debug:improve test coverage between matlab and python cases

typo

complete rebase

ncarglow/base.py

@@ -42,7 +42,10 @@ def simple(time: datetime, glat: float, glon: float,
                                   stderr=subprocess.DEVNULL,
                                   universal_newlines=True)
 
-    return glowparse(dat)
+    iono = glowparse(dat)
+    iono.attrs['geomag'] = ip
+
+    return iono
 
 
 def ebins(time: datetime, glat: float, glon: float,
@@ -87,9 +90,12 @@ def glowparse(raw: str) -> xarray.Dataset:
     dat = np.genfromtxt(table, skip_header=2, max_rows=NALT)
     alt_km = dat[:, 0]
 
-    states = ['Tn', 'O', 'N2', 'N', 'NO', 'NeIn', 'NeOut', 'ionrate',
+    states = ['Tn', 'O', 'N2', 'NO', 'NeIn', 'NeOut', 'ionrate',
               'O+', 'O2+', 'NO+', 'N2D', 'pedersen', 'hall']
 
+    if len(states) != dat.shape[1]-1:
+        raise ValueError('did not read raw output from GLOW correctly, please file a bug report.')
+
     d: dict = {k: ('alt_km', v) for (k, v) in zip(states, dat[:, 1:].T)}
     iono = xarray.Dataset(d, coords={'alt_km': alt_km})
 # %% VER

tests/test_basic.py

@@ -23,10 +23,12 @@ def test_simple():
         pytest.skip('CI internet FTP issue')
 
     assert iono['alt_km'].size == Nbins
-    assert iono.alt_km[32] == approx(101.8)
-    assert iono['Tn'][32] == approx(188.)
-    assert iono['ver'].loc[:, '5577'][32] == approx(20.45)
-    assert iono['ionrate'][32] == approx(335.)
+    i = 32
+    assert iono.alt_km[i] == approx(101.8)
+    assert iono['Tn'][i] == approx(188.)
+    assert iono['ver'].loc[:, '5577'][i] == approx(20.45)
+    assert iono['ionrate'][i] == approx(335.)
+    assert iono['hall'][i].item() == approx(6.98e-05)
 
 
 def test_ebins():

tests/test_basic.py.orig

@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+import ncarglow as glow
+import pytest
+from pytest import approx
+from datetime import datetime
+import numpy as np
+
+
+def test_simple():
+    time = datetime(2015, 12, 13, 10, 0, 0)
+    glat = 65.1
+    glon = -147.5
+    # %% flux [erg cm-2 s-1 == mW m-2 s-1]
+    Q = 1
+    # %% characteristic energy [eV]
+    Echar = 100e3
+    # %% Number of energy bins
+    Nbins = 250
+
+    try:
+        iono = glow.simple(time, glat, glon, Q, Echar, Nbins)
+    except ConnectionError:
+        pytest.skip('CI internet FTP issue')
+
+    assert iono['alt_km'].size == Nbins
+    assert iono.alt_km[32] == approx(101.8)
+    assert iono['Tn'][32] == approx(188.)
+    assert iono['ver'].loc[:, '5577'][32] == approx(20.45)
+<<<<<<< HEAD
+    assert iono['ionrate'][32] == approx(473.)
+=======
+    assert iono['ionrate'][32] == approx(0.488)
+>>>>>>> db1f403... upgrade API for use as subproject
+
+
+def test_ebins():
+    time = datetime(2015, 12, 13, 10, 0, 0)
+    glat = 65.1
+    glon = -147.5
+    # %% Energy grid [eV]
+    Emin = 0.1
+    Emax = 1e6
+    E0 = 100e3
+    Nbins = 250
+    # %% monoenergetic beam
+    Ebins = np.logspace(np.log10(Emin), np.log10(Emax), Nbins).astype(np.float32)
+    Phitop = np.zeros_like(Ebins)
+    Phitop[abs(Ebins-E0).argmin()] = 1.
+    Phitop = Phitop.astype(np.float32)
+    # %% run glow
+    try:
+        iono = glow.ebins(time, glat, glon, Ebins, Phitop)
+    except ConnectionError:
+        pytest.skip('CI internet FTP issue')
+
+    assert iono['alt_km'].size == Nbins
+    assert iono['Tn'][32] == approx(188.0)
+    assert iono['ver'].loc[:, '5577'][32] == approx(0.04)
+
+
+if __name__ == '__main__':
+    pytest.main(['-r', 'a', '-v', __file__])

tests/test_build.py.orig

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+import pytest
+import ncarglow.build as build
+from pathlib import Path
+
+R = Path(__file__).parent
+
+
+@pytest.mark.parametrize('build_sys', ['cmake', 'meson'])
+def test_build(build_sys, tmp_path):
+    build.build(build_sys, R.parent, tmp_path)
+
+
+<<<<<<< HEAD
+=======
+def test_bad(tmp_path):
+    with pytest.raises(ValueError):
+        build.build('fake', R.parent, tmp_path)
+
+
+>>>>>>> db1f403... upgrade API for use as subproject
+if __name__ == '__main__':
+    pytest.main(['-r', 'a', '-v', '-s', __file__])

tests/test_matlab.py

@@ -34,7 +34,7 @@ def test_matlab_build(build_sys, tmp_path):
 
 @pytest.mark.skipif(not MATLAB, reason="Matlab not available")
 def test_matlab_api():
-    subprocess.check_call([MATLAB, '-batch', 'test_mod'],
+    subprocess.check_call([MATLAB, '-batch', 'runtests'],
                           cwd=R, timeout=60)
 
