diff options
Diffstat (limited to 'pkgs/applications/science/math')
8 files changed, 35 insertions, 164 deletions
diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 561c9c66a50ec..3cd9384ecf1fd 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2023-12-31"; + version = "unstable-2024-01-22"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "cc92936e226b0a4c77cdc5d00b7a02c472746f6f"; - hash = "sha256-wY06pZzqcgYdBS7ecB3ZnvmK74ve651n6aHHAN5DWdw="; + rev = "db4b22cd536cefbdf0b6c928f11c793a5580da0b"; + hash = "sha256-T1GXh1go08XVTToEg5Dq4BuwTCxxqYwQsx+c8g1RPxg="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index a4173d1f5e6d8..765c691c95551 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -32,6 +32,7 @@ let }); }; + # matches src/sage/repl/ipython_kernel/install.py:kernel_spec jupyter-kernel-definition = { displayName = "SageMath ${sage-src.version}"; argv = [ @@ -42,7 +43,7 @@ let "-f" "{connection_file}" ]; - language = "sagemath"; + language = "sage"; # just one 16x16 logo is available logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png"; logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png"; diff --git a/pkgs/applications/science/math/sage/patches/disable-slow-glpk-test.patch b/pkgs/applications/science/math/sage/patches/disable-slow-glpk-test.patch index c04463e7e99c4..89f0613589d4c 100644 --- a/pkgs/applications/science/math/sage/patches/disable-slow-glpk-test.patch +++ b/pkgs/applications/science/math/sage/patches/disable-slow-glpk-test.patch @@ -1,12 +1,12 @@ diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py -index 0070705f78..ac19818f1b 100644 +index 2deb533f7f..663ff2cd13 100644 --- a/src/sage/graphs/generic_graph.py +++ b/src/sage/graphs/generic_graph.py -@@ -6699,12 +6699,6 @@ class GenericGraph(GenericGraph_pyx): +@@ -6953,12 +6953,6 @@ class GenericGraph(GenericGraph_pyx): sage: G = DiGraph(d6, format='dig6') sage: G.edge_connectivity() 5 -- sage: G.edge_disjoint_spanning_trees(5) # long time +- sage: G.edge_disjoint_spanning_trees(5) # long time # needs sage.numerical.mip - [Digraph on 28 vertices, - Digraph on 28 vertices, - Digraph on 28 vertices, diff --git a/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch b/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch deleted file mode 100644 index 539afc4b3b77d..0000000000000 --- a/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py -index aa153fd4cd..eebbe87aff 100644 ---- a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py -+++ b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py -@@ -134,11 +134,11 @@ Sage example in ./graphique.tex, line 1120:: - sage: t = srange(0, 5, 0.1); p = Graphics() - sage: for k in srange(0, 10, 0.15): - ....: y = integrate.odeint(f, k, t) -- ....: p += line(zip(t, flatten(y))) -+ ....: p += line(zip(t, y.flatten())) - sage: t = srange(0, -5, -0.1); q = Graphics() - sage: for k in srange(0, 10, 0.15): - ....: y = integrate.odeint(f, k, t) -- ....: q += line(zip(t, flatten(y))) -+ ....: q += line(zip(t, y.flatten())) - sage: y = var('y') - sage: v = plot_vector_field((1, -cos(x*y)), (x,-5,5), (y,-2,11)) - sage: g = p + q + v; g.show() diff --git a/pkgs/applications/science/math/sage/python-modules/sage-setup.nix b/pkgs/applications/science/math/sage/python-modules/sage-setup.nix index