Subject: [bug#55104] [PATCH 000/232] Update IPython to latest, fix texlive-polyglossia, add more

From: Maxim Cournoyer <[email-masked]>
Date: Sun, 24 Apr 2022 23:57:14 -0400

Hello Guix!

This is the result of a quest to update IPython (to fix a reported CVE) and
wanting to fix its Texinfo/PDF doc generation.  The later ended up being a
rather deep rabbit hole, hence the following slurry of commits.  The end
result is that we now have an up-to-date IPython and better support to build
Sphinx-based documentation, a working texlive-polyglossia package (at least
for XeLaTeX) and many new font tools that should allow us to build more fonts
from source.

The branch wip-ipython-polyglossia has been used to bulid the branch, so
should you be interested in trying it, the new packages should have
substitutes.

Thanks, and happy 10th Guix anniversary!

Maxim Cournoyer (232):
  gnu: python-ipython: Re-order fields.
  gnu: python-astroid: Propagate python-typing-extensions.
  gnu: Add python-pure-eval.
  gnu: Add python-asttokens.
  gnu: Add python-littleutils.
  gnu: Add python-stack-data.
  gnu: python-traitlets: Update to 5.1.1.
  gnu: python-jinja2: Update to 3.1.1.
  gnu: python-prompt-toolkit: Update to 3.0.29.
  gnu: python-ipython: Update to 8.2.0 [fixes CVE-2022-21699].
  gnu: python-nbformat: Update to 5.3.0.
  gnu: Add texlive-paralist.
  gnu: Add texlive-stix2-otf.
  gnu: Add texlive-metalogo.
  gnu: Add texlive-makecmds.
  gnu: Add texlive-csplain.
  gnu: Add texlive-cs.
  gnu: Add texlive-zref.
  gnu: Add python-pcpp.
  gnu: Add opentype-sanitizer.
  gnu: Add python-opentype-sanitizer.
  gnu: Add python-defcon-bootstrap.
  gnu: Add python-fontmath.
  gnu: Add python-unicodedata2.
  gnu: python-fonttools-with-test: Rename to python-fonttools-full.
  gnu: Add python-mutatormath.
  gnu: Add python-fontpens-bootstrap.
  gnu: Add python-booleanoperations.
  gnu: Add python-fontparts-bootstrap.
  gnu: Add python-fontpens.
  gnu: Add python-defcon.
  gnu: Add python-fontparts.
  gnu: Add python-cu2qu.
  gnu: Add python-ufoprocessor.
  gnu: Add python-ufonormalizer.
  gnu: Add python-types-toml.
  gnu: Add python-pytest-mypy.
  gnu: Add python-jaraco-context-bootstrap.
  gnu: Add python-jaraco-functools-bootstrap.
  gnu: Add python-autocommand.
  gnu: Add python-types-freezegun.
  gnu: Add python-types-pytz.
  gnu: Add python-pytest-freezegun.
  gnu: Add python-pytest-enabler-bootstrap.
  gnu: Add python-path-bootstrap.
  gnu: Add python-pip-run-bootstrap.
  gnu: python-importlib-metadata: Update to 4.11.3.
  gnu: python-pytest-black: Update to 0.3.12.
  gnu: python-mypy: Update to 0.942 and fix search path.
  gnu: Add python-types-docutils.
  gnu: python-pytest-checkdocs: Update to 2.7.1.
  gnu: Add python-jaraco-classes.
  gnu: Add python-jaraco-context.
  gnu: Add python-jaraco-functools.
  gnu: Add python-pytest-enabler.
  gnu: Add python-path.
  gnu: Add python-pip-run.
  gnu: Add python-tempora.
  gnu: Add python-pytest-perf.
  gnu: python-factory-boy: Update to 3.2.1.
  gnu: python-faker: Update to 13.3.4 and honor TESTS?.
  gnu: Add python-pytest-randomly.
  gnu: Add psautohint-font-data.
  gnu: Add psautohint.
  gnu: Add python-ordered-set.
  gnu: Add python-xdoctest.
  gnu: Add python-ubelt.
  gnu: python-setuptools: Update to 62.0.0.
  gnu: python-pathpy: Deprecate by python-path.
  gnu: python-pytest-shutil: Adjust to use python-path.
