create_JupyterLab_kernel.sh

@@ -20,7 +20,12 @@ spack repo add /srv/$INSTALLATION_ROOT/ebrains-spack-builds
 #spack env activate $SPACKIFIED_ENV
 
 module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-broadwell/
+module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-x86_64/
 source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads
+# add also user's .local python3.8 packages to allow package installation at runtime
+# by the user using pip
+export PYTHONPATH=$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages
+export PATH=$PATH:/opt/app-root/src/.local/bin
 
 # capture the env after spack activation
 cd /opt/app-root/src
@@ -49,8 +54,8 @@ chmod +x $LAB_KERNEL_PATH/bin/env.sh
 mkdir $LAB_KERNEL_PATH/spack_python_kernel_release_20210930
 cat <<EOF >$LAB_KERNEL_PATH/spack_python_kernel_release_20210930/kernel.json
 {
- "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}"],
- "display_name": "EBRAINS_release_20210930",
+ "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
+ "display_name": "EBRAINS_release_v0.1_202109",
  "name": "spack_python_kernel_release_20210930",
  "language": "python"
 }

create_job.sh

@@ -25,9 +25,9 @@ spec:
       #    level: s0:c25,c10
       containers:
       - name: simplejob
-        image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env:latest
+        image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env:release_v0.1_202109
         securityContext:
-          runAsUser: 1000410000
+          runAsUser: 1000430000
         volumeMounts:
           - name: sharedbin
             mountPath: /srv

packages/clb-nb-utils/package.py

+from spack import *
+
+# Usage
+# from clb_nb_utils import oauth
+# oauth.get_token()
+class ClbNbUtils(PythonPackage):
+    url      = 'https://github.com/HumanBrainProject/clb-nb-utils/archive/refs/heads/master.zip'
+    maintainers = ['akarmas']
+    version('0.1.0','aa079ed0a8c4806db4657a6e7b534f4d')
+    depends_on('python@3.8:', type=('build','run'))
+    depends_on('py-setuptools', type=('build','run'))
+    depends_on('py-requests', type=('build','run'))

packages/log4cxx/log4cxx-0.10.0-llvm-libcxx.patch

+--- apache-log4cxx-0.10.0/src/main/cpp/stringhelper.cpp2018-04-19 09:48:50.762552	436 +0200
++++ apache-log4cxx-0.10.0-old/src/main/cpp/stringhelper.cpp2	008-04-01 00:34:09.000000000 +0200
+@@ -28,7 +28,6 @@
+ #endif
+ #include <log4cxx/private/log4cxx_private.h>
+ #include <cctype>
+-#include <cstdlib>
+ #include <apr.h>
+ 
+ 
+diff -rpu apache-log4cxx-0.10.0/src/main/include/log4cxx/helpers/simpledateformat.h apache-log4cxx-0.10.0-old/src/main/include/log4cxx/helpers/simpledateformat.h
+--- apache-log4cxx-0.10.0/src/main/include/log4cxx/helpers/simpledateformat.h2018-04-19 09:4	8:19.010260662 +0200
++++ apache-log4cxx-0.10.0-old/src/main/include/log4cxx/helpers/simpledateformat.h2008-04-01 00:34:26.000000000 +0200
+@@ -26,1	0 +26,11 @@
+ 
+ 
+ #include <log4cxx/helpers/dateformat.h>
+-#include <locale>
+ #include <vector>
+ #include <time.h>
+ 
++namespace std { class locale; }
++
+ namespace log4cxx
+ {
+         namespace helpers

