Packaging Third-Party Code

One of the mottoes of the Sage project is to not reinvent the wheel: If an algorithm is already implemented in a well-tested library then consider incorporating that library into Sage. The current list of available packages are the subdirectories of SAGE_ROOT/build/pkgs/. The installation of packages is done through a bash script located in SAGE_ROOT/build/bin/sage-spkg. This script is typically invoked by giving the command:

[[email protected]]$ sage -i <options> <package name>...

options can be:

  • -f: install a package even if the same version is already installed
  • -s: do not delete temporary build directory
  • -c: after installing, run the test suite for the spkg. This should override the settings of SAGE_CHECK and SAGE_CHECK_PACKAGES.
  • -d: only download the package

The section Directory Structure describes the structure of each individual package in SAGE_ROOT/build/pkgs. In section Building the package we see how you can install and test a new spkg that you or someone else wrote. Finally, Inclusion Procedure for New and Updated Packages explains how to submit a new package for inclusion in the Sage source code.

Package types

Not all packages are built by default, they are divided into standard, optional and experimental ones:

  • standard packages are built by default. For a few packages, configure checks whether they are available from the system, in which case the build of those packages is skipped. Standard packages have stringent quality requirements: they should work on all supported platforms. In order for a new standard package to be accepted, it should have been optional for a while, see Inclusion Procedure for New and Updated Packages.
  • optional packages are subject to the same requirements, they should also work on all supported platforms. If there are optional doctests in the Sage library, those tests must pass. Note that optional packages are not tested as much as standard packages, so in practice they might break more often than standard packages.
  • for experimental packages, the bar is much lower: even if there are some problems, the package can still be accepted.

Directory Structure

Third-party packages in Sage consist of two parts:

  1. The tarball as it is distributed by the third party, or as close as possible. Valid reasons for modifying the tarball are deleting unnecessary files to keep the download size manageable, regenerating auto-generated files or changing the directory structure if necessary. In certain cases, you may need to (additionally) change the filename of the tarball. In any case, the actual code must be unmodified: if you need to change the sources, add a patch instead. See also Modified Tarballs for automating the modifications to the upstream tarball.
  2. The build scripts and associated files are in a subdirectory SAGE_ROOT/build/pkgs/<package>, where you replace <package> with a lower-case version of the upstream project name. If the project name contains characters which are not alphanumeric and are not an underscore, those characters should be removed or replaced by an underscore. For example, the project FFLAS-FFPACK is called fflas_ffpack in Sage and path.py is renamed pathpy in Sage.

As an example, let us consider a hypothetical FoO project. They (upstream) distribute a tarball FoO-1.3.tar.gz (that will be automatically placed in SAGE_ROOT/upstream during the installation process). To package it in Sage, we create a subdirectory containing as a minimum the following files:

SAGE_ROOT/build/pkgs/foo
|-- checksums.ini
|-- dependencies
|-- package-version.txt
|-- spkg-install
|-- SPKG.txt
`-- type

The following are some additional files which can be added:

SAGE_ROOT/build/pkgs/foo
|-- patches
|   |-- bar.patch
|   `-- baz.patch
|-- spkg-check
`-- spkg-src

We discuss the individual files in the following sections.

Package type

The file type should contain a single word, which is either standard, optional or experimental. See Package types for the meaning of these types.

Build and install scripts

The spkg-build and spkg-install files are shell scripts or Python scripts which build and install the package. In the best case, the upstream project can simply be installed by the usual configure / make / make install steps. In that case, the build script would simply consist of:

#!/usr/bin/env bash

cd src

./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib"
if [ $? -ne 0 ]; then
    echo >&2 "Error configuring PACKAGE_NAME."
    exit 1
fi

$MAKE
if [ $? -ne 0 ]; then
    echo >&2 "Error building PACKAGE_NAME."
    exit 1
fi

The install script would consist of:

#!/usr/bin/env bash

cd src
$MAKE install
if [ $? -ne 0 ]; then
    echo >&2 "Error installing PACKAGE_NAME."
    exit 1
fi

Note that the top-level directory inside the tarball is renamed to src before calling the spkg-build and spkg-install scripts, so you can just use cd src instead of cd foo-1.3.

