fix merge conflict

README.md

@@ -38,9 +38,9 @@ Clone this repository. You can use the `ebrains-yy-mm` branches to install the E
 git clone --branch {branch-name} https://gitlab.ebrains.eu/technical-coordination/project-internal/devops/platform/ebrains-spack-builds.git
 ```
 
-Clone Spack. We currently use version v0.18.1:
+Clone Spack. We currently use version v0.19.2:
 ```
-git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.18.1 https://github.com/spack/spack
+git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.19.2 https://github.com/spack/spack
 ```
 
 Activate Spack:

packages/biobb-analysis/package.py

@@ -20,6 +20,16 @@ class BiobbAnalysis(PythonPackage):
     depends_on('gromacs')
     depends_on('ambertools')
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+        filter_file(
+            "'Programming Language :: Python :: 3.9'",
+            "'Programming Language :: Python :: 3.9',\r\n        "
+            "'Programming Language :: Python :: 3.10'",
+            "setup.py",
+        )
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-chemistry/package.py

@@ -21,6 +21,16 @@ class BiobbChemistry(PythonPackage):
     depends_on('ambertools')
     depends_on('acpype')
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+        filter_file(
+            "'Programming Language :: Python :: 3.9'",
+            "'Programming Language :: Python :: 3.9',\r\n        "
+            "'Programming Language :: Python :: 3.10'",
+            "setup.py",
+        )
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-common/package.py

@@ -20,6 +20,10 @@ class BiobbCommon(PythonPackage):
     depends_on('py-requests', type=('build', 'run'))
     depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
 
+    # Custom patch to enable python 3.10.8 for this package
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<=3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-gromacs/package.py

@@ -16,6 +16,10 @@ class BiobbGromacs(PythonPackage):
     depends_on('biobb-common')
     depends_on('gromacs')
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-io/package.py

@@ -15,6 +15,16 @@ class BiobbIo(PythonPackage):
     depends_on('biobb-common')
     depends_on('python@3.8:', type=('build', 'run'))
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+        filter_file(
+            "'Programming Language :: Python :: 3.9'",
+            "'Programming Language :: Python :: 3.9',\r\n        "
+            "'Programming Language :: Python :: 3.10'",
+            "setup.py",
+        )
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-model/package.py

@@ -16,6 +16,16 @@ class BiobbModel(PythonPackage):
     depends_on('biobb-common')
     depends_on('biobb-structure-checking')
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+        filter_file(
+            "'Programming Language :: Python :: 3.9'",
+            "'Programming Language :: Python :: 3.9',\r\n        "
+            "'Programming Language :: Python :: 3.10'",
+            "setup.py",
+        )
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/biobb-structure-utils/package.py

@@ -16,6 +16,16 @@ class BiobbStructureUtils(PythonPackage):
     depends_on('biobb-common')
     depends_on('biobb-structure-checking')
 
+    # Patching to enable python 3.10 (not official, might not be stable)
+    def patch(self):
+        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")
+        filter_file(
+            "'Programming Language :: Python :: 3.9'",
+            "'Programming Language :: Python :: 3.9',\r\n        "
+            "'Programming Language :: Python :: 3.10'",
+            "setup.py",
+        )
+
     # Test
     @run_after('install')
     @on_package_attributes(run_tests=True)

packages/genpybind/package.py

@@ -50,6 +50,9 @@ class Genpybind(WafPackage):
 
     extends('python')
 
+    patch('v0.2.1-python3.10.patch', when='@:0.2.1 ^python@3.10:')
+
+
     def configure_args(self):
         args = super(Genpybind, self).configure_args()
 

packages/genpybind/v0.2.1-python3.10.patch

+diff --git a/genpybind/annotations.py b/genpybind/annotations.py
+index 1dfd1f4..871ef4d 100644
+--- a/genpybind/annotations.py
++++ b/genpybind/annotations.py
+@@ -3,7 +3,7 @@
+ from __future__ import unicode_literals
