passagemath: General purpose mathematical software system, a fork of SageMath

passagemath is open source mathematical software released under the GNU General Public Licence GPLv2+.

It is a fork of SageMath, created in October 2024 with the following goals:

providing modularized installation with pip,
establishing first-class membership in the scientific Python ecosystem,
giving clear attribution of upstream projects,
inviting collaborations with upstream projects,
maintaining a professional, respectful, inclusive community,
developing a port to Pyodide for serverless deployment with Javascript,
developing a native Windows port.

People all around the globe have contributed to the development of SageMath, and hence of passagemath.

Full installation

Unless you need to install passagemath into a specific existing environment, we recommend to create and activate a fresh virtual environment over a suitable Python (3.9.x-3.12.x), for example ~/passagemath-venv/:

        $ python3 --version
        Python 3.12.7
        $ python3 -m venv ~/passagemath-venv
        $ source ~/passagemath-venv/bin/activate

Next, if you want to build from PyPI, use the following command:

        passagemath $ export SAGE_CONF_TARGETS=build

If you want to build from a local clone of the passagemath repository instead, use the following command first.

        passagemath $ export SAGE_ROOT=$(pwd)
        passagemath $ export PIP_CONSTRAINT="$(pwd)/constraints_pkgs.txt"
        passagemath $ export SAGE_CONF_TARGETS=build-local

As the first installation step, install , which builds various prerequisite non-Python packages in a subdirectory of ~/.sage/. The build can be customized by setting SAGE_CONF_CONFIGURE_ARGS.

        (passagemath-venv) $ python3 -m pip install -v passagemath-conf

After a successful installation, a wheelhouse provides various Python packages. You can list the wheels using the command:

        (passagemath-venv) $ ls $(sage-config SAGE_SPKG_WHEELS)

If this gives an error saying that sage-config is not found, check any messages that the pip install command may have printed. You may need to adjust your PATH, for example by:

        $ export PATH="$(python3 -c 'import sysconfig; print(sysconfig.get_path("scripts", "posix_user"))'):$PATH"

Now install the packages from the wheelhouse:

        (passagemath-venv) $ python3 -m pip install $(sage-config SAGE_SPKG_WHEELS)/*.whl

Next, install the package:

        (passagemath-venv) $ python3 -m pip install passagemath-setup

Finally, install the Sage library from the package :

        (passagemath-venv) $ python3 -m pip install --no-build-isolation -v passagemath-standard

The above instructions install the latest stable release of passagemath. To install the latest development version instead, add the switch --pre to all invocations of python3 -m pip install.

Modularized distributions

The passagemath library is provided by a number of distributions (pip-installable packages).

Distributions named after a basic mathematical structure

The packages may also cover a wide range of generalizations/applications of the structure after which they are named. Users who work in a specialized research area will, of course, recognize what structures they need. The down-to-earth naming also creates discoverability by a broader audience. Not many more distribution packages than these 7 are needed:

provides "everything combinatorial", except for graphs. It provides the functionality of SYMMETRICA, the library for representation theory of the symmetric group, combinatorics of tableaux, symmetric functions, etc.

provides directed and undirected graphs, but also posets, combinatorial designs, abstract simplicial complexes, quivers, etc. It uses the Boost Graph Library, with additional functionality from NetworkX and several other libraries.

provides groups and invariant theory.

provides vector spaces, modules, matrices, tensors, homology, coding theory, abelian groups, etc.

provides convex polyhedra in arbitrary dimension on the basis of the Parma Polyhedra Library, but also provides fans, hyperplane arrangements, polyhedral complexes, linear and mixed-integer optimization, lattice point sets, and toric varieties.

provides algebraic varieties, schemes, elliptic curves, modular forms, etc.

provides symbolic expressions implemented in Pynac, a fork of GiNaC, symbolic calculus using Maxima, and interfaces to various other symbolic software systems including SymPy, as well as differential geometry (SageManifolds).

Distributions named after a third-party non-Python dependency

This makes technical sense because the dependencies will be localized to this distribution package, but it also helps give attribution and visibility to these libraries and projects that Sage depends on.

