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.
* 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
* 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.
* 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.
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in
repeatmasker.
- the main RepeatMasker script
- SimpleBatcher.pm
- wublastToCrossmatch.pl
The ISO-8859 encoding prevented the sbang replacement of long paths when
spack uses python3.
* Update the icu4c package
This PR makes several changes to the icu4c package
1. add updated version to 65.1
2. modify the default url as project has moved to github
3. set UTF-8 locale to support building from source files in UTF-8
format
Note that the older versions are not available on github so explicit urls
were used. This PR will close#14399.
* Consolidate the urls
Consolidate the URLs in the `version` directives by using an if test in
`url_for_version`.
* Put version and sha256 on same line
* Put top level url back
* Update and fix bcftools package
This PR updates bcftools to 1.10.2 and is dependent on PR #14504.
This PR also fixes builds of other versions. Versions 1.2-1.4 did not
use autotools so when the packaeg was converted to use autotools with
version 1.6 those older versions could no longer build. Also, those
versions needed to be patched to use an external htsllib. The method of
finding the external htslib is also different for those older versions.
In addition, this PR adds two variants to bcftools:
- libgsl
- perl-filters
Finally, dependencies for perl and python are added, and an unused
dependency for libzip was removed.
* Do not use '@' in variant description
The '@' character in a variant description will cause a problem with
`spack info`.
```
==> Error: Incomplete color format: '@' in
expressions, for @1.8:
```
* Fix error with python2 processing this package
* Update htslib and add libcurl variant
This PR updates htslib to version 1.10.2 and adds a libcurl variant. The
libcurl variant defaults to True because, while it is optional, it is
highly recommended by the project developers.
Other things done:
- be consistent with quotes
* Change version in variant description
Apparently, `spack info` does not like the `@` character in a variant
description.
```
==> Error: Incomplete color format: '@' in
@1.3:.
```
The pathadd function was using setopt to configure zsh for word
splitting, which leaks out of the function and breaks default
functionality in a number of external zsh plugins and packages. This
switches to emulate -L, just as the spack function uses, to keep the
setting local to the function.
* libcircle: add develop version from git master branch
* Update var/spack/repos/builtin/packages/libcircle/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* libcircle: flake8 fix i think
* libcircle: naming things
* libcircle: 🐑 my sacrifice to the flake8 gods
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
