Merge pull request #51 from pyccel/pip-install

Clean up installation procedure with pip

.travis.yml

@@ -24,24 +24,16 @@ before_install:
   - h5pcc -showconfig -echo || true
   - export CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
   - python -m pip install --upgrade pip
-  - python -m pip install -r requirements.txt
   - python -m pip uninstall -y psydac
   - python -m pip uninstall -y sympde
-  - python -m pip uninstall -y gelato
   - python -m pip uninstall -y pyccel
-  - wget https://raw.githubusercontent.com/pyccel/pyccel/master/requirements.txt -O requirements_pyccel.txt
-  - python -m pip install -r requirements_pyccel.txt
-  - python -m pip install git+https://github.com/pyccel/pyccel@master
-  - wget https://raw.githubusercontent.com/pyccel/sympde/master/requirements.txt -O requirements_sympde.txt
-  - python -m pip install -r requirements_sympde.txt
-  - python -m pip install git+https://github.com/pyccel/sympde@master
-  - wget https://raw.githubusercontent.com/pyccel/gelato/master/requirements.txt -O requirements_gelato.txt
-  - python -m pip install -r requirements_gelato.txt
-  - python -m pip install git+https://github.com/pyccel/gelato@master
+  - python -m pip uninstall -y gelato
+  - python -m pip install -r requirements.txt
 
 # command to install project
 install:
   - python -m pip install .
+  - python -m pip freeze
 
 before_script:
   - mkdir pytest

TODO.rst

@@ -50,7 +50,7 @@ API
 
 - add other solvers to the solver_driver (only cg is available now)
 
-- remove psydac/run_tests.sh. however, we need to clear the cache of sympy after 1d, 2d and 3d tests, otherwise pytest will crash.
+- however, we need to clear the cache of sympy after 1d, 2d and 3d tests, otherwise pytest will crash.
 
 - add sympde and pyccel install procedure; maybe wget to download the requierements files as requirements_pyccel.txt etc then call pip3
 

psydac/__init__.py

@@ -1,8 +1,9 @@
 # -*- coding: UTF-8 -*-
-__version__ = "0.1"
-__all__     = ['api', 'cad', 'core', 'ddm', 'feec', 'fem',
+__all__     = ['__version__', 'api', 'cad', 'core', 'ddm', 'feec', 'fem',
                'linalg', 'mapping', 'utilities']
 
+from psydac.version import __version__
+
 from psydac import api
 from psydac import cad
 from psydac import core

psydac/api/ast/evaluation.py

@@ -7,7 +7,10 @@
 from sympde.topology             import ScalarField
 from sympde.topology             import VectorField
 from sympde.topology             import SymbolicExpr
-from sympde.topology.space       import ScalarTestFunction
+from sympde.topology.space       import element_of
+from sympde.topology.space       import ScalarFunctionSpace
+from sympde.topology.space       import VectorFunctionSpace
+from sympde.topology.datatype    import dtype_space_registry
 from sympde.topology.derivatives import _logical_partial_derivatives
 
 from pyccel.ast.core      import IndexedVariable
@@ -35,6 +38,21 @@ def __new__(cls, space, mapping, discrete_boundary=None, name=None,
         if not isinstance(mapping, Mapping):
             raise TypeError('> Expecting a Mapping object')
 
+        #.....................................................................
+        # If vector space is of undefined type, we assume that each component
+        # lives in H1; otherwise we raise an error. TODO: improve!
+        if isinstance(space, VectorFunctionSpace):
+            if space.kind == dtype_space_registry['undefined']:
+                space = ScalarFunctionSpace(
+                    name   = space.name,
+                    domain = space.domain,
+                    kind   = 'H1'
+                )
+            else:
+                msg = 'Cannot evaluate vector spaces of kind {}'.format(space.kind)
+                raise NotImplementedError(msg)
+        #.....................................................................
+
         obj = SplBasic.__new__(cls, mapping, name=name,
                                prefix='eval_mapping', mapping=mapping,
                                is_rational_mapping=is_rational_mapping)
@@ -173,7 +191,7 @@ def _initialize(self):
         weights_elements = []
         if self.is_rational_mapping:
             # TODO check if 'w' exist already
-            weights_pts = ScalarField(self.space, name='w')
+            weights_pts = element_of(self.space, name='w')
 
             weights_elements = [weights_pts]
 
@@ -217,7 +235,7 @@ def _initialize(self):
         # ...
 
