add patch to Python easyconfigs to fix ctypes when $LD_LIBRARY_PATH is not being set

easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb

@@ -11,7 +11,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.10.4.tgz': 'f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.10.4.tgz': 'f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb

@@ -11,7 +11,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.10.8.tgz': 'f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.10.8.tgz': 'f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.11.2-GCCcore-12.2.0-bare.eb

@@ -11,7 +11,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['2411c74bda5bbcfcddaf4531f66d1adc73f247f529aee981b029513aefdbf849']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.11.2.tgz': '2411c74bda5bbcfcddaf4531f66d1adc73f247f529aee981b029513aefdbf849'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.11.3.tgz': '1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['a12a0a013a30b846c786c010f2c19dd36b7298d888f7c4bd1581d90ce18b5e58']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.11.5.tgz': 'a12a0a013a30b846c786c010f2c19dd36b7298d888f7c4bd1581d90ce18b5e58'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.11.5-custom-ctypes.patch

@@ -0,0 +1,162 @@
+Ctypes heavily relies on LD_LIBRARY_PATH in it's find_library, ctypes.CDLL, ctypes.cdll.LoadLibrary functions.
+This patch is meant for systems where LD_LIBRARY_PATH is filtered. It will rely on LIBRARY_PATH instead.
+It makes the following essential changes:
+- Whereever find_library searched LD_LIBRARY_PATH, LIBRARY_PATH will be searched instead
+- find_library is adapted so that it returns the full library path, not just the library name, which replaces
+  https://github.com/easybuilders/easybuild-easyblocks/pull/3352
+- The internal function _findLib_gcc, one of the functions called by find_library to locate libraries, is adapted
+  so that it also works when called by full library name (e.g. libfoo.so.1) instead of the short name (foo) only
+  This is necessary since CDLL is typically called by full name, and needs to be able to call find_library 9see below)
+- The initialization of CDLL is adapted so that it calls find_library. Then, it overwrites the name
+  with the full library path. This defers all the library localization issues to the (patched) find_library
+Authors: Danilo Gonzalez (DoItNow group), Caspar van Leeuwen (SURF) and Alan O'cais (CECAM)
+diff -Nru Python-3.11.5.orig/Lib/ctypes/__init__.py Python-3.11.5/Lib/ctypes/__init__.py
+--- Python-3.11.5.orig/Lib/ctypes/__init__.py	2025-10-13 15:58:38.405564000 +0200
++++ Python-3.11.5/Lib/ctypes/__init__.py	2025-10-13 16:01:08.717507706 +0200
+@@ -14,6 +14,9 @@
+
+ from struct import calcsize as _calcsize
+
++# Add util to use find_library capabilities
++from ctypes import util
++
+ if __version__ != _ctypes_version:
+     raise Exception("Version number mismatch", __version__, _ctypes_version)
+
+@@ -349,6 +352,12 @@
+             flags |= _FUNCFLAG_USE_ERRNO
+         if use_last_error:
+             flags |= _FUNCFLAG_USE_LASTERROR
++        # define CDLL instance name as fullpath
++        if _os.name == "posix":
++            if name:
++                fullpath = util.find_library(name)
++                if fullpath is not None:
++                    self._name = fullpath
+         if _sys.platform.startswith("aix"):
+             """When the name contains ".a(" and ends with ")",
+                e.g., "libFOO.a(libFOO.so)" - this is taken to be an
+diff -Nru Python-3.11.5.orig/Lib/ctypes/util.py Python-3.11.5/Lib/ctypes/util.py
+--- Python-3.11.5.orig/Lib/ctypes/util.py	2025-10-13 15:58:38.306949000 +0200
++++ Python-3.11.5/Lib/ctypes/util.py	2025-10-13 17:17:07.589997890 +0200
+@@ -99,12 +99,19 @@
+         with open(filename, 'br') as thefile:
+             return thefile.read(4) == elf_header
+
+-    def _findLib_gcc(name):
++    def _findLib_gcc(name, name_is_fullname=False):
+         # Run GCC's linker with the -t (aka --trace) option and examine the
+         # library name it prints out. The GCC command will fail because we
+         # haven't supplied a proper program with main(), but that does not
+         # matter.
+-        expr = os.fsencode(r'[^\(\)\s]*lib%s\.[^\(\)\s]*' % re.escape(name))
++        # If the name is a full library name (e.g. libfoo.so), this function calls gcc with -l:<name> instead of
++        # -l<name> and uses a slightly more strict regular expression to avoid matching the error
++        # '/path/to/ld: cannot find -l:libfoo.so: No such file or directory'
++        # since we only want a regex match if the library exists
++        if name_is_fullname:
++            expr = os.fsencode(r'^[^\(\)\s]*%s[^\(\)\s]*' % re.escape(name))
++        else:
++            expr = os.fsencode(r'[^\(\)\s]*lib%s\.[^\(\)\s]*' % re.escape(name))
+
+         c_compiler = shutil.which('gcc')
+         if not c_compiler:
+@@ -115,7 +122,10 @@
+
+         temp = tempfile.NamedTemporaryFile()
+         try:
+-            args = [c_compiler, '-Wl,-t', '-o', temp.name, '-l' + name]
++            if name_is_fullname:
++                args = [c_compiler, '-Wl,-t', '-o', temp.name, '-l:' + name]
++            else:
++                args = [c_compiler, '-Wl,-t', '-o', temp.name, '-l' + name]
+
+             env = dict(os.environ)
+             env['LC_ALL'] = 'C'
+@@ -136,7 +146,12 @@
+                 # Raised if the file was already removed, which is the normal
+                 # behaviour of GCC if linking fails
+                 pass
+-        res = re.findall(expr, trace)
++        # If name_is_fullname, the regex in expr starts wity ^.
++        # Use re.MULTILINE, to make surethat ^ matches the start of EACH line in trace
++        if name_is_fullname:
++            res = re.findall(expr, trace, re.MULTILINE)
++        else:
++            res = re.findall(expr, trace)
+         if not res:
+             return None
+
+@@ -146,8 +161,11 @@
+             # shared objects. See bpo-41976 for more details
+             if not _is_elf(file):
+                 continue
+-            return os.fsdecode(file)
+-
++            file = os.fsdecode(file)
++            # Avoid returning CUDA stubs libraries, as those are not intended for runtime use
++            if re.search(r'cuda.*stubs', file, re.IGNORECASE):
++                continue
++            return file
+
+     if sys.platform == "sunos5":
+         # use /usr/ccs/bin/dump on solaris
+@@ -283,7 +301,8 @@
+             abi_type = mach_map.get(machine, 'libc6')
+
+             # XXX assuming GLIBC's ldconfig (with option -p)
+-            regex = r'\s+(lib%s\.[^\s]+)\s+\(%s'
++            # Regular expresion that captures complete line of ldconfig -p output that matches with library name.
++            regex = r'\s+(lib%s\.[^\s]+)\s+\(%s\)\s+=>\s+(\S+)'
+             regex = os.fsencode(regex % (re.escape(name), abi_type))
+             try:
+                 with subprocess.Popen(['/sbin/ldconfig', '-p'],
+@@ -293,7 +312,8 @@
+                                       env={'LC_ALL': 'C', 'LANG': 'C'}) as p:
+                     res = re.search(regex, p.stdout.read())
+                     if res:
+-                        return os.fsdecode(res.group(1))
++                        # return the regex second group, that is the full path to the library
++                        return os.fsdecode(res.group(2))
+             except OSError:
+                 pass
+
+@@ -301,10 +321,17 @@
+             # See issue #9998 for why this is needed
+             expr = r'[^\(\)\s]*lib%s\.[^\(\)\s]*' % re.escape(name)
+             cmd = ['ld', '-t']
+-            libpath = os.environ.get('LD_LIBRARY_PATH')
++            # use LIBRARY_PATH instead of LD_LIBRARY_PATH to use EB provided shared libraries
++            libpath = os.environ.get('LIBRARY_PATH')
+             if libpath:
+                 for d in libpath.split(':'):
+-                    cmd.extend(['-L', d])
++                    # Avoid picking up CUDA stubs libraries, as those are not intended for runtime use
++                    parts = d.split('/')
++                    # We want to add 'd' in all cases EXCEPT if the path contains both CUDA (as partial
++                    # directory name) and stubs (as full directory name). I.e. /my/bar/stubs and /my/cudafoo
++                    # will be added to cmd, but /my/cudafoo/bar/stubs won't be
++                    if not (any('cuda' in p.lower() for p in parts) and 'stubs' in parts):
++                        cmd.extend(['-L', d])
+             cmd.extend(['-o', os.devnull, '-l%s' % name])
+             result = None
+             try:
+@@ -325,9 +352,15 @@
+             return result
+
+         def find_library(name):
+-            # See issue #9998
+-            return _findSoname_ldconfig(name) or \
+-                   _get_soname(_findLib_gcc(name)) or _get_soname(_findLib_ld(name))
++            # Redefine find_library function, it will return the provided name if
++            # path exist, else it will use the set of functions to find the full library path.
++            # it will return the one that has a match.
++            if os.path.isabs(name) and os.path.exists(name):
++                return name
++            else:
++                return _findSoname_ldconfig(name) or \
++                   _findLib_gcc(name) or _findLib_ld(name) or \
++                   _findLib_gcc(name, name_is_fullname=True)
+
+ ################################################################
+ # test code