Standard packages	Optional Packages
provides modules depending on FLINT, the Fast Library for Number Theory.	provides the functionality of bliss, a tool for computing automorphism groups and canonical forms of graphs.
provides modules depending on GAP, the system for computational discrete algebra with particular emphasis on Computational Group Theory.	provides the functionality of BRiAl, a Boolean Ring Algebra implementation using binary decision diagrams, the successor to PolyBoRi.
provides the functionality of Giac, a general purpose computer algebra system.
provides a mixed integer linear optimization backend using GLPK, the GNU Linear Programming Kit.
provides the functionality of libhomfly, the library to compute the homfly polynomial of knots and links.
provides the functionality of lcalc, the L-function calculator.
provides the functionality of libbraiding, the library to compute several properties of braids, including centralizer and conjugacy check.	provides the functionality of treedec, algorithms concerning tree decompositions of graphs.
provides the functionality of GMP-ECM, the elliptic curve method for integer factorization.

provides the functionality of NTL, a library for doing number theory.
provides the functionality of PARI/GP, the computer algebra system for fast computations in number theory.
provides functionality from Singular, the computer algebra system for polynomial computations, algebraic geometry, singularity theory.

Distributions named after a technical functionality

Sage extends Python's object system by dynamic mix-in classes that are driven by categories and axioms. It is loosely modeled on concepts of category theory and inspired by Scratchpad/Axiom/FriCAS, Magma, and MuPAD. This distribution package makes Sage objects, the element/parent framework, basic categories and functors, the coercion system and the related metaclasses available. It only depends on the basic arithmetic libraries GMP, MPFR, MPC, on the Cython interface gmpy2 to these libraries, and on cysignals.

This distribution package contains the full set of categories defined by Sage, as well as basic mathematical objects such as integers and rational numbers, a basic implementation of polynomials, and affine spaces. None of this brings in additional dependencies.

provides the sage script for launching the Sage REPL and accessing various developer tools and Python modules that provide the connection to the system and software environment.

The top-level interactive environment with the preparser that defines the surface language of Sage. This distribution also includes the doctesting facilities (sage -t), as the doctests are written in the surface language.

Plotting facilities, depending on matplotlib.

Ideally an empty meta-package that depends on everything that is not in passagemath-symbolics; as a catch-all mechanism, this distribution ships all modules that do not carry a # sage_setup: distribution = ... directive.

Everything as provided by a standard installation of the Sage distribution. This is reduced to an empty meta-package.

Confectionery and configuration system.

Build system for the Sage library.

Build system for the Sage documentation.

Getting Started
Supported Platforms
[Windows] Preparing the Platform
[macOS] Preparing the Platform
Instructions to Build from Source
SageMath Docker Images
Troubleshooting
Contributing to Sage
Directory Layout
Build System
Relocation
Redistribution
Build System
Changes to Included Software

Getting Started

Those who are impatient may use prebuilt Sage available online from any of

[![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/passagemath/passagemath/tree/main

)

without local installation. Otherwise read on.

The Sage Installation Guide provides a decision tree that guides you to the type of installation that will work best for you. This includes building from source, obtaining Sage from a package manager, using a container image, or using Sage in the cloud.

This README contains self-contained instructions for building Sage from source. This requires you to clone the git repository (as described in this README) or download the sources in the form of a tarball.

If you have questions or encounter problems, please do not hesitate to email the sage-support mailing list or ask on the Ask Sage questions and answers site.

Supported Platforms

Sage attempts to support all major Linux distributions, recent versions of macOS, and Windows (using Windows Subsystem for Linux or virtualization).

Detailed information on supported platforms for a specific version of Sage can be found in the section Availability and installation help of the release notes for this version.

We highly appreciate contributions to Sage that fix portability bugs and help port Sage to new platforms; let us know at the sage-devel mailing list.

[Windows] Preparing the Platform

The preferred way to run Sage on Windows is using Windows Subsystem for Linux (WSL). Follow the official WSL setup guide to install Ubuntu (or another Linux distribution). Make sure you allocate WSL sufficient RAM; 5GB is known to work, while 2GB might be not enough for building Sage from source. Then all instructions for installation in Linux apply.

As an alternative, you can also run Linux on Windows using Docker (see below) or other virtualization solutions.

