Merge branch 'master' into core-updates

6 files changed, 285 insertions, 0 deletions

diff --git a/gnu/packages/patches/beets-werkzeug-compat.patch b/gnu/packages/patches/beets-werkzeug-compat.patch
new file mode 100644
index 0000000000..1a91c3a3f9
--- /dev/null
+++ b/gnu/packages/patches/beets-werkzeug-compat.patch
@@ -0,0 +1,18 @@
+Be compatible with python-werkzeug 1.0.0.
+
+Taken from upstream:
+https://github.com/beetbox/beets/commit/d43d54e21cde97f57f19486925ab56b419254cc8
+
+diff --git a/beetsplug/web/__init__.py b/beetsplug/web/__init__.py
+index f53fb3a954..21ff5d94ed 100644
+--- a/beetsplug/web/__init__.py
++++ b/beetsplug/web/__init__.py
+@@ -169,7 +169,7 @@ def to_python(self, value):
+         return ids
+ 
+     def to_url(self, value):
+-        return ','.join(value)
++        return ','.join(str(v) for v in value)
+ 
+ 
+ class QueryConverter(PathConverter):
diff --git a/gnu/packages/patches/bidiv-update-fribidi.patch b/gnu/packages/patches/bidiv-update-fribidi.patch
new file mode 100644
index 0000000000..d000cfeda4
--- /dev/null
+++ b/gnu/packages/patches/bidiv-update-fribidi.patch
@@ -0,0 +1,50 @@
+https://sources.debian.org/data/main/b/bidiv/1.5-6/debian/patches/fribidi_019
+
+Description: Fix building with fribidi 1.9
+Author: أحمد المحمودي <aelmahmoudy@users.sourceforge.net>
+Bug-Debian: http://bugs.debian.org/568130
+
+--- a/bidiv.c
++++ b/bidiv.c
+@@ -141,8 +141,9 @@ bidiv(FILE *fp)
+ 				*/
+ 				if(c1<0x80||c1>0xbf){
+ 					ungetc(c1, fp);
+-					unicode_in[len]=
+-						fribidi_iso8859_8_to_unicode_c(c);
++					fribidi_charset_to_unicode(
++						FRIBIDI_CHAR_SET_ISO8859_8,
++						&c, 1, &unicode_in[len]);
+ 				} else
+ 				unicode_in[len]=((c & 037) << 6) + (c1 & 077);
+ 				newline=0;
+@@ -153,8 +154,9 @@ bidiv(FILE *fp)
+ 				   In the future we will have a language
+ 				   option, which will control this (as well
+ 				   as the output encoding). */
+-				unicode_in[len]=
+-					fribidi_iso8859_8_to_unicode_c(c);
++				fribidi_charset_to_unicode(
++					FRIBIDI_CHAR_SET_ISO8859_8,
++					&c, 1, &unicode_in[len]);
+ #else
+ 				in[len]=c;
+ #endif
+@@ -206,11 +208,11 @@ bidiv(FILE *fp)
+ 			rtl_line=0;
+ 
+ 		if(out_utf8)
+-			fribidi_unicode_to_utf8(unicode_out, len,
+-					     out);
++			fribidi_unicode_to_charset(FRIBIDI_CHAR_SET_UTF8,
++					unicode_out, len, out);
+ 		else
+-			fribidi_unicode_to_iso8859_8(unicode_out, len,
+-						     out);
++			fribidi_unicode_to_charset(FRIBIDI_CHAR_SET_ISO8859_8,
++				unicode_out, len, out);
+ 		/* if rtl_line (i.e., base_dir is RL), and we didn't fill the
+ 		   entire width, we need to pad with spaces. Maybe in the
+ 		   future this should be an option.
+--
+
diff --git a/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch b/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch
new file mode 100644
index 0000000000..b95b46077a
--- /dev/null
+++ b/gnu/packages/patches/eigen-stabilise-sparseqr-test.patch
@@ -0,0 +1,74 @@
+From: Tobias Geerinckx-Rice <me@tobias.gr>
+Date: Mon, 16 Mar 2020 22:51:37 +0000
+Subject: gnu: eigen: Stabilise sparseqr test.
+
+Taken verbatim from this[0] upstream commit.
+
+[0]: https://gitlab.com/libeigen/eigen/-/commit/3b5deeb546d4017b24846f5b0dc3296a50a039fe
+
+From 3b5deeb546d4017b24846f5b0dc3296a50a039fe Mon Sep 17 00:00:00 2001
+From: Gael Guennebaud <g.gael@free.fr>
+Date: Tue, 19 Feb 2019 22:57:51 +0100
+Subject: [PATCH] bug #899: make sparseqr unit test more stable by 1) trying
+ with larger threshold and 2) relax rank computation for rank-deficient
+ problems.
