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authorTravis Scrimshaw <tscrimsh at umn.edu>2015-10-16 13:31:29 -0500
committerTravis Scrimshaw <tscrimsh at umn.edu>2015-10-16 13:31:29 -0500
commit8b851a05c2569a55063539bbc8a19937851f4c93 (patch)
treea7334a2b12dc62d41d7d683926ecbf4e00abdd73
parentFixing doctest failures and letting a few other rings know they are metric sp... (diff)
parentUpdated Sage version to 6.10.beta0 (diff)
Merge branch 'develop' into public/categories/topological_metric_spaces-18175
-rw-r--r--VERSION.txt2
-rw-r--r--build/make/deps6
-rw-r--r--build/pkgs/boehm_gc/dependencies5
-rw-r--r--build/pkgs/boost_cropped/dependencies5
-rw-r--r--build/pkgs/buckygen/dependencies5
-rw-r--r--build/pkgs/cephes/dependencies5
-rw-r--r--build/pkgs/cliquer/dependencies5
-rw-r--r--build/pkgs/combinatorial_designs/dependencies5
-rw-r--r--build/pkgs/compilerwrapper/dependencies5
-rw-r--r--build/pkgs/configure/checksums.ini6
-rw-r--r--build/pkgs/configure/package-version.txt2
-rw-r--r--build/pkgs/cryptominisat/dependencies5
-rw-r--r--build/pkgs/cython/checksums.ini6
-rw-r--r--build/pkgs/cython/package-version.txt2
-rw-r--r--build/pkgs/d3js/dependencies5
-rw-r--r--build/pkgs/database_cremona_ellcurve/dependencies5
-rw-r--r--build/pkgs/database_jones_numfield/dependencies5
-rw-r--r--build/pkgs/database_stein_watkins/dependencies5
-rw-r--r--build/pkgs/database_stein_watkins_mini/dependencies5
-rw-r--r--build/pkgs/database_symbolic_data/dependencies5
-rwxr-xr-xbuild/pkgs/gcc/spkg-install4
-rw-r--r--build/pkgs/graphs/dependencies5
-rw-r--r--build/pkgs/iconv/dependencies5
-rw-r--r--build/pkgs/libogg/dependencies5
-rw-r--r--build/pkgs/lrcalc/dependencies5
-rw-r--r--build/pkgs/nauty/dependencies5
-rw-r--r--build/pkgs/ncurses/dependencies5
-rw-r--r--build/pkgs/networkx/checksums.ini6
-rw-r--r--build/pkgs/networkx/dependencies2
-rw-r--r--build/pkgs/networkx/package-version.txt2
-rwxr-xr-xbuild/pkgs/networkx/spkg-install2
-rw-r--r--build/pkgs/notebook/package-version.txt2
-rw-r--r--build/pkgs/notebook/patches/jupyter_notebook_config.py7
-rwxr-xr-xbuild/pkgs/notebook/spkg-install5
-rw-r--r--build/pkgs/openssl/dependencies5
-rw-r--r--build/pkgs/pari/checksums.ini6
-rw-r--r--build/pkgs/pari/package-version.txt2
-rw-r--r--build/pkgs/pari/patches/KERNELCFLAGS.patch16
-rw-r--r--build/pkgs/pari/patches/README.txt10
-rw-r--r--build/pkgs/pari/patches/det_garbage.patch55
-rw-r--r--build/pkgs/pari/patches/perl_regex.patch200
-rwxr-xr-xbuild/pkgs/pari/spkg-install9
-rw-r--r--build/pkgs/pari_galdata/dependencies5
-rw-r--r--build/pkgs/pari_seadata_small/dependencies5
-rw-r--r--build/pkgs/patch/dependencies5
-rw-r--r--build/pkgs/patchbot/SPKG.txt26
-rw-r--r--build/pkgs/patchbot/checksums.ini4
-rw-r--r--build/pkgs/patchbot/dependencies1
-rw-r--r--build/pkgs/patchbot/package-version.txt1
-rwxr-xr-xbuild/pkgs/patchbot/spkg-install14
-rw-r--r--build/pkgs/patchbot/type1
-rw-r--r--build/pkgs/planarity/dependencies5
-rw-r--r--build/pkgs/plantri/dependencies5
-rw-r--r--build/pkgs/polytopes_db/dependencies5
-rw-r--r--build/pkgs/rubiks/dependencies5
-rw-r--r--build/pkgs/rw/dependencies5
-rw-r--r--build/pkgs/saclib/dependencies5
-rw-r--r--build/pkgs/symmetrica/dependencies5
-rw-r--r--build/pkgs/sympow/dependencies5
-rw-r--r--build/pkgs/termcap/dependencies5
-rw-r--r--build/pkgs/valgrind/dependencies5
-rw-r--r--build/pkgs/zeromq/dependencies5
-rw-r--r--build/pkgs/zlib/dependencies5
-rw-r--r--build/sage_bootstrap/cmdline.py44
-rw-r--r--src/bin/sage-banner2
-rwxr-xr-xsrc/bin/sage-sdist8
-rw-r--r--src/bin/sage-version.sh4
-rw-r--r--src/doc/en/developer/coding_in_python.rst2
-rw-r--r--src/doc/en/reference/algebras/index.rst4
-rw-r--r--src/doc/en/reference/categories/index.rst4
