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This file contains a description of the major changes to the easybuild-easyconfigs EasyBuild package.
For more detailed information, please see the git log.
These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
The latest version of easybuild-easyconfig provides 6,718 easyconfig files, for 1,182 different software packages,
25 different (compiler) toolchains, 13 software bundles and 1 meta-package.
v3.1.2 (March 20th 2017)
------------------------
bugfix/update release
- add patch to FFTW 3.3.6 easyconfigs to fix MPI F03 interface (#4334)
- note that this warrants rebuilding FFTW that is a part of foss/2017a
- added example easyconfig files for 14 new software packages:
- DBG2OLC (#4281), disambiguate (#4125), fqtrim (#4280), GFOLD (#4293), Kaiju (#4349), LSMS (#4335),
L_RNA_scaffolder (#4282), PileOMeth (#4289), psycopg2 (#4319), QGIS (#4307, #4332), QJson (#4305),
QScintilla (#4306, #4313), sketchmap (#4360), snaphu (#4362)
- added additional easyconfigs for various supported software packages, including GROMACS 2016.3, PGI 17.1, SAMtools 1.4
- various enhancements, including:
- fix style in several easyconfigs (#4267-#4271, #4274, #4275, #4277, #4279, #4286-#4288, #4318)
- various bug fixes, including:
- correctly set $PYTHONPATH in ROOT easyconfigs (#4239, #4331)
- correct libjpeg turbo references in GDAL (#4276)
- make sure that HDF5 provided via EasyBuild is used in BLASR easyconfigs (#4278)
- fix issues with miRDeep2 installation (#4291, #4301, #4316)
- also run tests with Tcl module syntax, Lua is the default in EasyBuild v3.x (#4315)
- fix PostgreSQL homepage + minor style fixes (#4318)
- detect use of '$root', which is not compatible with module files in Lua syntax (#4330)
- fix homepage/source_urls for ViennaRNA (#4338)
- pass down $FFLAGS via FLAGS_OPT in SWASH easyconfigs (#4341)
- remove include/GL/wglext.h from Mesa sanity check (#4354)
- rename S.A.G.E. to SAGE, can't have directories with trailing dot in Windows (#4368)
v3.1.1 (March 7th 2017)
-----------------------
bugfix/update release
- added example easyconfig files for 16 new software packages:
- Caffe (#3667), DIAMOND (#4107), fmt (#4131), googletest (#4132), igraph (#4172), MEGA (#4202), meRanTK (#4175),
meshio (#4178), miRDeep2 (#4229, #4255), OOMPA (#4211), PBSuite (#4224, #4230), randfold (#4217), skewer (#4246),
Smoldyn (#4110), SpiecEasi (#4215), stress (#4180)
- added additional easyconfigs for various supported software packages, including:
- binutils 2.28, Cantera 2.3.0, CGAL 4.9, GMP 6.1.2, IPython 5.2.2, JasPer 2.0.10, NWChem 6.6, matplotlib 2.0.0,
PCRE 8.40, Qt5 5.8.0, Vim 8.0, X11 bundle v20170129, VTK 7.1.0, Yade 2017.01a
- added new easyconfigs for existing toolchains:
- iomkl/2017a (#4216), intel/2017.02 (#4248)
- various enhancements, including:
- fix style in several easyconfigs (#4174, #4176, #4190, #4233)
- add sanity check command to Yade easyconfig to make sure that 'import yade' works, include bzip2 as dep (#4193)
- add PDF::API2 extension to Perl 5.24.0 easyconfigs + sync exts_list (#4221)
- various bug fixes, including:
- add Bison and gettext as build deps for X11 (#4111)
- clean up dependencies in libdrm (#4113)
- make sure Ghostscript picks up external libraries (#4118)
- fix ippicv source download and library install for OpenCV v3.1.0 (#4126)
- fix software name for OrthoMCL + modernise OrthoMCL easyconfigs (#4134, #4135)
- get rid of backticks in gettext descriptions, causes problems when packaging with FPM (#4146)
- remove duplicate sources specification in OpenMPI (#4150)
- fix definition of buildopts/installopts in Cantera easyconfig (#4133, #4164, #4177)
- use http rather than ftp source URLs in CFITSIO easyconfigs (#4167)
- add patch for XZ 5.2.2 to include 5.1.2alpha symbols required by 'rpm' command on CentOS 7.x (#4179)
- add patch for Boost v1.61-1.63 to fix problem with make_array/array_wrapper in boost serialization library (#4192)
- set CMAKE_PREFIX_PATH to ncurses install directory in CMake easyconfigs (#4196)
- switch to lowopt=True for libxc v2.2.* and v3.* (#4199)
- remove custom sanity_check_paths, since it's identical to that used by the R easyblock (#4200)
- fix version (& homepage) in ea-utils easyconfigs (#4205)
- remove --with-threads configure option in OpenMPI-2.* (#4213)
- fix check for Szip library in configure script for netCDF 4.1.3 (#4226)
- fix source_urls in several easyconfigs, including:
- bsoft, cutadapt, EMBOSS, GnuTLS, ImageMagick, LibTIFF, Mercurial, netCDF, netCDF-Fortran, pigz, ROOT and Subversion (#4227)
v3.1.0 (February 3rd 2017)
--------------------------
feature release
- added easyconfigs for foss/2017a and intel/2017a common toolchains (#3968, #3969)
- added example easyconfig files for 16 new software packages:
- ack (#3983), cclib (#4065), ConnectomeWorkbench (#3411), GroIMP (#3994), hyperspy (#3991), I-TASSER (#1216),
ImageJ (#4023, #4062), libconfig (#4051), libspatialindex (#4002), mahotas (#3990), Minia (#3949), muParser (#4007),
NetLogo (#3941), QIIME (#3868), QwtPolar (#4019), Tensorflow (#4084, #4095)
- added additional easyconfigs for various supported software packages, including:
- Boost 1.62.0 + 1.63.0, CP2K 4.1, GSL 2.3, PLUMED 2.3.0, Qt5 5.7.1, WRF 3.8, WPS 3.8, Yade 2016.06a, zlib 1.2.11
- various enhancements, including:
- update FFTW 3.3.5 easyconfigs to use FFTW easyblock & enable running of tests (#3985)
- add FME extensions (+ deps) in R 3.3.1 easyconfigs (#4063)
- various bug fixes, including:
- add libxml2 dependency on HDF5 (#3759)
- remove unnecessary dependency in libmatheval (#3988)
- fix permissions on SWASH binaries (#4003)
- add conda-forge channel to perl-app-cpanminus (#4012)
- add missing deps (libpthread-stubs, libpciaccess) to libdrm 2.4.70 (#4032)
- modloadmsg style fixes in multiple easyconfigs (#4035)
- include X11 as dep for Molden (#4082)
- remove incorrect definition for $ROSETTA3_DB, now (correctly) defined via Rosetta easyblock (#4083)
- fix source URLs for several easyconfigs, including:
- arpack-ng 3.1.3 + 3.1.5 (#4050), ChIP-Seq 1.5-1 (#4050), Ghostscript 9.10, 9.14 + 9.16 (#4050),
Git 1.7.12, 1.8.2 + 1.8.3.1 (#4050), HBase 1.0.2 (#4043), libevent 2.0.22 (#4037), libsodium 1.0.3 (#4046),
lynx 2.8.7 (#4050), Maven 3.2.2 and 3.3.3 (#4039), MEME 4.8.0 (#4050), PCC 20131024 (#4044), S-Lang 2.3.0 (#4045),
Spark 1.3.0 (#4041), splitRef 0.0.2 (#4040)
v3.0.2 (December 22nd 2016)
---------------------------
bugfix release
- added example easyconfig files for 13 new software packages:
- CryptoMiniSat (#3952), MATSim (#3902), Molcas (#2084), ne (#3376), psmc (#3910), PyCogent (#3897),
PyNAST (#3897), RASPA2 (#3903, #3946), SimPEG (#3876), SolexaQA++ (#3892), taco (#3882),
UCLUST (#3896), USPEX (#3767)
- added additional easyconfigs for various supported software packages, including:
- Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02
- various enhancements, including:
- trivial style fixes (#3878, #3893, #3895)
- various bug fixes, including:
- add X11 develop libs to ncview easyconfig (#3881)
- fix source_urls in pkg-config easyconfigs (#3907)
- install numpy/scipy as .egg to ensure shadowing of numpy/scipy in parent Python installation (#3921)
- fix broken source URL + homepage for Infernal (#3928)
- fix test that verifies dumped easyconfig, take into account that dumped dependencies may include hardcoded dependency (#3932)
- include libGLU as dependency in freeglut easyconfigs with recent Mesa (#3936)
- add patch for FreeSurfer to fix issue with MATLAB 2013 (#3954)
v3.0.1 (November 30th 2016)
---------------------------
bugfix release
- added example easyconfig files for 7 new software packages:
- Cookiecutter (#3827), ETE (#3857), findhap (#3860), graphviz (Python bindings, #3826), LoFreq (#3856),
PhyloBayes-MPI (#3859), XGBoost (#3849)
- added additional easyconfigs for various supported software packages
- various enhancements, including:
- add ipywidgets and widgetsnbextension extensions to IPython 5.1.0 easyconfigs (#3818, #3823)
- run dadi test suite as a sanity check command (#3858)
- various bug fixes, including:
- fix incorrect descriptions for ifort (#3817)
- fix modulename for Jinja2 and Pygments (#3823)
- fix download URL in BLAST 2.2.26 easyconfig (#3861)
v3.0.0 (November 16th 2016)
---------------------------
feature release
- backwards incompatible changes:
- archive easyconfigs using old inactive toolchains
- see #3725, #3728, #3729, #3730, #3731, #3732, #3733, #3735, #3736, #3737, #3738
- only taken into account by EasyBuild if --consider-archived-easyconfigs is enabled
- no easyconfigs available outside of archive for QLogicMPI + 15 toolchains:
- ClangGCC, cgmpich, cgmpolf, cgmvapich2, cgmvolf, cgompi, cgoolf, gmacml,
goalf, gpsmpi, gpsolf, iiqmpi, intel-para, ipsmpi, iqacml
- fix name in PyTables easyconfigs (was pyTables) (#3785)
- added example easyconfig files for 32 new software packages:
- 3to2 (#3655), Anaconda2 (#3337), Anaconda3 (#3337), ART (#3724), atools (#3631),
awscli (#3645), behave (#3751), Blosc (#3785), bokeh (#3790), Cantera (#3655),
Cargo (#3764), dadi v1.7.0, distributed (#3786), ea-utils (#3634), Elk (#3644),
FGSL (#3638), gencore_variant_detection (#3337), help2man (#3768), lbzip2 (#3791),
Log-Log4perl (#3574), Minimac2 (#3783), mypy (#3694), OBITools (#3573),
perl-app-cpanminus (#3337), PGDSpider (#3625), prokka (#3755), Reads2snp (#3609),
spglib-python (#3620), SUNDIALS (#3654, #3655), SelEstim (#3626), XMLStarlet (#3797),
x265 (#3090)
- added easyconfigs for new 'intelcuda' toolchain (#3750)
- added new easyconfigs for existing toolchains:
- goolfc/2016.08 (#3796), goolfc/2016.10 (#3666, #3775), intel/2017.00 (#3543), intel/2017.01 (#3757),
iomkl/2016.09-GCC-4.9.3-2.25 (#3680), iomkl/2016.09-GCC-5.4.0-2.26 (#3772)
- added additional easyconfigs for various supported software packages, including:
