Merge branch 'master' into new_e-antic

# Conflicts: //SOLVED
#	NormalizModule.cpp

Author: Winfried Bruns

.ci-install-normaliz.sh

@@ -24,6 +24,7 @@ fi
 
 [ "$COCOALIB" == "yes" ] && ./install_scripts_opt/install_nmz_cocoa.sh && echo "cocoalib complete!"
 [ "$FLINT" == "yes" ] && ./install_scripts_opt/install_nmz_flint.sh && echo "flint complete!"
+[ "$EANTIC" == "yes" ] && ./install_scripts_opt/install_nmz_flint.sh && echo "flint complete!"
 [ "$EANTIC" == "yes" ] && ./install_scripts_opt/install_nmz_arb.sh && echo "arb complete!"
 [ "$EANTIC" == "yes" ] && ./install_scripts_opt/install_nmz_e-antic.sh && echo "e-antic complete!"
 [ "$NAUTY" == "yes" ] && ./install_scripts_opt/install_nmz_nauty.sh && echo "nauty complete!"

.github/workflows/ci.yml

@@ -15,10 +15,13 @@ jobs:
       - uses: actions/checkout@v2
       - name: "Install prerequisites and Normaliz"
         run: |
-          sudo apt-get install libgmp-dev libflint-dev
-          pip install coverage
-          pip3 install coverage
-          pip install setuptools
+          sudo apt-get install libgmp-dev
+          sudo apt-get install libpython2-dev
+          sudo apt-get install libpython3-dev
+          # pip2 install coverage
+          # pip3 install coverage
+          # pip install setuptools
+          sudo apt-get install python-setuptools
           pip3 install setuptools
           ./.ci-install-normaliz.sh
       - name: "Install PyNormaliz"
@@ -38,10 +41,13 @@ jobs:
       - uses: actions/checkout@v2
       - name: "Install prerequisites and Normaliz"
         run: |
-          sudo apt-get install libgmp-dev 
-          pip install coverage
-          pip3 install coverage
-          pip install setuptools
+          sudo apt-get install libgmp-dev
+          sudo apt-get install libpython2-dev
+          sudo apt-get install libpython3-dev
+          # pip2 install coverage
+          # pip3 install coverage
+          # pip install setuptools
+          sudo apt-get install python-setuptools
           pip3 install setuptools
           ./.ci-install-normaliz.sh
       - name: "Install PyNormaliz"

NormalizModule.cpp

@@ -177,11 +177,11 @@ static PyObject* CallPythonFuncOnOneArg(PyObject* function, PyObject* single_arg
 #ifndef NMZ_RELEASE
 static_assert(
     false,
-    "Your Normaliz version (unknown) is to old! Update to 3.8.10 or newer.");
+    "Your Normaliz version (unknown) is to old! Update to 3.9.0 or newer.");
 #endif
-#if NMZ_RELEASE < 30810
+#if NMZ_RELEASE < 30900
 static_assert(false,
-              "Your Normaliz version is to old! Update to 3.8.10 or newer.");
+              "Your Normaliz version is to old! Update to 3.9.0 or newer.");
 #endif
 
 /***************************************************************************
@@ -473,10 +473,11 @@ static bool prepare_nf_input(vector< vector< NumberFieldElem > >& out,
                 if (!current_res) {
                     return false;
                 }
-                current_elem = renf_elem_class(nf->shared_from_this(),current_vector);
+                current_elem = NumberFieldElem(*nf, current_vector);
             }
             if (string_check(current_element)) {
-                current_elem =renf_elem_class(nf->shared_from_this(),PyUnicodeToString(current_element));
+                current_elem = NumberFieldElem(*nf);
+                current_elem = PyUnicodeToString(current_element);
             }
             if (PyFloat_Check(current_element)){
                 throw PyNormalizInputException("Nonintegral numbers must be given as strings"); 
@@ -713,27 +714,60 @@ template < typename Integer >
 static PyObject*
 NmzAutomorphismsToPython(const AutomorphismGroup< Integer >& grp)
 {
+    int list_size = 6;
+    if(grp.IsInput() || grp.IsAmbient())
+        list_size =7;    
 
-    PyObject* list = PyList_New(4);
+    PyObject* list = PyList_New(list_size);
 
     PyList_SetItem(list, 0, NmzToPyNumber(grp.getOrder()));
+    PyList_SetItem(list, 1, BoolToPyBool(grp.IsIntegralityChecked()));
+    PyList_SetItem(list, 2, BoolToPyBool(grp.IsIntegral()));
+    
+    if(grp.IsInput() || grp.IsAmbient()){
+        PyList_SetItem(list, 6, NmzMatrixToPyList(grp.getGens().get_elements()));
+        PyObject* current = PyList_New(2);        
+        PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getGensPerms()));
+        PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getGensOrbits()));
+        PyList_SetItem(list, 3, current);
+        
+        current = PyList_New(2);
+        vector<vector<long> > Empty;
+        PyList_SetItem(current, 0, NmzMatrixToPyList(Empty));
+        PyList_SetItem(current, 1, NmzMatrixToPyList(Empty));
+        PyList_SetItem(list, 4, current);
+        
+        if(grp.IsAmbient()){
+            current = PyList_New(2);
+            PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getLinFormsPerms()));
+            PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getLinFormsOrbits()));
+            PyList_SetItem(list, 5, current);            
+        }
+        else{
+            vector<vector<long> > Empty;
+            PyList_SetItem(current, 0, NmzMatrixToPyList(Empty));
+            PyList_SetItem(current, 1, NmzMatrixToPyList(Empty));
+            PyList_SetItem(list, 5, current);            
+        }        
+    }    
+    else{
+        PyObject* current = PyList_New(2);
+        PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getExtremeRaysPerms()));
+        PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getExtremeRaysOrbits()));
+        PyList_SetItem(list, 3, current);
 