  gnu: python-pytest-cov: Update to 3.0.0.
  gnu: Add python-scikit-build.
  gnu: python-jupyter-packaging: Update to 0.12.0, run test suite.
  gnu: python-scipy: Move input fields below arguments field.
  gnu: python-scipy: Update to 1.8.0 and enable parallel build.
  gnu: Add java-antlr4-runtime-cpp.
  gnu: Add python-fonttools-next.
  gnu: Add python-afdko.
  gnu: Add python-cffsubr.
  gnu: Add skia.
  gnu: Add python-skia-pathops.
  gnu: Add python-ufolib2.
  gnu: Add python-compreffor.
  gnu: Add python-ufo2ft.
  gnu: Add python-sfdlib.
  gnu: Add font-amiri.
  gnu: Add font-sil-ezra.
  gnu: Add texlive-bidi.
  gnu: Add font-gfs-ambrosia.
  gnu: python-click: Update to 8.1.2 and honor TESTS?.
  gnu: python-flask: Update to 2.1.1.
  gnu: Add python-untangle.
  gnu: python-black: Update to 22.3.0.
  gnu: pylint: Run tests in parallel.
  gnu: python-trio: Update to 0.20.0.
  gnu: Add python-pydevd.
  gnu: Add python-debugpy.
  gnu: python-greenlet: Update to 1.1.2.
  gnu: Add python-pytest-forked-next.
  gnu: python-pytest-xdist-next: Update to 2.5.0.
  gnu: Add python-ipyparallel-bootstrap.
  gnu: python-nest-asyncio: Update to 1.5.5.
  gnu: python-jupyter-core: Update to 4.10.0.
  gnu: python-jupyter-client: Update to 7.2.2.
  gnu: python-ipykernel: Update to 6.13.0.
  gnu: Add python-pytest-tornado.
  gnu: python-ipyparallel: Update to 8.2.1.
  gnu: python-anyio: Update to 3.5.0.
  gnu: python-nbclient: Update to 0.6.0.
  gnu: python-bleach: Update to 5.0.0.
  gnu: Add texlive-unicode-math.
  gnu: Add texlive-lm-math.
  gnu: python-nbconvert: Update to 6.5.0.
  gnu: Add python-jupyter-server-mathjax.
  gnu: python-nbval: Fix build.
  gnu: python-send2trash: Update to 1.8.0 and update home page.
  gnu: python-notebook: Update to 6.4.10.
  gnu: Add python-nbdime.
  gnu: Add python-docrepr.
  gnu: python-sphinx: Propagate TexLive dependencies.
  gnu: Add python-pep621.
  gnu: Add python-sphinx-theme-builder.
  gnu: Add python-sphinx-sitemap.
  gnu: texlive-fontspec: Add missing propagated inputs.
  gnu: texlive-polyglossia: Rename and fix package.
  gnu: Add texlive-cbfonts-fd.
  gnu: Add texlive-cbfonts.
  download: Add a mirror for CTAN.
  gnu: texlive-latex-geometry: Propagate texlive-latex-graphics.
  gnu: Add texlive-cm-lgc.
  gnu: Add texlive-xindy.
  gnu: python-ipython-documentation: Also build info and pdf targets.
  gnu: python-websockets: Update to 10.3 and enable tests.
  gnu: Add python-strict-rfc3339.
  gnu: Add python-rfc3339-validator.
  gnu: Add python-openapi-schema-validator.
  gnu: Add python-openapi-spec-validator.
  gnu: Add python-cbor2.
  gnu: python-httpcore: Update to 0.14.7 and enable tests.
  gnu: Add python-httpcore-bootstrap.
  gnu: Add python-httpx-bootstrap.
  gnu: python-httpx: Update to 0.22.0.
  gnu: python-uvicorn: Update to 0.17.6.
  gnu: Add python-socksio.
  gnu: python-sqlalchemy: Run tests in parallel via xdist.
  gnu: python-sqlalchemy: Update to 1.4.35.
  gnu: Add python-pecan.
  gnu: Add python-aioredis.
  gnu: python-fakeredis: Update to 1.7.1.
  gnu: python-falcon: Update to 3.1.0.
  gnu: Add python-dictpath.
  gnu: Add python-openapi-core.
  gnu: Add python-jupyterlab-server.
  gnu: python-hypothesis-6.23: Update to 6.43.3.
  gnu: python-numpy: Update to 1.21.6 and parallelize build/tests.
  gnu: python-llvmlite: Update to 0.38.0.
  gnu: python-numba: Update to 0.55.1.
