diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
deleted file mode 100644
index a51e30312ed9..000000000000
--- a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
+++ /dev/null
@@ -1,127 +0,0 @@
-diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
-index 25f94f7b7d..9f6139ea4a 100644
---- a/src/doc/common/conf.py
-+++ b/src/doc/common/conf.py
-@@ -622,9 +622,9 @@ def call_intersphinx(app, env, node, contnode):
- Check that the link from the thematic tutorials to the reference
- manual is relative, see :trac:`20118`::
-
-- sage: from sage.env import SAGE_DOC
-- sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html")
-- sage: for line in open(thematic_index).readlines():
-+ sage: from sage.env import SAGE_DOC # optional - dochtml
-+ sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") # optional - dochtml
-+ sage: for line in open(thematic_index).readlines(): # optional - dochtml
- ....: if "padics" in line:
- ....: sys.stdout.write(line)
- Introduction to the -adics
-diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index 4236fd05e0..8e499cbaf7 100644
---- a/src/sage/doctest/control.py
-+++ b/src/sage/doctest/control.py
-@@ -87,7 +87,7 @@ class DocTestDefaults(SageObject):
- self.sagenb = False
- self.long = False
- self.warn_long = None
-- self.optional = set(['sage']) | auto_optional_tags
-+ self.optional = set(['sage', 'dochtml']) | auto_optional_tags
- self.randorder = None
- self.global_iterations = 1 # sage-runtests default is 0
- self.file_iterations = 1 # sage-runtests default is 0
-@@ -343,7 +343,8 @@ class DocTestController(SageObject):
- if not optionaltag_regex.search(o):
- raise ValueError('invalid optional tag {!r}'.format(o))
-
-- options.optional |= auto_optional_tags
-+ if "sage" in options.optional:
-+ options.optional |= auto_optional_tags
-
- self.options = options
- self.files = args
-@@ -741,7 +742,7 @@ class DocTestController(SageObject):
- sage: DC = DocTestController(DD, [dirname])
- sage: DC.expand_files_into_sources()
- sage: sorted(DC.sources[0].options.optional) # abs tol 1
-- ['guava', 'magma', 'py3']
-+ ['guava', 'magma']
-
- We check that files are skipped appropriately::
-
-@@ -968,7 +969,7 @@ class DocTestController(SageObject):
- sage: from sage.doctest.control import DocTestDefaults, DocTestController
- sage: DC = DocTestController(DocTestDefaults(), [])
- sage: DC._optional_tags_string()
-- 'sage'
-+ 'dochtml,sage'
- sage: DC = DocTestController(DocTestDefaults(optional="all,and,some,more"), [])
- sage: DC._optional_tags_string()
- 'all'
-diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 9255aa848f..cc4712d3ec 100644
---- a/src/sage/misc/sagedoc.py
-+++ b/src/sage/misc/sagedoc.py
-@@ -18,9 +18,9 @@ TESTS:
- Check that argspecs of extension function/methods appear correctly,
- see :trac:`12849`::
-
-- sage: from sage.env import SAGE_DOC
-- sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html')
-- sage: with open(docfilename) as fobj:
-+ sage: from sage.env import SAGE_DOC # optional - dochtml
-+ sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') # optional - dochtml
-+ sage: with open(docfilename) as fobj: # optional - dochtml
- ....: for line in fobj:
- ....: if "#sage.symbolic.expression.Expression.numerical_approx" in line:
- ....: print(line)
-@@ -790,11 +790,12 @@ def _search_src_or_doc(what, string, extra1='', extra2='', extra3='',
-
- ::
-
-- sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1
-+ sage: from sage.misc.sagedoc import _search_src_or_doc # optional - dochtml
-+ sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 # optional - dochtml
- True
-- sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # long time (4s on sage.math, 2012)
-+ sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # optional - dochtml, long time (4s on sage.math, 2012)
- True
-- sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False)
-+ sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) # optional - dochtml
- True
- """
- # process keywords
-@@ -1160,9 +1161,9 @@ def search_doc(string, extra1='', extra2='', extra3='', extra4='',
- counting the length of ``search_doc('tree',
- interact=False).splitlines()`` gives the number of matches. ::
-
-- sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # long time
-+ sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # optional - dochtml, long time
- True
-- sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # long time
-+ sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # optional - dochtml, long time
- True
- """
- return _search_src_or_doc('doc', string, extra1=extra1, extra2=extra2,
-@@ -1332,9 +1333,9 @@ class _sage_doc:
-
- EXAMPLES::
-
-- sage: browse_sage_doc._open("reference", testing=True)[0] # indirect doctest
-+ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml, indirect doctest
- 'http://localhost:8000/doc/live/reference/index.html'
-- sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47]
-+ sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] # optional - dochtml
- 'Full MatrixSpace of 3 by 3 sparse matrices over Integer Ring'
- """
- def __init__(self):
-@@ -1494,9 +1495,9 @@ class _sage_doc:
-
- EXAMPLES::
-