easybuild/easyconfigs/p/Python/Python-3.12.3-GCCcore-13.3.0.eb

@@ -11,9 +11,15 @@ toolchainopts = {'pic': True}
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
 patches = ['Python-3.12.3_avoid-tkinter-build.patch']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
 checksums = [
     {'Python-3.12.3.tgz': 'a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0'},
     {'Python-3.12.3_avoid-tkinter-build.patch': '34fa44ca67fc08d41c58db2e289317f12f32777a352a982dca2e63459fc089e3'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
 ]
 
 builddependencies = [

easybuild/easyconfigs/p/Python/Python-3.13.1-GCCcore-14.2.0.eb

@@ -10,14 +10,21 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
+
 patches = [
     'Python-3.12.3_avoid-tkinter-build.patch',
     'Python-3.13.1_runshared-ld-preload.patch',
 ]
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
 checksums = [
     {'Python-3.13.1.tgz': '1513925a9f255ef0793dbf2f78bb4533c9f184bdd0ad19763fd7f47a400a7c55'},
     {'Python-3.12.3_avoid-tkinter-build.patch': '34fa44ca67fc08d41c58db2e289317f12f32777a352a982dca2e63459fc089e3'},
     {'Python-3.13.1_runshared-ld-preload.patch': 'ca9ec56c71aafa881e7ddf6fba23fbecc016be48c2d912e5ccd92962ddd38edf'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'},
 ]
 
 builddependencies = [

easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb

@@ -11,7 +11,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.9.5.tgz': 'e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.9.5.tgz': 'e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb

@@ -11,7 +11,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.9.6.tgz': 'd0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),

easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb

@@ -10,7 +10,15 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
 sources = [SOURCE_TGZ]
-checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866']
+
+# Like patches, but these will only be applied if EasyBuild is configured to filter $LD_LIBRARY_PATH
+# In that scenario, ctypes needs to be patched since it heavily relies on $LD_LIBRARY_PATH to find libraries
+patch_ctypes_ld_library_path = 'Python-3.11.5-custom-ctypes.patch'
+
+checksums = [
+    {'Python-3.9.6.tgz': 'd0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'},
+    {'Python-3.11.5-custom-ctypes.patch': 'b29c22f47587460149e05296ff09b29bf790a83e2b3b13fb2f42f5f236ad8ea7'}
+]
 
 builddependencies = [
     ('UnZip', '6.0'),