Merge pull request #16 from tsutterley/testing

directly call matlab program in test suite

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]         
+        os: [ubuntu-20.04, macos-latest]
         python-version: [3.5, 3.6, 3.7, 3.8]
 
     steps:
@@ -25,12 +25,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies for Linux
-      if: matrix.os == 'ubuntu-latest'
+      if: matrix.os == 'ubuntu-20.04'
       run: |
-        sudo apt-get install libproj-dev proj-data proj-bin libgeos-dev
+        sudo apt-get install libproj-dev proj-data proj-bin libgeos-dev octave
         sudo apt-get install libhdf5-dev libnetcdf-dev
         pip install --upgrade pip
-        pip install flake8 pytest pytest-cov numpy
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install dependencies for MacOS
       if: matrix.os == 'macos-latest'
@@ -39,8 +39,9 @@ jobs:
         brew install geos
         brew install hdf5
         brew install netcdf
+        brew install octave
         pip install --upgrade pip
-        pip install flake8 pytest pytest-cov numpy
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |
@@ -51,4 +52,6 @@ jobs:
     - name: Test with pytest
       run: |
         pip install --no-deps .
-        pytest
+        git clone ${{ secrets.TMD_MATLAB_TOOLBOX }}
+        pytest --username=${{ secrets.EARTHDATA_USERNAME }} \
+            --password=${{ secrets.EARTHDATA_PASSWORD }}

.github/workflows/python-request.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]         
+        os: [ubuntu-20.04, macos-latest]
         python-version: [3.5, 3.6, 3.7, 3.8]
 
     steps:
@@ -22,12 +22,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies for Linux
-      if: matrix.os == 'ubuntu-latest'
+      if: matrix.os == 'ubuntu-20.04'
       run: |
-        sudo apt-get install libproj-dev proj-data proj-bin libgeos-dev
+        sudo apt-get install libproj-dev proj-data proj-bin libgeos-dev octave
         sudo apt-get install libhdf5-dev libnetcdf-dev
         pip install --upgrade pip
-        pip install flake8 pytest pytest-cov numpy
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install dependencies for MacOS
       if: matrix.os == 'macos-latest'
@@ -36,8 +36,9 @@ jobs:
         brew install geos
         brew install hdf5
         brew install netcdf
+        brew install octave
         pip install --upgrade pip
-        pip install flake8 pytest pytest-cov numpy
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |
@@ -48,4 +49,6 @@ jobs:
     - name: Test with pytest
       run: |
         pip install --no-deps .
-        pytest
+        git clone ${{ secrets.TMD_MATLAB_TOOLBOX }}
+        pytest --username=${{ secrets.EARTHDATA_USERNAME }} \
+            --password=${{ secrets.EARTHDATA_PASSWORD }}

doc/source/conf.py

@@ -22,7 +22,7 @@
 author = 'Tyler C. Sutterley'
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.2.6'
+release = '1.0.2.7'
 
 
 # -- General configuration ---------------------------------------------------

pyTMD/bilinear_interp.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-bilinear_interp.py (07/2020)
+bilinear_interp.py (08/2020)
 Bilinear interpolation of input data to output coordinates
 
 CALLING SEQUENCE:
@@ -25,6 +25,7 @@
         https://numpy.org/doc/stable/user/numpy-for-matlab-users.html
 
 UPDATE HISTORY:
+    Updated 08/2020: check that output coordinates are within bounds
     Updated 07/2020: split into separate function
     Updated 06/2020: use argmin and argmax in bilinear interpolation
     Updated 09/2017: Rewritten in Python
@@ -57,29 +58,36 @@ def bilinear_interp(ilon,ilat,idata,lon,lat,dtype=np.float):
     #-- grid step size of tide model
     dlon = np.abs(ilon[1] - ilon[0])
     dlat = np.abs(ilat[1] - ilat[0])
+    #-- find valid points (within bounds)
+    valid, = np.nonzero((lon >= ilon.min()) & (lon <= ilon.max()) &
+        (lat > ilat.min()) & (lat < ilat.max()))
     #-- Convert input coordinates to radians
     phi = ilon*dtr
     th = (90.0 - ilat)*dtr
     #-- Convert output data coordinates to radians
     xphi = lon*dtr
     xth = (90.0 - lat)*dtr
     #-- interpolate gridded data values to data
-    data = np.zeros_like(lon,dtype=dtype)
-    for i,l in enumerate(lon):
+    npts = len(lon)
+    data = np.ma.zeros((npts),dtype=dtype)
+    data.mask = np.ones((npts),dtype=np.bool)
+    data.mask[valid] = False
+    #-- for each valid point
+    for i in valid:
         #-- calculating the indices for the original grid
         dx = (ilon - np.floor(lon[i]/dlon)*dlon)**2
         dy = (ilat - np.floor(lat[i]/dlat)*dlat)**2
         iph = np.argmin(dx)
         ith = np.argmin(dy)
         #-- if on corner value: use exact
         if ((lat[i] == ilat[ith]) & (lon[i] == ilon[iph])):
-            data[i] = idata[ith,iph]
+            data.data[i] = idata[ith,iph]
         elif ((lat[i] == ilat[ith+1]) & (lon[i] == ilon[iph])):
-            data[i] = idata[ith+1,iph]
+            data.data[i] = idata[ith+1,iph]
         elif ((lat[i] == ilat[ith]) & (lon[i] == ilon[iph+1])):
-            data[i] = idata[ith,iph+1]
+            data.data[i] = idata[ith,iph+1]
         elif ((lat[i] == ilat[ith+1]) & (lon[i] == ilon[iph+1])):
-            data[i] = idata[ith+1,iph+1]
+            data.data[i] = idata[ith+1,iph+1]
         else:
             #-- corner weight values for i,j
             Wa = (xphi[i]-phi[iph])*(xth[i]-th[ith])
@@ -94,6 +102,6 @@ def bilinear_interp(ilon,ilat,idata,lon,lat,dtype=np.float):
             Ic = idata[ith+1,iph]#-- (0,1)
             Id = idata[ith+1,iph+1]#-- (1,1)
             #-- calculate interpolated value for i
-            data[i] = (Ia*Wa + Ib*Wb + Ic*Wc + Id*Wd)/W
+            data.data[i] = (Ia*Wa + Ib*Wb + Ic*Wc + Id*Wd)/W
     #-- return interpolated values
     return data

