Merge branch 'develop' into ocaisa_develop

RELEASE_NOTES

@@ -3,6 +3,67 @@ 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.
 
+v2.0.0 (March 6th 2015)
+-----------------------
+
+feature + bugfix release
+- requires vsc-base v2.0.3 or more recent
+    - avoid deprecation warnings w.r.t. use of 'message' attribute (hpcugent/vsc-base#155)
+    - fix typo in log message rendering --ignoreconfigfiles unusable (hpcugent/vsc-base#158)
+- removed functionality that was deprecated for EasyBuild version 2.0 (#1143)
+    - see http://easybuild.readthedocs.org/en/latest/Removed-functionality.html
+    - the fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (#1151, #1206, #1207)
+    - for more information about this script, see http://easybuild.readthedocs.org/en/latest/Useful-scripts.html#fix-broken-easyconfigs-py
+- stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (#1160, #1194)
+    - vsc-base is automatically installed as a dependency for easybuild-framework, if a Python installation tool is used
+    - see http://easybuild.readthedocs.org/en/latest/Installation.html#required-python-packages
+- various other enhancements, including:
+    - add support for Linux/POWER systems (#1044)
+    - major cleanup in tools/systemtools.py + significantly enhanced tests (#1044)
+    - add support for 'eb -a rst', list available easyconfig parameters in ReST format (#1131)
+    - add support for specifying one or more easyconfigs in combination with --from-pr (#1132)
+        - see http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html#using-easyconfigs-from-pull-requests-via-from-pr
+    - define __contains__ in EasyConfig class (#1155)
+    - restore support for downloading over a proxy (#1158)
+        - i.e., use urllib2 rather than urllib
+        - this involved sacrificing the download progress report (which was only visible in the log file)
+    - let mpi_family return None if MPI is not supported by a toolchain (#1164)
+    - include support for specifying system-level configuration files for EasyBuild via $XDG_CONFIG_DIRS (#1166)
+        - see http://easybuild.readthedocs.org/en/latest/Configuration.html#default-configuration-files
+    - make unit tests more robust (#1167, #1196)
+        - see http://easybuild.readthedocs.org/en/latest/Unit-tests.html
+    - add hierarchical module naming scheme categorizing modules by 'moduleclass' (#1176)
+    - enhance bootstrap script to allow bootstrapping using supplied tarballs (#1184)
+        - see http://easybuild.readthedocs.org/en/latest/Installation.html#advanced-bootstrapping-options
+    - disable updating of Lmod user cache by default, add configuration option --update-modules-tool-cache (#1185)
+        - for now, only the Lmod user cache can be updated using --update-modules-tool-cache
+    - use available which() function, rather than running 'which' via run_cmd (#1192)
+    - fix install-EasyBuild-develop.sh script w.r.t. vsc-base dependency (#1193)
+    - also consider robot search path when looking for specified easyconfigs (#1201)
+        - see http://easybuild.readthedocs.org/en/latest/Using_the_EasyBuild_command_line.html#specifying-easyconfigs
+- various bug fixes, including:
+    - stop triggering deprecated/no longer support functionality in unit tests (#1126)
+    - fix from_pr test by including dummy easyblocks for HPL and ScaLAPACK (#1133)
+    - escape use of '%' in string with command line options with --job (#1135)
+    - fix handling specified patch level 0 (+ enhance tests for fetch_patches method) (#1139)
+    - fix formatting issues in generated easyconfig file obtained via --try-X (#1144)
+    - use log.error in tools/toolchain/toolchain.py where applicable (#1145)
+    - stop hardcoding /tmp in mpi_cmd_for function (#1146, #1200)
+    - correctly determine variable name for $EBEXTLIST when generating module file (#1156)
+    - do not ignore exit code of failing postinstall commands (#1157)
+    - fix rare case in which used easyconfig and copied easyconfig are the same (#1159)
+    - always filter hidden deps from list of dependencies (#1161)
+    - fix implementation of path_matches function in tools/filetools.py (#1163)
+    - make sure plain text keyring is used by unit tests (#1165)
+    - suppress creation of module symlinks for HierarchicalMNS (#1173)
+    - sort all lists obtained via glob.glob, since they are in arbitrary order (#1187)
+    - stop modifying $MODULEPATH directly in setUp/tearDown of toolchain tests (#1191)
+
+v1.16.2 (March 6th 2015)
+------------------------
+
+(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)
+
 v1.16.1 (December 19th 2014)
 ----------------------------
 

easybuild/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/framework/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/framework/easyblock.py