 

tests/test_matlab.py.orig

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+r"""
+On Windows with Octave >= 5, you may need to add to PATH like:
+    C:\Octave\Octave-5.1.0.0\mingw64\bin
+to get at octave.exe instead of octave.vbs
+"""
+from pathlib import Path
+import subprocess
+import pytest
+import shutil
+
+R = Path(__file__).parent
+Rcode = R.parent / 'matlab'
+
+OCTAVE = shutil.which('octave-cli')
+MATLAB = shutil.which('matlab')
+
+
+@pytest.mark.skipif(not OCTAVE, reason="GNU Octave not available")
+@pytest.mark.parametrize('build_sys', ['cmake', 'meson'])
+def test_octave_build(build_sys, tmp_path):
+    subprocess.check_call([OCTAVE, '--eval',
+<<<<<<< HEAD
+                           f"setup('{build_sys}', '{R.parent}', '{tmp_path}')"],
+=======
+                           f"build('{build_sys}', '{R.parent}', '{tmp_path}')"],
+>>>>>>> db1f403... upgrade API for use as subproject
+                          cwd=Rcode, timeout=120)
+
+
+@pytest.mark.skipif(not MATLAB, reason="Matlab not available")
+@pytest.mark.parametrize('build_sys', ['cmake', 'meson'])
+def test_matlab_build(build_sys, tmp_path):
+    subprocess.check_call([MATLAB, '-batch',
+<<<<<<< HEAD
+                           f"setup('{build_sys}', '{R.parent}', '{tmp_path}')"],
+=======
+                           f"build('{build_sys}', '{R.parent}', '{tmp_path}')"],
+>>>>>>> db1f403... upgrade API for use as subproject
+                          cwd=Rcode, timeout=120)
+
+
+@pytest.mark.skipif(not MATLAB, reason="Matlab not available")
+def test_matlab_api():
+    subprocess.check_call([MATLAB, '-batch', 'test_mod'],
+                          cwd=R, timeout=60)
+
+
+@pytest.mark.skipif(not OCTAVE, reason='octave not found')
+def test_octave_api():
+    subprocess.check_call([OCTAVE, 'test_mod.m'],
+                          cwd=R, timeout=60)
+
+
+if __name__ == '__main__':
+    pytest.main(['-r', 'a', '-v', '-s', __file__])

tests/test_mod.m

@@ -2,10 +2,10 @@
 time = datenum(2015,12,13,10,0,0);
 glat = 65.1;
 glon = -147.5;
-Ap = 4;
-f107 = 100;
-f107a = 100;
-f107p = 100;
+Ap = 7;
+f107 = 118.7;
+f107a = 78.7;
+f107p = 113.1;
 Q = 1;
 Echar = 100e3;
 Nbins = 250;
@@ -15,9 +15,10 @@
 
 iono = glow(time, glat, glon, f107a, f107, f107p, Ap, Q, Echar, Nbins);
 
-i = 32-1;
+i = 32+1;
 
-assert(abs(iono.altkm(i)  -  101.8) < 0.1, 'wrong altitude?')
-assert(abs(iono.Tn(i)  - 188.) < 0.01, 'Tn error')
-assert(abs(iono.A5577(i) - 20.45) < 0.0001,  'A5577 error')
-assert(abs(iono.ionrate(i) - 335.) < 0.01, 'ionrate error')
+assert(abs(iono.altkm(i)  -  101.8) < 0.1, ['alt_km: expected 101.8, but got: ', num2str(iono.altkm(i))])
+assert(abs(iono.Tn(i)  - 188.) < 0.01, ['Tn: expected 188., but got: ', num2str(iono.Tn(i))])
+assert(abs(iono.A5577(i) - 20.45) < 0.0001,   ['A5577: expected 20.45, but got: ', num2str(iono.A5577(i))])
+assert(abs(iono.ionrate(i) - 335.) < 0.01, ['ionrate: expected 335. but got: ', num2str(iono.ionrate(i))])
+assert(abs(iono.hall(i) - 6.98e-5) < 1e-7, ['hall: expected 6.98e-5 but got: ', num2str(iono.hall(i))])

tests/test_mod.m.orig

@@ -0,0 +1,32 @@
+%% simple
+time = datenum(2015,12,13,10,0,0);
+glat = 65.1;
+glon = -147.5;
+Ap = 4;
+f107 = 100;
+f107a = 100;
+f107p = 100;
+Q = 1;
+Echar = 100e3;
+Nbins = 250;
+
+cwd = fileparts(mfilename('fullpath'));
+addpath([cwd, filesep, '..', filesep, 'matlab'])
+
+iono = glow(time, glat, glon, f107a, f107, f107p, Ap, Q, Echar, Nbins);
+
+<<<<<<< HEAD
+i = 32;
+
+assert(abs(iono.altkm(i)  -  99.8) < 0.1, 'wrong altitude?')
+assert(abs(iono.Tn(i)  - 188.) < 0.01, 'Tn error')
+assert(abs(iono.A5577(i) - 27.32) < 0.0001,  'A5577 error')
+assert(abs(iono.ionrate(i) - 473.) < 0.01, 'ionrate error')
+=======
+i = 32-1;
+
+assert(abs(iono.altkm(i)  -  101.8) < 0.1, 'wrong altitude?')
+assert(abs(iono.Tn(i)  - 188.) < 0.01, 'Tn error')
+assert(abs(iono.A5577(i) - 20.45) < 0.0001,  'A5577 error')
+assert(abs(iono.ionrate(i) - 0.488) < 0.01, 'ionrate error')
+>>>>>>> db1f403... upgrade API for use as subproject