Merge branch 'master' into docs

.travis.yml

@@ -13,11 +13,13 @@ language: generic
 
 env:
   matrix:
-    # test with the latest version of Python 3.x
-    - PY=3   NUMPY=1.18 SCIPY=1.4 PETSc=3.12 UPLOAD_DOCS=1 SNOPT_VERSION=7.7 PYOPTSPARSE_VERSION=v2.1.0
-    - PY=3 NUMPY=1.17 SCIPY=1.3 SNOPT_VERSION=7.2 PYOPTSPARSE_VERSION=v1.2
-    - PY=3.7 NUMPY=1.17 SCIPY=1.3 SNOPT_VERSION=7.7 PYOPTSPARSE_VERSION=v2.1.0
-    - PY=3.6 NUMPY=1.16 SCIPY=1.2 PETSc=3.10.2 SNOPT_VERSION=7.7 PYOPTSPARSE_VERSION=v2.1.0
+    # latest versions
+    - PY=3   NUMPY=1    SCIPY=1   PYOPTSPARSE=v2.1.0 SNOPT=7.7 PETSc=3
+    # baseline versions
+    - PY=3.8 NUMPY=1.18 SCIPY=1.4 PYOPTSPARSE=v2.1.0 SNOPT=7.7 PETSc=3.12 UPLOAD_DOCS=1
+    # older versions
+    - PY=3.7 NUMPY=1.17 SCIPY=1.3 PYOPTSPARSE=v2.1.0 SNOPT=7.7
+    - PY=3.6 NUMPY=1.16 SCIPY=1.2 PYOPTSPARSE=v1.2   SNOPT=7.2 PETSc=3.10.2
 
 git:
   depth: 99999
@@ -72,7 +74,7 @@ install:
     echo "KEY NOT FOUND";
   fi
 
-# if we don't have a cached conda environment then build one, otherwise just activate the cached one
+# build Python environment
 - |
   echo ">>> Building python environment";
   echo " >> Installing conda";
@@ -87,46 +89,42 @@ install:
   conda create --yes -n PY$PY python=$PY numpy=$NUMPY scipy=$SCIPY cython swig;
   source $HOME/miniconda/bin/activate PY$PY;
 
-  echo " >> Installing non-pure Python dependencies from conda";
+  pip install --upgrade pip;
 
   if [ "$PETSc" ]; then
-    echo "Installing PETSc";
+    echo " >> Installing PETSc";
     conda install -c anaconda mpi4py --yes;
     conda install -c conda-forge petsc=$PETSc petsc4py --yes;
   fi
 
-  pip install --upgrade pip;
-
-  echo " >> Installing forked python packages";
-  pip install git+https://github.com/swryan/coveralls-python@work;
+  if [ "$PYOPTSPARSE" ]; then
+    echo " >> Installing pyOptSparse";
+    git clone -q https://github.com/OpenMDAO/build_pyoptsparse;
 
-  echo " >> Installing pyOptSparse";
-  git clone https://github.com/OpenMDAO/build_pyoptsparse;
-  cd build_pyoptsparse;
-  chmod 755 ./build_pyoptsparse.sh;
+    cd build_pyoptsparse;
+    chmod 755 ./build_pyoptsparse.sh;
 
-  echo " >> Checking SNOPT and PyoptSparse version"
-  if [[ "$SNOPT_VERSION" == "7.7" && "$PYOPTSPARSE_VERSION" == "v2.1.0" ]] || [[ "$SNOPT_VERSION" == "7.2" && "$PYOPTSPARSE_VERSION" == "v1.2" ]]; then
-    echo " >> Found SNOPT and PyoptSparse"
-    if [ "$SNOPT_VERSION" == "7.7" ] && [ "$SNOPT_LOCATION_77" ]; then
+    if [ "$SNOPT" == "7.7" ] && [ "$SNOPT_LOCATION_77" ]; then
       echo "  > Secure copying SNOPT 7.7 over SSH";
       mkdir SNOPT;
-      scp -r "$SNOPT_LOCATION_77" SNOPT;
-      ./build_pyoptsparse.sh -s SNOPT/src -b "$PYOPTSPARSE_VERSION";
+      scp -qr "$SNOPT_LOCATION_77" SNOPT;
+      ./build_pyoptsparse.sh -b "$PYOPTSPARSE" -s SNOPT/src;
 
