This PR adds the CudaPackage mixin class to py-theano. This replaces the
`gpu` variant with the `cuda` variant.

* Add new kcov package

* Fix linking error and add test

Signed-off-by: Sean Smith <seaam@amazon.com>

* capnproto: New package.

* capnproto: Fix flake8 errors.

* Remove characters invalid in Python 2.

Unfortunately UCX 1.7.0 is appearing in RPMS before it's officially released.
There's a problem with Open MPI 4.0.x where x < 3 and this version of UCX,
namely that the UCT BTL fails to compile.

See https://github.com/open-mpi/ompi/issues/7128



This patch works around the problem by disabling the build of the UCT BTL
for releases 4.0.0 to 4.0.2.

add hppritcha (me) as maintainer

Signed-off-by: Howard Pritchard <howardp@lanl.gov>

* Added py-spdlog package

* pleasing flake-8

* pleasing flake-8

* addressed some comments from adamjstewart

* changed URL for archive

* replaced with pypi.io url

* Add +cfitsio variant to wcslib dependency

* Replace ncurses dependency with readline dependency

casacore explicitly may depend on readline, not ncurses

* Add workaround for casacore's readline dependency

casacore optionally depends upon readline, but it's CMakeLists.txt provides no
user control over whether or not readline becomes a dependency. As readline is
often present by default on systems, it's better for this package to explicitly
depend on readline in order to prevent linking to whatever system version of the
library happens to be found during the build process. This should be considered
a workaround until casacore's CMakeLists.txt is fixed.

* Apply workaround for casacore's dependency on SOFA

Similar to the issues with casacore's readline dependency, casacore's optional
dependency on SOFA does not provide the user with a means of controlling the
dependency during build time. Unlike the readline library, the SOFA library is
unlikely to exist on most systems by default. As the SOFA dependency is only
optionally used for testing casacore, requiring it by default is not a good
workaround. Until casacore's CMakeLists.txt is fixed, this variant has been
removed to avoid unexpected library dependencies in the installed package.

* Add newer casacore versions

* Add mpokorny to maintainer field

Co-authored-by: mlhardware <57849932+mlhardware@users.noreply.github.com>

- The suite-sparse author publishes new versions starting with 5.5.0 on GitHub, see https://github.com/DrTimothyAldenDavis/SuiteSparse/releases and http://faculty.cse.tamu.edu/davis/SuiteSparse/
  - change spack to download from there
  - updated sha256 checksums from GitHub for all available releases
- For versions 5.4.0, 5.5.0, 5.6.0 there is a slightly different compilation necessary: first `make default` then `make install`.

Summary of the version changes (+ added, -removed [because not available on GitHub]):
```
+ 5.6.0
+ 5.5.0
+ 5.4.0
  5.3.0
  5.2.0
+ 5.1.2
  5.1.0
+ 5.0.0
+ 4.5.6
  4.5.5
- 4.5.4
  4.5.3
- 4.5.1
```

* Added new hashes for the protobuf and py-protobuf packates.

* Fixed flake8

* Fix use of sys.executable for module/env commands

* Fix unit tests

* More consistent quotation, less duplication

* Fix import syntax

This updates the UnifyFS package to account for the latest 0.9.0
version and removes support for version 0.2.0.

to disabled use of libunwind.  Without this mesa fails to build
using recent Cray compilers - cce 9 and higher -  on aarch64 systems.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>

* add new package : geode

* remove provides for gemfire

This PR adds CudaPackage in order to pick up the cuda/compiler conflicts
defined in CudaPackage.

It seems that stable versions of perl also install a `perlX.Y.Z` binary.
However, it seems that this binary can hang if used in conjunction with
Spack's sbang workaround, as observed during automake's build.

Add version Octave 5.1.0 including sha256.

* Update py-csvkit

This PR updates the py-csvkit package. This version requires a python
stack based on agate and this PR includes the new dependency packages.

- py-agate-dbf
- py-agate-excel
- py-agate-sql
- py-agate
- py-dbfread
- py-isodate
- py-leather
- py-parsedatetime
- py-python-slugify
- py-pytimeparse
- py-text-unidecode

* Replace the copy/pasted apostrophes

Python 2 can not process the copy/pasted apostrophes so replace them
with standard single quote character.

* Add version constraints on dependencies

* rocksdb: Fix for rocksdb issue 5303

* rocksdb: Explicitly disable features

* rocksdb: Add TBB variant.

* rocksdb: New version 5.18.3 and 6.5.3

* Add version contraint to graphviz patches

This PR restricts the graphviz version that the patches for building
with the Intel compiler apply to. The two patches that were needed for
building graphviz-2.40.1 with the Intel compiler are not needed for
graphviz-2.42.2.

* Adjust the qt dependencies

The qt5 patch is only needed for graphviz-2.40.1. However, that version
will only compile with GCC-6 or greater.

This also fixes actually building the development releases.

Add version 2019.12.28 and update the prereqs for the latest master.

* add variant for enabling testing

* add variant for enabling testing

* enable tests and clean up other options

* enable tests and clean up other options

* add numbered versions

* add numbered versions

* updates to avoid enable_tests variant; correct versioning

* updates to avoid enable_tests variant; correct versioning

* fixes for style

* appropriate partitioners are enabled if 'all' is specified - so no need to check in spec

* revert accidental change to copyright

* remove erroneously re-introduced line about tests

* new spack recipe for build Jali - unstructured mesh infrastructure for multiphysics applications

* remove the +parallel condition for mstk, update 1.1.1 sha256sum and whitespace cleanup

* reformat description

* cut down description

* Fixes:
1. MPI_THREAD_MULTIPLE problem with OpenMPI and UCX.

Changes:
1. OpenMPI provides two new depends_on options which result in UCX being compiled with multiple threads support. One implicit when OpenMPI 3.x is used, MPI_THREAD_MULTIPLE is enabled by default, and one explicit for OpenMPI <= 2.x, MPI_THREAD_MULTIPLE is disabled by default.
2. Extends UCX package to allow "Enable thread support in UCP and UCT" option.
3. Adds sha256 sums of UCX releases 1.6.1 and 1.2.0.

More details:
Fixes the issue with OpenMPI where programs which use MPI_THREAD_MULTIPLE will fail to execute because UCP worker didn't support it.
During the OpenMPI package installation it's the +thread_multiple spec was not propagated to UCX nor UCX handled it at all.
Now, the OpenMPI package is capable of handling +thread_multiple spec when UCX is request and the UCX package correctly handles +thread_multiple and compiles with the --enable-mt option.
Error message during runtime:
pml_ucx.c:226 Error: UCP worker does not support MPI_THREAD_MULTIPLE

* Adapts check of specs to read better and is the suggested form in the docs.

* Explicitly disables multithreading of UCX if +thread_multiple option is not used.

* Rework texlive package to install from source

This PR reworks the texlive package so that it installs from versioned
source distibution files. This is preferred over installing the binary
package for several reasons. For the binary installation:

1. Each component is downloaded, so can not use a spack mirror.
2. Changes in components over time are not reflected in spack hash.
3. Some of the binaries do not run due to glibc issues, depending on OS.

This PR keeps the binary installation as an option but it should be
considered deprecated, and probably rewmoved at some point.

This PR depends on zziplib from PR #14318.

* Fix flake8 issues

One of the perl scripts was encoded with ISO-8859-1, which caused the
sbang replacement process to fail when spack uses python3. This PR
converts the ps_scan script to UTF-8 encoding.