packages/log4cxx/log4cxx-0.10.0-missing_includes.patch

+diff -Naur apache-log4cxx-0.10.0.orig/src/examples/cpp/console.cpp apache-log4cxx-0.10.0/src/examples/cpp/console.cpp
+--- apache-log4cxx-0.10.0.orig/src/examples/cpp/console.cpp	2008-04-01 00:34:52.000000000 +0200
++++ apache-log4cxx-0.10.0/src/examples/cpp/console.cpp	2008-05-06 05:40:52.000000000 +0200
+@@ -15,7 +15,10 @@
+  * limitations under the License.
+  */
+ 
+-#include <stdlib.h>
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <stdint.h>
+ #include <log4cxx/logger.h>
+ #include <log4cxx/consoleappender.h>
+ #include <log4cxx/simplelayout.h>
+diff -Naur apache-log4cxx-0.10.0.orig/src/main/cpp/inputstreamreader.cpp apache-log4cxx-0.10.0/src/main/cpp/inputstreamreader.cpp
+--- apache-log4cxx-0.10.0.orig/src/main/cpp/inputstreamreader.cpp	2008-04-01 00:34:09.000000000 +0200
++++ apache-log4cxx-0.10.0/src/main/cpp/inputstreamreader.cpp	2008-05-06 05:32:31.000000000 +0200
+@@ -21,6 +21,8 @@
+ #include <log4cxx/helpers/pool.h>
+ #include <log4cxx/helpers/bytebuffer.h>
+ 
++#include <cstring>
++
+ using namespace log4cxx;
+ using namespace log4cxx::helpers;
+ 
+diff -Naur apache-log4cxx-0.10.0.orig/src/main/cpp/socketoutputstream.cpp apache-log4cxx-0.10.0/src/main/cpp/socketoutputstream.cpp
+--- apache-log4cxx-0.10.0.orig/src/main/cpp/socketoutputstream.cpp	2008-04-01 00:34:09.000000000 +0200
++++ apache-log4cxx-0.10.0/src/main/cpp/socketoutputstream.cpp	2008-05-06 05:35:55.000000000 +0200
+@@ -20,6 +20,8 @@
+ #include <log4cxx/helpers/socket.h>
+ #include <log4cxx/helpers/bytebuffer.h>
+ 
++#include <cstring>
++
+ using namespace log4cxx;
+ using namespace log4cxx::helpers;
\ No newline at end of file