If there is any meaningful documentation included but not installed by make install, then you can add something like the following to install it:

if [ "$SAGE_SPKG_INSTALL_DOCS" = yes ] ; then
    $MAKE doc
    if [ $? -ne 0 ]; then
        echo >&2 "Error building PACKAGE_NAME docs."
        exit 1
    fi
    mkdir -p "$SAGE_SHARE/doc/PACKAGE_NAME"
    cp -R doc/* "$SAGE_SHARE/doc/PACKAGE_NAME"
fi

Many packages currently do not separate the build and install steps and only provide a spkg-install file that does both. The separation is useful in particular for root-owned install hierarchies:

  • If spkg-build exists, it is first called, followed by $SAGE_SUDO spkg-install.
  • Otherwise, only spkg-install is called (without $SAGE_SUDO). Such packages would prefix all commands in spkg-install that write into the installation hierarchy with $SAGE_SUDO.

Self-Tests

The spkg-check file is an optional, but highly recommended, script to run self-tests of the package. It is run after building and installing if the SAGE_CHECK environment variable is set, see the Sage installation guide. Ideally, upstream has some sort of tests suite that can be run with the standard make check target. In that case, the spkg-check script would simply contain:

#!/usr/bin/env bash

cd src
$MAKE check

The SPKG.txt File

The SPKG.txt file should follow this pattern:

= PACKAGE_NAME =

== Description ==

What does the package do?

== License ==

What is the license? If non-standard, is it GPLv3+ compatible?

== Upstream Contact ==

Provide information for upstream contact.

== Dependencies ==

Put a bulleted list of dependencies here:

* python
* readline

== Special Update/Build Instructions ==

If the tarball was modified by hand and not via a spkg-src
script, describe what was changed.

with PACKAGE_NAME replaced by the package name. Legacy SPKG.txt files have an additional changelog section, but this information is now kept in the git repository.

Package dependencies

Many packages depend on other packages. Consider for example the eclib package for elliptic curves. This package uses the libraries PARI, NTL and FLINT. So the following is the dependencies file for eclib:

pari ntl flint

----------
All lines of this file are ignored except the first.
It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

If there are no dependencies, you can use

# no dependencies

----------
All lines of this file are ignored except the first.
It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

There are actually two kinds of dependencies: there are normal dependencies and order-only dependencies, which are weaker. The syntax for the dependencies file is

normal dependencies | order-only dependencies

If there is no |, then all dependencies are normal.

  • If package A has an order-only dependency on B, it simply means that B must be built before A can be built. The version of B does not matter, only the fact that B is installed matters. This should be used if the dependency is purely a build-time dependency (for example, a dependency on Python simply because the spkg-install file is written in Python).
  • If A has a normal dependency on B, it means additionally that A should be rebuilt every time that B gets updated. This is the most common kind of dependency. A normal dependency is what you need for libraries: if we upgrade NTL, we should rebuild everything which uses NTL.

In order to check that the dependencies of your package are likely correct, the following command should work without errors:

[[email protected]]$ make distclean && make base && make PACKAGE_NAME

Finally, note that standard packages should only depend on standard packages and optional packages should only depend on standard or optional packages.

Patching Sources

Actual changes to the source code must be via patches, which should be placed in the patches/ directory, and must have the .patch extension. GNU patch is distributed with Sage, so you can rely on it being available. Patches must include documentation in their header (before the first diff hunk), and must have only one “prefix” level in the paths (that is, only one path level above the root of the upstream sources being patched). So a typical patch file should look like this:

Add autodoc_builtin_argspec config option

Following the title line you can add a multi-line description of
what the patch does, where you got it from if you did not write it
yourself, if they are platform specific, if they should be pushed
upstream, etc...

diff -dru Sphinx-1.2.2/sphinx/ext/autodoc.py.orig Sphinx-1.2.2/sphinx/ext/autodoc.py
--- Sphinx-1.2.2/sphinx/ext/autodoc.py.orig  2014-03-02 20:38:09.000000000 +1300
+++ Sphinx-1.2.2/sphinx/ext/autodoc.py  2014-10-19 23:02:09.000000000 +1300
@@ -1452,6 +1462,7 @@

     app.add_config_value('autoclass_content', 'class', True)
     app.add_config_value('autodoc_member_order', 'alphabetic', True)
+    app.add_config_value('autodoc_builtin_argspec', None, True)
     app.add_config_value('autodoc_default_flags', [], True)
     app.add_config_value('autodoc_docstring_signature', True, True)
     app.add_event('autodoc-process-docstring')

