From 8f6d0b5bb2e8d0b05bf57f27b160155feb1668ac Mon Sep 17 00:00:00 2001
From: thopri <thopri@noc.ac.uk>
Date: Thu, 26 Mar 2020 11:22:14 +0000
Subject: [PATCH] added unit testing to setup.py script

---
 README.rst                                    | 52 ++++++++++---------
 pynemo/pynemo_exe.py                          |  3 +-
 {unit_tests => pynemo}/unit_test.py           | 22 ++++----
 .../unit_tests}/gen_tools.py                  |  0
 .../unit_tests}/namelist_unit_test_offset.bdy | 16 +++---
 .../unit_tests}/namelist_unit_test_orth.bdy   | 16 +++---
 .../namelist_unit_test_rotated.bdy            | 16 +++---
 .../unit_tests}/resample_netcdf.py            |  0
 {unit_tests => pynemo/unit_tests}/test_gen.py | 28 +++++-----
 .../unit_tests}/unit_tests.ncml               |  8 +--
 setup.py                                      |  2 +-
 11 files changed, 84 insertions(+), 79 deletions(-)
 rename {unit_tests => pynemo}/unit_test.py (85%)
 rename {unit_tests => pynemo/unit_tests}/gen_tools.py (100%)
 rename {unit_tests => pynemo/unit_tests}/namelist_unit_test_offset.bdy (86%)
 rename {unit_tests => pynemo/unit_tests}/namelist_unit_test_orth.bdy (87%)
 rename {unit_tests => pynemo/unit_tests}/namelist_unit_test_rotated.bdy (86%)
 rename {unit_tests => pynemo/unit_tests}/resample_netcdf.py (100%)
 rename {unit_tests => pynemo/unit_tests}/test_gen.py (82%)
 rename {unit_tests => pynemo/unit_tests}/unit_tests.ncml (84%)

diff --git a/README.rst b/README.rst
index af36ede..1f749a2 100644
--- a/README.rst
+++ b/README.rst
@@ -21,15 +21,15 @@ Steps to take to install PyNEMO, creating a specific conda virtual environment i
 - Create conda environment for PyNEMO::
 
     $ cd to/PyNEMO/directory
-    $ conda env create -f environment_pynemo.yml
+    $ conda env create -f pynemo_37.yml
 
 - Activate the new virtual environment::
 
-   $ source activate pynemo_env
+   $ source activate pynemo3
 
-- Install Jave JRE (outside scope of this readme) and link libjvm.dylib to LD_LIBRARY_PATH variable::
+- Install Jave JDK (outside scope of this readme) and link Java Home to conda environment::
 
-    $ export LD_LIBRARY_PATH=/path/to/java/library/folder/containing/libjvm.dylib:$LD_LIBARY_PATH # see notes below
+    $ export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home # see notes below
 
 - Install PyNEMO::
   
@@ -39,45 +39,39 @@ Steps to take to install PyNEMO, creating a specific conda virtual environment i
 
 This should result in PyNEMO being installed in the virtual environment, and can be checked by entering::  
 
-    $ pynemo -v
+    $ pynemo -h
 
 Resulting in a help usage prompt::
  
-    $ usage: pynemo -g -s <namelist.bdy> 
+    $ usage: pynemo [-g] -s -d <namelist.bdy>
+       -g (optional) will open settings editor before extracting the data
+       -s <bdy filename> file to use
+       -d (optional) will download CMEMS data using provided bdy file
 
 The virtual environment can be deactivated to return you to the normal prompt by typing::  
     
-$ conda deactivate
+    $ conda deactivate
+
 To reactivate, the following needs to be typed::
 
-    $ source activate pynemo_env
+    $ source activate pynemo3
 
 
 To use PyNEMO, the following command is entered: (the example will run an benchmarking test)::
 
     $ pynemo -s /path/to/namelist/file (e.g. PyNEMO/inputs/namelist_remote.bdy)
 
