Extra packages wishlist

[slel]

This issue is devoted to requests for extra packages (as found in various discussion channels for instance).

Included in SageMath-9.4 with optional packages (see releases):

• [x] 4ti2
• [x] benzene
• [x] biopython
• [x] bliss
• [x] buckygen
• [x] cbc
• [x] coxeter3
• [x] cryptominisat
• [x] csdp
• [x] e_antic
• [x] frobby
• [x] gap_packages
• [x] glucose
• [x] gp2c
• [x] igraph
• [x] ipympl
• [x] isl
• [x] kenzo
• [x] latte_int
• [x] libnauty
• [x] libsemigroups
• [x] lrslib
• [x] mcqd
• [x] meataxe
• [x] mpfrcx
• [x] normaliz
• [x] p_group_cohomology
• [x] pari_elldata
• [x] pari_galpol
• [x] pari_nftables
• [x] plantri
• [x] primecount
• [x] pycosat
• [x] pynormaliz
• [x] pysingular
• [x] qhull
• [x] saclib
• [x] sage_numerical_backends_coin
• [x] sirocco
• [x] symengine
• [x] symengine_py
• [x] tdlib
• [x] tides
• [x] topcom

Other requests:

• [ ] dot2tex -- see Ask Sage question 60815

[culler]

The dot2tex package is can be installed with pip. To make it available to the macOS app, run %pip install dot2tex It will be installed in the user's .sage directory.

While the app does not support sage -i it does support installing pypi packages and our policy is that we do not include sage optional packages that can be installed with pip.

[slel]

Would it make sense for the error message to suggest that too?

Currently:

$ sage -i dot2tex
Sorry, this binary distribution does not support installing sage packages.

Proposed:

$ sage -i dot2tex
Sorry, this binary distribution does not support installing extra packages with `sage -i`.
If dot2tex is pip-installable, use the following from within Sage: `%pip install dot2tex`.

[culler]

Sure. I'll reopen the ticket to remind me to make that change.

[sudeepan]

A lot of these packages failed for version 9.5. Only kbmag seems to work.

I'm using the arm64 dmg on M1-Pro Mac.

(base) > ~ % sage ┌────────────────────────────────────────────────────────────────────┐ │ SageMath version 9.5, Release Date: 2022-01-30 │ │ Using Python 3.9.9. Type "help()" for help. │ └────────────────────────────────────────────────────────────────────┘ sage: libgap.LoadPackage("PackageManager")
true sage: libgap.InstallPackage("topcom")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmcCLlF1/exec-log.txt

I Package "topcom" not found in package list

false sage: libgap.InstallPackage("pynormaliz")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmQZS3On/exec-log.txt

I Package "pynormaliz" not found in package list

false sage: libgap.InstallPackage("kenzo")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmqTa5Zk/exec-log.txt

I Package "kenzo" not found in package list

false sage: libgap.InstallPackage("4ti2")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmzc0RsZ/exec-log.txt

I Package "4ti2" not found in package list

false sage: libgap.InstallPackage("gap_packages")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmZBeDqZ/exec-log.txt

I Package "gap_packages" not found in package list

false sage: libgap.InstallPackage("frobby")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tml4Lrdn/exec-log.txt

I Package "frobby" not found in package list

false sage: libgap.InstallPackage("normaliz")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmkeSLx2/exec-log.txt

I Package "normaliz" not found in package list

false sage: libgap.InstallPackage("qhull")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmy3NqxW/exec-log.txt

I Package "qhull" not found in package list

false sage: libgap.InstallPackage("symengine")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmNvL0L0/exec-log.txt

I Package "symengine" not found in package list

false sage: libgap.InstallPackage("saclib")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmr7ml2F/exec-log.txt

I Package "saclib" not found in package list

false sage: libgap.InstallPackage("kbmag")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmU2kKYO/exec-log.txt

I Retrieving PackageInfo.g from https://gap-packages.github.io/kbmag/PackageInfo.g ...

I Possible error detected: see log at /tmp/tm17YHZt/exec-log.txt

I The newest version of package "kbmag" is already installed

true sage: libgap.InstallPackage("libnauty")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmRgQbxn/exec-log.txt

I Package "libnauty" not found in package list

false sage: libgap.InstallPackage("libnauty")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmDhlIGG/exec-log.txt

I Package "libnauty" not found in package list

false sage: libgap.InstallPackage("glucose")

I Getting PackageInfo URLs...

I Possible error detected: see log at /tmp/tmnNVMma/exec-log.txt

I Package "glucose" not found in package list

false sage:

Upon checking these log files such as /tmp/tmcCLlF1/exec-log.txt for example, all of them turned out to be blank.

[slel]

@sudeepan

The command libgap.InstallPackage is to install GAP packages. Most of the packages you tried to install are not GAP packages, and the failure you observed is therefore not surprising.

Furthermore all packages listed in the first comment of this issue are already shipped with Sage-macOS in its extended form, except for dot2tex, which is a Python package listed on PyPI, and can therefore be installed by running:

sage: %pip install dot2tex

[sudeepan]

Thanks! I had been using sage (compiled from source) on linux so thought packages like topcom need to be installed manually. Checked just now that in the dmg it could be used off-the-shelf, just as you said.

[slel]

This ticket seems to be creating confusion. I opened #38 for the remaining issue.