-    elif [ "$SNOPT_VERSION" == "7.2" ]  && [ "$SNOPT_LOCATION_72" ]; then
+    elif [ "$SNOPT" == "7.2" ] && [ "$SNOPT_LOCATION_72" ]; then
       echo "  > Secure copying SNOPT 7.2 over SSH";
       mkdir SNOPT;
-      scp -r "$SNOPT_LOCATION_72" SNOPT;
-      ./build_pyoptsparse.sh -s SNOPT/source -b "$PYOPTSPARSE_VERSION";
+      scp -qr "$SNOPT_LOCATION_72" SNOPT;
+      ./build_pyoptsparse.sh -b "$PYOPTSPARSE" -s SNOPT/source;
 
     else
-      ./build_pyoptsparse.sh -b "$PYOPTSPARSE_VERSION";
+      if [ "$SNOPT" ]; then
+        echo "SNOPT version $SNOPT was requested but source is not available";
+      fi
+      ./build_pyoptsparse.sh -b "$PYOPTSPARSE";
     fi
-  else
-    echo "Incompatible versions of SNOPT and PyoptSparse"
+
+    cd ..;
   fi
-  cd ..;
 
   echo " >> Installing optional packages for test coverage";
   pip install psutil objgraph git+https://github.com/mdolab/pyxdsm;
@@ -145,7 +143,7 @@ script:
 - export OMPI_MCA_btl=^openib
 # newer versions of OpenMPI require this
 - export OMPI_MCA_rmaps_base_oversubscribe=1
-# IPOPT Requires
+# IPOpt requires this
 - export LD_LIBRARY_PATH=/home/travis/ipopt/lib
 
 # make docs first
@@ -166,6 +164,9 @@ after_success:
 # again, only run coverage operations on the upload machine after success.
 # strip the site-package path so that links works on coveralls.io
 - if [ "$UPLOAD_DOCS" ]; then
+    echo " >> Installing forked version of coveralls";
+    pip install git+https://github.com/swryan/coveralls-python@work;
+
     coveralls --rcfile=../../.coveragerc --output=coveralls.json;
     SITE=`python -c 'import site; print(site.getsitepackages()[0])'`;
     sed "s/${SITE//\//\\/}\///g" < coveralls.json > coveralls-upd.json;
@@ -181,4 +182,4 @@ deploy:
       python _utils/upload_doc_version.py;
     fi
   on:
-    branch: master
+    branch: master

openmdao/components/add_subtract_comp.py

@@ -79,8 +79,8 @@ def __init__(self, output_name=None, input_names=None, vec_size=1, length=1,
         self._input_names = {}
 
         if isinstance(output_name, str):
-            self.add_equation(output_name, input_names, vec_size, length, val, scaling_factors,
-                              kwargs)
+            self.add_equation(output_name, input_names, vec_size, length, val,
+                              scaling_factors=scaling_factors, **kwargs)
         elif isinstance(output_name, collections.Iterable):
             raise NotImplementedError(self.msginfo + ': Declaring multiple addition systems '
                                       'on initiation is not implemented.'

openmdao/components/exec_comp.py

@@ -7,6 +7,7 @@
 
 from openmdao.core.explicitcomponent import ExplicitComponent
 from openmdao.utils.units import valid_units
+from openmdao.utils.general_utils import warn_deprecation
 
 # regex to check for variable names.
 VAR_RGX = re.compile(r'([.]*[_a-zA-Z]\w*[ ]*\(?)')
@@ -132,6 +133,7 @@ def __init__(self, exprs=[], **kwargs):
         exp(x)                     Exponential function
         expm1(x)                   exp(x) - 1
         factorial(x)               Factorial of all numbers in x
+                                   (DEPRECATED, not available with SciPy >=1.5)
         fmax(x, y)                 Element-wise maximum of x and y
         fmin(x, y)                 Element-wise minimum of x and y
         inner(x, y)                Inner product of arrays x and y
@@ -634,8 +636,26 @@ def _import_functs(mod, dct, names=None):
 except ImportError:
     pass
 else:
-    _import_functs(scipy.special, _expr_dict,
-                   names=['factorial', 'erf', 'erfc'])
+    _import_functs(scipy.special, _expr_dict, names=['erf', 'erfc'])
+
+    from distutils.version import LooseVersion
+    if LooseVersion(scipy.__version__) >= LooseVersion("1.5.0"):
+        def factorial(*args):
+            """
+            Raise a RuntimeError stating that the factorial function is not supported.
+            """
+            raise RuntimeError("The 'factorial' function is not supported for SciPy "
+                               f"versions >= 1.5, current version: {scipy.__version__}")
+    else:
+        def factorial(*args):
+            """
+            Raise a warning stating that the factorial function is deprecated.
+            """
+            warn_deprecation("The 'factorial' function is deprecated. "
+                             "It is no longer supported for SciPy versions >= 1.5.")
+            return scipy.special.factorial(*args)
+
+    _expr_dict['factorial'] = factorial
 