- Advisor 2017 update 1, Amber 16, ATLAS 3.10.2, GROMACS 2016, Octave 4.0.3,
OpenFOAM 3.0.1, PyTables 3.3.0, QuantumESPRESSO 6.0, Rust v1.12.1
- various other enhancements, including:
- STREAM builds using ~56GiB and ~111GiB (#3670)
- various bug fixes, including:
- fix source spec in VASP easyconfig, ensure static linking with Intel MKL (#3381)
- fix source URL in GCCcore 6.2.0 easyconfig (#3608)
- correct STAMP dependency in i-cisTarget, must be 1.3 (#3613)
- consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#3623)
- fix source URLs for Cython (#3636)
- add Bison as build dep and M4 as runtime dep for flex 2.6.0 (#3656)
- enable parallel building of flex 2.6.0 (#3630)
- add zlib and bzip2 dependencies to X11 bundle (#3662)
- use 'letter_dir_for' function rather than just grabbing 1st letter of software name in easyconfigs tests (#3664)
- add patch to fix typo in GRIT 2.0.5 (#3675)
- fix typo in patch for WRF 3.8.0 (#3702)
- use $CC,$CXX rather than $I_MPI_CC,$I_MPI_CXX in patch for OpenFOAM 4.0 (#3703)
- patch FLTK to fix 'undefined symbol' issue when building Octave (#3704)
- include Pillow as a proper dep for scikit-image rather than as extension, since it has deps itself (#3723)
- update Travis config w.r.t. changes framework config defaults and required Lmod version (#3773)
- don't limit parallellism to 4 in recent GCC easyconfigs (#3776, #3777, #3778)
- include M4 as dependency in flex 2.5.39 easyconfigs + fix consistency issues (#3782)
- consistently apply patch for ncurses 6.0 (#3792)
- eliminate dependency on mpi-mic-rt in ifort (#3793)
- include Autotools as build dependency in all beagle-lib and MrBayes easyconfigs (#3794)
- make OpenBLAS use the LAPACK version specified in the easyconfig (v0.2.18 & v0.2.19) (#3795)
- include original download URL for ISL source tarball in GCC easyconfigs (#3798)
- disable installing libiberty for binutils built with intel toolchain (#3802)
v2.9.0 (September 23rd 2016)
----------------------------
feature release
- added example easyconfig files for 88 new software packages:
ADMIXTURE (#3359), angsd (#3593), ASHS (#3429), AutoDock (#3465), AutoGrid (#3466), BayeScan (#2748, #3356),
BayPass (#3451), Bazel (#3379), Blender (#3553, #3558), bwakit (#3567), BXH_XCEDE_TOOLS (#3410), CastXML (#3403),
CHASE (#3304), configparser (#3368, #3424), configurable-http-proxy (#3380), cppcheck (#3508), CRPropa (#779),
DicomBrowser (#3432), DMTCP (#3422), entrypoints (#3368, #3424), f90cache (#3570), fastPHASE (#3343),
fastQValidator (#3192), FFindex (#1135), FragGeneScan (#1198), gdc-client (#3399), gflags (#3417), glog (#3417),
GRIT (#3561), H5hut (#3431), HAPGEN2 (#3344), HEALPix (#779), IMOD (#1187, #3347), IronPython (#607),
jhbuild (#3476), jupyterhub (#3380), Keras (#3581), khmer (#1158), LeadIT (#3345, #3599), LevelDB (#3417),
libbitmask (#3481), libcpuset (#3481), LMDB (#3417), log4cplus (#1136), MACH (#3346), Mako (#3460), Maq (#3428),
MetaGeneAnnotator (#3307), Metal (#3324), Mono (#607), MyMediaLite (#607), nco (#2575), nose-parameterized (#3579),
OpenEXR (#3553), OpenImageIO (#3553), path.py (#3368, #3424), PCRE2 (#3325), pftoolsV3 (#3317), PHASE (#3385),
PLAST (#3288), PLINKSEQ (#3402), POV-Ray (#3551), ProbABEL (#3108), prompt-toolkit (#3368, #3424),
protobuf-python (#3563), PSORTb (#3317), py (#3403, #3482), pygccxml (#3403, #3482), pyGIMLi (#3403, #3482),
pyplusplus (#3403, #3482), PyQt5 (#3533), Pyro4 (#3527), pytest (#3403, #3482), QCA (#3595), RDMC (#1137),
S.A.G.E. (#3427), SDL2 (#3551), SHORE (#3531), SimVascular (#3555), SortMeRNA (#3326), SUMACLUST (#3316),
SUMATRA (#3316), Text-CSV (#3323), Triangle (#3403), VEGAS (#3457), VirSorter (#3307), wcwidth (#3368, #3424),
X11 (#3340)
- added new easyconfigs for existing toolchains:
- CrayGNU + CrayIntel 2016.06 (#3377)
- foss 2016.07 (#3517) + 2016.09 (#3523),
- iomkl 2016.07 (#3458)
- pomkl 2016.09 (#3516)
- added additional easyconfigs for various supported software packages, including:
FFTW 3.3.5, GCC 4.9.4 + 6.2.0, GROMACS 5.1.4, IPython 5.1.0, LLVM 3.9.0, Mesa 12.0.1, OpenCV 3.1.0, OpenFOAM 4.0,
OpenMPI 2.0.1, ParaView 5.1.2, PGI 16.7, QuantumESPRESSO 5.4.0, Qt5 5.7.0, R-bundle-Bioconductor 3.3, VTK 7.0.0,
Yade 2016.06a
- various enhancements, including:
- adjust PSI4 easyconfigs for updated easyblock (#3312)
- clean up libxml2 easyconfigs according to updated libxml2 easyblock (#3479, #3509)
- significantly speed up verifying of dumped easyconfig by resorting to 'shallow' parsing (#3520)
- include sanity checks for all MATIO config files (#3528)
- remove --with-tcl-config/--with-tk-config from R easyconfig, already done in R easyblock (#3580)
- various bug fixes, including:
- disable testing in all ParaView 4.4.0 easyconfigs, required download is too much of a PITA (#3178)
- add SQLite as dep to GDAL 2.1.0 easyconfigs (#3342)
- add zlib/SQLite/LibTIFF as dep to R 3.3.1 easyconfigs (#3342)
- add bzip2 as a dependency of freetype (#3464)
- specify correct MPI target in FDS easyconfigs (#3488)
- add tcsh as OS dep in NAMD easyconfigs (#3491)
- statically link ncurses/libreadline in Lua easyconfig with 'dummy' toolchain (#3545)
- add M4 as dep for flex 2.6.x (#3542, #3550)
- add bzip2 and libxcb dependencies to FFmpeg 3.x easyconfigs (#3548)
- make sure & check that Graphviz does not install Tcl bindings in Tcl install prefix (#3556)
- add missing patches for extensions in Python 3.x easyconfigs (#3557)
- add missing XZ dependency to libxml2 2.9.4 easyconfigs, change gettext dep of XZ to build-only dep (#3568)
- enable running of tests for HPCG (#3578)
- fix buildopts in tabix easyconfigs (#3584)
v2.8.2 (July 13th 2016)
-----------------------
bugfix release
- added example easyconfig files for 54 new software packages:
Amber (#3200), Bullet (#3175), CONTRAlign (#690), Cluster-Buster (#3191), damageproto (#3222, #3308),
DCA++ (#3219), EIGENSOFT (#3147, #3163), Extrae (#507), fdstools (#3237), ffnet (#3273), GP2C (#3257),
Gurobi (#3239), gc (#3202, #3261), gputools (#546), IMa2p (#3300), IOzone (#3253), i-cisTarget (#3191, #3194),
icmake (#3243), io_lib (#3255), Kent_tools (#3191), libcmaes (#3256), libpsortb (#3259), libxsmm (#3099),
MEGACC (#3263), MM-align (#1428), MOSAIK (#880), MView (#1345), MySQL-python (#3172, #3189), magma (#3219),
mrFAST (#862), mrsFAST (#862), mysqlclient (#3172, #3232), NTL (#3183), PARI-GP (#3257), Paraver (#508),
psutil (#3171, #3231), PSI4 (#3293), Qwt (#3157), RMBlast (#3142), STAMP (#3191), Seqmagick (#3264),
splitRef (#946), TAU (#509), TRF (#3141), TVB (#3053, #3247, #3251), TVB-deps (#3053, #3247, #3251),
tvb-data (#3053, #3247, #3251), tvb-framework (#3053, #3247, #3251), tvb-library (#3053, #3247, #3251),
VampirTrace (#509), Voro++ (#3174), wheel (#3235), wxPropertyGrid (#508), xonsh (#3159)
- added easyconfigs for update of common toolchains: foss/2016b (#3271), intel/2016b (#3270)
- added new easyconfigs for existing toolchains: CrayGNU 2016.03 & 2016.04 (#3291), foss/2016.06 (#3184), intel/2016.03-GCC-5.4 (#3185)
- added additional easyconfigs for various supported software packages, including:
Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2,
Python 2.7.12, Python 3.5.2, Qt 3.3.8, R 3.3.1
- various enhancements, including:
- use check_conflicts function in easyconfigs tests (#2981)
- also include vsc-install in list of sources for recent EasyBuild easyconfigs, to support offline installation (#3203)
- enable building of libmysqld.* in MariaDB easyconfigs (#3230)
- add ALDEx2, phyloseq to bundles for Bioconductor 3.2 (#3211, #3241)
- add biom, geepack, lubridate, pim to list of R 3.2.3 extensions (#3186, #3211, #3275)
- various bug fixes, including:
- add patch for Boost 1.60.0 to fix bug resulting in TypeError (#3162)
- add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU (#3176)
- fix location of libelf.h, only (also) installed as include/libelf.h is there's no /usr/include/libelf.h (#3201)
- fix software name for Guile & GnuTLS (was 'guile' & 'gnutls') (#3207)
- added missing space in Geant4 configopts to specify -DGEANT4_INSTALL_DATA (#3209)
- fix Cython download URL in Python 2.7.11 easyconfigs (#3212)
- add missing build deps for X stack in easyconfigs using foss/2016a or intel/2016a (#3222, #3308)
- fix overruling of exts_list in Perl 5.22.2 easyconfig (#3224)
- add missing dependency on GMP in R 3.2.3 easyconfigs (#3226)
- don't hard specify toolchain for binutils build dep in likwid easyconfig, since it matches parent toolchain (#3240)
- fix homepage & source_urls in HMMER easyconfigs (#3246)
- stick to pydot 1.1.0 for Python 2.6 in Travis config (#3282)
- add python-dev(el) to osdeps in GC3Pie easyconfigs (#3310)
v2.8.1 (May 30th 2016)
----------------------
- added example easyconfig files for 13 new software packages:
drFAST (#906), git-lfs (#2478), grabix (#3127), JWM (#3007), libcroco (#3007), librsvg (#3007), MaCH (#3136),
mayavi (#3106), OpenMM (#2762), Pysam (#3080), SeqPrep (#3097), vt (#3128), wkhtmltopdf (#3098)
- added new easyconfigs for existing toolchains: intel/2016.03-GCC-4.9 (#3088)
- added additional easyconfigs for various supported software packages, including:
Boost 1.61.0, ESMF 7.0.0, Inspector 2016 update 3, IPython 4.2, netCDF-C++4 4.3.0, netCDF-Fortran 4.4.4, Perl 5.22.2, VTune 2016 update 3
- various bug fixes, including:
- apply libreadline patch to fix bug triggering segmentation fault (#3086)
v2.8.0 (May 18th 2016)
----------------------
feature + bugfix release
- added example easyconfig files for 69 new software packages:
ALPS (#2888), annovar (#3010), BayeScEnv (#2765), BayesAss (#2870), BerkeleyGW (#2925), Blitz++ (#2784, #3004),
bam-readcount (#2850), Commet (#2938), CrossTalkZ (#2939), cuDNN (#2882), DBus (#2855), DFT-D3 (#2107),
DIAL (#3056), dask (#2885), dbus-glib (#2855), FFLAS-FFPACK (#2793), FLAC (#2824), FLANN (#3015, #3029),
