Refactoring after PR#53 code review by mdmitry1 · Pull Request #59 · SMLP-Systems/smlp

mdmitry1 · 2026-03-17T16:33:20Z

Regression passed in all five configurations, all Docker images are uploaded

2) Preparation for gmp library reuse instead of compilation

2. Changed pre-built wheel location

mdmitry1

Regression passed after the first refactoring round.

Main fixes:

Write access to system directory is removed
<repo>/dist directory is removed
<repo>/manylinux_2_28 directory is removed
Optional git switch is removed
Z3_PREFIX is set automatically - tested on Ubuntu 24.04

Validation:

pip install <repo> use case - validated on Ubuntu 24.04
Manylinux wheel build use case - validated on Ubuntu 22.04

…ing forward

2. Updated wheel location in Dockerfile

…on fails on AlmaLinux

2. Rebuild wheel with new setup.py version

2. Replaced hard-coded branch name by parameter

2) Meson and ninja search code cleanup

mdmitry1

Finished second round of refactoring

Fixed build issue in the case of user_config.jam file present in home directory
Added meson and ninja to build-system.requires
Removed redundant meson and ninja search code
For Debian only: started using precompiled gmp libraries
For manylinux build got compilation error in SMLP C++ code

Validation

DORA test passed in Ubuntu 24.04 python virtual environment with manylinux wheel.

fbrausse · 2026-03-18T14:13:00Z

4. For manylinux build got compilation error in SMLP C++ code

Could you post the log containing the error? I'll take a look what might have gone wrong. Also the version number of GMP they install might be helpful, if you know it.

mdmitry1 · 2026-03-18T16:26:23Z

1) ../src/reals.hh: In function ‘kay::Z smlp::reals::eager::ubound_log2(const R&)’:
../src/reals.hh:62:39: error: invalid initialization of reference of type ‘const kay::Z&’ {aka ‘const mpz_class&’} from expression of type ‘__gmp_expr<__mpq_struct [1], __gmp_unary_expr<__gmp_expr<__mpq_struct [1], __gmp_unary_expr<__gmp_expr<__mpq_struct [1], __mpq_struct [1]>, __gmp_abs_function> >, __gmp_ceil_function> >’

gmp version is 6.3.0

fbrausse · 2026-03-18T17:22:46Z

../src/reals.hh: In function ‘kay::Z smlp::reals::eager::ubound_log2(const R&)’: ../src/reals.hh:62:39: error: invalid initialization of reference of type ‘const kay::Z&’ {aka ‘const mpz_class&’} from expression of type ‘__gmp_expr<__mpq_struct [1], __gmp_unary_expr<__gmp_expr<__mpq_struct [1], __gmp_unary_expr<__gmp_expr<__mpq_struct [1], __mpq_struct [1]>, __gmp_abs_function> >, __gmp_ceil_function> >’

gmp version is 6.3.0

I can't reproduce this locally, neither with gcc-{13,14,15} nor with clang++-{20,21}. I also don't understand why the ceil function would return an mpq_class, it (kay's, that is) should return an mpz_class object. It could be an include path issue (since kay's ceil doesn't seem to be used) or sth. else. While I can't run manylinux here, yet, the full compile log (including the compiler commands run) might help.

mdmitry1

Refactoring is done.
The only remaining step: merge with
commit a44b1d2
Author: Konstantin Korovin kostyakor@gmail.com
Date: Wed Mar 11 14:23:24 2026 +0000

pyproject.toml: patch for standalone smlp

fbrausse · 2026-03-21T17:26:11Z

merge with commit a44b1d2

No need to merge branches. Cherry-pick should be fine.

pyproject.toml: patch for standalone smlp

2. Added smlp command support

… files 2. Fixed inaccuracies in scripts/bin/README.md

Reference: #62

fbrausse

Thanks, Dmitry. For now I have a few comments, will test it tomorrow.

src/run_smlp.py

setup.py

pyproject.toml

fbrausse · 2026-03-23T00:04:03Z

pyproject.toml

 [tool.setuptools.packages.find]
 where = ["."]
-exclude = ["src*", "smlp_py*", "regr_smlp*", "utils*"]
+exclude = ["scripts*","src*", "smlp_py*", "regr_smlp*", "utils*"]


While on a clean source tree this (mostly, sometimes a __pycache__ directory is included as well)
works, might I suggest to explicitly include the files instead of excluding only some? For instance, it is quite common, to put temporary directories and other files while testing / developing. Being explicit about the files part of the wheel is also more future-proof.

This is just to exclude looking for *whl files. If we decided not to have *whl files in our distribution, probably the safest thing to do is remove these lines.

This is just to exclude looking for *whl files. If we decided not to have *whl files in our distribution, probably the safest thing to do is remove these lines.

This is just to exclude looking for *whl files. If we decided not to have *whl files in our distribution, probably the safest thing to do is remove these lines.

What this does, is include everything and then selectively exempt some files/dirs from everything. There is a separate include option for tool.setuptools.packages.find, which instead includes only the given things and excludes everything else. That is what I'm suggesting. See https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

We need to exclude everything.

We don't need to include and/or discover anything.

