Opened 16 months ago

Last modified 3 days ago

#29705 new task

Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages) sagemath-...

Reported by: mkoeppe Owned by:
Priority: major Milestone: sage-9.5
Component: refactoring Keywords: sd109, sd110, sd111
Cc: vdelecroix, mjo, fbissey, isuruf, tscrim, gh-kliem, jhpalmieri, gh-tobiasdiez, defeo, gh-thierry-FreeBSD Merged in:
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Description (last modified by mkoeppe)

(From https://groups.google.com/d/msg/sage-devel/M9QTWtln6zU/UHwkrmTKBQAJ)

Modularize sagelib into separate distributions (pip-installable packages), so that these can be built and run with a much smaller set of libraries. The packages can be made available individually on PyPI using the naming scheme sagemath-....

The goal is do this without changing the overall structure of the source tree.

Current status of pip-installability (Sage release tour)

Presentation video: https://researchseminars.org/talk/SageDays110/11/

  1. In particular, create a package sagemath-objects that makes Sage objects, the element/parent framework, categories, the coercion system and the related metaclasses available. This package would, for example, not provide or know about integers, polynomials, or matrices (thus avoiding all the dependencies on the various libraries implementing these). Ideally it would only have a build dependency on Cython and no runtime dependencies.

(Doctesting sagemath-objects would still need more of Sage, but some it could also be done by mocking instead of with the real classes.)

a) These facilities could see a wider use in the mathematical Python community, and in this way we could hope to benefit from a larger developer base. For example, we would hope that sagemath-objects could be ported for use with PyPy instead of CPython.

b) Building and deploying a user package would be easier if it could depend on a small package such as sagemath-objects only instead of the whole multigigabyteness of Sage.

  1. Remove the mechanism of OptionalExtensions from sagelib.

Currently, a user would install, for example, the optional package tdlib and then rebuild sagelib so that the OptionalExtension sage.graphs.graph_decompositions.tdlib is built and installed.

With this ticket, the user would instead install a new optional package sagemath-tdlib (which has tdlib as a dependency); this installs the Extension sage.graphs.graph_decompositions.tdlib (as a namespace package).

This has been completed in Sage 9.2 (#29701).

Not within the scope of this ticket:

  • We will not change the overall structure of the source tree (SAGE_ROOT/src/sage). We will achieve this by using the mechanism of native namespace packages introduced in Python 3.3 (PEP 420, see https://trac.sagemath.org/ticket/28925).
  • It is not a prerequisite to fight against all circular imports. In particular, a parent class and its corresponding element class would certainly not be separated into separate distutils packages.

Constraints and challenges:

  • Inconsistent handling of symlinks by pip/setuptools. We cannot simply create a distribution of a subset of the files in src by creating a flock of symlinks (see #29850) and expect everything to work; notably, pip fails because of longstanding issues with installs from local directories (see discussion in #29854).

Solution (implemented in Sage 9.2, #29500): Do not use pip for installations from local source directories. Use setup.py bdist_wheel, followed by pip install of the wheel.

  • The category framework can not really be separated from the Parent/Element/CategoryObject (e.g. coercion is involved in comparisons and binary operations).

Solution: These should therefore be in the same package sagemath-objects.

  • The category framework cannot live without the integers (e.g. the output of .cardinality() expects an integer).

Possible solution: The coercion system already has the notion of a global coercion model - which is determined at runtime, not compile time (sage.structure.element.get_coercion_model). When methods in sagemath-objects need to create an integer, they should obtain the appropriate class of integers in the same way. An existing function provides this interface already (but has a static implementation):

sage: py_scalar_parent(int)
Integer Ring

#29875 will make this implementation dynamic.

  • Imports in sage.categories:
      bimodules imports QQ, RR
      classical_crystals imports SR
      finite_coxeter_groups imports QQbar
    

One can try to not populate the whole category system.