[macOS] Preparing the Platform

If your Mac uses the Apple Silicon (M1, M2, M3, M4; arm64) architecture and you set up your Mac by transferring files from an older Mac, make sure that the directory /usr/local does not contain an old copy of Homebrew (or other software) for the x86_64 architecture that you may have copied over. Note that Homebrew for the M1 is installed in /opt/homebrew, not /usr/local.
If you wish to use conda, please see the section on conda in the Sage Installation Manual for guidance.
Otherwise, we strongly recommend to use Homebrew ("the missing package manager for macOS") from https://brew.sh/, which provides the gfortran compiler and many libraries.
Otherwise, if you do not wish to install Homebrew, you will need to install the latest version of Xcode Command Line Tools. Open a terminal window and run xcode-select --install; then click "Install" in the pop-up window. If the Xcode Command Line Tools are already installed, you may want to check if they need to be updated by typing softwareupdate -l.

Instructions to Build from Source

Like many other software packages, Sage is built from source using ./configure, followed by make. However, we strongly recommend to read the following step-by-step instructions for building Sage.

The instructions cover all of Linux, macOS, and WSL.

More details, providing a background for these instructions, can be found in the section Install from Source Code in the Installation Guide.

Decide on the source/build directory (SAGE_ROOT):
- On personal computers, any subdirectory of your :envvar:HOME directory should do.
- For example, you could use SAGE_ROOT=~/sage/sage, which we will use as the running example below.
- You need at least 10 GB of free disk space.
- The full path to the source directory must contain no spaces.
- After starting the build, you cannot move the source/build directory without breaking things.
- You may want to avoid slow filesystems such as network file systems (NFS) and the like.
- [macOS] macOS allows changing directories without using exact capitalization. Beware of this convenience when compiling for macOS. Ignoring exact capitalization when changing into :envvar:SAGE_ROOT can lead to build errors for dependencies requiring exact capitalization in path names.
Clone the sources with git:
- To check that git is available, open a terminal and enter the following command at the shell prompt ($):
```
  $ git --version
  git version 2.42.0
```
  The exact version does not matter, but if this command gives an error, install git using your package manager, using one of these commands:
```
  $ sudo pacman -S git                          # on Arch Linux
  $ sudo apt-get update && apt-get install git  # on Debian/Ubuntu
  $ sudo yum install git                        # on Fedora/Redhat/CentOS
  $ sudo zypper install git                     # on openSUSE
  $ sudo xbps-install git                       # on Void Linux
```
- Create the directory where SAGE_ROOT should be established:
```
  $ mkdir -p ~/sage
  $ cd ~/sage
```
- Clone the passagemath git repository:
```
  $ git clone -c core.symlinks=true --filter blob:none  \
              --origin passagemath \
              https://github.com/passagemath/passagemath.git
```
  This will create the subdirectory ~/sage/passagemath. (See the section Setting up git and the following sections in the Sage Developer's Guide for more information.)
- Change into the created subdirectory:
```
  $ cd passagemath
```
- [Windows] The Sage source tree contains symbolic links, and the build will not work if Windows line endings rather than UNIX line endings are used.
  
  Therefore it is recommended (but not necessary) to use the WSL version of git.
Install system packages.

Either refer for this to the section on installation from source in the Sage Installation Manual for compilations of system packages that you can install. When done, skip to step 7 (bootstrapping).

Alternatively, follow the more fine-grained approach below.
[Linux, WSL] Install the required minimal build prerequisites:
- Compilers: gcc, gfortran, g++ (GCC versions from 8.4.0 to 13.x and recent versions of Clang (LLVM) are supported). See build/pkgs/gcc/SPKG.rst and build/pkgs/gfortran/SPKG.rst for a discussion of suitable compilers.
- Build tools: GNU make, GNU m4, perl (including ExtUtils::MakeMaker), ranlib, git, tar, bc. See build/pkgs/_prereq/SPKG.rst for more details.
- Python 3.4 or later, or Python 2.7, a full installation including urllib; but ideally version 3.9.x, 3.10.x, 3.11.x, 3.12.x, which will avoid having to build Sage's own copy of Python 3. See build/pkgs/python3/SPKG.rst for more details.
We have collected lists of system packages that provide these build prerequisites. See, in the folder build/pkgs/_prereq/distros, the files arch.txt, debian.txt (also for Ubuntu, Linux Mint, etc.), fedora.txt (also for Red Hat, CentOS), opensuse.txt, slackware.txt, and void.txt, or visit https://doc.sagemath.org/html/en/reference/spkg/_prereq.html#spkg-prereq
Optional: It is recommended that you have both LaTeX and the ImageMagick tools (e.g. the "convert" command) installed since some plotting functionality benefits from them.
[Development] If you plan to do Sage development or otherwise work with ticket branches and not only releases, install the bootstrapping prerequisites. See the files in the folder build/pkgs/_bootstrap/distros, or visit https://doc.sagemath.org/html/en/reference/spkg/_bootstrap.html#spkg-bootstrap
Bootstrap the source tree using the following command:
```
$ make configure
```
(If the bootstrapping prerequisites are not installed, this command will download a package providing pre-built bootstrap output instead.)
Sanitize the build environment. Use the command
```
$ env
```
to inspect the current environment variables, in particular PATH, PKG_CONFIG_PATH, LD_LIBRARY_PATH, CFLAGS, CPPFLAGS, CXXFLAGS, and LDFLAGS (if set).