  gnu: python-pandas: Build and run tests in parallel.
  gnu: python-pandas: Update to 1.4.2.
  gnu: python-scikit-learn: Parallelize build and test suite.
  gnu: python-pynndescent: Update to 0.5.6.
  gnu: python-umap-learn: Update to 0.5.3.
  gnu: python-jupyter-server: Update to 1.16.0.
  gnu: python-voila: Update to 0.3.5.
  gnu: python-sparqlwrapper: Update to 2.0.0.
  gnu: python-sparqlkernel: Use gexps and fix inputs.
  gnu: python-jupyter-protocol: Update to 0.2.0.
  gnu: python-jupyter-kernel-mgmt: Update to 0.5.1 and disable tests.
  gnu: xeus: Update to 2.4.1.
  gnu: python-types-dataclasses: Fix typo.
  gnu: python-cmarkgfm: Update to 0.8.0.
  gnu: python-readme-renderer: Update to 34.0.
  gnu: mbed-tools: Update to 7.53.0 and relax click version requirement.
  gnu: conan: Update to 1.47.0 and relax PyYAML requirement.
  gnu: python-parse-type: Update to 0.6.0, fixing build.
  gnu: Add python-bson.
  gnu: python-can: Update to 4.0.0.
  gnu: python-amqp: Update to 5.1.1 and enable tests.
  gnu: python-kombu: Update to 5.2.4.
  gnu: python-celery: Update to 5.2.6 and enable tests.
  gnu: Add python-argparse-addons.
  gnu: python-bitstruct: Update to 8.14.0.
  gnu: Add python-toolrack.
  gnu: sshoot: Update to 1.5.1.
  gnu: python-multipart: Fix build with PyYAML 6.
  gnu: Add python-mergedeep.
  gnu: Add python-pyyaml-env-tag.
  gnu: python-ghp-import: Update to 2.0.2.
  gnu: Add python-mdx-gh-links.
  gnu: python-mkdocs: Update to 1.3.0.
  gnu: Add python-crccheck.
  gnu: python-cantools: Update to 37.0.7.
  gnu: python-locust: Update to 2.8.6.
  gnu: Remove python2-jmespath.
  gnu: python-croniter: Update to 1.3.4.
  gnu: python-miio: Update to 0.5.11.
  gnu: Remove python-orator due to being broken and unmaintained.
  gnu: Add python-pydyf.
  gnu: weasyprint: Update to 54.3.
  gnu: seed: Use webkitgtk-with-libsoup2.
  gnu: markets: Add python-wrapper to fix build.
  gnu: libgrss: Use libsoup-minimal-2 to fix build.
  gnu: setzer: Add python-wrapper to fix build.
  gnu: emacsy: Use webkitgtk-with-libsoup2.
  gnu: python-keyring: Fix test suite.
  gnu: Remove python2-keyring.
  gnu: python-pingouin: Update to 0.5.1.
  gnu: python-flask-wtf: Update to 1.0.1.
  gnu: python-flask-login: Update to 0.6.0.
  snippets: Add a 'remove' snippet.
  gnu: python2-sqlalchemy: Skip a failing test.
  gnu: dynaconf: Fix build following python-click upgrade.
  gnu: python-numpydoc: Update to 1.2.1.
  gnu: python-sphinx: Update to 4.5.0.
  gnu: python-pydata-sphinx-theme: Update to 0.7.2.
  gnu: python-sphinx-copybutton: Update to 0.5.0.
  gnu: python-sphinx-click: Update to 4.0.3 and enable tests.
  gnu: python-sphinxcontrib-websupport: Update to 1.2.4.
  gnu: python-sphinxcontrib-programoutput: Update to 0.17 and enable
    tests.
  gnu: python-sphinx-argparse: Update to 0.3.1.
  gnu: python-sphinx-cloud-sptheme: Update to 1.10.1 [still broken].
  gnu: Add python-beartype.
  gnu: Add python-nptyping.
  gnu: python-sphinx-autodoc-typehints: Update to 1.18.1.
  gnu: python-sphinxext-opengraph: Update to 0.6.3.
  gnu: python-sphinx-rtd-theme: Update to 1.0.0.
  gnu: python-numpy-documentation: Overhaul package definition.
  gnu: Add python-ipdb.
  gnu: python-pudb: Update to 2022.1.1 and rename from pudb.
  gnu: Add python-mpl-sphinx-theme.
  gnu: Add texlive-underscore.
  gnu: python-matplotlib-documentation: Fix build.