@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -52,8 +52,8 @@
 from easybuild.tools import config, filetools
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ITERATE_OPTIONS, EasyConfig, ActiveMNS
-from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
+from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
 from easybuild.tools.build_details import get_build_stats
@@ -937,7 +937,7 @@ def make_module_req(self):
             txt = "\n"
             for key in sorted(requirements):
                 for path in requirements[key]:
-                    paths = glob.glob(path)
+                    paths = sorted(glob.glob(path))
                     if paths:
                         txt += self.module_generator.prepend_paths(key, paths)
             try:
@@ -1652,7 +1652,10 @@ def make_module_step(self, fake=False):
 
         self.log.info("Module file %s written" % self.module_generator.filename)
 
-        self.modules_tool.update()
+         # only update after generating final module file
+        if not fake:
+            self.modules_tool.update()
+
         self.module_generator.create_symlinks()
 
         if not fake:
@@ -1825,15 +1828,17 @@ def run_all_steps(self, run_test_cases):
         return True
 
 
-def build_and_install_one(module, orig_environ):
+def build_and_install_one(ecdict, orig_environ):
     """
     Build the software
-    @param module: dictionary contaning parsed easyconfig + metadata
+    @param ecdict: dictionary contaning parsed easyconfig + metadata
     @param orig_environ: original environment (used to reset environment)
     """
     silent = build_option('silent')
 
-    spec = module['spec']
+    spec = ecdict['spec']
+    rawtxt = ecdict['ec'].rawtxt
+    name = ecdict['ec']['name']
 
     print_msg("processing EasyBuild easyconfig %s" % spec, log=_log, silent=silent)
 
@@ -1847,12 +1852,11 @@ def build_and_install_one(module, orig_environ):
     # load easyblock
     easyblock = build_option('easyblock')
     if not easyblock:
-        easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
+        easyblock = fetch_parameters_from_easyconfig(rawtxt, ['easyblock'])[0]
 
-    name = module['ec']['name']
     try:
         app_class = get_easyblock_class(easyblock, name=name)
-        app = app_class(module['ec'])
+        app = app_class(ecdict['ec'])
         _log.info("Obtained application instance of for %s (easyblock: %s)" % (name, easyblock))
     except EasyBuildError, err:
         tup = (name, easyblock, err.msg)
@@ -1909,9 +1913,9 @@ def build_and_install_one(module, orig_environ):
                 # upload spec to central repository
                 currentbuildstats = app.cfg['buildstats']
                 repo = init_repository(get_repository(), get_repositorypath())
-                if 'original_spec' in module:
+                if 'original_spec' in ecdict:
                     block = det_full_ec_version(app.cfg) + ".block"
-                    repo.add_easyconfig(module['original_spec'], app.name, block, buildstats, currentbuildstats)
+                    repo.add_easyconfig(ecdict['original_spec'], app.name, block, buildstats, currentbuildstats)
                 repo.add_easyconfig(spec, app.name, det_full_ec_version(app.cfg), buildstats, currentbuildstats)
                 repo.commit("Built %s" % app.full_mod_name)
                 del repo
@@ -1976,22 +1980,23 @@ def build_and_install_one(module, orig_environ):
     return (success, application_log, errormsg)
 
 
-def get_easyblock_instance(easyconfig):
+def get_easyblock_instance(ecdict):
     """
     Get an instance for this easyconfig
     @param easyconfig: parsed easyconfig (EasyConfig instance)
 
     returns an instance of EasyBlock (or subclass thereof)
     """
-    spec = easyconfig['spec']
-    name = easyconfig['ec']['name']
+    spec = ecdict['spec']
+    rawtxt = ecdict['ec'].rawtxt
+    name = ecdict['ec']['name']
 
     # handle easyconfigs with custom easyblocks
     # determine easyblock specification from easyconfig file, if any
-    easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
+    easyblock = fetch_parameters_from_easyconfig(rawtxt, ['easyblock'])[0]
 
     app_class = get_easyblock_class(easyblock, name=name)
-    return app_class(easyconfig['ec'])
+    return app_class(ecdict['ec'])
 
 
 def build_easyconfigs(easyconfigs, output_dir, test_results):

easybuild/framework/easyconfig/__init__.py

@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/framework/easyconfig/constants.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

easybuild/framework/easyconfig/default.py

@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),