-**Additional NOTES** 
-
-For Macbook Pro 2015, macOS Mojave and Java SDK 13 and JRE 8 the following path for the libjvm library should be correct:: 
-
-    /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server
+Other commands include -d which downloads the specified CMEMS data in the namelist bdy file.::
 
-Resulting in the following command: (this will be different for different java versions and operating systems)::
+    $ pynemo -d /PyNEMO/inputs/namelist_cmems.bdy
 
-    $ export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server:$LD_LIBRARY_PATH
-
-For an iMac 2013, macOS Catalina and JRE 8 only the followinng path was found to be correct::
-    
-   /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server
-   
-With the following command being required to set the environment variable::
+**Additional NOTES**
 
-    $ export LD_LIBRARY_PATH=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server:$LD_LIBRARY_PATH
+The above path for Java Home was valid for a Macbook Pro 2015 with macOS Catalina and Java SDK 13.0.2
+however for different java versions, operating systems etc this may be different
 
-The conda environment creation command has not yet been tested. The yml document (can be opened using text editor) gives a list of all the modules and their versions that are required for PyNEMO so a environment can be constructed using this document as reference (or if you use pip!)
+The conda environment yaml file has been tested with Miniconda 3.7 and found to install the enironment correctly.
 
-**Update** conda environment yaml file has been tested (and works!) on a Macbook Pro 2015 and iMac 2013 running Anaconda 3.7 and Miniconda 3.7 respectively. 
 
 Contribution guidelines
 -----------------------
@@ -101,6 +95,16 @@ The PyNEMO module can be tested using the bench marking namelist bdy file in the
   :width: 800
   :alt: Example BDY coords output
 
+Unit Tests
+-------------------
+
+To test operation of the PyNEMO module, running the PyTest script in the unit tests folder will perform a range tests on different child grids,
+checking the interpolation of the source data on to the child grid. To do this the following command is required::
+
+    $ pytest -q unit_tests/unit_test.py
+
+The command should be run from the main PyNEMO directory to enable modules to be imported correctly.
+
 Who do I talk to?
 -----------------
 
diff --git a/pynemo/pynemo_exe.py b/pynemo/pynemo_exe.py
index b441a3e..5c9aa96 100644
--- a/pynemo/pynemo_exe.py
+++ b/pynemo/pynemo_exe.py
@@ -18,7 +18,7 @@ def main():
     setup_file = ''
     mask_gui = False
     try:
-        opts, dummy_args = getopt.getopt(sys.argv[1:], "hsdg", ["help", "setup=", "download_cmems=", "mask_gui"])
+        opts, dummy_args = getopt.getopt(sys.argv[1:], "hs:dg", ["help", "setup=", "download_cmems=", "mask_gui"])
     except getopt.GetoptError:
         print("usage: pynemo -g -s -d <namelist.bdy> ")
         sys.exit(2)
@@ -41,6 +41,7 @@ def main():
             t1 = time.time()
             print("CMEMS download time: %s" % (t1 - t0))
             sys.exit(0)
+
     if setup_file == "":
         print("usage: pynemo [-g] -s <namelist.bdy> ")
         sys.exit(2)
diff --git a/unit_tests/unit_test.py b/pynemo/unit_test.py
similarity index 85%
rename from unit_tests/unit_test.py
rename to pynemo/unit_test.py
index 1daf0fe..ae95d17 100644
--- a/unit_tests/unit_test.py
+++ b/pynemo/unit_test.py
@@ -11,7 +11,7 @@ import os
 
 # generate test data by import test gen script and executing main function
 # TODO: Maybe simplify this, as this import imports other scripts and is abit clunky.
-import unit_tests.test_gen as tg
+from pynemo.unit_tests import test_gen as tg
 gen_data = tg._main()
 # if a non zero is return than the grid and data generation has failed.
 if gen_data != 0:
@@ -19,7 +19,7 @@ if gen_data != 0:
 