packages/log4cxx/log4cxx-0.10.0-narrowing-fixes-from-upstream.patch

+diff --git a/src/main/cpp/locationinfo.cpp b/src/main/cpp/locationinfo.cpp
+index e76ea29..bd22a1d 100644
+--- a/src/main/cpp/locationinfo.cpp
++++ b/src/main/cpp/locationinfo.cpp
+@@ -149,18 +149,21 @@ void LocationInfo::write(ObjectOutputStream& os, Pool& p) const {
+          os.writeNull(p);
+     } else {
+         char prolog[] = {
+-         0x72, 0x00, 0x21, 0x6F, 0x72, 0x67, 0x2E, 
+-         0x61, 0x70, 0x61, 0x63, 0x68, 0x65, 0x2E, 0x6C, 
+-         0x6F, 0x67, 0x34, 0x6A, 0x2E, 0x73, 0x70, 0x69, 
+-         0x2E, 0x4C, 0x6F, 0x63, 0x61, 0x74, 0x69, 0x6F, 
+-         0x6E, 0x49, 0x6E, 0x66, 0x6F, 0xED, 0x99, 0xBB, 
+-         0xE1, 0x4A, 0x91, 0xA5, 0x7C, 0x02, 0x00, 0x01, 
+-         0x4C, 0x00, 0x08, 0x66, 0x75, 0x6C, 0x6C, 0x49, 
+-         0x6E, 0x66, 0x6F, 
+-            0x74, 0x00, 0x12, 0x4C, 0x6A, 
+-                0x61, 0x76, 0x61, 0x2F, 0x6C, 0x61, 0x6E, 0x67, 
+-                0x2F, 0x53, 0x74, 0x72, 0x69, 0x6E, 0x67, 0x3B,
+-         0x78, 0x70 };
++         0x72,
++         0x00,
++         0x21, 0x6F, 0x72, 0x67, 0x2E, 0x61, 0x70, 0x61, 0x63, 0x68, 0x65, 0x2E,
++         0x6C, 0x6F, 0x67, 0x34, 0x6A, 0x2E, 0x73, 0x70, 0x69, 0x2E, 0x4C, 0x6F,
++         0x63, 0x61, 0x74, 0x69, 0x6F, 0x6E, 0x49, 0x6E, 0x66, 0x6F, static_cast<char>(0xED),
++         static_cast<char>(0x99), static_cast<char>(0xBB), static_cast<char>(0xE1),
++         0x4A, static_cast<char>(0x91), static_cast<char>(0xA5), 0x7C, 0x02,
++         0x00,
++         0x01, 0x4C,
++         0x00,
++         0x08, 0x66, 0x75, 0x6C, 0x6C, 0x49, 0x6E, 0x66, 0x6F, 0x74,
++         0x00,
++         0x12, 0x4C, 0x6A, 0x61, 0x76, 0x61, 0x2F, 0x6C, 0x61, 0x6E, 0x67, 0x2F,
++         0x53, 0x74, 0x72, 0x69, 0x6E, 0x67, 0x3B, 0x78, 0x70
++        };
+       os.writeProlog("org.apache.log4j.spi.LocationInfo", 2, prolog, sizeof(prolog), p);
+         char* line = p.itoa(lineNumber);
+         //
+diff --git a/src/main/cpp/loggingevent.cpp b/src/main/cpp/loggingevent.cpp
+index 1c0d4be..edbf40b 100644
+--- a/src/main/cpp/loggingevent.cpp
++++ b/src/main/cpp/loggingevent.cpp
+@@ -242,7 +242,7 @@ void LoggingEvent::writeProlog(ObjectOutputStream& os, Pool& p)  {
+         0x68, 0x65, 0x2E, 0x6C, 0x6F, 0x67, 0x34, 0x6A, 
+         0x2E, 0x73, 0x70, 0x69, 0x2E, 0x4C, 0x6F, 0x67, 
+         0x67, 0x69, 0x6E, 0x67, 0x45, 0x76, 0x65, 0x6E, 
+-        0x74, 0xF3, 0xF2, 0xB9, 0x23, 0x74, 0x0B, 0xB5, 
++        0x74, static_cast<char>(0xF3), static_cast<char>(0xF2), static_cast<char>(0xB9), 0x23, 0x74, 0x0B, static_cast<char>(0xB5), 
+         0x3F, 0x03, 0x00, 0x0A, 0x5A, 0x00, 0x15, 0x6D, 
+         0x64, 0x63, 0x43, 0x6F, 0x70, 0x79, 0x4C, 0x6F, 
+         0x6F, 0x6B, 0x75, 0x70, 0x52, 0x65, 0x71, 0x75, 
+diff --git a/src/main/cpp/objectoutputstream.cpp b/src/main/cpp/objectoutputstream.cpp
+index 7cd696b..5442420 100644
+--- a/src/main/cpp/objectoutputstream.cpp
++++ b/src/main/cpp/objectoutputstream.cpp
+@@ -36,7 +36,7 @@ ObjectOutputStream::ObjectOutputStream(OutputStreamPtr outputStream, Pool& p)
+        objectHandle(0x7E0000),
+        classDescriptions(new ClassDescriptionMap())
+ {
+-   char start[] = { 0xAC, 0xED, 0x00, 0x05 };
++   char start[] = { static_cast<char>(0xAC), static_cast<char>(0xED), 0x00, 0x05 };
+    ByteBuffer buf(start, sizeof(start));
+    os->write(buf, p);
+ }
+@@ -81,15 +81,15 @@ void ObjectOutputStream::writeObject(const MDC::Map& val, Pool& p) {
+     //
+     //  TC_OBJECT and the classDesc for java.util.Hashtable
+     //
+-    char prolog[] = {
+-        0x72, 0x00, 0x13, 0x6A, 0x61, 0x76, 0x61, 
+-        0x2E, 0x75, 0x74, 0x69, 0x6C, 0x2E, 0x48, 0x61, 
+-        0x73, 0x68, 0x74, 0x61, 0x62, 0x6C, 0x65, 0x13, 
+-        0xBB, 0x0F, 0x25, 0x21, 0x4A, 0xE4, 0xB8, 0x03, 
+-        0x00, 0x02, 0x46, 0x00, 0x0A, 0x6C, 0x6F, 0x61, 
+-        0x64, 0x46, 0x61, 0x63, 0x74, 0x6F, 0x72, 0x49, 
+-        0x00, 0x09, 0x74, 0x68, 0x72, 0x65, 0x73, 0x68, 
+-        0x6F, 0x6C, 0x64, 0x78, 0x70  };
++	char prolog[] = {
++		0x72, 0x00, 0x13, 0x6A, 0x61, 0x76, 0x61,
++		0x2E, 0x75, 0x74, 0x69, 0x6C, 0x2E, 0x48, 0x61,
++		0x73, 0x68, 0x74, 0x61, 0x62, 0x6C, 0x65, 0x13,
++		static_cast<char>(0xBB), 0x0F, 0x25, 0x21, 0x4A, static_cast<char>(0xE4), static_cast<char>(0xB8), 0x03,
++		0x00, 0x02, 0x46, 0x00, 0x0A, 0x6C, 0x6F, 0x61,
++		0x64, 0x46, 0x61, 0x63, 0x74, 0x6F, 0x72, 0x49,
++		0x00, 0x09, 0x74, 0x68, 0x72, 0x65, 0x73, 0x68,
++		0x6F, 0x6C, 0x64, 0x78, 0x70  };
+     writeProlog("java.util.Hashtable", 1, prolog, sizeof(prolog), p);
+     //
+     //   loadFactor = 0.75, threshold = 5, blockdata start, buckets.size = 7
+diff --git a/src/test/cpp/xml/domtestcase.cpp b/src/test/cpp/xml/domtestcase.cpp
+index a500628..29d67dd 100644
+--- a/src/test/cpp/xml/domtestcase.cpp
++++ b/src/test/cpp/xml/domtestcase.cpp
+@@ -190,9 +190,9 @@ public:
+                 DOMConfigurator::configure(LOG4CXX_TEST_STR("input/xml/DOMTestCase3.xml"));
+                 LOG4CXX_INFO(logger, "File name is expected to end with a superscript 3");
+ #if LOG4CXX_LOGCHAR_IS_UTF8
+-                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, 0xC2, 0xB3, 0 };
++                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, static_cast<logchar>(0xC2), static_cast<logchar>(0xB3), 0 };
+ #else
+-                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, 0xB3, 0 };
++                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, static_cast<logchar>(0xB3), 0 };
+ #endif
+                 File file;
+                 file.setPath(fname);
+@@ -209,9 +209,9 @@ public:
+                 DOMConfigurator::configure(LOG4CXX_TEST_STR("input/xml/DOMTestCase4.xml"));
+                 LOG4CXX_INFO(logger, "File name is expected to end with an ideographic 4");
+ #if LOG4CXX_LOGCHAR_IS_UTF8
+-                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, 0xE3, 0x86, 0x95, 0 };
++                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, static_cast<logchar>(0xE3), static_cast<logchar>(0x86), static_cast<logchar>(0x95), 0 };
+ #else
+-                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, 0x3195, 0 };
++                const logchar fname[] = { 0x6F, 0x75, 0x74, 0x70, 0x75, 0x74, 0x2F, 0x64, 0x6F, 0x6D, static_cast<logchar>(0x3195), 0 };
+ #endif
+                 File file;
+                 file.setPath(fname);
\ No newline at end of file

