From ada57517cbdc2ed6893edaf486da8381c06e3e0a Mon Sep 17 00:00:00 2001 From: Raspbian forward porter Date: Mon, 13 Feb 2023 15:21:51 +0000 Subject: [PATCH] Import scipy_1.10.0-4+rpi1.debian.tar.xz [dgit import tarball scipy 1.10.0-4+rpi1 scipy_1.10.0-4+rpi1.debian.tar.xz] --- changelog | 1755 +++++++++++++++++ control | 96 + copyright | 423 ++++ gbp.conf | 3 + get-submodules | 41 + ...t-treat-warnings-as-errors-in-pytest.patch | 20 + ...documentation-referencing-the-source.patch | 125 ++ ...s_parameter_k_which-to-fail-on-armel.patch | 25 + patches/0018-Drop-intersphinx.patch | 18 + patches/Use-system-LBFGSB.patch | 46 + patches/build_sh4_FE.patch | 15 + patches/docs_no_sphinx_design.patch | 335 ++++ patches/find_cython3.patch | 30 + patches/fix_cast_PR17726.patch | 62 + patches/fix_highs_atomic_PR17777.patch | 43 + patches/manage_docs.patch | 37 + patches/manage_tests.patch | 382 ++++ patches/pythran_type_PR16646.patch | 32 + patches/qhull-lfs.patch | 24 + patches/readonly_interpolate_PR17717.patch | 122 ++ patches/series | 16 + patches/use_local_mathjax.patch | 20 + python-scipy-doc.doc-base | 14 + python-scipy-doc.docs | 1 + python-scipy-doc.lintian-overrides | 1 + python3-scipy.lintian-overrides | 1 + rules | 171 ++ salsa-ci.yml | 4 + source/format | 1 + source/lintian-overrides | 2 + tests/atlas | 1 + tests/blis | 1 + tests/control | 22 + tests/openblas | 21 + tests/python3 | 139 ++ tests/python3-smoke | 18 + upstream/metadata | 15 + watch | 5 + 38 files changed, 4087 insertions(+) create mode 100644 changelog create mode 100644 control create mode 100644 copyright create mode 100644 gbp.conf create mode 100755 get-submodules create mode 100644 patches/0008-Don-t-treat-warnings-as-errors-in-pytest.patch create mode 100644 patches/0009-Remove-some-documentation-referencing-the-source.patch create mode 100644 patches/0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch create mode 100644 patches/0018-Drop-intersphinx.patch create mode 100644 patches/Use-system-LBFGSB.patch create mode 100644 patches/build_sh4_FE.patch create mode 100644 patches/docs_no_sphinx_design.patch create mode 100644 patches/find_cython3.patch create mode 100644 patches/fix_cast_PR17726.patch create mode 100644 patches/fix_highs_atomic_PR17777.patch create mode 100644 patches/manage_docs.patch create mode 100644 patches/manage_tests.patch create mode 100644 patches/pythran_type_PR16646.patch create mode 100644 patches/qhull-lfs.patch create mode 100644 patches/readonly_interpolate_PR17717.patch create mode 100644 patches/series create mode 100644 patches/use_local_mathjax.patch create mode 100644 python-scipy-doc.doc-base create mode 100644 python-scipy-doc.docs create mode 100644 python-scipy-doc.lintian-overrides create mode 100644 python3-scipy.lintian-overrides create mode 100755 rules create mode 100644 salsa-ci.yml create mode 100644 source/format create mode 100644 source/lintian-overrides create mode 120000 tests/atlas create mode 120000 tests/blis create mode 100644 tests/control create mode 100755 tests/openblas create mode 100755 tests/python3 create mode 100755 tests/python3-smoke create mode 100644 upstream/metadata create mode 100644 watch diff --git a/changelog b/changelog new file mode 100644 index 00000000..d91ae4bd --- /dev/null +++ b/changelog @@ -0,0 +1,1755 @@ +scipy (1.10.0-4+rpi1) bookworm-staging; urgency=medium + + [changes brought forward from 1.8.1-14+rpi1 by Peter Michael Green at Mon, 26 Sep 2022 01:12:43 +0000] + * Disable testsuite. + * Add build-conflicts on git, the documenation seems to fail to + build if it is installed. + + -- Raspbian forward porter Mon, 13 Feb 2023 15:21:51 +0000 + +scipy (1.10.0-4) unstable; urgency=medium + + * Team upload. + * skip more build-time tests + - hurd-i386: test_find_peaks_exact test_find_peaks_withnoise + test_examples[True-float64] test_rv_sample + test_location_scale[pdf + - x32: test_basic + * update debian/tests + - armhf with openblas: skip test_array_smoothing + - i386 with blis: skip test_random_complex_exact + * debian patch fix_cast_PR17726.patch applies upstream PR17726 + to fix 32-bit/64-bit casting. Closes: #1029690. + * add Breaks: python3-skbio (<< 0.5.8-3~) to aid migration + + -- Drew Parsons Tue, 07 Feb 2023 09:49:03 +0100 + +scipy (1.10.0-3) unstable; urgency=medium + + * Team upload. + * drop scipy/_lib/boost/ from debian/copyright + (no longer provided in upstream source) + * skip build-time tests + - hurd-i386: test_mip1 + - ia64: test_maxiter_worsening[lgmres] + - x32: test_input_validation + * update skips in debian/tests: + - i386: skip test_simple_overdet_complex with blis + - armhf: skip test_rosenbrock_with_no_exception + * update debian patch Use-system-LBFGSB.patch for the new meson build + Closes: #1030142. + + -- Drew Parsons Fri, 03 Feb 2023 10:48:29 +0100 + +scipy (1.10.0-2) unstable; urgency=medium + + * Team upload. + + [ Andreas Tille ] + * Add missing copyright for submodules + + [ Drew Parsons ] + * update debian/tests + - i386: fix test skips + - armel: skip test_brunnermunzel_normal_dist + - armhf with openblas: skip test_pdist_calling_conventions + test_pdist_dtype_equivalence test_striding + - s390x with atlas: skip test_aligned_mem + * debian patch readonly_interpolate_PR17717.patch applies upstream + PR17717 to fix interpolate.interpn. Closes: #1029692. + * drop debian patch fix_numpy1.24_PR17035.patch (applied upstream) + + -- Drew Parsons Sun, 29 Jan 2023 10:13:42 +0100 + +scipy (1.10.0-1exp6) experimental; urgency=medium + + * Team upload. + * powerpc: skip test_maxiter_worsening[lgmres] + * mipsel: skip test_integrator test_double_integrator + + -- Drew Parsons Wed, 25 Jan 2023 11:05:38 +0100 + +scipy (1.10.0-1exp5) experimental; urgency=medium + + * Team upload. + * mipsel skip test_fht_special_cases test_integrality (also mips64el) + * armel skip test_brunnermunzel_normal_dist + * riscv64 skip test_maxiter_worsening[lgmres] + + -- Drew Parsons Tue, 24 Jan 2023 12:37:59 +0100 + +scipy (1.10.0-1exp4) experimental; urgency=medium + + * Team upload. + * debian patch fix_highs_atomic_PR17777.patch applies upstream + PR17777 to fix handling of libatomic (with gcc) in _highs. + Fixes build for armel, mipsel, powerpc. + * skip tests on mips64el: test_integrator test_double_integrator + + -- Drew Parsons Mon, 23 Jan 2023 23:01:47 +0100 + +scipy (1.10.0-1exp3) experimental; urgency=medium + + * Team upload. + * skip more tests: + - i386: test_examples[True-float64] + test_pdf_nolan_samples[pct_range0-alpha_range0-beta_range0] + - ppc64: test_maxiter_worsening + + -- Drew Parsons Mon, 23 Jan 2023 12:39:03 +0100 + +scipy (1.10.0-1exp2) experimental; urgency=medium + + * Team upload. + * Build-Depends: libblas-dev not libopenblas-dev. Preferred BLAS + implementation must be installed by the system administrator not + at build time, and OpenBLAS is not available on all arches. + * handle failing tests, see https://github.com/scipy/scipy/issues/17839 + - relax more tolerances in debian patch manage_tests.patch to enable + i386 to pass tests + - i386: skip test_x0_equals_Mb[bicgstab] + test_rv_sample test_location_scale[pdf + - s390x: skip test_atol[bicg] + - ppc64: skip test_precond_dummy + - armhf (in debian/tests, build-time tests pass fine) + + -- Drew Parsons Mon, 23 Jan 2023 02:41:59 +0100 + +scipy (1.10.0-1exp1) experimental; urgency=medium + + [ Drew Parsons ] + * Team upload. + * New upstream major release. + - no longer uses local boost source + (drop debian patch hppa-boost-long-double-config.patch) + - Build-Depends: meson (>= 0.62.2~) + - Build-Depends-Indep: python3-sphinx-tabs for docs + - update versioned Build-Depends: cython3 (>= 0.29.21~), + python3-pythran (>= 0.9.12~), python3-pythran (<< 0.12) + * update debian/watch with uversionmangle=s/rc/~rc/ to order + RC releases below final release versions + + [ Andreas Tille ] + * Standards-Version: 4.6.2 (routine-update) + * Multi-Arch: foreign + * Reorder sequence of d/control fields by cme (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Fix field name typo in debian/copyright (Comments ⇒ Comment). + * Build-Depends: s/libblas-dev/libopenblas-dev/ + * Build-Depends: pkg-config + * Symlink submodules from submodules source tarball + TODO: + - Integrate submodules via additional tarball that can be + created with script debian/get-submodules + + [ Drew Parsons ] + * debian/control: allow use of pythran 0.12 + * add _build_utils/cythoner.py to find_cython3.patch, + see upstream scipy Issue#17808 + * Build-Depends: python3-mesonpy + * Build-Depends: python3-pooch (used by datasets test_data.py) + - skip test_data (datasets) pooch tests at build time, which need + internet or cached datafiles. test_existence_all, test_ascent, + test_face, test_electrocardiogram. + * update debian patch manage_tests.patch to only copy .coveragerc if + it exists (it is no longer shipped with the source) + * debian patch manage_docs.patch enables doc build to complete + - drops sphinx_design (not yet packaged for Debian) + - ignores imp deprecation warnings (from invoke via pooch, see + https://github.com/pyinvoke/invoke/issues/675 and #829) + - skips switcher themes (needs updated pydata-sphinx-theme, + see Bug##1029009) + - don't treat doc warnings as errors. Life is too short for that. + * debian patch docs_no_sphinx_design.patch works around the missing + sphinx_design extension, replacing docs using grid: with the + scipy 1.8 version using panel:, and removing tab-set:. + * update debian/copyright: scipy-mathjax, sphinxext no longer + present in doc dirs + * meson build is still work-in-progress, installs residual cython + (pyx) files, see cython_special comments in scipy/special/meson.build + So remove any python3.X (not python3) files left after dh_python3. + More work is needed to manage these cython files, see + https://github.com/scipy/scipy/issues/14890 + + -- Drew Parsons Fri, 20 Jan 2023 11:47:47 +0100 + +scipy (1.8.1-22) unstable; urgency=medium + + * Team upload. + * skip test_atol[bicg] on s390x. Closes: #1029550. + + -- Drew Parsons Wed, 25 Jan 2023 15:32:10 +0100 + +scipy (1.8.1-21) unstable; urgency=medium + + * Team upload. + * debian patch fix_numpy1.24_PR17035.patch applies upstream PR17035 + to fix build with numpy 1.24. Closes: #1027244 + + -- Drew Parsons Thu, 19 Jan 2023 14:54:51 +0100 + +scipy (1.8.1-20) unstable; urgency=medium + + * Team upload. + * Fix sphinx build with Python 3.11 + + -- Jochen Sprickerhof Tue, 03 Jan 2023 21:59:59 +0100 + +scipy (1.8.1-19) unstable; urgency=medium + + * Team upload. + * Add upstream patch to fix flapack (Closes: #1027460) + * Add upstream patch for numpy 1.24 + * Use dh-sequence-* + + -- Jochen Sprickerhof Tue, 03 Jan 2023 11:32:39 +0100 + +scipy (1.8.1-18) unstable; urgency=medium + + * Team upload. + * Skip one more failing test on ppc64el + + -- Jochen Sprickerhof Mon, 26 Dec 2022 09:33:52 +0100 + +scipy (1.8.1-17) unstable; urgency=medium + + * Team upload. + * Ignore some test in autopkgtests + + -- Jochen Sprickerhof Sun, 25 Dec 2022 12:03:29 +0100 + +scipy (1.8.1-16) unstable; urgency=medium + + * Team upload. + * Ignore some failing unit tests on some archs + + -- Jochen Sprickerhof Fri, 23 Dec 2022 23:53:47 +0100 + +scipy (1.8.1-15) unstable; urgency=medium + + * Team upload. + * Fix FTBFS with new numpy (deprecated numpy.distutils) + (Closes: #1026210, #1026342, #1026516) + * Add workaround for FTBFS with new sphinx + * Ignore test failure on armel (Closes: #1025699) + + -- Jochen Sprickerhof Tue, 20 Dec 2022 19:47:35 +0100 + +scipy (1.8.1-14) unstable; urgency=medium + + * Team upload. + * debian/tests: skip all test_complex* tests on i386 with blis + * once again drop pythran support on armhf. + Still causes many packages to fail tests even after revised + version of PR16646 (possibly due to memory exhaustion?) + + -- Drew Parsons Thu, 08 Sep 2022 16:01:54 +0200 + +scipy (1.8.1-13) unstable; urgency=medium + + * Team upload. + * skip build-time tests + - armel: test_random_exact in linalg/tests/test_basic.py (segfaults) + * update debian patch pythran_type_PR16646.patch to latest PR16646 + + -- Drew Parsons Wed, 07 Sep 2022 09:53:04 +0200 + +scipy (1.8.1-12) unstable; urgency=medium + + * Team upload. + * skip build-time tests + - armel: linalg/tests/test_decomp.py (started segfaulting) + - hppa: test_nodata test_cont_basic[500-200-semicircular-arg89] + - riscv64: test_vector test_iterative_refinements_dense (segfaults) + * skip more tests in debian/test + - i386 with blis: test_complex_dotc (segfaults) + - armhf with openblas: test_solver_selection + - ppc64el with atlas: sparse test_svd_v0, test_svd_random_state{_2} + * update debian patch pythran_type_PR16646.patch to latest PR16646 + - reinstate TestMLS tests + - reinstate pythran on armhf to test if PR16646 now fixes problems + - Closes: #1017862 + + -- Drew Parsons Tue, 30 Aug 2022 20:12:18 +0200 + +scipy (1.8.1-11) unstable; urgency=medium + + * Team upload. + * skip more tests in debian/tests + - arm64: test_atol[cgs] with blis + - armel: skip linalg test_aligned_mem in test_decomp.py + - armhf with openblas: some optimize tests in TestRRSVD, TestDogbox + - i386 with blis: test_complex_dotu + - ppc64el: test_svds_parameter_tol, test_bug_6139 (with atlas) + - s390x with atlas: test_bug_6139, test_solver_select + - riscv64: avoid failures and segfaults + * skip tests failing on powerpc in stats/tests/test_stats.py: + overflow encountered in _hypergeom_*. Skip test_hypergeom_cdf, + test_hypergeom_sf, test_nch_hypergeom, test_precision, + test_precise, test_less_greater + * debian/tests: restrict openblas tests to supported architectures + only (i.e. not armel) + + -- Drew Parsons Fri, 26 Aug 2022 00:29:59 +0200 + +scipy (1.8.1-10) unstable; urgency=medium + + * Team upload. + * skip TestSmirnovp (test_kolmogorov) also on hurd-i386 + * skip test_first_step and test_classes on mips64el + (integrate/_ivp/tests/test_ivp.py) + See https://github.com/scipy/scipy/issues/16883 + * skip test_large_rank_deficient on armhf with blis. Segfaults in + test_lsq_linear.py::TestBVLS + * once again drop pythran support on armhf. + It does work successfully, but shifts numerical results enough to + break tests on a dozen packages (astropy, pandas, pyfai, skimage etc) + + -- Drew Parsons Wed, 24 Aug 2022 11:43:19 +0200 + +scipy (1.8.1-9) unstable; urgency=medium + + * Team upload. + * drop asyncio_mode=auto from debian patch manage_tests.patch. + Only relevant when python3-pytest-asyncio is installed + (causes errors if not installed, but scipy doesn't need it) + * use runtests.py to manage build-time tests + * skip failing tests + - signal TestMLS fails due to broken pythran support on 32 bit + arches. See Bug#1017862. + - special test_kolmogorov.py (TestSmirnovp) segfaults on i386. + Closes: Bug#1017864. + - stats test_cont_basic[500-200-ncf-arg74] fails with + IntegrationWarning. See upstream Issue 14519 + * update debian/watch (uscan) for latest github format + + -- Drew Parsons Mon, 22 Aug 2022 17:24:17 +0200 + +scipy (1.8.1-8) unstable; urgency=medium + + * Team upload. + * overhaul debian/tests to run debci tests using upstream's + runtests.py. Previous approach was overcomplicated and unable to + skip test_hermitian_modes for blis on i386. Keep specific skips for + BLAS tests but drop general tests previously skipped in order to + verify if they still need skipping. + * debian patch pythran_type_PR16646.patch applies upstream PR#16646 + to properly define pythran types for 32 bit arches. + - reinstate pythran support on armhf + * fix determination of python3 versions in debian/rules + + -- Drew Parsons Mon, 25 Jul 2022 00:20:58 +0200 + +scipy (1.8.1-7) unstable; urgency=medium + + * Team upload. + * drop pythran completely from armhf. Still causes errors from built + components even if pythran is not installed at runtime. + cf. https://github.com/serge-sans-paille/pythran/issues/2002 + * reorganise test skip list in debian/tests to ensure i386 properly + skips test_hermitian_modes + + -- Drew Parsons Mon, 18 Jul 2022 13:36:40 +0200 + +scipy (1.8.1-6) unstable; urgency=medium + + * Team upload. + * on armhf, demote python3-scipy Depends: pythran to Suggests. + Causes armhf debci test failure on dozens of dependent packages, + mainly with MemoryError. Only individual tests fail, probably + depends on the specific usage. + + -- Drew Parsons Thu, 30 Jun 2022 22:14:11 +0200 + +scipy (1.8.1-5) unstable; urgency=medium + + * Team upload. + * debian/tests: skip more blas-specific tests + - armhf/openblas: test_large_rank_deficient and all TestTRF + (in optimize/tests/test_lsq_linear.py; times out or segfaults) + - armhf/openblas: test_disp in optimize/tests/test_linprog.py + (times out) + - armhf/atlas: test_aligned_mem in linalg/tests/test_decomp.py + (illegal value for DHSEQR parameter) + - fix i386 skip of test_hermitian_modes (_eigen not eigen) + * update debian patch manage_tests.patch + - alpha: special test_round.py skip all + * Depends: python3-pythran on all arches. Even arches without full + SIMD support should benefit from the dynamic C++ compilation. + cf. https://github.com/scipy/scipy/issues/13308#issuecomment-1168579164 + Closes: #1013568. + + -- Drew Parsons Wed, 29 Jun 2022 01:17:22 +0200 + +scipy (1.8.1-4) unstable; urgency=medium + + * Team upload. + * update debian patch manage_tests.patch + - add asyncio_mode=auto to pytest.ini. Required in order to launch + tests from toplevel source directory. + - hppa (parisc64): io/arff test_arffread.py + skip TestNoData + - hppa (parisc64): special test_round.py skip all + - hurd: platform.machine() is 'i686-AT386', so use + machine.startswith('i686') instead of machine=='i686' + to skip tests for both i386 (linux) and hurd-i386 + * return an exit code from scipy.test() otherwise 0 is always + returned so test failure is not detected + * disable pythran support on i386 because of test errors + "TypeError: Invalid call to pythranized function" + cf. https://github.com/serge-sans-paille/pythran/issues/1025 + Revisit once pythran 0.11.0 is packaged. + * debian/tests: skip test_hermitian_modes with BLIS on i386 + (in sparse/linalg/eigen/arpack/arpack.py). Closes: Bug#1003880. + * in BLAS tests, only use first alternative for BLAS implementation + + -- Drew Parsons Wed, 15 Jun 2022 18:35:03 +0200 + +scipy (1.8.1-3) unstable; urgency=medium + + * Team upload. + * debian/tests specific blas tests Depend on -dev versions of blas + packages in order to not hardcode ABI versions + (blis recently bumped to libblis.so.4) + * update debian patch manage_tests.patch: + - mips64el: fft test_fftlog.py skip test_fht_special_cases + - mips64el: sparse/csgraph test_shortest_path.py + skip test_NaN_warnings + - mips64el: stats test_distributions.py skip test_moments_warnings + - on i386 platform.machine() is 'i686' not 'i386' + - on armel and armhf platform.machine() is "armv7l' not simply 'arm' + Use startswith('arm') not =='arm' to allow the general case. + - on powerpc platform.machine() is "ppc" + * reinstate handling of nocheck in DEB_BUILD_OPTIONS to run tests + * run tests with set -e to ensure errors are not ignored. + Closes: #1003417. + * debian patch build_sh4_FE.patch ensures FE_UPWARD and FE_DOWNWARD + are defined for sh4 architecture. Closes: #1007769. + * add pythran support for i386 + + -- Drew Parsons Tue, 14 Jun 2022 16:11:24 +0200 + +scipy (1.8.1-2) experimental; urgency=medium + + * Team upload. + * rename debian patch skip_tests.patch to manage_tests.patch and + update to increase test successes + - all: linalg test_lapack.py test_sygst + raise tol from 1e-4 to 2e-4 + - armel, powerpc: stats test_stats skip various tests + - armel: special test_round.py skip all + - armel: optimize test_linprog.py skip test_bounds_infeasible_2 + - armel: interpolate test_fitpack.py skip test_kink + - armhf: linalg test_interpolative.py + skip test_estimate_spectral_norm_diff + - i386: relax tolerance in spatial/transform test_rotation.py + and spatial test_distance.pytest_pdist_jensenshannon_iris + - i386: sparse/linalg/_isolve test_iterative.py skip + test_maxiter_worsening + - i386: signal test_spectral.py skip test_nd_axis_m1, + test_nd_axis_0 + - s390x, powerpc, ppc64, sparc64: io/arff test_arffread.py + skip TestNoData + + -- Drew Parsons Mon, 13 Jun 2022 01:36:20 +0200 + +scipy (1.8.1-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - Depends: python3-numpy (>= 1:1.17.3~) + * Build-Depends: pybuild-plugin-pyproject to use pyproject.toml. + Closes: #1008680. + * Simplify debian/rules back to minimal dh (with python,sphinxdoc) + * drop debian/python3-scipy.install: pybuild/pyproject installs + directly into debian package dirs + * launch build-time tests from /tmp (needs to start outside the + source dir) + * debian patch skip_tests.patch skips failing tests + - linalg: test_decomp.py TestSchur.test_sort and + test_solvers.py test_solve_discrete_are + see https://github.com/scipy/scipy/issues/14517 + - optimize test_optimize.py: test_minimize_l_bfgs_maxls passes but + marked as expected to fail + * Standards-Version: 4.6.1 + + -- Drew Parsons Sun, 12 Jun 2022 02:03:37 +0200 + +scipy (1.8.0-1exp2) experimental; urgency=medium + + * build scipy with pythran support where available [amd64 arm64 m68k] + Depends: python3-pythran [amd64 arm64 m68k] + Closes: #991753. + + -- Drew Parsons Tue, 15 Feb 2022 01:41:52 +0100 + +scipy (1.8.0-1exp1) experimental; urgency=medium + + * Team upload. + * New upstream release. + * update debian/copyright: vendored libraries SuperLU and arpack + used by sparse/linalg are now treated as private via an + _underscore prefix (_dsolve, _eigen) + + -- Drew Parsons Fri, 11 Feb 2022 22:05:09 +0100 + +scipy (1.7.3-2) unstable; urgency=medium + + * Team upload. + * debian patch hppa-boost-long-double-config.patch disables + LONG_DOUBLE in the boost submodule on hppa. Adapted from the boost + patch hppa-long-double-config.patch. + See https://github.com/scipy/scipy/issues/15260 + for discussion of why boost has been vendored for scipy. + Closes: #1004197. + + -- Drew Parsons Fri, 11 Feb 2022 12:11:29 +0100 + +scipy (1.7.3-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + * Build-Depends-Indep: python3-sphinx-panels + Drop debian patch docs_skip_panels.patch. Closes: #991752. + * remove upper bound on python3-pybind11 build-dependency. It's not + used upstream in dev code, gets applied only to release versions + to make local pip virtualenv installations use known-good versions. + Closes: #1002065. + * remove upper bound in Build-Depends: python3-numpy, python3-wheel + * raise versioned Build-Depends python3-numpy (>= 1.21.4) for + python3.10 support. + * don't compress woff font files. Apply the same + override_dh_compress used for numpy. Closes: #1003282. + * add a source lintian override for fortran-si4-11x1x10.dat + (source-contains-prebuilt-windows-binary). It's a test data + file, not a DOS executable. + * Standards-Version: 4.6.0 + * update debian/copyright + - remove deprecated files debian/patches/css_font_OpenSans.patch, + doc/scipy-sphinx-theme/*, scipy/_lib/six.py + - acknowledge Jonathan Neal's code snippet "font-family: no-parens" + from https://codepen.io/jonneal/pen/bXLEdB (MIT licence) + in doc/source/_static/scipy.css + - scipy/fft/_pocketfft/ licence applies to all _pocketfft not only + pocketfft.cxx + - scipy/_lib/uarray/ renamed to _uarray + + -- Drew Parsons Sun, 09 Jan 2022 14:11:52 +0100 + +scipy (1.7.1-2) unstable; urgency=medium + + * Drop -dbg package; Closes: #994375 + + -- Sandro Tosi Wed, 10 Nov 2021 23:57:11 -0500 + +scipy (1.7.1-1) unstable; urgency=medium + + * Team upload. + + [ Debian Janitor ] + * Use secure URI in Homepage field. + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. + + [ Drew Parsons ] + * New upstream release + * update upper-versioned Build-Depends + - python3-numpy (<< 1.23.0) (see pyproject.toml) + - python3-pybind11 (<< 2.8) (build is stable with pybind11 2.7) + + -- Drew Parsons Wed, 18 Aug 2021 02:07:15 +0200 + +scipy (1.7.0-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - deprecates debian patches css_font_OpenSans.patch and + css_font_local.patch + * Build with SCIPY_USE_PYTHRAN=0 since pythran is not yet available. + pythran packaging requested in Bug#991143. + * Build-Depends-Indep: python3-pydata-sphinx-theme, + python3-sphinx (>> 3.1) + * debian patch docs_skip_panels.patch skips use of sphinx-panels in + docs. Not available yet (RFP#991684). + * update debian/rules + - allow for spaces in filenames in override_dh_fixperms-arch. + sobol_vec.gz is no longer installed. + - drop special handling for weave. It was removed in scipy 0.15.0. + * mark python3-scipy as Multi-Arch: no + * lintian fixes + - mark scipy/optimize/lbfgsb_src/*.f as License: BSD-generic not BSD + - packages override bogus-mail-host-in-debian-changelog + Debian/i386 Build Daemon + - source override obsolete-url-in-packaging debian/copyright + https://code.google.com/archive/p/ampgo + * remove deprecated debian/README.source + + -- Drew Parsons Sat, 31 Jul 2021 01:40:57 +0200 + +scipy (1.6.2-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - fixes matrix dtypes. Closes: #983404. + - introduces upper-versioned Build-Depends: cython3 (<< 3.0), + python3-pybind11 (<< 2.7), + python3-wheel (<< 0.37.0) + (leave python3-setuptools uncapped) + - also Build-Depends: python3-all-dev (>= 3.7) + * Stop ignoring build-time errors in debian/rules. Closes: #967977. + + -- Drew Parsons Fri, 26 Mar 2021 19:21:49 +0100 + +scipy (1.6.1-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + * Depends: python3-numpy (>= 1:1.16.5) + + -- Drew Parsons Sun, 21 Feb 2021 20:46:00 +0100 + +scipy (1.6.0-2) unstable; urgency=medium + + * Team upload. + * upload new upstream version to unstable + + -- Drew Parsons Sat, 16 Jan 2021 23:26:56 +1100 + +scipy (1.6.0-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + * Standards-Version: 4.5.1 + * drop debian/python3-scipy.docs: Thanks.txt no longer shipped. + * update debian/copyright for new features + - benchmarks/benchmarks/go_benchmark_functions/*.py + Copyright: 2013 Andrea Gavana + License: expat + - scipy/fft/_pocketfft/pocketfft.cxx + Copyright: 2010-2019 Max-Planck-Society, Martin Reinecke + 2019 Peter Bell. License: BSD-3-clause + - scipy/fft/_pocketfft/pocketfft_hdronly.h + Copyright: 2010-2019 Max-Planck-Society, Martin Reinecke + 2019 Peter Bell, 2003,2007-2014 Matteo Frigo, + Massachusetts Institute of Technology. License: BSD-3-clause + - scipy/optimize/_highs/* + Copyright: 2020 ERGO-Code + License: Expat + - scipy/sparse/csgraph/_matching.pyx + Copyright: 1987, A. Volgenant/Amsterdam School of Economics, + University of Amsterdam. License: BSD-3-clause + - scipy/_lib/uarray/* + Copyright: 2018, Quansight-Labs + License: BSD-3-clause + + -- Drew Parsons Wed, 06 Jan 2021 19:57:43 +1100 + +scipy (1.5.4-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + + -- Drew Parsons Sat, 14 Nov 2020 13:36:06 +0800 + +scipy (1.5.3-2) unstable; urgency=medium + + * Team upload. + * push new upstream release to unstable + + -- Drew Parsons Thu, 05 Nov 2020 03:33:52 +0800 + +scipy (1.5.3-1) experimental; urgency=medium + + * Team upload. + + [ Ondřej Nový ] + * d/control: Update Maintainer field with new Debian Python Team + contact address. + * d/control: Update Vcs-* fields with new Debian Python Team Salsa + layout. + + [ Drew Parsons ] + * New upstream release. + + -- Drew Parsons Tue, 03 Nov 2020 13:32:21 +0800 + +scipy (1.5.2-2) unstable; urgency=medium + + * Team upload. + * debian/tests (autopkgtest): add a new test case using BLAS=libblis3 + + -- Drew Parsons Sat, 01 Aug 2020 12:49:57 +0800 + +scipy (1.5.2-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - update versioned Build-Depends: cython3 (>= 0.29.18), + python3-numpy (>= 1:1.14.5), python3-pybind11 (>= 2.4.3) + - builds with gfortran 10. Closes: #957780. + * debhelper compatibility level 13 + + -- Drew Parsons Fri, 24 Jul 2020 15:17:18 +0800 + +scipy (1.4.1-2) unstable; urgency=medium + + * Team upload. + * bring new upstream version to unstable + + -- Drew Parsons Sat, 18 Apr 2020 11:08:42 +0800 + +scipy (1.4.1-1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - applies debian patches fix_custom_sampling_input_2b3ed61.patch + and fix_test_NAN_input_iv_7806757.diff + - deprecates debian patch use_local_objects.inv.patch + - Build-Depends: python3-pybind11 (>= 2.4.0) + - Build-Depends-Indep: python3-sphinx (>= 2~) + * provide PYTHONPATH as env variable with make doc + * Standards-Version: 4.5.0 + + -- Drew Parsons Fri, 17 Apr 2020 01:11:18 +0800 + +scipy (1.3.3-3) unstable; urgency=medium + + * Team upload. + * skip sparsetools.TestInt32Overflow tests test_bsr_1_block and + test_bsr_n_block (they regularly timeout) + + -- Drew Parsons Fri, 06 Dec 2019 10:22:05 +0800 + +scipy (1.3.3-2) unstable; urgency=medium + + * Team upload. + * add debian patches to avoid internet connections when using docs + - css_font_OpenSans.patch adapts font settings from + https://fonts.googleapis.com/css?family=Open+Sans + (Apache 2.0 licence) + - css_font_local.patch uses local font_OpenSans.css from + css_font_OpenSans.patch + - python-scipy-doc Depends: fonts-open-sans + - Closes: #873433. + * debian patch fix_custom_sampling_input_2b3ed61.patch applies + upstream commit 2b3ed61 to fix syntax. Closes: #945093. + + -- Drew Parsons Thu, 05 Dec 2019 00:30:25 +0800 + +scipy (1.3.3-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + * change source package name to scipy for python3-only, to + distinguish from python-scipy which supports python2. + * update Vcs salsa repo name to scipy (from python-scipy) + + -- Drew Parsons Wed, 27 Nov 2019 20:53:58 +0800 + +python-scipy (1.3.1-1exp3) experimental; urgency=medium + + * Team upload. + * update versioned Build-Depends: python3-numpy (>= 1:1.13.3) + and cython3 (>= 0.29.2) + * Patch fix_test_NAN_input_iv_7806757.diff applies upstream commit + 7806757 to fix tests on hppa, riscv64, sparc64. Closes: #934806. + + -- Drew Parsons Fri, 16 Aug 2019 13:20:27 +0800 + +python-scipy (1.3.1-1exp2) experimental; urgency=medium + + * Team upload. + * build binaries before building docs + + -- Drew Parsons Tue, 13 Aug 2019 18:45:38 +0800 + +python-scipy (1.3.1-1exp1) experimental; urgency=medium + + * Team upload. + * New upstream release. + - drops support for Python 2 (python-scipy is no longer provided) + - applies patches + matrix_API_614847c5.patch + matrix_API_filter_check_87e48c3c5.patch + matrix_API_more_e0cfa29e2.patch + fix_test_optim_canonical_constraint_2d7e7e8c.patch + * adjust skipping of spatial tests according to context of test + (openblas,atlas specify scipy.spatial) + + -- Drew Parsons Tue, 13 Aug 2019 15:04:07 +0800 + +python-scipy (1.2.2-8) unstable; urgency=medium + + * Team upload. + + [ Ondřej Nový ] + * Bump Standards-Version to 4.4.1. + + [ Drew Parsons ] + * only build docs for default python3. Closes: #942794. + - apply dh_auto_install to arch-dependent packages only + + -- Drew Parsons Tue, 19 Nov 2019 02:32:19 +0800 + +python-scipy (1.2.2-7) unstable; urgency=medium + + * Team upload. + * Patch fix_test_NAN_input_iv_7806757.diff applies upstream commit + 7806757 to fix tests on mipsel, hppa, riscv64, sparc64 + (taken from 1.3.1-1exp3) + + -- Drew Parsons Sun, 25 Aug 2019 20:37:32 +0800 + +python-scipy (1.2.2-6) unstable; urgency=medium + + * Team upload. + * atlas, openblas tests Depends: python3 + + -- Drew Parsons Sun, 25 Aug 2019 01:47:34 +0800 + +python-scipy (1.2.2-5) unstable; urgency=medium + + * Team upload. + * adjust skipping of sparse and spatial tests according to context + of test (openblas and atlas specify scipy.sparse, scipy.spatial) + * run atlas and openblas tests with python3 not python2 + + -- Drew Parsons Sat, 24 Aug 2019 11:42:02 +0800 + +python-scipy (1.2.2-4) unstable; urgency=medium + + * Team upload. + * debian patch Use-system-LBFGSB.patch: + run test_minimize_l_bfgs_maxls with rtol=1e-5 + + -- Drew Parsons Tue, 30 Jul 2019 09:28:55 +0800 + +python-scipy (1.2.2-3) unstable; urgency=medium + + * Team upload. + * run build-time tests over all versions of python3 + * Build-Depends: liblbfgsb-dev and add Debian patch + Use-system-LBFGSB.patch to use the system L-BFGS-B library (which + uses LAPACK rather than the scipy-bundled LINPACK) + Enables test_minimize_l_bfgs_maxls in scipy.optimize to succeed. + Thanks Gard Spreemann. Closes: #778635. + + -- Drew Parsons Tue, 30 Jul 2019 00:26:20 +0800 + +python-scipy (1.2.2-2) unstable; urgency=medium + + * Team upload. + * debhelper compatibility level 12 + - run configure build step through pybuild to get consistent + build directories + - set PYLIBPATH to pybuild build directory + * debian/rules: use AUTOPKGTEST_TMP instead of ADTTMP to run tests + * v1.2.2 fixes indexing in fftpack. Closes: #924396. + * drop ignore_DeprecationWarning_diff1.2.patch (already applied in + scipy 1.2) + * Register docs with doc-base. Closes: #846253. + * debian/tests/python3: skip tests of + scipy.spatial.tests.test__plotutils.TestPlotting + (see https://github.com/scipy/scipy/issues/9946) + + -- Drew Parsons Mon, 29 Jul 2019 18:43:34 +0800 + +python-scipy (1.2.2-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + * configure debian/watch to grab tar.xz rather than tar.gz + (for smaller tarballs) + * debian/rules: build with dh --buildsystem=pybuild + * Standards-Version: 4.4.0 + + -- Drew Parsons Fri, 26 Jul 2019 15:22:36 +0800 + +python-scipy (1.2.1-1exp1) experimental; urgency=medium + + * Team upload. + * New upstream release. + + -- Drew Parsons Thu, 28 Feb 2019 11:16:38 +0800 + +python-scipy (1.2.0-1) experimental; urgency=medium + + * New upstream release + + -- Julian Taylor Tue, 15 Jan 2019 12:27:45 +0100 + +python-scipy (1.1.0-7) unstable; urgency=medium + + * Team upload. + * Patch fix_test_optim_canonical~onstraint_2d7e7e8c.patch applies + upstream patch 2d7e7e8 to fix occasional random failures in + test_canonical_constraint.test_concatenation. + + -- Drew Parsons Fri, 12 Apr 2019 00:46:35 +0800 + +python-scipy (1.1.0-6) unstable; urgency=medium + + * Team upload. + * skip sparsetools.TestInt32Overflow matvec tests on python3 also. + + -- Drew Parsons Thu, 11 Apr 2019 09:38:17 +0800 + +python-scipy (1.1.0-5) unstable; urgency=medium + + * Team upload. + * Skip sparsetools.TestInt32Overflow matvec tests on python2 + (MemoryError). Closes: #919929. + + -- Drew Parsons Wed, 10 Apr 2019 16:41:47 +0800 + +python-scipy (1.1.0-4) unstable; urgency=medium + + * Team upload. + * Replace patch ignore_DeprecationWarning_diff1.2.patch with + matrix_API_614847c5.patch + matrix_API_filter_check_87e48c3c5.patch + matrix_API_more_e0cfa29e2.patch + adapting the indicated upstream commits to scipy 1.1.0 + (use numpy.matmul instead of @ for matrix multiplication, since @ + is not available in python2) + Removes sources of matrix DeprecationWarnings. + Addresses: Bug#919929. + + -- Drew Parsons Thu, 14 Mar 2019 14:12:00 +0800 + +python-scipy (1.1.0-3) unstable; urgency=medium + + * Team upload. + * Debian patch