sagemath · vbraun · Apr 6, 2023 · Mar 21, 2023 · Mar 21, 2023 · Mar 21, 2023
diff --git a/src/doc/en/reference/combinat/module_list.rst b/src/doc/en/reference/combinat/module_list.rst
@@ -367,7 +367,7 @@ Comprehensive Module List
     sage/combinat/tutorial
     sage/combinat/vector_partition
     sage/combinat/words/abstract_word
-    sage/combinat/words
+    sage/combinat/words/all
     sage/combinat/words/alphabet
     sage/combinat/words/finite_word
     sage/combinat/words/infinite_word

diff --git a/src/doc/en/reference/modules/index.rst b/src/doc/en/reference/modules/index.rst
@@ -29,7 +29,7 @@ Modules with basis
 .. toctree::
    :maxdepth: 1
 
-   sage/modules/with_basis/__init__
+   sage/modules/with_basis/all
    sage/modules/with_basis/cell_module
    sage/modules/with_basis/indexed_element
    sage/modules/with_basis/invariant

diff --git a/src/sage/algebras/__init__.py → src/sage/algebras/letterplace/all.py b/src/sage/algebras/__init__.py → src/sage/algebras/letterplace/all.py
diff --git a/...s/finite_dimensional_algebras/__init__.py → src/sage/categories/examples/all.py b/...s/finite_dimensional_algebras/__init__.py → src/sage/categories/examples/all.py
diff --git a/src/sage/algebras/fusion_rings/__init__.py → src/sage/coding/codecan/all.py b/src/sage/algebras/fusion_rings/__init__.py → src/sage/coding/codecan/all.py
diff --git a/src/sage/algebras/hecke_algebras/__init__.py → src/sage/coding/guruswami_sudan/all.py b/src/sage/algebras/hecke_algebras/__init__.py → src/sage/coding/guruswami_sudan/all.py
diff --git a/src/sage/combinat/all.py b/src/sage/combinat/all.py
@@ -26,7 +26,7 @@
 - :ref:`sage.combinat.species.all`
 - :ref:`sage.combinat.designs.all`
 - :ref:`sage.combinat.posets.all`
-- :ref:`sage.combinat.words`
+- :ref:`sage.combinat.words.all`
 - :ref:`sage.combinat.bijectionist`
 
 Utilities

diff --git a/src/sage/combinat/sf/__init__.py b/src/sage/combinat/sf/__init__.py
diff --git a/src/sage/combinat/species/__init__.py b/src/sage/combinat/species/__init__.py
diff --git a/src/sage/combinat/words/__init__.py b/src/sage/combinat/words/__init__.py
diff --git a/src/sage/combinat/words/all.py b/src/sage/combinat/words/all.py
@@ -1,3 +1,48 @@
+r"""
+Combinatorics on words
+
+**Main modules and their methods:**
+
+- :ref:`sage.combinat.words.abstract_word`
+- :ref:`sage.combinat.words.finite_word`
+- :ref:`sage.combinat.words.infinite_word`
+- :ref:`sage.combinat.words.alphabet`
+- :ref:`sage.combinat.words.words`
+- :ref:`sage.combinat.words.paths`
+- :ref:`sage.combinat.words.morphism`
+- :ref:`sage.combinat.words.shuffle_product`
+- :ref:`sage.combinat.words.suffix_trees`
+
+Main classes and functions meant to be used by the user:
+
+    :func:`~sage.combinat.words.word.Word`,
+    :class:`~sage.combinat.words.words.FiniteWords`,
+    :class:`~sage.combinat.words.words.InfiniteWords`,
+    :func:`~sage.combinat.words.words.Words`,
+    :func:`~sage.combinat.words.alphabet.Alphabet`,
+    :class:`~sage.combinat.words.morphism.WordMorphism`,
+    :class:`~sage.combinat.words.paths.WordPaths`.
+
+A list of common words can be accessed through ``words.<tab>`` and are listed in
+the :ref:`words catalog <sage.combinat.words.word_generators>`.
+
+**Internal representation of words:**
+
+- :ref:`sage.combinat.words.word`
+- :ref:`sage.combinat.words.word_char`
+- :ref:`sage.combinat.words.word_datatypes`
+- :ref:`sage.combinat.words.word_infinite_datatypes`
+
+**Options:**
+
+- :ref:`sage.combinat.words.word_options`
+
+See :func:`~sage.combinat.words.word_options.WordOptions`.
+"""
+# install the docstring of this module to the containing package
+from sage.misc.namespace_package import install_doc
+install_doc(__package__, __doc__)
+
 from .alphabet import Alphabet, build_alphabet
 from .morphism import WordMorphism
 from .paths import WordPaths