+
+---
+ test/sparseqr.cpp | 31 ++++++++++++++++++++++++++-----
+ 1 file changed, 26 insertions(+), 5 deletions(-)
+
+diff --git a/test/sparseqr.cpp b/test/sparseqr.cpp
+index 3ffe62314..3576cc626 100644
+--- a/test/sparseqr.cpp
++++ b/test/sparseqr.cpp
+@@ -43,6 +43,7 @@ int generate_sparse_rectangular_problem(MatrixType& A, DenseMat& dA, int maxRows
+ 
+ template<typename Scalar> void test_sparseqr_scalar()
+ {
++  typedef typename NumTraits<Scalar>::Real RealScalar;
+   typedef SparseMatrix<Scalar,ColMajor> MatrixType; 
+   typedef Matrix<Scalar,Dynamic,Dynamic> DenseMat;
+   typedef Matrix<Scalar,Dynamic,1> DenseVector;
+@@ -91,14 +92,34 @@ template<typename Scalar> void test_sparseqr_scalar()
+     exit(0);
+     return;
+   }
+-  
+-  VERIFY_IS_APPROX(A * x, b);
+-  
+-  //Compare with a dense QR solver
++
++  // Compare with a dense QR solver
+   ColPivHouseholderQR<DenseMat> dqr(dA);
+   refX = dqr.solve(b);
+   
+-  VERIFY_IS_EQUAL(dqr.rank(), solver.rank());
++  bool rank_deficient = A.cols()>A.rows() || dqr.rank()<A.cols();
++  if(rank_deficient)
++  {
++    // rank deficient problem -> we might have to increase the threshold
++    // to get a correct solution.
++    RealScalar th = RealScalar(20)*dA.colwise().norm().maxCoeff()*(A.rows()+A.cols()) * NumTraits<RealScalar>::epsilon();
++    for(Index k=0; (k<16) && !test_isApprox(A*x,b); ++k)
++    {
++      th *= RealScalar(10);
++      solver.setPivotThreshold(th);
++      solver.compute(A);
++      x = solver.solve(b);
++    }
++  }
++
++  VERIFY_IS_APPROX(A * x, b);
++  
++  // For rank deficient problem, the estimated rank might
++  // be slightly off, so let's only raise a warning in such cases.
++  if(rank_deficient) ++g_test_level;
++  VERIFY_IS_EQUAL(solver.rank(), dqr.rank());
++  if(rank_deficient) --g_test_level;
++
+   if(solver.rank()==A.cols()) // full rank
+     VERIFY_IS_APPROX(x, refX);
+ //   else
+-- 
+2.24.1
+
diff --git a/gnu/packages/patches/python-alembic-exceptions-cause.patch b/gnu/packages/patches/python-alembic-exceptions-cause.patch
new file mode 100644
index 0000000000..b9844e5ad0
--- /dev/null
+++ b/gnu/packages/patches/python-alembic-exceptions-cause.patch
@@ -0,0 +1,69 @@
+Fix a test failure with newer versions of SQLalchemy due to missing
+"causes" for some exceptions.
+
+diff --git a/alembic/operations/ops.py b/alembic/operations/ops.py
+index 5ec2762..7129472 100644
+--- a/alembic/operations/ops.py
++++ b/alembic/operations/ops.py
+@@ -108,6 +108,7 @@ def from_constraint(cls, constraint):
+             "primary_key_constraint": "primary",
+             "check_constraint": "check",
+             "column_check_constraint": "check",
++            "table_or_column_check_constraint": "check",
+         }
+ 
+         constraint_table = sqla_compat._table_for_constraint(constraint)
+@@ -707,6 +708,7 @@ def batch_create_foreign_key(
+     "create_check_constraint", "batch_create_check_constraint"
+ )
+ @AddConstraintOp.register_add_constraint("check_constraint")
++@AddConstraintOp.register_add_constraint("table_or_column_check_constraint")
+ @AddConstraintOp.register_add_constraint("column_check_constraint")
+ class CreateCheckConstraintOp(AddConstraintOp):
+     """Represent a create check constraint operation."""
