Merge remote-tracking branch 'upstream/ebrains-23-02' into ebrains-23-02-with-site-config

.gitlab-ci.yml

@@ -227,7 +227,7 @@ sync-gitlab-spack-instance:
     - read-write
   image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/gitlab_runners_nfs:gitlab_runners_nfs_22.09 
   variables:
-    SPACK_NFS_ENV: ebrains-runner-build
+    SPACK_NFS_ENV: ebrains-runner-build-23-02
     SPACK_PATH: /mnt/spack_v0.18.1_t
     SPACK_USER_CACHE_PATH: $SPACK_PATH/.spack
     SPACK_USER_CONFIG_PATH: $SPACK_PATH/.spack
@@ -289,5 +289,5 @@ sync-gitlab-spack-instance:
       - spack_logs
     when: always
   rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /technical-coordination/
+    - if: $CI_COMMIT_BRANCH == "ebrains-23-02" && $CI_PROJECT_NAMESPACE =~ /technical-coordination/
       when: manual

packages/apbs/package.py

@@ -30,7 +30,7 @@ class Apbs(CMakePackage):
     version('3.4.0', sha256='572ff606974119430020ec948c78e171d8525fb0e67a56dad937a897cac67461')
 
     # Dependencies.
-    depends_on('cmake@3.19',        type=('build'))
+    depends_on('cmake@3.19:',       type=('build'))
     depends_on('bison',             type=('build')) 
     depends_on('flex',              type=('build'))
     depends_on('swig',              type=('build'))
@@ -48,14 +48,18 @@ class Apbs(CMakePackage):
         # See tests/CMakeLists.txt lines 6-14.
         python_version = str(self.spec['python'].version)
         args = [
-                '-DPYTHON_MIN_VERSION='+python_version,
-                '-DPYTHON_MAX_VERSION='+python_version
-                ]
+            self.define('PYTHON_MIN_VERSION', python_version),
+            self.define('PYTHON_MAX_VERSION', python_version),
+            self.define('BLAS_FOUND', True),
+            self.define('BLAS_INCLUDE_DIRS', self.spec['blas'].prefix.include),
+            self.define('BLAS_LIBRARIES', self.spec['blas'].libs.joined(';'))
+            ]
         return args
 
     def setup_build_environment(self, env):
         # add suite-sparse libs to path because tests can't find them
-        env.prepend_path("LD_LIBRARY_PATH", self.spec['suite-sparse'].prefix.lib)
+        env.prepend_path('LD_LIBRARY_PATH', self.spec['suite-sparse'].prefix.lib)
+        env.prepend_path('LD_LIBRARY_PATH', self.spec['blas'].prefix.lib)
 
     def setup_dependent_build_environment(self, env, dependent_spec):
         self.setup_build_environment(env)

packages/hxtorch/package.py

@@ -14,10 +14,10 @@ class Hxtorch(WafPackage):
     # This repo provides a waf binary used for the build below
     git      = "https://github.com/electronicvisions/pynn-brainscales.git"
 
-    version('4.0-rc1-fixup1', branch='waf')
+    version('4.0-rc1-fixup2', branch='waf')
 
     # PPU compiler dependencies
-    depends_on('oppulance@4.0-rc1-fixup1')
+    depends_on('oppulance@4.0-rc1-fixup2')
 
     # host software dependencies
     depends_on('bitsery', type=('build', 'link', 'run'))
@@ -133,29 +133,12 @@ class Hxtorch(WafPackage):
     def configure(self, spec, prefix):
         """Setup and configure the project."""
 
-        self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-munge',
-            '--project=hxtorch@ebrains-' + str(spec.version),
-            '--project=haldls@ebrains-' + str(spec.version),
-            '--project=grenade@ebrains-' + str(spec.version),
-            '--project=code-format@ebrains-' + str(spec.version),
-            '--project=logger@ebrains-' + str(spec.version),
-            '--project=halco@ebrains-' + str(spec.version),
-            '--project=hate@ebrains-' + str(spec.version),
-            '--project=fisch@ebrains-' + str(spec.version),
-            '--project=ztl@ebrains-' + str(spec.version),
-            '--project=hxcomm@ebrains-' + str(spec.version),
-            '--project=rant@ebrains-' + str(spec.version),
-            '--project=pywrap@ebrains-' + str(spec.version),
-            '--project=lib-boost-patches@ebrains-' + str(spec.version),
-            '--project=sctrltp@ebrains-' + str(spec.version),
-            '--project=hwdb@ebrains-' + str(spec.version),
-            '--project=visions-slurm@ebrains-' + str(spec.version),
-            '--project=flange@ebrains-' + str(spec.version),
-            '--project=lib-rcf@ebrains-' + str(spec.version),
-            '--project=bss-hw-params@ebrains-' + str(spec.version),
-            '--project=nhtl-extoll@ebrains-' + str(spec.version),
-            '--project=librma@ebrains-' + str(spec.version),
-            '--project=libnux@ebrains-' + str(spec.version)
+        self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+            '--without-munge',
+            '--without-hxcomm-hostarq',
+            '--without-hxcomm-extoll',
+            '--project=hxtorch',
+            '--release-branch=ebrains-' + str(spec.version)
          )
 
         args = ['--prefix={0}'.format(self.prefix)]

