Merge branch '5.0.x' of github.com:easybuilders/easybuild-framework into 5.0.x

Author: boegel

.github/workflows/container_tests.yml

@@ -74,7 +74,7 @@ jobs:
           ls dist
           export PREFIX=/tmp/$USER/$GITHUB_SHA
           pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
-          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/develop.tar.gz
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz
 
     - name: run test
       run: |
@@ -95,7 +95,7 @@ jobs:
           echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
           # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
           # see https://docs.easybuild.io/en/latest/Containers.html
-          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/5.0.x/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
           export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
           eb bzip2-1.0.8.eb --containerize --experimental --container-build-image

.github/workflows/container_tests_apptainer.yml

@@ -74,7 +74,7 @@ jobs:
           ls dist
           export PREFIX=/tmp/$USER/$GITHUB_SHA
           pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
-          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/develop.tar.gz
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz
 
     - name: run test
       run: |
@@ -95,7 +95,7 @@ jobs:
           echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
           # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
           # see https://docs.easybuild.io/en/latest/Containers.html
-          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/5.0.x/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
           export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
           export EASYBUILD_CONTAINER_TYPE='apptainer'

.github/workflows/eb_command.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
+        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
       fail-fast: false
     steps:
     - uses: actions/checkout@v3
@@ -91,7 +91,7 @@ jobs:
           pymajver=$(python -c 'import sys; print(sys.version_info[0])')
           pymajminver=$(python -c 'import sys; print(".".join(str(x) for x in sys.version_info[:2]))')
           # check patterns in verbose output
-          for pattern in "^>> Considering .python.\.\.\." "^>> .python. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: python \(.*/bin/python\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+          for pattern in "^>> Considering .python3.\.\.\." "^>> .python3. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python3' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: python3 \(.*/bin/python3\)" "^This is EasyBuild 5\.[0-9.]\+"; do
               echo "Looking for pattern \"${pattern}\" in eb_version.out..."
               grep "$pattern" eb_version.out
           done
@@ -103,7 +103,7 @@ jobs:
           for eb_python in "python${pymajver}" "python${pymajminver}"; do
               export EB_PYTHON="${eb_python}"
               eb --version | tee eb_version.out 2>&1
-              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 5\.[0-9.]\+"; do
                   echo "Looking for pattern \"${pattern}\" in eb_version.out..."
                   grep "$pattern" eb_version.out
               done

.github/workflows/end2end.yml

@@ -7,7 +7,6 @@ jobs:
     strategy:
       matrix:
         container:
-          - centos-7.9
           - centos-8.5
           - fedora-36
           - opensuse-15.4
@@ -26,17 +25,17 @@ jobs:
         run: |
           cd $HOME
           for pkg in easyblocks easyconfigs; do
-              curl -OL https://github.com/easybuilders/easybuild-${pkg}/archive/develop.tar.gz
-              tar xfz develop.tar.gz
-              rm -f develop.tar.gz
+              curl -OL https://github.com/easybuilders/easybuild-${pkg}/archive/5.0.x.tar.gz
+              tar xfz 5.0.x.tar.gz
+              rm -f 5.0.x.tar.gz
           done
 
       - name: Set up environment
         shell: bash
         run: |
           # collect environment variables to be set in subsequent steps in script that can be sourced
           echo "export PATH=$PWD:$PATH" > /tmp/eb_env
-          echo "export PYTHONPATH=$PWD:$HOME/easybuild-easyblocks-develop:$HOME/easybuild-easyconfigs-develop" >> /tmp/eb_env
+          echo "export PYTHONPATH=$PWD:$HOME/easybuild-easyblocks-5.0.x:$HOME/easybuild-easyconfigs-5.0.x" >> /tmp/eb_env
 
       - name: Run commands to check test environment
         shell: bash

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3
@@ -30,10 +30,4 @@ jobs:
 
     - name: Run flake8 to verify PEP8-compliance of Python code
       run: |
-        # don't check py2vs3/py3.py when testing with Python 2, and vice versa
-        if [[ "${{ matrix.python-version }}" =~ "2." ]]; then
-            py_excl=py3
-        else
-            py_excl=py2
-        fi
-        flake8 --exclude ./easybuild/tools/py2vs3/${py_excl}.py
+        flake8