Therefore, correct lines are:

[tool.setuptools.packages.find] where = ["."] exclude = ["*"]

Without exclude statement, some extra files are written in the distribution area.
Please, run installation and if something is incorrect, let me know.
For me everything works fine:

find /usr/local/lib/python3.11/dist-packages -name smlp'*'

/usr/local/lib/python3.11/dist-packages/smlp-1.0.1.dist-info /usr/local/lib/python3.11/dist-packages/smlp /usr/local/lib/python3.11/dist-packages/smlp/smlp_py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_verify.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_terms.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_solver.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_plots.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_correlations.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_config.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_verify.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_refine.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_doe.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_mrmr.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_constants.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_flows.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_optimize.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_terms.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_precisions.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_frontier.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_data.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_models.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_discretize.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_utils.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_spec.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_logs.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_query.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/__pycache__/smlp_subgroups.cpython-311.pyc /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_optimize.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_plots.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_models.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_flows.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_solver.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_precisions.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_query.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_correlations.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_doe.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_refine.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_frontier.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_spec.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_logs.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_discretize.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_subgroups.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_constants.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_config.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_data.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_utils.py /usr/local/lib/python3.11/dist-packages/smlp/smlp_py/smlp_mrmr.py /usr/local/lib/python3.11/dist-packages/bin/smlp

Thanks, I'll try it. Looks weird, though.

mdmitry1

Updates according to release plan

…commit

mdmitry1

Implemented requested changes after review

mdmitry1 added 10 commits March 16, 2026 14:41

Initial commit for issue# 58 fix

53e88ea

Wheel build and test scripts refactoring

0f7fc60

Reverted scikit-learn back to 1.4.2 due to pycaret requirement

2e5adfb

Refactoring after code review

6a9613a

1) Updated Z3_PREFIX to synch with setup.py change

cfe5319

2) Preparation for gmp library reuse instead of compilation

Removed branch switching

f107386

Removed redundant setting of PKG_CONFIG_PATH

072d97a

1. Added default Z3_PREFIX definition for Ubuntu 24.04

4b1da46

2. Changed pre-built wheel location

Made existing wheel invisible for setup.py

008f394

Replaced wheel by the result of clean build

c1b8794

mdmitry1 marked this pull request as draft March 17, 2026 16:34

mdmitry1 added 2 commits March 17, 2026 19:16

Added support of image build from current branch

a133938

Fixed typo

bcbee68

mdmitry1 commented Mar 17, 2026

View reviewed changes

mdmitry1 added 12 commits March 18, 2026 09:15

Fixed build crash due to existing ~/user-config.jam

9e5d1db

Removed redundant build files, as only manylinux will be supported go…

84124a9

…ing forward

1. Removed redundant files

271c1cf

2. Updated wheel location in Dockerfile

Removed redundant code

8a5c67a

Fixed typo

61ff498

Added support of preinstalled gmp package

343c7e6

Leaving using prebuilt GMP library only for Ubuntu, as smlp compilati…

591dcf2

…on fails on AlmaLinux

1. Reverted back Dockerfile to compile gmp

afc221c

2. Rebuild wheel with new setup.py version

1. Updated wheel location

0d61874

2. Replaced hard-coded branch name by parameter

Using meson from build.system

d455ff5

1) Using ninja from build system

9e50a9a

2) Meson and ninja search code cleanup

Rebuilt wheel after build scripts update

e32580f

mdmitry1 commented Mar 18, 2026

View reviewed changes

mdmitry1 commented Mar 21, 2026

View reviewed changes

mdmitry1 added 7 commits March 21, 2026 21:44

Fixed inaccuracies in README.md

64a9446

Merge with a44b1d2

f002e41

pyproject.toml: patch for standalone smlp

Updated wheel after adding smlp command support

cbfe16e

1. Fixed refactoring issue

2a0e7d7

2. Added smlp command support

1. Removed unnecessary gpg package from OpenSuse and AlmaLinux docker…

fc6c4ad

… files 2. Fixed inaccuracies in scripts/bin/README.md

Removed redundant files

af470c4

Removing redundant file.

4ac2665

Reference: #62

mdmitry1 marked this pull request as ready for review March 22, 2026 20:00

mdmitry1 requested review from fbrausse and zurabksmlp March 22, 2026 20:01

fbrausse reviewed Mar 23, 2026

View reviewed changes

mdmitry1 added 5 commits March 23, 2026 09:30

Implemented fixes, recommended by @fbrausse

791c0fe

Updated wheel version 0.1.0 -> 1.0.1

69762cd

Updated wheel name

71ddb76

Added smlp command support to mdmitry1/python311-dev container

720f261

Removed redundant comment

b1374e7

fbrausse mentioned this pull request Mar 23, 2026

macos: Use @rpath for libraries bundled in wheel #67

Open

mdmitry1 added 3 commits March 23, 2026 12:59

Fixed package description

4684922

Moved repair_wheel.py from repository root to this directory

978d0a1

Moved bench directory from repository root to here

7746fc7

mdmitry1 commented Mar 23, 2026

View reviewed changes

mdmitry1 added 2 commits March 23, 2026 17:12

No files should be copied to distribution area

2fd3ca1

Synch wheel with pyproject.toml bug fix. See details in the previous …

5b85173

…commit

mdmitry1 requested a review from fbrausse March 23, 2026 15:53

mdmitry1 added 2 commits March 23, 2026 19:05

Removed erroneous comments

c6d11ff

Removed redundant comments

c63ac15

mdmitry1 commented Mar 23, 2026

View reviewed changes

Synchronized requirements.txt with pyproject.toml

a734cc4

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Regression passed after the first refactoring round.

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Finished second round of refactoring

Validation

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