packages/neuron/nrn_find_ncurses.patch

+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -275,6 +275,7 @@
+   # If we are not using self contained, static readline library created for building wheel then only
+   # look for curses and termcap
+   if(NOT NRN_WHEEL_STATIC_READLINE)
++    set(CURSES_NEED_NCURSES TRUE)
+     find_package(Curses QUIET)
+     find_package(Termcap QUIET)
+   endif()
\ No newline at end of file

packages/neuron/package.py

@@ -53,6 +53,7 @@ class Neuron(CMakePackage):
     conflicts("+rx3d", when="~python")
 
     patch("patch-v782-git-cmake-avx512.patch", when="@7.8.2")
+    patch("nrn_find_ncurses.patch", when="@8.2.2")
 
     def cmake_args(self):
         spec = self.spec

packages/oppulance/package.py

@@ -22,8 +22,8 @@ class Oppulance(Package):
 
     releases = [
         {
-            'version': '4.0-rc1-fixup1',
-            'tag': 'ebrains-4.0-rc1-fixup1'
+            'version': '4.0-rc1-fixup2',
+            'tag': 'ebrains-4.0-rc1-fixup2'
         },
     ]
 

packages/py-elephant/package.py

@@ -76,6 +76,7 @@ class PyElephant(PythonPackage):
     @run_after('install')
     @on_package_attributes(run_tests=True)
     def install_test(self):
-        # run tests here (this is just an example):
         pytest = which('pytest')
-        pytest()
+        # skip some tests that seem to fail on HPC deployments,
+        # see https://gitlab.ebrains.eu/technical-coordination/project-internal/devops/platform/ebrains-spack-builds/-/issues/38
+        pytest('-k', 'not test_WPLI_ground_truth_consistency_real_LFP_dataset and not test_multitaper_cohere_perfect_cohere')

packages/pynn-brainscales/package.py

@@ -13,10 +13,10 @@ class PynnBrainscales(WafPackage):
     homepage = "https://github.com/electronicvisions/pynn-brainscales"
     git      = "https://github.com/electronicvisions/pynn-brainscales.git"
 
-    version('4.0-rc1-fixup1', branch='waf')
+    version('4.0-rc1-fixup2', branch='waf')
 
     # PPU compiler dependencies
-    depends_on('oppulance@4.0-rc1-fixup1')
+    depends_on('oppulance@4.0-rc1-fixup2')
 
     # host software dependencies
     depends_on('bitsery', type=('build', 'link', 'run'))
@@ -110,29 +110,12 @@ class PynnBrainscales(WafPackage):
     def configure(self, spec, prefix):
         """Setup and configure the project."""
 
-        self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-munge',
-            '--project=pynn-brainscales@ebrains-' + str(spec.version),
-            '--project=haldls@ebrains-' + str(spec.version),
-            '--project=grenade@ebrains-' + str(spec.version),
-            '--project=code-format@ebrains-' + str(spec.version),
-            '--project=logger@ebrains-' + str(spec.version),
-            '--project=halco@ebrains-' + str(spec.version),
-            '--project=hate@ebrains-' + str(spec.version),
-            '--project=fisch@ebrains-' + str(spec.version),
-            '--project=ztl@ebrains-' + str(spec.version),
-            '--project=hxcomm@ebrains-' + str(spec.version),
-            '--project=rant@ebrains-' + str(spec.version),
-            '--project=pywrap@ebrains-' + str(spec.version),
-            '--project=lib-boost-patches@ebrains-' + str(spec.version),
-            '--project=sctrltp@ebrains-' + str(spec.version),
-            '--project=hwdb@ebrains-' + str(spec.version),
-            '--project=visions-slurm@ebrains-' + str(spec.version),
-            '--project=flange@ebrains-' + str(spec.version),
-            '--project=lib-rcf@ebrains-' + str(spec.version),
-            '--project=bss-hw-params@ebrains-' + str(spec.version),
-            '--project=nhtl-extoll@ebrains-' + str(spec.version),
-            '--project=librma@ebrains-' + str(spec.version),
-            '--project=libnux@ebrains-' + str(spec.version)
+        self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+            '--without-munge',
+            '--without-hxcomm-hostarq',
+            '--without-hxcomm-extoll',
+            '--project=pynn-brainscales',
+            '--release-branch=ebrains-' + str(spec.version)
          )
 
         args = ['--prefix={0}'.format(self.prefix)]

packages/sda/package.py

@@ -49,7 +49,11 @@ class Sda(MakefilePackage):
         install_tree('bin', prefix.bin)
         install_tree('examples', prefix.examples)
         install_tree('lib', prefix.lib)
-        install_tree('src', prefix.src)
+
+    @run_before('build')
+    def make_clean(self):
+        with working_dir('src'):
+            make("clean")
 
     @run_after('install')
     def test_install(self):

spack.yaml

@@ -21,8 +21,8 @@ spack:
     - py-tvb-library@2.7.3
     - py-tvb-storage@2.7.3
     - py-tvb-framework@2.7.3.1
-    - pynn-brainscales@4.0-rc1-fixup1
-    - hxtorch@4.0-rc1-fixup1
+    - pynn-brainscales@4.0-rc1-fixup2
+    - hxtorch@4.0-rc1-fixup2
     - py-nestml@5.2.0
     - py-neo@0.12.0
     - py-hdmf@3.4.6