 # run PyNEMO with test data
 # generate list of namelist.bdy files to run
-namelist_files = glob.glob('unit_tests/namelist*')
+namelist_files = glob.glob('pynemo/unit_tests/namelist*')
 for n in namelist_files:
     # run each of the namelist files
     stdout, stderr = Popen(['pynemo', '-s', n], stdout=PIPE, stderr=PIPE,
@@ -34,7 +34,7 @@ for n in namelist_files:
 
 # perform tests
 def test_temp():
-    test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+    test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
     if len(test_files) == 0:
         raise Exception('DONT PANIC: no temperature test files found')
     for t in test_files:
@@ -47,7 +47,7 @@ def test_temp():
         assert abs(temp_[temp_ != 0.0].min() - 15) <= 0.001
 
 def test_salinty():
-    test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+    test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
     if len(test_files) == 0:
         raise Exception('DONT PANIC: no salinity test files found')
     for t in test_files:
@@ -63,7 +63,7 @@ def test_salinty():
 #  U and V and SSH tests are required. e.g. ln_dyn2d is set to true.
 
 def test_ssh():
-    test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+    test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
     if len(test_files) == 0:
         raise Exception('DONT PANIC: no SSH test files found')
     for t in test_files:
@@ -76,7 +76,7 @@ def test_ssh():
         assert abs(ssh_[ssh_ != 0.0].min() - 1.0) <= 0.001
 
 def test_U():
-    test_files = glob.glob('unit_tests/test_outputs/*bdyU*')
+    test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyU*')
     if len(test_files) == 0:
         raise Exception('DONT PANIC: no U current test files found')
     for t in test_files:
@@ -89,7 +89,7 @@ def test_U():
         assert abs(U_[U_ != 0.0].min() - 0.5) <= 0.001
 
 def test_V():
-    test_files = glob.glob('unit_tests/test_outputs/*bdyV*')
+    test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyV*')
     if len(test_files) == 0:
         raise Exception('DONT PANIC: no V current test files found')
     for t in test_files:
@@ -103,16 +103,16 @@ def test_V():
 
 # clean up test I/O
 def test_rm_out():
-    files = glob.glob('unit_tests/test_outputs/*')
+    files = glob.glob('pynemo/unit_tests/test_outputs/*')
     for f in files:
         os.remove(f)
-    files = glob.glob('unit_tests/test_outputs/*')
+    files = glob.glob('pynemo/unit_tests/test_outputs/*')
     assert len(files) == 0
 
 
 def test_rm_in():
-    files = glob.glob('unit_tests/test_inputs/*')
+    files = glob.glob('pynemo/unit_tests/test_inputs/*')
     for f in files:
         os.remove(f)
-    files = glob.glob('unit_tests/test_inputs/*')
+    files = glob.glob('pynemo/unit_tests/test_inputs/*')
     assert len(files) == 0
diff --git a/unit_tests/gen_tools.py b/pynemo/unit_tests/gen_tools.py
similarity index 100%
rename from unit_tests/gen_tools.py
rename to pynemo/unit_tests/gen_tools.py
diff --git a/unit_tests/namelist_unit_test_offset.bdy b/pynemo/unit_tests/namelist_unit_test_offset.bdy
similarity index 86%
rename from unit_tests/namelist_unit_test_offset.bdy
rename to pynemo/unit_tests/namelist_unit_test_offset.bdy
index 10d164b..d50f053 100644
--- a/unit_tests/namelist_unit_test_offset.bdy
+++ b/pynemo/unit_tests/namelist_unit_test_offset.bdy
@@ -30,18 +30,18 @@
 !------------------------------------------------------------------------------
 !  grid information 
 !------------------------------------------------------------------------------
-   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
-   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
-   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
-   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
-   sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
-   sn_bathy   = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_bathy.nc'
+   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_hgr_zps.nc'
+   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_zgr_zps.nc'
+   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
+   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
+   sn_src_msk = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/mask.nc'
+   sn_bathy   = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_offset_dst_bathy.nc'
 