Patches directly under the patches/ directly are applied automatically before running the spkg-install script (so long as they have the .patch extension). If you need to apply patches conditionally (such as only on a specifically platform), you can place those patches in a subdirectory of patches/ and apply them manually using the sage-apply-patches script. For example, considering the layout:

SAGE_ROOT/build/pkgs/foo
|-- patches
|   |-- solaris
|   |   |-- solaris.patch
|   |-- bar.patch
|   `-- baz.patch

The patches bar.patch and baz.patch are applied to the unpacked upstream sources in src/ before running spkg-install. To conditionally apply the patch for Solaris the spkg-install should contain a section like this:

if [ $UNAME == "SunOS" ]; then
    sage-apply-patches -d solaris
fi

where the -d flag applies all patches in the solaris/ subdirectory of the main patches/ directory.

When to patch, when to repackage, when to autoconfiscate

  • Use unpatched original upstream tarball when possible.

    Sometimes it may seem as if you need to patch a (hand-written) Makefile because it “hard-codes” some paths or compiler flags:

    --- a/Makefile
    +++ b/Makefile
    @@ -77,7 +77,7 @@
     # This is a Makefile.
     # Handwritten.
    
    -DESTDIR = /usr/local
    +DESTDIR = $(SAGE_ROOT)/local
     BINDIR   = $(DESTDIR)/bin
     INCDIR   = $(DESTDIR)/include
     LIBDIR   = $(DESTDIR)/lib
    

    Don’t use patching for that. Makefile variables can be overridden from the command-line. Just use the following in spkg-install:

    $(MAKE) DESTDIR="$SAGE_ROOT/local"
    
  • Check if Debian or another distribution already provides patches for upstream. Use them, don’t reinvent the wheel.

  • If the upstream Makefile does not build shared libraries, don’t bother trying to patch it.

    Autoconfiscate the package instead and use the standard facilities of Automake and Libtool. This ensures that the shared library build is portable between Linux and macOS.

  • If you have to make changes to configure.ac or other source files of the autotools build system (or if you are autoconfiscating the package), then you can’t use patching; make a modified tarball instead.

  • If the patch would be huge, don’t use patching. Make a modified tarball instead.

  • Otherwise, maintain a set of patches.

How to maintain a set of patches

We recommend the following workflow for maintaining a set of patches.

  • Fork the package and put it on a public git repository.

    If upstream has a public version control repository, import it from there. If upstream does not have a public version control repository, import the current sources from the upstream tarball. Let’s call the branch upstream.

  • Create a branch for the changes necessary for Sage, let’s call it sage_package_VERSION, where version is the upstream version number.

  • Make the changes and commit them to the branch.

  • Generate the patches against the upstream branch:

    rm -Rf SAGE_ROOT/build/pkgs/PACKAGE/patches
    mkdir SAGE_ROOT/build/pkgs/PACKAGE/patches
    git format-patch -o SAGE_ROOT/build/pkgs/PACKAGE/patches/ upstream
    
  • Optionally, create an spkg-src file in the Sage package’s directory that regenerates the patch directory using the above commmands.

  • When a new upstream version becomes available, merge (or import) it into upstream, then create a new branch and rebase in on top of the updated upstream:

    git checkout sage_package_OLDVERSION
    git checkout -b sage_package_NEWVERSION
    git rebase upstream
    

    Then regenerate the patches.

Modified Tarballs

The spkg-src file is optional and only to document how the upstream tarball was changed. Ideally it is not modified, then there would be no spkg-src file present either.

However, if you really must modify the upstream tarball then it is recommended that you write a script, called spkg-src, that makes the changes. This not only serves as documentation but also makes it easier to apply the same modifications to future versions.

Package Versioning

The package-version.txt file containts just the version. So if upstream is FoO-1.3.tar.gz then the package version file would only contain 1.3.

If the upstream package is taken from some revision other than a stable version or if upstream doesn’t have a version number, you should use the date at which the revision is made. For example, the database_stein_watkins package with version 20110713 contains the database as of 2011-07-13. Note that the date should refer to the contents of the tarball, not to the day it was packaged for Sage. This particular Sage package for database_stein_watkins was created in 2014, but the data it contains was last updated in 2011.

