sagemath · mkoeppe · Feb 6, 2024 · Aug 3, 2024 · Feb 8, 2024 · Feb 8, 2024
diff --git a/src/sage/features/__init__.py b/src/sage/features/__init__.py
@@ -299,7 +299,7 @@ def resolution(self):
                 lines.append(ps.spkg_installation_hint(self.spkg, feature=self.name))
         if self.url:
             lines.append("Further installation instructions might be available at {url}.".format(url=self.url))
-        self._cache_resolution = "\n".join(lines)
+        self._cache_resolution = "\n\n".join(lines)
         return self._cache_resolution
 
     def joined_features(self):
@@ -463,6 +463,7 @@ def __str__(self):
             lines.append(self.reason)
         resolution = self.resolution
         if resolution:
+            lines.append('')
             lines.append(str(resolution))
         return "\n".join(lines)
 

diff --git a/src/sage/features/databases.py b/src/sage/features/databases.py
@@ -195,7 +195,7 @@ def __init__(self):
             sage: isinstance(DatabaseKnotInfo(), DatabaseKnotInfo)
             True
         """
-        PythonModule.__init__(self, 'database_knotinfo', spkg='database_knotinfo')
+        PythonModule.__init__(self, 'database_knotinfo', spkg='pkg:pypi/database-knotinfo')
 
 
 class DatabaseMatroids(PythonModule):
@@ -221,7 +221,7 @@ def __init__(self):
             sage: isinstance(DatabaseMatroids(), DatabaseMatroids)
             True
         """
-        PythonModule.__init__(self, 'matroid_database', spkg='matroid_database')
+        PythonModule.__init__(self, 'matroid_database', spkg='pkg:pypi/matroid-database')
 
 
 class DatabaseCubicHecke(PythonModule):
@@ -247,7 +247,7 @@ def __init__(self):
             sage: isinstance(DatabaseCubicHecke(), DatabaseCubicHecke)
             True
         """
-        PythonModule.__init__(self, 'database_cubic_hecke', spkg='database_cubic_hecke')
+        PythonModule.__init__(self, 'database_cubic_hecke', spkg='pkg:pypi/database-cubic-hecke')
 
 
 class DatabaseReflexivePolytopes(StaticFile):
@@ -289,7 +289,7 @@ def __init__(self, name='polytopes_db'):
 
 
 def all_features():
-    return [PythonModule('conway_polynomials', spkg='conway_polynomials', type='standard'),
+    return [PythonModule('conway_polynomials', spkg='pkg:pypi/conway-polynomials', type='standard'),
             DatabaseCremona(),
             DatabaseCremona('cremona_mini', type='standard'),
             DatabaseEllcurves(),

diff --git a/src/sage/features/igraph.py b/src/sage/features/igraph.py
@@ -37,7 +37,7 @@ def __init__(self):
             True
         """
         JoinFeature.__init__(self, 'python_igraph',
-                             [PythonModule('igraph', spkg='python_igraph',
+                             [PythonModule('igraph', spkg='pkg:pypi/igraph',
                                             url='http://igraph.org')])
 
 def all_features():

diff --git a/src/sage/features/mip_backends.py b/src/sage/features/mip_backends.py
@@ -52,7 +52,7 @@ def __init__(self):
             FeatureTestResult('cplex', True)
         """
         MIPBackend.__init__(self, 'cplex',
-                            spkg='sage_numerical_backends_cplex')
+                            spkg='pkg:pypi/sage-numerical-backends-cplex')
 
 
 class Gurobi(MIPBackend):
@@ -68,7 +68,7 @@ def __init__(self):
             FeatureTestResult('gurobi', True)
         """
         MIPBackend.__init__(self, 'gurobi',
-                            spkg='sage_numerical_backends_gurobi')
+                            spkg='pkg:pypi/sage-numerical-backends-gurobi')
 
