times, pos(out_pelton), '-', label='Pelton et al. (1978) Resistivity')
-plt.plot(times, neg(out_pelton), '--', label='')
+plt.plot(times, pos(-out_pelton), '--', label='')
 
 plt.legend()
 plt.yscale('log')

tests/test_cli.py

@@ -26,7 +26,7 @@ def test_main(script_runner):
 
     # help
     for inp in ['--help', '-h']:
-        ret = script_runner.run('empymod', inp)
+        ret = script_runner.run(['empymod', inp])
         assert ret.success
         assert "3D electromagnetic modeller for 1D VTI media" in ret.stdout
 
@@ -37,27 +37,27 @@ def test_main(script_runner):
     assert "empymod v" in ret.stdout
 
     # report
-    ret = script_runner.run('empymod', '--report')
+    ret = script_runner.run(['empymod', '--report'])
     assert ret.success
     # Exclude time to avoid errors.
     # Exclude empymod-version (after 300), because if run locally without
     # having empymod installed it will be "unknown" for the __main__ one.
     assert empymod.utils.Report().__repr__()[115:300] in ret.stdout
 
     # version        -- VIA empymod/__main__.py by calling the folder empymod.
-    ret = script_runner.run('python', 'empymod', '--version')
+    ret = script_runner.run(['python', 'empymod', '--version'])
     assert ret.success
     assert "empymod v" in ret.stdout
 
     # Wrong function -- VIA empymod/__main__.py by calling the file.
     ret = script_runner.run(
-            'python', join('empymod', '__main__.py'), 'wrong')
+            ['python', join('empymod', '__main__.py'), 'wrong'])
     assert not ret.success
     assert "error: argument routine: invalid choice: 'wrong'" in ret.stderr
 
     # try to run
     ret = script_runner.run(
-            'empymod', 'bipole', 'test.json', 'output.txt')
+            ['empymod', 'bipole', 'test.json', 'output.txt'])
     assert not ret.success
     assert "No such file or directory" in ret.stderr