add mpi4py to pyproject.toml to ensure access to parallel tests

anuga/parallel/setup.py

@@ -7,13 +7,8 @@ def configuration(parent_package='',top_path=None):
 
     config = Configuration('parallel', parent_package, top_path)
 
-    try:
-        import mpi4py
-    except:
-        pass
-    else:
-        config.add_data_dir('tests')
-        config.add_data_dir('data')
+    config.add_data_dir('tests')
+    config.add_data_dir('data')
 
     return config
 

anuga/parallel/tests/test_parallel_distribute_mesh.py

@@ -15,7 +15,7 @@
 import os
 import subprocess
 
-verbose = True
+verbose = False
 
 path = os.path.dirname(__file__)  # Get folder where this script lives
 run_filename = os.path.join(path, 'run_parallel_distribute_mesh.py')
@@ -31,6 +31,7 @@ def setUp(self):
         extra_options = '--oversubscribe'
         cmd = 'mpiexec -np 3 ' + extra_options + ' echo '
 
+        # See if we get an error with --oversubscribe option
         result = subprocess.run(cmd.split(), capture_output=True)
         if result.returncode != 0:
             extra_options = ' '

docs/source/installation.rst

@@ -85,6 +85,50 @@ via the command:
 
 You might even like to set this up in your `.bashrc` file. 
 
+Installing on Ubuntu using apt and pip
+--------------------------------------
+
+ANUGA can be installed using `pip`, but a complication arrise when installing 
+the `gdal` package. 
+
+First set up a python virtual environment and activate  via:
+
+.. code-block:: bash
+
+    python3 -m venv anuga_env
+    course anuga_env/bin/activate
+
+Now we first need to install the `gdal` python package. First install the 
+gdal library, via:
+
+.. code-block:: bash
+    sudo apt-get install -y gdal-bin libgdal-dev
+
+We need to ascertain the version of  `gdal` installed using the following command: 
+
+.. code-block:: bash
+
+    ogrinfo --version
+
+THe version of `gdal` to install via `pip` should match the version of the library. 
+For instance on Ubuntu 20.04 the previous command produces:
+
+.. code-block:: bash
+
+    GDAL 3.0.4, released 2020/01/28
+
+So in this case we install the `gdal` python package as follows
+
+.. code-block:: bash
+
+    pip install gdal==3.0.4
+
+Now we complete the installation of `anuga` simply by:
+
+.. code-block:: bash
+
+    pip install anuga
+
 Installing on Ubuntu using apt and pip
 ---------------------------------------
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "future", "Cython", "wheel", "numpy", "gitpython"]
+requires = ["setuptools", "future", "Cython", "wheel", "numpy", "gitpython", "mpi4py"]
 build-backend = "setuptools.build_meta"
 
 

requirements.txt

@@ -2,14 +2,15 @@ numpy
 scipy 
 matplotlib 
 nose 
+pytest
 cython 
 netcdf4 
 dill 
 future 
 gitpython
 pyproj 
 pymetis 
-triangle 
+meshpy
 Pmw
 pytz
 nbsphinx