FLEUR (#3043), GConf (#2855), GROMOS++ (#1297), GST-plugins-base (#2855), GStreamer (#2855), GTOOL (#2805),
Givaro (#2793), gdist (#2935), gromosXX (#1297), HISAT2 (#2809), i-PI (#2940), Kraken (#3037, #3041), LAME (#2823),
LASTZ (#3002), LinBox (#2793), Loki (#2839), libQGLViewer (#2923, #3008), libXxf86vm (#2855),
MDSplus (#2787, #2838, #3027), MRIcron (#2831), Mawk (#2732), minieigen (#2839), mpmath (#3058), NBO (#3047, 3048),
NGS (#2803), NGS-Python (#2810), ncbi-vdb (#2808), OptiX (#2795), PCL (#3024), PEAR (#2731), PLplot (#2990),
Postgres-XL (#2891), PyGTS (#2969), RSeQC (#2788), Rust (#2920, #2943), rainbow (#2730), SHAPEIT (#2806),
SIONlib (#2908), Saxon-HE (#2773), Singularity (#2901), SoX (#2825), Subread (#2790), SuperLU (#2665),
travis (#2953), VASP (#2950), Wannier90 (#2906, #3042), wget (#3041), wxPython (#2855), xf86vidmodeproto (#2855),
Yade (#2839), Yambo (#2932)
- add test configuration for Travis (#2942, #2944, #2954, #3061)
- added easyconfigs for new PGI-based toolchains
- pomkl/2016.03 (#2899, #2900, #3046), pomkl/2016.04 (#3044), CrayPGI/2016.04 (#2927)
- added new easyconfigs for existing toolchains:
foss/2016.04 (#3013), intel/2016.02-GCC-5.3 (#2523), intel/2016.03-GCC-5.3 (#3009)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
incl. CGAL 4.8, Clang 3.8.0, icc/ifort 2016.2.181 & 2016.3.210, imkl 11.3.2.181 & 11.3.3.210, impi 5.1.3.181,
LLVM 3.8.0, OpenCV 2.4.12, pandas 0.18.0, Qt 5.6.0, Scalasca 2.3, Score-P 2.0.1, SuiteSparse 4.5.2, WRF 3.8
- various other enhancements, including:
- enhance ORCA easyconfig for compatibility with SLURM (#1819)
- enable -fPIC in GraphicsMagick easyconfig, required by Octave (#2764)
- clean up binutils easyconfigs to use binutils easyblock (#3006)
- add include/GraphicsMagick to $CPATH in GraphicsMagick easyconfigs (#3034)
- update SuiteSparse easyconfigs according to updated SuiteSparse easyblock (#3050)
- various bug fixes, including:
- fix Perl extensions download urls (#2738)
- add Autoconf as build dep for GCCcore (#2772)
- fix versions of extensions in Bioconductor 3.2 bundles (#2769)
- fix (build) deps for intel/2016a easyconfigs of cairo, libXext, libXrender (#2785, #2874)
- use 'env' wherever preconfig/build/installopts is used to set environmental variables (#2807, #2811, #2812)
- add zlib as explicit dep in Tk easyconfigs (#2815)
- consistently specify to use -fgnu89-inline flag in M4 1.4.17 easyconfigs (#2774, #2779, #2816)
- fix homepage and description in Pygments easyconfigs (#2822)
- include pkg-config as build dependencies for libXau, libXdmcp, libxcb (#2827)
- consistently use XORG_*_SOURCE constants (#2829, #2830, #2848)
- update source URLs in ScientificPython easyconfig files (#2847)
- add checksums in SuiteSparse easyconfigs (#2849)
- fix build deps for GObject-Introspection (#2852)
- correctly specify Perl location in git easyconfig (#2866)
- fix bitstring 3.1.3 download URL in Python easyconfigs, source tarball on PyPI disappeared (#2880)
- fix Perl dependency in worker easyconfig, it requires non-standard Perl modules (#2884)
- add XZ as dependency in Python 3.5.1 easyconfigs, required for lzma (#2887)
- fix download URL for packmol (#2902)
- drop usempi toolchain in numexpr easyconfigs, not needed (#2937)
- fix use of resolve_dependencies in tests according to changes in framework (#2952)
- add dependency extensions for MarkupSafe and jsonscheme in IPython 3.2.3 easyconfigs (#2967)
- add patch for matplotlib 1.5.1 to fix Tcl/Tk library paths being used (#2971)
- add xproto build dependency for makedepend v1.0.5 (#2982)
- disable parallel build for Doxygen (#2986)
- fix source URLs for FreezeThaw and Tie::Function extensions for Perl v5.22.1 (#2988)
- add sed command in worker easyconfig files to fix module_path in conf/worker.conf (#2997, #3000)
- drop toolchainopts from Eigen easyconfigs, since it is headers-only (#3025)
- clean up dummy bzip2 easyconfig, define buildopts rather than defining $CC and $CFLAGS via os.environ (#3036)
- use %(pyshortver)s template rather than hardcoding 2.7 in VTK easyconfigs (#3052)
- correct install location of OpenCV Python bindings (#3054)
- include XZ as dependency for libunwind (#3055)
- add patch to fix broken OpenSSL tests due to expired certificates (#3057)
- fix broken link to VSC website in license headers (#3062)
v2.7.0 (March 20th 2016)
------------------------
feature + bugfix release
- added example easyconfig files for 63 new software packages:
ATSAS (#616, #2587), astropy (#2724, #2727), attr (#2706), BamUtil (#2654), BBMap (#2322), BH (#2508),
CheMPS2 (#2445), CosmoloPy (#2723, #2727), csvkit (#2639), Firefox (#2648), FreeXL (#2422), GL2PS (#2667),
Glade (#2631), htop (#2538), IGV (#2019), IGVTools (#2019), ImageMagick (#2438), jModelTest (#2529),
KEALib (#2420), libcerf (#2656), libgcrypt (#2201), libglade (#2631), libgpg-error (#2201), libspatialite (#2431),
LittleCMS (#2438), MAST (#2542), MLC (#2577), MPJ-Express (#2529), mutil (#2201), neon (#758), NextClip (#2544),
npstat (#2686, #2703), Octopus (#2643), QuickFF (#2721), p4vasp (#2328), PCMSolver (#2445), PFFT (#2643),
PHYLIP (#2694), pkgconfig (#2475, #2476), Platypus (#2618), pplacer (#1056), PRINSEQ (#2437, #2444, #2585),
PyFFmpeg (#2501, #2519), PyGObject (#2443), PyGTK (#2443), PyOpenGL (#2628), pyringe (#2533), qrupdate (#2675),
rgeos (#2635), rpmrebuild (#2402), shift (#2201), SNAPE-pooled (#2688), SNPhylo (#2701), sratoolkit (#2715),
STAR-Fusion (#2463), statsmodels (#2719), StringTie (#2527), synchronicity (#2508), testpath (#2461),
USEARCH (#2537), VarScan (#2464), vsc-install (#2165), Whoosh (#2725), xprop (#2645)
- added new easyconfigs for existing toolchains:
intel/2016.02-GCC-4.9 (#2620), gmpolf/2016a & gmvolf/2016a (#2589)
- stable Cray-specific easyconfigs
- delete deprecated Cray toolchains and easyconfig files (#2400)
- don't hardcode PrgEnv version, remove craype and fftw components in Cray toolchains (#2554)
- remove -XC versionsuffix for stable definitions for Cray* toolchains (#2714)
- support for various software packages with CrayGNU and CrayIntel toolchains: CP2K, GROMACS, WRF
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BWA 0.7.13, CMake 3.4.3, GATE 7.2, GROMACS 5.1.2, Mesa 11.1.2, netCDF 4.4.0, Perl 5.22.1, Python 3.5.1,
R 3.2.3, R-bundle-Bioconductor 3.2, scipy 0.17.0, SuiteSparse 4.5.1
- various other enhancements, including:
- copy contrib dir in Velvet easyconfigs so scripts are also available (#2456)
- redefine matplotlib 1.5.1 easyconfig as a bundle, also include cycler extension (dep for matplotlib) (#2470)
- add bitstring extension to Python 2.7.11 easyconfigs (#2471)
- enable building of MetaVelvet in Velvet 1.2.10 easyconfigs (#2473)
- add custom sanity check for libjpeg-turbo (#2480)
- add Velvet easyconfigs that include BioPerl dependency, so VelvetOptimizer can use it (#2495, #2729, #2733)
- add source URL in RAxML 7.2.6 easyconfigs (#2536)
- update MPICH easyconfigs to use new MPICH easyblock (#2589)
- free libX11 & co from unneeded Python dependency/versionsuffix (#2549, #2563, #2605, #2664)
- add '--enable-utf --enable-unicode-properties' configure options in PCRE easyconfigs (#2561)
- required for latest R versions
- add HCsnip, metagenomeSeq in Bioconductor 3.1 bundles (#2553, #2578)
- add additional extensions in R 3.2.x easyconfigs that are required for extra Bioconductor extensions (#2547, #2556)
- update psmpi easyconfig files to use the new psmpi easyblock (#2619)
- add easyconfig for Python 2.7.11 on top of X11-enabled Tk (#2614, #2621)
- add virtualenv as extension in Python 2.7.11 easyconfigs (#2660)
- various bug fixes, including:
- fix software name for GTK+ (was 'gtk+'), PyCairo (was 'pycairo') and Gdk-Pixbuf (was 'gdk-pixbuf') (#2468)
- don't hardcode CC/CXX in OpenMPI easyconfigs (#2472)
- remove Google Code source URL for mpi4py (#2474)
- rename ffmpeg to FFmpeg (#2425, #2481)
- use available easyblock for flex (#2486)
- fix determining list of easyconfigs in unit test suite, don't assume locations are correct (#2530)
- fix specifying DB dependency in DB_File easyconfigs (#2539)
- remove hard-coded -xSSE4.2 for numpy/scipy with Intel compilers (#2546)
- fix license headers: Hercules foundation is now FWO (#2550)
- add --with-zlib configure argument in libxml easyconfigs (#2555)
- don't hardcode optarch=True in xextproto/xtrans easyconfigs (#2601)
- change toolchain version to '' in easyconfigs that use dummy toolchain and include dependencies (#2612)
- GLib doesn't require libxml2 with Python bindings (#2632)
- add patch file to imkl 10.2.6.038 32-bit easyconfig to fix installer not being able to deal with '--' in build path (#2634)
- add missing 'pkgconfig' dependency for h5py (#2476, #2650)
- correct software name in FastQC easyconfigs (was 'fastqc'), use 'dummy' toolchain for all FastQC version (#2657, #2666)
- add missing libxml2 dependencies in GLib easyconfigs (#2658)
- fix Xerces-C++ download location (#2668)
- enable XML::Bare extension in all Perl easyconfigs (#2672)
- update dead link for SuiteSparse (#2679)
- remove custom exts_filter in easyconfigs used PythonPackage easyblock (#2683, #2685)
- add M4 as build dep for binutils & flex (#2681)
- add missing dependencies in Python 3.5.x easyconfigs: SQLite, Tk, GMP (#2704)
- fix (OS) deps, add checksums, remove parameter definition with default values in MVAPICH2 easyconfigs (#2707)
- style cleanup in various easyconfigs (#2378, #2387, #2395, #2396, #2488-#2493, #2496-#2500, #2502-#2504, #2602)
- working towards automated style review of pull requests
v2.6.0 (January 26th 2016)
--------------------------
feature + bugfix release
- add easyconfigs for foss/2016a and intel/2016 common toolchains (#2310, #2311, #2339, #2363)
incl. easyconfigs for Boost, CMake, Python, Perl using these toolchains
- added example easyconfig files for 21 new software packages:
BLASR (#922), BioKanga (#2247), BoltzTraP (#2365), basemap (#2221), CppUnit (#2271), EggLib (#2335),
FLASH (#2281), GLM (#2288), hub (#2249), MACS2 (#1983), MotEvo (#843), numba (#2243), PGI (#1833, #2367),
PLY (#2305), PaStiX (#2319, #2326), patchelf (#2327), pip (#2284), RSEM (#2316), RcppArmadillo (#2289),
SCDE (#2289), slepc4py (#2318)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BamTools 2.4.0, Boost 1.60.0, Clang 3.7.1, DOLFIN/FFC/FIAT/Instant/UFL 1.6.0, GATE 7.0, GCC 5.3.0,
LLVM 3.7.1, pandas 0.17.1, PETSc 3.6.3, SAMtools 1.3, scipy 0.16.1, SLEPc 3.6.2, Trilinos 12.4.2,
Trinity 2.1.1, VTK 6.3.0
- various other enhancements, including:
- added new Cray* toolchain versions with pinned dependency versions (#2222)
- don't hardcode .so, use SHLIB_EXT constant instead (#2245)
- add custom sanity check in GEOS easyconfigs (#2285)
- various bug fixes, including:
- add Autotools (M4) as a build dependency in GMP v6.x easyconfigs (#2096)
- remove argparse from list of extensions in Python 3.2+ easyconfigs, since it became part of stdlib (#2323)
- various style fixes, including:
- get rid of tabs (#2302)
- remove trailing whitespace (#2341)
v2.5.0 (December 17th 2015)
---------------------------
feature + bugfix release
- add GCCcore easyconfig that can be used as base for all compilers (without getting in the way) (#2214)
- + easyconfig for GCC/4.9.3-2.25: bundle of GCCcore 4.9.3 and binutils 2.25
- intended to replace the GNU toolchain
- added example easyconfig files for 39 new software packages:
DIRAC (#2212), GeoIP (#2172, #2185), GeoIP-C (#2172, #2185), graph-tool (#1591), gtkglext (#2217),
Intel Advisor (#2210), InterProScan (#2225, #2227, #2234), intltool (#2136), kallisto (#2173), LibUUID (#1930),
LuaJIT (#2153), libXcursor (#2136), libXrandr (#2136), libXtst (#2143), libdap (#1930), libtasn1 (#2208),
libxkbcommon (#2136), MRtrix (#2217, #2218), MultiNest (#2166, #2168), Nipype (#2150), PPfold (#2183, #2187),
p11-kit (#2208), pangox-compat (#2217), Qt5 (#2136), randrproto (#2136), rhdf5 (#2175), Stampy (#2180, #2182),
scikit-umfpack (#2061), scp (Python pkg) (#2196), sleuth (#2175), traits (#2150), vincent (#2169, #2185),
XKeyboardConfig (#2136), xcb-util (#2136), xcb-util-image (#2136), xcb-util-keysyms (#2136),
xcb-util-renderutil (#2136), xcb-util-wm (#2136), zlibbioc (#2175)
- added new easyconfigs for existing toolchains:
intel/2015.08 (#2194), intel/2016.00 (#2209), intel/2016.01 (#2219), iomkl/2015.03 (#2155)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including CMake 3.4.1, HDF5 1.8.16, netCDF 4.3.3.1, netCDF-Fortran 4.4.2, numpy 1.10.1, Octave 4.0.0,
OpenFOAM 3.0.0, OpenFOAM-Extend 3.2, Python 2.7.11
- various other enhancements, including:
- add tidyr to R 3.2.1 easyconfigs (#2174)
- enable C++ support in MIGRATE-N (#2178)
- also installed shared libraries for AMD and UMFPACK in SuiteSparse (#2061)
- fix software name for ParaView (was: Paraview) (#2132)
- enable building of shared libraries for binutils (#2133)
- harden binutils built with dummy toolchain by linking to system libraries via RPATH (#2228)
- enhance easyconfig unit tests to check that each easyconfig file is in the right subdirectory (#2232)
- various bug fixes, including:
- fix ALADIN patch file to not use relative paths, and adjust list of ALADIN sources accordingly (#2207, #2213)
- rename patch files for OpenFOAM to be in line with other patches (#2226)
- fix typo in bzip2 source URLs (#2204)
- force linking of ncurses in libreadline (#2206)
- enable -fPIC in all zlib 1.2.8 easyconfigs (#2220)
- move Net-LibIDN/SRA-Toolkit/bbftpPRO/o2scl easyconfigs to right location (#2232)
- restrict parallel build in OpenFOAM-Extend easyconfigs via 'maxparallel', not 'parallel' (#2233)
v2.4.0 (November 10th 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 45 new software packages:
animation (#2007), ANSYS CFD (#1969), ANTLR (#1191, #1980), APR (#1970), APR-util (#1970), Aspera Connect (#2005),
ChIP-Seq (#2119), deap (#2082), DISCOVARdenovo (#1932), FastQC (#1984), fontsproto (#1618, #2038),
GraphicsMagick (#2007), HBase (#1990), ISIS (#1972), libedit (#293), libfontenc (#1618, #2038), libGLU (#1627),
libXdamage (#1618, #2038), libXfont (#1618, #2038), LLVM (#1620, #1989, #2031), MIGRATE-N (#1944), MIRA (#1938),
mympingpong (#2049), MySQLdb (#2011), NCO (#1191, #1980), NIPY (#2064), Nilearn (#2064), NiBabel (#2064),
PBZIP2 (#1038), PIL (#2062), PhyloCSF (#2018), pycairo (#2085), pydicom (#2063), Salmon (#2051), Samcef (#1941),
scikit-image (#1974, #2006), Serf (#1970), SSAHA2 (#1039), Subversion (#1970), SWASH (#2059, #2128), time (#1954),
Trim_Galore (#1984), Trimmomatic (#1987), WEKA (#1986), x264 (#2017)
- added new easyconfigs for existing toolchains: gimkl/2.11.5 (#2093)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Clang + LLVM 3.7.0, CMake 3.3.2, CUDA 7.5.18, hanythingondemand v3.0.1, Mesa 11.0.2, mpi4py v2.0.0,
ncurses 6.0, OpenFOAM 2.4.0, Paraview 4.4.0, Python 3.5.0, QuantumESPRESSO v5.2.1
- various other enhancements, including:
- enable 'pic' toolchain option in libxml2 easyconfigs (#1993)
- extend list of R libraries included in R v3.2.1 easyconfigs (#2042, #2046, #2067, #2072)
- add Rsubread in Bioconductor easyconfigs (#1971)
- various bug fixes, including:
- fix software name for BEEF (was 'libbeef') (#1679)
- add patch to install qhull.pc (pkgconfig) file with Qhull (#1975)
- don't enable experimental nouveau API in libdrm easyconfigs (#1994)
- fix dev version to follow PEP-440, as required by recent setuptools versions (#1997)
- required to avoid that setuptools transforms the version itself
- see also https://www.python.org/dev/peps/pep-0440/#developmental-releases
- correct homepage in Cufflinks easyconfigs (#2060)
- fix imports for set_tmpdir in easyblock unit tests after function was moved in EasyBuild framework (#2097)
- add patch for Tk 8.6.4 to fix problem with tk.tcl not being found (#2102)
- don't use %(version)s template in toolchain version, causes problems with HierarchicalMNS (#2104)
- fix sanity check paths in several easyconfig (#2109, #2120, #2121, #2125)
- required because of bug fix in sanity_check_step implementation
- CVXOPT, h5py, LIBSVM, libunistring, MDP, monty, PhyloCSF, Pyke, pandas, pycosat, pyhull, pymatgen,
python-dateutils, Seaborn, Theano, XML-LibXML, XML-Simple
v2.3.0 (September 2nd 2015)
---------------------------
feature + bugfix release
- added example easyconfig files for 19 new software packages:
ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780),
gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677),
Molpro (#1880), NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859)
- added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696)
add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1,
Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0
- various other enhancements, including:
- enhance texinfo easyconfig w.r.t. texmf, only use it as a build dependency (#1840)
- enable building of ld.gold in binutils 2.25 (#1885)
- various bug fixes, including:
- fix enabling MPI support for h5py 2.5.0 (#1825)
- fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917)
- put dummy values in place for builddir/installdir templates in easyconfigs unit tests (#1835)
- fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875)
- add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858)
- specify installation prefix for SIP (#1888, #1892)
- add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909)
- required because of fix in EasyBuild framework, causing default sanity check paths to be considered
for extensions that are installed as a module
- affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql,
evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx,
ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn,
SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck
- don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911)
- add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925)
v2.2.0 (July 15th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 62 new software packages:
ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171),
Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995),
EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440),
frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762),
GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760),
libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116),
ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412),
Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776),
rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658),
SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512),
VampirServer (#512), verifyBamID (#1675)
- added easyconfigs for 4 new software bundles:
R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759),
R-bundle-pbd (#1659)
- added easyconfigs for new GNU toolchain (#1346, #1669)
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added example easyconfig for generating buildenv module (#1503)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1,
Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1
- various other enhancements, including:
- update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337)
- update PDT easyconfigs to use PDT easyblock (#1687)
- add custom sanity_check_paths in libxml2 easyconfigs (#1690)
- enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761)
- include snappy as dependency in Hadoop easyconfigs (#1758, #1773)
- enable SSL support in CMake v3.2.3 easyconfigs (#1784)
- add additional extensions in R easyconfigs (#1637)
- various bug fixes, including:
- add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631)
- fix issue with OpenMPI dependency in ECore easyconfigs (#777)
- don't run the Bloom tests for Jellyfish, they can randomly fail (#1016)
- fix source URLs in BioPerl easyconfigs (#1075)
- patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576)
- consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722)
- include Tcl and Tk as dependencies in R easyconfig (#1623)
- add patch for installing paycheck as Py3 extension (#1629)
- add Perl dependency in git 2.x easyconfigs (#1631)
- fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635)
- fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652)
- include Tk as dependency in Python 2.7.9 easyconfigs (#1654)
- include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655)
- drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657)
- include missing libxml2 dep in GLib easyconfigs (#1666)
- fix source URLs in Qt easyconfigs (#1673)
- fix source URLs for argparse Python extension (#1697)
- fix source URLs for deap Python extension (#1699)
- fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708)
- fix names for Xmipp easyconfigs and patches (#1719)
- add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734)
- add M4 as build dep for GCC 5.1.0 (#1735)
- fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748)
- remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765)
- fix source_urls in netCDF easyconfigs (#1766)
- fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767)
v2.1.1 (May 18th 2015)
----------------------
bugfix release
- added example easyconfig files for 3 new software packages:
networkx (#1592), Platanus (#1597), SaguaroGW (#1600)
- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40
- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3
- various bug fixes, including:
- enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590)
- use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595)
- only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609)
v2.1.0 (April 30th 2015)
------------------------
feature + bugfix release
- added example easyconfig files for 27 new software packages:
AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530),
mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036),
Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536),
seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369),
Xmipp (#1489)
- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE
- initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558)
- see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray
- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1
- various other enhancements, including:
- include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540)
- include SQLite as dependency in Python v2.7.9 easyconfigs (#1468)
- set $LD_PRELOAD for Hoard and jemalloc (#1470)
- fix homepage in SCOTCH easyconfigs (#1485)
- adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510)
- enable pic toolchain option in expat easyconfigs (#1562)
- extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568)
- various bug fixes, including:
- adding missing zlib dependency in all Tcl easyconfig files (#1344)
- fix homepage in FLUENT easyconfigs (#1472)
- use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511)
- stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512)
- replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532)
- stop relying on $MKLROOT in ROOT easyconfigs (#1537)
- use proper Bundle easyblock for biodeps/PRACE (#1566)
- make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574)
- add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574)
v2.0.0 (March 6th 2015)
-----------------------
feature + bugfix release
- added example easyconfig files for 29 new software packages:
bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568),
fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389),
jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242),
rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370),
ZPAQ (#1242)
- added easyconfigs for new (common) toolchains
foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238),
intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401)
- added new software bundle: Autotools (#1385)
- various other enhancements, including:
- don't define $LDSHARED in zlib easyconfigs (#1350)
- this fixes the long-standing "no version information available" issue with zlib
- see also https://github.com/hpcugent/easybuild-framework/issues/108
- add unit test to check that all extra_options keys are defined in EasyConfig instance (#1378)
- add source MD5 checksums in all GCC easyconfigs (#1391)
- speeding up the unit tests by avoiding rereading of same easyconfig file (#1432)
- fix conflict detection in unit tests by considering build deps separately from runtime deps (#1447)
- fix toolchain for Bison build dep in MVAPICH2-1.9-iccifort-2011.13.367.eb easyconfig (#1448)
- use Bundle generic easyblock for HPCBIOS bundles and fix moduleclass (#1451)
- various bug fixes, including:
- revert version of Libint dependency to 1.1.4 in CP2K v2.5.1 easyconfig (#1144)
- added Java dependencies to EMBOSS easyconfigs (#1167)
- don't list 'lto' as a language in GCC easyconfigs (#1286)
- related to the fixes in the GCC easyblock, see hpcugent/easybuild-easyblocks#535
- rename libint2 easyconfigs as Libint v2 easyconfigs (#1287)
- fix mpi4py source_urls in Python easyconfigs (#1306)
- consistently use CLooG 0.18.0 for GCC 4.8 series (#1392)
- rename GenomeAnalysisTk easyconfigs to GATK (#1399)
- include openssl-devel SLES11 OS dependency in cURL/MySQL/Python easyconfigs (#1422)
- add missing Perl dependency in parallel easyconfigs (#1430)
- correct name in BLAST+ easyconfigs (#1443)
- fix name for sparsehash easyconfigs (#1452)
v1.16.2.0 (March 6th 2015)
--------------------------
(no changes compared to v1.16.1.0, simple version bump to stay in sync with easybuild-easyblocks)
v1.16.1.0 (December 19th 2014)
------------------------------
- set default easyblock to ConfigureMake in TEMPLATE.eb (#1277)
v1.16.0.0 (December 18th 2014)
------------------------------
feature + bugfix release
- added example easyconfig files for 39 new software packages:
ANTs (#1232), BEOPS (#1264), Chhimera (#1255), ctffind (#1249), DBD-SQLite (#1064), DBD-mysql (#1063),
DIALIGN-TX (#668), ffmpeg (#1088), GObject-Introspection (#1079), GTS (#1079), Graphviz (#1079), GraphViz2 (#1079),
grace (#1131), HarfBuzz (#1079), HTSlib (#1161), GSSAPI (#1048), Kerberos_V5 (#1048), libevent (#1063),
libXdmcp (#1129), libXft (#1017), libXinerama (#1017), libXrender (#1017), Maven (#1094), MySQL (#1063),
Net-LibIDN (#1060), OpenCV (#1088), OpenMD (#1105), Qhull (#1105), Pango (#1079), psmpi (#1245, #1246),
RELION (#1017), renderproto (#1017), rjags (#1125), runjags (#1125), SPRNG (#1138, #1141), xineramaproto (#1017),
XML-Dumper (#1061), XML-Parser (#1061), XML-Twig (#1061)
- added easyconfigs for new toolchains
intel/2014.10 & intel/2014.11 (#1219), intel-para/2014.12 (#1246), gpsolf/2014.12 (#1245), iompi/6.6.4 (#1215)
- include easyblock = 'ConfigureMake' in relevant easyconfigs to deal with deprecation of automagic fallback to ConfigureMake (#1248)
- see also easybuild-framework#1113 and Automagic fallback to ConfigureMake
- clean up use of deprecated functionality in existing easyconfigs (#1252, #1259)
- stop using deprecated makeopts, premakeopts and shared_lib_ext
- check for use of deprecated functionality in easyconfigs unit tests
- see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#easyconfig-parameters
- various other enhancements, including:
- also build fftw3_threads libraries, and enhance sanity checks (#1013)
- add unit test to verify specified sanity_check_paths (#1119)
- update and clean up README, refer to http://easybuild.readthedocs.org documentation (#1184, #1224)
- various bug fixes, including:
- fix unit tests w.r.t. changes in framework (#1146)
- remove unnecessary build dependencies for OpenMPI (#1168)
- remove duplicate line in OpenMPI easyconfigs (#1207)
- fix affiliation/mail address for Fotis in headers (#1237)
- fix permissions of easyconfig files for consistency (#1210)
- disable symbol lookup feature in cairo to fix build on SL6 (#1241)
- fix easyconfig gmpolf toolchain w.r.t. MPICH software name (#1217)
- see also easybuild-framework#1112
- fix source_urls for WRF and WPS (#1225)
- fix and clean up GATE easyconfigs (#1228)
- fix broken CLHEP builds by including -gcc in $CXXFLAGS (#1254)
- add patch to fix broken test in Go (#1257)
- fix name of GMAP easyconfigs, should be GMAP-GSNAP (#1268)
- fix easyconfig filenames, enhance unit test to check easyconfig filenames (#1271)
v1.15.2.0 (October 7th 2014)
----------------------------
bugfix release
- disable parallel build for slalib (#968)
- fix compatibility of goolfc with HierarchicalMNS by using GCC toolchain for installing CUDA (#1106, #1115)
- fix zlib OS dependency spec for Debian in Boost easyconfigs (#1109)
- fix compatibility of gimkl with HierarchicalMNS by using gimpi subtoolchain (#1110)
- make both GCC and Clang first-class members in Clang-based toolchains to fix compatibility with HierarchicalMNS (#1113)
v1.15.1.0 (September 23rd 2014)
-------------------------------
bugfix release
- minor bug fixes, including:
- use SHLIB_EXT in GMP/MPFR easyconfigs (#1090)
- fix TopHat homepage and source_urls since page moved (#1092)
- make iomkl toolchain compatible with HierarchicalMNS (#1099)
v1.15.0.0 (September 12th 2014)
-------------------------------
feature + bugfix release
- added example easyconfig files for 13 new software packages:
Circos (#780), DB_File (#913), Emacs (#970), evmix (#1077), GD (#780), gsl (#1077), IOR (#949), JAGS (#1076),
libgd (#780), MethPipe (#1070), Modeller (#825), NAMD (#835), netCDF-C++4 (#1015)
- added easyconfigs for new toolchains (#986, #1051):
gimkl/1.5.9, ictce/7.1.2
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
including Python 2.7.8/3.4.1, Perl 5.20.0, R 3.1.1, NWChem 6.3, OpenFOAM-Extend 3.1, GCC 4.9.1, Clang 3.4.2, ...