diff --git a/src/sage/crypto/block_cipher/__init__.py b/src/sage/crypto/block_cipher/__init__.py
diff --git a/src/sage/crypto/public_key/__init__.py b/src/sage/crypto/public_key/__init__.py
diff --git a/src/sage/data_structures/__init__.py b/src/sage/data_structures/__init__.py
diff --git a/src/sage/databases/__init__.py b/src/sage/databases/__init__.py
diff --git a/src/sage/dynamics/__init__.py b/src/sage/dynamics/__init__.py
diff --git a/src/sage/dynamics/arithmetic_dynamics/__init__.py b/src/sage/dynamics/arithmetic_dynamics/__init__.py
diff --git a/src/sage/dynamics/cellular_automata/__init__.py b/src/sage/dynamics/cellular_automata/__init__.py
diff --git a/src/sage/dynamics/complex_dynamics/__init__.py b/src/sage/dynamics/complex_dynamics/__init__.py
diff --git a/src/sage/functions/__init__.py b/src/sage/functions/__init__.py
diff --git a/src/sage/game_theory/__init__.py b/src/sage/game_theory/__init__.py
diff --git a/src/sage/games/__init__.py b/src/sage/games/__init__.py
diff --git a/src/sage/geometry/__init__.py b/src/sage/geometry/__init__.py
diff --git a/src/sage/geometry/hyperbolic_space/__init__.py b/src/sage/geometry/hyperbolic_space/__init__.py
diff --git a/src/sage/geometry/hyperplane_arrangement/__init__.py b/src/sage/geometry/hyperplane_arrangement/__init__.py
diff --git a/src/sage/algebras/letterplace/__init__.py → ...ge/geometry/hyperplane_arrangement/all.py b/src/sage/algebras/letterplace/__init__.py → ...ge/geometry/hyperplane_arrangement/all.py
diff --git a/src/sage/geometry/polyhedron/__init__.py b/src/sage/geometry/polyhedron/__init__.py
diff --git a/src/sage/geometry/polyhedron/combinatorial_polyhedron/__init__.py b/src/sage/geometry/polyhedron/combinatorial_polyhedron/__init__.py
diff --git a/src/sage/algebras/lie_algebras/__init__.py → ...olyhedron/combinatorial_polyhedron/all.py b/src/sage/algebras/lie_algebras/__init__.py → ...olyhedron/combinatorial_polyhedron/all.py
diff --git a/src/sage/geometry/polyhedron/modules/__init__.py b/src/sage/geometry/polyhedron/modules/__init__.py
diff --git a/...gebras/lie_conformal_algebras/__init__.py → src/sage/geometry/polyhedron/modules/all.py b/...gebras/lie_conformal_algebras/__init__.py → src/sage/geometry/polyhedron/modules/all.py
diff --git a/src/sage/geometry/riemannian_manifolds/__init__.py b/src/sage/geometry/riemannian_manifolds/__init__.py
diff --git a/src/sage/geometry/triangulation/__init__.py b/src/sage/geometry/triangulation/__init__.py
diff --git a/src/sage/graphs/base/__init__.py b/src/sage/graphs/base/__init__.py
diff --git a/src/sage/algebras/quantum_groups/__init__.py → src/sage/graphs/base/all.py b/src/sage/algebras/quantum_groups/__init__.py → src/sage/graphs/base/all.py
diff --git a/src/sage/graphs/generators/__init__.py b/src/sage/graphs/generators/__init__.py
diff --git a/src/sage/algebras/quatalg/__init__.py → src/sage/graphs/generators/all.py b/src/sage/algebras/quatalg/__init__.py → src/sage/graphs/generators/all.py
diff --git a/src/sage/groups/__init__.py b/src/sage/groups/__init__.py
diff --git a/src/sage/groups/abelian_gps/__init__.py b/src/sage/groups/abelian_gps/__init__.py
diff --git a/src/sage/groups/additive_abelian/__init__.py b/src/sage/groups/additive_abelian/__init__.py
diff --git a/src/sage/groups/affine_gps/__init__.py b/src/sage/groups/affine_gps/__init__.py
diff --git a/src/sage/algebras/steenrod/__init__.py → src/sage/groups/affine_gps/all.py b/src/sage/algebras/steenrod/__init__.py → src/sage/groups/affine_gps/all.py
diff --git a/src/sage/groups/lie_gps/__init__.py b/src/sage/groups/lie_gps/__init__.py
diff --git a/src/sage/calculus/__init__.py → src/sage/groups/lie_gps/all.py b/src/sage/calculus/__init__.py → src/sage/groups/lie_gps/all.py
