Merge branch 'main' into post-meeting

.github/workflows/test.yaml

@@ -0,0 +1,16 @@
+name: unit_testing
+
+on:
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    container: iquod/wodpy:test-base-230716
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+      - name: run_tests
+        run: pytest 

Dockerfile-testing-base

@@ -1,4 +1,4 @@
 FROM python:3.9
 
 RUN apt-get update -y && apt-get install -y libhdf5-serial-dev netcdf-bin libnetcdf-dev
-RUN pip install numpy pandas cftime netCDF4 nose
+RUN pip install numpy pandas cftime netCDF4 pytest

tests/netcdf_test.py

@@ -0,0 +1,149 @@
+from datetime import datetime, timedelta
+from wodpy import wodnc
+import numpy, math, pandas, pytest
+
+@pytest.fixture
+def classic1():
+    # example from pp 124 of http://data.nodc.noaa.gov/woa/WOD/DOC/wodreadme.pdf
+    # with IQuOD flags
+    r = wodnc.Ragged("tests/testData/ocldb1570984477.6279_OSD.nc")
+    return wodnc.ncProfile(r, 55)
+
+def test_latitude(classic1):
+    '''
+    check latitude == 61.93
+    '''
+
+    latitude = classic1.latitude()
+    assert round(latitude, 2) == 61.93, 'latitude should have been approx 61.93, instead read %f' % latitude
+
+def test_longitude(classic1):
+    '''
+    check latitude == -172.270
+    '''
+
+    longitude = classic1.longitude()
+    assert round(longitude, 2) == -172.270, 'longitude should have been approx -172.270, instead read %f' % latitude
+
+def test_uid(classic1):
+    '''
+    check profile ID == 67064
+    '''
+
+    uid = classic1.uid()
+    assert uid == 67064, 'uid should have been 67064, instead read %f' % uid
+
+def test_n_levels(classic1):
+    '''
+    check the number of levels == 4
+    '''
+
+    levels = classic1.n_levels()
+    assert levels == 4, 'levels should have been 4, instead read %f' % levels
+
+def test_year(classic1):
+    '''
+    check year == 1934
+    '''
+
+    year = classic1.year()
+    assert year == 1934, 'year should have been 1934, instead read %f' % year
+
+def test_month(classic1):
+    '''
+    check month == 8
+    '''
+
+    month = classic1.month() 
+    assert month == 8, 'month should have been 8, instead read %f' % month
+
+def test_day(classic1):
+    '''
+    check day == 7
+    '''
+
+    day = classic1.day()
+    assert day == 7, 'day should have been 7, instead read %f' % day
+
+def test_time(classic1):
+    ''' 
+    check time == 10.37
+    '''
+
+    time = classic1.time()
+    assert round(time,2) == 10.37, 'time should have been 10.37, instead read %f' % time
+
+def test_datetime(classic1):
+    '''
+    check datetime is close to 1934-8-7 10:22:12
+    allow a 36 second (== 0.01 hour) deviation for round off error in the time
+    '''
+
+    d = classic1.datetime()
+    assert timedelta(seconds=-18) < (d - datetime(1934, 8, 7, 10, 22, 12)) < timedelta(seconds=18), 'time should have been close to 1934-08-07 10:22:12, instead read %s' % d
+
+def test_probe_type(classic1):
+    '''
+    check probe type == 7
+    '''
+
+    probe = classic1.probe_type() 
+    assert probe == 7, 'probe should have been 7, instead read %f' % probe
+
+def test_depth(classic1):
+    '''
+    check depths == [0.0, 10.0, 25.0, 50.0]
+    '''
+
+    truth = [0.0, 10.0, 25.0, 50.0]
+    truth = [numpy.float32(t) for t in truth]
+    z = classic1.z()
+    assert numpy.array_equal(z, truth), 'depths should have been [0, 10, 25, 50], instead read %s' % z.__str__()
+
+def test_temperature(classic1):
+    '''
+    check temperatures == [8.960, 8.950, 0.900, -1.230]
+    '''
+
+    truth = [8.960, 8.950, 0.900, -1.230]
+    truth = [numpy.float32(t) for t in truth]
+    t = classic1.t()
+    assert numpy.array_equal(t, truth), 'temperatures should have been [8.96, 8.95, 0.9, -1.23], instead read %s' % t.__str__()
+
+def test_salinity(classic1):
+    '''
+    check salinities == [30.900, 30.900, 31.910, 32.410]
+    '''
+
+    truth = [30.900, 30.900, 31.910, 32.410]
+    truth = [numpy.float32(t) for t in truth]
+    s = classic1.s()
+    assert numpy.array_equal(s, truth), 'salinities should have been [30.9, 30.9, 31.91, 32.41], instead read %s' % s.__str__()
+
+def test_oxygen(classic1):
+    truth = [293.90298, 291.90366, 375.3761,  317.39523]
+    truth = [numpy.float32(t) for t in truth]
+    s = classic1.oxygen()
+    assert numpy.array_equal(s, truth), 'dissolved oxygen should have been [293.90298, 291.90366, 375.3761,  317.39523], instead read %s' % s.__str__()
+
+def test_phosphate(classic1):
+    truth = [0.63, 0.69, 0.88, 1.14]
+    truth = [numpy.float32(t) for t in truth]
+    s = classic1.phosphate()
+    assert numpy.array_equal(s, truth), 'phosphate should have been [0.63, 0.69, 0.88, 1.14], instead read %s' % s.__str__()
+
+def test_silicate(classic1):
+    truth = [20, 12, 15, 25]
+    truth = [numpy.float32(t) for t in truth]
+    s = classic1.silicate()
+    assert numpy.array_equal(s, truth), 'silicate should have been [20, 12, 15, 25], instead read %s' % s.__str__()
+
+def test_pH(classic1):
+    truth = [8.100, 8.100, 8.100, 8.050]
+    truth = [numpy.float32(t) for t in truth]
+    s = classic1.pH()
+    assert numpy.array_equal(s, truth), 'pH should have been [8.100, 8.100, 8.100, 8.050], instead read %s' % s.__str__()
+
+
+
+