packages/log4cxx/package.py

+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Log4cxx(AutotoolsPackage):
+    """A C++ port of Log4j"""
+
+    homepage = "https://logging.apache.org/log4cxx/latest_stable/"
+    url      = "http://mirror.netcologne.de/apache.org/logging/log4cxx/0.10.0/apache-log4cxx-0.10.0.tar.gz"
+
+    version('0.10.0', sha256='0de0396220a9566a580166e66b39674cb40efd2176f52ad2c65486c99c920c8c')
+
+    depends_on('apr-util')
+    depends_on('apr')
+    depends_on('zip')
+
+    build_directory = 'spack-build'
+
+    # patches from https://aur.archlinux.org/packages/log4cxx/
+    patch('log4cxx-0.10.0-missing_includes.patch')
+    patch('log4cxx-0.10.0-narrowing-fixes-from-upstream.patch')
+    patch('log4cxx-0.10.0-llvm-libcxx.patch', when='@0.10.0%clang')
+
+    def configure_args(self):
+        args = ['--disable-static']
+
+        return args

packages/nest/package.py

@@ -176,3 +176,8 @@ class Nest(CMakePackage):
     @on_package_attributes(run_tests=True)
     def installcheck(self):
         make("installcheck")
+
+    # quick-fix to add lib64/python3.8/site-packages to the PYTHONPATH;
+    # this should happen automatically for packages extending Python...
+    def setup_run_environment(self, env):
+        env.prepend_path('PYTHONPATH', self.prefix.lib64.join('python3.8/site-packages'))

spack.yaml

@@ -7,6 +7,8 @@ spack:
     - py-ipython %gcc@10.3.0
     - py-ipykernel %gcc@10.3.0
     - py-notebook %gcc@10.3.0
+    # Collab utils
+    - clb-nb-utils@0.1.0 %gcc@10.3.0
     # General
     - py-pip %gcc@10.3.0
     - py-numpy %gcc@10.3.0
@@ -26,4 +28,4 @@ spack:
     - py-formencode %gcc@10.3.0
     - tvb-framework ^binutils+ld+gold %gcc@10.3.0
     - meta-brainscales %gcc@10.3.0
-    - pynn-brainscales@1.0-rc2 ^googletest@1.11.0:+gmock %gcc@10.3.0
+    - pynn-brainscales@1.0-rc2 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock %gcc@10.3.0