-    PyObject* current = PyList_New(2);
-    PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getExtremeRaysPerms()));
-    PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getExtremeRaysOrbits()));
-    PyList_SetItem(list, 1, current);
-
-    current = PyList_New(2);
-    PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getVerticesPerms()));
-    PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getVerticesOrbits()));
-    PyList_SetItem(list, 2, current);
+        current = PyList_New(2);
+        PyList_SetItem(current, 0, NmzMatrixToPyList(grp.getVerticesPerms()));
+        PyList_SetItem(current, 1, NmzMatrixToPyList(grp.getVerticesOrbits()));
+        PyList_SetItem(list, 4, current);
 
-    current = PyList_New(2);
-    PyList_SetItem(current, 0,
-                   NmzMatrixToPyList(grp.getSupportHyperplanesPerms()));
-    PyList_SetItem(current, 1,
-                   NmzMatrixToPyList(grp.getSupportHyperplanesOrbits()));
-    PyList_SetItem(list, 3, current);
+        current = PyList_New(2);
+        PyList_SetItem(current, 0,
+                    NmzMatrixToPyList(grp.getSupportHyperplanesPerms()));
+        PyList_SetItem(current, 1,
+                    NmzMatrixToPyList(grp.getSupportHyperplanesOrbits()));
+        PyList_SetItem(list, 5, current);    
+    }
 
     return list;
 }
@@ -1012,6 +1046,7 @@ static PyObject* _NmzConeIntern_renf(PyObject* kwargs)
     }
 
 
+    renf_class* renf;
     // number_field_data contains 3 entries: poly, var, emb
     // All are strings
     string poly = PyUnicodeToString(PySequence_GetItem(number_field_data, 0));
@@ -1041,7 +1076,7 @@ static PyObject* _NmzConeIntern_renf(PyObject* kwargs)
                 continue;
             vector< vector< renf_elem_class > > Mat;
             try {
-                prepare_nf_input(Mat, current_value, my_renf);
+                prepare_nf_input(Mat, current_value, renf);
             }
             catch (PyNormalizInputException& e) {
                 PyErr_SetString(PyNormaliz_cppError,
@@ -1730,6 +1765,10 @@ _NmzResultImpl(Cone< Integer >* C, PyObject* prop_obj, const void* nf = nullptr)
         case libnormaliz::ConeProperty::AmbientAutomorphisms:
             return NmzAutomorphismsToPython(C->getAutomorphismGroup(
                 libnormaliz::ConeProperty::AmbientAutomorphisms));
+            
+        case libnormaliz::ConeProperty::InputAutomorphisms:
+            return NmzAutomorphismsToPython(C->getAutomorphismGroup(
+                libnormaliz::ConeProperty::InputAutomorphisms));
 
         case libnormaliz::ConeProperty::CombinatorialAutomorphisms:
             return NmzAutomorphismsToPython(C->getAutomorphismGroup(
@@ -2427,7 +2466,7 @@ static PyObject* NmzGetRenfInfo(PyObject* self, PyObject* args)
     }
     const renf_class* renf = get_cone_renf_renf(cone_py);
     std::string minpoly_str;
-    minpoly_str = fmpq_poly_get_str_pretty(renf->get_renf()->nf->pol, renf->gen_name().c_str());
+    minpoly_str = fmpq_poly_get_str_pretty(renf->get_renf()->nf->pol, renf->gen_name.c_str());
     std::string res1 = arb_get_str(renf->get_renf()->emb, 64, 0);
     // long prec = renf->get_renf()->prec;
     return PyTuple_Pack(2, StringToPyUnicode(minpoly_str), StringToPyUnicode(res1));

