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encoding scheme for class names #98

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99b50ee
Cedric was here
Jul 17, 2012
0dc201e
Added the *.eb files created so far. Should work, typos however possi…
Jul 18, 2012
f683261
Added the easyblocks files for bowtie2 and bwa.
Jul 18, 2012
7f02a77
Renamed fastx_toolkit eb-file.
Jul 18, 2012
149d036
Changed names of fastx_toolkit and its dependency libgtextutils to ma…
Jul 18, 2012
05c08c6
handy-bash-functions.txt gives some handy functions for applied usage…
Jul 18, 2012
d8a1f2a
Necessary changes to bowtie2 eb-file: The download parameter was miss…
Jul 18, 2012
a6157ca
Added the eb file for bwa. Should work in combination with bwa.py eas…
Jul 18, 2012
7c7993a
Modified Hello World
fgeorgatos Jul 18, 2012
316fe62
Modified Hello World again
fgeorgatos Jul 18, 2012
b837b09
Update master
fgeorgatos Jul 18, 2012
132fa67
Update master
fgeorgatos Jul 18, 2012
2ed74bc
Update master
fgeorgatos Jul 18, 2012
8853a37
Modified Hello World again too
fgeorgatos Jul 18, 2012
9c5f7a3
Modified Hello World again too
fgeorgatos Jul 18, 2012
8e8e0e1
Modified Hello World again too
fgeorgatos Jul 18, 2012
44b88fd
Fixed headers for all EB files
fgeorgatos Jul 18, 2012
bbb2cf0
striped unneeded comments for all .eb files
fgeorgatos Jul 18, 2012
315e0d0
Added header to *py files
fgeorgatos Jul 18, 2012
b09b5ff
Adjusted the header
Jul 23, 2012
4035c15
fixed whitespace, no big deal
claczny Jul 23, 2012
e4891a4
fixed whitespace & corrected sourceURL tuple
claczny Jul 23, 2012
a0c04f5
fixed whitespace, no big deal
claczny Jul 23, 2012
e49bd2b
fixed whitespace & corrected sourceURL tuple
claczny Jul 23, 2012
b3fa5bb
fixed whitespace, no big deal
claczny Jul 23, 2012
b644a71
fixed whitespace, no big deal
claczny Jul 23, 2012
3d42421
fixed whitespace & removed commented preconfigopts
claczny Jul 23, 2012
6e6d95c
fixed whitespace & gave up on EB way to automate download
claczny Jul 23, 2012
67609c7
fixed whitespace, no big deal
claczny Jul 23, 2012
3d74f80
Added easyblocks/configs/tarballs for: MUMmer, MetaVelvet, SOAPdenovo…
claczny Jul 23, 2012
e69cd81
Merge branch 'develop' of github.com:hpcugent/easybuild into develop
fgeorgatos Aug 17, 2012
17b2d5f
Modified all *py files to refer to eb_ style new encoding
fgeorgatos Aug 17, 2012
e7fdaf3
Added encode_string function
fgeorgatos Aug 17, 2012
b57d934
Modified application.py to use the new eb_ encoding scheme
fgeorgatos Aug 17, 2012
257bb7d
Merge branch 'develop' of https://github.com/hpcugent/easybuild into …
fgeorgatos Aug 17, 2012
b72557f
fixed eb_ prefix for fortran python package
fgeorgatos Aug 17, 2012
6938f84
bugfixes around encode_string business
fgeorgatos Aug 17, 2012
3459eb9
Merge branch 'develop' of https://github.com/hpcugent/easybuild into …
fgeorgatos Aug 17, 2012
412aa6d
undo additions to the experimental directory
fgeorgatos Aug 17, 2012
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2 changes: 1 addition & 1 deletion easybuild/easyblocks/a/atlas.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from easybuild.tools.modules import get_software_root


class ATLAS(Application):
class eb_ATLAS(Application):
"""
Support for building ATLAS
- configure (and check if it failed due to CPU throttling being enabled)
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/b/binary.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.framework.application import Application


class Binary(Application):
class eb_Binary(Application):
"""Support for installing a binary package.
Just copy it's sources to the installdir"""

Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/b/blacs.py
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ def det_interface(log, path):
log.error("Failed to determine interface, output for xintface: %s" % out)


class BLACS(Application):
class eb_BLACS(Application):
"""
Support for building/installing BLACS
- configure: symlink BMAKES/Bmake.MPI-LINUX to Bmake.inc
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/c/cp2k.py
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
from easybuild.tools.modules import get_software_root, get_software_version


class CP2K(Application):
class eb_CP2K(Application):
"""
Support for building CP2K
- prepare module include files if required
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/c/cplex.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
from easybuild.tools.filetools import run_cmd_qa


class CPLEX(Binary):
class eb_CPLEX(Binary):
"""
Support for installing CPLEX.
Version 12.2 has a self-extracting package with a Java installer
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/d/doxygen.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
from easybuild.tools.filetools import run_cmd


class Doxygen(Application):
class eb_Doxygen(Application):
"""Support for building/installing Doxygen"""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/f/fsl.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
from easybuild.tools.filetools import run_cmd


class FSL(Application):
class eb_FSL(Application):
"""Support for building and installing FSL."""

def __init__(self,*args,**kwargs):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/g/g2clib.py
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
from easybuild.tools.modules import get_software_root


class G2clib(Application):
class eb_g2clib(Application):
"""Support for building g2clib GRIB2 C library."""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/g/g2lib.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.tools.modules import get_software_root


class G2lib(Application):
class eb_g2lib(Application):
"""Support for building g2clib GRIB2 library."""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/g/gcc.py
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
from easybuild.tools.systemtools import get_kernel_name, get_shared_lib_ext, get_platform_name


class GCC(Application):
class eb_GCC(Application):
"""
Self-contained build of GCC.
Uses system compiler for initial build, then bootstraps.
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/h/hdf5.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
from easybuild.tools.modules import get_software_root


class HDF5(Application):
class eb_HDF5(Application):
"""Support for building/installing HDF5"""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/h/hpl.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.tools.filetools import run_cmd


class HPL(Application):
class eb_HPL(Application):
"""
Support for building HPL (High Performance Linpack)
- create Make.UNKNOWN
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/icc.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
from easybuild.easyblocks.i.intelbase import IntelBase


class Icc(IntelBase):
class eb_icc(IntelBase):
"""Support for installing icc

- tested with 11.1.046
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/ifort.py
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
from easybuild.easyblocks.i.icc import Icc, IntelBase


class Ifort(Icc):
class eb_ifort(Icc):
"""
Class that can be used to install ifort
- tested with 11.1.046
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/imkl.py
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
from easybuild.tools.modules import Modules


class Imkl(IntelBase):
class eb_imkl(IntelBase):
"""
Class that can be used to install mkl
- tested with 10.2.1.017
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/impi.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.tools.filetools import run_cmd


class Impi(IntelBase):
class eb_impi(IntelBase):
"""
Support for installing Intel MPI library
"""
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/intelbase.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from easybuild.tools.filetools import run_cmd


class IntelBase(Application):
class eb_intelBase(Application):
"""
Base class for Intel software
- no configure/make : binary release
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/ipp.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
from easybuild.easyblocks.i.intelbase import IntelBase


class Ipp(IntelBase):
class eb_ipp(IntelBase):

def sanitycheck(self):

Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/i/itac.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.tools.filetools import run_cmd


class Itac(IntelBase):
class eb_itac(IntelBase):
"""
Class that can be used to install itac
- tested with Intel Trace Analyzer and Collector 7.2.1.008
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/l/lapack.py
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ def get_blas_lib(log):
return blaslib


class LAPACK(Application):
class eb_LAPACK(Application):
"""
Support for building LAPACK
- read make.inc.example and replace BLAS line with configtops
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/l/libsmm.py
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
from easybuild.tools.modules import get_software_root, get_software_version


class Libsmm(Application):
class eb_libsmm(Application):
"""
Support for the CP2K small matrix library
Notes: - build can take really really long, and no real rebuilding needed for each version
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/m/maple.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.tools.filetools import run_cmd_qa


class Maple(Application):
class eb_Maple(Application):
"""Support for installing Maple."""

def unpack_src(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/m/mrbayes.py
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
from easybuild.tools.modules import get_software_root


class MrBayes(Application):
class eb_MrBayes(Application):
"""Support for building/installing MrBayes."""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/m/mvapich2.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.framework.easyconfig import CUSTOM


class MVAPICH2(Application):
class eb_MVAPICH2(Application):
"""
Support for building the MVAPICH2 MPI library.
- some compiler dependent configure options
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/n/ncl.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
from easybuild.tools.modules import get_software_root, get_software_version


class NCL(Application):
class eb_NCL(Application):
"""Support for building/installing NCL."""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/n/netcdf.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from easybuild.tools.modules import get_software_root, get_software_version


class NetCDF(Application):
class eb_netCDF(Application):
"""Support for building/installing netCDF"""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/n/netcdf_fortran.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.framework.application import Application


class NetCDF_Fortran(Application):
class eb_netCDF_Fortran(Application):
"""Support for building/installing the netCDF-Fortran library"""

def configure(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/o/openfoam.py
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
from easybuild.tools.modules import get_software_root


class OpenFOAM(Application):
class eb_OpenFOAM(Application):
"""Support for building and installing OpenFOAM."""

def __init__(self,*args,**kwargs):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/p/packedbinary.py
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
from easybuild.easyblocks.b.binary import Binary


class PackedBinary(Binary, Application):
class eb_PackedBinary(Binary, Application):
"""Support for installing a packed binary package.
Just unpack its source in the installdir
"""
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/p/pasha.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
from easybuild.tools.modules import get_software_root


class Pasha(Application):
class eb_Pasha(Application):
"""Support for building and installing Pasha"""

def configure(self):
Expand Down
28 changes: 14 additions & 14 deletions easybuild/easyblocks/p/python.py
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
from easybuild.tools.modules import get_software_root


class Python(Application):
class eb_Python(Application):
"""Support for building/installing Python
- default configure/make/make install works fine

