Merge pull request #3279 from boegel/develop

sync develop with master after EasyBuild v4.2.0 release + bump version to 4.2.1dev

Author: Micket

RELEASE_NOTES

@@ -3,6 +3,69 @@ 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.
 
+v4.2.0 (April 14th 2020)
+------------------------
+
+feature release
+
+- add support for --try-update-deps (experimental feature), to upgrade dependencies based on available easyconfigs (#2599)
+- adding locking to prevent two parallel builds of the same installation directory (#3009)
+  - for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html
+- significantly speed up -D/--dry-run by avoiding useless 'module show' (#3203)
+- add support for creating an index & using it when searching for easyconfigs (#3210)
+  - for more information, see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html
+- additional GitHub integration features:
+    - add support for targeting easyblocks and framework repositories in --new-pr (#1876, #3189)
+    - add support for --include-easyblocks-from-pr (#3206)
+    - for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html
+- various other enhancements, including:
+  - add a contrib/hooks dir with some examples of hooks used (#2777)
+  - also mention working directory + input passed via stdin (if any) in trace output of run_cmd (#3168)
+  - probe external modules for missing metadata that is not provided via extermal module metadata file (#3174)
+  - also update $CMAKE_PREFIX_PATH and $CMAKE_LIBRARY_PATH in generated module file (#3176)
+  - optionally call log.warning in print_warning (#3195)
+  - add an option to git_config to retain the .git directory (#3197)
+  - allow use of SYSTEM as --try-toolchain option (#3213)
+  - mention CPU arch name in comment for uploaded test report, if it's known by archspec (#3227)
+  - make --merge-pr take into account --pr-target-branch (#3236)
+  - make --check-contrib print a warning when None is used for checksums (#3244)
+  - update install-EasyBuild-develop.sh script and create script for 2020a merge sprint (#3245)
+  - add template for mpi_cmd_prefix (#3264)
+  - update copy_dir to include option to merge directories (#3270)
+  - support template name for CUDA version (#3274)
+- various bug fixes, including:
+  - use correct module for errors_found_in_log (#3119)
+  - fix EasyConfig.update code to handle both strings and lists as input (#3170)
+  - fix removing temporary branch on --check-github (#3182)
+  - fix shebang even if first line doesn't start with '#!' (#3183)
+  - make boostrap script work with Python 3 (#3186)
+  - read patch files as bytestring to avoid UnicodeDecodeError for patches that include funky characters (#3191)
+  - fix online check in --check-github: try repeatedly and with different URLs to cater for HTTP issues (#3194)
+  - don't crash when GitPython is not installed when using Python 3 (#3198)
+  - fix os_name_map for RHEL8 (#3201)
+  - don't add shebang to binary files (#3208)
+  - use checkout@v2 in GitHub Actions to fix broken re-triggered tests (#3219)
+  - don't filter out None values in to_checksums, leave them in place (#3225)
+  - fix defining of $MPI_INC_* and $MPI_LIB_* environment variables for impi version 2019 and later (#3229)
+  - use correct target account/repo when creating test report & posting comment in PR (#3234)
+  - reorganize EasyBlock.extensions_step to ensure correct filtering of extensions (#3235)
+  - also support %(installdir)s and %(builddir)s templates for extensions (#3237)
+  - unset $GITHUB_TOKEN in Travis after installing token, to avoid failing test_from_pr_token_log (#3252)
+  - fix reporting when skipping extensions (#3254)
+  - avoid API rate limit errors on online check in --check-github (#3257)
+  - show easyconfig filenames for parallel build (#3258)
+  - make EasyConfig.dump aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (#3261)
+  - fix use of --copy-ec with a single argument, assume copy to current working directory (#3262)
+  - fix posting of comment in PR with --upload-test-report (#3272)
+  - take into account dependencies marked as external modules when composing template values like %(pyver)s (#3273)
+- other changes:
+  - increase timeout & use api.github.com for connectivity check in check_github (#3192)
+  - restore flake8 default ignores (#3193)
+  - enable tracking of test suite coverage using coveralls (#3204)
+  - make tests use easybuilders/testrepository rather than hpcugent/testrepository after it was moved (#3238)
+  - improve raised error in remove_dir and deprecate rmtree2 (#3228)
+
+
 v4.1.2 (March 16th 2020)
 ------------------------
 
@@ -11,6 +74,8 @@ bugfix release
 - fix gitdb dependency on Python 2.6 in test configuration (#3212)
 - fix broken test for --review-pr by using different PR to test with (#3226)
 - censor authorization part of headers before logging ReST API request (#3248)
+  - see also https://github.com/easybuilders/easybuild-framework/security/advisories/GHSA-2wx6-wc87-rmjm
+
 
 v4.1.1 (January 16th 2020)
 --------------------------

easybuild/tools/version.py

@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.2.0.dev0')
+VERSION = LooseVersion('4.2.1.dev0')
 UNKNOWN = 'UNKNOWN'
 
 

test/framework/filetools.py

@@ -1292,8 +1292,8 @@ def test_pypi_source_urls(self):
         eb340_url += 'easybuild-3.4.0.tar.gz#md5=267a056a77a8f77fccfbf56354364045'
         self.assertTrue(eb340_url, res)
         pattern = '^https://pypi.python.org/packages/[a-f0-9]{2}/[a-f0-9]{2}/[a-f0-9]{60}/'
-        pattern_md5 = pattern + 'easybuild-[0-9rc.]+.tar.gz#md5=[a-f0-9]{32}$'
-        pattern_sha256 = pattern + 'easybuild-[0-9rc.]+.tar.gz#sha256=[a-f0-9]{64}$'
+        pattern_md5 = pattern + 'easybuild-[0-9a-z.]+.tar.gz#md5=[a-f0-9]{32}$'
+        pattern_sha256 = pattern + 'easybuild-[0-9a-z.]+.tar.gz#sha256=[a-f0-9]{64}$'
         regex_md5 = re.compile(pattern_md5)
         regex_sha256 = re.compile(pattern_sha256)
         for url in res: