From 5e4c67665dd9416b508d88cc0596a9b96b62d0ba Mon Sep 17 00:00:00 2001
From: Andrew Davison <andrew.davison@cnrs.fr>
Date: Fri, 29 Apr 2022 13:43:54 +0200
Subject: [PATCH 01/22] Add py-quantities, which is a dependency for py-neo.
This same version is available in upstream Spack, adding it here in case we
need to add new versions quickly
---
packages/py-quantities/package.py | 41 +++++++++++++++++++++++++++++++
spack.yaml | 1 +
2 files changed, 42 insertions(+)
create mode 100644 packages/py-quantities/package.py
diff --git a/packages/py-quantities/package.py b/packages/py-quantities/package.py
new file mode 100644
index 00000000..6bc6c11b
--- /dev/null
+++ b/packages/py-quantities/package.py
@@ -0,0 +1,41 @@
+# 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 import *
+
+
+class PyQuantities(PythonPackage):
+ """Support for physical quantities with units, based on numpy"""
+
+ homepage = "https://python-quantities.readthedocs.org"
+ pypi = "quantities/quantities-0.12.1.tar.gz"
+ maintainers = ['apdavison']
+
+ version('0.13.0', sha256='0fde20115410de21cefa786f3aeae69c1b51bb19ee492190324c1da705e61a81')
+ version('0.12.5', sha256='67546963cb2a519b1a4aa43d132ef754360268e5d551b43dd1716903d99812f0')
+ version('0.12.4', sha256='a33d636d1870c9e1127631185d89b0105a49f827d6aacd44ad9d8f151f331d8b')
+ version('0.12.3', sha256='582f3c7aeba897846761e966615e01202a5e5d06add304492931b05085d19883')
+ version('0.12.2', sha256='92e8397938516483f4fd1855097ec11953ab10dd0bf3293954559226679f76f0')
+ version('0.12.1', sha256='0a03e8511db603c57ca80dee851c43f08d0457f4d592bcac2e154570756cb934')
+ version('0.11.1', sha256='4382098a501b55bf0fdb3dba2061a161041253697d78811ecfd7c55449836660',
+ url="https://pypi.io/packages/source/q/quantities/quantities-0.11.1.zip")
+
+ conflicts('^py-numpy@1.13:', when='@:0.11')
+
+ depends_on('python@2.6:2.7,3.3:3.4', type=('build', 'run'), when='@:0.11')
+ depends_on('python@2.7.0:2.7,3.4:3.6', type=('build', 'run'), when='@0.12.0:0.12.2')
+ depends_on('python@2.7.0:2.7,3.4:3.7', type=('build', 'run'), when='@0.12.3')
+ depends_on('python@2.7.0:2.7,3.4:3.8', type=('build', 'run'), when='@0.12.4:0.12.5')
+ depends_on('python@3.7:3.10', type=('build', 'run'), when='@0.13:')
+
+ # pip silently replaces distutils with setuptools
+ depends_on('py-setuptools', type='build')
+
+ depends_on('py-numpy@1.7.1:1.9', type=('build', 'run'), when='@:0.11')
+ depends_on('py-numpy@1.8.2:1.13', type=('build', 'run'), when='@0.12.0:0.12.1')
+ depends_on('py-numpy@1.8.2:1.14', type=('build', 'run'), when='@0.12.2')
+ depends_on('py-numpy@1.8.2:1.16', type=('build', 'run'), when='@0.12.3')
+ depends_on('py-numpy@1.8.2:1.17', type=('build', 'run'), when='@0.12.4:0.12')
+ depends_on('py-numpy@1.16:', type=('build', 'run'), when='@0.13.0:')
diff --git a/spack.yaml b/spack.yaml
index 4e967314..4503e0b4 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -32,6 +32,7 @@ spack:
#- py-cerebunit
- py-cerebrus
- py-sciunit@0.2.5.1
+ - py-quantities
- py-quantities-scidash@0.12.4.3
#- py-ebrains-drive@0.4.0
#- py-vf-client@0.6.3
--
GitLab
From 2298d0d11708300f3dbdb7208bf59b71af02ed0c Mon Sep 17 00:00:00 2001
From: Andrew Davison <andrew.davison@cnrs.fr>
Date: Fri, 29 Apr 2022 13:46:38 +0200
Subject: [PATCH 02/22] Add py-neo, which is a dependency for py-elephant and
py-pynn. An older version is available in upstream Spack.
