Merge pull request #3 from easybuilders/develop

Bringing our develop branch up to date

.gitignore

@@ -8,3 +8,7 @@ build/
 dist/
 *egg-info/
 *.swp
+
+Dockerfile.*
+Singularity.*
+test-reports/

.hound.yml

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

.travis.yml

@@ -5,13 +5,14 @@ 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
+    - ENV_MOD_VERSION=4.1.2 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
@@ -47,8 +48,10 @@ before_install:
     - 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"
@@ -74,6 +77,8 @@ 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/
@@ -86,14 +91,16 @@ 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 $EB_BOOTSTRAP_SHA256SUM"
-    - EB_BOOTSTRAP_EXPECTED="20180201.01 9d6278409b3d9ecf034bd28384da25c14ebfe773606d4fa800e51ed11667e851"
+    - EB_BOOTSTRAP_EXPECTED="20180531.01 21d9704055c4fcf2cd42fe9825dd5925fa508268e4c7c423cb5958a0903d7c2e"
     - test "$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

CONTRIBUTING.md

@@ -43,7 +43,7 @@ Pull the _develop_ branch from the main easybuild-framework repository:
 
 ```bash
 cd easybuild
-git remote add github_easybuilders git@github.com/easybuilders/easybuild-framework.git
+git remote add github_easybuilders git@github.com:easybuilders/easybuild-framework.git
 git branch develop
 git checkout develop
 git pull github_easybuilders develop

RELEASE_NOTES

@@ -3,6 +3,121 @@ 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.
 
+v3.6.2 (July 11th 2018)
+-----------------------
+
+bugfix release
+- various enhancements, including:
+  - add support for including environment variable that is resolved at "module load time" in user module path (#2395)
+    - {RUNTIME_ENV::EXAMPLE} is replaced by value of $EXAMPLE when module is loaded
+  - also support generating Docker container recipes & image via --containerize (still experimental) (#2479)
+  - add support for specifying source URLs directly in 'sources' (#2520)
+  - perform early 'raw' parse of provided easyconfig file to check for syntax error or faulty inputs (#2523)
+  - add 'bitbucket_account' easyconfig parameter and template, and let BITBUCKET* templates use it (#2525)
+- various bug fixes, including:
+  - take into account --filter-deps when re-loading build dependencies in extensions_step (#2516)
+  - fix for offline use of bootstrap script: ignore errors when determining source URLs if source tarballs are provided (#2517)
+  - fix error message that is raised for incorrect type of value in sanity_check_paths (#2524)
+- other changes:
+  - move flake8 config into setup.cfg + fix style issues in easybuild/tools/options.py (#2511)
+  - make test that verifies that BuildOptions does not support updating a bit more flexible (#2518)
+
+
+v3.6.1 (May 28th 2018)
+----------------------
+
+bugfix release
+- various enhancements, including:
+  - add support for enabling fallback in sanity check to consider lib64 equivalent for seemingly missing libraries (#2477)
+  - add GITHUB_LOWER_SOURCE constant (#2491)
+  - add 'exts_download_dep_fail' as known easyconfig parameter (#2493)
+  - add support for passing custom messages on failing sanity check for extensions (#2494)
+  - add definition for fosscuda toolchain (#2507)
+- various bug fixes, including:
+  - make --inject-checksums always re-order source_urls/sources/patches/checksums (#2487)
+  - fix git remote url in CONTRIBUTING.md (#2490)
+  - make flake8 happy in easyblock.py (#2492)
+  - handle missing permissions for adding labels in --new-pr (#2497)
+  - restore tweaked $TMPDIR value after loading module (for sanity check) (#2498)
+  - enhance get_module_path function to auto-detect generic vs software-specific easyblock class names (#2502)
+  - don't blindly overwrite an existing easyconfig in tweak_one (#2504)
+  - take account that PlaintextKeyring may be provided via keyrings.alt (#2505)
+  - prepend location for temporary module file to $MODULEPATH with high priority + mark it as default in load_fake_module method (#2506)
+
+
+v3.6.0 (April 26th 2018)
+------------------------
+
+feature release
+- (experimental) support for generating Singularity container recipes & (optionally) images via 'sudo singularity' (#2332, #2480, #2481, #2482, #2483)
+  - see documentation at http://easybuild.readthedocs.io/en/latest/Containers.html
+- include -ftree-vectorize and -fno-math-errno in default compiler optimisation flags for GCC (#2388)
+  - this significantly improves performance of generated binaries when building with a GCC-based toolchain
+  - can be disabled if needed via the 'vectorize' toolchain option
+- several enhancements/fixes to GitHub integration support:
+  - loosen commit message requirements for --new-pr w.r.t. to patches as long as all easyconfigs are new (#2438)
+  - automatically add 'new' and/or 'update' labels in --new-pr (#2384)
+  - add force_in_dry_run=True to copy_file in copy_patch_files (#2442)
+  - test for custom commit message when deleting a file instead of when adding a patch (#2443)
+  - make diff_stat pattern also match output of older git versions in tests for --new/update-pr (#2444)
+  - remove duplicates from --new-pr title (#2478)
+- add support for "eb --fetch" to only download sources (even without having a modules tool installed) (#2457)
+- add definitions for a bunch of new toolchains:
+  - golf (#2458), gmkl (#2460), gomkl (#2455), pmkl (#2460)
+  - toolchains including CUDA: gmklc, gomklc, iimklc, iompic, iomklc (#2461)
+- various minor enhancements, including:
+  - avoid that '--inject-checksums' adds lines longer than 120 characters (#2434)
+  - enable caching of $HOME/.cache/pip in Travis config (#2435)
+  - replace raw strings with bytes literal as iterator sentinels in checksum calculation (#2446)
+  - new command-line option '--job-max-jobs' to cap nr of submitted build jobs with GC3Pie (#2378)
+  - add configuration for houndci + flake8 (#2451)
+  - add Accept header when downloading file (#2437)
+  - include running of 'eb --check-github' in Travis config (#2449, #2454)
+  - flesh out common code blocks in test/framework/options.py (#2452)
+  - support 'depends_on' load statements in generated modules via --module-depends-on and module_depends_on easyconfig parameter (#2391)
+  - fix compatibility with Modules v4.1.x (#2470)
+  - add support to run_cmd to enable streaming output (#2476)
+- various bug fixes, including:
+  - determine whether included easyblocks are generic or not based on class they define (#2432)
+  - make sure GitHub token is used in test for --preview-pr (#2436)
+  - take into account that toolchain components may be hidden when determining toolchain composition (#2440)
+  - stick to autopep8 1.3.4 when testing with Python 2.6 (#2462)
+  - strip off .lua extension when backing up modules to ensure Lmod 6.x doesn't pick up on them (#2463)
+  - check for modulecmd.tcl before modulecmd in bootstrap script to discriminate between Modules 4.1.x vs 3.2.10 (#2468)
+  - fix derive_alt_pypi_url after PyPI switching to sha256 in package URLs + fix broken test for pypi_source_urls + fix bootstrap script (#2471)
+  - make sure that both 'get_git_revision' and 'this_is_easybuild' return regular strings rather than Unicode strings (#2472)
+
+
+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)
 --------------------------