-rw-r--r--src/doc/en/reference/coding/index.rst4
-rw-r--r--src/doc/en/reference/combinat/module_list.rst2
-rw-r--r--src/doc/en/reference/data_structures/index.rst1
-rw-r--r--src/doc/en/reference/graphs/index.rst1
-rw-r--r--src/doc/en/reference/index.rst1
-rw-r--r--src/doc/en/reference/polynomial_rings/polynomial_rings_univar.rst1
-rw-r--r--src/doc/en/reference/rings/asymptotic_expansions_index.rst1
-rw-r--r--src/doc/en/reference/sat/index.rst38
-rw-r--r--src/module_list.py4
-rw-r--r--src/sage/algebras/associated_graded.py341
-rw-r--r--src/sage/algebras/catalog.py2
-rw-r--r--src/sage/algebras/clifford_algebra.py80
-rw-r--r--src/sage/algebras/free_zinbiel_algebra.py253
-rw-r--r--src/sage/algebras/weyl_algebra.py47
-rw-r--r--src/sage/all.py1
-rw-r--r--src/sage/categories/algebras.py2
-rw-r--r--src/sage/categories/algebras_with_basis.py2
-rw-r--r--src/sage/categories/bialgebras.py5
-rw-r--r--src/sage/categories/cartesian_product.py38
-rw-r--r--src/sage/categories/category_with_axiom.py2
-rw-r--r--src/sage/categories/coalgebras.py39
-rw-r--r--src/sage/categories/coalgebras_with_basis.py3
-rw-r--r--src/sage/categories/covariant_functorial_construction.py4
-rw-r--r--src/sage/categories/examples/filtered_algebras_with_basis.py178
-rw-r--r--src/sage/categories/examples/filtered_modules_with_basis.py151
-rw-r--r--src/sage/categories/examples/graded_modules_with_basis.py5
-rw-r--r--src/sage/categories/filtered_algebras.py62
-rw-r--r--src/sage/categories/filtered_algebras_with_basis.py541
-rw-r--r--src/sage/categories/filtered_modules.py161
-rw-r--r--src/sage/categories/filtered_modules_with_basis.py928
-rw-r--r--src/sage/categories/finite_posets.py16
-rw-r--r--src/sage/categories/graded_algebras.py19
-rw-r--r--src/sage/categories/graded_algebras_with_basis.py137
-rw-r--r--src/sage/categories/graded_modules.py119
-rw-r--r--src/sage/categories/graded_modules_with_basis.py164
-rw-r--r--src/sage/categories/groups.py1
-rw-r--r--src/sage/categories/hopf_algebras.py3
-rw-r--r--src/sage/categories/hopf_algebras_with_basis.py1
-rw-r--r--src/sage/categories/modules.py137
-rw-r--r--src/sage/categories/modules_with_basis.py9
-rw-r--r--src/sage/categories/monoids.py3
-rw-r--r--src/sage/categories/posets.py3
-rw-r--r--src/sage/categories/pushout.py426
-rw-r--r--src/sage/categories/sets_cat.py57
-rw-r--r--src/sage/categories/super_algebras.py67
-rw-r--r--src/sage/categories/super_algebras_with_basis.py61
-rw-r--r--src/sage/categories/super_hopf_algebras_with_basis.py30
-rw-r--r--src/sage/categories/super_modules.py229
-rw-r--r--src/sage/categories/super_modules_with_basis.py185
-rw-r--r--src/sage/categories/unique_factorization_domains.py81
-rw-r--r--src/sage/coding/all.py15
-rw-r--r--src/sage/coding/codes_catalog.py9
-rw-r--r--src/sage/coding/encoder.py325
-rw-r--r--src/sage/coding/encoders_catalog.py16
-rw-r--r--src/sage/coding/linear_code.py415
-rw-r--r--src/sage/combinat/all.py2
-rw-r--r--src/sage/combinat/alternating_sign_matrix.py19
-rw-r--r--src/sage/combinat/cluster_algebra_quiver/cluster_seed.py160
-rw-r--r--src/sage/combinat/colored_permutations.py1097
-rw-r--r--src/sage/combinat/combinat.py45
-rw-r--r--src/sage/combinat/designs/block_design.py23
-rw-r--r--src/sage/combinat/designs/incidence_structures.py97
-rw-r--r--src/sage/combinat/diagram_algebras.py166
-rw-r--r--src/sage/combinat/integer_list.py10
-rw-r--r--src/sage/combinat/kazhdan_lusztig.py2
-rw-r--r--src/sage/combinat/ncsf_qsym/generic_basis_code.py5
-rw-r--r--src/sage/combinat/partition.py522
-rw-r--r--src/sage/combinat/perfect_matching.py29
-rw-r--r--src/sage/combinat/posets/__init__.py2
-rw-r--r--src/sage/combinat/posets/cartesian_product.py505
-rw-r--r--src/sage/combinat/posets/elements.py11