Remove items from these (colon-separated) environment variables that Sage should not use for its own build. In particular, remove items if they refer to a previous Sage installation.
- [WSL] In particular, WSL imports many items from the Windows PATH variable into the Linux environment, which can lead to confusing build errors. These items typically start with /mnt/c. It is best to remove all of them from the environment variables. For example, you can set PATH using the command:
```
  $ export PATH=/usr/sbin/:/sbin/:/bin/:/usr/lib/wsl/lib/
```
- [macOS with homebrew] Set required environment variables for the build:
```
  $ source ./.homebrew-build-env
```
  This is to make some of Homebrew's packages (so-called keg-only packages) available for the build. Run it once to apply the suggestions for the current terminal session. You may need to repeat this command before you rebuild Sage from a new terminal session, or after installing additional homebrew packages. (You can also add it to your shell profile so that it gets run automatically in all future sessions.)
Optionally, decide on the installation prefix (SAGE_LOCAL):
- Traditionally, and by default, Sage is installed into the subdirectory hierarchy rooted at SAGE_ROOT/local/.
- This can be changed using ./configure --prefix=SAGE_LOCAL, where SAGE_LOCAL is the desired installation prefix, which must be writable by the user.
  
  Unless you use this option in combination with --enable-editable, you can delete the entire Sage source tree after completing the build process. What is installed in SAGE_LOCAL will be a self-contained installation of Sage.
- Note that in Sage's build process, make builds and installs (make install is a no-op). Therefore the installation hierarchy must be writable by the user.
- See the Sage Installation Manual for options if you want to install into shared locations such as /usr/local/. Do not attempt to build Sage as root.
Optionally, review the configuration options, which includes many optional packages:
```
$ ./configure --help
```
Notable options for Sage developers are the following:
- Use the option --config-cache to have configure keep a disk cache of configuration values. This gives a nice speedup when trying out ticket branches that make package upgrades, which involves automatic re-runs of the configuration step.
- Use the option --enable-ccache to have Sage install and use the optional package ccache, which is preconfigured to keep a disk cache of object files created from source files. This can give a great speedup when switching between different branches, at the expense of disk space use.
Optional, but highly recommended: Set some environment variables to customize the build.

For example, the MAKE environment variable controls whether to run several jobs in parallel. On a machine with 4 processors, say, typing export MAKE="make -j4" will configure the build script to perform a parallel compilation of Sage using 4 jobs. On some powerful machines, you might even consider -j16, as building with more jobs than CPU cores can speed things up further.

To reduce the terminal output during the build, type export V=0. (V stands for "verbosity".)

Some environment variables deserve a special mention: CC, CXX and FC. These variables defining your compilers can be set at configuration time and their values will be recorded for further use at build time and runtime.

For an in-depth discussion of more environment variables for building Sage, see the installation guide.
Type ./configure, followed by any options that you wish to use. For example, to build Sage with gf2x package supplied by Sage, use ./configure --with-system-gf2x=no.

At the end of a successful ./configure run, you may see messages recommending to install extra system packages using your package manager.

For a large list of Sage packages, Sage is able to detect whether an installed system package is suitable for use with Sage; in that case, Sage will not build another copy from source.