- various enhancements, including:
- make existing ictce/intel toolchains compatible with HierarchicalMNS (#1069)
- this involves installing impi with an iccifort toolchain, and imkl with an iimpi toolchain
- various bug fixes, including:
- download link for Perl modules changed to use cpan.metapan.org
- fix missing MPI-based OpenFOAM libraries (Pstream, (pt)scotchDecomp), make sure provided SCOTCH is used (#957)
v1.14.0.0 (July 9th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 17 new software packages:
ANSYS (#836), Beast (#912), ELPH (#910, #911), FastTree (#900, #947), GEM-library (#858), HPCG (#853),
mdtest (#925), ncview (#648), PRANK (#917), RDP-Classifier (#903), SDPA (#955), SIBELia (#886),
SOAPaligner (#857), SPAdes (#884), stemming (#891), WHAM (#872), YAXT (#656)
- added easyconfigs for new toolchains (#935, #944, #948):
foss/2014b, ictce/6.3.5, intel/2014b
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- various enhancements, including:
- replace use of deprecated (pre)makeopts with (pre)buildopts in all easyblocks (#954)
- disable running embossupdate on installation of EMBOSS (#963)
- various bug fixes, including:
- really enable OpenMP support in FastTree easyconfigs (#947)
- fix easyconfigs unit tests after changes in framework (#958)
v1.13.0.0 (May 29th 2014)
-------------------------
feature + bugfix release
- added example easyconfig files for 32 new software packages:
APBS (#742), BayesTraits (#770), bc (#888), BitSeq (#791), CEM (#789), CVS (#888), eXpress (#786), file (#888),
GEMSTAT (#861), GMAP (#594), Go (#887), iscp (#602), IsoInfer (#773), Jellyfish (#868), less (#888),
libcircle (#883), mcpp (#602), MMSEQ (#795), MUSTANG (#800), OpenFOAM-Extend (#437), popt (#759), pscom (#759),
psmpi2 (#759), QuadProg++ (#773), rSeq (#771), RSEQtools (#870), Ruby (#873), segemehl (#792), SOAPec (#879),
SOAPdenovo2 (#874), SRA-Toolkit (#793), texinfo (#888)
- added easyconfig for new toolchain goolfc/1.4.10
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- e.g. older versions of Boost (1.47.0), GCC (4.1-4.4), & recent versions of Clang, GCC, Lmod, etc.
- various enhancements, including:
- add OpenSSL dependency for cURL, to enable HTTPS support (#881)
- also install esl-X binaries for HMMER (#889)
- various bug fixes, including:
- properly pass down compiler flags for ParMGridGen (#437)
- specify proper make options for PLINK, fixing the build on SL6 (#594, #772)
- fix netloc version (0.5 rather than 0.5beta) (#707)
- remove Windows-style line ending in netCDF patch file (#796)
- bump version of OpenSSL dep for BOINC (#882)
v1.12.1.0 (April 25th 2014)
---------------------------
(no changes compared to v1.12.0, simple version bump to stay in sync with easybuild-framework)
v1.12.0.0 (April 4th 2014)
--------------------------
feature + bugfix release
- added example easyconfig files for 6 new software packages:
CLooG (#653), ELPA (#738), LIBSVM (#788), netaddr (#753), netifcas (#753), slalib-c (#750)
- added easyconfigs for new toolchains:
ClangGCC/1.3.0 (#653), goolf/1.4.10-no-OFED (#749), goolf/1.5.14(-no-OFED) (#764, #767), ictce/6.2.5 (#726), iomkl (#747)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- various enhancements, including:
- tweak BOINC easyconfig to make use of glob support available for files_to_copy (#781)
- enable -fPIC for libreadline, so it can be linked into shared libs (e.g. libpython2.x.so) (#798)
- various bug fixes, including:
- fix Qt source_urls (#756)
- enable -fPIC in ncurses 5.9 ictce/5.2.0 easyconfig, just like in the others (#801)
- fix unit tests after changes to framework (#763, #766, #769)
v1.11.1.0 (February 28th 2014)
------------------------------
(no changes compared to v1.11.0, simple version bump to stay in sync with easybuild-framework)
v1.11.0.0 (February 16th 2014)
------------------------------
feature + bugfix release
- added example easyconfig files for 30 new software packages:
argtable (#669), Clustal-Omega (#669), Coreutils (#582), GMT (#560), gperftools (#596), grep (#582), h4toh5 (#597),
libunwind (#596), Lmod (#600, #692), Lua (#600, #692), MAFFT (#654), Molekel (#597), NEdit (#597),
netcdf4-python (#660), nodejs (#678), OCaml (#704), patch (#582), PhyML (#664),
PRACE Common Production Environment (#599), protobuf (#680), python-dateutil (#438), sed (#582), sickle (#651),
Tesla-Deployment-Kit (#489), TREE-PUZZLE (#662), VCFtools (#626), Vim (#665), vsc-mympirun-scoop (#661),
vsc-processcontrol (#661), XZ (#582)
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- OpenSSL with ictce toolchain (#703)
- various enhancements, including:
- using more constants and templates (#613, #615)
- specify OS dependency for SSL support, with OpenSSL dependency as fallback (#703)
- various bug fixes, including:
- fix unit tests after (internal) framework API changes (#667, #672)
- fix homepage in vsc-mympirun easyconfig file (#681)
- align OpenMPI easyconfigs (#650)
- add additional source URL in Qt easyconfigs (#676)
- specify correct $PATH specification and define $CHPL_HOME for Chapel (#683)
v1.10.0.0 (December 24th 2013)
------------------------------
feature + bugfix release
- added example easyconfig files for 18 new software packages:
BEDTools (#579, #632, #635), CAP3 (#548), CHARMM (#584), cutadapt (#620), ErlangOTP (#556, #630),
Ghostscript (#547, #632), HTSeq (#554, #632), Jansson (#545), libjpeg-turbo (#574), Molden (#566),
netloc (#545), o2scl (#633), packmol (#566), PP (#405), qtop (#500), TAMkin (#566), vsc-base (#621),
vsc-mympirun (#621)
- added easyconfigs for new toolchains (#545, #609, #629):
gcccuda/2.6.10, gompic/2.6.10, goolfc/2.6.10, ictce/6.0.5, ictce/6.1.5
- added additional easyconfigs for various supported software packages: version updates, different toolchains, ...
- new versions of icc, ifort, imkl, impi (#609, #629)
- large collection of ictce/5.3.0 easyconfigs (#627)
- various enhancements, including:
- extended list of Python packages as extensions to Python (#625)
- add MPI-enabled version of GROMACS + easyconfigs using ictce (#606, #636)
- clean up templating of source_urls (#637)
- various bug fixes, including:
- provide alternative download URL for Mesa (#532)
- add Python versionsuffix in OpenBabel filenames (#566)
- apply no-gets patch in all M4 v1.4.16 easyconfigs (#623)
- fix patching of Python w.r.t. libffi/_ctypes issues (#625, #642)
- bug fixes in GROMACS easyconfigs (#606)
- change versionsuffix for non-MPI GROMACS easyconfigs to '-mt'
- stop using 'CMakeMake' easyblock for GROMACS now that there's a dedicated GROMACS easyblock,
which correctly specifies building against external BLAS/LAPACK libraries
- fix Qt dependency for CGAL (#642)
- fix libctl, libmatheval, Meep, PSI build issues caused by full paths in guile-config/python-config shebang (#642)
- make sure HDF easyconfigs specify dedicated 'include/hdf' include dir (#642)
- this is required to avoid build issues with NCL, because HDF ships it's own netcdf.h
- this also triggered removal of patch files for NCL that rewrote 'include/hdf' to 'include'
- fix WPS v3.5.1 patch file after upstream source tarball was changed, supply checksum for verification (#642)
v1.9.0.0 (November 17th 2013)
-----------------------------
feature + bugfix release
- added example easyconfig files for 58 new software packages:
- Allinea (#468), ARB + dependencies (#396, #493, #495), arpack-ng (#451, #481), CDO (#484, #521), Cube (#505),
ed (#503), FLTK (#503), GenomeAnalysisTK (#467), GIMPS (#527), GTI (#511), IPython (#485, #519), LWM2 (#510),
MPICH2 (#460), MUST (#511), ncdf (#496, #522), OPARI2 (#505), OpenBabel (#504, #524), OTF (#505), OTF2 (#505),
PandaSEQ (#475), ParaView (#498, #514), ParFlow (#483, #520), PCC (#486, #528), PDT (#505), picard (#467),
PnMPI (#511), PyQuante (#499, #523), pysqlite (#519), Scalasca (#505), Score-P (#505), SDCC (#486, #528),
Silo (#483, #520), Stride (#503), SURF (#503), TCC (#486, #528)
- ARB dependencies (23): fixesproto, imake, inputproto, kbproto, libICE, libSM, libX11, libXau, libXaw,
libXext, libXfixes, libXi, libXmu, libXp, libXpm, libXt, lynx, motif, printproto,
Sablotron, xbitmaps, xextproto, xtrans
- added easyconfigs for new gmpich2/1.4.8, gmpolf/1.4.8 and goolf/1.6.10 toolchains (#460, #525, #530)
- added additional easyconfigs for various software packages (list too long to include here)
- version updates, different toolchains, ...
