Trac #33465: sage.graphs: Use Executable.absolute_filename()

This is so that the Sage library becomes fully functional even when not
being run from within sage-env (which sets PATH).

We add `sage.features.nauty` to provide features for nauty executables.

To test:
{{{
$ venv/bin/python3 -c 'from sage.all import graphs;
print(len(list(graphs.fullerenes(60))))'
}}}

URL: https://trac.sagemath.org/33465
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): David Coudert

src/sage/features/nauty.py

@@ -0,0 +1,59 @@
+r"""
+Features for testing the presence of nauty executables
+"""
+
+from sage.env import SAGE_NAUTY_BINS_PREFIX
+
+from . import Executable
+from .join_feature import JoinFeature
+
+
+class NautyExecutable(Executable):
+    r"""
+    A :class:`~sage.features.Feature` which checks for nauty executables.
+
+    EXAMPLES::
+
+        sage: from sage.features.nauty import NautyExecutable
+        sage: NautyExecutable('converseg').is_present()         # optional - nauty
+        FeatureTestResult('nauty_converseg', True)
+    """
+    def __init__(self, name):
+        r"""
+        TESTS::
+
+            sage: from sage.features.nauty import NautyExecutable
+            sage: isinstance(NautyExecutable('geng'), NautyExecutable)
+            True
+        """
+        Executable.__init__(self, name=f"nauty_{name}",
+                            executable=f"{SAGE_NAUTY_BINS_PREFIX}{name}",
+                            spkg="nauty")
+
+
+class Nauty(JoinFeature):
+    r"""
+    A :class:`~sage.features.Feature` describing the presence of the executables
+    which comes as a part of ``nauty``.
+
+    EXAMPLES::
+
+        sage: from sage.features.nauty import Nauty
+        sage: Nauty().is_present()                              # optional - nauty
+        FeatureTestResult('nauty', True)
+    """
+    def __init__(self):
+        r"""
+        TESTS::
+
+            sage: from sage.features.nauty import Nauty
+            sage: isinstance(Nauty(), Nauty)
+            True
+        """
+        JoinFeature.__init__(self, "nauty",
+                             [NautyExecutable(name)
+                              for name in ('directg', 'gentourng', 'geng', 'genbg', 'converseg')])
+
+
+def all_features():
+    return [Nauty()]

src/sage/graphs/digraph_generators.py

@@ -63,7 +63,6 @@
 #                         http://www.gnu.org/licenses/
 ################################################################################
 from sage.cpython.string import bytes_to_str
-from sage.env import SAGE_NAUTY_BINS_PREFIX as nautyprefix
 
 import sys
 from sage.misc.randstate import current_randstate
@@ -528,7 +527,12 @@ def tournaments_nauty(self, n,
 
         nauty_input +=  " " + str(n) + " "
 
-        sp = subprocess.Popen(nautyprefix+"gentourng {0}".format(nauty_input), shell=True,
+        import shlex
+        from sage.features.nauty import NautyExecutable
+        gentourng_path = NautyExecutable("gentourng").absolute_filename()
+
+        sp = subprocess.Popen(shlex.quote(gentourng_path) + " {0}".format(nauty_input),
+                              shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE, close_fds=True)
 
@@ -636,8 +640,13 @@ def nauty_directg(self, graphs, options="", debug=False):
             options += ' -q'
 
         # Build directg input (graphs6 format)
-        input = ''.join(g.graph6_string()+'\n' for g in graphs)
-        sub = subprocess.Popen(nautyprefix+'directg {0}'.format(options),
+        input = ''.join(g.graph6_string() + '\n' for g in graphs)
+
+        import shlex
+        from sage.features.nauty import NautyExecutable
+        directg_path = NautyExecutable("directg").absolute_filename()
+
+        sub = subprocess.Popen(shlex.quote(directg_path) + ' {0}'.format(options),
                                shell=True,
                                stdout=subprocess.PIPE,
                                stdin=subprocess.PIPE,

src/sage/graphs/graph_generators.py

@@ -15,7 +15,6 @@
 More interestingly, one can get the list of all graphs that Sage knows how to
 build by typing ``graphs.`` in Sage and then hitting tab.
 """
-from sage.env import SAGE_NAUTY_BINS_PREFIX as nautyprefix
 
 import subprocess
 
@@ -956,8 +955,10 @@ def nauty_geng(self, options="", debug=False):
             sage: list(graphs.nauty_geng("-c 3", debug=True))
             ['>A ...geng -cd1D2 n=3 e=2-3\n', Graph on 3 vertices, Graph on 3 vertices]
         """
-
-        sp = subprocess.Popen(nautyprefix+"geng {0}".format(options), shell=True,
+        import shlex
+        from sage.features.nauty import NautyExecutable
+        geng_path = NautyExecutable("geng").absolute_filename()
+        sp = subprocess.Popen(shlex.quote(geng_path) + " {0}".format(options), shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE, close_fds=True,
                               encoding='latin-1')
@@ -1292,7 +1293,9 @@ def fullerenes(self, order, ipr=False):
         from sage.features.graph_generators import Buckygen
         Buckygen().require()
 
-        command = 'buckygen -'+('I' if ipr else '')+'d {0}d'.format(order)
+        import shlex
+        command = shlex.quote(Buckygen().absolute_filename())
+        command += ' -' + ('I' if ipr else '') + 'd {0}d'.format(order)
 
         sp = subprocess.Popen(command, shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
@@ -1379,7 +1382,9 @@ def fusenes(self, hexagon_count, benzenoids=False):
         from sage.features.graph_generators import Benzene
         Benzene().require()
 
-        command = 'benzene '+('b' if benzenoids else '')+' {0} p'.format(hexagon_count)
+        import shlex
+        command = shlex.quote(Benzene().absolute_filename())
+        command += (' b' if benzenoids else '') + ' {0} p'.format(hexagon_count)
 
         sp = subprocess.Popen(command, shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
@@ -1563,7 +1568,10 @@ def plantri_gen(self, options=""):
         from sage.features.graph_generators import Plantri
         Plantri().require()
 
-        sp = subprocess.Popen('plantri {}'.format(options), shell=True,
+        import shlex
+        command = '{} {}'.format(shlex.quote(Plantri().absolute_filename()),
+                                 options)
+        sp = subprocess.Popen(command, shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE, close_fds=True,
                               encoding='latin-1')

src/sage/graphs/hypergraph_generators.py

@@ -30,7 +30,6 @@
 Functions and methods
 ---------------------
 """
-from sage.env import SAGE_NAUTY_BINS_PREFIX as nautyprefix
 
 class HypergraphGenerators():
     r"""
@@ -149,6 +148,9 @@ def nauty(self, number_of_sets, number_of_vertices,
             raise ValueError("cannot have more than 64 sets+vertices")
 
         import subprocess
+        import shlex
+        from sage.features.nauty import NautyExecutable
+        genbgL_path = NautyExecutable("genbgL").absolute_filename()
 
         nauty_input = options
 
@@ -181,7 +183,7 @@ def nauty(self, number_of_sets, number_of_vertices,
 
         nauty_input +=  " " + str(number_of_vertices) + " " + str(number_of_sets) + " "
 
-        sp = subprocess.Popen(nautyprefix + "genbgL {0}".format(nauty_input), shell=True,
+        sp = subprocess.Popen(shlex.quote(genbgL_path) + " {0}".format(nauty_input), shell=True,
                               stdin=subprocess.PIPE, stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE, close_fds=True)