+ 
+ import ast
+-import collections
++from collections.abc import Sequence
+ 
+ from clang.cindex import CursorKind
+ 
+@@ -25,7 +25,7 @@ LOZENGE = u"◊"
+ SPECIAL_NAMES = {"true": True, "false": False, "default": None, "none": None}
+ 
+ 
+-class Annotations(collections.Sequence):
++class Annotations(Sequence):
+     def __init__(self, annotations=None):
+         # type: (Union[None, Text, Iterable[Text]]) -> None
+         self._annotations = []  # type: List[AnnotationT]
+diff --git a/genpybind/registry.py b/genpybind/registry.py
+index 4f66ace..75ba7a9 100644
+--- a/genpybind/registry.py
++++ b/genpybind/registry.py
+@@ -1,6 +1,6 @@
+ from __future__ import unicode_literals
+ 
+-import collections
++from collections.abc import Mapping
+ import re
+ 
+ from clang import cindex
+@@ -16,7 +16,7 @@ if False:  # pylint: disable=using-constant-test
+ RE_NON_IDENTIFIER = re.compile(r"[^a-zA-Z0-9_]+")
+ 
+ 
+-class Registry(collections.Mapping):
++class Registry(Mapping):
+     def __init__(self, tags=None):
+         # type: (Optional[Iterable[Text]]) -> None
+         self._declarations = {}  # type: Dict[Text, Optional[Declaration]]

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('6.0-rc1', branch='waf')
+    version('6.0-rc2', branch='waf')
 
     # PPU compiler dependencies
-    depends_on('oppulance@6.0-rc1')
+    depends_on('oppulance@6.0-rc2')
 
     # host software dependencies
     depends_on('bitsery', type=('build', 'link', 'run'))
@@ -135,6 +135,11 @@ class Hxtorch(WafPackage):
     def configure(self, spec, prefix):
         """Setup and configure the project."""
 
+        env = os.environ
+        if 'SPACK_COMPILER_IMPLICIT_RPATHS' in env:
+            env['LIBRARY_PATH'] = env['SPACK_COMPILER_IMPLICIT_RPATHS'] + ':' + env['LIBRARY_PATH']
+            env['WAF_CONFIGURE_LD_LIBRARY_PATH'] = env['SPACK_COMPILER_IMPLICIT_RPATHS'] + ':' + env['WAF_CONFIGURE_LD_LIBRARY_PATH']
+
         self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects',
             '--without-munge',
             '--without-hxcomm-hostarq',
@@ -146,7 +151,6 @@ class Hxtorch(WafPackage):
         args = ['--prefix={0}'.format(self.prefix)]
         args += self.configure_args()
 
-        env = os.environ
         env['LD_LIBRARY_PATH'] = env.get('WAF_CONFIGURE_LD_LIBRARY_PATH')
         self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
 

packages/nest/package.py

@@ -26,7 +26,7 @@ class Nest(CMakePackage):
     git      = "https://github.com/nest/nest-simulator.git"
 
     version('master', branch='master')
-    version('3.5',    sha256='4504ff7f9cfa051c91a5e85a0761bdd09d23aeeadac22c45f6be18b7fbe2db43')
+    version('3.5',    sha256='3cdf5720854a4d8a7d359f9de9d2fb3619a0be2e36932028d6940360741547bd')
     version('3.4',    sha256='c56699111f899045ba48e55e87d14eca8763b48ebbb3648beee701a36aa3af20')
     version('3.3',    sha256='179462b966cc61f5785d2fee770bc36f86745598ace9cd97dd620622b62043ed')
     version('3.2',    sha256='583d5725882ad5e8fd4fc7ffab425da97cbbb91fadbc327e940c184e8892b958')

packages/oppulance/package.py

@@ -22,8 +22,8 @@ class Oppulance(Package):
 
     releases = [
         {
-            'version': '6.0-rc1',
-            'tag': 'ebrains-6.0-rc1'
+            'version': '6.0-rc2',
+            'tag': 'ebrains-6.0-rc2'
         },
     ]
 

packages/py-cerebrus/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 PyCerebrus(PythonPackage):
-    """Lightweight, extensible schema and data validation tool for Python dictionaries
-    """
-
-    homepage = "http://docs.python-cerberus.org/"
-    pypi     = "Cerberus/Cerberus-1.3.4.tar.gz"
-    git      = "https://github.com/pyeve/cerberus.git"
-
-    version('1.3.4', sha256='d1b21b3954b2498d9a79edf16b3170a3ac1021df88d197dc2ce5928ba519237c')
-
-    depends_on('python@3.6.9:')
-    depends_on('py-setuptools',     type=('build', 'run'))
-    depends_on('py-pytest',         type=('test'))

packages/py-csa/package.py

+# Copyright 2013-2022 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.package import *
+
+
+class PyCsa(PythonPackage):
+    """This provides basic utility functions and classes to other parts of
+    SpiNNaker"s tooling. Nothing in here knows anything about SpiNNaker
+    functionality."""
