If you are producing code to add new functionality to Sage, you might consider turning it into a package (an “spkg”) instead of a patch file. If your code is very large (for instance) and should be offered as an optional download, a package is the right choice. Similarly, if your code depends on some other optional component of Sage, you should produce a package. When in doubt, ask for advice on the sage-devel mailing list.
This chapter covers issues relevant to producing a package. The directory structure of a package is discussed along with scripts for installing a package and running the test suite (if any) contained in an upstream project’s source distribution. For guidelines on patching an existing Sage package, see the chapter Patching a Sage Package.
The abbreviation “spkg” stands for “Sage package”. The directory SAGE_ROOT/spkg/standard contains spkg’s. In a source install, these are all Sage spkg files (actually .tar or .tar.bz2 files), which are the source code that defines Sage. In a binary install, some of these may be small placeholder files to save space.
Sage packages are distributed as .spkg files, which are .tar.bz2 files (or tar files) but have the extension .spkg to discourage confusion. Although Sage packages are packed using tar and/or bzip2, note that .spkg files contain control information (installation scripts and metadata) that are necessary for building and installing them. When you compile Sage from a source distribution (or when you run sage -i <pkg> or sage -f <pkg>), the file SAGE_ROOT/spkg/bin/sage-spkg takes care of the unpacking, compilation, and installation of Sage packages for you. You can type
tar -jxvf mypackage-version.spkg
to extract an spkg and see what is inside. If you want to create a new Sage package, it is recommended that you start by examining some existing spkg’s. In a source distribution of Sage, the standard spkg’s can be found under SAGE_ROOT/spkg/standard/. The URL http://www.sagemath.org/download-packages.html lists standard spkg’s available for download.
Each Sage spkg has a name of the following form:
BASENAME is the name of the package; it may contain lower-case letters, numbers, and underscores, but no hyphens. VERSION is the version number; it should start with a number and may contain numbers, letters, dots, and hyphens; it may end in a string of the form “pNUM”, where “NUM” is a non-negative integer. If your spkg is a “vanilla” (unmodified) version of some piece of software, say version 5.3 of “my-python-package”, then BASENAME would be “my_python_package” – note the change from hyphens to underscores, because BASENAME should not contain any hyphens – and VERSION would be “5.3”. If you need to modify the software to use it with Sage (as described below and in the chapter Patching a Sage Package), then VERSION would be “5.3.p0”, the “p0” indicating a patch-level of 0. If someone adds more patches, later, this would become “p1”, then “p2”, etc.
The string VERSION must be present. If you are using a piece software with no obvious version number, use a date: you can see several such names among the standard Sage packages: http://www.sagemath.org/packages/standard/.
To give your spkg a name like this, create a directory called BASENAME-VERSION and put your files in that directory – the next section describes the directory structure.
Put your files in a directory with a name like mypackage-0.1, as described above. If you are porting another software package, then the directory should contain a subdirectory src/, containing an unaltered copy of the package. Every file not in src/ should be under version control, i.e. checked into an hg repository.
More precisely, the directory should contain the following:
src/: this directory contains vanilla upstream code, with a few exceptions, e.g. when the spkg shipped with Sage is in effect upstream, and development on that code base is happening in close coordination with Sage. See John Cremona’s eclib spkg, for instance. The directory src/ must not be under revision control.
.hg, .hgignore, and .hgtags: The Sage project uses Mercurial for its revision control system (see Producing Patches with Mercurial). The hidden directory .hg is part of the standard Sage spkg layout. It contains the Mercurial repository for all files not in the src/ directory. To create this Mercurial repository from scratch, you should do
The files .hgignore and .hgtags also belong to the Mercurial repository. The file .hgtags is optional, and is frequently omitted. You should make sure that the file .hgignore contains “src/”, since we are not tracking its content. Indeed, frequently this file contains only a single line,
spkg-install: this file contains the install script. See The file spkg-install for more information and a template.