---
packages/py-neo/package.py | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
create mode 100644 packages/py-neo/package.py
diff --git a/packages/py-neo/package.py b/packages/py-neo/package.py
new file mode 100644
index 00000000..8d4116ee
--- /dev/null
+++ b/packages/py-neo/package.py
@@ -0,0 +1,33 @@
+# 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 import *
+
+
+class PyNeo(PythonPackage):
+ """Neo is a package for representing electrophysiology data in Python,
+ together with support for reading a wide range of neurophysiology
+ file formats"""
+
+ homepage = "https://neuralensemble.org/neo"
+ pypi = "neo/neo-0.4.1.tar.gz"
+
+ version('0.10.2', sha256='2d4218b0826daeea880e155227060029ec38a00238ceb5f097138d9467c6399b')
+ version('0.10.0', sha256='e591a53e18cfa4478603a0e133f3fa0e07bc016b2a279d21d72cf8196eca8353')
+ version('0.9.0', sha256='6e31c88d7c52174fa2512df589b2b5003e9471fde27fca9f315f4770ba3bd3cb')
+ version('0.8.0', sha256='3382a37b24a384006238b72981f1e9259de9bfa71886f8ed564d35d254ace458')
+ version('0.5.2', sha256='1de436b7d5e72a5b4f1baa68bae5b790624a9ac44b2673811cb0b6ef554d3f8b')
+
+ depends_on('py-setuptools', type='build')
+
+ depends_on('py-numpy@1.7.1:', type=('build', 'run'), when='@0.5.2:0.8.0')
+ depends_on('py-numpy@1.13.0:', type=('build', 'run'), when='@0.9.0')
+ depends_on('py-numpy@1.16.1:', type=('build', 'run'), when='@0.10.0:')
+
+ depends_on('py-quantities@0.9.0:', type=('build', 'run'), when='@0.5.2:0.8.0')
+ depends_on('py-quantities@0.12.1:', type=('build', 'run'), when='@0.9.0:')
+
+ 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:')
--
GitLab
From 2227a10f1acb851444128ab617e89434d8fb4085 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Wed, 11 May 2022 15:50:52 +0200
Subject: [PATCH 03/22] Add BrainScaleS' cross-compiler for its embedded CPUs
---
packages/oppulance/package.py | 65 +++++++++++++++++++++++++++++++++++
spack.yaml | 1 +
2 files changed, 66 insertions(+)
create mode 100644 packages/oppulance/package.py
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
new file mode 100644
index 00000000..ffc1acab
--- /dev/null
+++ b/packages/oppulance/package.py
@@ -0,0 +1,65 @@
+# 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 import *
+import os
+
+class Oppulance(Package):
+ """SDK for embedded processors on BrainScaleS-2"""
+
+ homepage = "https://github.com/electronicvisions/oppulance"
+
+ # PPU compiler dependencies
+ depends_on('gettext')
+ depends_on('zlib')
+ depends_on('bison')
+ depends_on('flex')
+ depends_on('m4')
+ depends_on('texinfo')
+ depends_on('wget')
+ conflicts('flex', when='@2.6.3', msg='Binutils 2.25 for Nux doesn\'t build with flex 2.6.3.')