+
+    homepage = "https://github.com/SpiNNakerManchester/SpiNNUtils"
+    pypi = "csa/csa-0.1.12.tar.gz"
+
+    version("0.1.12", sha256="15e7103f3df32871951785880b2fe6a18056768ba31a7cc053ba553717c4b2de")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))

packages/py-elephant/package.py

@@ -17,6 +17,7 @@ class PyElephant(PythonPackage):
     maintainers = ["Moritz-Alexander-Kern"]
 
     version('develop', branch='master')
+    version("0.13.0", sha256="2c6463cf9ace41631f2af196c5b80b468bf1c4b264d3a6b1ea0fb587d9e7dd67")
     version("0.12.0", sha256="81f8d668f92d8688344bb7a9c5abaa8438d824560c935a411e6e36ddf7dc7c72")
     version("0.11.2", sha256="f8759fff0bbb136ae4ffc8d1eacadeea8ba56610d705c3bf207de87ada3ba240")
     version("0.11.1", sha256="d604a202583440fdf9d95d42cef50a410bd74fcaaa1a925b139435f27ab012ef")

packages/py-frites/package.py

@@ -18,6 +18,7 @@ class PyFrites(PythonPackage):
     # notify when the package is updated.
     # maintainers = ['github_user1', 'github_user2']
 
+    version('0.4.4', sha256='280ca9f3f711da0550eceec8ce94108b891369b63ea3cc1b8c960825ed20fb3f')
     version('0.4.3', sha256='41a0aa2414196f1a08b7668b3e6be5872eda0f6814171408ef33af4904619f3a')
     version('0.4.2', sha256='5da63f6f91515ff0dbed0252a75fcbdeade4311bfd28d08cd644c89c85e6ac5a')
 

packages/py-neo/package.py

@@ -41,3 +41,6 @@ class PyNeo(PythonPackage):
 
     depends_on('py-scipy@0.12.0:',      type=('build', 'run'), when='@0.5.2:0.8.0')
     depends_on('py-scipy@1.0.0:',       type=('build', 'run'), when='@0.9.0:')
+
+    depends_on('py-nixio@1.5.0:',       type=('build', 'run'))
+    depends_on('py-pynwb',              type=('build', 'run'))

packages/py-netpyne/package.py

@@ -10,20 +10,22 @@ class PyNetpyne(PythonPackage):
     """NetPyNE (Networks using Python and NEURON) is a Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biological neuronal networks using the NEURON simulator."""
 
     homepage = "netpyne.org"
-    url = "https://github.com/suny-downstate-medical-center/netpyne/archive/refs/tags/v1.0.4.1.tar.gz"
+    url = "https://github.com/suny-downstate-medical-center/netpyne/archive/refs/tags/v1.0.4.2.tar.gz"
     git = "https://github.com/suny-downstate-medical-center/netpyne.git"
 
     # list of GitHub accounts to notify when the package is updated.
     maintainers = ["salvadord", "vvbragin"]
 
+    version("1.0.4.2", sha256="4191464386bbc2ecad3b224302c19edb9a26fe0da57c0d9b234cb9c2dd918c8d")
     version("1.0.4.1", sha256="2ed12807f9b3d3e3a8ba9910f8d22c5c17635e0cdea0af09fa3a230e68876df6")
 
     depends_on("py-setuptools", type="build")
-    
+
     depends_on("neuron", type=("build", "run"))
     depends_on("py-numpy", type=("build", "run"))
     depends_on("py-scipy", type=("build", "run"))
-    depends_on("py-matplotlib@:3.5.1", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-matplotlib@:3.5.1", type=("build", "run"), when="@:1.0.4.1")
     depends_on("py-matplotlib-scalebar", type=("build", "run"))
     depends_on("py-future", type=("build", "run"))
     depends_on("py-pandas", type=("build", "run"))