 !------------------------------------------------------------------------------
 !  I/O 
 !------------------------------------------------------------------------------
-   sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
-   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
+   sn_src_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/unit_tests.ncml' ! src_files/'
+   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_outputs'
    sn_fn      = 'unit_test_offset'             ! prefix for output files
    nn_fv      = -1e20                 !  set fill value for output files
    nn_src_time_adj = 0                ! src time adjustment
diff --git a/unit_tests/namelist_unit_test_orth.bdy b/pynemo/unit_tests/namelist_unit_test_orth.bdy
similarity index 87%
rename from unit_tests/namelist_unit_test_orth.bdy
rename to pynemo/unit_tests/namelist_unit_test_orth.bdy
index 8542652..ff4ac6c 100644
--- a/unit_tests/namelist_unit_test_orth.bdy
+++ b/pynemo/unit_tests/namelist_unit_test_orth.bdy
@@ -30,18 +30,18 @@
 !------------------------------------------------------------------------------
 !  grid information 
 !------------------------------------------------------------------------------
-   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
-   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
-   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_hgr_zps.nc'
-   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_zgr_zps.nc'
-   sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
-   sn_bathy   = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_bathy.nc'
+   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_hgr_zps.nc'
+   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_zgr_zps.nc'
+   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_dst_hgr_zps.nc'
+   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_dst_zgr_zps.nc'
+   sn_src_msk = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/mask.nc'
+   sn_bathy   = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_dst_bathy.nc'
 
 !------------------------------------------------------------------------------
 !  I/O 
 !------------------------------------------------------------------------------
-   sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
-   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
+   sn_src_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/unit_tests.ncml' ! src_files/'
+   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_outputs'
    sn_fn      = 'unit_test_orth'             ! prefix for output files
    nn_fv      = -1e20                 !  set fill value for output files
    nn_src_time_adj = 0                ! src time adjustment
diff --git a/unit_tests/namelist_unit_test_rotated.bdy b/pynemo/unit_tests/namelist_unit_test_rotated.bdy
similarity index 86%
rename from unit_tests/namelist_unit_test_rotated.bdy
rename to pynemo/unit_tests/namelist_unit_test_rotated.bdy
index f970101..baa850d 100644
--- a/unit_tests/namelist_unit_test_rotated.bdy
+++ b/pynemo/unit_tests/namelist_unit_test_rotated.bdy
@@ -30,18 +30,18 @@
 !------------------------------------------------------------------------------
 !  grid information 
 !------------------------------------------------------------------------------
-   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
-   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
-   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
-   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
-   sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
-   sn_bathy   = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_bathy.nc'
+   sn_src_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_hgr_zps.nc'
+   sn_src_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_src_zgr_zps.nc'
+   sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
+   sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
+   sn_src_msk = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/mask.nc'
+   sn_bathy   = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/test_rot_dst_bathy.nc'
 
 !------------------------------------------------------------------------------
 !  I/O 
 !------------------------------------------------------------------------------
-   sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
-   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
+   sn_src_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/unit_tests.ncml' ! src_files/'
+   sn_dst_dir = '/Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_outputs'
    sn_fn      = 'unit_test_rotated'             ! prefix for output files
    nn_fv      = -1e20                 !  set fill value for output files
    nn_src_time_adj = 0                ! src time adjustment
diff --git a/unit_tests/resample_netcdf.py b/pynemo/unit_tests/resample_netcdf.py
similarity index 100%
rename from unit_tests/resample_netcdf.py
rename to pynemo/unit_tests/resample_netcdf.py
diff --git a/unit_tests/test_gen.py b/pynemo/unit_tests/test_gen.py
similarity index 82%
rename from unit_tests/test_gen.py
rename to pynemo/unit_tests/test_gen.py
index 9c27327..5150576 100644
--- a/unit_tests/test_gen.py
+++ b/pynemo/unit_tests/test_gen.py
@@ -6,7 +6,7 @@ occurs, the results are then plotted in a figure showing original (blue points)
 The source coordinate grid is also plotted (green).
 