ignore_DeprecationWarning_diff1.2.patch applies diff + of pytest.ini between scipy 1.1 and 1.2 to ignore + DeprecationWarnings from numpy 1.16. Addresses Bug#919929. + * Use default gfortran-8 on s390x. unroll-loops was fixed in + gcc-8 8.2.0-18. Closes: #906198, #915738. + + -- Drew Parsons Fri, 08 Mar 2019 00:31:29 +0800 + +python-scipy (1.1.0-2) unstable; urgency=medium + + * Team upload. + * Remove Alexandre Fayolle from the Uploaders list. Thanks for your + previous contributions! Closes: #833329 + * Use gfortran-7 on s390x to work around a regression causing the imexam + test suite to fail when scipy is built with gfortran 8. Addresses: #906198 + * Add some Multi-Arch markers suggested by the m-a hinter. + + -- Mattia Rizzolo Sun, 04 Nov 2018 19:01:19 +0100 + +python-scipy (1.1.0-1) unstable; urgency=medium + + [ Julian Taylor ] + * New upstream release + Closes: #896060, #901380, #896635 + * update to debian/compat 9 and standard 4.1.4 + + [ Ondřej Nový ] + * d/control: Set Vcs-* to salsa.debian.org + * d/copyright: Use https protocol in Format field + * d/tests: Use AUTOPKGTEST_TMP instead of ADTTMP + * d/control: Remove ancient X-Python-Version field + * d/control: Remove ancient X-Python3-Version field + + -- Julian Taylor Sun, 01 Jul 2018 14:34:28 +0200 + +python-scipy (0.19.1-2) unstable; urgency=medium + + * Replace python-imaging recomments with python-pil (Closes: #866468) + * build documentation with python3-sphinx + * Fix atlas and openblas tests for openblas and atlas multiarch locations + Thanks to Matthias Klose for the patch (Closes: #876007) + * Depend on python-all-dbg for autopkgtests + Thanks to Michael Hudson-Doyle for the patch (Closes: #864699) + * bump standard to 4.1.3 + - debian/control: replace priority extra with optional + + -- Julian Taylor Sun, 07 Jan 2018 14:38:57 +0100 + +python-scipy (0.19.1-1) unstable; urgency=medium + + * New upstream release + * weave has been removed, drop its patch blitz++.patch + * drop cap-ld-precision.patch, fixed in numpy + + -- Julian Taylor Wed, 06 Sep 2017 18:07:38 +0200 + +python-scipy (0.18.1-2.1) unstable; urgency=high + + * Non-maintainer upload. + * No-change rebuild to build without _PyFPE symbols. + + -- Matthias Klose Tue, 05 Sep 2017 16:36:34 +0200 + +python-scipy (0.18.1-2) unstable; urgency=medium + + * fix dbg package import (Closes: #840264) + * add dbg package import adt tests + + -- Julian Taylor Fri, 21 Oct 2016 16:10:57 +0200 + +python-scipy (0.18.1-1) unstable; urgency=medium + + [ Julian Taylor ] + * New upstream bugfix release + + [ Sebastian Humenda ] + * make the build-indep target execute the build target to allow the usage of + the module for generating the documentation (Closes: #806867) + + -- Julian Taylor Sun, 25 Sep 2016 11:25:21 +0200 + +python-scipy (0.18.0-1) unstable; urgency=medium + + * New upstream release + * add python-setuptools to build depends + + -- Julian Taylor Sat, 30 Jul 2016 19:05:17 +0200 + +python-scipy (0.17.1-1) unstable; urgency=medium + + [ Julian Taylor ] + * New upstream bugfix release + * enable parallel build based on DEB_BUILD_OPTIONS + * bump standard to 3.9.7, no changes required + + [ Ondřej Nový ] + * Fixed VCS URL (https) + + -- Julian Taylor Mon, 23 May 2016 20:02:14 +0200 + +python-scipy (0.17.0-1) unstable; urgency=medium + + * New upstream release + + -- Julian Taylor Sat, 23 Jan 2016 20:39:44 +0100 + +python-scipy (0.16.1-1) unstable; urgency=medium + + * New upstream bugfix release + * update adt-tests to new layout + * remove duplicate files in -doc package + + -- Julian Taylor Sun, 25 Oct 2015 11:51:34 +0100 + +python-scipy (0.16.0-2) unstable; urgency=medium + + [ Julian Taylor ] + * bump cython build-depend to required 0.22 + + [ Jean-Christophe Jaskula ] + * fix build of documentation in arch only builds + + -- Julian Taylor Mon, 24 Aug 2015 09:51:10 +0200 + +python-scipy (0.16.0-1) unstable; urgency=medium + + [ Varun Hiremath ] + * New upstream release + * Bump Standards-Version to 3.9.6 + * Remove upstream applied patches: + - fitpack-alias.patch + - fix-undefined-behavior-in-alngam.patch + - relax-bounds-of-interpolate-test.patch + * d/rules: minor build fixes + + [ Jean-Christophe Jaskula ] + * Pointed debian/watch to github.com (cleaner sources) + * d/control: + - Added dh_python to B-d + - Removed unnecessary XS-Testsuite field + * Linking to local javascript libraries + - use_local_mathjax.patch + * Using local intersphinx objects + - use_local_objects.patch + * Cleaned debian/copyright + + -- Varun Hiremath Sun, 23 Aug 2015 23:01:46 -0400 + +python-scipy (0.14.1-1) unstable; urgency=medium + + * New upstream bugfix release + remove upstream applied patches: + - numpy-version-fix.patch + - numpy_ufunc.patch + - put-_gen-classes-back.patch + - put-back-veccdf.patch + - sparse-fix-omitted-types.patch + - sparse-superlu-fix.patch + * add python-gmpy2 dependency to autopkgtest to speed up mpmath tests + * add suggest on python-scipy-doc (Closes: #760522) + * debian/copyright: add bootstrap Apache 2.0 license + + -- Julian Taylor Fri, 05 Sep 2014 18:56:54 +0200 + +python-scipy (0.14.0-2) unstable; urgency=medium + + * add patches to fix test failures on i386 and mips: + - fix-undefined-behavior-in-alngam.patch (Closes: #756905) + - relax-bounds-of-interpolate-test.patch + * add patches from 0.14.x maintenance branch: + - sparse-superlu-fix.patch: fix crash + - sparse-fix-omitted-types.patch: fix crash + - put-back-veccdf.patch: restore stats api + - put-_gen-classes-back.patch: restore stats api + - numpy-version-fix.patch: fix wrong version check + - numpy_ufunc.patch: compatibility with numpy 1.9 + + -- Julian Taylor Wed, 27 Aug 2014 14:40:24 +0200 + +python-scipy (0.14.0-1) unstable; urgency=low + + [ Denis Laxalde ] + * Add the documentation binary package (Closes: #600547). + + [ Julian Taylor ] + * New upstream release + * drop not swig build dependency and reswig.patch, not needed anymore + * use embedded six, current unstable version not compatible + * fitpack-alias.patch: fix wrong aliasing in interpolate.splder + + -- Julian Taylor Fri, 23 May 2014 10:37:06 +0200 + +python-scipy (0.13.3-2) unstable; urgency=medium + + * upload to unstable + * add build-essential dependency to adt tests, needed for weave + + -- Julian Taylor Mon, 31 Mar 2014 23:32:16 +0200 + +python-scipy (0.13.3-1) experimental; urgency=low + + * New upstream release + * ignore TestSplder.test_kink adt failure, probably numerical error + + -- Julian Taylor Tue, 04 Feb 2014 19:48:01 +0100 + +python-scipy (0.13.2-1) experimental; urgency=low + + * New upstream release + * update X-Python-Version to >= 2.6 + * require python3-numpy (>= 1:1.7.2) for hashing fixes + * bump standard to 3.9.5, no changes required + * bump cython dependency to >= 0.19 to avoid leaks with fused types + + -- Julian Taylor Mon, 21 Oct 2013 18:59:29 +0200 + +python-scipy (0.13.0~b1-1) experimental; urgency=low + + [ Julian Taylor ] + * New upstream beta release + * require python-six >= 1.3.0, scipy ships a slightly patched 1.2.0, + version 1.3.0 includes the patches + + [ Varun Hiremath ] + * Fix debian/watch file + + -- Julian Taylor Sat, 07 Sep 2013 18:06:00 +0200 + +python-scipy (0.12.0-3) unstable; urgency=high + + * temporary-directory-usage.patch: + fix insecure temporary directory usage of weave module. (Closes: #726093) + Thanks to Tomas Tomecek for the patch. + + -- Julian Taylor Tue, 22 Oct 2013 23:44:47 +0200 + +python-scipy (0.12.0-2) unstable; urgency=low + + * ignore testsuite failures to not block python3.3 transition + only masks issues on hardly used ports + + -- Julian Taylor Mon, 01 Jul 2013 20:09:40 +0200 + +python-scipy (0.12.0-1) unstable; urgency=low + + [ Julian Taylor ] + * New upstream release, no repackaging required anymore + - Closes: #707315 + - Closes: #691254 + * also fail on test failures not only test errors + * skip failing test_mio on big endian python3 >= 3.2 + * print skipped tests and unused skips in autopkgtest scripts + * add-swig-filetypes.patch, reswig.patch: + reswigging from setup.py, dropped from debian/rules + * cython-wraparound.patch: fix issue in ckdtree.pyx + * qhull-lfs.patch: enable large file support + * cap-ld-precision.patch: fix test failures due to broken np.finfo on ppc + * refresh patches and remove upstream applied: + - BUG-fix-dependency-on-dict-ordering-in-test.patch + - BUG-remove-inline-statement-rejected-by-cython.patch + - fix-dbg-crash.patch + - fix-f2py-dependencies.patch + - fix-test_basic.py-cephes_vs_amos_mass_te.patch + - python3.3-incdir.diff + * Bump standard to 3.9.4, no changes required + * drop unused sharutils build depend and python-profiler from suggests + * use system python-six and python-decorator instead of embedded copies + * don't install setup.py and generator scripts + + [ Jakub Wilk ] + * Use canonical URIs for Vcs-* fields. + * Remove DM-Upload-Allowed; it's no longer used by the archive + software. + + -- Julian Taylor Thu, 09 May 2013 11:35:07 +0200 + +python-scipy (0.11.0+dfsg1-1) experimental; urgency=low + + * New upstream release + * bump required cython to >= 0.17 + * refresh patches: + - drop upstream applied: + - interpnd-generator.patch + - dtype.diff, + - kolmogorov.diff, + - up_minpack_ints.diff + - kde.diff + - new patches for python3.3 compatibility and test fixing: + - BUG-remove-inline-statement-rejected-by-cython.patch + - BUG-fix-dependency-on-dict-ordering-in-test.patch + - fix-test_basic.py-cephes_vs_amos_mass_te.patch + - python3.3-incdir.diff + - fix-dbg-crash.patch + - fix-f2py-dependencies.patch + * add autopkgtests + * run fast tests during build + * update debian/copyright to dep5 + + -- Julian Taylor Fri, 25 Jan 2013 23:54:43 +0100 + +python-scipy (0.10.1+dfsg2-1) unstable; urgency=low + + * add missing cython and swig sources from git tag (Closes: #589731) + * generate cython c files, requires python-mako and cython build depends + * ensure that all swig files are regenerated + * update debian/orig-tar.sh appropriately + * interpnd-generator.patch: fix the interpnd.pyx generation + + -- Julian Taylor Thu, 29 Nov 2012 21:56:31 +0100 + +python-scipy (0.10.1+dfsg1-4) unstable; urgency=low + + [ Julian Taylor ] + * use dh_numpy3 + - build depend on python3-numpy >= 1:1.6.2~rc1-1~ + * debian/rules: remove reference to pyshared + + [ Varun Hiremath ] + * debian/patches: + - add dtype.diff (Closes: #682030) + - add up_minpack_ints.diff, thanks to Yaroslav Halchenko (Closes: #681270) + + -- Varun Hiremath Sat, 21 Jul 2012 17:23:02 -0400 + +python-scipy (0.10.1+dfsg1-3) unstable; urgency=low + + * wrap-and-sort debian folder + * add python3 packages (Closes: #664785) + * debian/rules: + - split the build into build and install step + - use .install files instead of direct setup.py install + + -- Julian Taylor Fri, 20 Apr 2012 21:59:33 +0200 + +python-scipy (0.10.1+dfsg1-2) unstable; urgency=low + + * debian/control: + - Recommends: python-imaging (Closes: #648036) + - Recommends: python-dev (Closes: #651760) + * debian/patches: + - Add kolmogorov.diff, thanks to Yaroslav Halchenko (Closes: #653948) + - Add kde.diff (Closes: #648034) + + -- Varun Hiremath Fri, 20 Apr 2012 02:37:28 -0400 + +python-scipy (0.10.1+dfsg1-1) unstable; urgency=low + + * New upstream release (Closes: #653262) + * Update debian/orig-tar.sh script + * debian/patches + - updated restore_sys_argv.patch + - removed string_exception.patch, not needed + + -- Varun Hiremath Thu, 19 Apr 2012 16:14:28 -0400 + +python-scipy (0.9.0+dfsg1-1) unstable; urgency=low + + * New upstream release (Closes: #614407, #579041, #569008) + * Convert to dh_python2 (Closes: #617028) + + -- Varun Hiremath Wed, 06 Apr 2011 21:26:25 -0400 + +python-scipy (0.8.0+dfsg1-1) experimental; urgency=low + + [ Varun Hiremath ] + * New upstream release + * Build-Depend on python-numpy-* (>= 1:1.5.1) + * Update all the debian/patches/* + + [ Luca Falavigna ] + * Remove myself from Uploaders. + + [ Stefano Rivera ] + * debian/patches/blitz++.patch: Fix scipy.weave.inline compilations. Thanks + to Sameer Morar (Closes: #598520, LP: #302649) + + -- Varun Hiremath Fri, 24 Dec 2010 08:20:54 -0500 + +python-scipy (0.7.2+dfsg1-1) unstable; urgency=low + + * Release with a new source tarball with missing cython source files + * debian/rules: Add get-orig-source target + * Add debian/README.source explaining the repackaging of source tarball + * Add debian/orig-tar.sh to add missing cython source files to the + source tarball (Closes: #589731) + * debian/rules: add call to dh_numpy to generate stricter versioned + depends on python-numpy (Closes: #590763) + * Bump Standards-Version to 3.9.1 + * Add myself to Uploaders + + -- Varun Hiremath Fri, 30 Jul 2010 18:29:18 -0400 + +python-scipy (0.7.2-2) unstable; urgency=low + + * debian/patches/string_exceptions.patch: + - Do not use string exceptions, not supported by Python 2.6. + + -- Luca Falavigna Mon, 07 Jun 2010 14:52:40 +0200 + +python-scipy (0.7.2-1) unstable; urgency=low + + * New upstream release. + * Switch to debhelper 7. + * Provide python-scipy-dbg package (Closes: #525329). + * Add myself to Uploaders. + + -- Luca Falavigna Sun, 25 Apr 2010 17:21:21 +0200 + +python-scipy (0.7.1-1) unstable; urgency=low + + [ Sandro Tosi ] + * debian/control + - removed Marco Presi from uploaders: thanks for your work! + + [ Luca Falavigna ] + * New upstream release. + - Fix KeyError exception in sparse module (Closes: #525109). + - Fix SyntaxWarning exception with python2.6 (Closes: #567148). + * debian/patches/restore_sys_argv.patch: + - Restore sys.argv in case of exception (Closes: #500814). + * debian/control: + - Depend on ${misc:Depends}. + - Drop useless Conflicts/Replaces fields. + - Bump Standards-Version to 3.8.4, no changes required. + * debian/README.Debian: + - Remove obsolete information. + * debian/pycompat: + - Remove, useless. + + -- Debian Python Modules Team Mon, 05 Apr 2010 17:10:56 +0200 + +python-scipy (0.7.0-2) unstable; urgency=medium + + [ Julien Lavergne ] + * debian/copyright : Update Copyright holders (Closes: #524131) + * From Ubuntu, prepare for the future python transition: + - debian/rules: + + Include /usr/share/python/python.mk + + Add $(py_setup_install_args) to setup.py install + + Replace site-packages by *-packages + - debian/control: + + Bump build-depends to python-all-dev (>= 2.5.4-1~) + + [ Luca Falavigna ] + * Remove patches, they are no longer needed and also causing FTBFS with + recent python-numpy. Remove quilt machinery too (Closes: #545606). + * debian/copyright: add missing copyright holder (Closes: #540504). + * debian/control: bump Standards-Version to 3.8.3, no changes required. + * debian/watch: fix regex to report correct upstream stable version. + + -- Debian Python Modules Team Tue, 15 Sep 2009 23:30:12 +0200 + +python-scipy (0.7.0-1) unstable; urgency=low + + [ Ondrej Certik ] + * Beta version + * debian/patches: scipy_include_fix.diff and segfault.patch removed (applied + upstream), swig_ftbfs.dpatch and umfpack.dpatch updated to new paths + + [ Sandro Tosi ] + * debian/control + - switch Vcs-Browser field to viewsvn + + [ David Cournapeau ] + * New upstream version + * Remove obsolete dependencies on libfftw3-dev, libx11-dev and libnetcdf-dev + * Update version for numpy dependency: scipy requires version >= 1.2.0 + * Set ATLAS to None when building scipy to avoid depending on ATLAS API, and + only use BLAS/LAPACK public API, even when ATLAS is installed on the build + machine + + -- Ondrej Certik Sun, 08 Mar 2009 18:47:03 -0700 + +python-scipy (0.6.0-12) unstable; urgency=low + + * The description updated to match the current SciPy (Closes: #489149). + * Standards-Version bumped to 3.8.0 (no action needed) + * Build-Depends: netcdf-dev changed to libnetcdf-dev + + -- Ondrej Certik Mon, 16 Jun 2008 22:58:01 +0200 + +python-scipy (0.6.0-11.1) unstable; urgency=low + + * Non-maintainer upload. + * Change description to refer to python-numpy package instead of Numeric + to avoid confusion with python-numeric package. + + -- Chris AtLee Wed, 23 Apr 2008 15:45:22 -0400 + +python-scipy (0.6.0-11) unstable; urgency=low + + * Fixes FTBFS, by unexporting LDFLAGS and setting FFLAGS directly, the same + hack as in numpy (Closes: #475990) + + -- Ondrej Certik Mon, 14 Apr 2008 14:53:57 +0200 + +python-scipy (0.6.0-10) unstable; urgency=low + + [Sandro Tosi] + * Fixes a dangling symlink (Closes: #471825) + + -- Ondrej Certik Thu, 20 Mar 2008 14:50:31 +0100 + +python-scipy (0.6.0-9) unstable; urgency=medium + + * Uses correct pycentral locations (Closes: #471549) + + -- Ondrej Certik Wed, 19 Mar 2008 21:41:12 +0100 + +python-scipy (0.6.0-8) unstable; urgency=low + + * Build depend on libsuitesparse (>= 3.1.0-3) + * Build depends fixed to use gfortran based lapack and blas (Closes: #466868) + + -- Ondrej Certik Sat, 23 Feb 2008 01:21:51 +0100 + +python-scipy (0.6.0-7) unstable; urgency=low + + * Bumped the version, because python-numpy conflicts with python-scipy (<= + 0.6.0-6). This compiles against the old suitesparse, but it makes the + package installable and working again. + + -- Ondrej Certik Thu, 21 Feb 2008 15:38:00 +0100 + +python-scipy (0.6.0-6) UNRELEASED; urgency=low + + * debian/control + - uniforming both Vcs-Svn and Vcs-Browser fields + + -- Sandro Tosi Thu, 03 Jan 2008 12:18:46 +0100 + +python-scipy (0.6.0-5.1) unstable; urgency=low + + * Non-maintainer upload. + * Changed `fftw3-dev' to `libfftw3-dev' to get rid of that dependency + on a virtual package. + * Fix FTBFS with relation to swig with a patch provided by + Kumar Appaiah (Closes: #456892) + + -- Philipp Kern Mon, 31 Dec 2007 13:45:10 +0100 + +python-scipy (0.6.0-5) unstable; urgency=low + + * DM-Upload-Allowed changed to XS-DM-Upload-Allowed + * standards-version made uptodate (3.7.3) + * don't create an empty dir usr/share/doc/python-scipy/weave/ + + -- Ondrej Certik Tue, 04 Dec 2007 22:27:48 +0100 + +python-scipy (0.6.0-4) unstable; urgency=low + + * Use quilt (much eaiser to use) instead of dpatch + * Paul's patch added (Closes: #452991) + * Add DM-Upload-Allowed: yes + + -- Ondrej Certik Mon, 03 Dec 2007 15:33:24 +0100 + +python-scipy (0.6.0-3) unstable; urgency=low + + [ Piotr Ożarowski ] + * Rename XS-Vcs-* fields to Vcs-* (dpkg supports them now) + + [ Ondrej Certik ] + * Depending on libsuitesparse-dev directly instead of libufsparse-dev + (Closes: #445771) + + -- Ondrej Certik Mon, 15 Oct 2007 20:09:07 +0200 + +python-scipy (0.6.0-2) unstable; urgency=medium + + * Replaced fftw-dev with fftw3-dev in Build-Depends (closes: #444124) + + -- Piotr Ożarowski Wed, 26 Sep 2007 23:52:25 +0200 + +python-scipy (0.6.0-1) unstable; urgency=low + + [Ondřej Čertík] + * New upstream release + * watch file added + + [Piotr Ożarowski] + * Homepage field added + + -- Ondrej Certik Sun, 23 Sep 2007 16:14:35 +0200 + +python-scipy (0.5.2.1-2) unstable; urgency=low + + * Got rid of all lintian and linda warnings (removed "SciPy is an open + source library of scientific tools for Python" (first sentence) from the + long description) + * debian/control: Added XS-Vcs-Svn and XS-Vcs-Browser fields to the Source + section + + -- Ondrej Certik Fri, 31 Aug 2007 04:29:55 +0200 + +python-scipy (0.5.2.1-1) unstable; urgency=low + + * Adopting the package + * New upstream release (Closes: #426012) + * Removed unnecessary patches + * Removing LICENSE.txt, since it is unnecessary (and it fixes a lintian + warning) + + -- Ondrej Certik Tue, 28 Aug 2007 12:03:29 +0200 + +python-scipy (0.5.2-9) experimental; urgency=low + + * Added Build-Dep on python-numpy (Closes: 422389) + * Made build independent of the python version (Closes: 414626) + * Added a new patch on sandbox/montecarlo to fix py2.5 compatibility + + -- Marco Presi (Zufus) Fri, 18 May 2007 11:12:31 +0100 + +python-scipy (0.5.2-8) experimental; urgency=low + + * Fixed compatibility with numpy >= 1.0.2, by importing parts from upstream svn + + -- Marco Presi (Zufus) Sat, 21 Apr 2007 22:46:29 +0100 + +python-scipy (0.5.2-7+b1) unstable; urgency=low + + * Binary-only non-maintainer upload for i386; no source changes. + * Rebuild to fix binaries built against experimental + + -- Debian/i386 Build Daemon Tue, 27 Feb 2007 02:01:45 -0600 + +python-scipy (0.5.2-7) unstable; urgency=low + + * Added 'm86k' among the archs on which xplt should not build. + + -- Marco Presi (Zufus) Sat, 24 Feb 2007 13:40:42 +0000 + +python-scipy (0.5.2-6) unstable; urgency=low + + * Merged patch for image viwer from upstream svn + + -- Marco Presi (Zufus) Sat, 24 Feb 2007 01:39:18 +0000 + +python-scipy (0.5.2-5) experimental; urgency=low + + * Added a fix in sandbox/montecarlo tests that prevented installation + + -- Marco Presi (Zufus) Thu, 22 Feb 2007 01:33:18 +0000 + +python-scipy (0.5.2-4) experimental; urgency=low + + * Incorporated code from setup_without_xplt.py into patches/sandbox.dpatch, in order to + build sandbox/xplt only on supported archs (Closes: #407869). + * Added libx11-dev among Build-Deps to support xplt. + + -- Marco Presi (Zufus) Thu, 22 Feb 2007 00:33:51 +0000 + +python-scipy (0.5.2-3) experimental; urgency=low + + * Added netcdfg-dev Build-Deps (completed sandbox inclusion) + + -- Marco Presi (Zufus) Tue, 20 Feb 2007 23:28:43 +0000 + +python-scipy (0.5.2-2) experimental; urgency=low + + * Enabled sandbox modules. To this aim randomkit.[ch] are included from + pyhon-numpy sources. See debian/patches/sandbox.dpatch + (Closes: #407869). + + -- Marco Presi (Zufus) Mon, 19 Feb 2007 19:26:22 +0000 + +python-scipy (0.5.2-1) unstable; urgency=low + + * Fixed scipy.signal segfault (closes: #410757) + * Replaced hard-coded xv command with "see" (from mime-support). + Additionally, the environment variable SCIPY_PIL_IMAGE_VIEWER can be set. + (Closes: #395198) + + -- Marco Presi (Zufus) Sun, 18 Feb 2007 16:22:03 +0000 + +python-scipy (0.5.2-0.1) unstable; urgency=medium + + * Remove build dependency on python-numpy-dev. + * python-scipy: Depend on python-numpy instead of python-numpy-dev. + * Package builds on other archs than i386. Closes: #402783. + + -- Matthias Klose Sun, 7 Jan 2007 14:12:12 +0100 + +python-scipy (0.5.2-0) experimental; urgency=low + + * New upstream version (compatible with python-numpy-1.0.x). + * (Build-)depend on python-numpy (>= 1:1.0.1). + * Remove redundant (build-)dependencies. + * weave examples and docs are removed from the upstream tarball. + + -- Matthias Klose Wed, 3 Jan 2007 22:37:49 +0100 + +python-scipy (0.5.1-3) unstable; urgency=low + + * Moved weave/examples into /usr/share/doc/python-scipy/ + and removed *.so files that prevented building on non x86 archs + (closes: #397241) + + -- Marco Presi (Zufus) Sat, 16 Sep 2006 18:46:56 +0200 + +python-scipy (0.5.1-2) unstable; urgency=low + + * Added swig and libufsparse-dev among Build-deps + + -- Marco Presi (Zufus) Mon, 11 Sep 2006 22:05:45 +0200 + +python-scipy (0.5.1-1) unstable; urgency=low + + * New upstream release + + -- Marco Presi (Zufus) Thu, 7 Sep 2006 00:32:07 +0200 + +python-scipy (0.5.0-3) unstable; urgency=low + + * Re-compiled to reflect C-API changes in numpy. + + -- Marco Presi (Zufus) Fri, 18 Aug 2006 01:06:06 +0200 + +python-scipy (0.5.0-2) unstable; urgency=low + + * Re-added fftw-dev among build-deps. + + -- Marco Presi (Zufus) Tue, 8 Aug 2006 17:34:44 -0400 + +python-scipy (0.5.0-1) unstable; urgency=low + + * New upstream release + * Removed debian/patches/python2.3.dpatch now included in upstream release + + -- Marco Presi (Zufus) Sun, 30 Jul 2006 00:33:21 +0200 + +python-scipy (0.4.9-2) unstable; urgency=low + + * Build against new release of python-numpy. + + -- José Fonseca Wed, 05 Jul 2006 18:06:41 +0100 + +python-scipy (0.4.9-1) unstable; urgency=low + + * New upstream version. + + -- José Fonseca Tue, 04 Jul 2006 16:11:01 +0100 + +python-scipy (0.3.2-9) unstable; urgency=low + + * Updated to new python policy (closes: #373352) + * Updated standards to 3.7.2 + + -- Alexandre Fayolle Thu, 15 Jun 2006 17:10:49 +0200 + +python-scipy (0.3.2-8) unstable; urgency=low + + * Changed dependency on libwxgtk2.4-1-python to python-wxgtk2.4 (closes: #333795) + * Added cow progress bar fix by Glen W. Mabey (closes: #322796) + + -- Alexandre Fayolle Tue, 8 Nov 2005 11:56:51 +0100 + +python-scipy (0.3.2-7) unstable; urgency=low + + * Depend on libwxgtk2.4-1-python due to new C++ ABI. + * Do not depend on obsolete blas-dev (Closes: #320441) + * Drop the python2.2 version due to python2.2-numeric removal. + * Applied Andreas Jochens' patch fixing gcc4.0 storage class + error (Closes: #302598) + + -- José Fonseca Sun, 31 Jul 2005 11:11:42 +0100 + +python-scipy (0.3.2-6) unstable; urgency=low + + * Added a Suggests: python2.X-profiler in debian/control, made the + import of pstats optional by patching stats/__init__.py + (Closes: #296796) + + -- Alexandre Fayolle Fri, 11 Mar 2005 10:54:35 +0100 + +python-scipy (0.3.2-5) unstable; urgency=low + + * Applied Adam Conrad's patch to allow build on m68k (Closes: #292919) + * Applied Andreas Jochens' patch fixing gcc4.0 incompatibility and + syntax error in debian/control (Closes: #288181) + + -- Alexandre Fayolle Thu, 17 Feb 2005 14:49:03 +0100 + +python-scipy (0.3.2-4) unstable; urgency=low + + * Build for python 2.4. + + -- José Fonseca Mon, 24 Jan 2005 12:25:16 +0000 + +python-scipy (0.3.2-3) unstable; urgency=low + + * fixed build dependencies on arm (Closes: #277897) + + -- Alexandre Fayolle Sat, 23 Oct 2004 11:28:51 +0200 + +python-scipy (0.3.2-2) unstable; urgency=low + + * Updated package description + * removed scipy.xplt on hppa, s390, ia64, mips, mipsel (Closes: #277485) + * Added note about the missing module in README.Debian + + -- Alexandre Fayolle Fri, 22 Oct 2004 15:05:00 +0200 + +python-scipy (0.3.2-1) unstable; urgency=low + + * New version. + + -- José Fonseca Mon, 18 Oct 2004 16:28:16 +0100 + +python-scipy (0.3.0+266.4239-1) unstable; urgency=low + + * Updated to release. + * Recommends c++-compiler. + * Dropped python2.1 support. + * Official package (closes: #126037). + * Added Alexandre Fayolle and Marco Presi as uploaders + * Added missing build dependencies + + -- Alexandre Fayolle Mon, 13 Sep 2004 23:04:34 +0200 + +python-scipy (0.2.0+cvs20031002-1) unstable; urgency=low + + * Moved scipy_core into a seperate package. + * Default to python-2.3. + + -- José Fonseca Thu, 02 Oct 2003 13:31:30 +0100 + +python-scipy (0.2.0+alpha144.4350-1) unstable; urgency=low + + * Initial Release. + + -- José Fonseca Tue, 01 Jul 2003 13:35:03 +0100 diff --git a/control b/control new file mode 100644 index 00000000..576a3bcf --- /dev/null +++ b/control @@ -0,0 +1,96 @@ +Source: scipy +Maintainer: Debian Python Team +Uploaders: Ondrej Certik , + David Cournapeau , + Varun Hiremath +Section: python +Priority: optional +Build-Depends: cython3 (>= 0.29.21~), + cython3 (<< 3.0), + debhelper-compat (= 13), + dh-sequence-python3, + pybuild-plugin-pyproject, + gfortran, + libblas-dev, + liblapack-dev, + liblbfgsb-dev, + libsuitesparse-dev, + python3-mesonpy, + pkg-config, + python3-all-dev, + python3-decorator, + python3-numpy (>= 1:1.21.4), + python3-pooch, + python3-pybind11 (>= 2.4.3), + python3-pytest, + python3-setuptools, + python3-wheel, + python3-pythran, + python3-pythran (<< 0.13) [!armhf] +Build-Depends-Indep: dvipng, + dh-sequence-sphinxdoc, + python3-doc, + python3-docutils, + python3-matplotlib, + python3-numpydoc, + python3-pydata-sphinx-theme, + python3-sphinx, + python3-sphinx-panels, + python3-sphinx-tabs, + rdfind, + symlinks, + texlive-latex-base, + texlive-latex-extra +Build-Conflicts: git +Standards-Version: 4.6.2 +Homepage: https://www.scipy.org/ +Vcs-Git: https://salsa.debian.org/python-team/packages/scipy.git +Vcs-Browser: https://salsa.debian.org/python-team/packages/scipy +Rules-Requires-Root: no + +Package: python3-scipy +Architecture: any +Multi-Arch: foreign +Depends: python3-decorator, + python3-numpy (>= 1:1.17.3~), + python3-pythran [!armhf], + ${misc:Depends}, + ${python3:Depends}, + ${shlibs:Depends} +Recommends: g++ | c++-compiler, + python3-pil +Suggests: python-scipy-doc +Breaks: python3-skbio (<< 0.5.8-3~) +Description: scientific tools for Python 3 + SciPy supplements the popular NumPy module (python-numpy package), gathering a + variety of high level science and engineering modules together as a single + package. + . + SciPy is a set of Open Source scientific and numeric tools for Python. It + currently supports special functions, integration, ordinary differential + equation (ODE) solvers, gradient optimization, genetic algorithms, parallel + programming tools, an expression-to-C++ compiler for fast execution, and + others. + +Package: python-scipy-doc +Architecture: all +Multi-Arch: foreign +Section: doc +Depends: fonts-open-sans, + libjs-jquery, + libjs-mathjax, + libjs-underscore, + ${misc:Depends}, + ${sphinxdoc:Depends} +Description: scientific library for Python - documentation + SciPy supplements the popular NumPy module (python-numpy package), gathering a + variety of high level science and engineering modules together as a single + package. + . + SciPy is a set of Open Source scientific and numeric tools for Python. It + currently supports special functions, integration, ordinary differential + equation (ODE) solvers, gradient optimization, genetic algorithms, parallel + programming tools, an expression-to-C++ compiler for fast execution, and + others. + . + This package contains documentation for the SciPy library. diff --git a/copyright b/copyright new file mode 100644 index 00000000..c225b27a --- /dev/null +++ b/copyright @@ -0,0 +1,423 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: SciPy +Source: http://www.scipy.org/ + +Files: * +Copyright: 2003-2019 SciPy Developers + 1999-2005 Travis Oliphant + 2001-2002 Enthought, Inc. + 2002 Eric Jones + 2002 Patrick J. Miller + 2002-2003 Jochen Kuepper + 2002-2004 Pearu Peterson + 2002-2005 Jean-Sebastien Roy + 2003-2005 Peter J. Verveer + 2003-2006 Ed Schofield + 2003-2012 SciPy Developers. + 2004 David M. Cooke + 2006 Bart Vandereycken + 2006 BasSw + 2006 Johannes Loehnert + 2007 Andrew D Straw + 2007 John Travers, Robert Hetland + 2007-2008 Damian Eads + 2008 Tiziano Zito + Gary Strangman + 2010 Pauli Virtanen + 2010, 2011 Pim Schellart + 2009 Yosef Meller +License: BSD-3-clause +Comment: the files in scipy/io/tests/data/*.sav are IDL formatted test data files + and can be read with the functions in scipy/io/idl.py + they contain a EULA notice which is likely invalid and ignored by debian, see + also https://lists.debian.org/debian-legal/2014/06/msg00001.html + +Files: doc/source/_static/scipy.css +Copyright: 2009-2017 The MathJax Consortium + 2019 Jonathan Neal "font-family: no-parens" +License: Apache-2.0+MIT + Code snippet "font-family: no-parens" under MIT licence: + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + . + Other parts of scipy.css released under the standard SciPy Apache-2.0 + licence. +Comment: + Code snippet "font-family: no-parens" retrieved + from https://codepen.io/jonneal/pen/bXLEdB (MIT) + +Files: benchmarks/benchmarks/go_benchmark_functions/*.py +Copyright: 2013 Andrea Gavana +License: expat +Comment: Functions for testing global optimizers, + forked from the AMPGO project, https://code.google.com/archive/p/ampgo + +Files: scipy/fft/_pocketfft/* +Copyright: 2010-2019 Max-Planck-Society +License: BSD-3-clause + +Files: scipy/fft/_pocketfft/pocketfft_hdronly.h +Copyright: 2010-2019 Max-Planck-Society, Martin Reinecke + 2019 Peter Bell + 2003,2007-2014 Matteo Frigo, Massachusetts Institute of Technology +License: BSD-3-clause + +Files: scipy/linalg/src/id_dist/* +Copyright: 2014, P.-G. Martinsson, V. Rokhlin, Y. Shkolnisky, M. Tygert +License: BSD-3-clause + +Files: scipy/misc/ascent.dat +Copyright: public-domain +License: public-domain + No permission whatsoever is needed to copy or use public domain works. Public + domain material is available for anyone to use for any purpose, private and + commercial. Public domain works can serve as the foundation for new creative + works. Public domain works can also be copied and distributed without any + permission or paying royalties + +Files: scipy/ndimage/* +Copyright: 2003-2005, Peter J. Verveer +License: BSD-3-clause + +Files: scipy/optimize/_highs/* +Copyright: 2020 ERGO-Code +License: Expat + +Files: scipy/optimize/lbfgsb_src/*.f +Copyright: 2011 Ciyou Zhu, Richard Byrd, and Jorge Nocedal +License: BSD-generic + The version included here (in lbfgsb.f) is 3.0 (released April 25, 2011). It was + written by Ciyou Zhu, Richard Byrd, and Jorge Nocedal . It + carries the following condition for use: + . + """ + This software is freely available, but we expect that all publications + describing work using this software, or all commercial products using it, + quote at least one of the references given below. This software is released + under the BSD License. + . + References + * R. H. Byrd, P. Lu and J. Nocedal. A Limited Memory Algorithm for Bound + Constrained Optimization, (1995), SIAM Journal on Scientific and + Statistical Computing, 16, 5, pp. 1190-1208. + * C. Zhu, R. H. Byrd and J. Nocedal. L-BFGS-B: Algorithm 778: L-BFGS-B, + FORTRAN routines for large scale bound constrained optimization (1997), + ACM Transactions on Mathematical Software, 23, 4, pp. 550 - 560. + * J.L. Morales and J. Nocedal. L-BFGS-B: Remark on Algorithm 778: L-BFGS-B, + FORTRAN routines for large scale bound constrained optimization (2011), + ACM Transactions on Mathematical Software, 38, 1. + """ + +Files: scipy/optimize/lbfgsb_src/lbfgsb.pyf +Copyright: 2004 David M. Cooke + 2012 Joonas Paalasmaa +License: Expat + +Files: scipy/sparse/csgraph/_matching.pyx +Copyright: 1987, A. Volgenant/Amsterdam School of Economics, + University of Amsterdam +License: BSD-3-clause + +Files: scipy/sparse/linalg/_dsolve/SuperLU/* +Copyright: 2003, The Regents of the University of California, + through Lawrence Berkeley National Laboratory (subject to receipt + of any required approvals from U.S. Dept. of Energy) +License: BSD-3-clause + +Files: scipy/sparse/linalg/_eigen/arpack/* +Copyright: 1996-2008 Rice University, + 1996-2008 D.C. Sorensen, R.B. Lehoucq, C. Yang, and K. Maschhoff + 2001-2011 Scilab Enterprises, Allan Cornet, Sylvestre Ledru + 2007 - Sébastien Fabbro (gentoo patch) + 2010 - Jordi Gutiérrez Hermoso (Octave patch) +License: BSD-3-clause + +Files: scipy/spatial/qhull_src/* +Copyright: 1993-2015, The Geometry Center (University of Minnesota) + 1993-2015, C.B. Barber +License: qhullbsd + This software includes Qhull from C.B. Barber and The Geometry Center. + Qhull is copyrighted as noted above. Qhull is free software and may + be obtained via http from www.qhull.org. It may be freely copied, modified, + and redistributed under the following conditions: + . + 1. All copyright notices must remain intact in all files. + . + 2. A copy of this text file must be distributed along with any copies + of Qhull that you redistribute; this includes copies that you have + modified, or copies of programs or other software products that + include Qhull. + . + 3. If you modify Qhull, you must include a notice giving the + name of the person performing the modification, the date of + modification, and the reason for such modification. + . + 4. When distributing modified versions of Qhull, or other software + products that include Qhull, you must provide notice that the original + source code may be obtained as noted above. + . + 5. There is no warranty or other guarantee of fitness for Qhull, it is + provided solely "as is". Bug reports or fixes may be sent to + qhull_bug@qhull.org; the authors may or may not act on them as + they desire. + +Files: scipy/special/cephes/* +Copyright: 1984, 1987, 1989, 2000 Stephen L. 