 .../guix-commit-message-remove-package        |   13 +
 gnu/local.mk                                  |    4 +
 gnu/packages/android.scm                      |   22 +-
 gnu/packages/benchmark.scm                    |   24 +-
 gnu/packages/c.scm                            |   32 +
 gnu/packages/check.scm                        |  258 +-
 gnu/packages/databases.scm                    |  124 +-
 gnu/packages/documentation.scm                |   57 +
 gnu/packages/embedded.scm                     |   10 +-
 gnu/packages/fonts.scm                        |   91 +
 gnu/packages/fontutils.scm                    |  767 +++-
 gnu/packages/gnome-xyz.scm                    |    2 +
 gnu/packages/gnome.scm                        |    7 +-
 gnu/packages/graphics.scm                     |  135 +
 gnu/packages/guile-xyz.scm                    |   10 +-
 gnu/packages/java.scm                         |   35 +-
 gnu/packages/jupyter.scm                      |  330 +-
 gnu/packages/llvm.scm                         |    6 +-
 gnu/packages/machine-learning.scm             |   77 +-
 gnu/packages/markup.scm                       |    4 +-
 gnu/packages/matrix.scm                       |    2 +-
 gnu/packages/package-management.scm           |   12 +-
 .../python-debugpy-unbundle-pydevd.patch      |  254 ++
 .../python-ipython-documentation-chars.patch  |   18 +
 .../python-ipython-documentation-repro.patch  |   25 +
 .../patches/python-mypy-use-sys-path.patch    |  130 +
 gnu/packages/pdf.scm                          |  130 +-
 gnu/packages/python-check.scm                 |  160 +-
 gnu/packages/python-crypto.scm                |   30 +-
 gnu/packages/python-science.scm               |  172 +-
 gnu/packages/python-web.scm                   |  498 ++-
 gnu/packages/python-xyz.scm                   | 3388 +++++++++++------
 gnu/packages/rdf.scm                          |   13 +-
 gnu/packages/sphinx.scm                       |  302 +-
 gnu/packages/tex.scm                          |  744 +++-
 gnu/packages/version-control.scm              |   11 +-
 gnu/packages/vpn.scm                          |   20 +-
 gnu/packages/xml.scm                          |   30 +
 guix/download.scm                             |    5 +
 39 files changed, 6249 insertions(+), 1703 deletions(-)
 create mode 100644 etc/snippets/text-mode/guix-commit-message-remove-package
 create mode 100644 gnu/packages/patches/python-debugpy-unbundle-pydevd.patch
 create mode 100644 gnu/packages/patches/python-ipython-documentation-chars.patch
 create mode 100644 gnu/packages/patches/python-ipython-documentation-repro.patch
 create mode 100644 gnu/packages/patches/python-mypy-use-sys-path.patch

-- 
2.34.0