Sometimes, the messages will recommend to install packages that are already installed on your system. See the earlier configure messages or the file config.log for explanation. Also, the messages may recommend to install packages that are actually not available; only the most recent releases of your distribution will have all of these recommended packages.
Optional: If you choose to install the additional system packages, a re-run of ./configure will test whether the versions installed are usable for Sage; if they are, this will reduce the compilation time and disk space needed by Sage. The usage of packages may be adjusted by ./configure parameters (check again the output of ./configure --help).
Type make. That's it! Everything is automatic and non-interactive.

If you followed the above instructions, in particular regarding the installation of system packages recommended by the output of ./configure (step 11), and regarding the parallel build (step 10), building Sage takes less than one hour on a modern computer. (Otherwise, it can take much longer.)

The build should work fine on all fully supported platforms. If it does not, we want to know!
Type ./sage to try it out. In Sage, try for example 2 + 2, plot(x^2), plot3d(lambda x, y: x*y, (-1, 1), (-1, 1)) to test a simple computation and plotting in 2D and 3D. Type Ctrl+D or quit to quit Sage.
Optional: Type make ptestlong to test all examples in the documentation (over 200,000 lines of input!) -- this takes from 10 minutes to several hours. Don't get too disturbed if there are 2 to 3 failures, but always feel free to email the section of logs/ptestlong.log that contains errors to the sage-support mailing list. If there are numerous failures, there was a serious problem with your build.
The HTML version of the documentation is built during the compilation process of Sage and resides in the directory local/share/doc/sage/html/. You may want to bookmark it in your browser.
Optional: If you want to build the PDF version of the documentation, run make doc-pdf (this requires LaTeX to be installed).
Optional: Install optional packages of interest to you: get a list by typing ./sage --optional or by visiting the packages documentation page.
Optional: Create a symlink to the installed sage script in a directory in your PATH, for example /usr/local. This will allow you to start Sage by typing sage from anywhere rather than having to either type the full path or navigate to the Sage directory and type ./sage. This can be done by running:
```
$ sudo ln -s $(./sage -sh -c 'ls $SAGE_ROOT/venv/bin/sage') /usr/local/bin
```
Optional: Set up SageMath as a Jupyter kernel in an existing Jupyter notebook or JupyterLab installation, as described in the section Launching SageMath in the Sage Installation Guide.

Troubleshooting

If you have problems building Sage, check the Sage Installation Guide, as well as the version-specific installation help in the release tour corresponding to the version that you are installing.

Please do not hesitate to ask for help in the SageMath forum or the sage-support mailing list. The Troubleshooting section in the Sage Installation Guide provides instructions on what information to provide so that we can provide help more effectively.

Contributing to Sage

If you'd like to contribute to Sage, we strongly recommend that you read the Developer's Guide.

Sage has significant components written in the following languages: C/C++, Python, Cython, Common Lisp, Fortran, and a bit of Perl.

Directory Layout

Simplified directory layout (only essential files/directories):

SAGE_ROOT                 Root directory (create by git clone)
├── build
│   └── pkgs              Every package is a subdirectory here
│       ├── 4ti2/
│       …
│       └── zlib/
├── configure             Top-level configure script
├── COPYING.txt           Copyright information
├── pkgs                  Source trees of Python distribution packages
│   ├── sage-conf
│   │   ├── sage_conf.py
│   │   └── setup.py
│   ├── sage-docbuild
│   │   ├── sage_docbuild/
│   │   └── setup.py
│   ├── sage-setup
│   │   ├── sage_setup/
│   │   └── setup.py
│   ├── sage-sws2rst
│   │   ├── sage_sws2rst/
│   │   └── setup.py
│   └── sagemath-standard
│       ├── bin/
│       ├── sage -> ../../src/sage
│       └── setup.py
├── local  (SAGE_LOCAL)   Installation hierarchy for non-Python packages
│   ├── bin               Executables
│   ├── include           C/C++ headers
│   ├── lib               Shared libraries, architecture-dependent data
│   ├── share             Databases, architecture-independent data, docs
│   │   └── doc           Viewable docs of Sage and of some components
│   └── var
│       ├── lib/sage
│       │   ├── installed/
│       │   │             Records of installed non-Python packages
│       │   ├── scripts/  Scripts for uninstalling installed packages
│       │   └── venv-python3.9  (SAGE_VENV)
│       │       │         Installation hierarchy (virtual environment)
│       │       │         for Python packages
│       │       ├── bin/  Executables and installed scripts
│       │       ├── lib/python3.9/site-packages/
│       │       │         Python modules/packages are installed here
│       │       └── var/lib/sage/
│       │           └── wheels/
│       │                 Python wheels for all installed Python packages
│       │
│       └── tmp/sage/     Temporary files when building Sage
├── logs
│   ├── install.log       Full install log
│   └── pkgs              Build logs of individual packages
│       ├── alabaster-0.7.12.log
│       …
│       └── zlib-1.2.11.log
├── m4                    M4 macros for generating the configure script
│   └── *.m4
├── Makefile              Running "make" uses this file
├── prefix -> SAGE_LOCAL  Convenience symlink to the installation tree
├── README.md             This file
├── sage                  Script to start Sage
├── src                   Monolithic Sage library source tree
│   ├── bin/              Scripts that Sage uses internally
│   ├── doc/              Sage documentation sources
│   └── sage/             The Sage library source code
├── upstream              Source tarballs of packages
│   ├── Babel-2.9.1.tar.gz
│   …
│   └── zlib-1.2.11.tar.gz
├── venv -> SAGE_VENV     Convenience symlink to the virtual environment
└── VERSION.txt

