* Make texlive untrusted
TeXLive updates their installer without changing its name. We've been
playing keep-up with them, but I'm proposing it's not worth it.
I seem to end up installing it '--no-checksum' anyway.
This commit updates the package to make that approach official,
removing the checksum, adding a note to the description and a bigger
note/comment inthe package body.
* Pull installer from stable source (packages are still *live*)
This pulls the installer script from the "historic" repository. It
appears to be stable, so that we can use a checksum with it (one
hopes, time will tell).
The installer still pulls the packages from the live repos so
installations aren't reproducible.
Add r-biobase package. Remove explicit R dependency from r-biocgenerics
package (since it is an instance of RPackage). Update version for
r-biocgenerics and remove github versions.
* First draft package for sambamba
Depends on the ldc package (#5279) that alalazo's working on.
It requires a patch to the Makefile because one of ldc's library
functions mentions dlopen. I *think* that ldc should be handling
this. See the discusssion in #5279.
It also requires a "static" ldc. Again, see #5279.
Finally, it needs "undeaD" as a resource, but I'm guessing at the
appropriate release. See
https://github.com/lomereiter/sambamba/issues/312.
* alalazo renamed the shared_libs variant, keep up...
+ The recipe for cgns seems to be wrong. CMake complains about variables set but
not used (`HDF5_NEEDS_ZLIB`, `HDF5_NEEDS_MPI` and `HDF5_NEEDS_SZIP`) and fails
to find HDF5.
+ This change set removes these variables from the cmake configure line,
replacing them with `'-DHDF5_DIR=%s' % spec['hdf5'].prefix`
+ cgns also has trouble with parallel make, so I set `parallel = False`.
* 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.
* fixing build issues for gcc on osx
* reverting inadvertent change on develop
* fixing typesetting of bsws description
* very minor update to RTD docs footer to ref github contributors
* Revert "very minor update to RTD docs footer to ref github contributors"
This reverts commit c40d75da7f3b918350a263e7a9ef34df56b7fb01.
* switch fastmath to depend_on arpack_ng; remove arpack/parpack
* Module files now are generated using a template engine refers #2902#3173
jinja2 has been hooked into Spack.
The python module `modules.py` has been splitted into several modules
under the python package `spack/modules`. Unit tests stressing module
file generation have been refactored accordingly.
The module file generator for Lmod has been extended to multi-providers
and deeper hierarchies.
* Improved the support for templates in module files.
Added an entry in `config.yaml` (`template_dirs`) to list all the
directories where Spack could find templates for `jinja2`.
Module file generators have a simple override mechanism to override
template selection ('modules.yaml' beats 'package.py' beats 'default').
* Added jinja2 and MarkupSafe to vendored packages.
* Spec.concretize() sets mutual spec-package references
The correct place to set the mutual references between spec and package
objects at the end of concretization. After a call to concretize we
should now be ensured that spec is the same object as spec.package.spec.
Code in `build_environment.py` that was performing the same operation
has been turned into an assertion to be defensive on the new behavior.
* Improved code and data layout for modules and related tests.
Common fixtures related to module file generation have been extracted
in `conftest.py`. All the mock configurations for module files have been
extracted from python code and have been put into their own yaml file.
Added a `context_property` decorator for the template engine, to make
it easy to define dictionaries out of properties.
The default for `verbose` in `modules.yaml` is now False instead of True.
* Extendable module file contexts + short description from docstring
The contexts that are used in conjunction with `jinja2` templates to
generate module files can now be extended from package.py and
modules.yaml.
Module files generators now infer the short description from package.py
docstring (and as you may expect it's the first paragraph)
* 'module refresh' regenerates all modules by default
`module refresh` without `--module-type` specified tries to
regenerate all known module types. The same holds true for `module rm`
Configure options used at build time are extracted and written into the
module files where possible.
* Fixed python3 compatibility, tests for Lmod and Tcl.
Added test for exceptional paths of execution when generating Lmod
module files.
Fixed a few compatibility issues with python3.
Fixed a bug in Tcl with naming_scheme and autoload + unit tests
* Updated module file tutorial docs. Fixed a few typos in docstrings.