 
 # Put any functions here that need special versions to work under

openmdao/components/tests/test_add_subtract_comp.py

@@ -263,6 +263,57 @@ def test_partials(self):
         assert_check_partials(partials)
 
 
+class TestAddSubtractInit(unittest.TestCase):
+
+    def setUp(self):
+        self.nn = 5
+
+        self.p = om.Problem()
+
+        ivc = om.IndepVarComp()
+        ivc.add_output(name='a', shape=(self.nn, 3), units='ft')
+        ivc.add_output(name='b', shape=(self.nn, 3), units='m')
+        ivc.add_output(name='c', shape=(self.nn, 3), units='m')
+
+        self.p.model.add_subsystem(name='ivc',
+                                   subsys=ivc,
+                                   promotes_outputs=['a', 'b','c'])
+
+        # verify proper handling of constructor args
+        adder = om.AddSubtractComp(output_name='adder_output',
+                                   input_names=['input_a', 'input_b', 'input_c'],
+                                   vec_size=self.nn, length=3,
+                                   scaling_factors=[2., 1., -1],
+                                   units='ft')
+
+        self.p.model.add_subsystem(name='add_subtract_comp', subsys=adder)
+
+        self.p.model.connect('a', 'add_subtract_comp.input_a')
+        self.p.model.connect('b', 'add_subtract_comp.input_b')
+        self.p.model.connect('c', 'add_subtract_comp.input_c')
+
+        self.p.setup()
+
+        self.p['a'] = np.random.rand(self.nn, 3)
+        self.p['b'] = np.random.rand(self.nn, 3)
+        self.p['c'] = np.random.rand(self.nn, 3)
+
+        self.p.run_model()
+
+    def test_results(self):
+        a = self.p['a']
+        b = self.p['b']
+        c = self.p['c']
+        out = self.p['add_subtract_comp.adder_output']
+        m_to_ft = 3.280839895
+        expected = 2*a + b*m_to_ft - c*m_to_ft
+        assert_near_equal(out, expected, 1e-8)
+
+    def test_partials(self):
+        partials = self.p.check_partials(method='fd', out_stream=None)
+        assert_check_partials(partials)
+
+
 class TestForExceptions(unittest.TestCase):
 
     def test_for_bad_scale_factors(self):

openmdao/components/tests/test_exec_comp.py

@@ -6,14 +6,16 @@
 from numpy.testing import assert_almost_equal
 import scipy
 
+from distutils.version import LooseVersion
+
 try:
     from parameterized import parameterized
 except ImportError:
     from openmdao.utils.assert_utils import SkipParameterized as parameterized
 
 import openmdao.api as om
 from openmdao.components.exec_comp import _expr_dict
-from openmdao.utils.assert_utils import assert_near_equal, assert_check_partials
+from openmdao.utils.assert_utils import assert_near_equal, assert_check_partials, assert_warning
 
 _ufunc_test_data = {
     'abs': {
@@ -115,11 +117,6 @@
         'check_func': np.expm1,
         'args': {'f': {'value': np.zeros(6)},
                  'x': {'value': np.random.random(6)}}},
-    'factorial': {
-        'str': 'f=factorial(x)',
-        'check_func': scipy.special.factorial,
-        'args': {'f': {'value': np.zeros(6)},
-                 'x': {'value': np.random.random(6)}}},
     'fmax': {
         'str': 'f=fmax(x, y)',
         'check_func': np.fmax,
@@ -254,6 +251,28 @@
 }
 