diff --git a/src/sage/groups/matrix_gps/__init__.py b/src/sage/groups/matrix_gps/__init__.py
diff --git a/src/sage/groups/misc_gps/__init__.py b/src/sage/groups/misc_gps/__init__.py
diff --git a/src/sage/calculus/transforms/__init__.py → src/sage/groups/misc_gps/all.py b/src/sage/calculus/transforms/__init__.py → src/sage/groups/misc_gps/all.py
diff --git a/src/sage/groups/perm_gps/__init__.py b/src/sage/groups/perm_gps/__init__.py
diff --git a/src/sage/groups/perm_gps/partn_ref/__init__.py b/src/sage/groups/perm_gps/partn_ref/__init__.py
diff --git a/src/sage/categories/examples/__init__.py → src/sage/groups/perm_gps/partn_ref/all.py b/src/sage/categories/examples/__init__.py → src/sage/groups/perm_gps/partn_ref/all.py
diff --git a/src/sage/groups/perm_gps/partn_ref2/__init__.py b/src/sage/groups/perm_gps/partn_ref2/__init__.py
diff --git a/src/sage/coding/__init__.py → src/sage/groups/perm_gps/partn_ref2/all.py b/src/sage/coding/__init__.py → src/sage/groups/perm_gps/partn_ref2/all.py
diff --git a/src/sage/groups/semimonomial_transformations/__init__.py b/src/sage/groups/semimonomial_transformations/__init__.py
diff --git a/src/sage/coding/codecan/__init__.py → ...roups/semimonomial_transformations/all.py b/src/sage/coding/codecan/__init__.py → ...roups/semimonomial_transformations/all.py
diff --git a/src/sage/homology/__init__.py b/src/sage/homology/__init__.py
diff --git a/src/sage/interacts/__init__.py b/src/sage/interacts/__init__.py
diff --git a/src/sage/knots/__init__.py b/src/sage/knots/__init__.py
diff --git a/src/sage/lfunctions/__init__.py b/src/sage/lfunctions/__init__.py
diff --git a/src/sage/libs/gap/__init__.py b/src/sage/libs/gap/__init__.py
diff --git a/src/sage/logic/__init__.py b/src/sage/logic/__init__.py
diff --git a/src/sage/manifolds/__init__.py b/src/sage/manifolds/__init__.py
diff --git a/src/sage/manifolds/differentiable/__init__.py b/src/sage/manifolds/differentiable/__init__.py
diff --git a/src/sage/coding/guruswami_sudan/__init__.py → src/sage/manifolds/differentiable/all.py b/src/sage/coding/guruswami_sudan/__init__.py → src/sage/manifolds/differentiable/all.py
diff --git a/src/sage/manifolds/differentiable/examples/__init__.py b/src/sage/manifolds/differentiable/examples/__init__.py
diff --git a/src/sage/coding/source_coding/__init__.py → .../manifolds/differentiable/examples/all.py b/src/sage/coding/source_coding/__init__.py → .../manifolds/differentiable/examples/all.py
diff --git a/src/sage/manifolds/subsets/__init__.py b/src/sage/manifolds/subsets/__init__.py
diff --git a/src/sage/combinat/__init__.py → src/sage/manifolds/subsets/all.py b/src/sage/combinat/__init__.py → src/sage/manifolds/subsets/all.py
diff --git a/src/sage/matroids/__init__.py b/src/sage/matroids/__init__.py
diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py
@@ -211,6 +211,28 @@ def cython(filename, verbose=0, compile_message=False,
         sage: cython('''
         ....: cdef size_t foo = 3/2
         ....: ''')
+
+    Check that Cython supports PEP 420 packages::
+
+        sage: cython('''
+        ....: cimport sage.misc.cachefunc
+        ....: ''')
+
+        sage: cython('''
+        ....: from sage.misc.cachefunc cimport cache_key
+        ....: ''')
+
+    In Cython 0.29.33 using `from PACKAGE cimport MODULE` is broken
+    when `PACKAGE` is a namespace package, see :trac:`35322`::
+
+        sage: cython('''
+        ....: from sage.misc cimport cachefunc
+        ....: ''')
+        Traceback (most recent call last):
+        ...
+        RuntimeError: Error compiling Cython file:
+        ...
+        ...: 'sage/misc.pxd' not found
     """
     if not filename.endswith('pyx'):
         print("Warning: file (={}) should have extension .pyx".format(filename), file=sys.stderr)