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By copying, installing or otherwise using Python, Licensee + agrees to be bound by the terms and conditions of this License + Agreement. diff --git a/gbp.conf b/gbp.conf new file mode 100644 index 00000000..9280931d --- /dev/null +++ b/gbp.conf @@ -0,0 +1,3 @@ +[DEFAULT] +component = submodules +debian-branch = experimental diff --git a/get-submodules b/get-submodules new file mode 100755 index 00000000..ecd91e01 --- /dev/null +++ b/get-submodules @@ -0,0 +1,41 @@ +#!/bin/sh -e +# According to https://github.com/scipy/scipy/issues/16331 +# some git submodules are needed to build scipy since version 1.9.x +# This script clones the scipy repository initialises the submodules +# and creates a submodules tarball + +COMPONENT=submodules +EXT=gz + +if [ $(basename $PWD) = "debian" ] ; then + cd .. +fi + +VERSION=$(dpkg-parsechangelog | grep '^Version' | cut -d' ' -f2 | cut -f1 -d-) + +TMPDIR=$(mktemp -d /tmp/scipy.XXXXXX) +cd $TMPDIR +git clone https://github.com/scipy/scipy +cd scipy +git submodule update --init + +MODULES=$(grep 'path =' .gitmodules | sed 's/^.*path = *//') +set -x +mkdir ../scipy-${VERSION} +cd ../scipy-${VERSION} +for m in $MODULES ; do + mkdir -p $m + rsync -a -v ../scipy/$m $(dirname $m) +done +cd .. +pwd + +tar caf scipy_${VERSION}.orig-${COMPONENT}.tar.${EXT} scipy-${VERSION} + +cat < +Date: Sun, 18 Dec 2022 10:33:23 +0100 +Subject: Don't treat warnings as errors in pytest + +--- + pytest.ini | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/pytest.ini b/pytest.ini +index a4deb42..3438da8 100644 +--- a/pytest.ini ++++ b/pytest.ini +@@ -3,7 +3,6 @@ addopts = -l + junit_family=xunit2 + + filterwarnings = +- error + always::scipy._lib._testutils.FPUModeChangeWarning + ignore:.*deprecated and ignored since IPython.*:DeprecationWarning + once:.*LAPACK bug 0038.*:RuntimeWarning diff --git a/patches/0009-Remove-some-documentation-referencing-the-source.patch b/patches/0009-Remove-some-documentation-referencing-the-source.patch new file mode 100644 index 00000000..5b5b355b --- /dev/null +++ b/patches/0009-Remove-some-documentation-referencing-the-source.patch @@ -0,0 +1,125 @@ +From: Jochen Sprickerhof +Date: Tue, 20 Dec 2022 09:45:22 +0100 +Subject: Remove some documentation referencing the source + +These break in sbuild with: + +Traceback (most recent call last): + File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 281, in build_main + app.build(args.force_all, args.filenames) + File "/usr/lib/python3/dist-packages/sphinx/application.py", line 341, in build + self.builder.build_update() + File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 310, in build_update + self.build(to_build, + File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 376, in build + self.write(docnames, list(updated_docnames), method) + File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 571, in write + self._write_serial(sorted(docnames)) + File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 574, in _write_serial + with logging.pending_warnings(): + File "/usr/lib/python3.10/contextlib.py", line 142, in __exit__ + next(self.gen) + File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 218, in pending_warnings + memhandler.flushTo(logger) + File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 183, in flushTo + logger.handle(record) + File "/usr/lib/python3.10/logging/__init__.py", line 1634, in handle + self.callHandlers(record) + File "/usr/lib/python3.10/logging/__init__.py", line 1696, in callHandlers + hdlr.handle(record) + File "/usr/lib/python3.10/logging/__init__.py", line 964, in handle + rv = self.filter(record) + File "/usr/lib/python3.10/logging/__init__.py", line 821, in filter + result = f.filter(record) + File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 499, in filter + record.location = get_node_location(location) + File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 519, in get_node_location + source = abspath(source) + File "/usr/lib/python3/dist-packages/sphinx/util/osutil.py", line 136, in abspath + pathdir = path.abspath(pathdir) + File "/usr/lib/python3.10/posixpath.py", line 378, in abspath + path = os.fspath(path) +TypeError: expected str, bytes or os.PathLike object, not StringList +--- + doc/source/reference/optimize.qap-2opt.rst | 8 -------- + doc/source/reference/optimize.qap-faq.rst | 8 -------- + doc/source/reference/sparse.linalg.svds-arpack.rst | 8 -------- + doc/source/reference/sparse.linalg.svds-lobpcg.rst | 8 -------- + doc/source/reference/sparse.linalg.svds-propack.rst | 8 -------- + 5 files changed, 40 deletions(-) + delete mode 100644 doc/source/reference/optimize.qap-2opt.rst + delete mode 100644 doc/source/reference/optimize.qap-faq.rst + delete mode 100644 doc/source/reference/sparse.linalg.svds-arpack.rst + delete mode 100644 doc/source/reference/sparse.linalg.svds-lobpcg.rst + delete mode 100644 doc/source/reference/sparse.linalg.svds-propack.rst + +diff --git a/doc/source/reference/optimize.qap-2opt.rst b/doc/source/reference/optimize.qap-2opt.rst +deleted file mode 100644 +index f2ac70e..0000000 +--- a/doc/source/reference/optimize.qap-2opt.rst ++++ /dev/null +@@ -1,8 +0,0 @@ +-.. _optimize.qap-2opt: +- +-quadratic_assignment(method='2opt') +----------------------------------------- +- +-.. scipy-optimize:function:: scipy.optimize.quadratic_assignment +- :impl: scipy.optimize._qap._quadratic_assignment_2opt +- :method: 2opt +diff --git a/doc/source/reference/optimize.qap-faq.rst b/doc/source/reference/optimize.qap-faq.rst +deleted file mode 100644 +index 385274a..0000000 +--- a/doc/source/reference/optimize.qap-faq.rst ++++ /dev/null +@@ -1,8 +0,0 @@ +-.. _optimize.qap-faq: +- +-quadratic_assignment(method='faq') +----------------------------------------- +- +-.. scipy-optimize:function:: scipy.optimize.quadratic_assignment +- :impl: scipy.optimize._qap._quadratic_assignment_faq +- :method: faq +diff --git a/doc/source/reference/sparse.linalg.svds-arpack.rst b/doc/source/reference/sparse.linalg.svds-arpack.rst +deleted file mode 100644 +index 6651c94..0000000 +--- a/doc/source/reference/sparse.linalg.svds-arpack.rst ++++ /dev/null +@@ -1,8 +0,0 @@ +-.. _sparse.linalg.svds-arpack: +- +-svds(solver='arpack') +----------------------------------------- +- +-.. scipy-optimize:function:: scipy.sparse.linalg.svds +- :impl: scipy.sparse.linalg._eigen._svds_doc._svds_arpack_doc +- :method: arpack +diff --git a/doc/source/reference/sparse.linalg.svds-lobpcg.rst b/doc/source/reference/sparse.linalg.svds-lobpcg.rst +deleted file mode 100644 +index 52e91e6..0000000 +--- a/doc/source/reference/sparse.linalg.svds-lobpcg.rst ++++ /dev/null +@@ -1,8 +0,0 @@ +-.. _sparse.linalg.svds-lobpcg: +- +-svds(solver='lobpcg') +----------------------------------------- +- +-.. scipy-optimize:function:: scipy.sparse.linalg.svds +- :impl: scipy.sparse.linalg._eigen._svds_doc._svds_lobpcg_doc +- :method: lobpcg +diff --git a/doc/source/reference/sparse.linalg.svds-propack.rst b/doc/source/reference/sparse.linalg.svds-propack.rst +deleted file mode 100644 +index ac282f9..0000000 +--- a/doc/source/reference/sparse.linalg.svds-propack.rst ++++ /dev/null +@@ -1,8 +0,0 @@ +-.. _sparse.linalg.svds-propack: +- +-svds(solver='propack') +----------------------------------------- +- +-.. scipy-optimize:function:: scipy.sparse.linalg.svds +- :impl: scipy.sparse.linalg._eigen._svds_doc._svds_propack_doc +- :method: propack diff --git a/patches/0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch b/patches/0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch new file mode 100644 index 00000000..ebe68bb6 --- /dev/null +++ b/patches/0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch @@ -0,0 +1,25 @@ +From: Jochen Sprickerhof +Date: Tue, 20 Dec 2022 19:29:15 +0100 +Subject: Allow test_svds_parameter_k_which to fail on armel + +--- + scipy/sparse/linalg/_eigen/tests/test_svds.py | 3 +++ + 1 file changed, 3 insertions(+) + +--- a/scipy/sparse/linalg/_eigen/tests/test_svds.py ++++ b/scipy/sparse/linalg/_eigen/tests/test_svds.py +@@ -1,4 +1,5 @@ + import os ++import platform + import re + import copy + import numpy as np +@@ -283,6 +284,8 @@ class SVDSCommonTests: + _check_svds(A, k, *res, which=which, atol=8e-10) + + # loop instead of parametrize for simplicity ++ @pytest.mark.xfail(platform.machine() == 'armv8l', ++ reason="fails on armel") + def test_svds_parameter_tol(self): + if self.solver == 'propack': + if not has_propack: diff --git a/patches/0018-Drop-intersphinx.patch b/patches/0018-Drop-intersphinx.patch new file mode 100644 index 00000000..3018fa27 --- /dev/null +++ b/patches/0018-Drop-intersphinx.patch @@ -0,0 +1,18 @@ +From: Jochen Sprickerhof +Date: Tue, 3 Jan 2023 14:35:03 +0100 +Subject: Drop intersphinx + +--- + doc/source/conf.py | 1 - + 1 file changed, 1 deletion(-) + +--- a/doc/source/conf.py ++++ b/doc/source/conf.py +@@ -42,7 +42,6 @@ extensions = [ + 'sphinx.ext.autosummary', + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', +- 'sphinx.ext.intersphinx', + 'numpydoc', + 'sphinx_design', + 'scipyoptdoc', diff --git a/patches/Use-system-LBFGSB.patch b/patches/Use-system-LBFGSB.patch new file mode 100644 index 00000000..6d7f9177 --- /dev/null +++ b/patches/Use-system-LBFGSB.patch @@ -0,0 +1,46 @@ +From: Gard Spreemann +Date: Sun, 29 Jan 2023 19:55:15 +0100 +Subject: Use system LBFGSB. + +--- + scipy/optimize/meson.build | 5 +---- + scipy/optimize/setup.py | 4 +++- + 2 files changed, 4 insertions(+), 5 deletions(-) + +diff --git a/scipy/optimize/meson.build b/scipy/optimize/meson.build +index c7079e7..78a006f 100644 +--- a/scipy/optimize/meson.build ++++ b/scipy/optimize/meson.build +@@ -100,15 +100,12 @@ lbfgsb_module = custom_target('lbfgsb_module', + + _lbfgsb = py3.extension_module('_lbfgsb', + [ +- 'lbfgsb_src/lbfgsb.f', +- 'lbfgsb_src/linpack.f', +- 'lbfgsb_src/timer.f', + lbfgsb_module, + ], + c_args: numpy_nodepr_api, + fortran_args: fortran_ignore_warnings, + include_directories: [inc_np, inc_f2py], +- link_args: version_link_args, ++ link_args: version_link_args + ['-llbfgsb'], + dependencies: [lapack, fortranobject_dep], + install: true, + link_language: 'fortran', +diff --git a/scipy/optimize/setup.py b/scipy/optimize/setup.py +index c24ef50..1dabc2b 100644 +--- a/scipy/optimize/setup.py ++++ b/scipy/optimize/setup.py +@@ -64,8 +64,10 @@ def configuration(parent_package='', top_path=None): + pre_build_hook = None + + lapack = combine_dict(lapack, numpy_nodepr_api) ++ lapack.setdefault('libraries', []) ++ lapack['libraries'].append('lbfgsb') + +- sources = ['lbfgsb.pyf', 'lbfgsb.f', 'linpack.f', 'timer.f'] ++ sources = ['lbfgsb.pyf'] + ext = config.add_extension('_lbfgsb', + sources=[join('lbfgsb_src', x) + for x in sources], diff --git a/patches/build_sh4_FE.patch b/patches/build_sh4_FE.patch new file mode 100644 index 00000000..e53dd944 --- /dev/null +++ b/patches/build_sh4_FE.patch @@ -0,0 +1,15 @@ +--- a/scipy/special/_round.h ++++ b/scipy/special/_round.h +@@ -68,5 +68,12 @@ int fegetround() + + #endif + ++/* SH4 is not C99 compliant, see https://github.com/scipy/scipy/issues/15584 */ ++#ifndef FE_UPWARD ++#define FE_UPWARD -1 ++#endif ++#ifndef FE_DOWNWARD ++#define FE_DOWNWARD -1 ++#endif + + #endif /* _round.h */ diff --git a/patches/docs_no_sphinx_design.patch b/patches/docs_no_sphinx_design.patch new file mode 100644 index 00000000..65b07fda --- /dev/null +++ b/patches/docs_no_sphinx_design.patch @@ -0,0 +1,335 @@ +Index: scipy/doc/source/dev/contributor/building.rst +=================================================================== +--- scipy.orig/doc/source/dev/contributor/building.rst 2023-01-19 18:02:21.338559648 +0100 ++++ scipy/doc/source/dev/contributor/building.rst 2023-01-19 18:02:21.334559614 +0100 +@@ -25,9 +25,9 @@ + You can skip these steps if you are using ``conda``, as these dependencies + will be installed automatically. + +-.. tab-set:: ++.. note:: + +- .. tab-item:: Linux ++ Linux + + If you want to use the system Python and ``pip``, you will need: + +@@ -41,9 +41,9 @@ + `ATLAS `__ and + `MKL `__. + +- .. tab-set:: ++ .. note:: + +- .. tab-item:: Debian/Ubuntu Linux ++ Debian/Ubuntu Linux + + .. note:: + +@@ -67,7 +67,7 @@ + See also :ref:`ubuntu-guide`. + + +- .. tab-item:: Fedora ++ Fedora + + To install SciPy build requirements, you can do:: + +@@ -81,7 +81,7 @@ + advantage that new dependencies or updates to required versions are + handled by the package managers. + +- .. tab-item:: CentOS/RHEL ++ CentOS/RHEL + + To install SciPy build requirements, you can do:: + +@@ -95,7 +95,7 @@ + advantage that new dependencies or updates to required versions are + handled by the package managers. + +- .. tab-item:: Arch ++ Arch + + To install SciPy build requirements, you can do:: + +@@ -115,7 +115,7 @@ + If you are using conda, these dependencies can be installed in the conda + environment itself. See :ref:`conda-guide` for more details. + +- .. tab-item:: OSX ++ OSX + + Install Apple Developer Tools. An easy way to do this is to + `open a terminal window `_, +@@ -129,7 +129,7 @@ + `git `_, the software we need to download and manage the + SciPy source code. See also :ref:`build-osx`. + +- .. tab-item:: Windows ++ Windows + + See :ref:`build-windows`. + +Index: scipy/doc/source/dev/dev_quickstart.rst +=================================================================== +--- scipy.orig/doc/source/dev/dev_quickstart.rst 2023-01-19 18:02:21.338559648 +0100 ++++ scipy/doc/source/dev/dev_quickstart.rst 2023-01-19 18:02:21.334559614 +0100 +@@ -47,9 +47,9 @@ + + Next, set up your development environment. + +-.. tab-set:: ++.. note:: + +- .. tab-item:: conda ++ conda + + With ``conda`` installed (through + `Miniforge or Mambaforge `_, +@@ -66,7 +66,7 @@ + Your command prompt now lists the name of your new environment, like so + ``(scipy-dev)$``. + +- .. tab-item:: pip+venv ++ pip+venv + + **With** :ref:`system-level dependencies ` **installed**, execute + the following commands at the terminal from the base directory of your +Index: scipy/doc/source/getting_started.rst +=================================================================== +--- scipy.orig/doc/source/getting_started.rst 2023-01-19 18:02:21.338559648 +0100 ++++ scipy/doc/source/getting_started.rst 2023-01-19 18:02:21.334559614 +0100 +@@ -7,47 +7,53 @@ + Installation + ------------ + +-.. grid:: 2 ++.. panels:: ++ :card: + install-card ++ :column: col-lg-6 col-md-6 col-sm-12 col-xs-12 p-3 + +- .. grid-item-card:: ++ Working with conda? ++ ^^^^^^^^^^^^^^^^^^^ + +- Working with conda? +- ^^^^^^^^^^^^^^^^^^^ ++ SciPy is part of the `Anaconda `__ ++ distribution and can be installed with Anaconda or Miniconda: + +- SciPy is part of the `Anaconda `__ +- distribution and can be installed with Anaconda or Miniconda: ++ ++++++++++++++++++++++ + +- ++++++++++++++++++++++ ++ .. code-block:: bash + +- .. code-block:: bash ++ conda install scipy + +- conda install scipy ++ --- + +- .. grid-item-card:: ++ Prefer pip? ++ ^^^^^^^^^^^ + +- Prefer pip? +- ^^^^^^^^^^^ ++ SciPy can be installed via pip from `PyPI `__. + +- SciPy can be installed via pip from `PyPI `__. ++ ++++ + +- ++++ ++ .. code-block:: bash + +- .. code-block:: bash ++ pip install scipy + +- pip install scipy ++ --- ++ :column: col-12 p-3 + +- .. grid-item-card:: +- :columns: 12 ++ In-depth instructions? ++ ^^^^^^^^^^^^^^^^^^^^^^ + +- In-depth instructions? +- ^^^^^^^^^^^^^^^^^^^^^^ ++ Installing a specific version? Installing from source? Check the advanced ++ installation page. + +- Installing a specific version? Installing from source? Check the +- installation page. ++ .. container:: custom-button + +- .. container:: custom-button ++ :ref:`Learn more ` + +- `Learn more `__ ++.. toctree:: ++ :maxdepth: 1 ++ :hidden: ++ ++ install_upgrade + + Tutorials + --------- +Index: scipy/doc/source/index.rst +=================================================================== +--- scipy.orig/doc/source/index.rst 2023-01-19 18:02:21.338559648 +0100 ++++ scipy/doc/source/index.rst 2023-01-19 18:02:21.334559614 +0100 +@@ -20,81 +20,75 @@ + **SciPy** (pronounced "Sigh Pie") is an open-source software for mathematics, + science, and engineering. + +-.. grid:: 2 ++.. panels:: ++ :card: + intro-card text-center ++ :column: col-lg-6 col-md-6 col-sm-6 col-xs-12 d-flex + +- .. grid-item-card:: +- :img-top: _static/index_getting_started.png ++ --- ++ :img-top: _static/index_getting_started.png + +- Getting started +- ^^^^^^^^^^^^^^^ ++ Getting started ++ ^^^^^^^^^^^^^^^ + +- New to *SciPy*? Check out the getting started guides. They contain an +- introduction to *SciPy's* main concepts and links to additional tutorials. ++ New to *SciPy*? Check out the getting started guides. They contain an ++ introduction to *SciPy'* main concepts and links to additional tutorials. + +- +++ ++ +++ + +- .. button-ref:: getting_started_ref +- :expand: +- :color: secondary +- :click-parent: ++ .. link-button:: getting_started_ref ++ :type: ref ++ :text: To the getting started guides ++ :classes: btn-block btn-secondary stretched-link + +- To the getting started guides ++ --- ++ :img-top: _static/index_user_guide.png + +- .. grid-item-card:: +- :img-top: _static/index_user_guide.png ++ User guide ++ ^^^^^^^^^^ + +- User guide +- ^^^^^^^^^^ ++ The user guide provides in-depth information on the ++ key concepts of SciPy with useful background information and explanation. + +- The user guide provides in-depth information on the +- key concepts of SciPy with useful background information and explanation. ++ +++ + +- +++ ++ .. link-button:: user_guide ++ :type: ref ++ :text: To the user guide ++ :classes: btn-block btn-secondary stretched-link + +- .. button-ref:: user_guide +- :expand: +- :color: secondary +- :click-parent: ++ --- ++ :img-top: _static/index_api.png + +- To the user guide ++ API reference ++ ^^^^^^^^^^^^^ + +- .. grid-item-card:: +- :img-top: _static/index_api.png ++ The reference guide contains a detailed description of ++ the SciPy API. The reference describes how the methods work and which parameters can ++ be used. It assumes that you have an understanding of the key concepts. + +- API reference +- ^^^^^^^^^^^^^ ++ +++ + +- The reference guide contains a detailed description of +- the SciPy API. The reference describes how the methods work and which parameters can +- be used. It assumes that you have an understanding of the key concepts. ++ .. link-button:: scipy-api ++ :type: ref ++ :text: To the reference guide ++ :classes: btn-block btn-secondary stretched-link + +- +++ ++ --- ++ :img-top: _static/index_contribute.png + +- .. button-ref:: scipy-api +- :expand: +- :color: secondary +- :click-parent: ++ Developer guide ++ ^^^^^^^^^^^^^^^ + +- To the reference guide ++ Saw a typo in the documentation? Want to improve ++ existing functionalities? The contributing guidelines will guide ++ you through the process of improving SciPy. + +- .. grid-item-card:: +- :img-top: _static/index_contribute.png ++ +++ + +- Developer guide +- ^^^^^^^^^^^^^^^ +- +- Saw a typo in the documentation? Want to improve +- existing functionalities? The contributing guidelines will guide +- you through the process of improving SciPy. +- +- +++ +- +- .. button-ref:: scipy-development +- :expand: +- :color: secondary +- :click-parent: +- +- To the development guide ++ .. link-button:: scipy-development ++ :type: ref ++ :text: To the development guide ++ :classes: btn-block btn-secondary stretched-link + + .. toctree:: + :maxdepth: 1 +Index: scipy/doc/source/conf.py +=================================================================== +--- scipy.orig/doc/source/conf.py 2023-01-19 18:02:21.338559648 +0100 ++++ scipy/doc/source/conf.py 2023-01-19 18:03:10.810990305 +0100 +@@ -43,6 +43,7 @@ + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'numpydoc', ++ 'sphinx_panels', + 'scipyoptdoc', + 'doi_role', + 'matplotlib.sphinxext.plot_directive', +@@ -148,6 +149,7 @@ + r"OpenSSL\.rand is deprecated", # OpenSSL package in linkcheck + r"distutils Version", # distutils + r"the imp module is deprecated", # invoke (via pooch) ++ r"open_text is deprecated", # sphinx_panels + ): + warnings.filterwarnings( # deal with other modules having bad imports + 'ignore', message=".*" + key, category=DeprecationWarning) diff --git a/patches/find_cython3.patch b/patches/find_cython3.patch new file mode 100644 index 00000000..4ca0a652 --- /dev/null +++ b/patches/find_cython3.patch @@ -0,0 +1,30 @@ +Author: Andreas Tille +Last-Update: Tue, 13 Dec 2022 14:11:49 +0100 +Description: cython is actually cython3 + +Index: scipy/meson.build +=================================================================== +--- scipy.orig/meson.build 2023-01-18 02:19:58.182097975 +0100 ++++ scipy/meson.build 2023-01-18 02:19:58.182097975 +0100 +@@ -112,7 +112,7 @@ + version_link_args = [] + endif + +-cython = find_program('cython') ++cython = find_program('cython3') + generate_f2pymod = files('tools/generate_f2pymod.py') + tempita = files('scipy/_build_utils/tempita.py') + +Index: scipy/scipy/_build_utils/cythoner.py +=================================================================== +--- scipy.orig/scipy/_build_utils/cythoner.py 2023-01-17 18:14:49.363744124 +0100 ++++ scipy/scipy/_build_utils/cythoner.py 2023-01-18 02:20:17.462283940 +0100 +@@ -17,7 +17,7 @@ + def main(): + in_fname, out_fname = (op.abspath(p) for p in sys.argv[1:3]) + +- sbp.run(['cython', '-3', '--fast-fail', ++ sbp.run(['cython3', '-3', '--fast-fail', + '--output-file', out_fname, + '--include-dir', os.getcwd()] + + sys.argv[3:] + [in_fname], diff --git a/patches/fix_cast_PR17726.patch b/patches/fix_cast_PR17726.patch new file mode 100644 index 00000000..74bb28b4 --- /dev/null +++ b/patches/fix_cast_PR17726.patch @@ -0,0 +1,62 @@ +From 0a6f149beaea60c4b70923e861e8fd0d9e6e5747 Mon Sep 17 00:00:00 2001 +From: Evgeni Burovski +Date: Thu, 5 Jan 2023 12:29:15 +0300 +Subject: [PATCH 1/2] BUG: interpolate/RGI: upcast float32 to float64 + +--- + scipy/interpolate/_rgi.py | 1 + + scipy/interpolate/tests/test_rgi.py | 27 +++++++++++++++++++++++++++ + 2 files changed, 28 insertions(+) + +Index: scipy/scipy/interpolate/_rgi.py +=================================================================== +--- scipy.orig/scipy/interpolate/_rgi.py 2023-02-07 00:46:37.290167643 +0100 ++++ scipy/scipy/interpolate/_rgi.py 2023-02-07 00:46:37.290167643 +0100 +@@ -332,6 +332,7 @@ + indices, norm_distances = self._find_indices(xi.T) + if (ndim == 2 and hasattr(self.values, 'dtype') and + self.values.ndim == 2 and self.values.flags.writeable and ++ self.values.dtype in (np.float64, np.complex128) and + self.values.dtype.byteorder == '='): + # until cython supports const fused types, the fast path + # cannot support non-writeable values +Index: scipy/scipy/interpolate/tests/test_rgi.py +=================================================================== +--- scipy.orig/scipy/interpolate/tests/test_rgi.py 2023-02-07 00:46:37.290167643 +0100 ++++ scipy/scipy/interpolate/tests/test_rgi.py 2023-02-07 00:46:37.290167643 +0100 +@@ -588,6 +588,35 @@ + v2 = np.expand_dims(vs, axis=0) + assert_allclose(v, v2, atol=1e-14, err_msg=method) + ++ @pytest.mark.parametrize( ++ "dtype", ++ [np.float32, np.float64, np.complex64, np.complex128] ++ ) ++ @pytest.mark.parametrize("xi_dtype", [np.float32, np.float64]) ++ def test_float32_values(self, dtype, xi_dtype): ++ # regression test for gh-17718: values.dtype=float32 fails ++ def f(x, y): ++ return 2 * x**3 + 3 * y**2 ++ ++ x = np.linspace(1, 4, 11) ++ y = np.linspace(4, 7, 22) ++ ++ xg, yg = np.meshgrid(x, y, indexing='ij', sparse=True) ++ data = f(xg, yg) ++ ++ data = data.astype(dtype) ++ ++ interp = RegularGridInterpolator((x, y), data) ++ ++ pts = np.array([[2.1, 6.2], ++ [3.3, 5.2]], dtype=xi_dtype) ++ ++ # the values here are just what the call returns; the test checks that ++ # that the call succeeds at all, instead of failing with cython not ++ # having a float32 kernel ++ assert_allclose(interp(pts), [134.10469388, 153.40069388], atol=1e-7) ++ ++ + class MyValue: + """ + Minimal indexable object diff --git a/patches/fix_highs_atomic_PR17777.patch b/patches/fix_highs_atomic_PR17777.patch new file mode 100644 index 00000000..11dafdb7 --- /dev/null +++ b/patches/fix_highs_atomic_PR17777.patch @@ -0,0 +1,43 @@ +Index: scipy/scipy/meson.build +=================================================================== +--- scipy.orig/scipy/meson.build 2023-01-23 17:24:52.527541297 +0100 ++++ scipy/scipy/meson.build 2023-01-23 17:24:52.527541297 +0100 +@@ -292,6 +292,25 @@ + use_math_defines = [] + endif + ++# Determine whether it is necessary to link libatomic. This could be the case ++# e.g. on 32-bit platforms when atomic operations are used on 64-bit types. ++# The check is copied from Mesa . ++atomic_dep = dependency('', required : false) ++if cc.get_id() != 'msvc' ++ if not cc.links(''' ++ #include ++ int main() { ++ struct { ++ uint64_t *v; ++ } x; ++ return (int)__atomic_load_n(x.v, __ATOMIC_ACQUIRE) & ++ (int)__atomic_add_fetch(x.v, (uint64_t)1, __ATOMIC_ACQ_REL); ++ }''', ++ name : 'GCC atomic builtins required -latomic') ++ atomic_dep = cc.find_library('atomic') ++ endif ++endif ++ + # Suppress warning for deprecated Numpy API. + # (Suppress warning messages emitted by #warning directives). + # Replace with numpy_nodepr_api after Cython 3.0 is out +Index: scipy/scipy/optimize/_highs/meson.build +=================================================================== +--- scipy.orig/scipy/optimize/_highs/meson.build 2023-01-23 17:24:52.527541297 +0100 ++++ scipy/scipy/optimize/_highs/meson.build 2023-01-23 17:24:52.527541297 +0100 +@@ -237,7 +237,7 @@ + '../../_lib/highs/src/lp_data/', + '../../_lib/highs/src/util/' + ], +- dependencies: thread_dep, ++ dependencies: [thread_dep, atomic_dep], + link_args: version_link_args, + link_with: [highs_lib, ipx_lib, basiclu_lib], + cpp_args: [highs_flags, highs_define_macros, cython_c_args], diff --git a/patches/manage_docs.patch b/patches/manage_docs.patch new file mode 100644 index 00000000..3bdd29a3 --- /dev/null +++ b/patches/manage_docs.patch @@ -0,0 +1,37 @@ +Index: scipy/doc/source/conf.py +=================================================================== +--- scipy.orig/doc/source/conf.py 2023-01-19 18:30:16.581879951 +0100 ++++ scipy/doc/source/conf.py 2023-01-19 18:31:24.970440822 +0100 +@@ -43,7 +43,6 @@ + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'numpydoc', +- 'sphinx_design', + 'scipyoptdoc', + 'doi_role', + 'matplotlib.sphinxext.plot_directive', +@@ -141,13 +140,14 @@ + # be strict about warnings in our examples, we should write clean code + # (exceptions permitted for pedagogical purposes below) + warnings.resetwarnings() +-warnings.filterwarnings('error') ++warnings.filterwarnings('default') + # allow these and show them + warnings.filterwarnings('default', module='sphinx') # internal warnings + # global weird ones that can be safely ignored + for key in ( + r"OpenSSL\.rand is deprecated", # OpenSSL package in linkcheck + r"distutils Version", # distutils ++ r"the imp module is deprecated", # invoke (via pooch) + ): + warnings.filterwarnings( # deal with other modules having bad imports + 'ignore', message=".*" + key, category=DeprecationWarning) +@@ -181,7 +181,7 @@ + html_theme_options = { + "github_url": "https://github.com/scipy/scipy", + "twitter_url": "https://twitter.com/SciPy_team", +- "navbar_end": ["theme-switcher", "version-switcher", "navbar-icon-links"], ++# "navbar_end": ["theme-switcher", "version-switcher", "navbar-icon-links"], + "switcher": { + "json_url": "https://scipy.github.io/devdocs/_static/version_switcher.json", + "version_match": version, diff --git a/patches/manage_tests.patch b/patches/manage_tests.patch new file mode 100644 index 00000000..d793c169 --- /dev/null +++ b/patches/manage_tests.patch @@ -0,0 +1,382 @@ +Index: scipy/scipy/linalg/tests/test_solvers.py +=================================================================== +--- scipy.orig/scipy/linalg/tests/test_solvers.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/linalg/tests/test_solvers.py 2023-01-23 22:46:22.470014403 +0100 +@@ -306,7 +306,7 @@ + for ind, case in enumerate(cases): + _test_factory(case, min_decimal[ind]) + +- ++@pytest.mark.skip(reason="test fails, see https://github.com/scipy/scipy/issues/14517") + def test_solve_discrete_are(): + + cases = [ +Index: scipy/scipy/optimize/tests/test_optimize.py +=================================================================== +--- scipy.orig/scipy/optimize/tests/test_optimize.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/optimize/tests/test_optimize.py 2023-01-23 22:46:22.470014403 +0100 +@@ -1001,6 +1001,7 @@ + + assert_allclose(v, self.func(self.solution), rtol=tol) + ++ @pytest.mark.skip(reason="contradictory: expected to fail but succeeds") + def test_minimize_l_bfgs_maxls(self): + # check that the maxls is passed down to the Fortran routine + sol = optimize.minimize(optimize.rosen, np.array([-1.2, 1.0]), +Index: scipy/scipy/linalg/tests/test_lapack.py +=================================================================== +--- scipy.orig/scipy/linalg/tests/test_lapack.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/linalg/tests/test_lapack.py 2023-01-23 22:46:22.474014482 +0100 +@@ -1023,7 +1023,7 @@ + + eig, _, info = syevd(a) + assert_(info == 0) +- assert_allclose(eig, eig_gvd, rtol=1e-4) ++ assert_allclose(eig, eig_gvd, rtol=2e-4) + + + def test_hegst(): +Index: scipy/scipy/interpolate/tests/test_fitpack.py +=================================================================== +--- scipy.orig/scipy/interpolate/tests/test_fitpack.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/interpolate/tests/test_fitpack.py 2023-01-23 22:46:22.474014482 +0100 +@@ -6,6 +6,7 @@ + assert_almost_equal, assert_array_almost_equal) + from pytest import raises as assert_raises + import pytest ++import platform + from scipy._lib._testutils import check_free_memory + + from scipy.interpolate import RectBivariateSpline +@@ -279,6 +280,7 @@ + def test_order0_diff(self): + assert_raises(ValueError, splder, self.spl, 4) + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armel") + def test_kink(self): + # Should refuse to differentiate splines with kinks + +Index: scipy/scipy/optimize/tests/test_linprog.py +=================================================================== +--- scipy.orig/scipy/optimize/tests/test_linprog.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/optimize/tests/test_linprog.py 2023-01-23 22:46:22.474014482 +0100 +@@ -14,6 +14,7 @@ + from scipy.linalg import LinAlgWarning + import scipy.sparse + import pytest ++import platform + + has_umfpack = True + try: +@@ -605,6 +606,7 @@ + if do_presolve: + assert_equal(res.nit, 0) + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armel") + def test_bounds_infeasible_2(self): + + # Test ill-valued bounds (lower inf, upper -inf) +Index: scipy/scipy/special/tests/test_round.py +=================================================================== +--- scipy.orig/scipy/special/tests/test_round.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/special/tests/test_round.py 2023-01-23 22:46:22.474014482 +0100 +@@ -1,8 +1,14 @@ + import numpy as np + import pytest ++import platform + + from scipy.special import _test_internal + ++machine=platform.machine() ++if ( machine.startswith('arm') or ++ machine=='alpha' or ++ machine=='parisc64' ): ++ pytest.skip("rounding tests known to fail on armel, alpha and hppa", allow_module_level=True) + + @pytest.mark.skipif(not _test_internal.have_fenv(), reason="no fenv()") + def test_add_round_up(): +Index: scipy/scipy/stats/tests/test_stats.py +=================================================================== +--- scipy.orig/scipy/stats/tests/test_stats.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/stats/tests/test_stats.py 2023-01-23 22:46:22.478014561 +0100 +@@ -19,6 +19,7 @@ + assert_array_less) + import pytest + from pytest import raises as assert_raises ++import platform + import numpy.ma.testutils as mat + from numpy import array, arange, float32, float64, power + import numpy as np +@@ -499,6 +500,7 @@ + [1] 1.701815e-09 + """ + ++ @pytest.mark.skipif(platform.machine()=='ppc', reason="test known to fail on powerpc") + def test_basic(self): + fisher_exact = stats.fisher_exact + +@@ -6198,14 +6200,17 @@ + with pytest.raises(ValueError, match='Invalid array input'): + stats.gstd('This should fail as it can not be cast to an array.') + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armel") + def test_raises_value_error_zero_entry(self): + with pytest.raises(ValueError, match='Non positive value'): + stats.gstd(np.append(self.array_1d, [0])) + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armel") + def test_raises_value_error_negative_entry(self): + with pytest.raises(ValueError, match='Non positive value'): + stats.gstd(np.append(self.array_1d, [-1])) + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armel") + def test_raises_value_error_inf_entry(self): + with pytest.raises(ValueError, match='Infinite value'): + stats.gstd(np.append(self.array_1d, [np.inf])) +Index: scipy/scipy/signal/tests/test_spectral.py +=================================================================== +--- scipy.orig/scipy/signal/tests/test_spectral.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/signal/tests/test_spectral.py 2023-01-23 22:46:22.478014561 +0100 +@@ -4,6 +4,7 @@ + assert_array_almost_equal_nulp, suppress_warnings) + import pytest + from pytest import raises as assert_raises ++import platform + + from scipy import signal + from scipy.fft import fftfreq +@@ -94,6 +95,7 @@ + assert_raises(ValueError, periodogram, np.zeros(4, np.complex128), + scaling='foo') + ++ @pytest.mark.skipif(platform.machine().startswith('i686'), reason="test known to fail on i386 linux and hurd") + def test_nd_axis_m1(self): + x = np.zeros(20, dtype=np.float64) + x = x.reshape((2,1,10)) +@@ -104,6 +106,7 @@ + f0, p0 = periodogram(x[0,0,:]) + assert_array_almost_equal_nulp(p0[np.newaxis,:], p[1,:], 60) + ++ @pytest.mark.skipif(platform.machine().startswith('i686'), reason="test known to fail on i386 linux and hurd") + def test_nd_axis_0(self): + x = np.zeros(20, dtype=np.float64) + x = x.reshape((10,2,1)) +Index: scipy/scipy/sparse/linalg/_isolve/tests/test_iterative.py +=================================================================== +--- scipy.