 
 class COIN(JoinFeature):
@@ -85,7 +85,7 @@ def __init__(self):
         """
         JoinFeature.__init__(self, 'sage_numerical_backends_coin',
                              [MIPBackend('coin')],
-                             spkg='sage_numerical_backends_coin')
+                             spkg='pkg:pypi/sage-numerical-backends-coin')
 
 
 class CVXOPT(JoinFeature):
@@ -103,7 +103,7 @@ def __init__(self):
         JoinFeature.__init__(self, 'cvxopt',
                              [MIPBackend('CVXOPT'),
                               PythonModule('cvxopt')],
-                             spkg='cvxopt',
+                             spkg='pkg:pypi/cvxopt',
                              type='standard')
 
 

diff --git a/src/sage/features/normaliz.py b/src/sage/features/normaliz.py
@@ -36,7 +36,7 @@ def __init__(self):
             True
         """
         JoinFeature.__init__(self, 'pynormaliz',
-                             [PythonModule('PyNormaliz', spkg='pynormaliz')])
+                             [PythonModule('PyNormaliz', spkg='pkg:pypi/pynormaliz')])
 
 
 def all_features():

diff --git a/src/sage/features/phitigra.py b/src/sage/features/phitigra.py
@@ -35,7 +35,7 @@ def __init__(self):
             sage: isinstance(Phitigra(), Phitigra)
             True
         """
-        PythonModule.__init__(self, 'phitigra', spkg='phitigra')
+        PythonModule.__init__(self, 'phitigra', spkg='pkg:pypi/phitigra')
 
 
 def all_features():

diff --git a/src/sage/features/pkg_systems.py b/src/sage/features/pkg_systems.py
@@ -4,14 +4,20 @@
 """
 
 # *****************************************************************************
-#       Copyright (C) 2021-2022 Matthias Koeppe
+#       Copyright (C) 2021-2024 Matthias Koeppe
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
 #                  https://www.gnu.org/licenses/
 # *****************************************************************************
 
+import os
+import re
+import shlex
+import sys
+import sysconfig
+
 from . import Feature
 
 
@@ -56,6 +62,29 @@
             feature = spkgs
         return self._spkg_installation_hint(spkgs, prompt, feature)
 
+    def _system_packages(self, spkgs):
+        r"""
+        Return system packages corresponding to SPKG names or PURLs.
+
+        INPUT:
+
+        - ``spkgs`` -- string, whitespace-separated list of SPKG names or PURLs
+
+        OUTPUT: list of strings.
+
+        EXAMPLES::
+
+            sage: from sage.features.pkg_systems import PackageSystem
+            sage: debian = PackageSystem('debian')
+            sage: debian._system_packages('fflas_ffpack pypi/cvxopt pkg:generic/gmp')  # optional - SAGE_ROOT
+            ['fflas-ffpack', 'libgmp-dev']
+        """
+        from subprocess import run, CalledProcessError
+        system = self.name
+        proc = run(f'sage-get-system-packages {system} {spkgs}',
+                   shell=True, capture_output=True, text=True, check=True)
+        return proc.stdout.strip().split('\n')
+
     def _spkg_installation_hint(self, spkgs, prompt, feature):
         r"""
         Return a string that explains how to install ``feature``.
@@ -69,18 +98,17 @@
             sage: fedora.spkg_installation_hint('openblas')  # optional - SAGE_ROOT
             'To install openblas using the fedora package manager, you can try to run:\n!sudo yum install openblas-devel'
         """
-        from subprocess import run, CalledProcessError, PIPE
+        from subprocess import run, CalledProcessError
         lines = []
         system = self.name
         try:
-            proc = run(f'sage-get-system-packages {system} {spkgs}',
-                       shell=True, capture_output=True, text=True, check=True)
-            system_packages = proc.stdout.strip()
+            system_packages = ' '.join(shlex.quote(pkg)
+                                       for pkg in self._system_packages(spkgs))
             print_sys = f'sage-print-system-package-command {system} --verbose --sudo --prompt="{prompt}"'
             command = f'{print_sys} update && {print_sys} install {system_packages}'
             proc = run(command, shell=True, capture_output=True, text=True, check=True)
-            command = proc.stdout.strip()
-            if command:
+            command = proc.stdout
+            if command.strip():
                 lines.append(f'To install {feature} using the {system} package manager, you can try to run:')
                 lines.append(command)
                 return '\n'.join(lines)
@@ -148,11 +176,37 @@
             To install foobarability using the Sage package manager, you can try to run:
             ### sage -i foo bar
         """
+        spkgs = ' '.join(shlex.quote(pkg) for pkg in self._system_packages(spkgs))
         lines = []
         lines.append(f'To install {feature} using the Sage package manager, you can try to run:')
         lines.append(f'{prompt}sage -i {spkgs}')
         return '\n'.join(lines)
 