SPKG.txt: this file describes the spkg in wiki format. Each new revision needs an updated changelog entry or the spkg will get an automatic “needs work” at review time. See The file SPKG.txt for a template.
spkg-check: this file runs the test suite. This is somewhat optional since not all spkg’s have test suites. If possible, do create such a script since it helps isolate bugs in upstream packages.
patches/: this directory contains patches to source files in src/. See Patching a Sage Package. Patches to files in src/ should be applied in spkg-install, and all patches must be documented in SPKG.txt, i.e. what they do, if they are platform specific, if they should be pushed upstream, etc. To ensure that all patched versions of upstream source files under src/ are under revision control, the whole directory patches/ must be under revision control.
Never apply patches to upstream source files under src/ and then package up an spkg. Such a mixture of upstream source with Sage specific patched versions is a recipe for confusion. There must be a clean separation between the source provided by the upstream project and the patched versions that the Sage project generates based on top of the upstream source.
The only exception to this rule is for removals of unused files or directories. Some packages contain parts which are not needed for Sage. To save space, these may be removed directly from src/. But be sure to document this in the “Special Update/Build Instructions” section in SPKG.txt!
The script spkg-install is run during installation of the Sage package. In this script, you may make the following assumptions:
The PATH has the locations of sage and python (from the Sage installation) at the front. Thus the command
python setup.py install
will run the correct version of Python with everything set up correctly. Also, running gap or Singular, for example, will run the correct version.
The environment variable SAGE_ROOT points to the root directory of the Sage installation.
The environment variable SAGE_LOCAL points to the SAGE_ROOT/local directory of the Sage installation.
The environment variables LD_LIBRARY_PATH and DYLD_LIBRARY_PATH both have SAGE_ROOT/local/lib at the front.
The spkg-install script should copy your files to the appropriate place after doing any build that is necessary. Here is a template:
#!/usr/bin/env bash if [ -z "$SAGE_LOCAL" ]; then echo >&2 "SAGE_LOCAL undefined ... exiting" echo >&2 "Maybe run 'sage --sh'?" exit 1 fi cd src # Apply patches. See SPKG.txt for information about what each patch # does. for patch in ../patches/*.patch; do [ -r "$patch" ] || continue # Skip non-existing or non-readable patches patch -p1 <"$patch" if [ $? -ne 0 ]; then echo >&2 "Error applying '$patch'" exit 1 fi done ./configure --prefix="$SAGE_LOCAL" 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 $MAKE install if [ $? -ne 0 ]; then echo >&2 "Error installing PACKAGE_NAME." exit 1 fi if [ "$SAGE_SPKG_INSTALL_DOCS" = yes ] ; then # Before trying to build the documentation, check if any # needed programs are present. In the example below, we # check for 'latex', but this will depend on the package. # Some packages may need no extra tools installed, others # may require some. We use 'command -v' for testing this, # and not 'which' since 'which' is not portable, whereas # 'command -v' is defined by POSIX. # if [ `command -v latex` ] ; then # echo "Good, latex was found, so building the documentation" # else # echo "Sorry, can't build the documentation for PACKAGE_NAME as latex is not installed" # exit 1 # fi # make the documentation in a package-specific way # for example, we might have # cd doc # $MAKE html if [ $? -ne 0 ]; then echo >&2 "Error building PACKAGE_NAME docs." exit 1 fi mkdir -p "$SAGE_ROOT/local/share/doc/PACKAGE_NAME" # assuming the docs are in doc/* cp -R doc/* "$SAGE_ROOT/local/share/doc/PACKAGE_NAME" fi
Note that the first line is #!/usr/bin/env bash; this is important for portability. Next, the script checks that SAGE_LOCAL is defined to make sure that the Sage environment has been set. After this, the script may simply run cd src and then call either python setup.py install or the autotools sequence ./configure && make && make install, or something else along these lines.
Sometimes, though, it can be more complicated. For example, you might need to apply the patches from the patches directory in a particular order. Also, you should first build (e.g. with python setup.py build, exiting if there is an error), before installing (e.g. with python setup.py install). In this way, you would not overwrite a working older version with a non-working newer version of the spkg.
