Merge branch 'develop' into ext_sources

Author: Flamefire

.coveragerc

@@ -97,7 +97,7 @@ jobs:
           # see https://docs.easybuild.io/en/latest/Containers.html
           curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
-          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
+          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/rockylinux-8.10-amd64'
           eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
           singularity exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1)
           singularity exec bzip2-1.0.8.sif bzip2 --help

.github/workflows/container_tests.yml

@@ -91,7 +91,7 @@ jobs:
           # see https://docs.easybuild.io/en/latest/Containers.html
           curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
-          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
+          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/rockylinux-8.10-amd64'
           export EASYBUILD_CONTAINER_TYPE='apptainer'
           eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
           apptainer exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1)

.github/workflows/container_tests_apptainer.yml

@@ -24,7 +24,7 @@ jobs:
     - name: set up Python
       uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ matrix.python }}
 
     - name: install Python packages
       run: |

.github/workflows/linting.yml

@@ -2,7 +2,7 @@
    :align: center
    :height: 400px
 
-.. image:: https://github.com/easybuilders/easybuild-framework/workflows/EasyBuild%20framework%20unit%20tests/badge.svg?branch=develop
+.. image:: https://github.com/easybuilders/easybuild-framework/actions/workflows/unit_tests.yml/badge.svg?branch=develop
 
 `EasyBuild <https://easybuild.io>`_ is a software build
 and installation framework that allows you to manage (scientific) software

README.rst

@@ -4,9 +4,98 @@ For more detailed information, please see the git log.
 These release notes can also be consulted at https://docs.easybuild.io/release-notes .
 
 
+v5.1.1 (6 July 2025)
+--------------------
+
+update/bugfix release
+
+- enhancements:
+  - don't allow using `--pr-commit-msg` when only adding new files with `--new-pr` (unless `--force` is used) (#4498)
+  - update `install-EasyBuild-develop.sh` script to allow installation without forking (#4899)
+  - add blue, cyan, purple as known colors that can be used in colorize function (#4907)
+  - trigger `post_run_shell_cmd_hook` before raising error if shell command failed + pass down full `RunShellCmdResult` instance (#4908)
+  - also pass value of `fail_on_error` and `hidden` options of `run_shell_cmd` call down to pre/post `run_shell_cmd` hook (#4911)
+  - add configuration option to ignore unversioned (0.0.0) Python packages (#4912)
+  - add `required` option to `EasyConfig.get_cuda_cc_template_value` method (#4913)
+  - add total iteration count to trace output (#4919, #4952)
+  - add support for pre/post `easyblock` hook (#4923, #4938)
+  - catch `HTTPException` when doing GitHub API request (#4926)
+- bug fixes:
+  - fix reporting of method name in `EasyBlock.run_step` (#4920)
+  - fix handling of broken symlinks in `filetools.remove` (#4921)
+  - keep symlinks when copying build dirs of failed installations (#4933)
+  - also copy patches of extensions to easybuild subdirectory of installation directory (#4939, #4946)
+  - also copy easyblocks of bundle components to reprod dir (#4944)
+  - take into account that forked repository may not have same name as origin `--sync-pr-with-develop` (#4947)
+- enhancements and fixes for test suite:
+  - add support for passing valid unittest options to test suite (#3790)
+  - enhance `LooseVersion` test to add cases with leading alphabetical characters (#4901)
+  - prefer using `importlib.metadata` over the deprecated `pkg_resources` in `det_pypkg_version` + switch container tests to Rocky Linux 8.10 (#4904)
+  - fix `TypeError` for Python version comparison in `test_fetch_sources_git` (#4934)
+  - fix broken tests for GitHub integration features (#4954)
+- other changes:
+  - change value of architectures constants RISCV32 and RISCV64 (#4915)
+  - remove some superflous Python 2 checks (#4917)
+  - remove use of unsupported `source` key in patch spec (#4924)
+  - remove super() arguments from mk_tmpl_easyblock_for (#4936)
+
+
+v5.1.0 (26 May 2025)
+--------------------
+
+feature release
+
+- various enhancements, including:
+  - add support for data installations (#4474, #4873, #4874)
+  - allow specifying location for RPATH wrapper scripts via `rpath_wrappers_dir` (#4596)
+  - add a CUDA device code sanity check (#4692)
+  - add support for check_readelf_rpath easyconfig parameter to optionally skip RPATH checks (#4768)
+  - add support for using environment variables in value used in modextravars (#4855)
+  - print summary after the build in trace output (#4861, #4875)
+  - avoid leaking keys by mistake with `--upload-test-report` (#4877)
+  - obtain PR/commit diff via GitHub API rather than downloading `*.diff` file via github.com (#4878)
+  - support options for patch command (#4886)
+  - replace full trace message for extension check command with simple pass/fail message (#4892)
+- various bug fixes, including:
+  - also pass `rpath_include_dirs` when preparing build environment for extensions (#4596)
+  - fix `check_checksums` when `nosource: True` is used (#4806)
+  - fix help string of findPythonDeps.py script (#4821)
+  - take into account `job-output-dir` option in Slurm job backend (#4842)
+  - fix unbound variable in error case in `build_and_install_software` (#4843)
+  - avoid failure when only some passed easyconfigs exist (#4847)
+  - restore original value for non-list easyconfig parameter values that are considered for iterating over (#4848)
+  - add '-' before 'DMKL_ILP64' in $CFLAGS (#4850)
+  - enhance RPATH sanity check to skip anything whose absolute path resolves to outside the install dir (#4854)
+  - use new `ModEnvVarType.STRICT_PATH_WITH_FILES` with `CMAKE_LIBRARY_PATH` environment variable (#4858)
+  - fix `is_patch_for` for patch dicts (#4865)
+  - update fake module for each extension installed (#4868, #4888, #4895)
+  - implement exponential backoff in `download_file` (#4870, #4880)
+  - use `develop` branch for PRs that target removed `5.0.x` branch in `fetch_files_from_pr` (#4879)
+  - also ignore errors raised during test step when `--ignore-test-failure` is used (#4881)
+  - fix download progress bar (#4885)
+  - fix `--dep-graph` by using `graphviz` Python package (#4891)
+- fixes for test suite:
+  - fix `test_github_preview_pr` which got broken because there's no more easyconfigs for bzip2 1.0.6 in easyconfigs repo (#4827)
+  - fix tests after removal of 5.0.x branch (#4830)
+  - fix missed message in trivial equal-asserts (#4831)
+  - fix wrong variable name used for Python version in linting CI (#4839)
+  - fix failing GitHub integration CI tests (#4841)
+  - fix testsuite badge in README (#4845)
+- other changes:
+  - go back to using `develop` branch rather than `5.0.x` branch in GitHub Actions workflows (#4820)
+  - remove source tarball for Python 3.7.2 from test sources (#4828)
+  - delete .coveragerc (#4833)
+  - remove Python 2 constructs (#4834)
+  - remove superflous assignment in `_sanity_check_step` (#4851)
+  - replace deprecation warning about reproducible tarballs on Python older than 3.9 with a regular warning (#4852)
+  - move `EasyBlock.expand_module_search_path` into `ModuleEnvironmentVariable.expand_paths` (#4859)
+
+
 v5.0.0 (18 March 2025)
 ----------------------
 