+    def _system_packages(self, spkgs):
+        r"""
+        Return system packages corresponding to SPKG names or PURLs.
+
+        INPUT:
+
+        - ``spkgs`` -- string, whitespace-separated list of SPKG names or PURLs
+
+        OUTPUT: list of strings.
+
+        EXAMPLES::
+
+            sage: from sage.features.pkg_systems import SagePackageSystem
+            sage: SagePackageSystem()._system_packages('gfortran')
+            ['gfortran']
+            sage: SagePackageSystem()._system_packages('pkg:pypi/cvxopt')               # needs sage_spkg
+            ['cvxopt']
+        """
+        if 'pkg:' not in spkgs and 'pypi/' not in spkgs and 'generic/' not in spkgs:
+            return spkgs.split()
+        from subprocess import run, CalledProcessError
+        proc = run(f'sage-package list {spkgs}',
+                    shell=True, capture_output=True, text=True, check=True)
+        return proc.stdout.strip().split('\n')
+
 
 class PipPackageSystem(PackageSystem):
     r"""
@@ -193,3 +247,67 @@
             return True
         except CalledProcessError:
             return False
+
+    def _spkg_installation_hint(self, spkgs, prompt, feature):
+        r"""
+        Return a string that explains how to install ``feature``.
+
+        EXAMPLES::
+
+            sage: from sage.features.pkg_systems import PipPackageSystem
+            sage: print(PipPackageSystem().spkg_installation_hint(['admcycles'], feature='admcycles'))  # indirect doctest
+            To install admcycles...pip install admcycles...
+        """
+        lines = []
+        # https://github.com/pypa/pip/blob/51de88ca6459fdd5213f86a54b021a80884572f9/src/pip/_internal/utils/virtualenv.py#L14
+        is_virtualenv = sys.prefix != getattr(sys, "base_prefix", sys.prefix)
+        # https://github.com/pypa/pip/blob/51de88ca6459fdd5213f86a54b021a80884572f9/src/pip/_internal/utils/misc.py#L648
+        marker = os.path.join(sysconfig.get_path("stdlib"), "EXTERNALLY-MANAGED")
+        is_externally_managed = os.path.isfile(marker)
+        pip_packages = ' '.join(shlex.quote(pkg) for pkg in self._system_packages(spkgs))
+        if not is_virtualenv and is_externally_managed:
+            lines.append(f'To install {feature} using the pip package manager:')
+            lines.append(f'Note that this Sage is installed in an externally managed Python environment.')
+            lines.append(f'It is recommended to first create a virtual environment:')
+            lines.append(f'{prompt}sage -python -m venv --system-site-packages ~/.sage/venv')
+            lines.append(f'Then quit the current Sage:')
+            lines.append(f'  exit')
+            lines.append(f'Next, in the shell, activate the new virtual environment:')
+            lines.append(f' $ . ~/.sage/venv/bin/activate')
+            lines.append(f' $ pip install {pip_packages}')
+            lines.append(f'Finally, start Sage from the new virtual environment:')
+            lines.append(f' $ sage')
+            lines.append(f'To exit the virtual environment after use:')
+            lines.append(f' $ deactivate')
+            return '\n'.join(lines)
+        return super()._spkg_installation_hint(spkgs, prompt, feature)
+
+    def _system_packages(self, spkgs):
+        r"""
+        Return system packages corresponding to SPKG names or PURLs.
+
+        INPUT:
+
+        - ``spkgs`` -- string, whitespace-separated list of SPKG names or PURLs
+
+        OUTPUT: list of strings.
+
+        EXAMPLES::
+
+            sage: from sage.features.pkg_systems import PipPackageSystem
+            sage: PipPackageSystem()._system_packages('pypi/cvxopt pkg:pypi/pynormaliz')
+            ['cvxopt...', 'pynormaliz...']
+            sage: PipPackageSystem()._system_packages('pypi/cvxopt pkg:pypi/pynormaliz dateutil')  # optional - sage_spkg
+            ['cvxopt...', 'python-dateutil...', 'pynormaliz...']
+        """
+        result = super()._system_packages(spkgs)
+        if result:
+            return result
+        all_packages = spkgs.split()
+        pypi_packages = [m.group(2) for package in all_packages
+                         if (m := re.fullmatch('(pkg:)?pypi/(.*)', package))]
+        other_packages = [package for package in all_packages
+                          if not re.fullmatch('(pkg:)?pypi/(.*)', package)]
+        if other_packages:
+            return []
+        return sorted(pypi_packages)
diff --git a/src/sage/features/polymake.py b/src/sage/features/polymake.py
@@ -36,7 +36,7 @@ def __init__(self):
             True
         """
         JoinFeature.__init__(self, "jupymake",
-                             [PythonModule("JuPyMake", spkg='jupymake')])
+                             [PythonModule('JuPyMake', spkg='pkg:pypi/jupymake')])
 