 """
-import unit_tests.gen_tools as gt
+from pynemo.unit_tests import gen_tools as gt
 
 # TODO: remove hard coded file names and directories.
 # TODO: organise the variables better, (maybe in a single dict?)
@@ -21,8 +21,8 @@ def _main():
     max_dep = 100
     min_dep = 10
     z_end_dim = 1
-    h_fname = 'unit_tests/test_inputs/test_src_hgr_zps.nc'
-    z_fname = 'unit_tests/test_inputs/test_src_zgr_zps.nc'
+    h_fname = 'pynemo/unit_tests/test_inputs/test_src_hgr_zps.nc'
+    z_fname = 'pynemo/unit_tests/test_inputs/test_src_zgr_zps.nc'
     grid_h1 = gt.set_hgrid(dx,dy,jpi,jpj)
     grid_z1 = gt.set_zgrid(grid_h1,jpk,max_dep,min_dep,z_end_dim)
     write_coord_H = gt.write_coord_H(h_fname,grid_h1)
@@ -42,14 +42,14 @@ def _main():
     min_dep = 10
     z_end_dim = 1
     sf = 10
-    h_fname = 'unit_tests/test_inputs/test_dst_hgr_zps.nc'
-    z_fname = 'unit_tests/test_inputs/test_dst_zgr_zps.nc'
+    h_fname = 'pynemo/unit_tests/test_inputs/test_dst_hgr_zps.nc'
+    z_fname = 'pynemo/unit_tests/test_inputs/test_dst_zgr_zps.nc'
     grid_h2 = gt.set_hgrid(dx,dy,jpi,jpj,zoffx,zoffy,sf)
     grid_z2 = gt.set_zgrid(grid_h2,jpk,max_dep,min_dep,z_end_dim)
     write_coord_H = gt.write_coord_H(h_fname,grid_h2)
     write_coord_Z = gt.write_coord_Z(z_fname,grid_h2,grid_z2)
     # write bathy files (constant bathy)
-    bathy_fname = 'unit_tests/test_inputs/test_dst_bathy.nc'
+    bathy_fname = 'pynemo/unit_tests/test_inputs/test_dst_bathy.nc'
     bathy = gt.write_bathy(bathy_fname,grid_h2,grid_z2)
     if write_coord_H + write_coord_Z + bathy == 0:
         print("Org child grid generation successful!")
@@ -60,8 +60,8 @@ def _main():
     origin = (8,8)
 
     # rotate grid
-    rot_h_fname = 'unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
-    rot_z_fname = 'unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
+    rot_h_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
+    rot_z_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
     grid_rot = grid_h2.copy()
     grid_rot['latt'], grid_rot['lont'] = gt.rotate_around_point(grid_h2['latt'],grid_h2['lont'],theta,origin)
     grid_rot['latu'], grid_rot['lonu'] = gt.rotate_around_point(grid_h2['latu'], grid_h2['lonu'], theta, origin)
@@ -70,7 +70,7 @@ def _main():
     write_coord_H = gt.write_coord_H(rot_h_fname,grid_rot)
     write_coord_Z = gt.write_coord_Z(rot_z_fname,grid_rot,grid_z2)
     # write bathy files (constant bathy)
-    bathy_fname = 'unit_tests/test_inputs/test_rot_dst_bathy.nc'
+    bathy_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_bathy.nc'
     bathy = gt.write_bathy(bathy_fname,grid_rot,grid_z2)
     if write_coord_H + write_coord_Z + bathy == 0:
         print("Rotated child grid generation Successful!")
@@ -87,14 +87,14 @@ def _main():
     min_dep = 10
     z_end_dim = 1
     sf = 10
-    h_fname = 'unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
-    z_fname = 'unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
+    h_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
+    z_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
     grid_h3 = gt.set_hgrid(dx,dy,jpi,jpj,zoffx,zoffy,sf)
     grid_z3 = gt.set_zgrid(grid_h2,jpk,max_dep,min_dep,z_end_dim)
     write_coord_H = gt.write_coord_H(h_fname,grid_h3)
     write_coord_Z = gt.write_coord_Z(z_fname,grid_h3,grid_z3)
     # write bathy files (constant bathy)
-    bathy_fname = 'unit_tests/test_inputs/test_offset_dst_bathy.nc'
+    bathy_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_bathy.nc'
     bathy = gt.write_bathy(bathy_fname,grid_h3,grid_z3)
     if write_coord_H + write_coord_Z + bathy == 0:
         print("Offset child grid gneration successful!")
@@ -104,7 +104,7 @@ def _main():
     #           grid_h3['lont'],grid_h1['latt'],grid_h1['lont'])
 