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-01-23 22:46:22.482014639 +0100 +@@ -10,6 +10,7 @@ + assert_, assert_allclose, suppress_warnings) + import pytest + from pytest import raises as assert_raises ++import platform + + from numpy import zeros, arange, array, ones, eye, iscomplexobj + from scipy.linalg import norm +@@ -459,6 +460,7 @@ + pytest.param(bicgstab, marks=pytest.mark.xfail), + pytest.param(gcrotmk, marks=pytest.mark.xfail), + pytest.param(tfqmr, marks=pytest.mark.xfail)]) ++@pytest.mark.skipif(platform.machine().startswith('i686'), reason="needs tol=9 not 5 on i386 (linux and hurd)") + def test_maxiter_worsening(solver): + # Check error does not grow (boundlessly) with increasing maxiter. + # This can occur due to the solvers hitting close to breakdown, +Index: scipy/scipy/spatial/tests/test_distance.py +=================================================================== +--- scipy.orig/scipy/spatial/tests/test_distance.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/spatial/tests/test_distance.py 2023-01-23 22:46:22.482014639 +0100 +@@ -1176,7 +1176,7 @@ + def test_pdist_jensenshannon_iris(self): + if _is_32bit(): + # Test failing on 32-bit Linux on Azure otherwise, see gh-12810 +- eps = 1.5e-10 ++ eps = 2.5e-10 + else: + eps = 1e-12 + +Index: scipy/scipy/spatial/transform/tests/test_rotation.py +=================================================================== +--- scipy.orig/scipy/spatial/transform/tests/test_rotation.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/spatial/transform/tests/test_rotation.py 2023-01-23 22:46:22.482014639 +0100 +@@ -1,4 +1,5 @@ + import pytest ++import platform + + import numpy as np + from numpy.testing import assert_equal, assert_array_almost_equal +@@ -1115,9 +1116,14 @@ + + + def test_align_vectors_single_vector(): ++ if platform.machine().startswith("i686"): ++ # Test failing on 32-bit i386 (linux and hurd) ++ eps = 3e-8 ++ else: ++ eps = 1e-16 + with pytest.warns(UserWarning, match="Optimal rotation is not"): + r_estimate, rmsd = Rotation.align_vectors([[1, -1, 1]], [[1, 1, -1]]) +- assert_allclose(rmsd, 0, atol=1e-16) ++ assert_allclose(rmsd, 0, atol=eps) + + + def test_align_vectors_invalid_input(): +Index: scipy/scipy/io/arff/tests/test_arffread.py +=================================================================== +--- scipy.orig/scipy/io/arff/tests/test_arffread.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/io/arff/tests/test_arffread.py 2023-01-23 22:46:22.482014639 +0100 +@@ -11,6 +11,7 @@ + assert_array_equal, assert_equal, assert_) + import pytest + from pytest import raises as assert_raises ++import platform + + from scipy.io.arff import loadarff + from scipy.io.arff._arffread import read_header, ParseArffError +@@ -97,7 +98,12 @@ + for i in ['yop', 'yap']: + assert_array_almost_equal(data[i], expect_missing[i]) + +- ++machine=platform.machine() ++@pytest.mark.skipif(machine=='s390x' ++ or machine.startswith('ppc') ++ or machine=='parisc64' ++ or machine=='sparc64', ++ reason="test known to fail on s390x, powerpc, ppc64, hppa and sparc64") + class TestNoData: + def test_nodata(self): + # The file nodata.arff has no data in the @DATA section. +Index: scipy/scipy/linalg/tests/test_interpolative.py +=================================================================== +--- scipy.orig/scipy/linalg/tests/test_interpolative.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/linalg/tests/test_interpolative.py 2023-01-23 22:46:22.482014639 +0100 +@@ -36,6 +36,7 @@ + assert_array_equal) + import pytest + from pytest import raises as assert_raises ++import platform + import sys + _IS_32BIT = (sys.maxsize < 2**32) + +@@ -146,6 +147,7 @@ + norm_2_est = pymatrixid.estimate_spectral_norm(A) + assert_allclose(norm_2_est, s[0], rtol=1e-6, atol=1e-8) + ++ @pytest.mark.skipif(platform.machine().startswith('arm'), reason="test known to fail on armhf") + def test_estimate_spectral_norm_diff(self, A): + B = A.copy() + B[:, 0] *= 1.2 +Index: scipy/scipy/fft/tests/test_fftlog.py +=================================================================== +--- scipy.orig/scipy/fft/tests/test_fftlog.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/fft/tests/test_fftlog.py 2023-01-23 22:46:22.486014719 +0100 +@@ -2,6 +2,7 @@ + import numpy as np + from numpy.testing import assert_allclose + import pytest ++import platform + + from scipy.fft._fftlog import fht, ifht, fhtoffset + from scipy.special import poch +@@ -99,6 +100,7 @@ + assert_allclose(a, a_) + + ++@pytest.mark.skipif(platform.machine().startswith('mips64'), reason="test known to fail on mips64el") + def test_fht_special_cases(): + rng = np.random.RandomState(3491349965) + +Index: scipy/scipy/sparse/csgraph/tests/test_shortest_path.py +=================================================================== +--- scipy.orig/scipy/sparse/csgraph/tests/test_shortest_path.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/sparse/csgraph/tests/test_shortest_path.py 2023-01-23 22:46:22.486014719 +0100 +@@ -7,6 +7,7 @@ + NegativeCycleError) + import scipy.sparse + import pytest ++import platform + + directed_G = np.array([[0, 3, 3, 0, 0], + [0, 0, 0, 2, 4], +@@ -314,6 +315,7 @@ + shortest_path(G, method=method) + + ++@pytest.mark.skipif(platform.machine().startswith('mips64'), reason="test known to fail on mips64el") + def test_NaN_warnings(): + with warnings.catch_warnings(record=True) as record: + shortest_path(np.array([[0, 1], [np.nan, 0]])) +Index: scipy/scipy/stats/tests/test_distributions.py +=================================================================== +--- scipy.orig/scipy/stats/tests/test_distributions.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/stats/tests/test_distributions.py 2023-01-23 22:46:22.490014796 +0100 +@@ -2602,6 +2602,7 @@ + assert_(np.isfinite(s)) + assert_(not np.isfinite(k)) + ++ @pytest.mark.skipif(platform.machine().startswith('mips64'), reason="test known to fail on mips64el") + def test_moments_warnings(self): + # no warnings should be generated for dfd = 2, 4, 6, 8 (div by zero) + with warnings.catch_warnings(): +@@ -3918,7 +3919,7 @@ + # for alpha = 1. for linux 32 bit optimize.bisect + # has some issues for .01 and .99 percentile + [ +- 'piecewise', 1e-11, lambda r: ( ++ 'piecewise', 2e-10, lambda r: ( + (r['alpha'] == 1.) & + (not is_linux_32) & + np.isin(r['pct'], pct_range) & +@@ -4032,7 +4033,7 @@ + tests = [ + # piecewise generally good accuracy + [ +- 'piecewise', 1e-12, lambda r: ( ++ 'piecewise', 2e-12, lambda r: ( + np.isin(r['pct'], pct_range) & + np.isin(r['alpha'], alpha_range) & + np.isin(r['beta'], beta_range) & +Index: scipy/runtests.py +=================================================================== +--- scipy.orig/runtests.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/runtests.py 2023-01-23 22:46:22.490014796 +0100 +@@ -322,8 +322,9 @@ + if not os.path.isdir(test_dir): + os.makedirs(test_dir) + +- shutil.copyfile(os.path.join(ROOT_DIR, '.coveragerc'), +- os.path.join(test_dir, '.coveragerc')) ++ if os.path.exists(os.path.join(ROOT_DIR, '.coveragerc')): ++ shutil.copyfile(os.path.join(ROOT_DIR, '.coveragerc'), ++ os.path.join(test_dir, '.coveragerc')) + + cwd = os.getcwd() + try: +Index: scipy/scipy/special/tests/test_orthogonal.py +=================================================================== +--- scipy.orig/scipy/special/tests/test_orthogonal.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/special/tests/test_orthogonal.py 2023-01-23 22:46:22.490014796 +0100 +@@ -549,7 +549,7 @@ + vgq(rootf(170), evalf(170), weightf(170), -1., 1., 5, atol=1e-13) + vgq(rootf(170), evalf(170), weightf(170), -1., 1., 25, atol=1e-12) + vgq(rootf(170), evalf(170), weightf(170), -1., 1., 100, atol=1e-11) +- vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 5, atol=1e-13) ++ vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 5, atol=2e-13) + vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 25, atol=1e-12) + vgq(rootf(170.5), evalf(170.5), weightf(170.5), -1., 1., 100, atol=1e-11) + +Index: scipy/scipy/stats/tests/test_mstats_basic.py +=================================================================== +--- scipy.orig/scipy/stats/tests/test_mstats_basic.py 2023-01-23 22:46:22.494014875 +0100 ++++ scipy/scipy/stats/tests/test_mstats_basic.py 2023-01-23 22:48:18.483977720 +0100 +@@ -1768,8 +1768,8 @@ + r = stats.skewtest(x) + rm = stats.mstats.skewtest(xm) + +- assert_allclose(r[0][0], rm[0][0], rtol=2e-15) +- assert_allclose(r[0][1], rm[0][1], rtol=1e-15) ++ assert_allclose(r[0][0], rm[0][0], rtol=1e-14) ++ assert_allclose(r[0][1], rm[0][1], rtol=1e-14) + + def test_normaltest(self): + with np.errstate(over='raise'), suppress_warnings() as sup: diff --git a/patches/pythran_type_PR16646.patch b/patches/pythran_type_PR16646.patch new file mode 100644 index 00000000..42094266 --- /dev/null +++ b/patches/pythran_type_PR16646.patch @@ -0,0 +1,32 @@ +From 5874244209db676138bea3e1a3b1d32568c57419 Mon Sep 17 00:00:00 2001 +From: serge-sans-paille +Date: Tue, 19 Jul 2022 19:04:28 +0200 +Subject: [PATCH] Have get_index_dtype follow its documentation and return + int32 or int64 + +This also avoids np.intc which is a portability pain. +Adjust group_sparse signature accordingly. + +This should also fix https://github.com/serge-sans-paille/pythran/issues/2002 +--- + scipy/optimize/_group_columns.py | 8 ++++---- + scipy/sparse/_sputils.py | 2 +- + 2 files changed, 5 insertions(+), 5 deletions(-) + +--- a/scipy/optimize/_group_columns.py ++++ b/scipy/optimize/_group_columns.py +@@ -52,10 +52,10 @@ def group_dense(m, n, A): + return groups + + +-#pythran export group_sparse(int, int, int32[], int32[]) +-#pythran export group_sparse(int, int, int64[], int64[]) +-#pythran export group_sparse(int, int, int32[::], int32[::]) +-#pythran export group_sparse(int, int, int64[::], int64[::]) ++# pythran export group_sparse(int, int, int32[] or int32[::], ++# int32[] or int32[::]) ++# pythran export group_sparse(int, int, int64[] or int64[::], ++# int64[] or int64[::]) + def group_sparse(m, n, indices, indptr): + groups = -np.ones(n, dtype=np.intp) + current_group = 0 diff --git a/patches/qhull-lfs.patch b/patches/qhull-lfs.patch new file mode 100644 index 00000000..05c69102 --- /dev/null +++ b/patches/qhull-lfs.patch @@ -0,0 +1,24 @@ +From: Julian Taylor +Date: Mon, 12 Oct 2015 15:17:23 -0700 +Subject: enable large file support + + probably not needed as the file open api of qhull is not available in python +Forwarded: no + +Patch-Name: qhull-lfs.patch +--- + scipy/spatial/setup.py | 3 +++ + 1 file changed, 3 insertions(+) + +--- a/scipy/spatial/setup.py ++++ b/scipy/spatial/setup.py +@@ -52,6 +52,9 @@ def configuration(parent_package='', top + config.add_extension('_qhull', + sources=['_qhull.c', 'qhull_misc.c'] + qhull_src, + **cfg) ++ cfg.setdefault('define_macros', []).append(('_FILE_OFFSET_BITS','64')) ++ cfg.setdefault('define_macros', []).append(('_LARGEFILE_SOURCE','1')) ++ cfg.setdefault('define_macros', []).append(('_LARGEFILE64_SOURCE','1')) + + # cKDTree + ckdtree_src = ['query.cxx', diff --git a/patches/readonly_interpolate_PR17717.patch b/patches/readonly_interpolate_PR17717.patch new file mode 100644 index 00000000..8ac3343f --- /dev/null +++ b/patches/readonly_interpolate_PR17717.patch @@ -0,0 +1,122 @@ +Index: scipy/scipy/interpolate/_rgi.py +=================================================================== +--- scipy.orig/scipy/interpolate/_rgi.py 2023-01-27 14:16:48.632034939 +0100 ++++ scipy/scipy/interpolate/_rgi.py 2023-01-27 14:16:48.620034814 +0100 +@@ -23,11 +23,12 @@ + # input is descending, so make it ascending + descending_dimensions.append(i) + p = np.flip(p) +- p = np.ascontiguousarray(p) + else: + raise ValueError( + "The points in dimension %d must be strictly " + "ascending or descending" % i) ++ # see https://github.com/scipy/scipy/issues/17716 ++ p = np.ascontiguousarray(p) + grid.append(p) + return tuple(grid), tuple(descending_dimensions) + +@@ -330,7 +331,10 @@ + if method == "linear": + indices, norm_distances = self._find_indices(xi.T) + if (ndim == 2 and hasattr(self.values, 'dtype') and +- self.values.ndim == 2): ++ self.values.ndim == 2 and self.values.flags.writeable and ++ self.values.dtype.byteorder == '='): ++ # until cython supports const fused types, the fast path ++ # cannot support non-writeable values + # a fast path + out = np.empty(indices.shape[1], dtype=self.values.dtype) + result = evaluate_linear_2d(self.values, +Index: scipy/scipy/interpolate/_rgi_cython.pyx +=================================================================== +--- scipy.orig/scipy/interpolate/_rgi_cython.pyx 2023-01-27 14:16:48.632034939 +0100 ++++ scipy/scipy/interpolate/_rgi_cython.pyx 2023-01-27 14:16:48.620034814 +0100 +@@ -17,7 +17,7 @@ + @cython.boundscheck(False) + @cython.initializedcheck(False) + def evaluate_linear_2d(double_or_complex[:, :] values, # cannot declare as ::1 +- long[:, :] indices, # unless prior ++ const long[:, :] indices, # unless prior + double[:, :] norm_distances, # np.ascontiguousarray + tuple grid not None, + double_or_complex[:] out): +@@ -72,11 +72,13 @@ + @cython.boundscheck(False) + @cython.cdivision(True) + @cython.initializedcheck(False) +-def find_indices(tuple grid not None, double[:, :] xi): ++def find_indices(tuple grid not None, const double[:, :] xi): ++ # const is required for xi above in case xi is read-only + cdef: + long i, j, grid_i_size + double denom, value +- double[::1] grid_i ++ # const is required in case grid is read-only ++ const double[::1] grid_i + + # Axes to iterate over + long I = xi.shape[0] +Index: scipy/scipy/interpolate/tests/test_rgi.py +=================================================================== +--- scipy.orig/scipy/interpolate/tests/test_rgi.py 2023-01-27 14:16:48.632034939 +0100 ++++ scipy/scipy/interpolate/tests/test_rgi.py 2023-01-27 14:16:48.624034856 +0100 +@@ -933,3 +933,58 @@ + "RegularGridInterpolator has dimension 1") + with assert_raises(ValueError, match=msg): + interpn(points, values, xi) ++ ++ def test_readonly_grid(self): ++ # https://github.com/scipy/scipy/issues/17716 ++ x = np.linspace(0, 4, 5) ++ y = np.linspace(0, 5, 6) ++ z = np.linspace(0, 6, 7) ++ points = (x, y, z) ++ values = np.ones((5, 6, 7)) ++ point = np.array([2.21, 3.12, 1.15]) ++ for d in points: ++ d.flags.writeable = False ++ values.flags.writeable = False ++ point.flags.writeable = False ++ interpn(points, values, point) ++ RegularGridInterpolator(points, values)(point) ++ ++ def test_2d_readonly_grid(self): ++ # https://github.com/scipy/scipy/issues/17716 ++ # test special 2d case ++ x = np.linspace(0, 4, 5) ++ y = np.linspace(0, 5, 6) ++ points = (x, y) ++ values = np.ones((5, 6)) ++ point = np.array([2.21, 3.12]) ++ for d in points: ++ d.flags.writeable = False ++ values.flags.writeable = False ++ point.flags.writeable = False ++ interpn(points, values, point) ++ RegularGridInterpolator(points, values)(point) ++ ++ def test_non_c_contiguous_grid(self): ++ # https://github.com/scipy/scipy/issues/17716 ++ x = np.linspace(0, 4, 5) ++ x = np.vstack((x, np.empty_like(x))).T.copy()[:, 0] ++ assert not x.flags.c_contiguous ++ y = np.linspace(0, 5, 6) ++ z = np.linspace(0, 6, 7) ++ points = (x, y, z) ++ values = np.ones((5, 6, 7)) ++ point = np.array([2.21, 3.12, 1.15]) ++ interpn(points, values, point) ++ RegularGridInterpolator(points, values)(point) ++ ++ @pytest.mark.parametrize("dtype", ['>f8', ' +Date: Mon, 12 Oct 2015 15:17:20 -0700 +Subject: use_local_mathjax + +Setting mathjax_path variable to use the local mathjax javascript library +Patch-Name: use_local_mathjax.patch +--- + doc/source/conf.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +--- a/doc/source/conf.py ++++ b/doc/source/conf.py +@@ -224,6 +224,7 @@ html_file_suffix = '.html' + htmlhelp_basename = 'scipy' + + mathjax_path = "scipy-mathjax/MathJax.js?config=scipy-mathjax" ++mathjax_path='/usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML' + + # ----------------------------------------------------------------------------- + # Intersphinx configuration diff --git a/python-scipy-doc.doc-base b/python-scipy-doc.doc-base new file mode 100644 index 00000000..0490e435 --- /dev/null +++ b/python-scipy-doc.doc-base @@ -0,0 +1,14 @@ +Document: python-scipy-doc +Title: SciPy Manual +Author: The SciPy community +Abstract: This guide is intended as an introductory overview of SciPy + and explains how to install and make use of the most important + features of SciPy. + There is also a tutorial and an API reference manual which details + functions, modules, and objects included in SciPy, describing what + they are and what they do. +Section: Programming/Python + +Format: HTML +Index: /usr/share/doc/python-scipy-doc/html/index.html +Files: /usr/share/doc/python-scipy-doc/html/* diff --git a/python-scipy-doc.docs b/python-scipy-doc.docs new file mode 100644 index 00000000..8137b041 --- /dev/null +++ b/python-scipy-doc.docs @@ -0,0 +1 @@ +doc/build/html diff --git a/python-scipy-doc.lintian-overrides b/python-scipy-doc.lintian-overrides new file mode 100644 index 00000000..91bb3f73 --- /dev/null +++ b/python-scipy-doc.lintian-overrides @@ -0,0 +1 @@ +bogus-mail-host-in-debian-changelog Debian/i386 Build Daemon * diff --git a/python3-scipy.lintian-overrides b/python3-scipy.lintian-overrides new file mode 100644 index 00000000..91bb3f73 --- /dev/null +++ b/python3-scipy.lintian-overrides @@ -0,0 +1 @@ +bogus-mail-host-in-debian-changelog Debian/i386 Build Daemon * diff --git a/rules b/rules new file mode 100755 index 00000000..58b708c8 --- /dev/null +++ b/rules @@ -0,0 +1,171 @@ +#!