-rw-r--r--src/sage/combinat/posets/posets.py216
-rw-r--r--src/sage/combinat/rigged_configurations/kleber_tree.py56
-rw-r--r--src/sage/combinat/rigged_configurations/kr_tableaux.py14
-rw-r--r--src/sage/combinat/rigged_configurations/rigged_configuration_element.py119
-rw-r--r--src/sage/combinat/rigged_configurations/rigged_configurations.py22
-rw-r--r--src/sage/combinat/root_system/integrable_representations.py200
-rw-r--r--src/sage/combinat/similarity_class_type.py43
-rw-r--r--src/sage/combinat/skew_tableau.py109
-rw-r--r--src/sage/combinat/tableau.py2
-rw-r--r--src/sage/combinat/words/word_char.pyx174
-rw-r--r--src/sage/data_structures/mutable_poset.py3523
-rw-r--r--src/sage/databases/findstat.py13
-rw-r--r--src/sage/dynamics/interval_exchanges/template.py47
-rw-r--r--src/sage/functions/log.py44
-rw-r--r--src/sage/geometry/cone.py252
-rw-r--r--src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py4
-rw-r--r--src/sage/geometry/hyperplane_arrangement/arrangement.py112
-rw-r--r--src/sage/geometry/lattice_polytope.py19
-rw-r--r--src/sage/geometry/linear_expression.py17
-rw-r--r--src/sage/geometry/polyhedron/base.py30
-rw-r--r--src/sage/geometry/polyhedron/double_description.py2
-rw-r--r--src/sage/geometry/polyhedron/double_description_inhomogeneous.py4
-rw-r--r--src/sage/geometry/polyhedron/lattice_euclidean_group_element.py2
-rw-r--r--src/sage/geometry/polyhedron/palp_database.py10
-rw-r--r--src/sage/geometry/polyhedron/ppl_lattice_polytope.py17
-rw-r--r--src/sage/geometry/polyhedron/representation.py4
-rw-r--r--src/sage/graphs/asteroidal_triples.pyx2
-rw-r--r--src/sage/graphs/base/dense_graph.pyx148
-rw-r--r--src/sage/graphs/digraph.py170
-rw-r--r--src/sage/graphs/generators/classical_geometries.py183
-rw-r--r--src/sage/graphs/generators/families.py2
-rw-r--r--src/sage/graphs/generic_graph.py29
-rw-r--r--src/sage/graphs/graph.py568
-rw-r--r--src/sage/graphs/graph_generators.py4
-rw-r--r--src/sage/graphs/graph_input.py527
-rw-r--r--src/sage/graphs/hyperbolicity.pyx2
-rw-r--r--src/sage/graphs/hypergraph_generators.py19
-rw-r--r--src/sage/graphs/independent_sets.pyx2
-rw-r--r--src/sage/graphs/schnyder.py145
-rw-r--r--src/sage/graphs/strongly_regular_db.pyx314
-rw-r--r--src/sage/groups/abelian_gps/abelian_group_element.py1
-rw-r--r--src/sage/groups/abelian_gps/element_base.py10
-rw-r--r--src/sage/groups/additive_abelian/additive_abelian_group.py4
-rw-r--r--src/sage/groups/conjugacy_classes.py2
-rw-r--r--src/sage/groups/finitely_presented_named.py6
-rw-r--r--src/sage/groups/free_group.py11
-rw-r--r--src/sage/groups/matrix_gps/group_element.py13
-rw-r--r--src/sage/homology/simplicial_complex.py2
-rw-r--r--src/sage/interfaces/chomp.py8
-rw-r--r--src/sage/interfaces/octave.py262
-rw-r--r--src/sage/interfaces/sage0.py16
-rw-r--r--src/sage/libs/pari/paridecl.pxd101
-rw-r--r--src/sage/libs/singular/groebner_strategy.pyx4
-rw-r--r--src/sage/matrix/matrix_mod2_dense.pyx12
-rw-r--r--src/sage/matrix/operation_table.py22
-rw-r--r--src/sage/matroids/lean_matrix.pyx16
-rw-r--r--src/sage/matroids/matroid.pyx12
-rw-r--r--src/sage/misc/c3_controlled.pyx4
-rw-r--r--src/sage/misc/cython.py18
-rw-r--r--src/sage/misc/mrange.py107
-rw-r--r--src/sage/misc/rest_index_of_methods.py181
-rw-r--r--src/sage/misc/superseded.py38
-rw-r--r--src/sage/modular/modform_hecketriangle/abstract_ring.py4
-rw-r--r--src/sage/modular/overconvergent/weightspace.py14
-rw-r--r--src/sage/modules/fg_pid/fgp_element.py33
-rw-r--r--src/sage/modules/free_module_element.pyx15
-rw-r--r--src/sage/monoids/free_monoid_element.py17
-rw-r--r--src/sage/monoids/indexed_free_monoid.py27
-rw-r--r--src/sage/plot/arc.py253
-rw-r--r--src/sage/plot/hyperbolic_arc.py12