         # ...
-        Nj           = ScalarTestFunction(space, name='Nj')
+        Nj           = element_of(space, name='Nj')
         body         = []
         init_basis   = OrderedDict()
         updates      = []
@@ -364,7 +382,7 @@ def _initialize(self):
         # ...
 
         # ...
-        Nj = ScalarTestFunction(space, name='Nj')
+        Nj = element_of(space, name='Nj')
         body = []
         init_basis = OrderedDict()
         init_map   = OrderedDict()
@@ -503,7 +521,7 @@ def _initialize(self):
         # ...
 
         # ...
-        Nj = VectorField(space, name='Nj')
+        Nj = VectorField(space, name='Nj')  # TODO: use 'element_of'
         body = []
         init_basis = OrderedDict()
         init_map   = OrderedDict()
@@ -666,7 +684,7 @@ def _initialize(self):
         # ...
 
         # ...
-        Nj = ScalarTestFunction(space, name='Nj')
+        Nj = element_of(space, name='Nj')
         init_basis = OrderedDict()
         init_map   = OrderedDict()
 
@@ -860,7 +878,7 @@ def _initialize(self):
         weights_elements = []
         if self.is_rational_mapping:
             # TODO check if 'w' exist already
-            weights_pts = ScalarField(self.space, name='w')
+            weights_pts = element_of(self.space, name='w')
 
             weights_elements = [weights_pts]
 
@@ -905,7 +923,7 @@ def _initialize(self):
         # ...
 
         # ...
-        Nj             = ScalarTestFunction(space, name='Nj')
+        Nj             = element_of(space, name='Nj')
         body           = []
         init_basis     = OrderedDict()
         atomic_exprs   = self.elements + weights_elements

psydac/api/ast/fem.py

@@ -39,6 +39,7 @@
 from sympde.topology.space       import ProductSpace
 from sympde.topology.space       import ScalarTestFunction
 from sympde.topology.space       import VectorTestFunction
+from sympde.topology.space       import element_of
 from sympde.topology.space       import IndexedTestTrial
 from sympde.topology.derivatives import _partial_derivatives
 from sympde.topology.derivatives import _logical_partial_derivatives
@@ -617,13 +618,11 @@ def _initialize(self):
         if is_bilinear or is_linear:
             test_function = self.weak_form.test_functions
             if not isinstance(test_function, (tuple, Tuple)):
-                test_function = [test_function]
-                test_function = Tuple(*test_function)
+                test_function = Tuple(test_function)
 
         elif is_function:
-            test_function = ScalarTestFunction(self.weak_form.space, name='Nj')
-            test_function = [test_function]
-            test_function = Tuple(*test_function)
+            test_function = element_of(self.weak_form.space, name='Nj')
+            test_function = Tuple(test_function)
 
         # creation of symbolic vars
         if is_bilinear:

psydac/api/ast/utilities.py

@@ -12,6 +12,7 @@
 from sympde.topology.space       import ScalarTestFunction
 from sympde.topology.space       import VectorTestFunction
 from sympde.topology.space       import IndexedTestTrial
+from sympde.topology.space       import element_of
 from sympde.topology             import ScalarField
 from sympde.topology             import VectorField, IndexedVectorField
 from sympde.topology             import Mapping
@@ -462,7 +463,7 @@ def rationalize_eval_mapping(mapping, nderiv, space, indices_quad):
 
     # ... weights and their derivatives
     # TODO check if 'w' exist already
-    weights = ScalarField(space, name='w')
+    weights = element_of(space, name='w')
 
     weights_elements = [weights]
     if nderiv > 0:

psydac/api/tests/test_api_1d_compatible_spaces.py

@@ -1,37 +1,21 @@
 # -*- coding: UTF-8 -*-
 
-from sympy import pi, cos, sin, Tuple, Matrix
+from sympy               import pi, sin
+from scipy.sparse.linalg import spsolve
 
