Merge pull request #2 from boegel/package_singularity_develop

sync Singularity branch with develop

.flake8.ini

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 120

.hound.yml

@@ -0,0 +1,4 @@
+# configuration for houndci, see https://houndci.com/configuration#python
+flake8:
+  enabled: true
+  config_file: .flake8.ini

.travis.yml

@@ -5,12 +5,13 @@ env:
     # purposely specifying slowest builds first, to gain time overall
     - LMOD_VERSION=5.8
     - LMOD_VERSION=5.8 TEST_EASYBUILD_MODULE_SYNTAX=Tcl
-    - LMOD_VERSION=6.6.3
-    - LMOD_VERSION=6.6.3 TEST_EASYBUILD_MODULE_SYNTAX=Tcl
-    - LMOD_VERSION=7.4
-    - LMOD_VERSION=7.4 TEST_EASYBUILD_MODULE_SYNTAX=Tcl
+    - LMOD_VERSION=7.7.16
+    - LMOD_VERSION=7.7.16 TEST_EASYBUILD_MODULE_SYNTAX=Tcl
     - ENV_MOD_VERSION=3.2.10 TEST_EASYBUILD_MODULES_TOOL=EnvironmentModulesC TEST_EASYBUILD_MODULE_SYNTAX=Tcl
     - ENV_MOD_TCL_VERSION=1.147 TEST_EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl TEST_EASYBUILD_MODULE_SYNTAX=Tcl
+    - ENV_MOD_VERSION=4.0.0 TEST_EASYBUILD_MODULE_SYNTAX=Tcl TEST_EASYBUILD_MODULES_TOOL=EnvironmentModules
+cache:
+  pip: true
 matrix:
   # mark build as finished as soon as job has failed
   fast_finish: true
@@ -42,8 +43,14 @@ before_install:
     - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install 'GitPython<2.0'; else pip install GitPython; fi
     # pydot (dep for python-graph-dot) 1.2.0 and more recent doesn't work with Python 2.6
     - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install pydot==1.1.0; else pip install pydot; fi
+    # paramiko (dep for GC3Pie) 2.4.0 & more recent doesn't work with Python 2.6
+    - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install 'paramiko<2.4.0'; else pip install paramiko; fi
+    # SQLAlchemy (dep for GC3Pie) 1.2.0 & more recent doesn't work with Python 2.6
+    - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install 'SQLAlchemy<1.2.0'; else pip install SQLAlchemy; fi
+    # autopep8 1.3.4 is last one to support Python 2.6
+    - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install 'autopep8<1.3.5'; else pip install autopep8; fi
     # optional Python packages for EasyBuild
-    - pip install autopep8 GC3Pie pycodestyle python-graph-dot python-hglib PyYAML
+    - pip install GC3Pie pycodestyle python-graph-dot python-hglib PyYAML
     # git config is required to make actual git commits (cfr. tests for GitRepository)
     - git config --global user.name "Travis CI"
     - git config --global user.email "travis@travis-ci.org"
@@ -60,7 +67,7 @@ script:
     # make sure 'ml' alias is defined, otherwise sourcing the init script fails (silently) for Lmod (< 5.9.3)
     - if [ ! -z $MOD_INIT ] && [ ! -z $LMOD_VERSION ]; then alias ml=foobar; fi
     # set up environment for modules tool (if $MOD_INIT is defined)
-    - if [ ! -z $MOD_INIT ]; then source $MOD_INIT; fi
+    - if [ ! -z $MOD_INIT ]; then source $MOD_INIT; type module; fi
     # install GitHub token
     - if [ ! -z $GITHUB_TOKEN ]; then
         if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ];
@@ -69,6 +76,8 @@ script:
         fi;
         python -c "import keyring; $SET_KEYRING; keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
       fi
+    - if [ ! -z $TEST_EASYBUILD_MODULES_TOOL ]; then export EASYBUILD_MODULES_TOOL=$TEST_EASYBUILD_MODULES_TOOL; fi
+    - if [ ! -z $TEST_EASYBUILD_MODULE_SYNTAX ]; then export EASYBUILD_MODULE_SYNTAX=$TEST_EASYBUILD_MODULE_SYNTAX; fi
     # create 'source distribution' tarball, like we do when publishing a release to PyPI
     - cd $TRAVIS_BUILD_DIR; python setup.py sdist
     - ls -l $TRAVIS_BUILD_DIR/dist/
@@ -81,14 +90,16 @@ script:
     # to run tests on an *installed* version of the EasyBuild framework;
     # this is done to catch possible packaging issues
     - cd $HOME
+    # check GitHub configuration
+    - eb --check-github --github-user=easybuild_test
     # run test suite
     - python -O -m test.framework.suite
     # check bootstrap script version
     # version and SHA256 checksum are hardcoded below to avoid forgetting to update the version in the script along with contents
     - EB_BOOTSTRAP_VERSION=$(grep '^EB_BOOTSTRAP_VERSION' $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py | sed 's/[^0-9.]//g')
     - EB_BOOTSTRAP_SHA256SUM=$(sha256sum $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py | cut -f1 -d' ')
     - EB_BOOTSTRAP_FOUND="$EB_BOOTSTRAP_VERSION $EB_BOOTSTRAP_SHA256SUM"
-    - EB_BOOTSTRAP_EXPECTED="20170808.01 b78eac49374b26c78a16ea41efcde8c03d21649087f650e08f5339e8e48d7c6e"
+    - EB_BOOTSTRAP_EXPECTED="20180412.02 d05b0922f83ba7febfeb1dcfca4a854be93cbfefa6cdedcc87cc8c3835aa3fa3"
     - test "$EB_BOOTSTRAP_FOUND" = "$EB_BOOTSTRAP_EXPECTED" || (echo "Version check on bootstrap script failed $EB_BOOTSTRAP_FOUND" && exit 1)
     # test bootstrap script
     - python $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py /tmp/$TRAVIS_JOB_ID/eb_bootstrap