 
 def all_features():

diff --git a/src/sage/features/sat.py b/src/sage/features/sat.py
@@ -71,7 +71,7 @@ def __init__(self):
             True
         """
         PythonModule.__init__(self, "pycosat",
-                              spkg="pycosat", type="optional")
+                              spkg="pkg:pypi/pycosat", type="optional")
 
 
 class Pycryptosat(PythonModule):

diff --git a/src/sage/features/sphinx.py b/src/sage/features/sphinx.py
@@ -36,7 +36,7 @@ def __init__(self):
             sage: isinstance(Sphinx(), Sphinx)
             True
         """
-        PythonModule.__init__(self, 'sphinx', spkg='sphinx', type='standard')
+        PythonModule.__init__(self, 'sphinx', spkg='pkg:pypi/sphinx', type='standard')
 
 
 def all_features():

diff --git a/src/sage/features/standard.py b/src/sage/features/standard.py
@@ -19,20 +19,20 @@
 
 
 def all_features():
-    return [PythonModule('cvxopt', spkg='cvxopt', type='standard'),
-            PythonModule('fpylll', spkg='fpylll', type='standard'),
-            JoinFeature('ipython', (PythonModule('IPython'),), spkg='ipython', type='standard'),
-            JoinFeature('lrcalc_python', (PythonModule('lrcalc'),), spkg='lrcalc_python', type='standard'),
-            PythonModule('mpmath', spkg='mpmath', type='standard'),
-            PythonModule('networkx', spkg='networkx', type='standard'),
-            PythonModule('numpy', spkg='numpy', type='standard'),
-            PythonModule('pexpect', spkg='pexpect', type='standard'),
-            JoinFeature('pillow', (PythonModule('PIL'),), spkg='pillow', type='standard'),
-            JoinFeature('pplpy', (PythonModule('ppl'),), spkg='pplpy', type='standard'),
-            PythonModule('primecountpy', spkg='primecountpy', type='standard'),
-            PythonModule('ptyprocess', spkg='ptyprocess', type='standard'),
-            PythonModule('pyparsing', spkg='pyparsing', type='standard'),
-            PythonModule('requests', spkg='requests', type='standard'),
-            PythonModule('rpy2', spkg='rpy2', type='standard'),
-            PythonModule('scipy', spkg='scipy', type='standard'),
-            PythonModule('sympy', spkg='sympy', type='standard')]
+    return [PythonModule('cvxopt', spkg='pkg:pypi/cvxopt', type='standard'),
+            PythonModule('fpylll', spkg='pkg:pypi/fpylll', type='standard'),
+            JoinFeature('ipython', (PythonModule('IPython'),), spkg='pkg:pypi/ipython', type='standard'),
+            JoinFeature('lrcalc_python', (PythonModule('lrcalc'),), spkg='pkg:pypi/lrcalc', type='standard'),
+            PythonModule('mpmath', spkg='pkg:pypi/mpmath', type='standard'),
+            PythonModule('networkx', spkg='pkg:pypi/networkx', type='standard'),
+            PythonModule('numpy', spkg='pkg:pypi/numpy', type='standard'),