When copying documentation to $SAGE_ROOT/local/share/doc/PACKAGE_NAME, it may be necessary to check that only the actual documentation files intended for the user are copied. For example, if the documentation is built from .tex files, you may just need to copy the resulting pdf files, rather than copying the entire doc directory. When generating documentation using Sphinx, copying the build/html directory generally will copy just the actual output intended for the user.
The SPKG.txt file should follow this pattern:
= name of spkg = == Description == Describe the package here. == License == Describe the package's license here. == SPKG Maintainers == * Mary Smith * Bill Jones * Leonhard Euler == Upstream Contact == Provide information for upstream contact. == Dependencies == Put a bulleted list of dependencies here: * python * readline == Special Update/Build Instructions == List patches that need to be applied and what they do == Changelog == Provide a changelog of the spkg here, where the entries have this format: === mypackage-0.1.p0 (Mary Smith, 1 Jan 2012) === * Patch src/configure so it builds on Solaris. See Sage trac #137. === mypackage-0.1 (Leonhard Euler, 17 September 1783) === * Initial release. See Sage trac #007.
When the directory (say, mypackage-0.1) is ready, the command
sage --pkg mypackage-0.1
will create the file mypackage-0.1.spkg. As noted above, this creates a compressed tar file. Running sage --pkg_nc mypackage-0.1 creates an uncompressed tar file.
When your spkg is ready, you should post about it on sage-devel. If people there think it is a good idea, then post a link to the spkg on the Sage trac server (see The Sage Trac Server: Submitting Patches and Packages) so it can be refereed. Do not post the spkg itself to the trac server: you only need to provide a link to your spkg. If your spkg gets a positive review, it might be included into the core Sage library, or it might become an optional download from the Sage website, so anybody can automatically install it by typing sage -i mypackage-version.spkg.
For any spkg:
If your package is intended to be a standard Sage spkg, then you should make sure that any dependencies for your package are recorded in the makefile SAGE_ROOT/spkg/standard/deps. Also add a line for your package to the script SAGE_ROOT/spkg/install. For example, the relevant line for the readline package is
If your package is not a standard package and depends on another non-standard package, say fricas-1.0.9.spkg, then your package’s spkg-install script should check that the other package has been installed, with code like the following:
if [ ! -f "$SAGE_ROOT/spkg/installed/fricas-1.0.9" ]; then echo >&2 "The fricas spkg, version 1.0.9 is required; please install it." exit 1 fi
If you don’t care which version of the fricas spkg is installed, you could instead use
if ! ls -1 "$SAGE_ROOT/spkg/installed/" | grep '^fricas-.*' > /dev/null ; then echo >&2 "The fricas spkg is required; please install it." exit 1 fi
(The regular expression matches the package name followed by a hyphen and then other characters; in particular, it was chosen so that it wouldn’t match a package like fricasaldor-1.0.9 whose name also starts with “fricas”.)
This could be made more sophisticated, for example testing which version of fricas is installed vs. which version is required, etc. You could, instead of or in addition to checking the existence of the appropriate file in $SAGE_ROOT/spkg/installed/, check for the required functionality somehow. For instance, the spkg-install script for the p_group_cohomology package checks whether database_gap is installed using the following:
SMALL_GROUPS=`echo "SmallGroup(13,1); quit;" | $SAGE_ROOT/sage -gap -b -T | grep "13"` if [ "$SMALL_GROUPS" = "" ]; then echo "It seems that GAP's SmallGroups library is missing." echo "One way to install it is by doing" echo " sage: install_package('database_gap')" echo "in a Sage session." exit 1 fi
Caveat: Do not just copy to e.g. SAGE_ROOT/local/lib/gap*/ since that will copy your package to the lib directory of the old version of GAP if GAP is upgraded.
External Magma code goes in SAGE_ROOT/devel/ext/magma/user, so if you want to redistribute Magma code with Sage as a package that Magma-enabled users can use, that is where you would put it. You would also want to have relevant Python code to make the Magma code easily usable.
This section contains some guidelines on what an spkg must never do to a Sage installation. You are encouraged to produce an spkg that is as self-contained as possible.