Merge pull request #346 from xylar/fix_tmp_dir

Allow conversion tools to be called with a directory

compass/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "compass" %}
-{% set version = "0.1.10" %}
+{% set version = "0.1.11" %}
 {% set build = 0 %}
 
 {% if mpi == "nompi" %}
@@ -31,7 +31,7 @@ requirements:
   run:
     - python
     - geometric_features 0.1.11
-    - mpas_tools 0.0.12
+    - mpas_tools 0.0.13
     - jigsaw 0.9.12
     - jigsawpy 0.2.1
     - metis

conda_package/docs/versions.rst

@@ -9,6 +9,7 @@ Documentation    On GitHub
 `stable`_        `master`_
 `v0.0.11`_        `0.0.11`_
 `v0.0.12`_        `0.0.12`_
+`v0.0.13`_        `0.0.13`_
 ================ ===============
 
 .. _`stable`: ../stable/index.html
@@ -17,3 +18,5 @@ Documentation    On GitHub
 .. _`0.0.11`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/0.0.11
 .. _`v0.0.12`: ../0.0.12/index.html
 .. _`0.0.12`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/0.0.12
+.. _`v0.0.13`: ../0.0.13/index.html
+.. _`0.0.13`: https://github.com/MPAS-Dev/MPAS-Analysis/tree/0.0.13

conda_package/mpas_tools/__init__.py

@@ -1,2 +1,2 @@
-__version_info__ = (0, 0, 12)
+__version_info__ = (0, 0, 13)
 __version__ = '.'.join(str(vi) for vi in __version_info__)

conda_package/mpas_tools/mesh/conversion.py

@@ -1,17 +1,14 @@
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
 import os
 import xarray
 import subprocess
-from backports.tempfile import TemporaryDirectory
+from tempfile import TemporaryDirectory
 import shutil
 
 from mpas_tools.io import write_netcdf
 
 
-def convert(dsIn, graphInfoFileName=None, logger=None):
-    '''
+def convert(dsIn, graphInfoFileName=None, logger=None, dir=None):
+    """
     Use ``MpasMeshConverter.x`` to convert an input mesh to a valid MPAS
     mesh that is fully compliant with the MPAS mesh specification.
     https://mpas-dev.github.io/files/documents/MPAS-MeshSpec.pdf
@@ -29,13 +26,18 @@ def convert(dsIn, graphInfoFileName=None, logger=None):
     logger : ``logging.Logger``, optional
         A logger for the output if not stdout
 
+    dir : str, optional
+        A directory in which a temporary directory will be added with files
+        produced during conversion and then deleted upon completion.
+
     Returns
     -------
     dsOut : ``xarray.Dataset``
         The MPAS mesh
-    '''
-
-    with TemporaryDirectory() as tempdir:
+    """
+    if dir is not None:
+        dir = os.path.abspath(dir)
+    with TemporaryDirectory(dir=dir) as tempdir:
         inFileName = '{}/mesh_in.nc'.format(tempdir)
         write_netcdf(dsIn, inFileName)
 
@@ -64,8 +66,8 @@ def convert(dsIn, graphInfoFileName=None, logger=None):
 
 
 def cull(dsIn, dsMask=None, dsInverse=None, dsPreserve=None,
-         graphInfoFileName=None, logger=None):
-    '''
+         graphInfoFileName=None, logger=None, dir=None):
+    """
     Use ``MpasCellCuller.x`` to cull cells from a mesh based on the
     ``cullCell`` field in the input file or DataSet and/or the provided masks.
     ``cullCell``, dsMask and dsInverse are merged together so that the final
@@ -98,14 +100,19 @@ def cull(dsIn, dsMask=None, dsInverse=None, dsPreserve=None,
     logger : ``logging.Logger``, optional
         A logger for the output if not stdout
 
+    dir : str, optional
+        A directory in which a temporary directory will be added with files
+        produced during cell culling and then deleted upon completion.
+
     Returns
     -------
     dsOut : ``xarray.Dataset``
         The culled mesh
 
-    '''
-
-    with TemporaryDirectory() as tempdir:
+    """
+    if dir is not None:
+        dir = os.path.abspath(dir)
+    with TemporaryDirectory(dir=dir) as tempdir:
         inFileName = '{}/ds_in.nc'.format(tempdir)
         write_netcdf(dsIn, inFileName)
         outFileName = '{}/ds_out.nc'.format(tempdir)
@@ -158,8 +165,9 @@ def cull(dsIn, dsMask=None, dsInverse=None, dsPreserve=None,
     return dsOut
 
 
-def mask(dsMesh, fcMask=None, fcSeed=None, positiveLon=False, logger=None):
-    '''
+def mask(dsMesh, fcMask=None, fcSeed=None, positiveLon=False, logger=None,
+         dir=None):
+    """
     Use ``MpasMaskCreator.x`` to create a set of region masks either from
     mask feature collecitons or from seed points to be used to flood fill
 