The reference section for module files has been reorganized. The idea is
to have only three topics at the highest level:
- shell support + spack load/unload use/unuse
- module file generation (a.k.a. APIs + modules.yaml)
- module file maintenance (spack module refresh/rm)
Module file generation will cover the entries in modules.yaml
Also:
- Licenses have been updated to include NOTICE and extended to 2017
- docstrings have been reformatted according to Google style
* Removed redundant arguments to RPackage and WafPackage.
All the callbacks in `RPackage` and `WafPackage` that are not build
phases have been modified not to accept a `spec` and a `prefix`
argument. This permits to leverage the common `configure_args` signature
to insert by default the configuration arguments into the generated
module files. I think it's preferable to handling those packages
differently than `AutotoolsPackage`. Besides only one package seems
to override one of these methods.
* Fixed broken indentation + improved resiliency of refresh
Fixed broken indentation in `spack module refresh` (probably a rebase
gone silently wrong?). Filter the writers for blacklisted specs before
searching for name clashes. An error with a single writer will not
stop regeneration, but instead will print a warning and continue
the command.
* Add --with-mpi=spec['mpi'].name at configure step to avoid error when finding 2 MPI implementations
* Improve scorep package with different compilers and mpi providers
Merge work from multiple contributors on the mesa package. This
includes the following changes and decisions:
* Added in mesa +hwrender support
* make +swrender the default selection since this represents a very
common usage case (ie, cluster usage)
* leave ~llvm as the default, since inadvertently building this package
could take a very long time. May need to revisit this assumption in
the future since the performance difference can be quite substantial.
* build libGLESv1+2 and libGL for all variants
* avoid dependence on dri/libdrm when ~hwrender
* disable gallium drivers if none are requested
- '\b' in regular expression needs to be in a raw string (r'\b')
- Regression test that would've caught this was unintentionally disabled
- This fixes the string and the test
Fixes a problem in ymake-filter: The line buffer is currently hardcoded to be
2048 bytes large but some Makefiles contain lines longer than that. This
caused the Makefiles to sometimes not be generated, consequently failing parts
of the build.
Fixes#4112
This commit extends the support of the AutotoolsPackage methods
`with_or_without` and `enable_or_disable` to bool-valued variants. It
also defines for those functions a convenience short-cut if the
activation parameter is the prefix of a spec (like in
`--with-{pkg}={prefix}`).
This commit also includes:
* Updates to viennarna and adios accordingly: they have been modified to
use `enable_or_disable` and `with_or_without`
* Improved docstrings in `autotools.py`. Raise `KeyError` if name is
not a variant.
* fix armadillo macro expansions
- most compilers `#define linux 1`
- armadillo does raw pasting of include directories in code
- this means macro expansion of `linux-x86_64` -> `1-x86_64`
- new version, previous download url seems broken
- lib64 instead of lib?
- needs verification, was required for intel, works for others
* flake8: two spaces is modules, one for classes
* add some explanation of how the patch works
* use p1 patch file with -U0 to prepend undef linux
* armadillo v8.100.1
* Improve PDToolkit support for different compilers
PDT dependency of TAU profiler doesn't use CC, CXX eb variables and needs command line arguments for compiler identification. If we don't pass compiler id then it uses gcc and result in link time errors while building TAU. This patch fixes it; tested with PGI and Intel compilers.
Renames the existing bootstrap command to 'clone'. Repurposes
'spack bootstrap' to install packages that are useful to the
operation of Spack (for now this is just environment-modules).
For bash and ksh users running setup-env.sh, if a Spack-installed
instance of environment-modules is detected and environment modules
and dotkit are not externally available, Spack will define the
'module' command in the user's shell to use the environment-modules
built by Spack.
* Added support to query packages by tags.
- The querying commands `spack list`, `spack find` and `spack info` have
been modified to support querying by tags. Tests have been added to
check that the feature is working correctly under what should be the
most frequent use cases.
* Refactored Repo class to make insertion of new file caches easier.
- Added the class FastPackageChecker. This class is a Mapping from
package names to stat info, that gets memoized for faster access.
- Extracted the creation of a ProviderIndex to its own factory function.
* Added a cache file for tags.
- Following what was done for providers, a TagIndex class has been added.