 
+# 'factorial' will raise a RuntimeError or a deprecation warning depending on scipy version
+if LooseVersion(scipy.__version__) >= LooseVersion("1.5.0"):
+    _ufunc_test_data['factorial'] = {
+        'str': 'f=factorial(x)',
+        'args': {'f': {'value': np.zeros(6)},
+                 'x': {'value': np.random.random(6)}},
+        'error': (RuntimeError,
+                  "The 'factorial' function is not supported for SciPy "
+                  f"versions >= 1.5, current version: {scipy.__version__}")
+    }
+else:
+    _ufunc_test_data['factorial'] = {
+        'str': 'f=factorial(x)',
+        'check_func': scipy.special.factorial,
+        'args': {'f': {'value': np.zeros(6)},
+                 'x': {'value': np.random.random(6)}},
+        'warning': (DeprecationWarning,
+                    "The 'factorial' function is deprecated. "
+                    "It is no longer supported for SciPy versions >= 1.5.")
+    }
+
+
 class TestExecComp(unittest.TestCase):
 
     def test_no_expr(self):
@@ -1074,7 +1093,18 @@ def test_exec_comp_value(self, f):
         model.add_subsystem('comp', om.ExecComp(test_data['str'], **test_data['args']),
                             promotes_outputs=['f'])
         prob.setup()
-        prob.run_model()
+
+        if 'error' in test_data:
+            err, msg = test_data['error']
+            with self.assertRaises(err) as cm:
+                prob.run_model()
+            self.assertTrue(msg in str(cm.exception))
+            return
+        elif 'warning' in test_data:
+            with assert_warning(*test_data['warning']):
+                prob.run_model()
+        else:
+            prob.run_model()
 
         if 'check_func' in test_data:
             check_args = []
@@ -1121,7 +1151,18 @@ def test_exec_comp_jac(self, f):
                             om.ExecComp(test_data['str'], **test_data['args']),
                             promotes_outputs=['f'])
         prob.setup()
-        prob.run_model()
+
+        if 'error' in test_data:
+            err, msg = test_data['error']
+            with self.assertRaises(err) as cm:
+                prob.run_model()
+            self.assertTrue(msg in str(cm.exception))
+            return
+        elif 'warning' in test_data:
+            with assert_warning(*test_data['warning']):
+                prob.run_model()
+        else:
+            prob.run_model()
 
         if 'check_val' not in test_data:
             cpd = prob.check_partials(out_stream=None)

openmdao/utils/om.py

@@ -44,6 +44,7 @@
     split_ep, _compute_entry_points_setup_parser, _compute_entry_points_exec, \
         _find_plugins_setup_parser, _find_plugins_exec
 from openmdao.core.component import Component
+from openmdao.utils.general_utils import warn_deprecation
 
 
 def _n2_setup_parser(parser):
@@ -66,7 +67,7 @@ def _n2_setup_parser(parser):
                         action='store', dest='title', help='diagram title.')
     parser.add_argument('--use_declare_partial_info', action='store_true',
                         dest='use_declare_partial_info',
-                        help="use declare partial info for internal connectivity.")
+                        help="ignored, now always true.")
 
 
 def _n2_cmd(options, user_args):
@@ -87,10 +88,13 @@ def _n2_cmd(options, user_args):
         def _noraise(prob):
             prob.model._raise_connection_errors = False
 
+        if options.use_declare_partial_info:
+            warn_deprecation("'--use_declare_partial_info' is now the"
+                             " default and the option is ignored.")
+
         def _viewmod(prob):
             n2(prob, outfile=options.outfile, show_browser=not options.no_browser,
-               title=options.title, embeddable=options.embeddable,
-               use_declare_partial_info=options.use_declare_partial_info)
+                title=options.title, embeddable=options.embeddable)
             exit()  # could make this command line selectable later
 
         hooks._register_hook('setup', 'Problem', pre=_noraise)
@@ -100,8 +104,7 @@ def _viewmod(prob):
     else:
         # assume the file is a recording, run standalone
         n2(filename, outfile=options.outfile, title=options.title,
-           show_browser=not options.no_browser, embeddable=options.embeddable,
-           use_declare_partial_info=options.use_declare_partial_info)
+            show_browser=not options.no_browser, embeddable=options.embeddable)
 
 
 def _view_connections_setup_parser(parser):