e1c497678d50b..a96f7ccd5d4c0 100644 --- a/pkgs/applications/science/math/sage/python-modules/sage-setup.nix +++ b/pkgs/applications/science/math/sage/python-modules/sage-setup.nix @@ -1,7 +1,7 @@ { lib , buildPythonPackage , sage-src -, cython +, cython_3 , jinja2 , pkgconfig # the python module, not the pkg-config alias }: @@ -11,7 +11,7 @@ buildPythonPackage rec { pname = "sage-setup"; src = sage-src; - nativeBuildInputs = [ cython ]; + nativeBuildInputs = [ cython_3 ]; buildInputs = [ pkgconfig ]; propagatedBuildInputs = [ jinja2 ]; diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 96b1adb562f49..4149e9163a363 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -1,6 +1,7 @@ { stdenv , fetchFromGitHub , fetchpatch +, fetchurl }: # This file is responsible for fetching the sage source and adding necessary patches. @@ -9,14 +10,23 @@ # all get the same sources with the same patches applied. stdenv.mkDerivation rec { - version = "10.0"; + version = "10.2"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-zN/Lo/GBCjYGemuaYpgG3laufN8te3wPjXMQ+Me9zgY="; + sha256 = "sha256-VXnPdJhtw5Y/anecrVpevJDCyBVfnjksyuuZslNipm4="; + }; + + # contains essential files (e.g., setup.cfg) generated by the bootstrap script. + # TODO: investigate https://github.com/sagemath/sage/pull/35950 + configure-src = fetchurl { + # the hash below is the tagged commit's _parent_. it can also be found by looking for + # the "configure" asset at https://github.com/sagemath/sage/releases/tag/${version} + url = "mirror://sageupstream/configure/configure-b2813506039143e6f0abe859ab67a343abf72c2e.tar.gz"; + sha256 = "sha256-a1v0XyoKI+zO6Sjm8DzEwItRHbIgRDbpj4UfwVH+/hw="; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -52,99 +62,6 @@ stdenv.mkDerivation rec { # should come from or be proposed to upstream. This list will probably never # be empty since dependencies update all the time. packageUpgradePatches = [ - # https://github.com/sagemath/sage/pull/35584, landed in 10.1.beta1 - (fetchpatch { - name = "networkx-3.1-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/be0aab74fd7e399e146988ef27260d2837baebae.diff"; - sha256 = "sha256-xBGrylNaiF7CpfmX9/4lTioP2LSYKoRCkKlKSGZuv9U="; - }) - - # https://github.com/sagemath/sage/pull/35612, landed in 10.1.beta1 - (fetchpatch { - name = "linbox-1.7-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/35cbd2f2a2c4c355455d39b1424f05ea0aa4349b.diff"; - sha256 = "sha256-/TpvIQZUqmbUuz6wvp3ni9oRir5LBA2FKDJcmnHI1r4="; - }) - - # https://github.com/sagemath/sage/pull/35619, landed in 10.1.beta1 - (fetchpatch { - name = "maxima-5.46.0-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/4ddf9328e7598284d4bc03cd2ed890f0be6b6399.diff"; - sha256 = "sha256-f6YaZiLSj+E0LJMsMZHDt6vecWffSAuUHYVkegBEhno="; - }) - - # https://github.com/sagemath/sage/pull/35635, landed in 10.1.beta1 - (fetchpatch { - name = "sympy-1.12-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/1a73b3bbbfa0f4a297e05d49305070e1ed5ae598.diff"; - sha256 = "sha256-k8Oam+EiRcfXC7qCdLacCx+7vpUAw2K1wsjKcQbeGb4="; - }) - - # https://github.com/sagemath/sage/pull/35826, landed in 10.1.beta5 - (fetchpatch { - name = "numpy-1.25.0-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/ecfe06b8f1fe729b07e885f0de55244467e5c137.diff"; - sha256 = "sha256-G0xhl+LyNdDYPzRqSHK3fHaepcIzpuwmqRiussraDf0="; - }) - - # https://github.com/sagemath/sage/pull/35826#issuecomment-1658569891 - ./patches/numpy-1.25-deprecation.patch - - # https://github.com/sagemath/sage/pull/35842, landed in 10.1.beta5 - (fetchpatch { - name = "scipy-1.11-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/90ece168c3c61508baa36659b0027b7dd8b43add.diff"; - sha256 = "sha256-Y5TmuJcUJR+veb2AuSVODGs+xkVV+pTM8fWTm4q+NDs="; - }) - - # https://github.com/sagemath/sage/pull/35825, landed in 10.1.beta6 - (fetchpatch { - name = "singular-4.3.2p2-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/1a1b49f814cdf4c4c8d0ac8930610f3fef6af5b0.diff"; - sha256 = "sha256-GqMgoi0tsP7zcCcPumhdsbvhPB6fgw1ufx6gHlc6iSc="; - }) - - # https://github.com/sagemath/sage/pull/36006, landed in 10.2.beta2 - (fetchpatch { - name = "gmp-6.3-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/5e841de46c3baa99cd1145b36ff9163e9340a55c.diff"; - sha256 = "sha256-fJPDryLtGBQz9qHDiCkBwjiW2lN6v7HiHgxY7CTeHcs="; - }) - - # https://github.com/sagemath/sage/pull/36279, landed in 10.2.beta4 - (fetchpatch { - name = "matplotlib-3.8-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/0fcf88935908440930c5f79202155aca4ad57518.diff"; - sha256 = "sha256-mvqAHaTCXsxPv901L8HSTnrfghfXYdq0wfLoP/cYQZI="; - }) - - # https://github.com/sagemath/sage/pull/35658, landed in 10.1.beta2 - (fetchpatch { - name = "sphinx-7-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/cacd9a89b5c4fdcf84a8dd2b7d5bdc10cc78109a.diff"; - sha256 = "sha256-qJvliTJjR3XBc5pH6Q0jtm8c4bhtZcTcF3O04Ro1uaU="; - }) - - # https://github.com/sagemath/sage/pull/36296, landed in 10.2.beta4 - (fetchpatch { - name = "duplicate-args-region_plot.patch"; - url = "https://github.com/sagemath/sage/commit/461727b453712550a2c5dc0ae11933523255aaed.diff"; - sha256 = "sha256-mC8084VQoUBk4hocALF+Y9Cwb38Zt360eldi/SSjna8="; - }) - - # https://github.com/sagemath/sage/pull/36218, landed in 10.2.beta3 - (fetchpatch { - name = "sageenv-disable-file-validation.patch"; - url = "https://github.com/sagemath/sage/commit/31a764f4a9ec54d3ea970aa9514a088c4e603ebd.diff"; - sha256 = "sha256-NhYUTTmYlyjss3eS8HZXP8U11TElQY0cv6KW4wBOaJY="; - }) - - # https://github.com/sagemath/sage/pull/36235, landed in 10.2.beta3 - (fetchpatch { - name = "ecl-23.9.9.patch"; - url = "https://github.com/sagemath/sage/commit/b6b50a80e9660c002d069019f5b8f04e9324a423.diff"; - sha256 = "sha256-nF+5oKad1VYms6Dxr1t9/V0XBkoMfhy0KCY/ZPddrm0="; - }) ]; patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; @@ -158,11 +75,17 @@ stdenv.mkDerivation rec { sed -i \ "s|var(\"SAGE_ROOT\".*|var(\"SAGE_ROOT\", \"$out\")|" \ src/sage/env.py + + # sage --docbuild unsets JUPYTER_PATH, which breaks our docbuilding + # https://trac.sagemath.org/ticket/33650#comment:32 + sed -i "/export JUPYTER_PATH/d" src/bin/sage ''; buildPhase = "# do nothing"; installPhase = '' cp -r . "$out" + tar xkzf ${configure-src} -C "$out" + rm "$out/configure" ''; } diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix index 228b5aa2c609c..5e2191486bf08 100644 --- a/pkgs/applications/science/math/sage/sagedoc.nix +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -11,11 +11,6 @@ stdenv.mkDerivation rec { strictDeps = true; - nativeBuildInputs = [ - # for patchShebangs below - python3 - ]; - unpackPhase = '' export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage" export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc" @@ -29,18 +24,6 @@ stdenv.mkDerivation rec { export HOME="$TMPDIR/sage_home" mkdir -p "$HOME" - # run bootstrap script to generate Sage spkg docs, because unfortunately some unrelated doc - # pages link to them. it needs a few ugly (but self-contained) hacks for a standalone run. - cp -r "${src}/build" "$HOME" - chmod -R 755 "$HOME/build" - sed -i "/assert/d" "$HOME/build/sage_bootstrap/env.py" - sed -i "s|sage-bootstrap-python|python3|" "$HOME/build/bin/sage-package" - patchShebangs "$HOME/build/bin/sage-package" - pushd "$SAGE_DOC_SRC_OVERRIDE" - sed -i "s|OUTPUT_DIR=\"src/doc/|OUTPUT_DIR=\"$SAGE_DOC_SRC_OVERRIDE/|" bootstrap - PATH="$HOME/build/bin:$PATH" SAGE_ROOT="${src}" ./bootstrap - popd - # adapted from src/doc/Makefile (doc-src target), which tries to call Sage from PATH mkdir -p $SAGE_DOC_SRC_OVERRIDE/en/reference/repl ${sage-with-env}/bin/sage -advanced > $SAGE_DOC_SRC_OVERRIDE/en/reference/repl/options.txt @@ -51,12 +34,10 @@ stdenv.mkDerivation rec { # jupyter-sphinx calls the sagemath jupyter kernel during docbuild export JUPYTER_PATH=${jupyter-kernel-specs} - # sage --docbuild unsets JUPYTER_PATH, so we call sage_docbuild directly - # https://trac.sagemath.org/ticket/33650#comment:32 - ${sage-with-env}/bin/sage --python3 -m sage_docbuild \ + ${sage-with-env}/bin/sage --docbuild \ --mathjax \ --no-pdf-links \ - all html < /dev/null + all html ''; installPhase = '' @@ -80,7 +61,7 @@ stdenv.mkDerivation rec { # sagemath_doc_html tests assume sage tests are being run, so we # compromise: we run standard tests, but only on files containing # relevant tests. as of Sage 9.6, there are only 4 such files. - grep -PRl "#.*optional.*sagemath_doc_html" ${src}/src/sage{,_docbuild} | \ + grep -PRl "#.*(optional|needs).*sagemath_doc_html" ${src}/src/sage{,_docbuild} | \ xargs ${sage-with-env}/bin/sage -t --optional=sage,sagemath_doc_html ''; } diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index f8beabaac1ffa..5a1f4ee473c9b 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -48,7 +48,7 @@ , cvxopt , cypari2 , cysignals -, cython +, cython_3 , fpylll , gmpy2 , importlib-metadata @@ -152,7 +152,7 @@ buildPythonPackage rec { cvxopt cypari2 cysignals - cython + cython_3 fpylll gmpy2 importlib-metadata @@ -202,29 +202,13 @@ buildPythonPackage rec { mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" mkdir -p "var/lib/sage/installed" - 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 '/sage_conf/d' src/setup.cfg.m4 - sed -i '/sage_conf/d' src/requirements.txt.m4 - # version lower bounds are useful, but upper bounds are a hassle because # Sage tests already catch any relevant API breakage. # according to the discussion at https://trac.sagemath.org/ticket/33520, # upper bounds will be less noisy starting from Sage 9.6. - sed -i 's/==0.5.1/>=0.5.1/' ../ptyprocess/install-requires.txt - sed -i 's/, <[^, ]*//' ../*/install-requires.txt - - for infile in src/*.m4; do - if [ -f "$infile" ]; then - outfile="src/$(basename $infile .m4)" - m4 "$infile" > "$outfile" - fi - done + sed -i 's/, <[^, ]*//' build/pkgs/*/install-requires.txt - cd src + cd build/pkgs/sagelib/src ''; postInstall = '' |