diff --git a/src/sage/misc/dev_tools.py b/src/sage/misc/dev_tools.py
@@ -169,7 +169,7 @@ def load_submodules(module=None, exclude_pattern=None):
         load sage.geometry.polyhedron.palp_database... succeeded
         load sage.geometry.polyhedron.ppl_lattice_polygon... succeeded
     """
-    import pkgutil
+    from .package_dir import walk_packages
 
     if module is None:
         import sage
@@ -181,7 +181,7 @@ def load_submodules(module=None, exclude_pattern=None):
     else:
         exclude = None
 
-    for importer, module_name, ispkg in pkgutil.walk_packages(module.__path__, module.__name__ + '.'):
+    for importer, module_name, ispkg in walk_packages(module.__path__, module.__name__ + '.'):
         if ispkg or module_name in sys.modules:
             continue
 

diff --git a/src/sage/misc/package_dir.py b/src/sage/misc/package_dir.py
@@ -14,6 +14,7 @@
 
 import os
 import glob
+import sys
 from contextlib import contextmanager
 
 
@@ -154,29 +155,29 @@ def is_package_or_sage_namespace_package_dir(path, *, distribution_filter=None):
     :mod:`sage.cpython` is an ordinary package::
 
         sage: from sage.misc.package_dir import is_package_or_sage_namespace_package_dir
-        sage: directory = os.path.dirname(sage.cpython.__file__); directory
+        sage: directory = sage.cpython.__path__[0]; directory
         '.../sage/cpython'
         sage: is_package_or_sage_namespace_package_dir(directory)
         True
 
     :mod:`sage.libs.mpfr` only has an ``__init__.pxd`` file, but we consider
     it a package directory for consistency with Cython::
 
-        sage: directory = os.path.join(os.path.dirname(sage.libs.all.__file__), 'mpfr'); directory
+        sage: directory = os.path.join(sage.libs.__path__[0], 'mpfr'); directory
         '.../sage/libs/mpfr'
         sage: is_package_or_sage_namespace_package_dir(directory)
         True
 
     :mod:`sage` is designated to become an implicit namespace package::
 
-        sage: directory = os.path.dirname(sage.env.__file__); directory
+        sage: directory = sage.__path__[0]; directory
         '.../sage'
         sage: is_package_or_sage_namespace_package_dir(directory)
         True
 
     Not a package::
 