+diff --git a/alembic/testing/assertions.py b/alembic/testing/assertions.py
+index 3dc08f0..a78e5e8 100644
+--- a/alembic/testing/assertions.py
++++ b/alembic/testing/assertions.py
+@@ -2,10 +2,9 @@
+ 
+ import re
+ 
++from sqlalchemy import util
+ from sqlalchemy.engine import default
+ from sqlalchemy.testing.assertions import _expect_warnings
+-from sqlalchemy.testing.assertions import assert_raises  # noqa
+-from sqlalchemy.testing.assertions import assert_raises_message  # noqa
+ from sqlalchemy.testing.assertions import eq_  # noqa
+ from sqlalchemy.testing.assertions import is_  # noqa
+ from sqlalchemy.testing.assertions import is_false  # noqa
+@@ -17,6 +16,29 @@
+ from ..util.compat import py3k
+ 
+ 
++def assert_raises(except_cls, callable_, *args, **kw):
++    try:
++        callable_(*args, **kw)
++        success = False
++    except except_cls:
++        success = True
++
++    # assert outside the block so it works for AssertionError too !
++    assert success, "Callable did not raise an exception"
++
++
++def assert_raises_message(except_cls, msg, callable_, *args, **kwargs):
++    try:
++        callable_(*args, **kwargs)
++        assert False, "Callable did not raise an exception"
++    except except_cls as e:
++        assert re.search(msg, util.text_type(e), re.UNICODE), "%r !~ %s" % (
++            msg,
++            e,
++        )
++        print(util.text_type(e).encode("utf-8"))
++
++
+ def eq_ignore_whitespace(a, b, msg=None):
+     # sqlalchemy.testing.assertion has this function
+     # but not with the special "!U" detection part
diff --git a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch
new file mode 100644
index 0000000000..0e928ef455
--- /dev/null
+++ b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch
@@ -0,0 +1,36 @@
+We need one patch on top of 0.3.8 for compatibility with Werkzeug 1.0.
+
+Taken from upstream:
+https://github.com/flask-restful/flask-restful/commit/73376a488907af3042b52678ac4c23f8a8911e5b
+
+diff --git a/tests/test_api.py b/tests/test_api.py
+index f7f8e661..6795d362 100644
+--- a/tests/test_api.py
++++ b/tests/test_api.py
+@@ -445,7 +445,9 @@ def test_handle_non_api_error(self):
+ 
+         resp = app.get("/foo")
+         self.assertEquals(resp.status_code, 404)
+-        self.assertEquals('text/html', resp.headers['Content-Type'])
++        # in newer versions of werkzeug this is `text/html; charset=utf8`
++        content_type, _, _ = resp.headers['Content-Type'].partition(';')
++        self.assertEquals('text/html', content_type)
+ 
+     def test_non_api_error_404_catchall(self):
+         app = Flask(__name__)
+diff --git a/tests/test_reqparse.py b/tests/test_reqparse.py
+index 2f1fbedf..9776f17c 100644
+--- a/tests/test_reqparse.py
++++ b/tests/test_reqparse.py
+@@ -2,9 +2,9 @@
+ import unittest
+ from mock import Mock, patch
+ from flask import Flask
+-from werkzeug import exceptions, MultiDict
++from werkzeug import exceptions
+ from werkzeug.wrappers import Request
+-from werkzeug.datastructures import FileStorage
++from werkzeug.datastructures import FileStorage, MultiDict
+ from flask_restful.reqparse import Argument, RequestParser, Namespace
+ import six
+ import decimal
diff --git a/gnu/packages/patches/python-jedi-deleted-variables.patch b/gnu/packages/patches/python-jedi-deleted-variables.patch
new file mode 100644
index 0000000000..53bdc05cde
--- /dev/null
+++ b/gnu/packages/patches/python-jedi-deleted-variables.patch
@@ -0,0 +1,38 @@
+Fix test failure in some environments, including Guix.
+
+Taken from upstream:
+https://github.com/davidhalter/jedi/commit/bec87f7ff82b0731713c6520a14c213341b4cecf
+
+diff --git a/test/completion/basic.py b/test/completion/basic.py
+index b40068179..3ff919ca6 100644
+--- a/test/completion/basic.py
++++ b/test/completion/basic.py
+@@ -209,11 +209,11 @@ def global_as_import():
+ 
+ deleted_var = 3
+ del deleted_var
+-#? int()
++#?
+ deleted_var
+-#? ['deleted_var']
++#? []
+ deleted_var
+-#! ['deleted_var = 3']
++#! []
+ deleted_var
+ 
+ # -----------------
+diff --git a/test/test_api/test_full_name.py b/test/test_api/test_full_name.py
+index 4fdb861b0..6858b6ca8 100644
+--- a/test/test_api/test_full_name.py
++++ b/test/test_api/test_full_name.py
+@@ -112,7 +112,8 @@ def test_os_path(Script):
+ 
+ def test_os_issues(Script):
+     """Issue #873"""
+-    assert [c.name for c in Script('import os\nos.nt''').complete()] == ['nt']
++    # nt is not found, because it's deleted
++    assert [c.name for c in Script('import os\nos.nt''').complete()] == []
+ 
+ 
+ def test_param_name(Script):