Merge pull request #322 from LBL-EESA/release-3.0.0

finalizing release 3.0.0

MANIFEST.in

@@ -9,6 +9,6 @@ recursive-include apps *.*
 recursive-include python *.*
 recursive-include paraview *.*
 recursive-include test *.*
-recursive-include doc *.*
+recursive-include doc/release *.*
 global-exclude *.pdf
 global-exclude *.sw?

alg/teca_python_algorithm.py

@@ -1,4 +1,3 @@
-import teca_py
 
 class teca_python_algorithm(object):
     """
@@ -27,6 +26,7 @@ def initialize_implementation(self):
 
         # call overrides to get implementation for teca execution
         # phase implementations
+        import teca_py
         self.impl = teca_py.teca_programmable_algorithm.New()
         self.impl.set_number_of_input_connections(n_inputs)
         self.impl.set_number_of_output_ports(n_outputs)
@@ -70,7 +70,8 @@ def get_report_callback(self):
         phase of execution.
         """
         def report_callback(port, md_in):
-             return teca_py.teca_metadata(md_in[0])
+            import teca_py
+            return teca_py.teca_metadata(md_in[0])
         return report_callback
 
     def get_request_callback(self):
@@ -84,6 +85,7 @@ def get_request_callback(self):
         phase of execution.
         """
         def request_callback(port, md_in, req_in):
+            import teca_py
             return [teca_py.teca_metadata(req_in)]
         return request_callback
 
@@ -98,6 +100,7 @@ def get_execute_callback(self):
         phase of execution.
         """
         def execute_callback(port, data_in, req_in):
+            import teca_py
             if len(data_in):
                 data_out = data_in[0].new_instance()
                 data_out.shallow_copy(teca_py.as_non_const_teca_dataset(data_out))

doc/release/3.0.0.md

@@ -0,0 +1,44 @@
+# Release Notes for TECA 3.0.0 #
+
+This is a major release in support of:
+
+  T.A. O'Brien et al, **"Detection of Atmospheric Rivers with Inline
+  Uncertainty Quantification: TECA-BARD v1.0"**, Geoscientific Model
+  Development, submitted winter 2020
+
+The pipeline internals were refactored to be more general, the assumption that
+time was the dimension across which the reduction is applied was removed, as
+well as changes that enable nested map-reduce.
+
+The TECA User Guide was ported to "Read the Docs". https://teca.readthedocs.io
+
+Our Travis CI test infrastructure was updated to use Docker, and two new OS
+images Fedora 28, and Ubuntu 18.04 were deployed.
+
+More than 40 bug fixes
+
+## New algorithms included in this release: ##
+
+| Type                | Name                               | Description                                                                       |
+|---------------------|------------------------------------|-----------------------------------------------------------------------------------|
+| general puprose     | teca_2d_component_area             | Computes the area's of regions identified by the connected components filter.     |
+| general puprose     | teca_bayesian_ar_detect            | Detects atmospheric rivers using a Bayesian method.                               |
+| general puprose     | teca_bayesian_ar_detect_parameters | Parameters used by Bayesian AR detector.                                          |
+| general puprose     | teca_cartesian_mesh_source         | Used to create Cratesian meshes in memory and inject them into a pipeline.        |
+| general puprose     | teca_component_area_filter         | Masks regions with area out side a user specified range                           |
+| general puprose     | teca_component_statistics          | Gathers information about connected component regions into a tabular format       |
+| general puprose     | teca_latitude_damper               | Multiplies a field by an inverted Gaussian (user specified mean and HWHM)         |
+| general puprose     | teca_normalize_coordinates         | Transforms Cartesian meshes such that coordinates are always in ascending order   |
+| general puprose     | teca_python_algorithm              | Base class for TECA algorithm's written in Python. Handles internal plumbing      |
+| core infrastructure | teca_memory_profiler               | Supporting class that samples memory consumtion during application execution      |
+| core infrastructure | teca_profiler                      | Supporting class that logs start, stop, and duration of developer defined events  |
+| I/O                 | teca_cartesian_mesh_reader         | Reads TECA Cartesian meshes in TECA's internal binary format                      |
+| I/O                 | teca_cartesian_mesh_writer         | Writes TECA Cartesian meshes in TECA's internal binary format                     |
+| I/O                 | teca_cf_writer                     | Writes TECA Cratesian meshes in NetCDF CF2 conventions                            |
+
+## New applications included in this release: ##
+
+| Name                     | Description                                                             |
+|--------------------------|-------------------------------------------------------------------------|
+| teca_bayesian_ar_detect  | Command line application that can be used to detect AR's on HPC systems |
+| teca_profile_explorer    | Interactive tool for exploring run time profiling data                  |

setup.py

@@ -12,7 +12,7 @@
 # when compiled outside of the git repo we must set the version
 # manually. Also note that these must be unique per upload to PyPi
 # so be sure to use an 'rcX' for testing
-teca_version = "2.2.2"
+teca_version = "3.0.0"
 
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=''):
@@ -63,7 +63,7 @@ def build_extension(self, ext):
             raise RuntimeError('Windows is currrently unsupprted due to a lack of interest/funding')
         else:
             cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
-            build_args += ['--', '-j20']
+            build_args += ['--', '-j%d'%(nj)]
             install_args += ['--', '-j%d'%(nj), 'install']
 
         # make the build directory