Merge pull request #57 from cropsinsilico/debug

Matlab env variable issue on some OS

Author: langmm

.travis.yml

@@ -198,7 +198,7 @@ jobs:
           - $HOME/Library/Caches/pip
           - $HOME/Library/Caches/Homebrew
           - $HOME/R/Library
-      env: YGG_PYTHON=3.6 R_LIBS_USER=$HOME/R/Library YGG_TEST_FLAGS="tests/test_tools.py --test-suite=types --test-suite=timing --languages R c" INSTALLR=0
+      env: YGG_PYTHON=3.6 R_LIBS_USER=$HOME/R/Library YGG_TEST_FLAGS="tests/test_tools.py --test-suite=types --languages R c" INSTALLR=0
     - os: osx
       python: 3.7
       language: generic  # https://github.com/travis-ci/travis-ci/issues/2312
@@ -207,7 +207,7 @@ jobs:
         directories:
           - $HOME/Library/Caches/pip
           - $HOME/Library/Caches/Homebrew
-      env: YGG_CONDA=3.7 YGG_TEST_FLAGS="serialize --test-suite=examples_part1 communication/tests/test_IPCComm.py communication/tests/test_RMQAsyncComm.py" INSTALLZMQ=0
+      env: YGG_CONDA=3.7 YGG_TEST_FLAGS="serialize --test-suite=examples_part1 communication/tests/test_IPCComm.py communication/tests/test_RMQAsyncComm.py --test-suite=timing" INSTALLZMQ=0
       script:
         - yggconfig --remove-file
         - yggtest --ci tests/test_config.py $YGG_TEST_FLAGS

recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "yggdrasil" %}
-{% set version = "0.10.0" %}
+{% set version = "1.1.1" %}
 
 package:
   name: {{ name|lower }}
@@ -9,9 +9,9 @@ source:
   path: ../
 
 build:
-  number: 1
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv "
-  skip: true  # [win and vc<14]
+  skip: true  # [(win and vc<14) or py<35]
   entry_points:
     - ygginfo = yggdrasil.command_line:ygginfo
     - yggrun = yggdrasil.command_line:yggrun
@@ -33,9 +33,6 @@ build:
     - ygginstall = yggdrasil.command_line:ygginstall
 
 requirements:
-  # build:
-  #   - {{ compiler('c') }}
-  #   - {{ compiler('cxx') }}
   host:
     - czmq
     - pip
@@ -46,9 +43,10 @@ requirements:
     - cmake
     - czmq
     - flaky
+    - git
     - GitPython
     - jsonschema
-    - matplotlib
+    - matplotlib-base
     - numpy
     - pandas
     - pyperf

yggdrasil/drivers/MatlabModelDriver.py

@@ -562,22 +562,32 @@ def parse_arguments(self, args):
         self.wrapper_products.append(self.model_wrapper)
 
     @classmethod
-    def write_error_wrapper(cls, fname, try_lines, matlab_engine=None):
+    def write_error_wrapper(cls, fname, try_lines, env=None,
+                            matlab_engine=None):
         r"""Write a wrapper for the model that encloses it in a try except so
         that the error can be propagated appropriately.
 
         Args:
             fname (str): File where the wrapper should be written.
             try_lines (list): List of lines to go in the try block.
             model_file (str): Path to model that should be wrapped.
+            env (dict, optional): Dictionary of environment variables
+                that should be set before calling the model. Defaults
+                to None and is ignored.
             matlab_engine (MatlabEngine, optional): Matlab engine that will be
-               used to call the wrapper. If not provided, it is assumed the
-               error will be called using the Matlab interpreter on the command
-               line. Defautls to None.
+                used to call the wrapper. If not provided, it is assumed the
+                error will be called using the Matlab interpreter on the command
+                line. Defautls to None.
 
         Raises:
 
         """
+        # Add environment variables explicitly
+        lines = []
+        if env is not None:
+            for k, v in env.items():
+                lines.append('setenv(\'%s\', \'%s\')' % (
+                    k, v.encode("unicode_escape").decode('utf-8')))
         # Create lines based on use of engine or not
         if matlab_engine is not None:
             catch_block = ["error(e.message);"]
@@ -587,7 +597,7 @@ def write_error_wrapper(cls, fname, try_lines, matlab_engine=None):
             #                "disp(e.identifier);",
             #                "disp(e.stack);",
             #                "exit(0);"]
-        lines = cls.write_try_except(try_lines, catch_block)
+        lines += cls.write_try_except(try_lines, catch_block)
         if matlab_engine is None:
             lines.append("exit(0);")
         # Write lines
@@ -615,7 +625,7 @@ def run_code(cls, lines, **kwargs):
         kwargs.setdefault('process_kwargs', {})
         if not kwargs['process_kwargs'].get('dont_wrap_error', False):
             lines = cls.write_error_wrapper(
-                None, lines,
+                None, lines, env=kwargs.get('env', None),
                 matlab_engine=kwargs.get('matlab_engine', None))
             kwargs['process_kwargs']['dont_wrap_error'] = True
         return super(MatlabModelDriver, cls).run_code(lines, **kwargs)
@@ -677,6 +687,7 @@ def run_executable(cls, args, dont_wrap_error=False, fname_wrapper=None,
                 if working_dir is not None:
                     fname_wrapper = os.path.join(working_dir, fname_wrapper)
             cls.write_error_wrapper(fname_wrapper, try_block,
+                                    env=kwargs.get('env', None),
                                     matlab_engine=matlab_engine)
             assert(os.path.isfile(fname_wrapper))
             args = [os.path.splitext(os.path.basename(fname_wrapper))[0]]

yggdrasil/examples/gs_lesson3/src/gs_lesson3.m

@@ -1,4 +1,4 @@
-% Initialize input/output channels 
+% Initialize input/output channels
 in_channel = YggInterface('YggInput', 'input');
 out_channel = YggInterface('YggOutput', 'output');