diff options
Diffstat (limited to 'pkgs/applications/science/math/sage')
15 files changed, 256 insertions, 142 deletions
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index e9dae55fbae..2066087692a 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -14,13 +14,17 @@ let # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies sagelib = self.callPackage ./sagelib.nix { inherit flint arb; - inherit sage-src env-locations pynac singular; + inherit sage-src env-locations singular; inherit (maxima) lisp-compiler; linbox = pkgs.linbox.override { withSage = true; }; pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config }; - sage_docbuild = self.callPackage ./sage_docbuild.nix { + sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix { + inherit sage-src; + }; + + sage-setup = self.callPackage ./python-modules/sage-setup.nix { inherit sage-src; }; }; @@ -58,9 +62,9 @@ let # the env-locations file. sage-env = callPackage ./sage-env.nix { sagelib = python3.pkgs.sagelib; - sage_docbuild = python3.pkgs.sage_docbuild; + sage-docbuild = python3.pkgs.sage-docbuild; inherit env-locations; - inherit python3 singular palp flint pynac pythonEnv maxima; + inherit python3 singular palp flint pythonEnv maxima; pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config }; @@ -74,7 +78,7 @@ let sage-with-env = callPackage ./sage-with-env.nix { inherit python3 pythonEnv; inherit sage-env; - inherit pynac singular maxima; + inherit singular maxima; inherit three; pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config }; @@ -91,7 +95,7 @@ let pythonRuntimeDeps = with python3.pkgs; [ sagelib - sage_docbuild + sage-docbuild cvxopt networkx service-identity @@ -132,9 +136,6 @@ let }; }; - # *not* to confuse with the python package "pynac" - pynac = pkgs.pynac.override { inherit singular flint; }; - # With openblas (64 bit), the tests fail the same way as when sage is build with # openblas instead of openblasCompat. Apparently other packages somehow use flints # blas when it is available. Alternative would be to override flint to use diff --git a/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch b/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch new file mode 100644 index 00000000000..a478f50d92e --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch @@ -0,0 +1,46 @@ +diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py +index 01f32fb8e4..4d83dc7b47 100644 +--- a/src/sage/doctest/control.py ++++ b/src/sage/doctest/control.py +@@ -1253,6 +1253,7 @@ class DocTestController(SageObject): + + self.log("Using --optional=" + self._optional_tags_string()) + available_software._allow_external = self.options.optional is True or 'external' in self.options.optional ++ available_software._autodetect_safe = self.options.optional is True or 'sage' in self.options.optional + self.log("Features to be detected: " + ','.join(available_software.detectable())) + self.add_files() + self.expand_files_into_sources() +diff --git a/src/sage/doctest/external.py b/src/sage/doctest/external.py +index 84dae19ea5..badc61466e 100644 +--- a/src/sage/doctest/external.py ++++ b/src/sage/doctest/external.py +@@ -409,6 +409,7 @@ class AvailableSoftware(object): + [] + """ + self._allow_external = True ++ self._autodetect_safe = True + # For multiprocessing of doctests, the data self._seen should be + # shared among subprocesses. Thus we use Array class from the + # multiprocessing module. +@@ -430,6 +431,8 @@ class AvailableSoftware(object): + sage: 'internet' in available_software # random, optional - internet + True + """ ++ if not self._autodetect_safe: ++ return False + try: + idx = self._indices[item] + except KeyError: +diff --git a/src/sage/features/sagemath.py b/src/sage/features/sagemath.py +index 433338766d..233623b14a 100644 +--- a/src/sage/features/sagemath.py ++++ b/src/sage/features/sagemath.py +@@ -12,7 +12,7 @@ class sagemath_doc_html(StaticFile): + + EXAMPLES:: + +- sage: from sage.features.sagemath import sagemath_doc_html ++ sage: from sage.features.sagemath import sagemath_doc_html # optional - sagemath_doc_html + sage: sagemath_doc_html().is_present() # optional - sagemath_doc_html + FeatureTestResult('sagemath_doc_html', True) + """ diff --git a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch b/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch deleted file mode 100644 index d5c19a54fd9..00000000000 --- a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch +++ /dev/null @@ -1,26 +0,0 @@ -From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001 -From: Timo Kaufmann <timokau@zoho.com> -Date: Sun, 21 Oct 2018 17:52:40 +0200 -Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested - ---- - src/sage/doctest/control.py | 3 ++- - 1 file changed, 2 insertions(+), 1 deletion(-) - -diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py -index 2d93841e50..6d156e29a1 100644 ---- a/src/sage/doctest/control.py -+++ b/src/sage/doctest/control.py -@@ -375,7 +375,8 @@ 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 - --- -2.28.0 - diff --git a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch index 178cef3e54e..90a23f94cb5 100644 --- a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch +++ b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch @@ -1,8 +1,8 @@ diff --git a/src/sage/env.py b/src/sage/env.py -index 95980cc2df..37107a30e1 100644 +index c4953cfa65..47b880f9ad 100644 --- a/src/sage/env.py +++ b/src/sage/env.py -@@ -227,93 +227,12 @@ OPENMP_CXXFLAGS = var("OPENMP_CXXFLAGS", "") +@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1' SAGE_BANNER = var("SAGE_BANNER", "") SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes") @@ -29,20 +29,12 @@ index 95980cc2df..37107a30e1 100644 - - EXAMPLES:: - -- sage: import sys -- sage: from fnmatch import fnmatch - sage: from sage.env import _get_shared_lib_path -- sage: lib_filename = _get_shared_lib_path("Singular", "singular-Singular") -- sage: if sys.platform == 'cygwin': -- ....: pattern = "*/cygSingular-*.dll" -- ....: elif sys.platform == 'darwin': -- ....: pattern = "*/libSingular-*.dylib" -- ....: else: -- ....: pattern = "*/lib*Singular-*.so" -- sage: fnmatch(str(lib_filename), pattern) +- sage: "gap" in _get_shared_lib_path("gap") - True - sage: _get_shared_lib_path("an_absurd_lib") is None - True +- - """ - - for libname in libnames: @@ -87,11 +79,6 @@ index 95980cc2df..37107a30e1 100644 - # Just return None if no files were found - return None - - # locate singular shared object - # On Debian it's libsingular-Singular so try that as well --SINGULAR_SO = var("SINGULAR_SO", _get_shared_lib_path("Singular", "singular-Singular")) -+SINGULAR_SO = var("SINGULAR_SO", '/default') - # locate libgap shared object -GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", "")) +GAP_SO = var("GAP_SO", '/default') diff --git a/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch b/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch new file mode 100644 index 00000000000..91e080aa294 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch @@ -0,0 +1,58 @@ +diff --git a/src/sage/libs/linbox/conversion.pxd b/src/sage/libs/linbox/conversion.pxd +index 7794c9edc3..1753277b1f 100644 +--- a/src/sage/libs/linbox/conversion.pxd ++++ b/src/sage/libs/linbox/conversion.pxd +@@ -177,9 +177,8 @@ cdef inline Vector_integer_dense new_sage_vector_integer_dense(P, DenseVector_in + - v -- linbox vector + """ + cdef Vector_integer_dense res = P() +- cdef cppvector[Integer] * vec = &v.refRep() + cdef size_t i + for i in range(<size_t> res._degree): +- mpz_set(res._entries[i], vec[0][i].get_mpz_const()) ++ mpz_set(res._entries[i], v.getEntry(i).get_mpz_const()) + + return res +diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd +index 9112d151f8..dcc482960c 100644 +--- a/src/sage/libs/linbox/linbox.pxd ++++ b/src/sage/libs/linbox/linbox.pxd +@@ -32,7 +32,7 @@ cdef extern from "linbox/matrix/dense-matrix.h": + ctypedef Modular_double Field + ctypedef double Element + DenseMatrix_Modular_double(Field F, size_t m, size_t n) +- DenseMatrix_Modular_double(Field F, Element*, size_t m, size_t n) ++ DenseMatrix_Modular_double(Field F, size_t m, size_t n, Element*) + void setEntry(size_t i, size_t j, Element& a) + Element &getEntry(size_t i, size_t j) + +@@ -42,7 +42,7 @@ cdef extern from "linbox/matrix/dense-matrix.h": + ctypedef Modular_float Field + ctypedef float Element + DenseMatrix_Modular_float(Field F, size_t m, size_t n) +- DenseMatrix_Modular_float(Field F, Element*, size_t m, size_t n) ++ DenseMatrix_Modular_float(Field F, size_t m, size_t n, Element*) + void setEntry(size_t i, size_t j, Element& a) + Element &getEntry(size_t i, size_t j) + +@@ -101,7 +101,6 @@ cdef extern from "linbox/vector/vector.h": + DenseVector_integer (Field &F) + DenseVector_integer (Field &F, long& m) + DenseVector_integer (Field &F, cppvector[Integer]&) +- cppvector[Element]& refRep() + size_t size() + void resize(size_t) + void resize(size_t n, const Element&) +diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi +index 010365d76f..3d60726ff9 100644 +--- a/src/sage/matrix/matrix_modn_dense_template.pxi ++++ b/src/sage/matrix/matrix_modn_dense_template.pxi +@@ -219,7 +219,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_ + return 0,[] + + cdef ModField *F = new ModField(<long>modulus) +- cdef DenseMatrix *A = new DenseMatrix(F[0], <ModField.Element*>entries,<Py_ssize_t>nrows, <Py_ssize_t>ncols) ++ cdef DenseMatrix *A = new DenseMatrix(F[0], <Py_ssize_t>nrows, <Py_ssize_t>ncols, <ModField.Element*>entries) + cdef Py_ssize_t r = reducedRowEchelonize(A[0]) + cdef Py_ssize_t i,j + for i in range(nrows): diff --git a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch index 3c64be100d2..1ff081b25e0 100644 --- a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch +++ b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch @@ -1,8 +1,8 @@ diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py -index 79005b903a..fbe6fe2595 100644 +index 8a5c1a19d2..21fd192642 100644 --- a/src/sage_docbuild/__init__.py +++ b/src/sage_docbuild/__init__.py -@@ -85,27 +85,6 @@ def builder_helper(type): +@@ -89,27 +89,6 @@ def builder_helper(type): """ Returns a function which builds the documentation for output type ``type``. @@ -12,7 +12,7 @@ index 79005b903a..fbe6fe2595 100644 - Check that :trac:`25161` has been resolved:: - - sage: from sage_docbuild import DocBuilder, setup_parser -- sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set +- sage: DocBuilder._options = setup_parser().parse_args([]) # builder_helper needs _options to be set - - sage: import sage_docbuild.sphinxbuild - sage: def raiseBaseException(): @@ -30,7 +30,7 @@ index 79005b903a..fbe6fe2595 100644 """ def f(self, *args, **kwds): output_dir = self._output_dir(type) -@@ -127,10 +106,9 @@ def builder_helper(type): +@@ -131,10 +110,9 @@ def builder_helper(type): logger.debug(build_command) # Run Sphinx with Sage's special logger @@ -44,10 +44,10 @@ index 79005b903a..fbe6fe2595 100644 if ABORT_ON_ERROR: raise diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py -index f58f6c61d7..ef51a55411 100644 +index d917c3e9d4..551cc8028a 100644 --- a/src/sage_docbuild/sphinxbuild.py +++ b/src/sage_docbuild/sphinxbuild.py -@@ -326,3 +326,8 @@ def runsphinx(): +@@ -327,3 +327,8 @@ def runsphinx(): sys.stderr = saved_stderr sys.stdout.flush() sys.stderr.flush() diff --git a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix new file mode 100644 index 00000000000..1766cec3e35 --- /dev/null +++ b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix @@ -0,0 +1,28 @@ +{ lib +, buildPythonPackage +, sage-src +, sphinx +}: + +buildPythonPackage rec { + version = src.version; + pname = "sage-docbuild"; + src = sage-src; + + propagatedBuildInputs = [ + sphinx + ]; + + preBuild = '' + cd pkgs/sage-docbuild + ''; + + doCheck = false; # we will run tests in sagedoc.nix + + meta = with lib; { + description = "Build system of the Sage documentation"; + homepage = "https://www.sagemath.org"; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + }; +} diff --git a/pkgs/applications/science/math/sage/python-modules/sage-setup.nix b/pkgs/applications/science/math/sage/python-modules/sage-setup.nix new file mode 100644 index 00000000000..50346153123 --- /dev/null +++ b/pkgs/applications/science/math/sage/python-modules/sage-setup.nix @@ -0,0 +1,28 @@ +{ lib +, buildPythonPackage +, sage-src +, pkgconfig # the python module, not the pkg-config alias +}: + +buildPythonPackage rec { + version = src.version; + pname = "sage-setup"; + src = sage-src; + + buildInputs = [ + pkgconfig + ]; + + preBuild = '' + cd pkgs/sage-setup + ''; + + doCheck = false; # sagelib depends on sage-setup, but sage-setup's tests depend on sagelib + + meta = with lib; { + description = "Build system of the Sage library"; + homepage = "https://www.sagemath.org"; + license = licenses.gpl2Plus; + maintainers = teams.sage.members; + }; +} diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index ae0b9f7453b..e680c0c3b22 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -2,7 +2,7 @@ , lib , writeTextFile , sagelib -, sage_docbuild +, sage-docbuild , env-locations , gfortran , bash @@ -45,11 +45,10 @@ , flint , gmp , mpfr -, pynac , zlib , gsl , ntl -, jdk8 +, jdk , less }: @@ -60,8 +59,6 @@ assert (!blas.isILP64) && (!lapack.isILP64); # dependencies. let - jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731 - runtimepath = (lib.makeBinPath ([ "@sage-local@" "@sage-local@/build" @@ -163,7 +160,6 @@ writeTextFile rec { gmp mpfr pari - pynac zlib eclib gsl @@ -179,7 +175,6 @@ writeTextFile rec { glpk flint gap - pynac mpfr.dev ]) }' @@ -193,5 +188,5 @@ writeTextFile rec { ''; } // { # equivalent of `passthru`, which `writeTextFile` doesn't support lib = sagelib; - docbuild = sage_docbuild; + docbuild = sage-docbuild; } diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index eb07434b4cc..a51e92cde52 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -57,24 +57,29 @@ let ); in stdenv.mkDerivation rec { - version = "9.4"; + version = "9.5"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-jqkr4meG02KbTCMsGvyr1UbosS4ZuUJhPXU/InuS+9A="; + sha256 = "sha256-uOsLpsGpcIGs8Xr82X82MElnTB2E908gytyNJ8WVD5w="; }; # Patches needed because of particularities of nix or the way this is packaged. # The goal is to upstream all of them and get rid of this list. nixPatches = [ - # Make sure py2/py3 tests are only run when their expected context (all "sage" - # tests) are also run. That is necessary to test dochtml individually. See - # https://trac.sagemath.org/ticket/26110 for an upstream discussion. - # TODO: Determine if it is still necessary. - ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch + # Since https://trac.sagemath.org/ticket/32174, some external features are + # marked as "safe" and get auto-detected, in which case the corresponding + # optional tests are executed. We disable auto-detection of safe features if + # we are doctesting with an "--optional" argument which does not include + # "sage", because tests from autodetected features expect context provided + # by running basic sage tests. This is necessary to test sagemath_doc_html + # separately. See https://trac.sagemath.org/ticket/26110 for a related + # upstream discussion (from the time when Sage still had optional py2/py3 + # tags). + ./patches/Only-test-external-software-when-all-of-sage-is.patch # Fixes a potential race condition which can lead to transient doctest failures. ./patches/fix-ecl-race.patch @@ -117,46 +122,6 @@ stdenv.mkDerivation rec { # Let's just assume warnings are expected until we update to 4.27.0. ./patches/fonttools-deprecation-warnings.patch - # https://trac.sagemath.org/ticket/32305 - (fetchSageDiff { - base = "9.4"; - name = "networkx-2.6-upgrade.patch"; - rev = "9808325853ba9eb035115e5b056305a1c9d362a0"; - sha256 = "sha256-gJSqycCtbAVr5qnVEbHFUvIuTOvaxFIeffpzd6nH4DE="; - }) - - # https://trac.sagemath.org/ticket/32420 - (fetchSageDiff { - base = "9.5.beta2"; - name = "sympy-1.9-update.patch"; - rev = "beed4e16aff32e47d0c3b1c58cb1e2f4c38590f8"; - sha256 = "sha256-3eJPfWfCrCAQ5filIn7FbzjRQeO9QyTIVl/HyRuqFtE="; - }) - - # https://trac.sagemath.org/ticket/32567 - (fetchSageDiff { - base = "9.5.beta2"; - name = "arb-2.21.0-update.patch"; - rev = "eb3304dd521a3d5a9334e747a08e234bbf16b4eb"; - sha256 = "sha256-XDkaY4VQGyESXI6zuD7nCNzyQOl/fmBFvAESH9+RRvk="; - }) - - # https://trac.sagemath.org/ticket/32797 - (fetchSageDiff { - base = "9.5.beta7"; - name = "pari-2.13.3-update.patch"; - rev = "f5f7a86908daf60b25e66e6a189c51ada7e0a732"; - sha256 = "sha256-H/caGx3q4KcdsyGe+ojV9bUTQ5y0siqM+QHgDbeEnbw="; - }) - - # https://trac.sagemath.org/ticket/32909 - (fetchSageDiff { - base = "9.5.beta7"; - name = "matplotlib-3.5-deprecation-warnings.patch"; - rev = "a5127dc56fdf5c2e82f6bc781cfe78dbd04e97b7"; - sha256 = "sha256-p23qUu9mgEUbdbX6cy7ArxZAtpcFjCKbgyxN4jWvj1o="; - }) - # https://trac.sagemath.org/ticket/32968 (fetchSageDiff { base = "9.5.beta8"; @@ -164,6 +129,11 @@ stdenv.mkDerivation rec { rev = "fc84f82f52b6f05f512cb359ec7c100f93cf8841"; sha256 = "sha256-bBbfdcnw/9LUOlY8rHJRbFJEdMXK4shosqTNaobTS1Q="; }) + + # Upstream has not upgraded to linbox 1.7 yet because it conflicts with + # pre-4.2.1p3 versions of Singular, but we don't have this problem. + # https://trac.sagemath.org/ticket/32959 + ./patches/linbox-1.7-upgrade.patch ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix index b74ec4007e6..df3a1467d53 100644 --- a/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/pkgs/applications/science/math/sage/sage-with-env.nix @@ -18,7 +18,6 @@ , eclib , ntl , ecm -, pynac , pythonEnv }: @@ -36,7 +35,6 @@ let blas lapack singular three - pynac giac gap pari @@ -126,6 +124,10 @@ stdenv.mkDerivation rec { cp -r src/bin "$out/bin" cp -r build/bin "$out/build/bin" + # sage assumes the existence of sage-src-env-config.in means it's being executed in-tree. in this case, it + # adds SAGE_SRC/bin to PATH, breaking our wrappers + rm "$out/bin"/*.in "$out/build/bin"/*.in + cp -f '${sage-env}/sage-env' "$out/bin/sage-env" substituteInPlace "$out/bin/sage-env" \ --subst-var-by sage-local "$out" diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index 106f9eea309..5805a5c7b0c 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -62,7 +62,8 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; - license = licenses.gpl2; + homepage = "https://www.sagemath.org"; + license = licenses.gpl2Plus; maintainers = teams.sage.members; }; } diff --git a/pkgs/applications/science/math/sage/sage_docbuild.nix b/pkgs/applications/science/math/sage/sage_docbuild.nix deleted file mode 100644 index ed78d46b445..00000000000 --- a/pkgs/applications/science/math/sage/sage_docbuild.nix +++ /dev/null @@ -1,20 +0,0 @@ -{ buildPythonPackage -, sage-src -, sphinx -}: - -buildPythonPackage rec { - version = src.version; - pname = "sage_docbuild"; - src = sage-src; - - propagatedBuildInputs = [ - sphinx - ]; - - preBuild = '' - cd build/pkgs/sage_docbuild/src - ''; - - doCheck = false; # we will run tests in sagedoc.nix -} diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix index 6016b3baeb4..489fc2edfe5 100644 --- a/pkgs/applications/science/math/sage/sagedoc.nix +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { jmol cddlib ] ++ (with python3.pkgs; [ - sage_docbuild + sage-docbuild psutil future sphinx @@ -83,6 +83,6 @@ stdenv.mkDerivation rec { doCheck = true; checkPhase = '' - ${sage-with-env}/bin/sage -t --optional=dochtml --all + ${sage-with-env}/bin/sage -t --optional=sagemath_doc_html --all ''; } diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index a884ad8899d..8d685c8da60 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -2,6 +2,7 @@ , env-locations , perl , buildPythonPackage +, m4 , arb , blas , lapack @@ -37,7 +38,7 @@ , pkg-config , planarity , ppl -, pynac +, primecountpy , python , ratpoints , readline @@ -49,11 +50,24 @@ , singular , pip , jupyter_core +, sage-setup , libhomfly , libbraiding , gmpy2 , pplpy , sqlite +, jupyter-client +, ipywidgets +, mpmath +, rpy2 +, fpylll +, scipy +, sympy +, matplotlib +, pillow +, ipykernel +, networkx +, sphinx # TODO: this is in setup.cfg, bug should we override it? }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -73,8 +87,10 @@ buildPythonPackage rec { perl jupyter_core pkg-config + sage-setup pip # needed to query installed packages lisp-compiler + m4 ]; buildInputs = [ @@ -116,7 +132,7 @@ buildPythonPackage rec { pari planarity ppl - pynac + primecountpy rankwidth ratpoints singular @@ -130,6 +146,18 @@ buildPythonPackage rec { gmpy2 pplpy sqlite + mpmath + rpy2 + scipy + sympy + matplotlib + pillow + ipykernel + fpylll + networkx + jupyter-client + ipywidgets + sphinx ]; preBuild = '' @@ -148,8 +176,24 @@ buildPythonPackage rec { mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" mkdir -p "var/lib/sage/installed" - # src/setup.py should not be used, see https://trac.sagemath.org/ticket/31377#comment:124 - cd build/pkgs/sagelib/src + cd build/pkgs/sagelib + + # some files, like Pipfile, pyproject.toml, requirements.txt and setup.cfg + # are generated by the bootstrap script using m4. these can fetch data from + # build/pkgs, either directly or via sage-get-system-packages. + sed -i 's/==2.1.0rc1/>=2.1.1/' ../gmpy2/install-requires.txt + sed -i 's/, <3.4//' ../rpy2/install-requires.txt + sed -i 's/, <4.3//' ../sphinx/install-requires.txt + sed -i '/sage_conf/d' src/setup.cfg.m4 + sed -i '/sage_conf/d' src/requirements.txt.m4 + for infile in src/*.m4; do + if [ -f "$infile" ]; then + outfile="src/$(basename $infile .m4)" + m4 "$infile" > "$outfile" + fi + done + + cd src ''; postInstall = '' |