pyTMD/read_tide_model.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_tide_model.py (07/2020)
+read_tide_model.py (08/2020)
 Reads files for a tidal model and makes initial calculations to run tide program
 Includes functions to extract tidal harmonic constants from OTIS tide models for
     given locations
@@ -50,6 +50,7 @@
     bilinear_interp.py: bilinear interpolation of data to specified coordinates
 
 UPDATE HISTORY:
+    Updated 08/2020: check that interpolated points are within range of model
     Updated 07/2020: added function docstrings. separate bilinear interpolation
         update griddata interpolation. changed TYPE variable to keyword argument
     Updated 06/2020: output currents as numpy masked arrays
@@ -118,6 +119,7 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
         xi,yi,hz,mz,iob,dt = read_tide_grid(grid_file)
     #-- run wrapper function to convert coordinate systems of input lat/lon
     x,y = convert_ll_xy(ilon,ilat,EPSG,'F')
+    invalid = (x < xi.min()) | (x > xi.max()) | (y < yi.min()) | (y > yi.max())
     #-- grid step size of tide model
     dx = xi[1] - xi[0]
     dy = yi[1] - yi[0]
@@ -236,7 +238,7 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
                 z[z==0] = np.nan
                 #-- use quick bilinear to interpolate values
                 z1 = np.ma.zeros((npts),dtype=z.dtype)
-                z1.data = bilinear_interp(xi,yi,z,x,y,dtype=np.complex128)
+                z1.data[:] = bilinear_interp(xi,yi,z,x,y,dtype=np.complex128)
                 #-- replace nan values with fill_value
                 z1.mask = (np.isnan(z1.data) | (~mz1.astype(np.bool)))
                 z1.data[z1.mask] = z1.fill_value
@@ -257,7 +259,7 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
                 z[z==0] = np.nan
                 #-- use scipy griddata to interpolate values
                 z1 = np.ma.zeros((npts),dtype=z.dtype)
-                z1.data=scipy.interpolate.griddata(interp_points,
+                z1.data[:] = scipy.interpolate.griddata(interp_points,
                     z.flatten(), np.c_[x,y], method=METHOD)
                 #-- replace nan values with fill_value
                 z1.mask = (np.isnan(z1.data) | (~mz1.astype(np.bool)))
@@ -283,7 +285,7 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
                 u[u==0] = np.nan
                 #-- use quick bilinear to interpolate values
                 u1 = np.ma.zeros((npts),dtype=u.dtype)
-                u1.data = bilinear_interp(xi,yi,u,x,y,dtype=np.complex128)
+                u1.data[:] = bilinear_interp(xi,yi,u,x,y,dtype=np.complex128)
                 #-- replace nan values with fill_value
                 u1.mask = (np.isnan(u1.data) | (~mu1.astype(np.bool)))
                 u1.data[u1.mask] = u1.fill_value
@@ -303,7 +305,7 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
                 u[u==0] = np.nan
                 #-- use scipy griddata to interpolate values
                 u1 = np.ma.zeros((npts),dtype=u.dtype)
-                u1.data=scipy.interpolate.griddata(interp_points,
+                u1.data[:] = scipy.interpolate.griddata(interp_points,
                     u.flatten(), np.c_[x,y], method=METHOD)
                 #-- replace nan values with fill_value
                 u1.mask = (np.isnan(u1.data) | (~mu1.astype(np.bool)))
@@ -363,6 +365,9 @@ def extract_tidal_constants(ilon, ilat, grid_file, model_file, EPSG, TYPE='z',
             amplitude.mask[:,i] = np.copy(v1.mask)
             ph.data[:,i] = np.arctan2(-np.imag(v1),np.real(v1))
             ph.mask[:,i] = np.copy(v1.mask)
+        #-- update mask to invalidate points outside model domain
+        ph.mask[:,i] |= invalid
+        amplitude.mask[:,i] |= invalid
 
     #-- convert phase to degrees
     phase = ph*180.0/np.pi

pytest.ini

@@ -2,3 +2,5 @@
 minversion = 2.0
 norecursedirs = .git
 python_files = test*.py
+testpaths =
+    test

test/requirements.txt → requirements-dev.txt

@@ -1,2 +1,5 @@
+flake8
 pytest>=4.6
 pytest-cov
+numpy
+oct2py

setup.py

@@ -14,7 +14,7 @@
 
 setup(
     name='pyTMD',
-    version='1.0.2.6',
+    version='1.0.2.7',
     description='Tide Model Driver to read OTIS, GOT and FES formatted tidal solutions and make tidal predictions',
     long_description=long_description,
     long_description_content_type="text/markdown",

test/conftest.py

@@ -0,0 +1,15 @@
+import pytest
+
+def pytest_addoption(parser):
+    parser.addoption("--username", action="store", help="NASA Earthdata username")
+    parser.addoption("--password", action="store", help="NASA Earthdata password")
+
+@pytest.fixture
+def username(request):
+    """ Returns NASA Earthdata username """
+    return request.config.getoption("--username")
+
+@pytest.fixture
+def password(request):
+    """ Returns NASA Earthdata password """
+    return request.config.getoption("--password")