.github/workflows/unit_tests.yml

@@ -13,10 +13,7 @@ jobs:
   setup:
     runs-on: ubuntu-20.04
     outputs:
-        lmod7: Lmod-7.8.22
         lmod8: Lmod-8.7.6
-        modulesTcl: modules-tcl-1.147
-        modules3: modules-3.2.10
         modules4: modules-4.1.4
     steps:
       - run: "true"
@@ -29,16 +26,11 @@ jobs:
         modules_tool:
           # use variables defined by 'setup' job above, see also
           # https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#needs-context
-          - ${{needs.setup.outputs.lmod7}}
           - ${{needs.setup.outputs.lmod8}}
-          - ${{needs.setup.outputs.modulesTcl}}
-          - ${{needs.setup.outputs.modules3}}
           - ${{needs.setup.outputs.modules4}}
         lc_all: [""]
         include:
-          # Test different Python 3 versions with Lmod 8.x
-          - python: 3.5
-            modules_tool: ${{needs.setup.outputs.lmod8}}
+          # Test different Python 3 versions with Lmod 8.x (with both Lua and Tcl module syntax)
           - python: 3.7
             modules_tool: ${{needs.setup.outputs.lmod8}}
           - python: 3.8
@@ -160,11 +152,7 @@ jobs:
           export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH
           eb --version
           # tell EasyBuild which modules tool is available
-          if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then
-            export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl
-          elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then
-            export EASYBUILD_MODULES_TOOL=EnvironmentModulesC
-          elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then
+          if [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then
             export EASYBUILD_MODULES_TOOL=EnvironmentModules
           else
             export EASYBUILD_MODULES_TOOL=Lmod

.github/workflows/unit_tests_python2.yml

@@ -87,7 +87,6 @@
 import weakref
 
 from easybuild.tools import LooseVersion
-from easybuild.tools.py2vs3 import raise_with_traceback, string_type
 
 
 def _env_to_boolean(varname, default=False):
@@ -214,11 +213,11 @@ class MissingLevelName(KeyError):
 
 def getLevelInt(level_name):
     """Given a level name, return the int value"""
-    if not isinstance(level_name, string_type):
+    if not isinstance(level_name, str):
         raise TypeError('Provided name %s is not a string (type %s)' % (level_name, type(level_name)))
 
     level = logging.getLevelName(level_name)
-    if isinstance(level, string_type):
+    if isinstance(level, str):
         raise MissingLevelName('Unknown loglevel name %s' % level_name)
 
     return level
@@ -328,7 +327,7 @@ def raiseException(self, message, exception=None, catch=False):
             exception = self.RAISE_EXCEPTION_CLASS
 
         self.RAISE_EXCEPTION_LOG_METHOD(fullmessage)
-        raise_with_traceback(exception, message, tb)
+        raise exception(message).with_traceback(tb)
 
     # pylint: disable=unused-argument
     def deprecated(self, msg, cur_ver, max_ver, depth=2, exception=None, log_callback=None, *args, **kwargs):
@@ -588,7 +587,7 @@ def logToFile(filename, enable=True, filehandler=None, name=None, max_bytes=MAX_
             os.makedirs(directory)
         except Exception as ex:
             exc, detail, tb = sys.exc_info()
-            raise_with_traceback(exc, "Cannot create logdirectory %s: %s \n detail: %s" % (directory, ex, detail), tb)
+            raise exc("Cannot create logdirectory %s: %s \n detail: %s" % (directory, ex, detail)).with_traceback(tb)
 
     return _logToSomething(
         logging.handlers.RotatingFileHandler,
@@ -741,7 +740,7 @@ def setLogLevel(level):
     """
     Set a global log level for all FancyLoggers
     """
-    if isinstance(level, string_type):
+    if isinstance(level, str):
         level = getLevelInt(level)
     logger = getLogger(fname=False, clsname=False)
     logger.setLevel(level)

easybuild/base/fancylogger.py

@@ -21,10 +21,10 @@
 It can be used as a drop-in replacement for dictionaries where immutability is desired.
 """
 import operator
+from collections.abc import Mapping
 from functools import reduce
 
 from easybuild.base import fancylogger
-from easybuild.tools.py2vs3 import Mapping
 
