[geometric decomposition] support normaliz version 3.4.0

.travis.yml

@@ -11,6 +11,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-6 && export CXX=g++-6"
+        - NORMALIZ_VERSION=3.3.0
       before_install:
         - eval ${MATRIX_EVAL}
       python: 2.7
@@ -27,6 +28,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-7 && export CXX=g++-7"
+        - NORMALIZ_VERSION=3.4.0
       before_install:
         - eval ${MATRIX_EVAL}
       python: 2.7
@@ -43,6 +45,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-6 && export CXX=g++-6"
+        - NORMALIZ_VERSION=3.4.0
       before_install:
         - eval ${MATRIX_EVAL}
       python: 3.5
@@ -59,6 +62,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-7 && export CXX=g++-7"
+        - NORMALIZ_VERSION=3.3.0
       before_install:
         - eval ${MATRIX_EVAL}
       python: 3.5
@@ -75,6 +79,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-6 && export CXX=g++-6"
+        - NORMALIZ_VERSION=3.3.0
       python: 3.6
       before_install:
         - eval ${MATRIX_EVAL}
@@ -91,6 +96,7 @@ matrix:
             - graphviz
       env:
         - MATRIX_EVAL="export CC=gcc-7 && export CXX=g++-7"
+        - NORMALIZ_VERSION=3.4.0
       python: 3.6
       before_install:
         - eval ${MATRIX_EVAL}
@@ -100,6 +106,8 @@ matrix:
       osx_image: xcode8
       language: c++
       compiler: clang
+      env:
+        - NORMALIZ_VERSION=3.3.0
       before_install:
         - brew install graphviz
         - pip install nose
@@ -108,14 +116,15 @@ matrix:
       osx_image: xcode9
       language: c++
       compiler: clang
+      env:
+        - NORMALIZ_VERSION=3.4.0
       before_install:
         - brew install graphviz
         - sudo mkdir /usr/local/man
         - sudo chmod 777 /usr/local/man # `nose` installs there
         - pip install nose
 
 install:
-  - export NORMALIZ_VERSION=3.3.0
   - export PATH=${TRAVIS_BUILD_DIR}/dist_install/bin:$PATH
   - export SECDEC_CONTRIB=${TRAVIS_BUILD_DIR}/dist_install/
   - export PYTHONPATH=${TRAVIS_BUILD_DIR}/dist_install/pySecDec_install:$PYTHONPATH

README.MD

@@ -30,8 +30,8 @@ you need the `normaliz`  executable,
 which can be downloaded from https://www.normaliz.uni-osnabrueck.de
 [W. Bruns and B. Ichim and T. Römer and R. Sieg and C. Söger].
 The geometric decomposition module is
-designed for normaliz version 3 - currently versions 3.0.0, 3.1.0, 3.1.1 and
-3.3.0 are known to work. We recommend to set your $PATH such that the `normaliz`
+designed for normaliz version 3 - currently versions 3.0.0, 3.1.0, 3.1.1,
+3.3.0, and 3.4.0 are known to work. We recommend to set your $PATH such that the `normaliz`
 executable is found. Alternatively, you can pass the path to the `normaliz` executable
 directly to the functions that need it.
 

doc/source/installation.rst

@@ -61,9 +61,9 @@ If you want to use the :mod:`geometric decomposition <pySecDec.decomposition.geo
 module, you need the `normaliz` [BIR]_ command line executable.
 The :mod:`geometric decomposition <pySecDec.decomposition.geometric>` module is
 designed for `normaliz` version 3 - currently versions ``3.0.0``, ``3.1.0``, ``3.1.1``,
-and ``3.3.0`` are known to work. We recommend to set your ``$PATH`` such that the `normaliz`
-executable is found. Alternatively, you can pass the path to the `normaliz` executable
-directly to the functions that need it.
+``3.3.0``, and ``3.4.0`` are known to work. We recommend to set your ``$PATH`` such that the
+`normaliz` executable is found. Alternatively, you can pass the path to the `normaliz`
+executable directly to the functions that need it.
 