Tickets for Sage 9.2:

  • #29411: make sagelib a script package
  • #29702: Move all code from src/setup.py to sage_setup
  • #29706, #29720, #29721, #29785, #29786, #29790, #29791: Move Extension options from src/module_list.py to distutils: directives in the individual files
  • #29701 (depends on all of the above): Replace use of module_list and OptionalExtension by extending sage_setup.find_python_sources
  • #28197: upgrade to ipython 7 (old ipython completer crashes on namespace packages)
  • #29803: Upgrade setuptools, setuptools_scm, pip (2020-06), add package wheel; remove zope_interface
  • #21559: Install src/bin scripts by sagelib's setup.py, not make
  • #29950: Build sagelib from build/pkgs/sagelib/src, fix setup.py sdist, add spkg-src and tox.ini (supersedes: #21516: Fix sagelib sdist (src/setup.py sdist), #13190: make sagelib use setuptools instead of distutils)
  • #29869, #29873, #29892, #29883, #16351, #29881, #29880, #29916, #29922: Improve/repair filtered structure of sagelib.
  • #29171: Move giacpy_sage into sage source code
  • #30332: Merge sage_brial into sagelib
  • #29500 Install all Python packages via pip wheel, store wheels in $SAGE_LOCAL/var/lib/sage/wheels
  • #30606: sage.features.Feature.resolution: If SAGE_ROOT is available, recommend system packages
  • #30616: Replace use of sage.misc.package.PackageNotFoundError (2); lazy_import: Add keyword argument 'feature'

Tickets for Sage 9.3:

  • #30715 Remove a few .all imports
  • #30739 Remove a few more .all imports
  • #30784 sage.matrix: Resolve circular imports without using __init__.py
  • #30779 Duplicate src/setup.py
  • #30780 sage_setup: Separate installing and cleaning
  • #30579 Clean up sage_setup.library_order
  • #30580 sage_setup: Remove import-time dependency (setup_requires) on pkgconfig, numpy
  • #29355 Sagelib's scripts in src/bin should not use build/bin/sage-system-python; remove sage-pypkg-location
  • #30780 sage_setup: Separate installing and cleaning
  • #30719 Add build/pkgs/SPKG/install-requires.txt for all Python packages, remove some unneeded packages
  • #29951 src/bin/sage-env: Make SAGE_ROOT and SAGE_LOCAL optional
  • #29852 sage: Determine SAGE_LOCAL, SAGE_ROOT via sage-config if it exists
  • #22731: Replace $SAGE_LOCAL/bin by more specific variables to make Sage easier to package, use in venvs
  • #30013: src/bin/sage-env: Make sure $SAGE_VENV/bin is at the beginning of the PATH
  • #30587: Remove import of ppl at startup
  • #31261: Update pplpy to 0.8.6
  • #29850: Install sage-env-config as part of sage_conf
  • #31025: FPLLL 5.4.0 and FPyLLL 0.5.4
  • #31058: src/bin/sage-venv-config: Do not fail if sage_conf is not available
  • #31218: bootstrap: Fix "sage-venv-config: /doesnotexist/python3: bad interpreter"
  • #31270: Remove sage-location's "sage-force-relocate" mechanism, fix script to work without SAGE_ROOT
  • #31321: build/pkgs: Add some missing install-requires metadata, add some documentation to the developer's guide
  • #30912: sagelib: Update metadata for PyPI deployment as distribution sagemath-standard
  • #31357: Fixup src/VERSION.txt added in #30912
  • #31332: sage.misc.persist: Import SAGE_DB on need only
  • #31334: sage.doctest.control: Do not fail if sage.libs.arb cannot be imported
  • #30984: sage_setup: Replace imports from distutils by setuptools
  • #31365: Add NTL to cython_aliases and sage.misc.cython library search dirs
  • #31279: Add package argon2-cffi (dependency of Jupyter notebook)
  • #31362: make build-local, make build-venv
  • #31377 ./configure --enable-editable
  • #31045: pip, wheel, setuptools: Make wheels available in SAGE_SPKG_WHEELS
  • #30010: Split sage_setup.docbuild out to a separate distribution (distutils package)
  • #31278: widgetsnbextension should not depend on notebook
  • #30383: Add configure --disable-notebook; show descriptions of optional packages in configure --help
  • #31523: Fix dependencies of ipywidgets
  • #31409: Make it possible to disable build of r, rpy2 using ./configure --disable-r