RELEASE_NOTES

@@ -3,6 +3,72 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
 
+v3.5.3 (March 7th 2018)
+-----------------------
+
+bugfix release
+- various enhancements, including:
+  - re-enable testing against environment modules, bump Lmod to 7.7.16 (#2425)
+  - print which hook is being executed in the command line output (#2427)
+- various bug fixes, including:
+  - fix order in result of gen_list_easyblocks and gen_easyblocks_overview_rst (#2421)
+  - fix target account for branch pushed when using --new-pr (#2426)
+
+
+v3.5.2 (March 2nd 2018)
+-----------------------
+
+bugfix release
+- various enhancements, including:
+  - add functionality to skip devel module with naming scheme (#2374)
+  - add pagination support in clean_gists.py (#2379)
+  - allow basic compiler modulenames to be specified as keys in optarch (#2387)
+  - initial set of OHPC module meta data for EasyBuild (#2392)
+  - allow different target account in post_comment_in_issue (#2399)
+  - declare support for RPATH linking stable (#2409)
+- various bug fixes, including:
+  - update bootstrap script to be compatible with Modules v4 (#2390)
+  - avoid fatal error when determining glibc version on non-glibc Linux system (e.g. Alphine Linux) (#2398)
+  - exclude location of RPATH wrappers from $PATH to avoid fork bomb (#2410)
+  - fix target account for --update-pr in case it's different from GitHub account being used to push branch (#2419)
+
+
+v3.5.1 (January 16th 2018)
+--------------------------
+
+bugfix release
+- various enhancements, including:
+  - add definition of giolfc toolchain (#2359)
+  - add support for Environment Modules 4 (#2365)
+- various bug fixes, including:
+  - install SQLAlchemy < 1.2.0 with Python 2.6 in Travis config (#2367)
+  - make code in easybuild/tools/job/gc3pie.py forward-compatible with GC3Pie 2.5 (#2373)
+
+
+v3.5.0 (December 15th 2017)
+---------------------------
+
+feature release
+- add support for implementing pre- and post-step hooks (#2343)
+  - documentation available at http://easybuild.readthedocs.io/en/latest/Hooks.html
+- various enhancements, including:
+  - add support for foss-like toolchain with Spectrum MPI: gsolf (#2329)
+  - add support for --preview-pr (#2331, #2337, #2348)
+    - see also http://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html#previewing-easyconfig-pull-requests-preview-pr
+  - flesh out find_extension function, hoist dict with extract commands into a constant (#2336)
+  - add support for using self.start_dir rather than using self.cfg['start_dir'] (#2339)
+  - add support for 'exts_default_options' easyconfig parameter (#2345, #2346)
+  - allow use of 'start_dir' easyconfig parameter in extensions (#2353)
+- various bug fixes, including:
+  - fix typo in 'giolf' toolchain definition (#2327)
+  - fix minor issues with --inject-checksums (#2333)
+  - fix error message when 'gv' Python package is not available (#2340)
+  - install paramiko version < 2.4.0 for Python 2.6 in Travis config (#2344)
+  - disable broken log rotation, avoid duplicate logging of output of executed commands under '--debug' (#2347)
+  - also include $ORIGIN and absolute paths to 'lib' and 'lib64' subdirectories in RPATH locations (#2358)
+  - fix repo references in install-EasyBuild-develop.sh script (#2360)
+
+
 v3.4.1 (October 17th 2017)
 --------------------------
 

easybuild/__init__.py

@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2017 Ghent University
+# Copyright 2011-2018 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 2009-2017 Ghent University
+# Copyright 2009-2018 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),