 .. _installation_neato:
 

pySecDec/decomposition/geometric.py

@@ -272,23 +272,34 @@ def _make_run_card_facets2vertices(self):
 
     def _read_cst_file(self, filepath):
         with open(filepath, 'r') as f:
-            # the first two lines contain the array dimensions
-            shape = int(f.readline()), int(f.readline())
+            # the first two lines may contain the array dimensions
+            try:
+                shape = int(f.readline()), int(f.readline())
+            except ValueError:
+                # more than a single number in first two lines
+                # --> file does not contain dimensions
+                f.seek(0)
 
             # the reduced input comes next (space and newline separated) and is terminated by a line containing letters
-            array_as_str = ''
+            array_lines = []
             current_str = f.readline()
             while re.match(r'^[\-0-9 ]+$', current_str) is not None:
-                array_as_str += current_str
+                array_lines.append(current_str)
                 current_str = f.readline()
+            array_as_str = ''.join(array_lines)
 
-        return np.fromstring(array_as_str, sep=' ', dtype=int).reshape(shape)
+        return np.fromstring(array_as_str, sep=' ', dtype=int).reshape(len(array_lines),-1)
 
     def _read_ext_file(self, filepath):
         with open(filepath, 'r') as f:
-            # the first two lines contain the array dimensions
-            shape = int(f.readline()), int(f.readline())
-            return np.fromfile(f, sep=' ', dtype=int).reshape(shape)
+            # the first two lines may contain the array dimensions
+            try:
+                shape = int(f.readline()), int(f.readline())
+            except ValueError:
+                # more than a single number in first two lines
+                # --> file does not contain dimensions
+                f.seek(0)
+            return np.loadtxt(f, dtype=int)
 
 def triangulate(cone, normaliz='normaliz', workdir='normaliz_tmp', keep_workdir=False, switch_representation=False):
     '''
@@ -384,25 +395,36 @@ def triangulate(cone, normaliz='normaliz', workdir='normaliz_tmp', keep_workdir=
         # read normaliz output
         # normaliz reorders the rays and defines its ordering in "normaliz.tgn"
         with open(os.path.join(workdir, 'normaliz.tgn'),'r') as f:
-            # the first two lines contain the array dimensions
-            shape = int(f.readline()), int(f.readline())
-            original_cone = np.fromfile(f, sep=' ', dtype=int).reshape(shape)
+            # the first two lines may contain the array dimensions
+            try:
+                shape = int(f.readline()), int(f.readline())
+            except ValueError:
+                # more than a single number in first two lines
+                # --> file does not contain dimensions
+                f.seek(0)
+            original_cone = np.loadtxt(f, dtype=int)
 
         # the triangulation is given as indices of `original_cone`
         with open(os.path.join(workdir, 'normaliz.tri'),'r') as f:
-            # the first two lines contain the array dimensions
-            shape = int(f.readline()), int(f.readline())
+            # the first two lines may contain the array dimensions
+            try:
+                shape = int(f.readline()), int(f.readline())
+            except ValueError:
+                # more than a single number in first two lines
+                # --> file does not contain dimensions
+                f.seek(0)
 
             # it is terminated by a line containing letters
-            array_as_str = ''
+            array_lines = []
             current_str = f.readline()
             while re.match(r'^[\-0-9 ]+$', current_str) is not None:
-                array_as_str += current_str
+                array_lines.append(current_str)
                 current_str = f.readline()
+            array_as_str = ''.join(array_lines)
 
         # `[:,:-1]` to delete the last column (last column are the determiants)
         # `-1` normaliz starts counting at `1` while python starts at `0`
-        simplicial_cones_indices = np.fromstring(array_as_str, sep=' ', dtype=int).reshape(shape)[:,:-1] - 1
+        simplicial_cones_indices = np.fromstring(array_as_str, sep=' ', dtype=int).reshape(len(array_lines),-1)[:,:-1] - 1
 
         return original_cone[simplicial_cones_indices]
 

pySecDec/decomposition/test_geometric_decomposition.py

@@ -305,6 +305,7 @@ def test_3D_geometric_decomposition_selected_indices(self):
         indices = [0,2,3]
         subsectors = list( geometric_decomposition(sector, indices, workdir='tmpdir_test_3D_geometric_decomposition_selected_indices_python' + python_major_version) )
 
+#@attr('active')
 class TestPolytope(unittest.TestCase):
     def setUp(self):
         self.vertices = [[2,1],
@@ -574,6 +575,7 @@ def test_vertex_incidence_lists(self):
                 # The ordering is not important but must be fixed to compare the arrays
                 np.testing.assert_array_equal(sort_2D_array(polytope.facets[value]), sort_2D_array(target_incidence_lists[key]))
 
+    #@attr('active')
     def test_vertex2facet(self):
         polytope1 = Polytope(vertices=self.vertices)
         polytope2 = Polytope(vertices=self.vertices_with_inside)