-        sage: directory = os.path.join(os.path.dirname(sage.symbolic.__file__), 'ginac'); directory
+        sage: directory = os.path.join(sage.symbolic.__path__[0], 'ginac'); directory
         '.../sage/symbolic/ginac'
         sage: is_package_or_sage_namespace_package_dir(directory)
         False
@@ -211,3 +212,124 @@ def cython_namespace_package_support():
         yield
     finally:
         Cython.Utils.is_package_dir = Cython.Build.Cythonize.is_package_dir = Cython.Build.Dependencies.is_package_dir = orig_is_package_dir
+
+
+def walk_packages(path=None, prefix='', onerror=None):
+    r"""
+    Yield :class:`pkgutil.ModuleInfo` for all modules recursively on ``path``.
+
+    This version of the standard library function :func:`pkgutil.walk_packages`
+    addresses https://github.com/python/cpython/issues/73444 by handling
+    the implicit namespace packages in the package layout used by Sage;
+    see :func:`is_package_or_sage_namespace_package_dir`.
+
+    INPUT:
+
+    - ``path`` -- a list of paths to look for modules in or
+      ``None`` (all accessible modules).
+
+    - ``prefix`` -- a string to output on the front of every module name
+      on output.
+
+    - ``onerror`` -- a function which gets called with one argument (the
+      name of the package which was being imported) if any exception
+      occurs while trying to import a package.  If ``None``, ignore
+      :class:`ImportError` but propagate all other exceptions.
+
+    EXAMPLES::
+
+        sage: sorted(sage.misc.package_dir.walk_packages(sage.misc.__path__))  # a namespace package
+        [..., ModuleInfo(module_finder=FileFinder('.../sage/misc'), name='package_dir', ispkg=False), ...]
+    """
+    # Adapted from https://github.com/python/cpython/blob/3.11/Lib/pkgutil.py
+
+    def iter_modules(path=None, prefix=''):
+        """
+        Yield :class:`ModuleInfo` for all submodules on ``path``.
+        """
+        from pkgutil import get_importer, iter_importers, ModuleInfo
+
+        if path is None:
+            importers = iter_importers()
+        elif isinstance(path, str):
+            raise ValueError("path must be None or list of paths to look for modules in")
+        else:
+            importers = map(get_importer, path)
+
+        yielded = {}
+        for i in importers:
+            for name, ispkg in iter_importer_modules(i, prefix):
+                if name not in yielded:
+                    yielded[name] = 1
+                    yield ModuleInfo(i, name, ispkg)
+
+    def iter_importer_modules(importer, prefix=''):
+        r"""
+        Yield :class:`ModuleInfo` for all modules of ``importer``.
+        """
+        from importlib.machinery import FileFinder
+
+        if isinstance(importer, FileFinder):
+            if importer.path is None or not os.path.isdir(importer.path):
+                return
+
+            yielded = {}
+            import inspect
+            try:
+                filenames = os.listdir(importer.path)
+            except OSError:
+                # ignore unreadable directories like import does
+                filenames = []
+            filenames.sort()  # handle packages before same-named modules
+
+            for fn in filenames:
+                modname = inspect.getmodulename(fn)
+                if modname and (modname in ['__init__', 'all']
+                                or modname.startswith('all__')
+                                or modname in yielded):
+                    continue
+
+                path = os.path.join(importer.path, fn)
+                ispkg = False
+
+                if not modname and os.path.isdir(path) and '.' not in fn:
+                    modname = fn
+                    if not (ispkg := is_package_or_sage_namespace_package_dir(path)):
+                        continue
+
+                if modname and '.' not in modname:
+                    yielded[modname] = 1
+                    yield prefix + modname, ispkg
+
+        elif not hasattr(importer, 'iter_modules'):
+            yield from []
+
+        else:
+            yield from importer.iter_modules(prefix)
+
+    def seen(p, m={}):
+        if p in m:
+            return True
+        m[p] = True
+
+    for info in iter_modules(path, prefix):
+        yield info
+
+        if info.ispkg:
+            try:
+                __import__(info.name)
+            except ImportError:
+                if onerror is not None:
+                    onerror(info.name)
+            except Exception:
+                if onerror is not None:
+                    onerror(info.name)
+                else:
+                    raise
+            else:
+                path = getattr(sys.modules[info.name], '__path__', None) or []
+
+                # don't traverse path items we've seen before
+                path = [p for p in path if not seen(p)]
+
+                yield from walk_packages(path, info.name + '.', onerror)
diff --git a/src/sage/modular/__init__.py b/src/sage/modular/__init__.py
diff --git a/src/sage/modular/abvar/__init__.py b/src/sage/modular/abvar/__init__.py
diff --git a/src/sage/modular/arithgroup/__init__.py b/src/sage/modular/arithgroup/__init__.py
diff --git a/src/sage/modular/btquotients/__init__.py b/src/sage/modular/btquotients/__init__.py
diff --git a/src/sage/modular/hecke/__init__.py b/src/sage/modular/hecke/__init__.py
diff --git a/src/sage/modular/local_comp/__init__.py b/src/sage/modular/local_comp/__init__.py
diff --git a/src/sage/modular/modform/__init__.py b/src/sage/modular/modform/__init__.py
diff --git a/src/sage/modular/modform_hecketriangle/__init__.py b/src/sage/modular/modform_hecketriangle/__init__.py
diff --git a/src/sage/modular/modsym/__init__.py b/src/sage/modular/modsym/__init__.py
diff --git a/src/sage/modular/overconvergent/__init__.py b/src/sage/modular/overconvergent/__init__.py
diff --git a/src/sage/modular/pollack_stevens/__init__.py b/src/sage/modular/pollack_stevens/__init__.py
diff --git a/src/sage/modular/quasimodform/__init__.py b/src/sage/modular/quasimodform/__init__.py
diff --git a/src/sage/modular/quatalg/__init__.py b/src/sage/modular/quatalg/__init__.py
diff --git a/src/sage/modular/ssmod/__init__.py b/src/sage/modular/ssmod/__init__.py
diff --git a/src/sage/modules/__init__.py b/src/sage/modules/__init__.py
diff --git a/src/sage/modules/all.py b/src/sage/modules/all.py
@@ -23,6 +23,8 @@
 