+
+ releases = [
+ {
+ 'version': '2.0-rc1',
+ 'tag': 'ebrains_release-2-rc1'
+ },
+ ]
+
+ for release in releases:
+ version(
+ release['version'],
+ git='https://github.com/electronicvisions/oppulance',
+ tag=release['tag'],
+ expand=False,
+ )
+
+ for res in ['binutils-gdb', 'gcc', 'newlib']:
+ resource(
+ name=res,
+ git='https://github.com/electronicvisions/{}'.format(res),
+ tag=release['tag'],
+ expand=False,
+ )
+
+ def do_fetch(self, mirror_only=False):
+ super(Oppulance, self).do_fetch(mirror_only)
+ mkdirp(self.stage.source_path)
+ tar = which('tar')
+ bash = which('bash')
+ with working_dir(self.stage.source_path):
+ for key in self.resources:
+ for res in self.resources[key]:
+ tar('xf', res.fetcher.stage.archive_file)
+ tar('xf', self.stage.archive_file)
+ bash('gcc/ci/00_download_prerequisites.sh')
+
+ def install(self, spec, prefix):
+ bash = which('bash')
+ bash('binutils-gdb/ci/00_build_install.sh')
+ bash('gcc/ci/01_build_install_freestanding.sh')
+ bash('newlib/ci/00_build_install.sh')
+ bash('oppulance/ci/00_build_install_libstdc++.sh')
+ mkdirp(spec.prefix)
+ install_tree('install/.', spec.prefix)
diff --git a/spack.yaml b/spack.yaml
index 8ba0006e..32822f19 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -28,6 +28,7 @@ spack:
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
+ - oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
- py-cerebrus
--
GitLab
From 10230162f4b63fc905f8e572c53aa295219cf01f Mon Sep 17 00:00:00 2001
From: Moritz-Alexander-Kern <moritz.kern@ymail.com>
Date: Thu, 12 May 2022 13:46:44 +0200
Subject: [PATCH 04/22] add spack package py-elephant
---
packages/py-elephant/package.py | 54 +++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 packages/py-elephant/package.py
diff --git a/packages/py-elephant/package.py b/packages/py-elephant/package.py
new file mode 100644
index 00000000..67195d94
--- /dev/null
+++ b/packages/py-elephant/package.py
@@ -0,0 +1,54 @@
+# 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 import *
+
+
+class PyElephant(PythonPackage):
+ """Elephant is a package for analysis of electrophysiology data in Python
+ """
+
+ homepage = "http://neuralensemble.org/elephant/"
+ pypi = "elephant/elephant-0.11.0.tar.gz"
+ git = "https://github.com/NeuralEnsemble/elephant.git"
+
+ # list of GitHub accounts to notify when the package is updated.
+ maintainers = ['Moritz-Alexander-Kern']
+
+ version('0.11.1', sha256='d604a202583440fdf9d95d42cef50a410bd74fcaaa1a925b139435f27ab012ef')
+ version('0.11.0', sha256='7b547964dbd196361edc922db2c5a7c0c886ef1effcca6c6dc7adb06f966a3be')
+ version('0.10.0', sha256='7e69a113475e4db01b3563328953c037d37f1597d9f2edf0d51fb65e9aebf096')
+ version('0.9.0', sha256='3e3d4a8e45d708f48bdcadcc4933c66f757d1ede6a1e172af0c07331b64ca180')
+ version('0.8.0', sha256='f7c2649d5b7cfdbaa4442457c75f86af01cc8e7ce2c63f5b3d4687bb94e10af2')
+ version('0.7.0', sha256='76785fe10c40042504928fde2fc57182230bbe39cf0fb0dcaffaba76219b046a')
+ version('0.6.4', sha256='b8c5f2c00ad3249e1fe428d0b8a1dbcaee4a69464481f5f8fd55d2f7f22c45a3')
+ version('0.4.1', sha256='86b21a44cbacdc09a6ba6f51738dcd5b42ecd553d73acb29f71a0be7c82eac81')
+ version('0.3.0', sha256='747251ccfb5820bdead6391411b5faf205b4ddf3ababaefe865f50b16540cfef')
+
+ variant('docs', default=False, description='Install documentation dependencies')
+ variant('pandas', default=False, description='Build with pandas', when='@0.3.0:0.4.1')
+ variant('extras', default=True, description='Build with extras for GPFA, ASSET', when='@0.6.4:')
+
+ depends_on('py-setuptools', type='build')
+ depends_on('python@3.7:', type=('build', 'run'), when='@0.11.0:')
+ depends_on('py-neo@0.3.4:', type=('build', 'run'), when='@0.3.0:0.4.1') # > 0.3.3 ?