Tickets for Sage 9.4:

  • #30913: Generate pyproject.toml and setup.cfg [install_requires], requirements.txt, Pipfile, and src/Pipfile (supersedes #30578, #30581)
  • #31384: cython_aliases: Do not fail if one of the listed libraries is not known to pkgconfig
  • #29013: Add configure option --with-sage-venv=SAGE_VENV to create venv there instead of in SAGE_LOCAL
  • #31593: configure: Paths within $SAGE_LOCAL ($prefix) for sage_conf
  • #31338: sage_setup: Use paths within SAGE_LOCAL when provided via sage_conf
  • #31562: Patch giac so that libintl from /usr/local does not leak in on macOS
  • #28890: Install fewer static libraries
  • #32045 sage-env, sage.env: Remove unused environment and Python variables SAGE_ETC, SAGE_INC
  • #32036 sage.env: Remove direct uses of SAGE_LOCAL from the Sage library
  • #32057 sage_setup.setenv: Only set ...PATH variables and LDFLAGS if SAGE_LOCAL differs from SAGE_VENV
  • #31577: Move SAGE_ROOT/build/pkgs/*/src to SAGE_ROOT/pkgs/*
  • #31333: sage.env.sage_include_directories: Remove hard dependency on numpy
  • #32073: Remove sage.libs.readline

Tickets used for the deployment of Sage 9.4 to PyPI and sage-wheels:

  • #32046 Use pip --use-feature=in-tree-build, replace use of sdh_setup_bdist_wheel by sdh_pip_install
  • #29847: Install sage_setup with setuptools as a build prerequisite for building/installing sagelib. Deploy sage_setup to PyPI.
  • #32371 ptyprocess: Pin version to 0.5.1 in install-requires.txt
  • #29039: pip-installable version of package sage_conf - installs non-Python bits of the Sage distribution in ~/.sage/
  • #31396: relocatable wheel version of package sage_conf
  • #32373: sage_setup.library_order: Skip libraries that were not detected
  • #29865: Modularization of sagelib: Prepare experimental subset distributions sagemath-objects, sagemath-categories, depending on Cython, pkgconfig, cysignals, gmpy2. Use them as a testsuite for testing the filtered structure of sagelib.

Tickets for Sage 9.5:

  • #31031 Change sage_setup: distribution headers from sage-... to sagemath-...
  • #32386 Merge pynac sources as src/sage/symbolic/ginac (supersedes #30534)
  • #32412: Deprecate sage.libs.primecount/sage.interfaces.primecount
  • #32411/#32413/#32415/#32416: Remove unnecessary uses of SR and symbolic functions
  • #32501 Meta-ticket: Clear out init.py files in preparation for namespace packages
  • #32534 Remove .all imports
  • #29870: Move sage.structure.formal_sum to sage.modules
  • #32062: GH Actions: Deploy sdists to PyPI
  • #30022/#32441/#32455 Remove compile-time dependency on cypari2 and flint from some modules
  • #32431 cysignals: Replace compile-time dependency on pari by run-time dispatch
  • #30778 sage.doctest.control: Exclude doctests in files via file-level directives
  • #32432: Modularization of sagelib: Break out a separate package sagemath-polyhedra
  • #30746 sage.doctest.control: Replace use of sage.misc.package.list_packages

Tickets for Sage 9.6:

  • #32390 Make ./configure --enable-editable the default
  • #30911: src/tox.ini: Add "develop" environment
  • #29868: pip-installable packages sagemath-doc-...
  • #31386: Move list of scripts from setup.py to setup.cfg
  • possibly move pkgs/sage-conf/sage_conf.py[.in] into src/, mark it (and also src/bin/sage-env-config[.in]) # sage_setup: distribution = sage-conf.
  • #31543: Eliminate use of patches for Python packages
  • #28925 Modify find_python_sources, clean_stale_files to support modularization of sagelib by native namespace packages (PEP 420)
  • #30666 Add "sage_setup: distribution" directives to all Cython modules needing external libraries
  • #30036: sage_conf-pypi: API for incremental builds
  • #29041 sage_bootstrap: Add command sage -package list --output={install-requires,requirements,pipfile,debian,....}
  • #30896: ./configure --without-sage-venv
  • #30647: Make lazy_import more friendly to pyflakes and other static checkers
  • #30152: sage_setup: Modify clean_stale_files to support out-of-tree namespace packages
  • Deploy mildly modularized distributions sagemath-core, sagemath-tdlib, ... to PyPI.
    • #30151: Modularization of sagelib: Break out a separate package sagemath-meataxe
    • #29864: Modularization of sagelib: Break out a separate package sagemath-tdlib
    • sagemath-giac (ex giacpy_sage in sage.libs.giac + dependency on libgiac)
    • sagemath-brial (ex sage-brial in sage.rings.polynomial.pbori + sage.libs.polybori, sage.crypto.boolean_function)
    • #30716 Towards making Arb library optional
  • Further modularization:
    • Rework sagemath-objects, sagemath-categories as namespace packages.
    • #29912: Modularization of sagelib: Break out a separate package sagemath-ntl
    • Modularization of sagelib: Break out a separate package sage-flint-arb-e_antic
    • #29941: Modularization of sagelib: Break out a separate package sagemath-repl
    • Modularization of sagelib: Break out a separate package sagemath-maxima (depends on ecl and maxima, packages sage.interfaces.maxima*, sage.libs.ecl)... or sagemath-calculus(?)
    • sagemath-singular
    • #31444 Modularization of sagelib: Break out separate package sagemath-linbox
    • #31695 Modularization of sagelib: Break out separate package sagemath-symbolics
  • Perhaps move the top-level scripts (sage, sage-env) to a separate package sagemath-scripts. This will allow users to run, for example, sage -sh before sagelib is installed.
  • #29874: Mock integer class
  • #29875: sage.structure.coerce.py_scalar_parent, py_scalar_to_element: Make dynamic
  • #29877: sage.categories: Replace import of ZZ by py_scalar_parent(int)
  • #25009: Split out sage.libs.primecount/sage.interfaces.primecount as a separate Python library
  • #29845: PEP 517 buildapi for sage_setup
  • #30527: Create PEP 503 simple repository for wheels built during installation
  • #30371: In-place (editable) installs of sagelib in a venv

Related:

Change History (160)

comment:1 Changed 16 months ago by mkoeppe

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comment:7 Changed 16 months ago by mkoeppe

  • Keywords sd109 added

comment:8 Changed 16 months ago by mkoeppe

  • Branch set to u/mkoeppe/META-modularize-sagelib

comment:9 Changed 16 months ago by mkoeppe

  • Cc gh-kliem jhpalmieri added
  • Commit set to 06a59119edb6d28e9b7cf8ca1bb192d7991ed5d5

Last 10 new commits:

47cb578is_package_or_namespace_package_dir: Recognize namespace packages by file 'namespace'
381a507src/module_list.py: Remove explicit list of sage.numerical.backends extensions
4c51133sage_setup/command/sage_install.py: WIP: Disable cleaning
c0a2ed7src/module_list.py: Remove explicit listing of sage.graphs.graph_decompositions extensions
acaa409Merge branch 't/28925/modify_find_python_sources__clean_stale_files_to_support_modularization_of_sagelib_by_native_namespace_packages__pep_420_' into HEAD
6909e23build/pkgs/coxeter3/distros/fedora.txt: New
2b060aesrc/module_list.py: Move OptionalExtension options for sage.libs.coxeter3.coxeter to distutils directive
4f0d07dsrc/sage/libs/coxeter3/decl.pxd: Add coxeter/ prefix to all header includes; src/module_list.py: remove include_dirs option
1497f3fbuild/pkgs/coxeter3/spkg-configure.m4: New
06a5911Merge branch 't/29721/spkg_configure_m4_for_coxeter3' into HEAD

comment:10 Changed 16 months ago by mkoeppe

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comment:11 Changed 16 months ago by mkoeppe

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comment:12 Changed 16 months ago by git

  • Commit changed from 06a59119edb6d28e9b7cf8ca1bb192d7991ed5d5 to 4365e5d772cabee22c9eb269b44eeed5788ae5ea

Branch pushed to git repo; I updated commit sha1. New commits:

55bd7basrc/module_list.py: Move options for Extensions in sage.graphs to distutils directives
4365e5dMerge branch 't/29790/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_5__sage_graphs_' into t/29705/META-modularize-sagelib

comment:13 Changed 16 months ago by git

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Branch pushed to git repo; I updated commit sha1. New commits:

7d94648src/module_list.py: Move options for Extensions in sage.libs to distutils directives

comment:14 Changed 16 months ago by mkoeppe

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comment:15 Changed 16 months ago by git

  • Commit changed from 7d94648a8904b499a5d76df4a44e006927467bb4 to b3d3d2f3baa0e1700c51b7df58a5af1aeba5acc4

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

9dc7022Merge branch 't/29706/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files' into t/29791/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_6__last_
f78b06dsrc/module_list.py: Move options for Extensions in sage.libs to distutils directives
1b0e29dsrc/module_list.py: Move options for Extensions in sage.matrix to distutils directives
6421e2csrc/module_list.py: Move remaining options for Extensions in sage.libs, sage.rings to distutils directives
b3d3d2fMerge branch 't/29791/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_6__last_' into t/29705/META-modularize-sagelib

comment:16 Changed 16 months ago by git

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Branch pushed to git repo; I updated commit sha1. New commits:

2821934Fix sage_setup directives: Use distribution, not package
9052db4Merge branch 't/29720/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_2___optionalextensions_' into t/29705/META-modularize-sagelib
ff710eesrc/sage_setup/optional_extension.py (is_package_installed_and_updated): Factor out from OptionalExtension
891d12asrc/setup.py: Remove use of module_list.py; filter by distributions

comment:17 Changed 16 months ago by mkoeppe

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comment:18 Changed 16 months ago by mkoeppe

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comment:19 Changed 16 months ago by mkoeppe

  • Summary changed from Meta-ticket: Modularize sagelib into separate distutils packages to Meta-ticket: Modularize sagelib into separate distributions (distutils packages)

comment:20 Changed 16 months ago by mkoeppe

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comment:21 Changed 16 months ago by mkoeppe

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comment:22 Changed 16 months ago by git

  • Commit changed from 891d12aeacd439cd72e31d42399826f48dae624f to bd26ddfc501e27f8c0544833358ce9887b023b9d

Branch pushed to git repo; I updated commit sha1. New commits:

0295c8fsrc/module_list.py: Move options for Extensions in sage.graphs.graph_decompositions to distutils directives
b582789src/sage_setup/find.py: Filter by directive 'sage_setup: distribution = PKG', find Cython modules
63c64d5Merge branches 't/29720/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_2___optionalextensions_', 't/29721/spkg_configure_m4_for_coxeter3', 't/29785/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_3__get_rid_of_uname_specific_', 't/29786/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_4__sage_rings_', 't/29790/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_5__sage_graphs_' and 't/29791/move_extension_options_from_src_module_list_py_to__distutils___directives_in_the_individual_files__part_6__last_' into t/29701/replace_use_of_module_list_optionalextension
ae70c81src/sage_setup/optional_extension.py (is_package_installed_and_updated): Factor out from OptionalExtension
ec7e9c5src/setup.py: Remove use of module_list.py; filter by distributions
bd26ddfMerge branch 't/29701/replace_use_of_module_list_optionalextension' into t/29705/META-modularize-sagelib

comment:23 Changed 16 months ago by mkoeppe

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comment:24 Changed 16 months ago by git