+            PythonModule('pexpect', spkg='pkg:pypi/pexpect', type='standard'),
+            JoinFeature('pillow', (PythonModule('PIL'),), spkg='pkg:pypi/pillow', type='standard'),
+            JoinFeature('pplpy', (PythonModule('ppl'),), spkg='pkg:pypi/pplpy', type='standard'),
+            PythonModule('primecountpy', spkg='pkg:pypi/primecountpy', type='standard'),
+            PythonModule('ptyprocess', spkg='pkg:pypi/ptyprocess', type='standard'),
+            PythonModule('pyparsing', spkg='pkg:pypi/pyparsing', type='standard'),
+            PythonModule('requests', spkg='pkg:pypi/requests', type='standard'),
+            PythonModule('rpy2', spkg='pkg:pypi/rpy2', type='standard'),
+            PythonModule('scipy', spkg='pkg:pypi/scipy', type='standard'),
+            PythonModule('sympy', spkg='pkg:pypi/sympy', type='standard')]
diff --git a/src/sage/features/symengine_py.py b/src/sage/features/symengine_py.py
@@ -37,7 +37,7 @@ def __init__(self):
             True
         """
         JoinFeature.__init__(self, 'symengine_py',
-                             [PythonModule('symengine', spkg='symengine_py',
+                             [PythonModule('symengine', spkg='pkg:pypi/symengine.py',
                                             url='https://pypi.org/project/symengine')])
 
 def all_features():

diff --git a/src/sage/geometry/cone.py b/src/sage/geometry/cone.py
@@ -236,9 +236,9 @@
 from sage.features import PythonModule
 lazy_import('ppl', ['C_Polyhedron', 'Generator_System', 'Constraint_System',
                     'Linear_Expression', 'Poly_Con_Relation'],
-                    feature=PythonModule("ppl", spkg='pplpy', type='standard'))
+                    feature=PythonModule('ppl', spkg='pkg:pypi/pplpy', type='standard'))
 lazy_import('ppl', ['ray', 'point'], as_=['PPL_ray', 'PPL_point'],
-                    feature=PythonModule("ppl", spkg='pplpy', type='standard'))
+                    feature=PythonModule('ppl', spkg='pkg:pypi/pplpy', type='standard'))
 
 
 def is_Cone(x):

diff --git a/src/sage/geometry/lattice_polytope.py b/src/sage/geometry/lattice_polytope.py
@@ -135,9 +135,9 @@
 from sage.features import PythonModule
 from sage.features.palp import PalpExecutable
 lazy_import('ppl', ['C_Polyhedron', 'Generator_System', 'Linear_Expression'],
-                    feature=PythonModule("ppl", spkg='pplpy', type='standard'))
+                    feature=PythonModule('ppl', spkg='pkg:pypi/pplpy', type='standard'))
 lazy_import('ppl', 'point', as_='PPL_point',
-                    feature=PythonModule("ppl", spkg='pplpy', type='standard'))
+                    feature=PythonModule('ppl', spkg='pkg:pypi/pplpy', type='standard'))
 
 from sage.matrix.constructor import matrix
 from sage.structure.element import Matrix