-from sympde.core import Constant
-from sympde.calculus import grad, dot, inner, cross, rot, curl, div
-from sympde.calculus import laplace, hessian
-from sympde.topology import (dx, dy, dz)
-from sympde.topology import ScalarFunctionSpace, VectorFunctionSpace
+from sympde.calculus import dot, div
+from sympde.topology import ScalarFunctionSpace
 from sympde.topology import ProductSpace
 from sympde.topology import element_of
-from sympde.topology import Boundary, NormalVector, TangentVector
-from sympde.topology import Domain, Line, Square, Cube
-from sympde.topology import Trace, trace_0, trace_1
-from sympde.topology import Union
-from sympde.expr import BilinearForm, LinearForm
-from sympde.expr import integral
-from sympde.expr import Norm, TerminalExpr
-from sympde.expr import find, EssentialBC
-
-
-from psydac.fem.basic   import FemField
-from psydac.fem.vector   import VectorFemField
-from psydac.api.discretization import discretize
-
-from numpy import linspace, zeros, allclose
-from mpi4py import MPI
-import pytest
+from sympde.topology import Line
+from sympde.expr     import BilinearForm, LinearForm
+from sympde.expr     import integral
+from sympde.expr     import Norm
+from sympde.expr     import find
 
-from scipy.sparse.linalg import cg, gmres
-from scipy import linalg
-from scipy.sparse.linalg import spsolve
+from psydac.fem.basic          import FemField
+from psydac.api.discretization import discretize
 
-import matplotlib.pyplot as plt
 #==============================================================================
 
 def run_system_1_1d_dir(f0, sol, ncells, degree):
@@ -76,7 +60,7 @@ def run_system_1_1d_dir(f0, sol, ncells, degree):
 
     ah.assemble()
 
-    M   = ah.linear_system.lhs.tosparse()
+    M   = ah.linear_system.lhs.tosparse().tocsc()
     rhs = ah.linear_system.rhs.toarray()
     sol = spsolve(M, rhs)
 

psydac/api/tests/test_api_2d_compatible_spaces.py

@@ -1,39 +1,23 @@
 # -*- coding: UTF-8 -*-
 
-from sympy import pi, cos, sin, Tuple, Matrix
+import numpy as np
+from sympy import pi, cos, sin, Matrix
+from scipy import linalg
+from scipy.sparse.linalg import spsolve
 
-from sympde.core import Constant
-from sympde.calculus import grad, dot, inner, cross, rot, curl, div
-from sympde.calculus import laplace, hessian
-from sympde.topology import (dx, dy, dz)
+from sympde.calculus import grad, dot, inner, div
 from sympde.topology import ScalarFunctionSpace, VectorFunctionSpace
 from sympde.topology import ProductSpace
 from sympde.topology import element_of
-from sympde.topology import Boundary, NormalVector, TangentVector
-from sympde.topology import Domain, Line, Square, Cube
-from sympde.topology import Trace, trace_0, trace_1
-from sympde.topology import Union
+from sympde.topology import Square
 from sympde.expr import BilinearForm, LinearForm, integral
-from sympde.expr import Norm, TerminalExpr
+from sympde.expr import Norm
 from sympde.expr import find, EssentialBC
 
-
-from psydac.fem.basic   import FemField
-from psydac.fem.vector  import VectorFemField
+from psydac.fem.basic          import FemField
+from psydac.fem.vector         import VectorFemField
 from psydac.api.discretization import discretize
 
-from numpy import linspace, zeros, allclose
-import numpy as np
-from mpi4py import MPI
-import pytest
-
-from scipy.sparse.linalg import cg, gmres
-from scipy.sparse.linalg import spsolve
-from scipy import linalg
-
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-from matplotlib import animation
 #==============================================================================
 
 def run_system_1_2d_dir(f0, sol, ncells, degree):
@@ -83,7 +67,7 @@ def run_system_1_2d_dir(f0, sol, ncells, degree):
 