-- sage: browse_sage_doc._open("reference", testing=True)[0]
-+ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml
- 'http://localhost:8000/doc/live/reference/index.html'
-- sage: browse_sage_doc._open("tutorial", testing=True)[1]
-+ sage: browse_sage_doc._open("tutorial", testing=True)[1] # optional - dochtml
- '.../html/en/tutorial/index.html'
- """
- url = self._base_url + os.path.join(name, "index.html")
diff --git a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
index d06e1e6cedf2..986ae42aeb62 100644
--- a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
+++ b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
@@ -14,27 +14,3 @@ index 4417b59276..ae57ca2991 100644
"""
global instances
try:
-diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp
-index 5fd5693b53..d12468faa8 100644
---- a/src/sage/libs/eclib/wrap.cpp
-+++ b/src/sage/libs/eclib/wrap.cpp
-@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose)
-
-
- int mw_process(struct Curvedata* curve, struct mw* m,
-- const struct bigint* x, const struct bigint* y,
-- const struct bigint* z, int sat)
-+ const bigint* x, const bigint* y,
-+ const bigint* z, int sat)
- {
- Point P(*curve, *x, *y, *z);
- if (!P.isvalid())
-@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
- }
-
- /* Returns index and unsat long array, which user must deallocate */
--int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
-+int mw_saturate(struct mw* m, bigint* index, char** unsat,
- long sat_bd, int odd_primes_only)
- {
- vector v;
diff --git a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch b/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
deleted file mode 100644
index 13b47dbdd31b..000000000000
--- a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py
-index e451766474..77eda66097 100644
---- a/src/sage/libs/pari/__init__.py
-+++ b/src/sage/libs/pari/__init__.py
-@@ -205,6 +205,13 @@ def _get_pari_instance():
- # messages in Sage.
- P.default("debugmem", 0)
-
-+ # Make sure pari doesn't use threads, regardless of how it was compiled.
-+ # Threads cause some doctest failures (memory issues). Those could probably
-+ # be solved without disabling threads. But that would require figuring out
-+ # some sensible values for `threadsizemax`. See
-+ # https://pari.math.u-bordeaux.fr/dochtml/html/GP_defaults.html
-+ P.default("nbthreads", 1)
-+
- return P
-
- pari = _get_pari_instance()
diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
deleted file mode 100644
index febab3702771..000000000000
--- a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
-index aa23c8405d..8a87de0591 100644
---- a/src/sage/repl/ipython_kernel/install.py
-+++ b/src/sage/repl/ipython_kernel/install.py
-@@ -112,7 +112,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_mathjax()
- sage: mathjax = os.path.join(spec.nbextensions_dir, 'mathjax')
- sage: os.path.isdir(mathjax)
-@@ -129,7 +129,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_jsmol()
- sage: jsmol = os.path.join(spec.nbextensions_dir, 'jsmol')
- sage: os.path.isdir(jsmol)
-@@ -146,7 +146,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_threejs()
- sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs')
- sage: os.path.isdir(threejs)
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 3dd62817bde7..43360f76da69 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -3,20 +3,17 @@
, fetchpatch
}:
stdenv.mkDerivation rec {
- version = "8.4.beta0";
+ version = "8.4.beta1";
name = "sage-src-${version}";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
- sha256 = "1jph4slscpni0smp2fxs3s12282c9r3mdfbgxpyx67gic0d9iya8";
+ sha256 = "0yk5ndjr1kap7vhd2i6i5bpcfgmr4fhypn6x7myiymiy9s93d37j";
};
nixPatches = [
- # https://trac.sagemath.org/ticket/25722
- ./patches/test-in-tmpdir.patch
-
# https://trac.sagemath.org/ticket/25358
(fetchpatch {
name = "safe-directory-test-without-patch.patch";
@@ -30,21 +27,6 @@ stdenv.mkDerivation rec {
# https://trac.sagemath.org/ticket/25316
# https://github.com/python/cpython/pull/7476
./patches/python-5755-hotpatch.patch
-
- # https://trac.sagemath.org/ticket/25315
- (fetchpatch {
- name = "find-libraries-in-dyld-library-path.patch";
- url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06";
- sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc";
- })
-
- # https://trac.sagemath.org/ticket/25345
- # (upstream patch doesn't apply on 8.2 source)
- ./patches/dochtml-optional.patch
-
- # work with pari with threads enabled at compile time (disable them at runtime)
- # https://trac.sagemath.org/ticket/26002
- ./patches/pari-no-threads.patch
];
packageUpgradePatches = [
@@ -96,20 +78,6 @@ stdenv.mkDerivation rec {
url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
})
-
- # cddlib 0.94i -> 0.94j
- (fetchpatch {
- name = "cddlib-0.94j.patch";
- url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888";
- sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb";
- })
-
- # arb 2.13.0 -> 2.14.0
- (fetchpatch {
- name = "arb-2.14.0.patch";
- url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta0&id=8bef4fd2876a61969b516fe4eb3b8ad7cc076c5e";
- sha256 = "00p3hfsfn3w2vxgd9fjd23mz7xfxjfravf8ysjxkyd657jbkpjmk";
- })
];
patches = nixPatches ++ packageUpgradePatches ++ [