This class can serialize and deserialize objects from json. Repo and
RepoPath have a new method 'packages_with_tags', that uses the TagIndex
to compute a list of package names that have all the tags passed as
arguments.
On Ubuntu 14.04 the effect if the cache reduces the time for spack list
from ~3sec. to ~0.3sec. after the cache has been built.
* Fixed colorization of `spack info`
pkgconf is a new pkg-config implementation with additional features and
no external dependencies.
For a detailed comparison, see: http://pkgconf.org/features.html
Adds a development version of boost, based on their github master
repo.
Git clones the submodules forever, but installs! :)
Useful for testing since boost tends to break complex software
dependencies quite often. This helps testing it before releases.
* Package 'cdo': removed obsolete version 1.6.9.
* Package 'cdo': updated urls.
* Package 'cdo': added version 1.9.0.
* Package 'cdo': no need to specify per version urls.
* Package 'cdo': switched from Package to AutotoolsPackage.
* Package 'cdo': added new variant 'openmp'.
* Package 'cdo': variants 'curl' and 'magics' by default.
Users can now add an optional custom message to the conflicts directive.
Layout on screen has been changed to improve readability and the long
spec is shown in tree format. Two conflicts in `espresso` have been
modified to showcase the feature.
- Python I/O would not properly interleave (or appear) with output from
subcommands.
- Add a flusing wrapper around sys.stdout and sys.stderr when
redirecting, so that Python output is synchronous with that of
subcommands.
- This should speed-up Travis CI tests and refers to #5049
- Travis uses build-stages to group tests together
- The idea is to let fast tests fail first, then move to longer ones.
- Added external perl to avoid download failure from CPAN and reduce build time
- Disabling perl-dbi: continues to fail with (504 Gateway Time-out) on Travis
- We now cover all the build systems in tests:
- Add back `openblas` to Travis as a separate package.
- Switched `openblas` for `astyle` to build a simpler MakefilePackage.
- Added 'tut' (WafPackage)
- Added 'py-setuptools' (PythonPackage)
- Added 'perl-dbi' (PerlPackage)
- Added 'build_systems' directory to the ones for which we get a summary
- Added 'openjpeg' (CMakePackage)
- Added 'r-rcpp' (RPackage)
- Added comments to build tests to show the covered build system
+ gitk (and possibly other tools) expect to find the Tk executable `wish`, so
add a symlink with this name that points to the the versioned filename.
+ Example: `wish --> wish8.6`
Previously, when +graph and +mpi were enabled, the graph library
was replaced with the graph_parallel library. This alters the
logic for +graph+mpi to build both libraries.
* Gaussian: Gaussian install
* Adding Patch to spack installed files
* Adding extra environment variables for gaussian at run time
* Adding provides linda
* Adding linda as a provided package
* Shortning vars and fixing flake8 indentation and spacings
this is a fix to an installation that failed due to
configure for some reason not finding the libiconv
shipped with glibc, but still trying to link against it
see http://xmlsoft.org/FAQ.html
* Refactor IntelInstaller into IntelPackage base class
* Move license attributes from __init__ to class-level
* Flake8 fixes: remove unused imports
* Fix logic that writes the silent.cfg file
* More specific version numbers for Intel MPI
* Rework logic that selects components to install
* Final changes necessary to get intel package working
* Various updates to intel-parallel-studio
* Add latest version of every Intel package
* Add environment variables for Intel packages
* Update env vars for intel package
* Finalize components for intel-parallel-studio package
Adds a +tbb variant to intel-parallel-studio.
The tbb package was renamed to intel-tbb.
Now both intel-tbb and intel-parallel-studio+tbb
provide tbb.