- various bug fixes, including:
- enable building of shared libraries for MPICH (#482)
- fix HDF configure option for Szip, should be --with-szlib (#533)
- for HDF5, this issue is fixed in the HDF5 easyblock
- other
- add build status badges for master/develop branches to README (#490)
v1.8.2.0 (October 18th 2013)
----------------------------
bugfix release
- port thread pool patch to PSI 4.0b4 and include it to avoid hanging tests (#471)
v1.8.1.0 (October 14th 2013)
----------------------------
bugfix release
- added additional easyconfigs for various software packages (#457):
- Boost, bzip2, libreadline, ncurses, PSI, Python, zlib
- various bug fixes, including:
- fix faulty easyconfig file names for HPCBIOS_Math, MUSCLE, XML-LibXML and YAML-Syck (#459, #462)
- stop (re)specifying default maximum ratio for failed tests in NWChem easyconfig (#457)
v1.8.0.0 (October 4th 2013)
---------------------------
feature + bugfix release
- added example easyconfig files for 9 new software packages:
- BOINC (#436), DB (#343, #449), fastahack (#374), FDTD Solutions (#387), FoldX (#440, #442), Mathematica (#394),
Mesquite (#447), MUMPS (#447), ParMGridGen (#447)
- added additional easyconfigs for goalf, gompi, ClangGCC, cgmvapich2, cgmvolf toolchains (#350, #441)
- added additional easyconfigs for various software packages:
- ATLAS, Bison, bzip2, Clang, CMake, cURL, EasyBuild, expat, FFTW, GDB, gettext, git, HPL, LAPACK, libreadline,
M4, METIS, MVAPICH2, Mercurial, ncurses, OpenBLAS, OpenMPI, ParMETIS, Python, ScaLAPACK, SCOTCH, Valgrind, zlib
- various 'bug' fixes, including:
- fix source URL for lockfile in Python easyconfigs (#428)
- correct dependency specifications w.r.t. versionsuffix and toolchain (#431)
- this is required to support building the affected easyconfigs with a custom module naming scheme
- correct PSI patch file to avoid errors w.r.t. memcpy not being in scope (#446)
- fix gettext build with adding --without-emacs configure options, add gettext as dependency for a2ps (#448)
- exclude EMACS support in a2ps because of build failures (#452)
v1.7.0.0 (September 2nd 2013)
-----------------------------
feature + bugfix release
- added example easyconfig files for 15 new software packages:
- Glib (#294, #400), GLPK (#400), horton (#413), libint2 (#413), molmod (#413), Rosetta (#336), SCons (#336), Stacks (#367, #377), sympy (#413),
Qt (#294), XML-LibXML (#397), XML-Simple (#397), yaff (#413), YAML-Syck (#380), zsh (#376)
- added additional easyconfigs for various software packages:
- BLAST, BamTools, BioPerl, Bison, Boost, bzip2, CMake, Cython, CUDA, FFTW, FIAT, GCC, GMP, gettext, git, h5py,
HDF5, libffi, libreadline, libxc, matplotlib, METIS, ncurses, Oases, Python, RAxML, ScientificPython, Szip,
tcsh, imkl, MVAPICH2, TotalView, VTune, WRF, zlib
- added toolchain easyconfig files for HPCBIOS policies (#402, #407)
- HPCBIOS_BioInfo, HPCBIOS_Debuggers, HPCBIOS_LifeSciences, HPCBIOS_Math, HPCBIOS_Profilers
- various enhancements, including:
- added more XML Perl modules to non-bare Perl easyconfigs (#375)
- various 'bug' fixes, including:
- fix website/description in scipy easyconfigs (#399)
- specify OpenMPI libibverbs-dev(el) OS dependency in an OS-dependent way (#403)
- add patch file for M4 to fix building on systems with recent glibc (>=2.16) (#406)
- align moduleclass in R easyconfigs (#411)
- fixed filename of Biopython/CD-HIT easyconfig files (#407)
- disable parallel building of otcl (#419)
v1.6.0.0 (July 11th 2013)
-------------------------
feature + bugfix release
- added example easyconfig files for 26 new software packages:
- ALLPATHS-LG (#359), AutoMake (#347), BamTools (#319, #338), BLAT (#340), Biopython (#356), cairo (#361),
CCfits (#327), CD-HIT (#344), CFITSIO (#327), Diffutils (#347), FASTA (#358, #361), findutils (#347),
fontconfig (#361), gawk (#347), gettext (#361), GLIMMER (#357, #361), libidn (#361), LibTIFF (#347),
libungif (#347), make (#355), MUSCLE (#339), Oases (#354), pixman (#361), PLINK (#352), RCS (#347), SQLite (#347)
- added additional easyconfigs for various software packages:
- ant, Bash, Bison, bzip2, cURL, expat, GCC, EasyBuild, freetype, FFTW, GDB, git, HMMER, JUnit, libreadline, libpng,
libtool, libxml2, libxslt, M4, makedepend, Mothur, MVAPICH2, Mercurial, ncurses, OpenBLAS, Python, ScaLAPACK, Tcl,
tcsh, TopHat, Trinity, Valgrind, Velvet, VTune, zlib
(see #169, #297, #298, #301, #309, #323, #331, #332, #341, #347, #349, #351, #355, #361)
- various enhancements, including:
- added easyconfigs for ictce/5.4.0, ictce/5.5.0 and gmvolf/1.7.12 toolchain modules (#297, #332, #349)
- added a template sanity_check_paths as 'MUST' in TEMPLATE.eb (#329)
- introduced biodeps 'toolchain' to ease keeping common dependencies for bio* software in sync (#309)
- added collection of easyconfigs for ictce/5.3.0 (#309, #323)
- bam2fastq, bbFTP, BLAST, Boost, DL_POLY Classic, EMBOSS, FFTW, libharu, libxml2, libxslt, libyaml, lxml,
Mercurial, Mothur, mpi4py, ncurses, ns, orthomcl, otcl, PAML, Perl, PyYAML, pandas, problog, scikit-learn,
TiCCutils, TiMBL, TinySVM, TopHat, tclcl, YamCha
- added missing dependencies for various software packages (#323, #328, #348, #361)
- style fixes in various easyconfigs (#309, #323, #345, #349, #355, #361)
- various 'bug' fixes, including:
- added 'pic' toolchain option for Perl goolf easyconfig (#299)
- fixed source URLs for R (use correct template 'version_major') (#302)
- synced libreadline easyconfigs w.r.t. ncurses dependency (#303)
- make sure EasyBuild configuration is initialized when running unit tests (#334)
- specify 'lowopt' (-O1) optimization level for OpenIFS, to avoid floating-point related issues (#328)
- fix naming of 'beagle-lib' (used to be 'BEAGLE'), to avoid name clashes with other software package(s) (#346)
v1.5.0.0 (June 1st 2013)
------------------------
feature + bugfix release
- added example easyconfig files for 23 new software packages:
- bam2fastq (#287), CBLAS (#263), EMBOSS (#265, #290), FCM (#272), FRC_align (#273), freeglut (#271),
FreeSurfer (#271), FSL (#271), GATK (#287), libharu (#290), libxslt (#235), MariaDB (#292), Mothur (#265)
mpi4py (#276), OpenIFS (#272), orthomcl (#265), PAML (#287), pandas (#262), phonopy (#235), problog (#277),
PSI (#258), PyYAML (#235), RAxML (#277)
- added additional example easyconfig files for:
- ABINIT (#235), ACML (#267), BLAST (#275), Boost (#273), BWA (#270), bzip2 (#263), Chapel (#240), CMake (#290),
FFTW2 (#247, #267), flex (#267), freetype (#235), grib_api (#272), gzip (#265), Java (#279), libpng (#240, #279),
libreadline (#267), libxml2 (#235), libxml (#235), matplotlib (#235), MCL (#265), MUMmer (#265), ncurses (#267),
numpy (#267), OpenFOAM (#267), Perl (#265), Python (#276, #263), R (#240, #279), SCOTCH (#267), ScaLAPACK (#267),
TopHat (#289), Valgrind (#255), zlib (#267)
- various enhancements, including:
- enhance unit test suite, include testing for module conflicts (#256) and presence of patch files (#264)
- use provided constants and templates in easyconfig files where appropriate (#248, #266, #281)
- various 'bug' fixes, including:
- get rid of hardcoded license_file paths for VTune, Inspector (#253)
- assign proper moduleclass where they were missing (#278)
- fix naming for LZO (#280)
- make unit tests clean up after themselves more thoroughly (#283, #284, #285, #286)
- fix TopHat dependencies (#289)
- fix source URLs for XML (#279)
- fix versions for all listed R extensions (#279)
- fix CUDA easyconfig file for use on Debian Squeeze (#291)
- correct easyconfig filename and module name mismatches (bbcp, DL_POLY Classic, ...) (#295)
v1.4.0.0 (May 2nd 2013)
-----------------------
feature + bugfix release
- added a unit test suite for easyconfigs (#228, #230)
- added example easyconfig files for 20 new software packages:
- ABAQUS (#231), BioPerl (#242), Bowtie (#227), Clang (#177), CRF++ (#131), DL_POLY Classic (#132), ESMF, GROMACS (#165),
HH-suite (#219), Inspector (#232), likwid (#131), Perl (#242), scikit (#133), TiCCutils (#131), TiMBL (#131), TinySVM (#131),
UDUNITS (#167), VTune (#232), YamCha (#131)
- add example easyconfigs for new compiler toolchains (use `eb --list-toolchains` for a full list of supported toolchains):
- the newly added toolchains only differ in compilers/MPI library, and all feature OpenBLAS, LAPACK, ScaLAPACK and FFTW
- goolfc: GCC, CUDA (co-compiler), OpenMPI (#191)
- a goolfc easyconfig for GROMACS is inluded as proof-of-concept (#165)
- cgmpolf: Clang (C/C++ compilers), GCC (Fortran compilers), MPICH (#213)
- cgmvolf: Clang, GCC, MVAPICH2 (#218)
- cgoolf: Clang, GCC, OpenMPI (#213)
- gmvolf: GCC, MVAPICH (#202, #222)
- ported already available easyconfigs to new compiler toolchains:
- ictce-5.3.0: 193 easyconfigs (#229)
- cgmpolf: 11 easyconfigs (#213)
- cgmvolf: 11 easyconfigs (#218)
- cgoolf: 12 easyconfigs (#213)
- gmvolf: 10 easyconfigs (#215)
- added additional example easyconfig files for:
- CMake (#163), git (#210), Java (#206), #221, Mercurial (#201, #215), ncurses (#225), TotalView (#160)
- various enhancements, including:
- added ESMF and UDUNITS dependencies to NCL easyconfigs (#211)
- changed value of source_urls in R easyconfigs, to be generic enough for version 3.0 and possibly beyond (#251)
- various 'bug' fixes, including:
- add --enable-mpirun-prefix-by-default configure option for all OpenMPI easyconfigs (#205)
v1.3.0.0 (April 1st 2013)
-------------------------
feature + bugfix release
- added example easyconfig files for 13 new software packages:
- Bash, CUDA, ccache, Ferret, gzip, libxc, ns, numactl, OpenBLAS, otcl, Tar, tclcl, tcsh
- several of these easyconfig files were contributed by attendees of the EasyBuild hackathon in Cyprus!