For more details see our Developer's Guide.

Build System

This is a brief summary of the Sage software distribution's build system. There are two components to the full Sage system--the Sage Python library and its associated user interfaces, and the larger software distribution of Sage's main dependencies (for those dependencies not supplied by the user's system).

Sage's Python library is built and installed using a setup.py script as is standard for Python packages (Sage's setup.py is non-trivial, but not unusual).

Most of the rest of the build system is concerned with building all of Sage's dependencies in the correct order in relation to each other. The dependencies included by Sage are referred to as SPKGs (i.e. "Sage Packages") and are listed under build/pkgs.

The main entrypoint to Sage's build system is the top-level Makefile at the root of the source tree. Unlike most normal projects that use autoconf (Sage does as well, as described below), this Makefile is not generated. Instead, it contains a few high-level targets and targets related to bootstrapping the system. Nonetheless, we still run make <target> from the root of the source tree--targets not explicitly defined in the top-level Makefile are passed through to another Makefile under build/make/Makefile.

The latter build/make/Makefile is generated by an autoconf-generated configure script, using the template in build/make/Makefile.in. This includes rules for building the Sage library itself (make sagelib), and for building and installing each of Sage's dependencies (e.g. make gf2x).

The configure script itself, if it is not already built, can be generated by running the bootstrap script (the latter requires GNU autotools being installed). The top-level Makefile also takes care of this automatically.

To summarize, running a command like make python3 at the top-level of the source tree goes something like this:

make python3
run ./bootstrap if configure needs updating
run ./configure with any previously configured options if build/make/Makefile needs updating
change directory into build/make and run the install script--this is little more than a front-end to running make -f build/make/Makefile python3, which sets some necessary environment variables and logs some information
build/make/Makefile contains the actual rule for building python3; this includes building all of python3's dependencies first (and their dependencies, recursively); the actual package installation is performed with the sage-spkg program

Relocation

It is not supported to move the SAGE_ROOT or SAGE_LOCAL directory after building Sage. If you do move the directories, you will have to run make distclean and build Sage again from scratch.

For a system-wide installation, you have to build Sage as a "normal" user and then as root you can change permissions. See the Installation Guide for further information.

Redistribution

Your local Sage install is almost exactly the same as any "developer" install. You can make changes to documentation, source, etc., and very easily package the complete results up for redistribution just like we do.

To make a binary distribution with your currently installed packages, visit sagemath/binary-pkg.
To make your own source tarball of Sage, type:
```
$ make dist
```
The result is placed in the directory dist/.

Changes to Included Software

All software included with Sage is copyrighted by the respective authors and released under an open source license that is GPL version 3 or later compatible. See COPYING.txt for more details.

Sources are in unmodified (as far as possible) tarballs in the upstream/ directory. The remaining description, version information, patches, and build scripts are in the accompanying build/pkgs/<packagename> directory. This directory is part of the Sage git repository.

https://www.sagemath.org

n-WN/passagemath