     # ...
     ah.assemble()
-    M   = ah.linear_system.lhs.tosparse()
+    M   = ah.linear_system.lhs.tosparse().tocsc()
     rhs = ah.linear_system.rhs.toarray()
     x   = spsolve(M, rhs)
     # ...
@@ -194,23 +178,21 @@ def run_system_2_2d_dir(f1, f2,u1, u2, ncells, degree):
 #            SERIAL TESTS
 ###############################################################################
 
+def test_api_system_1_2d_dir_1():
+    from sympy.abc import x,y
+
+    f0 =  -2*(2*pi)**2*sin(2*pi*x)*sin(2*pi*y)
+    u  = sin(2*pi*x)*sin(2*pi*y)
+    x = run_system_1_2d_dir(f0,u, ncells=[10,10], degree=[2,2])
+
 #==============================================================================
 def test_api_system_2_2d_dir_1():
     from sympy.abc import x,y
-    from sympy import cos
-
+
     f1 = -x**2*(x - 1)**2*(24*y - 12) - 4*y*(x**2 + 4*x*(x - 1) + (x - 1)**2)*(2*y**2 - 3*y + 1) - 2*pi*cos(2*pi*x)
     f2 = 4*x*(2*x**2 - 3*x + 1)*(y**2 + 4*y*(y - 1) + (y - 1)**2) + y**2*(24*x - 12)*(y - 1)**2 + 2*pi*cos(2*pi*y)
     u1 = x**2*(-x + 1)**2*(4*y**3 - 6*y**2 + 2*y)
     u2 =-y**2*(-y + 1)**2*(4*x**3 - 6*x**2 + 2*x)
     p  = sin(2*pi*x) - sin(2*pi*y)
 
     x = run_system_2_2d_dir(f1, f2, u1, u2, ncells=[2**3,2**3], degree=[2,2])
-
-def test_api_system_1_2d_dir_1():
-    from sympy.abc import x,y
-
-    f0 =  -2*(2*pi)**2*sin(2*pi*x)*sin(2*pi*y)
-    u  = sin(2*pi*x)*sin(2*pi*y)
-    x = run_system_1_2d_dir(f0,u, ncells=[10,10], degree=[2,2])
-

psydac/api/tests/test_api_2d_scalar.py

@@ -1,31 +1,24 @@
 # -*- coding: UTF-8 -*-
 
+from mpi4py import MPI
 from sympy import pi, cos, sin
 from sympy.utilities.lambdify import implemented_function
+import pytest
 
-from sympde.core import Constant
-from sympde.calculus import grad, dot, inner, cross, rot, curl, div
-from sympde.calculus import laplace, hessian
-from sympde.topology import (dx, dy, dz)
-from sympde.topology import ScalarFunctionSpace, VectorFunctionSpace
-from sympde.topology import ProductSpace
+from sympde.calculus import grad, dot
+from sympde.calculus import laplace
+from sympde.topology import ScalarFunctionSpace
 from sympde.topology import element_of
-from sympde.topology import Boundary, NormalVector, TangentVector
-from sympde.topology import Domain, Line, Square, Cube
-from sympde.topology import Trace, trace_0, trace_1
+from sympde.topology import NormalVector
+from sympde.topology import Square
 from sympde.topology import Union
-from sympde.expr import BilinearForm, LinearForm, integral
-from sympde.expr import Norm
-from sympde.expr import find, EssentialBC
+from sympde.expr     import BilinearForm, LinearForm, integral
+from sympde.expr     import Norm
+from sympde.expr     import find, EssentialBC
 
-from psydac.fem.basic   import FemField
+from psydac.fem.basic          import FemField
 from psydac.api.discretization import discretize
 
-from numpy import linspace, zeros, allclose
-from mpi4py import MPI
-import pytest
-
-
 #==============================================================================
 def run_poisson_2d_dir(solution, f, ncells, degree, comm=None):