If you apply any patches, or if you made changes to the upstream tarball (see Directory Structure for allowable changes), then you should append a .p0 to the version to indicate that it’s not a vanilla package.

Additionally, whenever you make changes to a package without changing the upstream tarball (for example, you add an additional patch or you fix something in the spkg-install file), you should also add or increase the patch level. So the different versions would be 1.3, 1.3.p0, 1.3.p1, ... The change in version number or patch level will trigger re-installation of the package, such that the changes are taken into account.

Checksums

The checksums.ini file contains the filename pattern of the upstream tarball (without the actual version) and its checksums. So if upstream is $SAGE_ROOT/upstream/FoO-1.3.tar.gz, create a new file $SAGE_ROOT/build/pkgs/foo/checksums.ini containing only:

tarball=FoO-VERSION.tar.gz

Sage internally replaces the VERSION substring with the content of package-version.txt. To recompute the checksums, run:

[[email protected]]$ sage --package fix-checksum foo

which will modify the checksums.ini file with the correct checksums.

Utility script to create package

Assuming that you have downloaded $SAGE_ROOT/upstream/FoO-1.3.tar.gz, you can use:

[[email protected]]$ sage --package create foo --version 1.3 --tarball FoO-VERSION.tar.gz --type experimental

to create $SAGE_ROOT/build/pkgs/foo/package-version.txt, checksums.ini, and type in one step.

Building the package

At this stage you have a new tarball that is not yet distributed with Sage (FoO-1.3.tar.gz in the example of section Directory Structure). Now you need to manually place it in the SAGE_ROOT/upstream/ directory and run sage --fix-pkg-checksums if you have not done that yet.

Now you can install the package using:

[[email protected]]$ sage -i package_name

or:

[[email protected]]$ sage -f package_name

to force a reinstallation. If your package contains a spkg-check script (see Self-Tests) it can be run with:

[[email protected]]$ sage -i -c package_name

or:

[[email protected]]$ sage -f -c package_name

If all went fine, open a ticket, put a link to the original tarball in the ticket and upload a branch with the code under SAGE_ROOT/build/pkgs.

Inclusion Procedure for New and Updated Packages

Packages that are not part of Sage will first become optional or experimental (the latter if they will not build on all supported systems). After they have been in optional for some time without problems they can be proposed to be included as standard packages in Sage.

To propose a package for optional/experimental inclusion please open a trac ticket with the respective Component: field set to either packages:experimental or packages:optional. The associated code requirements are described in the following sections.

After the ticket was reviewed and included, optional packages stay in that status for at least a year, after which they can be proposed to be included as standard packages in Sage. For this a trac ticket is opened with the Component: field set to packages:standard. Then make a proposal in the Google Group sage-devel.

Upgrading packages to new upstream versions or with additional patches includes opening a ticket in the respective category too, as described above.

License Information

If you are patching a standard Sage spkg, then you should make sure that the license information for that package is up-to-date, both in its SPKG.txt file and in the file SAGE_ROOT/COPYING.txt. For example, if you are producing an spkg which upgrades the vanilla source to a new version, check whether the license changed between versions.

Prerequisites for New Standard Packages

For a package to become part of Sage’s standard distribution, it must meet the following requirements:

  • License. For standard packages, the license must be compatible with the GNU General Public License, version 3. The Free Software Foundation maintains a long list of licenses and comments about them.

  • Build Support. The code must build on all the fully supported platforms.

    A standard package should also work on all the platforms where Sage is expected to work and on which Sage almost works but since we don’t fully support these platforms and often lack the resources to test on them, you are not expected to confirm your packages works on those platforms.

  • Quality. The code should be “better” than any other available code (that passes the two above criteria), and the authors need to justify this. The comparison should be made to both Python and other software. Criteria in passing the quality test include:

    • Speed
    • Documentation
    • Usability
    • Absence of memory leaks
    • Maintainable
    • Portability
    • Reasonable build time, size, dependencies
  • Previously an optional package. A new standard package must have spent some time as an optional package. Or have a good reason why this is not possible.

  • Refereeing. The code must be refereed, as discussed in The Sage Trac Server.