 from .vector_space_morphism import linear_transformation
 
+from .with_basis.all import *
+
 from sage.misc.lazy_import import lazy_import
 
 lazy_import('sage.modules.filtered_vector_space', 'FilteredVectorSpace')

diff --git a/src/sage/modules/fg_pid/__init__.py b/src/sage/modules/fg_pid/__init__.py
diff --git a/src/sage/combinat/chas/__init__.py → src/sage/modules/fg_pid/all.py b/src/sage/combinat/chas/__init__.py → src/sage/modules/fg_pid/all.py
diff --git a/src/sage/modules/fp_graded/__init__.py b/src/sage/modules/fp_graded/__init__.py
diff --git a/...mbinat/cluster_algebra_quiver/__init__.py → src/sage/modules/fp_graded/all.py b/...mbinat/cluster_algebra_quiver/__init__.py → src/sage/modules/fp_graded/all.py
diff --git a/src/sage/modules/fp_graded/steenrod/__init__.py b/src/sage/modules/fp_graded/steenrod/__init__.py
diff --git a/src/sage/combinat/crystals/__init__.py → src/sage/modules/fp_graded/steenrod/all.py b/src/sage/combinat/crystals/__init__.py → src/sage/modules/fp_graded/steenrod/all.py
diff --git a/src/sage/modules/with_basis/__init__.py → src/sage/modules/with_basis/all.py b/src/sage/modules/with_basis/__init__.py → src/sage/modules/with_basis/all.py
@@ -8,3 +8,6 @@
 