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Branch pushed to git repo; I updated commit sha1. New commits:

38b6bcfMerge tag '9.2.beta0' into t/29411/make_sagelib_a_script_package
f9a30f6build/pkgs/sagelib/spkg-install: Fix up error exits
00a1d57Merge branch 't/29411/make_sagelib_a_script_package' into t/29702/move_all_code_from_src_setup_py__src_fpickle_setup_py_to_sage_setup
25a2340Merge branch 't/29702/move_all_code_from_src_setup_py__src_fpickle_setup_py_to_sage_setup' into t/29701/replace_use_of_module_list_optionalextension
d7bd69eMerge branch 't/29701/replace_use_of_module_list_optionalextension' into t/29705/META-modularize-sagelib
2d866a3src/sage/graphs/graph_decompositions/tdlib.pyx: Fixup
14f488fMerge branch 't/29701/replace_use_of_module_list_optionalextension' into t/29705/META-modularize-sagelib
0d9f653WIP: Add sage_tdlib package
26b5575Use sage_install

comment:25 Changed 16 months ago by mkoeppe

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comment:27 Changed 16 months ago by git

  • Commit changed from 26b557545a62fbcea64df8391be097098e6dbaa1 to 7dd469fdf92a45b80049cd0583c75550ce1032ff

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

29327d3build/pkgs/entrypoints: Do not provide setup.py, not needed for entrypoints 0.3
bcc79a5build/pkgs/entrypoints/spkg-install.in: Remove pyproject.toml so that setup.py is used
361b98bbuild/pkgs/terminado/spkg-install.in: Remove pyproject.toml so that setup.py is used
5040d7ebuild/pkgs/testpath/spkg-install.in: Remove pyproject.toml so that setup.py is used
371ede6build/pkgs/zope_interface: Change to a dummy script package
b7c63dfMerge branch 't/29803/upgrade_setuptools__pip__2020_06_' into t/29705/META-modularize-sagelib
5f33436src/setup.py: from setuptools import setup
93bbbfeAdd src/setup.cfg
a7de6c0Merge branch 't/13190/make_sagelib_use_setuptools_instead_of_distutils' into t/29705/META-modularize-sagelib
7dd469fWIP: Add sage_tdlib package, use symlinks for sagelib package

comment:28 Changed 16 months ago by mkoeppe

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comment:29 Changed 16 months ago by git

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24e9b30build/pkgs/sage_tdlib/src/MANIFEST.in: New

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9b59435fixup symlinks

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Branch pushed to git repo; I updated commit sha1. New commits:

60ed86csrc/setup.py: WIP: Do not use sage_install
19e061dbuild/pkgs/sage_tdlib/src/sage_setup: Remove, we use the installed one

comment:32 Changed 16 months ago by git

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c3593b2build/pkgs/sage_tdlib/src/sage_setup: Remove, we use the installed one

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2612091Use setup.py install --single-version-externally-managed
458d851build/pkgs/sage_tdlib/spkg-src: New

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5d4e8e7build/pkgs/sage_tdlib/dependencies: Add sagelib, python toolchain
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90b33d8Install sagelib, sage_tdlib via sdist defined by MANIFEST.in

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2ccf6b7Merge tag '9.2.beta1' into t/29705/META-modularize-sagelib

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  • Summary changed from Meta-ticket: Modularize sagelib into separate distributions (distutils packages) to Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages)

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  • Summary changed from Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages) to Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages) sagemath-...

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