/usr/bin/make -f + +export PYBUILD_NAME=scipy + +include /usr/share/dpkg/architecture.mk + +unexport LDFLAGS +export FFLAGS="-fPIC" +export ATLAS=None +export PATH := $(CURDIR)/debian/extra_bin:$(PATH) +export SCIPY_USE_PYTHRAN=0 + +PY3VERS:= $(shell py3versions -v -s) +PY3_DEFAULT:= $(shell py3versions -dv) +TMPDIR := $(CURDIR)/build/tmp +BASE=$(shell pwd)/debian + +ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + export NPY_NUM_BUILD_JOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) +endif + +export SCIPY_USE_PYTHRAN = $(shell if dpkg-query -s python3-pythran >/dev/null 2>/dev/null; then echo 1; else echo 0; fi ) + +# specify build against generic BLAS/LAPACK. Preferred optimised implementation should be installed +# by the end user, not by the package build. +export PYBUILD_BUILD_ARGS := -Csetup-args=-Dblas=blas -Csetup-args=-Dlapack=lapack + +# stats/tests/test_continuous_basic.py::test_cont_basic[500-200-ncf-arg74] test fails with IntegrationWarning +# https://github.com/scipy/scipy/issues/14519 +# test_data (pooch) needs internet or cached data files +SKIP_TEST_LIST += test_cont_basic[500-200-ncf-arg74] test_existence_all test_ascent test_face test_electrocardiogram + +ifneq (,$(findstring $(DEB_HOST_ARCH), arm64)) + SKIP_TEST_LIST += test_maxiter_worsening[lgmres] +endif + +# linalg/tests/test_decomp.py started segfaulting on armel +ifneq (,$(findstring $(DEB_HOST_ARCH), armel)) + SKIP_TEST_LIST += test_decomp test_random_exact test_brunnermunzel_normal_dist +endif + +# some tests broken on i386, see https://github.com/scipy/scipy/issues/17839 +ifneq (,$(findstring $(DEB_HOST_ARCH), i386)) + SKIP_TEST_LIST += test_find_peaks_exact test_find_peaks_withnoise test_x0_equals_Mb[bicgstab] test_rv_sample + SKIP_TEST_LIST += test_location_scale[pdf test_examples[True-float64] test_pdf_nolan_samples[pct_range0-alpha_range0-beta_range0] +endif + +# Bug#1017864 test_kolmogorov.py segfaults on i386 (including hurd) +SKIP_KOLMOGOROV_ARCH_LIST := i386 hurd-i386 +ifneq (,$(findstring $(space)$(DEB_HOST_ARCH)$(space), $(space)$(SKIP_KOLMOGOROV_ARCH_LIST)$(space))) + SKIP_TEST_LIST += TestSmirnovp +endif + +# integrate/_ivp/tests/test_ivp.py fail on mips64el +# see https://github.com/scipy/scipy/issues/16883 +# https://github.com/scipy/scipy/issues/17839#issuecomment-1400636840 +ifneq (,$(findstring $(DEB_HOST_ARCH), mips64el)) + SKIP_TEST_LIST += test_first_step test_classes test_integrality test_integrator test_double_integrator +endif + +ifneq (,$(findstring $(DEB_HOST_ARCH), mipsel)) + SKIP_TEST_LIST += test_NaN_warnings test_moments_warnings test_fht_special_cases test_integrality test_integrator test_double_integrator +endif + +ifneq (,$(findstring $(DEB_HOST_ARCH), hppa)) + SKIP_TEST_LIST += test_nodata test_cont_basic[500-200-semicircular-arg89] +endif + +# powerpc: failures in stats/tests/test_stats.py: overflow encountered in _hypergeom_* +ifneq (,$(findstring $(DEB_HOST_ARCH), powerpc)) + SKIP_TEST_LIST += test_hypergeom_cdf test_hypergeom_sf test_nch_hypergeom test_precision test_precise test_less_greater test_maxiter_worsening[lgmres] +endif + +# test_atol[bicg] only just misses tolerance on s390x, but the design of the test makes it difficult to workaround, +# so skip. See https://github.com/scipy/scipy/issues/17839#issuecomment-1399477182 +ifneq (,$(findstring $(DEB_HOST_ARCH), s390x)) + SKIP_TEST_LIST += test_maxiter_worsening test_atol[bicg] +endif + +ifneq (,$(findstring $(DEB_HOST_ARCH), hurd-i386)) + SKIP_TEST_LIST += test_mip1 test_find_peaks_exact test_find_peaks_withnoise test_examples[True-float64] test_rv_sample test_location_scale[pdf +endif + +ifneq (,$(findstring $(DEB_HOST_ARCH), ia64)) + SKIP_TEST_LIST += test_maxiter_worsening[lgmres] +endif + +# https://github.com/scipy/scipy/issues/17839#issuecomment-1399478853 +ifneq (,$(findstring $(DEB_HOST_ARCH), ppc64)) + SKIP_TEST_LIST += test_precond_dummy test_maxiter_worsening[lgmres] +endif + +# https://github.com/scipy/scipy/issues/17839#issuecomment-1401780853 +ifneq (,$(findstring $(DEB_HOST_ARCH), riscv64)) + SKIP_TEST_LIST += test_maxiter_worsening[lgmres] +endif + +ifneq (,$(findstring $(DEB_HOST_ARCH), x32)) + SKIP_TEST_LIST += test_input_validation test_basic +endif + +%: + dh $@ --buildsystem=pybuild + +execute_after_dh_auto_clean: + rm -rf build .pybuild + -find $(CURDIR) -name __pycache__ -type d -exec rm -rf {} + + -rm -rf doc/source/fontList* + -rm -rf doc/source/reference/generated + -rm -rf doc/build + +execute_before_dh_clean: + # make sure symlinks to submodules are cleaned up or empty directories from tarball are removed + rm -rf doc/source/_static/scipy-mathjax + rm -rf scipy/_lib/boost + rm -rf scipy/_lib/highs + rm -rf scipy/_lib/unuran + rm -rf scipy/sparse/linalg/_propack/PROPACK + +execute_before_dh_auto_configure: + echo "Symlink to submodules" + ln -sf ../../../submodules/doc/source/_static/scipy-mathjax doc/source/_static/scipy-mathjax + ln -sf ../../submodules/scipy/_lib/boost scipy/_lib/boost + ln -sf ../../submodules/scipy/_lib/highs scipy/_lib/highs + ln -sf ../../submodules/scipy/_lib/unuran scipy/_lib/unuran + ln -sf ../../../../submodules/scipy/sparse/linalg/_propack/PROPACK scipy/sparse/linalg/_propack/PROPACK + echo "Building scipy with SCIPY_USE_PYTHRAN=$(SCIPY_USE_PYTHRAN)" + +execute_before_dh_installdocs-indep: + (export MPLCONFIGDIR=. ; \ + PYLIBPATH=`pybuild --print build_dir -p$(PY3_DEFAULT) | awk '{print $$3}'`; \ + echo "building docs using PYLIBPATH=$$PYLIBPATH"; \ + PYTHONPATH=$$PYLIBPATH make -C doc html PYTHONPATH=$$PYLIBPATH PYVER=3) || /bin/true + +override_dh_auto_test: + echo "Build-time tests will be run after the installation dir is installed" + +ifeq (testsuitedisabled,$(filter nocheck,$(DEB_BUILD_OPTIONS))) +execute_after_dh_auto_install: + set -e; \ + SKIP_TESTS=""; \ + list_initialised=0; \ + for t in $(SKIP_TEST_LIST); do \ + if [ $${list_initialised} = 0 ]; then \ + SKIP_TESTS=$$t; \ + list_initialised=1; \ + else \ + SKIP_TESTS="$${SKIP_TESTS} or $$t"; \ + fi; \ + done; \ + if [ "x$${SKIP_TESTS}" != "x" ]; then \ + SKIP_TESTS="not ( $${SKIP_TESTS} )"; \ + fi; \ + echo "skipping tests: $${SKIP_TESTS}"; \ + for py in $(PY3VERS); do \ + PYLIBPATH=`pybuild --print build_dir -p$$py | awk '{print $$3}'`; \ + PYTHONPATH=$$PYLIBPATH python$$py \ + $(CURDIR)/runtests.py -n -- -k "$${SKIP_TESTS}"; \ + done +endif + +execute_after_dh_install: + dh_numpy3 + + +# meson build is still work-in-progress, installs residual cython (pyx) files +# See cython_special comments in scipy/special/meson.build +# and https://github.com/scipy/scipy/issues/14890 +# In the meantime clean up python3.X (not python3) files left after dh_python3 +execute_after_dh_python3: + rm -rf debian/python3-scipy/usr/lib/python$(PY3_DEFAULT) diff --git a/salsa-ci.yml b/salsa-ci.yml new file mode 100644 index 00000000..33c3a640 --- /dev/null +++ b/salsa-ci.yml @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff --git a/source/format b/source/format new file mode 100644 index 00000000..163aaf8d --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/lintian-overrides b/source/lintian-overrides new file mode 100644 index 00000000..aed80725 --- /dev/null +++ b/source/lintian-overrides @@ -0,0 +1,2 @@ +obsolete-url-in-packaging https://code.google.com/archive/p/ampgo [debian/copyright] +source-contains-prebuilt-windows-binary [scipy/io/tests/data/fortran-si4-11x1x10.dat] diff --git a/tests/atlas b/tests/atlas new file mode 120000 index 00000000..6d65db32 --- /dev/null +++ b/tests/atlas @@ -0,0 +1 @@ +openblas \ No newline at end of file diff --git a/tests/blis b/tests/blis new file mode 120000 index 00000000..6d65db32 --- /dev/null +++ b/tests/blis @@ -0,0 +1 @@ +openblas \ No newline at end of file diff --git a/tests/control b/tests/control new file mode 100644 index 00000000..eb32bff8 --- /dev/null +++ b/tests/control @@ -0,0 +1,22 @@ +Tests: python3 +Depends: build-essential, python3-scipy, python3-pytest, python3-all, python3-all-dev, python3-pil, python3-pooch + +# short test on all python versions including debug +Tests: python3-smoke +Depends: python3-scipy, python3-pytest, python3-all + +#needs root for update-alternatives, build-essential for libc6-dev (ctype libm.so) +Tests: openblas +Restrictions: needs-root +Depends: build-essential, python3-scipy, python3-pytest, python3, libopenblas-dev +Architecture: amd64 arm64 armhf i386 powerpc ppc64el ppc64 kfreebsd-i386 kfreebsd-amd64 mips64el riscv64 sparc64 s390x + +#needs root for update-alternatives, build-essential for libc6-dev (ctype libm.so) +Tests: atlas +Restrictions: needs-root +Depends: build-essential, python3-scipy, python3-pytest, python3, libatlas-base-dev + +#needs root for update-alternatives, build-essential for libc6-dev (ctype libm.so) +Tests: blis +Restrictions: needs-root +Depends: build-essential, python3-scipy, python3-pytest, python3, libblis-dev diff --git a/tests/openblas b/tests/openblas new file mode 100755 index 00000000..7cdc4cb0 --- /dev/null +++ b/tests/openblas @@ -0,0 +1,21 @@ +#!/bin/sh +set -efu +ma=$(dpkg-architecture -qDEB_HOST_MULTIARCH) +blaslib=$(update-alternatives --list libblas.so.3-$ma | grep -m1 $(basename $0)) +update-alternatives --set libblas.so.3-$ma $blaslib + +echo "=== testing "$(basename $0)" ===" + +# one python is enough +PYS=${PYS:-"$(py3versions -d 2>/dev/null)"} + +#test only modules that link against libblas +PYS=$PYS TESTPKG=odr debian/tests/python3 +PYS=$PYS TESTPKG=optimize debian/tests/python3 +PYS=$PYS TESTPKG=spatial debian/tests/python3 +PYS=$PYS TESTPKG=special debian/tests/python3 +PYS=$PYS TESTPKG=cluster debian/tests/python3 +PYS=$PYS TESTPKG=integrate debian/tests/python3 +PYS=$PYS TESTPKG=interpolate debian/tests/python3 +PYS=$PYS TESTPKG=sparse debian/tests/python3 +PYS=$PYS TESTPKG=linalg debian/tests/python3 diff --git a/tests/python3 b/tests/python3 new file mode 100755 index 00000000..8fa93837 --- /dev/null +++ b/tests/python3 @@ -0,0 +1,139 @@ +#!/bin/bash +set -efu + +PYS=${PYS:-"$(py3versions -s 2>/dev/null)"} +TESTMODE=${TESTMODE:-full} +TESTPKG=${TESTPKG:-} +export HOME=$AUTOPKGTEST_TMP +export TMPDIR=$AUTOPKGTEST_TMP + +SUBMODULE= +if [ "x${TESTPKG}" != "x" ]; then + SUBMODULE="-s ${TESTPKG}"; +fi + +MODE= +if [ "x${TESTMODE}" != "xfull" ]; then + MODE="-m full"; +fi + +# some tests are expected to fail +# so list tests to skip in array variable SKIP_TEST_LIST +declare -a SKIP_TEST_LIST + +# some arches fail some tests with specific BLAS implementations +# Bug#1003880: skip test_hermitian_modes with blis on i386 (sparse.linalg._eigen.arpack) +arch=$(dpkg-architecture -qDEB_HOST_ARCH) +ma=$(dpkg-architecture -qDEB_HOST_MULTIARCH) +DEB_HOST_ARCH_BITS=$(dpkg-architecture -q DEB_HOST_ARCH_BITS) +if [ "$arch" = "arm64" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q blis ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_atol[cgs]) +fi +if [ "$arch" = "i386" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q blis ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_hermitian_modes test_svd_linop \ + test_complex_nonsymmetric_modes test_standard_nonsymmetric_starting_vector test_general_nonsymmetric_starting_vector \ + test_complex test_simple_overdet_complex test_random_complex_exact) +fi +if [ "$arch" = "armhf" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q openblas ; then + # test_large_rank_deficient in scipy/optimize/tests/test_lsq_linear.py times out or segfaults with openblas on armhf + # and other TestTRF tests time out + # test_disp in optimize/tests/test_linprog.py times out with openblas on armhf + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_large_rank_deficient TestTRF test_disp test_m_eq_n_sparse test_magic_square2 \ + test_numerical_jac test_with_bounds test_bvp test_solver_selection \ + test_pdist_calling_conventions test_pdist_dtype_equivalence test_striding \ + test_array_smoothing) +fi +if [ "$arch" = "armhf" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q atlas ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_aligned_mem) +fi +# segfaults in test_lsq_linear.py::TestBVLS +# see https://ci.debian.net/data/autopkgtest/testing/armhf/s/scipy/25114019/log.gz +if [ "$arch" = "armhf" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q blis ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_large_rank_deficient) +fi + +if [ "$arch" = "armel" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_aligned_mem test_decomp test_brunnermunzel_normal_dist) +fi + + +# https://github.com/scipy/scipy/issues/17839#issuecomment-1399492309 +if [ "$arch" = "armhf" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_woodbury test_complex_data test_scale_invariance \ + test_extreme_domains test_polynomial_reproduction test_vector_data \ + test_interpolation_misfit_2d test_smoothing_limit test_pickleable \ + test_equivalent_to_rbf_interpolator test_rosenbrock_with_no_exception) +fi + +# some tests broken on i386, see https://github.com/scipy/scipy/issues/17839 +if [ "$arch" = "i386" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_find_peaks_exact test_find_peaks_withnoise \ + test_x0_equals_Mb[bicgstab] test_rv_sample test_location_scale[pdf \ + test_examples[True-float64] test_pdf_nolan_samples[pct_range0-alpha_range0-beta_range0]) +fi + +# Bug#1017864 test_kolmogorov.py segfaults on i386 (including hurd) +if [ "$arch" = "i386" ] || [ "$arch" = "hurd-i386" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} TestSmirnovp) +fi + +# integrate/_ivp/tests/test_ivp.py fail on mips64el +# see https://github.com/scipy/scipy/issues/16883 +# https://github.com/scipy/scipy/issues/17839#issuecomment-1400636840 +if [ "$arch" = "mips64el" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_first_step test_classes test_integrator test_double_integrator) +fi + +if [ "$arch" = "ppc64el" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_cossin test_cossin_separate testInitialization) +fi + +if [ "$arch" = "s390x" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_maxiter_worsening test_atol[bicg]) +fi + +if [ "$arch" = "ppc64el" ] || [ "$arch" = "arm64" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_svds_parameter_tol) +fi + +if [ "$arch" = "ppc64el" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q atlas ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_bug_6139 test_svd_v0 test_svd_random_state test_svd_random_state_2) +fi +if [ "$arch" = "s390x" ] && update-alternatives --query libblas.so.3-$ma | sed -n "/^Value:/p" | grep -q atlas ; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_bug_6139 test_solver_select test_aligned_mem) +fi + +# avoid segfaults and other failures on riscv64 +if [ "$arch" = "riscv64" ]; then + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_kmeans2_high_dim test_krandinit test_kmeans2_kpp_high_dim) + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_banded_ode_solvers test_singular_term test_vode test_zvode test_odeint_banded_jacobian test_odeint_banded_jac) + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_vector test_iterative_refinements_dense) + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_sine_weighted_finite test_sine_weighted_infinite test_cosine_weighted_infinite) + SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_scalar test_integrate_ppoly test_compare_dense_and_sparse) +fi + + +# stats/tests/test_continuous_basic.py::test_cont_basic[500-200-ncf-arg74] test fails with IntegrationWarning +# https://github.com/scipy/scipy/issues/14519 +SKIP_TEST_LIST=(${SKIP_TEST_LIST[@]} test_cont_basic[500-200-ncf-arg74]) + +SKIP_TESTS="" +list_initialised=0 +for t in ${SKIP_TEST_LIST[@]}; do + if [ ${list_initialised} = 0 ]; then + SKIP_TESTS=$t + list_initialised=1 + else + SKIP_TESTS="${SKIP_TESTS} or $t" + fi +done +if [ "x${SKIP_TESTS}" != "x" ]; then + SKIP_TESTS="not ( ${SKIP_TESTS} )" +fi +echo "skipping tests with SKIP_TEST_LIST=${SKIP_TEST_LIST[@]}" + +for py in $PYS; do + echo "=== Testing: $py $TESTPKG ===" + $py runtests.py -n -v ${MODE} ${SUBMODULE} -- -k "${SKIP_TESTS}" 2>&1 + echo "=== Done: $py $TESTPKG ===" +done diff --git a/tests/python3-smoke b/tests/python3-smoke new file mode 100755 index 00000000..2184d577 --- /dev/null +++ b/tests/python3-smoke @@ -0,0 +1,18 @@ +#!/bin/sh +set -efu +echo "=== testing "$(basename $0)" ===" + +PYS=${PYS:-"$(py3versions -s 2>/dev/null)"} +TESTMODE=${TESTMODE:-full} +TESTPKG=${TESTPKG:-scipy} +export HOME=$AUTOPKGTEST_TMP +export TMPDIR=$AUTOPKGTEST_TMP + +cd "$AUTOPKGTEST_TMP" + +# test imports and a fast test +for py in $PYS; do + echo "=== Testing: $py $TESTPKG ===" + $py -c "import scipy.interpolate, scipy.stats, scipy.ndimage; scipy.interpolate.test()" 2>&1 + echo "=== Done: $py $TESTPKG ===" +done diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 index 00000000..63aa7b52 --- /dev/null +++ b/upstream/metadata @@ -0,0 +1,15 @@ +--- +Bug-Database: https://github.com/scipy/scipy/issues +Bug-Submit: https://github.com/scipy/scipy/issues/new +Repository: https://github.com/scipy/scipy.git +Repository-Browse: https://github.com/scipy/scipy +Registry: + - Name: conda:conda-forge + Entry: scipy + - Name: bio.tools + Entry: NA + Checked: 2021-08-01 + - Name: guix + Entry: python-scipy + - Name: SciCrunch + Entry: SCR_008058 diff --git a/watch b/watch new file mode 100644 index 00000000..1651637f --- /dev/null +++ b/watch @@ -0,0 +1,5 @@ +version=4 +opts="uversionmangle=s/rc/~rc/, \ + filenamemangle=s%(?:.*?)?v?(\d[\d.]*@ARCHIVE_EXT@)%@PACKAGE@-$1%" \ + https://github.com/scipy/scipy/tags \ + (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@ -- 2.30.2