* py-rtree: Added package
* py-rtree = RTree (spatial indexing) data structure for Python
* libspatialindex = Underlying C library wrapped by py-rtree
* Flake8 and Copyright issues.
* Fix Python syntax error.
* Fixed dependency type error.
* Added new version, based on updates requested in upstream PR
* 1. Change cmake to build dependency.
2. Updated to CMakePackage
* Update go to 1.7.4 and 1.6.4 to fix security issues
The go team recently rolled out two releases to address security
issues. Details available on the [go release
site](https://golang.org/doc/devel/release.html).
This commit updates our explicitly supported versions.
It also includes a comment about two CentOS requirements (enable
user_namespace and ensure that the static c library is installed) that
are required for the pacakges to pass their tests.
* Flake8 cleanup
* Make X11 font install dir the font search default
We install the X11 fonts into `/share/fonts` beneath the font-util
installation prefix, but that directory is not one of the places that
the font subsystem searches.
This commit makes the fontconfig package depend on the font-util
package, and then it makes
```python
spec['font-util'].prefix + "/share/fonts"
```
be the fontconfig default font location.
Before this change, plots drawn by R have bounding boxes where font
glyphs should be. After this change fonts appear as expected.
* Enrich description string (trigger new CI run)
Improve the docstring for the package.
Also interested in the side effect of triggering another CI run
to see if the recent flake8 fix lets this PR run clean.
* Flake8 cleanups
* Update R&friends to use our X11 libs
Add `depends_on()`'s for R, Cairo, and Tk so that they use the Spack X
bits.
* Conditionalize X stuff on variant
Another step towards hooking up the X stuff.
There's still discussion happening on the issue, but this is better
than the 'everything must build with X' state that it was in.
- Added 'dap' and 'cdmremote' variants
This is based on work in #2324 with the following motivation:
Turn off DAP support by deafult. DAP requires curl, which has issues
with circular dependencies. For 95% of NetCDF users that do not need
DAP, turning it off avoides this rats nest of problems.
- Added 'parallel-netcdf' variant
To support work with parallel-netcdf
- Added 'shared' and 'static' build separation
* Update go-bootstrap package
The last C based Go src tree was the 1.4 series. For a while they
were cutting new releases so that people could bootstrap from a C only
system. Now they're recommending that you either use the release-1.4
branch or that you use a date-stamped tarball that they'll produce on
an as-needed basis.
There are several issues that keep 1.4.2 from building on a CentOS 7
system.
I've switched to the date based tarball.
The cgo bits were also mis-behaving, but they're not needed for the
bootstrapping task so I've set an environment variable that disables
them.
Details [on the install-from-source
page](https://golang.org/doc/install/source#go14) and these issues:
- https://github.com/golang/go/issues/17545
- https://github.com/golang/go/issues/16352.
* Update go package
Switched from pulling from the git repository to using the source
tarballs and added digest values.
Added support for 1.7.3, continued supporting 1.6.2, including patches
for a couple of problems (details in
[17545](https://github.com/golang/go/issues/17545) and
[17986](https://github.com/golang/go/issues/17986).
Dropped support for 1.5.4 and 1.4.2 because they no longer pass their
tests and the patches above to not apply.
* Updating SuperLU package file with ability to build version 4.3 (before they added cmake) with external blas or internal blas, and added capability to build the latest version 5.2.1 (with cmake) with internal blas.
* Updating SuperLU package file with suggested changes, i.e. reorganizing installation methods based on version, adding cmake dependency when necessary, removing any use of internal blas, and also adding fpic variant.
* Fixing flake8 failures.
* Update flex package url's and versions
The old sourceforge page for flex is now defunct. While version 2.6.0
still downloads fine, later versions are no longer hosted there.
Development continues on github. I've adjusted urls to point to this
new location.
In addition, from 2.6.0 onwards, a new naming scheme for releases seems
to have been adopted. I've created a url_for_version function to sort
this out.
* Change flex to an AutotoolsPackage
Also move the url_for_version function to the end of the package
definition.
* Implement the autoreconf function for flex
Adds the IceT compositing library from Sandia/Kitware.
Most default functionality needed for image compositing is
added, OpenGL acceleration for very large displays is disabled.
Downstream usage:
most VTK based software which supports parallel image compositing,
such as VisIt, Paraview and in our use-case
[ISAAC](https://github.com/ComputationalRadiationPhysics/isaac).
* Force the recipe for Lua to use the spack compiler.
I'm not sure how the old recipe worked for anyone. The Lua Makefiles set
`CC=gcc` and for my spack environment the first `gcc` found in my `PATH` is
`$SPACK_ROOT/lib/spack/env/gcc`, which is a directory. This caused the build
to fail. My change drops the `-std=gnu99`, but this option doesn't appear
to be required for a sucessful build.
* Preserve the '-std=gnu99' compile option.
* fix tau installation issue : setup_environment() is
called before install phase when 'Makefile.*' doesn't
exist (causing list index out of range error).
* Added detailed comment suggested by @alalazo
* November 1 seems to have brought a new texlive release, updating the
digest to match.
Also switching the url from their automagic mirror to an explicit
site to avoid inconsistencies during their updates.
It seems like only yesterday (#2073) that I updated this....
* Add comment to url warning about mirror updates
Add a comment to the download info warning to use a
specific site rather than the mirror, to avoid wobbles
during their asynchronous updates.
* Fix typo ('to no' -> 'do not')
On MacOS, brew installs /usr/local/bin/python but the Python prefix is not /usr/local/bin
Use the python command sys.exec to get the correct directory, instead of the ad hoc self.prefix
previously used
This was a bear to debug; been driving me nuts since I started using spack.
Since spack passes PYTHONHOME down to package builds in the environment
it was passing PYTHONHOME of /usr/local/bin to the PETSc build that uses Python so
the PETSc Python ./configure errored immediately with
ImportError: No module named site
since python could find no python modules. Todd Gamblin pointed out that my first try to fix
this was wrong since it assumed the spack python was the same python used to run spack. Elizabeth Fischer
suggested how to get it to work also with python3
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 7 hours
Thanks-to: Todd Gamblin, Elizabeth Fischer
