* 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>
* Add 20181226 release of pgmath
* 20190329 release of pgmath requires match for CMPLX macro.
* Add llvm-flang package for Flang fork of LLVM
* Add new and old flang releases.
* Add cmake and python dependencies.
* Update dependencies on llvm-flang and pgmath.
* Fix cmake args and change spec to reflect llvm-flang package.
* change copyright date through 2020.
* Reference Flang package more explicitly.
* More robust support for python executable.
* import os no longer needed, picked up by flake8.
* Use built-in target spec. Variant and targets follow style in main LLVM package.
* Get rid of targets list and only support one target for now.
* Sparc does not appear to be supported in Flang.
* Raise InstallError if architecture not supported.
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* Quick fix for relocation issues.
* elf relocation fix: cherry-picked from develop branch (#6889)
* Revert "Quick fix for relocation issues."
This reverts commit 57608a6dc4.
* Buildcache: relocate fixes (#6512)
* Updated function which checks if a binary file needs relocation.
Previously this was incorrectly identifying ELF binaries as symbolic
links (so they were being excluded from relocation). Added test to
check that ELF binaries are not considered symlinks.
* relocate_text was not replacing paths in text files. Added test to
check that text files are relocated properly (i.e. paths in the file
are converted to the new prefix).
* Exclude backup files created by filter_file when installing from
binary cache.
* Update write_buildinfo_file method signature to distinguish between
the spec prefix and the working directory for the binary cache
package.
* Final changes for v0.11.0 (#6318)
* Fix logo link in README.md to point to the develop branch. (#6969)
* Compiler flag handlers (#6415)
This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).
When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.
Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.
This also removes redundant build system definitions from tutorial
examples
* Fix type issues with setting flag handlers (#6960)
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
* Bump version to 0.11.1
* Added flags to unit tests + OSX build done once per day (#6988)
* Adding flags to codecov reports
* OSX builds are triggered once a day
* Pull R list_urls from upstream.
* travis: removed /usr/local/include/c++ before installing gcc on OSX (#6515) (#7027)
"brew install gcc" fails for travis build because of an existing
/usr/local/include/c++. This commit removes the offending file
as suggested by brew.
* Fix gfortran 7 detection (#7017)
* Add NameError to exceptions caught from configure_args in module generation (#7173)
* Revert "Binary caching: remove symlinks, copy files instead (#9747)"
This reverts commit 058cf81312.
* Make Spack relocate text files in build caches with relative binaries
* add the tfel package
* fix the tfel package
* fix the tfel package
* fix the tfel package
* Taking Adam J. Steward' remarks into account
* fixes trailing white spaces
* Update description
* Update dependencies following @adamjstewart adices
* Style fixes
* Style fixes
* Add java optional support
* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)
* flake8 fixes
* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)
* Style fixes
* Style fixes
* Fix test on python version
* Follow @adamjstewart advices: code is much cleaner and readable
* Small fix
* Small fix
* Add comment
* Small fix in cmake option
* try again (trying to overcome Travis CI unstable build process)
* Add support for the MFrontGenericInterfaceSupport project (MGIS)
* Style fixes
* Package documentation update
* Package documentation update
* Fix a typo thanks to Andreas Baumbach review
* Follow Adam J. Stewart advices
* Fix type
* bugfix: add back r's for invalid regexes
* tutorial basics section: fix gcc install version
* version bump: v0.12.1
* bugfix: bring in .travis.yml from develop
* Add new TFEL' versions (3.0.4, 3.1.4 and 3.2.1). Add new MGIS version (1.0.1). Fix MGIS dependency
* merge with spack:develop
* add missing dependency
* new versions of and
* Fix MGIS url. Fix duplicate variant in TFEL
* Fix tfel packaging according to Adam J. Stewart' advices
* Fix flake8 warning
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Peter Scheibel <scheibel1@llnl.gov>
Co-authored-by: Greg Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add ADF
* Fix typo and lint
* fix lint again
* one more lint fix
* fix identation
* still stying to fix identation
* one final fix
* import needed libraries
* changes as per reviewer's request
fix setup environment function, enhance recipe
* add import os once again
* chnages as per reviewer's request
When removing packages from a view, extensions were being deactivated
in an arbitrary order. Extensions must be deactivated in preorder
traversal (dependents before dependencies), so when this order was
violated the view update would fail.
This commit ensures that views deactivate extensions based on a
preorder traversal and adds a test for it.