Expand All @@ -51,10 +51,10 @@ def extra_packages_pre(self):
"""
We set some default configs here for packages included in python
"""
#insert new packages by building them with DefaultPythonPackage
#insert new packages by building them with eb_DefaultPythonPackage
self.log.debug("setting extra packages options")
# use __name__ here, since this is the module where DefaultPythonPackage is defined
self.setcfg('pkgdefaultclass', (__name__, "DefaultPythonPackage"))
# use __name__ here, since this is the module where eb_DefaultPythonPackage is defined
self.setcfg('pkgdefaultclass', (__name__, "eb_DefaultPythonPackage"))
self.setcfg('pkgfilter', ('python -c "import %(name)s"', ""))

def make_install(self):
Expand All @@ -71,7 +71,7 @@ def make_install(self):
self.log.error("Failed to symlink %s to %s: %s" % err)


class DefaultPythonPackage(ApplicationPackage):
class eb_DefaultPythonPackage(ApplicationPackage):
"""
Easyblock for python packages to be included in the python installation.
"""
Expand Down Expand Up @@ -189,19 +189,19 @@ def getcfg(self, *args, **kwargs):
return self.mself.getcfg(*args, **kwargs)


class Nose(DefaultPythonPackage):
class eb_Nose(eb_DefaultPythonPackage):
"""nose package"""
def __init__(self, mself, pkg, pkginstalldeps):
DefaultPythonPackage.__init__(self, mself, pkg, pkginstalldeps)
eb_DefaultPythonPackage.__init__(self, mself, pkg, pkginstalldeps)

# use extra unpack options to avoid problems like
# 'tar: Ignoring unknown extended header keyword `SCHILY.nlink'
# and tar exiting with non-zero exit code
self.unpack_options = ' --pax-option="delete=SCHILY.*" --pax-option="delete=LIBARCHIVE.*" '


class FortranPythonPackage(DefaultPythonPackage):
"""Extends DefaultPythonPackage to add a Fortran compiler to the make call"""
class eb_FortranPythonPackage(eb_DefaultPythonPackage):
"""Extends eb_DefaultPythonPackage to add a Fortran compiler to the make call"""

def make(self):
comp_fam = self.toolkit().comp_family()
Expand All @@ -227,11 +227,11 @@ def make(self):
run_cmd(cmd, log_all=True, simple=True)


class Numpy(FortranPythonPackage):
class eb_Numpy(eb_FortranPythonPackage):
"""numpy package"""

def __init__(self, mself, pkg, pkginstalldeps):
FortranPythonPackage.__init__(self, mself, pkg, pkginstalldeps)
eb_FortranPythonPackage.__init__(self, mself, pkg, pkginstalldeps)

self.pkgcfgs = mself.getcfg('pkgcfgs')
if self.pkgcfgs.has_key('numpysitecfglibsubdirs'):
Expand Down Expand Up @@ -302,19 +302,19 @@ def make_install(self):
"""Install numpy package
We remove the numpy build dir here, so scipy doesn't find it by accident
"""
FortranPythonPackage.make_install(self)
eb_FortranPythonPackage.make_install(self)
builddir = os.path.join(self.builddir, "numpy")
if os.path.isdir(builddir):
shutil.rmtree(builddir)
else:
self.log.debug("build dir %s already clean" % builddir)


class Scipy(FortranPythonPackage):
class eb_Scipy(eb_FortranPythonPackage):
"""scipy package"""

def __init__(self, mself, pkg, pkginstalldeps):
FortranPythonPackage.__init__(self, mself, pkg, pkginstalldeps)
eb_FortranPythonPackage.__init__(self, mself, pkg, pkginstalldeps)

# disable testing
test = False
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/s/scalapack.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
from easybuild.tools.modules import get_software_root


class ScaLAPACK(Application):
class eb_ScaLAPACK(Application):
"""
Support for building and installing ScaLAPACK, both versions 1.x and 2.x
"""
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/t/tarball.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
from easybuild.framework.application import Application


class Tarball(Application):
class eb_Tarball(Application):
"""
Precompiled software packaged as tarball:
- will unpack binary and copy it to the install dir
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/t/tbb.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from easybuild.easyblocks.i.intelbase import IntelBase


class Tbb(IntelBase):
class eb_tbb(IntelBase):
"""EasyBlock for tbb, threading building blocks"""

def make_install(self):
Expand Down
2 changes: 1 addition & 1 deletion easybuild/easyblocks/t/toolkit.py
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
from easybuild.framework.application import Application


class Toolkit(Application):
class eb_Toolkit(Application):
"""
Compiler toolkit: generate module file only, nothing to make/install
"""
Expand Down
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