     # write boundary files (constant parameters)
-    out_fname = 'unit_tests/test_inputs/output_boundary' #drop file extension
+    out_fname = 'pynemo/unit_tests/test_inputs/output_boundary' #drop file extension
     params_t = {'param1': {'name':'thetao','const_value':15.0,'longname':'temperature','units':'degreesC'},
               'param2': {'name':'so','const_value':35.0,'longname':'salinity','units':'PSU'},
               'param3': {'name': 'zos', 'const_value': 1.0, 'longname': 'sea surface height', 'units': 'metres'}
@@ -121,7 +121,7 @@ def _main():
         print('Boundary file generation successful!')
 
     #write_mask
-    mask_fname = 'unit_tests/test_inputs/mask.nc'
+    mask_fname = 'pynemo/unit_tests/test_inputs/mask.nc'
     mask = gt.write_mask(mask_fname,grid_h1,grid_z1)
     if mask == 0:
         print('Mask file generation successful!')
diff --git a/unit_tests/unit_tests.ncml b/pynemo/unit_tests/unit_tests.ncml
similarity index 84%
rename from unit_tests/unit_tests.ncml
rename to pynemo/unit_tests/unit_tests.ncml
index d376a10..c03b174 100644
--- a/unit_tests/unit_tests.ncml
+++ b/pynemo/unit_tests/unit_tests.ncml
@@ -2,22 +2,22 @@
   <ns0:aggregation type="union">
     <ns0:netcdf>
       <ns0:aggregation dimName="time" name="temperature" type="joinExisting">
-        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*T\.nc$" />
+        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/" regExp=".*T\.nc$" />
       </ns0:aggregation>
     </ns0:netcdf>
     <ns0:netcdf>
       <ns0:aggregation dimName="time" name="zonal_velocity" type="joinExisting">
-        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*U\.nc$" />
+        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/" regExp=".*U\.nc$" />
       </ns0:aggregation>
     </ns0:netcdf>
     <ns0:netcdf>
       <ns0:aggregation dimName="time" name="meridian_velocity" type="joinExisting">
-        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*V\.nc$" />
+        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/" regExp=".*V\.nc$" />
       </ns0:aggregation>
     </ns0:netcdf>
     <ns0:netcdf>
       <ns0:aggregation dimName="time" name="sea_surface_height" type="joinExisting">
-        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*T\.nc$" />
+        <ns0:scan location="file://Users/thopri/Projects/PyNEMO/pynemo/unit_tests/test_inputs/" regExp=".*T\.nc$" />
       </ns0:aggregation>
     </ns0:netcdf>
   </ns0:aggregation>
diff --git a/setup.py b/setup.py
index bdc2c36..5318e94 100644
--- a/setup.py
+++ b/setup.py
@@ -38,7 +38,7 @@ setup(
       
       keywords='Oceanography, NEMO',
       
-      packages=['pynemo','pynemo.tests','pynemo.gui','pynemo.utils','pynemo.tide','pynemo.reader'],
+      packages=['pynemo','pynemo.tests','pynemo.gui','pynemo.utils','pynemo.tide','pynemo.reader','pynemo.unit_tests'],
       
       install_requires=['netCDF4>=1.1.9','scipy','numpy','matplotlib', 'basemap', 'thredds_crawler', 'seawater'],
       
-- 
GitLab