+major release (includes breaking changes)
+
 - remove support for Python 2.7 and 3.5 (#4229, #4270, #4306, #4473, #4477, #4476, #4478, #4524, #4607, #4756, #4810, #4811) 
   - also run unit test suite with Python 3.12 + 3.13 (#4484, #4674)
 - changed defaults in EasyBuild configuration:

RELEASE_NOTES

@@ -31,6 +31,7 @@
 """
 import contextlib
 import functools
+import json
 import os
 import re
 import signal
@@ -96,6 +97,12 @@ def cache_aware_func(cmd, *args, **kwargs):
     return cache_aware_func
 
 
+def json_loads(body):
+    """Deprecated wrapper for json.loads"""
+    _log.deprecated("json_loads is deprecated, use json.loads", '6.0')
+    return json.loads(body)
+
+
 def get_output_from_process(proc, read_size=None, asynchronous=False, print_deprecation_warning=True):
     """
     Get output from running process (that was opened with subprocess.Popen).

easybuild/_deprecated.py

@@ -125,4 +125,4 @@ def __init__(self, msg, *args, **kwargs):
 
         getattr(logger, self.LOGGING_METHOD_NAME)(msg)
 
-        super(LoggedException, self).__init__(msg)
+        super().__init__(msg)

easybuild/base/exceptions.py

@@ -578,8 +578,7 @@ def logToFile(filename, enable=True, filehandler=None, name=None, max_bytes=MAX_
         'maxBytes': max_bytes,
         'backupCount': backup_count,
     }
-    if sys.version_info[0] >= 3:
-        handleropts['encoding'] = 'utf-8'
+    handleropts['encoding'] = 'utf-8'
     # logging to a file is going to create the file later on, so let's try to be helpful and create the path if needed
     directory = os.path.dirname(filename)
     if not os.path.exists(directory):

easybuild/base/fancylogger.py

@@ -52,7 +52,7 @@ def __repr__(self):
 
     def __hash__(self):
         if self.__hash is None:
-            self.__hash = reduce(operator.xor, map(hash, self.iteritems()), 0)
+            self.__hash = reduce(operator.xor, map(hash, self.items()), 0)
 
         return self.__hash
 
@@ -87,13 +87,13 @@ def __init__(self, *args, **kwargs):
                 msg = "Encountered unknown keys %s (known keys: %s)" % (unknown_keys, self.KNOWN_KEYS)
                 self.log.raiseException(msg, exception=KeyError)
 
-        super(FrozenDictKnownKeys, self).__init__(tmpdict)
+        super().__init__(tmpdict)
 
     # pylint: disable=arguments-differ
     def __getitem__(self, key, *args, **kwargs):
         """Redefine __getitem__ to provide a better KeyError message."""
         try:
-            return super(FrozenDictKnownKeys, self).__getitem__(key, *args, **kwargs)
+            return super().__getitem__(key, *args, **kwargs)
         except KeyError as err:
             if key in self.KNOWN_KEYS:
                 raise KeyError(err)