-rw-r--r--src/sage/plot/hyperbolic_polygon.py14
-rw-r--r--src/sage/repl/display/fancy_repr.py25
-rw-r--r--src/sage/repl/ipython_kernel/install.py20
-rw-r--r--src/sage/rings/all.py3
-rw-r--r--src/sage/rings/asymptotic/all.py1
-rw-r--r--src/sage/rings/asymptotic/asymptotic_ring.py1613
-rw-r--r--src/sage/rings/asymptotic/growth_group.py96
-rw-r--r--src/sage/rings/asymptotic/term_monoid.py213
-rw-r--r--src/sage/rings/cfinite_sequence.py12
-rw-r--r--src/sage/rings/complex_ball_acb.pyx143
-rw-r--r--src/sage/rings/complex_double.pyx20
-rw-r--r--src/sage/rings/complex_interval.pyx50
-rw-r--r--src/sage/rings/complex_interval_field.py9
-rw-r--r--src/sage/rings/complex_number.pyx8
-rw-r--r--src/sage/rings/finite_rings/element_givaro.pyx13
-rw-r--r--src/sage/rings/finite_rings/element_ntl_gf2e.pyx22
-rw-r--r--src/sage/rings/finite_rings/element_pari_ffelt.pyx56
-rw-r--r--src/sage/rings/finite_rings/hom_finite_field.pyx11
-rw-r--r--src/sage/rings/finite_rings/integer_mod.pyx12
-rw-r--r--src/sage/rings/laurent_series_ring_element.pyx3
-rw-r--r--src/sage/rings/morphism.pyx51
-rw-r--r--src/sage/rings/number_field/number_field_element.pyx5
-rw-r--r--src/sage/rings/number_field/number_field_element_quadratic.pyx21
-rw-r--r--src/sage/rings/polynomial/complex_roots.py129
-rw-r--r--src/sage/rings/polynomial/infinite_polynomial_element.py7
-rw-r--r--src/sage/rings/polynomial/laurent_polynomial.pyx34
-rw-r--r--src/sage/rings/polynomial/multi_polynomial_ideal.py51
-rw-r--r--src/sage/rings/polynomial/plural.pyx17
-rw-r--r--src/sage/rings/polynomial/polynomial_element.pyx103
-rw-r--r--src/sage/rings/polynomial/polynomial_element_generic.py68
-rw-r--r--src/sage/rings/polynomial/polynomial_real_mpfr_dense.pyx25
-rw-r--r--src/sage/rings/polynomial/refine_root.pyx141
-rw-r--r--src/sage/rings/power_series_poly.pyx18
-rw-r--r--src/sage/rings/power_series_ring_element.pyx28
-rw-r--r--src/sage/rings/qqbar.py26
-rw-r--r--src/sage/rings/rational.pyx7
-rw-r--r--src/sage/rings/real_arb.pyx341
-rw-r--r--src/sage/rings/real_lazy.pyx91
-rw-r--r--src/sage/rings/real_mpfi.pxd6
-rw-r--r--src/sage/rings/real_mpfi.pyx115
-rw-r--r--src/sage/sandpiles/sandpile.py70
-rw-r--r--src/sage/sat/all.py2
-rw-r--r--src/sage/sat/converters/polybori.py2
-rw-r--r--src/sage/sat/solvers/sat_lp.py145
-rw-r--r--src/sage/sat/solvers/satsolver.pyx60
-rw-r--r--src/sage/sets/cartesian_product.py60
-rw-r--r--src/sage/structure/element.pyx22
-rw-r--r--src/sage/symbolic/ring.pyx16
-rw-r--r--src/sage/tensor/coordinate_patch.py12
-rw-r--r--src/sage/tensor/differential_form_element.py13
-rw-r--r--src/sage/tensor/differential_forms.py4
-rw-r--r--src/sage/version.py4
-rw-r--r--src/sage_setup/autogen/pari/parser.py2
264 files changed, 18090 insertions, 3113 deletions
diff --git a/VERSION.txt b/VERSION.txt
index 2090599..9d90d56 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-Sage version 6.9.rc0, released 2015-09-25
+Sage version 6.10.beta0, released 2015-10-15
diff --git a/build/make/deps b/build/make/deps
index c9becf0..3d0fb93 100644
--- a/build/make/deps
+++ b/build/make/deps
@@ -44,6 +44,12 @@ all-sage: \
$(EXTCODE) \
$(SCRIPTS)
+# Download all packages which should be inside an sdist tarball (the -B
+# option to make forces all targets to be built unconditionally)
+download-for-sdist: base
+ env SAGE_INSTALL_FETCH_ONLY=yes $(MAKE) -B SAGERUNTIME= \
+ $(STANDARD_PACKAGES) gcc mpir python2
+
# TOOLCHAIN consists of dependencies determined by build/make/install,
# including for example the GCC package.
toolchain: $(TOOLCHAIN)
diff --git a/build/pkgs/boehm_gc/dependencies b/build/pkgs/boehm_gc/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/boehm_gc/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/boost_cropped/dependencies b/build/pkgs/boost_cropped/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/boost_cropped/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/buckygen/dependencies b/build/pkgs/buckygen/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/buckygen/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/cephes/dependencies b/build/pkgs/cephes/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/cephes/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/cliquer/dependencies b/build/pkgs/cliquer/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/cliquer/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/combinatorial_designs/dependencies b/build/pkgs/combinatorial_designs/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/combinatorial_designs/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/compilerwrapper/dependencies b/build/pkgs/compilerwrapper/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/compilerwrapper/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
index cf5c6b5..0c17054 100644
--- a/build/pkgs/configure/checksums.ini
+++ b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
tarball=configure-VERSION.tar.gz
-sha1=8cfd9c770b0b2b6740da8861b8e5fb55be6a1961
-md5=e24e7847a5df019a174b8a8f4d1928dd
-cksum=1203608624
+sha1=3e0d10789b34d6f890e1575c2a06894a90e4807e
+md5=020a9b7f31e61b57056969b6816455f1
+cksum=2662451870
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
index ee977b5..52bd8e4 100644
--- a/build/pkgs/configure/package-version.txt
+++ b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-115
+120
diff --git a/build/pkgs/cryptominisat/dependencies b/build/pkgs/cryptominisat/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/cryptominisat/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/cython/checksums.ini b/build/pkgs/cython/checksums.ini
index 9589980..f3ac441 100644
--- a/build/pkgs/cython/checksums.ini
+++ b/build/pkgs/cython/checksums.ini
@@ -1,4 +1,4 @@
tarball=Cython-VERSION.tar.gz
-sha1=2ff0f863d3b996d2265d0bf06e567e5dd23d004d
-md5=db3c5b365e1c3f71c7cd90e96473a3ab
-cksum=1672168057
+sha1=d5592dc3d529c55a5ef95346caccf11c556993bd
+md5=813df20f7ce5f00e60568e0371fbd07c
+cksum=365027876
diff --git a/build/pkgs/cython/package-version.txt b/build/pkgs/cython/package-version.txt
index e13359b..9e40e75 100644
--- a/build/pkgs/cython/package-version.txt
+++ b/build/pkgs/cython/package-version.txt
@@ -1 +1 @@
-0.23.1.p0
+0.23.3
diff --git a/build/pkgs/d3js/dependencies b/build/pkgs/d3js/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/d3js/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/database_cremona_ellcurve/dependencies b/build/pkgs/database_cremona_ellcurve/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/database_cremona_ellcurve/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/database_jones_numfield/dependencies b/build/pkgs/database_jones_numfield/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/database_jones_numfield/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/database_stein_watkins/dependencies b/build/pkgs/database_stein_watkins/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/database_stein_watkins/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/database_stein_watkins_mini/dependencies b/build/pkgs/database_stein_watkins_mini/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/database_stein_watkins_mini/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/database_symbolic_data/dependencies b/build/pkgs/database_symbolic_data/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/database_symbolic_data/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/gcc/spkg-install b/build/pkgs/gcc/spkg-install