@@ -178,14 +186,19 @@ def mask(dsMesh, fcMask=None, fcSeed=None, positiveLon=False, logger=None):
     logger : ``logging.Logger``, optional
         A logger for the output if not stdout
 
+    dir : str, optional
+        A directory in which a temporary directory will be added with files
+        produced during mask creation and then deleted upon completion.
+
     Returns
     -------
     dsMask : ``xarray.Dataset``
         The masks
 
-    '''
-
-    with TemporaryDirectory() as tempdir:
+    """
+    if dir is not None:
+        dir = os.path.abspath(dir)
+    with TemporaryDirectory(dir=dir) as tempdir:
         inFileName = '{}/mesh_in.nc'.format(tempdir)
         write_netcdf(dsMesh, inFileName)
         outFileName = '{}/mesh_out.nc'.format(tempdir)

conda_package/mpas_tools/mesh/creation/build_mesh.py

@@ -17,7 +17,8 @@
 
 
 def build_spherical_mesh(cellWidth, lon, lat, earth_radius,
-                         out_filename='base_mesh.nc', plot_cellWidth=True):
+                         out_filename='base_mesh.nc', plot_cellWidth=True,
+                         dir='./'):
     """
     Build an MPAS mesh using JIGSAW with the given cell sizes as a function of
     latitude and longitude.
@@ -46,6 +47,10 @@ def build_spherical_mesh(cellWidth, lon, lat, earth_radius,
     plot_cellWidth : bool, optional
         Whether to produce a plot of ``cellWidth``. If so, it will be written to
         ``cellWidthGlobal.png``.
+
+    dir : str, optional
+        A directory in which a temporary directory will be added with files
+        produced during mesh conversion and then deleted upon completion.
     """
 
     da = xarray.DataArray(cellWidth,
@@ -92,7 +97,7 @@ def build_spherical_mesh(cellWidth, lon, lat, earth_radius,
                      sphere_radius=earth_radius)
 
     print('Step 3. Convert from triangles to MPAS mesh')
-    write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc')),
+    write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc'), dir=dir),
                  out_filename)
 
 

conda_package/mpas_tools/ocean/moc.py

@@ -18,7 +18,8 @@ def make_moc_basins_and_transects(gf, mesh_filename,
                                   mask_and_transect_filename,
                                   geojson_filename=None,
                                   mask_filename=None,
-                                  logger=None):
+                                  logger=None,
+                                  dir=None):
     """
     Builds features defining the ocean basins and southern transects used in
     computing the meridional overturning circulation (MOC)
@@ -42,6 +43,10 @@ def make_moc_basins_and_transects(gf, mesh_filename,
     logger : ``logging.Logger``, optional
         A logger for the output if not stdout
 
+    dir : str, optional
+        A directory in which a temporary directory will be added with files
+        produced during conversion and then deleted upon completion.
+
     Returns
     -------
     fc : ``FeatureCollection``
@@ -58,7 +63,7 @@ def make_moc_basins_and_transects(gf, mesh_filename,
 
     dsMesh = xarray.open_dataset(mesh_filename)
     dsMasks = mpas_tools.mesh.conversion.mask(dsMesh=dsMesh, fcMask=fcMOC,
-                                              logger=logger)
+                                              logger=logger, dir=dir)
 
     if mask_filename is not None:
         write_netcdf(dsMasks, mask_filename)

conda_package/mpas_tools/viz/paraview_extractor.py

@@ -2142,11 +2142,13 @@ def _cull_files(fc_region_mask, temp_dir, mesh_filename, time_file_names,
     with xarray.open_dataset(mesh_filename) as ds_mesh:
         ds_mesh = ds_mesh[mesh_vars]
         print('Making a region mask file')
-        ds_mask = mask(dsMesh=ds_mesh, fcMask=fc_region_mask, logger=logger)
+        ds_mask = mask(dsMesh=ds_mesh, fcMask=fc_region_mask, logger=logger,
+                       dir=temp_dir)
         write_netcdf(ds_mask, '{}/mask.nc'.format(temp_dir))
         print('Cropping mesh to region')
         out_mesh_filename = '{}/mesh.nc'.format(temp_dir)
-        ds_culled = cull(dsIn=ds_mesh, dsInverse=ds_mask, logger=logger)
+        ds_culled = cull(dsIn=ds_mesh, dsInverse=ds_mask, logger=logger,
+                         dir=temp_dir)
         write_netcdf(ds_culled, out_mesh_filename)
 
         region_masks = dict()

conda_package/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "mpas_tools" %}
-{% set version = "0.0.12" %}
+{% set version = "0.0.13" %}
 
 package:
   name: {{ name|lower }}
@@ -45,7 +45,6 @@ requirements:
     - geometric_features
     - pyevtk
     - future
-    - backports.tempfile
     - jigsaw >=0.9.12
     - jigsawpy >=0.2.1
     - pyflann