- added example easyconfigs for goolf toolchain (#158)
- added example easyconfigs for builds with goolf toolchain, i.e. for all goalf easyconfigs (#189)
- for several software packages, a patch file was needed to get them to build with GCC 4.7:
AMOS, BEAGLE, Cufflinks, DOLFIN, GATE, ns, Pasha, Trilinos, Trinity
- for PETSc, a patch file was required to make it build with a toolchain that doesn't include BLACS
- added additional example easyconfig files for:
gompi, hwloc, LAPACK, MVAPICH2, OpenMPI, ScaLAPACK
- various enhancements, including:
- define a proper module class in *all* easyconfigs, cfr. default module classes defined in framework (#150, #159, #161, #162, #179, #181)
- extend FFTW easyconfig to 'fat' builds that include single, double, long double and quad precision libraries in the same module
- quad precision is disabled for Intel compiler based builds (it requires GCC v4.6+)
- the imkl easyconfigs used for the ictce 3.2.2.u3 toolchain now also enable FFTW interfaces
- various 'bug' fixes, including:
- fix filename for Mercurial and ROOT easyconfig files
- fix homepage/description for Hypre
- fix enabling OpenMP support in OpenMPI: use '--enable-openmp', not 'with-openmp'
- use correct configure flag for enabling OpenMPI threading support in v1.6 (#186)
- '--enable-mpi-thread-multiple' instead of '--enable-mpi-threads'
- explicitely add '--without-openib --without-udapl' configure options in OpenMPI easyconfig using versionsuffix -no-OFED (#168)
- this avoids that OpenMPI auto-detects that it can enable Infiniband (OpenIB) support, which doesn't fit the -no-OFED versionsuffix
- Note: this makes goalf-1.1.0-no-OFED effectively not suitable to produce software builds that are IB-capable!
- remove explicit '--with-udapl' from OpenMPI easyconfigs, does more harm than good (#178)
- remove libibvers, libibmad, libibumad as explicit dependencies for OpenMPI/MVAPICH2 (#173, #182)
leave it up to the OS to provide these, since the required version is too much tied to the version of IB drivers
- use 'license_file' in Intel tools easyconfigs, as opposed to the new generic 'license' parameter with a different meaning (#180)
- modify patch for impi to avoid installation problems due to hardcoded path in /tmp (#185)
- now uses '$USER-$RANDOM' subdir to avoid clashes between different users on the same system
- the patch file for numpy was extended to also supporting ATLAS and other BLAS libraries spread across multiple directories
- the extension for ATLAS is required because we now no longer rely on the automatic numpy mechanism to find the ATLAS libs
- fixed dependencies:
- libibumad as dependency for libibmad
- ncurses as dependency for libreadline
- ncurses and zlib as dependency for SAMtools (+ enhanced patch)
- remove explicit FFTW dependency for Meep, ... since toolchain already provided FFTW
v1.2.0.0 (February 28th 2013)
---------------------------
feature + bugfix release
- added example easyconfig files for 41 new software packages:
- a2ps, AnalyzeFMRI, aria, bbcp, bbFTP, bbftpPRO, binutils, Bonnie++, ccache, cflow, cgdb, Corkscrew, EasyBuild,
Elinks, EPD, FLUENT, fmri, GDB, GDAL, gnuplot, gnutls, gperf, Iperf, lftp, libyaml, lzo, MATLAB, mc, nano, NASM,
nettle, numexpr, parallel, pyTables, QLogic MPI, Stow, TotalView, Valgrind, VTK, Yasm, zsync
- added example easyconfigs for iqacml and iiqmpi toolchains
- added additional example easyconfig files for:
- ABINIT, ABySS, ACML, BFAST, Bison, BLACS, Cython, cURL, Doxygen, FFTW, flex, g2clib, g2lib, GHC, h5py, HDF, HDF5,
HMMER, JasPer, icc, ictce, ifort, imkl, impi, libpng, libreadline, M4, matplotlib, MCL, MEME, mpiBLAST, NCL,
ncurses, netCDF, netCDF-Fortran, NWChem, R, ScaLAPACK, Tcl, Tk, WPS, WRF, zlib
- various enhancements, including:
- fix version of xtable R library in list of extensions for R, to avoid installation failures
- various 'bug' fixes, including:
- fix toolchain and file names for ABINIT easyconfigs
- fix sanity check paths for cURL
- don't disable 'optarch' for WRF, it's not needed (only disable heavy optimizations is required)
- fix homepage/description for ALADIN
v1.1.0.0 (January 27th 2013)
--------------------------
feature + bugfix release
- added example easyconfig files for 48 new software packages:
- ABINIT, ABySS, ACML, ALADIN, ant, BFAST, BLAST, Chapel, CLHEP, Cufflinks, ESPRresSo, GATE, GHC, Geant4,
Greenlet, google-sparsehash, grib_api, HMMER, Java, JUnit, libibmad, libibumad, libibverbs, MCL, MDP,
MEME, mpiBLAST, NCBI Toolkit, NEURON, NWChem, numpy, MDP, Oger, OpenPGM, paycheck, PyZMQ, QuantumESPRESSO,
R, ROOT, SCOOP, scipy, Tophat, Trinity, util-linux, VSC-tools, wiki2beamer, XML, ZeroMQ
- added example easyconfigs for gmacml, gmvapich2, iccifort, ictce, iomkl toolchains
- added additional example easyconfig files for:
- ATLAS, BLACS, Boost, Bowtie2, bzip2, CP2K, Doxygen, FFTW, GCC, HDF5, hwloc, icc, ifort, imkl, impi,
JasPer, Libint, libreadline, libsmm, libxml, ncurses, netCDF, M4, Meep, MVAPICH2, OpenMPI, Python,
ScaLAPACK, Szip, zlib
- various enhancements, including:
- major style cleanup of all example easyconfig file (PEP008 compliance)
- added setuptools to list of Python extensions
- get rid of 'parallel' versionsuffix for HDF5, as its meaningless (MPI-enabled build is always parallel)
- various 'bug' fixes, i.e. added missing dependencies or replaced os dependencies with proper dependencies
v1.0.0.2 (December 8th 2012)
----------------------------
bugfix release
- fixed source URL for ligtextutils (toolchain refactoring error)
v1.0.0.1 (November 24th 2012)
-----------------------------
bugfix release
- remove patch file for OpenMPI to resolve issue with pax hanging configure
- tar_config_opts should be enabled as needed
- disable parallel build for PAPI, seems to be causing problems
v1.0.0 (November 13th 2012)
---------------------------
- split up EasyBuild across three repositories: framework, easyblocks and easyconfigs
- packaged EasyBuild, different parts can now be installed easily using easy_install
- added example easyconfig files for 106 new software packages:
AMOS, Armadillo, ASE, Autoconf, BiSearch, Boost, Bowtie2, BWA, byacc, bzip2, CGAL, ClustalW2, CMake,
CPLEX, cURL, CVXOPT, Cython, Docutils, DOLFIN, ECore, Eigen, expat, FASTX-Toolkit, FFC, FIAT,
freetype, FSL, GEOS, git, glproto, GMP, gmvapich2, gompi, GPAW, GSL, guile, h5py, h5utils, Harminv,
hwloc, Hypre, Infernal, Instant, Jinja2, libctl, libdrm, libffi, libgtextutils, libmatheval,
libpciaccess, libpthread-stubs, libreadline, libtool, libunistring, libxcb, libxml2, makedepend,
matplotlib, Meep, Mercurial, Mesa, MetaVelvet, METIS, MPFR, MTL4, MUMmer, ncurses, OpenFOAM, OpenSSL,
ORCA, PAPI, ParMETIS, Pasha, PCRE, PETSc, petsc4py, pkg-config, Primer3, python-meep, RNAz, SAMtools,
ScientificPython, SCOTCH, setuptools, Shapely, SHRiMP, SLEPc, SOAPdenovo, Sphinx, SuiteSparse, SWIG,
Tcl, Theano, Tk, Tornado, Trilinos, UFC, UFL, Velvet, ViennaRNA, Viper, WIEN2k, xcb-proto, XCrySDen,
xorg-macros, xproto
- added additional example easyconfig files (versions, builds) for several software packages
Bison, BLACS, Doxygen, flex, GCC, HDF5, icc, ifort, libpng, M4, MVAPICH2, OpenMPI, Szip, tbb, zlib
- replaced GCC/OpenMPI based easyconfig files with equivalents using the gompi toolchain
ATLAS, BLACS, FFTW, LAPACK, ScaLAPACK
- enhanced Python example easyconfig files (more dependencies required for features, e.g. libreadline, bzip2, zlib, ...)
- corrected file name of easyconfig files to adher to standard as followed by EasyBuild robot dependency resolver
- style cleanup in existing easyconfig files
v0.8 (June 29th 2012)
---------------------
- added support for building/installing 17 additional software packages:
- BEAGLE, Doxygen, g2clib, g2lib, HDF, HDF5, JasPer, libpng, Maple,
MrBayes, NCL, netCDF, netCDF-Fortran, Szip, WPS, WRF, zlib
- the build procedure for WRF and WPS includes running the tests available for these packages
- various bug fixes and enhancements:
- made support for interactive installers (run_cmd_qa) more robust
- fixed Python git package check
- implemented toolkit functions for determine compiler family, MPI type, MPI run command, ...
v0.7 (June 18th 2012)
---------------------
- fixed BLACS build
- diagnostic tools to determine INTERFACE and TRANSCOMM values are now used
- added support for building Bison, CP2K, flex
- with regression test enabled for CP2K as part of build process
- note: BLACS built with EasyBuild prior to v0.7 needs to be rebuilt for CP2K to work correctly
- added --enable-mpi-threads to OpenMPI example easyconfigs
- required for correct CP2K psmp build
- adjusted libsmm example easyconfig for lower build time
- to make the full regression test finish in a reasonable amount of time
- added script to make porting of easyblocks from old to new EasyBuild codebase easier
- takes care of refactoring, checks for PyLint warnings/errors, ...
- fixed several small bugs
- prefixed EasyBuild messages with "=="
- full regression test passed (58 easyconfigs tested)
v0.6 (May 11th 2012)
---------------------
- added support for Intel compiler toolkit (ictce)
- which included the Intel compilers, Intel Math Kernel Library (imkl) and Intel MPI library (impi)
- added support for building Python with nose/numpy/scipy packages
- added simple regression test
- this version is able to build all supplied example easyconfigs
v0.5 (April 6th 2012)
----------------------
- first public release of EasyBuild
- after a thorough cleanup of the EasyBuild framework of the in-house version
- supports building HPL with goalf compiler toolkit
- the goalf toolkit consists of the GCC compilers, and the OpenMPI, ATLAS, LAPACK, FFTW and ScaLAPACK libraries
- also support build and installation of MVAPICH2