index a934113..f9c7fe6 100755
--- a/build/pkgs/gcc/spkg-install
+++ b/build/pkgs/gcc/spkg-install
@@ -137,3 +137,7 @@ $MAKE install
# Force re-installation of mpir, mpfr and mpc with the GCC we just built.
cd "$SAGE_SPKG_INST"
rm -f mpir-* mpfr-* mpc-*
+
+# Force re-configuration: the next time that "make" is run, we don't
+# want GCC to be built again, see Trac #19324
+touch "$SAGE_ROOT/configure"
diff --git a/build/pkgs/graphs/dependencies b/build/pkgs/graphs/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/graphs/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/iconv/dependencies b/build/pkgs/iconv/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/iconv/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/libogg/dependencies b/build/pkgs/libogg/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/libogg/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/lrcalc/dependencies b/build/pkgs/lrcalc/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/lrcalc/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/nauty/dependencies b/build/pkgs/nauty/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/nauty/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/ncurses/dependencies b/build/pkgs/ncurses/dependencies
new file mode 100644
index 00000000..3546cda
--- /dev/null
+++ b/build/pkgs/ncurses/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/networkx/checksums.ini b/build/pkgs/networkx/checksums.ini
index 50122f0..9aaf119 100644
--- a/build/pkgs/networkx/checksums.ini
+++ b/build/pkgs/networkx/checksums.ini
@@ -1,4 +1,4 @@
tarball=networkx-VERSION.tar.gz
-sha1=d6c1524724d3e47f7621bb2072863463924bfb99
-md5=b4a9e68ecd1b0164446ee432d2e20bd0
-cksum=3256827710
+sha1=99292e464c25be5e96de295752880bf5e5f1848a
+md5=eb7a065e37250a4cc009919dacfe7a9d
+cksum=2520536431
diff --git a/build/pkgs/networkx/dependencies b/build/pkgs/networkx/dependencies
index edf2711..d4db0ff 100644
--- a/build/pkgs/networkx/dependencies
+++ b/build/pkgs/networkx/dependencies
@@ -1,4 +1,4 @@
-$(INST)/$(PYTHON)
+$(INST)/$(PYTHON) $(INST)/$(DECORATOR)
----------
All lines of this file are ignored except the first.
diff --git a/build/pkgs/networkx/package-version.txt b/build/pkgs/networkx/package-version.txt
index a8fdfda..c044b1a 100644
--- a/build/pkgs/networkx/package-version.txt
+++ b/build/pkgs/networkx/package-version.txt
@@ -1 +1 @@
-1.8.1
+1.10
diff --git a/build/pkgs/networkx/spkg-install b/build/pkgs/networkx/spkg-install
index 6769f79..5cd75ee 100755
--- a/build/pkgs/networkx/spkg-install
+++ b/build/pkgs/networkx/spkg-install
@@ -15,4 +15,4 @@ rm -rf "$SAGE_LOCAL"/spkg/network*
cd src
-python setup.py install --home="$SAGE_LOCAL" --force
+python setup.py install
diff --git a/build/pkgs/notebook/package-version.txt b/build/pkgs/notebook/package-version.txt
index c5106e6..61d8a2a 100644
--- a/build/pkgs/notebook/package-version.txt
+++ b/build/pkgs/notebook/package-version.txt
@@ -1 +1 @@
-4.0.4
+4.0.4.p1
diff --git a/build/pkgs/notebook/patches/jupyter_notebook_config.py b/build/pkgs/notebook/pa