 .. SEEALSO:: The category :class:`ModulesWithBasis`
 """
+# install the docstring of this module to the containing package
+from sage.misc.namespace_package import install_doc
+install_doc(__package__, __doc__)
diff --git a/src/sage/monoids/__init__.py b/src/sage/monoids/__init__.py
diff --git a/src/sage/parallel/__init__.py b/src/sage/parallel/__init__.py
diff --git a/src/sage/plot/__init__.py b/src/sage/plot/__init__.py
diff --git a/src/sage/plot/plot3d/__init__.py b/src/sage/plot/plot3d/__init__.py
diff --git a/src/sage/probability/__init__.py b/src/sage/probability/__init__.py
diff --git a/src/sage/quadratic_forms/__init__.py b/src/sage/quadratic_forms/__init__.py
diff --git a/src/sage/quadratic_forms/genera/__init__.py b/src/sage/quadratic_forms/genera/__init__.py
diff --git a/src/sage/quivers/__init__.py b/src/sage/quivers/__init__.py
diff --git a/src/sage/combinat/designs/__init__.py → src/sage/quivers/all.py b/src/sage/combinat/designs/__init__.py → src/sage/quivers/all.py
diff --git a/src/sage/rings/asymptotic/__init__.py b/src/sage/rings/asymptotic/__init__.py
diff --git a/src/sage/rings/convert/__init__.py b/src/sage/rings/convert/__init__.py
diff --git a/src/sage/combinat/matrices/__init__.py → src/sage/rings/convert/all.py b/src/sage/combinat/matrices/__init__.py → src/sage/rings/convert/all.py
diff --git a/src/sage/rings/function_field/__init__.py b/src/sage/rings/function_field/__init__.py
diff --git a/src/sage/rings/function_field/drinfeld_modules/__init__.py b/src/sage/rings/function_field/drinfeld_modules/__init__.py
diff --git a/src/sage/combinat/ncsf_qsym/__init__.py → ...gs/function_field/drinfeld_modules/all.py b/src/sage/combinat/ncsf_qsym/__init__.py → ...gs/function_field/drinfeld_modules/all.py
diff --git a/src/sage/rings/invariants/__init__.py b/src/sage/rings/invariants/__init__.py
diff --git a/src/sage/rings/padics/__init__.py b/src/sage/rings/padics/__init__.py
diff --git a/src/sage/rings/polynomial/padics/__init__.py b/src/sage/rings/polynomial/padics/__init__.py
diff --git a/src/sage/combinat/ncsym/__init__.py → src/sage/rings/polynomial/padics/all.py b/src/sage/combinat/ncsym/__init__.py → src/sage/rings/polynomial/padics/all.py
diff --git a/src/sage/rings/polynomial/weil/__init__.py b/src/sage/rings/polynomial/weil/__init__.py
diff --git a/src/sage/rings/semirings/__init__.py b/src/sage/rings/semirings/__init__.py
diff --git a/src/sage/rings/valuation/__init__.py b/src/sage/rings/valuation/__init__.py
diff --git a/src/sage/sandpiles/__init__.py b/src/sage/sandpiles/__init__.py
diff --git a/src/sage/sat/__init__.py b/src/sage/sat/__init__.py
diff --git a/src/sage/schemes/__init__.py b/src/sage/schemes/__init__.py
diff --git a/src/sage/schemes/affine/__init__.py b/src/sage/schemes/affine/__init__.py
diff --git a/src/sage/schemes/berkovich/__init__.py b/src/sage/schemes/berkovich/__init__.py
diff --git a/src/sage/schemes/curves/__init__.py b/src/sage/schemes/curves/__init__.py
diff --git a/src/sage/schemes/cyclic_covers/__init__.py b/src/sage/schemes/cyclic_covers/__init__.py
diff --git a/src/sage/schemes/elliptic_curves/__init__.py b/src/sage/schemes/elliptic_curves/__init__.py
diff --git a/src/sage/schemes/generic/__init__.py b/src/sage/schemes/generic/__init__.py
diff --git a/src/sage/schemes/hyperelliptic_curves/__init__.py b/src/sage/schemes/hyperelliptic_curves/__init__.py
diff --git a/src/sage/schemes/jacobians/__init__.py b/src/sage/schemes/jacobians/__init__.py
diff --git a/src/sage/schemes/plane_conics/__init__.py b/src/sage/schemes/plane_conics/__init__.py
diff --git a/src/sage/schemes/plane_quartics/__init__.py b/src/sage/schemes/plane_quartics/__init__.py
diff --git a/src/sage/schemes/product_projective/__init__.py b/src/sage/schemes/product_projective/__init__.py
diff --git a/src/sage/schemes/projective/__init__.py b/src/sage/schemes/projective/__init__.py
diff --git a/src/sage/schemes/riemann_surfaces/__init__.py b/src/sage/schemes/riemann_surfaces/__init__.py
diff --git a/src/sage/combinat/path_tableaux/__init__.py → src/sage/schemes/riemann_surfaces/all.py b/src/sage/combinat/path_tableaux/__init__.py → src/sage/schemes/riemann_surfaces/all.py
diff --git a/src/sage/schemes/toric/__init__.py b/src/sage/schemes/toric/__init__.py
diff --git a/src/sage/schemes/toric/sheaf/__init__.py b/src/sage/schemes/toric/sheaf/__init__.py
diff --git a/src/sage/combinat/posets/__init__.py → src/sage/schemes/toric/sheaf/all.py b/src/sage/combinat/posets/__init__.py → src/sage/schemes/toric/sheaf/all.py
diff --git a/src/sage/server/__init__.py b/src/sage/server/__init__.py
diff --git a/src/sage/stats/__init__.py b/src/sage/stats/__init__.py
diff --git a/src/sage/stats/distributions/__init__.py b/src/sage/stats/distributions/__init__.py
diff --git a/...ombinat/rigged_configurations/__init__.py → src/sage/stats/distributions/all.py b/...ombinat/rigged_configurations/__init__.py → src/sage/stats/distributions/all.py
diff --git a/src/sage/stats/hmm/__init__.py b/src/sage/stats/hmm/__init__.py
diff --git a/src/sage/symbolic/__init__.py b/src/sage/symbolic/__init__.py
diff --git a/src/sage/symbolic/integration/__init__.py b/src/sage/symbolic/integration/__init__.py
diff --git a/src/sage/combinat/root_system/__init__.py → src/sage/symbolic/integration/all.py b/src/sage/combinat/root_system/__init__.py → src/sage/symbolic/integration/all.py
diff --git a/src/sage/symbolic/pynac.pxi b/src/sage/symbolic/pynac.pxi
@@ -3,9 +3,9 @@ Declarations for pynac, a Python frontend for ginac
 