* Overhaul environment variables set by intel-parallel-studio
* Point dependent packages to the correct MPI wrappers
* Never default to intel-parallel-studio
* Gather env vars by sourcing setup scripts
* Use mpiicc instead of mpicc when using Intel compiler
* Undo change to ARCH
* Add changes from intel-mpi to intel-parallel-studio
* Add comment explaining mpicc vs mpiicc
* Prepend env vars containing 'PATH' or separators
* Flake8 fix
* Fix bugs in from_sourcing_file
* Indentation fix
* Prepend, not set if contains separator
* Fix license symlinking broken by changes to intel-parallel-studio
* Use comments instead of docstrings to document attributes
* Flake8 fixes
* Use a set instead of a list to prevent duplicate components
* Fix MKL and MPI library linking directories
* Remove +all variant from intel-parallel-studio
* It is not possible to build with MKL, GCC, and OpenMP at this time
* Found a workaround for locating GCC libraries
* Typos and variable names
* Fix initialization of empty LibraryList
* Added a package for the MDAnalysis toolkit.
* Openblas now builds with clang when using 0.2.20
* Fixed flake8 error
* Added a guard to fail for openblas+openmp when on OSX systems
* Changed the guard to look for Apple's build of clang and to improve
the error messages.
* Removed blank line.
`h5z-zfp` now builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
Adds the "buildcache" command to spack. The buildcache command is
used to create gpg signatures for archives of installed spack
packages; the signatures and archives are placed together in a
directory that can be added to a spack mirror. A user can retrieve
the archives from a mirror and verify their integrity using the
buildcache command. It is often the case that the user's Spack
instance is located in a different path compared to the Spack
instance used to generate the package archive and signature, so
this includes logic to relocate the RPATHs generated by Spack.
* py-networkx: adding older version py-networkx
* py-pypeflow: new package
* falcon: adding new package
pacbio-daligner: adding new package
pacbio-damasker: adding new package
pacbio-dazz-db: adding new package
pacbio-dextractor: adding new package
* py-networkx: modifying version order to be in line with convention
* falcon: tweaking py-networkx dependency to satisfy setuptools
py-pypeflow: adding missing dependency
* pacbio-dextractor: changing hdf5 dependency
* pacbio-daligner: adding gmake build dep
pacbio-damasker: adding gmake build dep
pacbio-dazz-db: adding gmake build dep
pacbio-dextractor: adding gmake build dep
* mpest: new package
* adding architecture env var and making more version-flexible
* fixing environment
* fixed build directory
* getting rid of duplicated code
* signalp: new package
* fixed homepage
* fixed url and phases
* refixed phase
* improved readability
* making path in execuatble adaptable to new versions
* 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.
* adding mfem variants; do not assume build defaults
* adjusting format to clarify options
* fixing some build issues
* fixing mfem+sundials
* removing mesquite variant...turns out it is obsolete
* adding examples to mfem; fixing sundials darwin installs
* adding some additional variants and setting some configure flags by fiat
* switching most check_variants logic to conflicts() directives
* adding comment about cmake config
* fixing flake8 issues; thought I had already done that
* moving func def into install method
* switch yes_no to no_yes; fix miss-spelling of miniapps
* switching make target all to lib
* changing yes_no to function as requested; fix problem with same in sundials
* fix missing import sys directive
* adding master and develop versions to amrex
* Added a package for the MDAnalysis toolkit.
* Added additional packages that Elemental depends on.
* Changed LBANN to not ask for the scalapack variant in Elemental.
* Removed variant control on scalapack
* New package: qbox
* API changes
* Use install instead of shutil for comd
* Use any BLAS library
* Fix typo
* Python2 fix
* python2 + fix backslashes
* Modified to respond to ld_flags correctly
* Modified to use ld_flags
* Add ld_flags support
* Updated Changes
* Updated AMG with required MPI
* Updated AMG with Version ' changes'
* Fixed Issues with flag's and variant checks
* Updated with MPI Alone and Changes - NO Serial Variant
* Updated with MPI Alone and Changes - NO Serial Variant
* Fixed Flake 8 line length error
* Updated Spack Issues
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit.
* Fix flake8 errors.
* Fix flake8 errors.
* Update bcl2fastq2 with info for 2.19.1.403
Heads up, the download location changed (domain name AND protocol).
* Flake8 fix
What's one space between friends?
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch.
* Using even lower bound for pnetcdf conflict in Trilinos.
* Added a package for the MDAnalysis toolkit.
* Changed cmake_options to args to be consistent with the rest of the
file and fix a cmake error about undefined errors. Additionally,
added guards for both png and zlib to not include their cmake options
when those variants are not specified.