PyNormaliz.py

@@ -27,12 +27,31 @@ def print_perms_and_orbits(data, name):
 
 def print_automs(Automs):
     print("order ", Automs[0])
-    if len(Automs[1][0]) >0:
-        print_perms_and_orbits(Automs[1],"extreme rays of (recession) cone")
-    if len(Automs[2][0]) >0:
-        print_perms_and_orbits(Automs[2],"vertices of polyhedron")
+    if Automs[1]:
+        if Automs[2]:
+            print("automorphisms are integral")
+        else:
+            print("automorphisms are not integral")
+    else:
+        print("integrality of automorphisms unknown")
+        
+    gen_name ="extreme rays of (recession) cone"
+    if len(Automs) == 7:
+        gen_name = "input vectors";        
+    lf_name = "support hyperplanes"
+    if len(Automs) == 7:
+        lf_name = "coordinates"
+
     if len(Automs[3][0]) >0:
-        print_perms_and_orbits(Automs[3],"support hyperplanes")
+        print_perms_and_orbits(Automs[3],gen_name)
+    if len(Automs[4][0]) >0:
+        print_perms_and_orbits(Automs[4],"vertices of polyhedron")
+    if len(Automs[5][0]) >0:
+        print_perms_and_orbits(Automs[5],lf_name)
+    
+    if len(Automs) == 7:
+        print("input vectors")
+        print_matrix(Automs[6])
     return
 
 def print_Stanley_dec(dec):
@@ -207,7 +226,7 @@ def isPositive(x):
     def getDenominator(coefficients):
         exponents = [(inner, coefficients.count(inner))
                         for inner in set(coefficients)]
-        denominator = ' '.join('(1 - t{}){}'. format(to_sup(x[0]) if x[0] is not 1 else '', to_sup(x[1]) if x[1] is not 1 else '') for x in exponents)
+        denominator = ' '.join('(1 - t{}){}'. format(to_sup(x[0]) if x[0] != 1 else '', to_sup(x[1]) if x[1] != 1 else '') for x in exponents)
         return denominator
 
     num = getNumerator(numCoefficients)

README.md

@@ -13,9 +13,9 @@ A full documentation is conatined in [Appendix E](doc/PyNormaliz.pdf) of the Nor
 ## Requirements
 
 * python 2.7 or higher or python 3.4 or higher
-* Normaliz 3.8.10 or higher <https://github.com/Normaliz/Normaliz/releases>
+* Normaliz 3.9.0 or higher <https://github.com/Normaliz/Normaliz/releases>
 
-(The current version of PyNormaliz is under construction. Normaliz 3.8.10 not yet released. Use current master of Normaliz for current master of PyNormaliz.) The source packages of the Normaliz realeases contain PyNormaliz.
+(The current version of PyNormaliz is under construction. Normaliz 3.9.0 not yet released. Use current master of Normaliz for current master of PyNormaliz.) The source packages of the Normaliz realeases contain PyNormaliz.
 
 ## Installation
 
@@ -137,7 +137,8 @@ By using Python functions, the functionality of Normaliz can be extended. For ex
 
     def intersection(cone1, cone2):
         intersection_ineq = cone1.SupportHyperplanes()+cone2.SupportHyperplanes()
-        C = Cone(inequalities = intersection_ineq)
+        intersection_equat = cone1.Equations()+cone2.Equations()
+        C = Cone(inequalities = intersection_ineq, equations = intersection_equat)
         return C
 
 computes the intersection of two cones. So

doc/PyNormaliz.pdf

@@ -1,6 +1,6 @@
 [metadata]
 name = PyNormaliz
-version = 2.14
+version = 2.15
 description = An interface to Normaliz
 author = Sebastian Gutsche, Richard Sieg
 author_email = [email protected]

setup.cfg

@@ -4,6 +4,6 @@ Test automorphism group
 >>> from PyNormaliz import Cone, NmzCone, NmzResult
 >>> V = [[-1, -1, 1], [-1, 0, 1], [-1, 1, 1], [0, -1, 1], [0, 0, 1], [0, 1, 1], [1, -1, 1], [1, 0, 1], [1, 1, 1]]
 >>> cube2 = NmzCone(vertices=V)
->>> NmzResult(cube2,"Automorphisms") == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+>>> NmzResult(cube2,"Automorphisms") == [8, True, True, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
 True
 

tests/autom.txt

@@ -192,7 +192,7 @@ class Test2(GenericPyNormalizTest):
 
     # expected results
     AffineDim = 2
-    Automorphisms = [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+    Automorphisms = [8, True, True, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
     Congruences = []
     Dehomogenization = normaliz_error
     EmbeddingDim = 5

tests/generic_test.py

@@ -67,17 +67,15 @@ True
 True
 >>> len(NmzResult(cube2, "FaceLattice")) == 10
 True
->>> cube1.Automorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+>>> cube1.Automorphisms() == [8, True, True, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]] 
 True
->>> cube1.Automorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]] 
+>>> cube1.CombinatorialAutomorphisms() == [8,  False, False, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
 True
->>> cube1.CombinatorialAutomorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+>>> cube1.RationalAutomorphisms() == [8, True, True, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
 True
->>> cube1.RationalAutomorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+>>> cube1.RationalAutomorphisms() == [8,  True, True, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
 True
->>> cube1.RationalAutomorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
-True
->>> cube1.EuclideanAutomorphisms() == [8, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
+>>> cube1.EuclideanAutomorphisms() == [8, False, False, [[], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
 True
 >>> cube1.Incidence() == [[0, 0, 1, 1], [0, 1, 0, 1], [1, 0, 1, 0], [1, 1, 0, 0]]
 True