 
 # minor adjustments:

easybuild/base/frozendict.py

@@ -31,6 +31,7 @@
 * Jens Timmerman (Ghent University)
 """
 
+import configparser
 import copy
 import difflib
 import inspect
@@ -39,13 +40,15 @@
 import re
 import sys
 import textwrap
+from configparser import ConfigParser
 from functools import reduce
+from io import StringIO
 from optparse import Option, OptionGroup, OptionParser, OptionValueError, Values
 from optparse import SUPPRESS_HELP as nohelp  # supported in optparse of python v2.4
 
 from easybuild.base.fancylogger import getLogger, setroot, setLogLevel, getDetailsLogLevels
 from easybuild.base.optcomplete import autocomplete, CompleterOption
-from easybuild.tools.py2vs3 import StringIO, configparser, ConfigParser, string_type, subprocess_popen_text
+from easybuild.tools.run import subprocess_popen_text
 from easybuild.tools.utilities import mk_md_table, mk_rst_table, nub, shell_quote
 
 try:
@@ -133,7 +136,7 @@ def get_empty_add_flex(allvalues, self=None):
     empty = None
 
     if isinstance(allvalues, (list, tuple)):
-        if isinstance(allvalues[0], string_type):
+        if isinstance(allvalues[0], str):
             empty = ''
 
     if empty is None:
@@ -464,7 +467,7 @@ def is_value_a_commandline_option(self, opt, value, index=None):
         # --longopt=value, so no issues there either.
 
         # following checks assume that value is a string (not a store_or_None)
-        if not isinstance(value, string_type):
+        if not isinstance(value, str):
             return None
 
         cmdline_index = None
@@ -1191,7 +1194,7 @@ def add_group_parser(self, opt_dict, description, prefix=None, otherdefaults=Non
                         # choices
                         nameds['choices'] = [str(x) for x in extra_detail]  # force to strings
                         hlp += ' (choices: %s)' % ', '.join(nameds['choices'])
-                    elif isinstance(extra_detail, string_type) and len(extra_detail) == 1:
+                    elif isinstance(extra_detail, str) and len(extra_detail) == 1:
                         args.insert(0, "-%s" % extra_detail)
                     elif isinstance(extra_detail, (dict,)):
                         # extract any optcomplete completer hints
@@ -1708,7 +1711,7 @@ class SimpleOption(GeneralOption):
     PARSER = SimpleOptionParser
     SETROOTLOGGER = True
 
-    def __init__(self, go_dict=None, descr=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
+    def __init__(self, go_dict=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
         """Initialisation
         :param go_dict: General Option option dict
         :param short_groupdescr: short description of main options
@@ -1737,18 +1740,13 @@ def __init__(self, go_dict=None, descr=None, short_groupdescr=None, long_groupde
 
         super(SimpleOption, self).__init__(**kwargs)
 
-        if descr is not None:
-            # TODO: as there is no easy/clean way to access the version of the vsc-base package,
-            # this is equivalent to a warning
-            self.log.deprecated('SimpleOption descr argument', '2.5.0', '3.0.0')
-
     def main_options(self):
         if self.go_dict is not None:
             prefix = None
             self.add_group_parser(self.go_dict, self.descr, prefix=prefix)
 
 
-def simple_option(go_dict=None, descr=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
+def simple_option(go_dict=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
     """A function that returns a single level GeneralOption option parser
 
     :param go_dict: General Option option dict
@@ -1762,5 +1760,5 @@ def simple_option(go_dict=None, descr=None, short_groupdescr=None, long_groupdes
 
     the generated help will include the docstring
     """
-    return SimpleOption(go_dict=go_dict, descr=descr, short_groupdescr=short_groupdescr,
-                        long_groupdescr=long_groupdescr, config_files=config_files)
+    return SimpleOption(go_dict=go_dict, short_groupdescr=short_groupdescr, long_groupdescr=long_groupdescr,
+                        config_files=config_files)