 Check that we can externally cimport this (:trac:`18825`)::
 
-    sage: cython(  # long time; random compiler warnings  # optional - sage.misc.cython
+    sage: cython(  # optional - sage.misc.cython
     ....: '''
-    ....: from sage.symbolic cimport expression
+    ....: cimport sage.symbolic.expression
     ....: ''')
 """
 

diff --git a/src/sage/tensor/__init__.py b/src/sage/tensor/__init__.py
diff --git a/src/sage/tensor/modules/__init__.py b/src/sage/tensor/modules/__init__.py
diff --git a/src/sage/topology/__init__.py b/src/sage/topology/__init__.py
diff --git a/src/sage/typeset/__init__.py b/src/sage/typeset/__init__.py
diff --git a/src/sage_setup/autogen/interpreters/__init__.py b/src/sage_setup/autogen/interpreters/__init__.py
@@ -199,6 +199,11 @@ def rebuild(dirname, force=False):
     except OSError:
         if not os.path.isdir(dirname):
             raise
+        # Remove leftover file from before move to namespace packages
+        try:
+            os.remove(os.path.join(dirname, '__init__.py'))
+        except FileNotFoundError:
+            pass
 
     # Although multiple files are generated by this function, since
     # they are all generated at once it suffices to make sure if just
@@ -208,7 +213,7 @@ class NeedToRebuild(Exception):
     try:
         if force:
             raise NeedToRebuild("-> Force rebuilding interpreters")
-        gen_file = os.path.join(dirname, '__init__.py')
+        gen_file = os.path.join(dirname, 'all.py')
         if not os.path.isfile(gen_file):
             raise NeedToRebuild("-> First build of interpreters")
 
@@ -230,5 +235,5 @@ class NeedToRebuild(Exception):
     for interp in _INTERPRETERS:
         build_interp(interp(), dirname)
 
-    with open(os.path.join(dirname, '__init__.py'), 'w') as f:
+    with open(os.path.join(dirname, 'all.py'), 'w') as f:
         f.write("# " + AUTOGEN_WARN)