+ depends_on('py-numpy@1.8.2:', type=('build', 'run'), when='@0.3.0:0.4.1')
+ depends_on('py-quantities@0.10.1:', type=('build', 'run'), when='@0.3.0:0.4.1')
+ depends_on('py-scipy@0.14.0:', type=('build', 'run'), when='@0.3.0:0.4.1')
+ depends_on('py-pandas@0.14.1:', type=('build', 'run'), when='+pandas')
+ depends_on('py-numpydoc@0.5:', type=('build', 'run'), when='+doc')
+ depends_on('py-sphinx@1.2.2:', type=('build', 'run'), when='+doc')
+ depends_on('py-pandas@0.18.0:', type=('build', 'run'), when='+extras')
+ depends_on('py-scikit-learn@0.23.2:', type=('build', 'run'), when='+extras')
+ depends_on('py-statsmodels@0.12.1:', type=('build', 'run'), when='+extras')
+ depends_on('py-jinja2@2.11.2:', type=('build', 'run'), when='+extras')
+ depends_on('py-neo@0.10.0:', type=('build', 'run'), when='@0.11.0:')
+ depends_on('py-neo@0.9.0', type=('build', 'run'), when='@0.9.0:0.10.0')
+ depends_on('py-neo@0.8.0', type=('build', 'run'), when='@0.6.4:0.8.0')
+ depends_on('py-numpy@1.18.1:', type=('build', 'run'), when='@0.6.4:')
+ depends_on('py-quantities@0.12.1:', type=('build', 'run'), when='@0.6.4:')
+ depends_on('py-scipy@1.5.4:', type=('build', 'run'), when='@0.6.4:')
+ depends_on('py-six@1.10.0:', type=('build', 'run'), when='@0.6.4:')
+ depends_on('py-tqdm', type=('build', 'run'), when='@0.6.4:')
--
GitLab
From 91eefeae2ff6cba93daf62f55ab631e1931870b3 Mon Sep 17 00:00:00 2001
From: Moritz-Alexander-Kern <moritz.kern@ymail.com>
Date: Thu, 12 May 2022 14:08:52 +0200
Subject: [PATCH 05/22] add py-elephant to spack.yml
---
spack.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/spack.yaml b/spack.yaml
index 4e967314..b29a7d76 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -44,6 +44,7 @@ spack:
- py-hbp-neuromorphic-platform@0.10.1
- py-torch~cuda~rocm~valgrind~mkldnn~mpi~gloo~tensorpipe~onnx_ml@1.9.1 ^protobuf@:3.17.999
- py-lfpy@2.2.6
+ - py-elephant
#- biobb-common
# demo for codejam12
#- funniest1022
--
GitLab
From 0be497a2703a0500598d130bb73088de492f95a7 Mon Sep 17 00:00:00 2001
From: Moritz-Alexander-Kern <moritz.kern@ymail.com>
Date: Thu, 12 May 2022 14:16:33 +0200
Subject: [PATCH 06/22] add py-viziphant package
---
packages/py-viziphant/package.py | 29 +++++++++++++++++++++++++++++
spack.yaml | 1 +
2 files changed, 30 insertions(+)
create mode 100644 packages/py-viziphant/package.py
diff --git a/packages/py-viziphant/package.py b/packages/py-viziphant/package.py
new file mode 100644
index 00000000..9853eb54
--- /dev/null
+++ b/packages/py-viziphant/package.py
@@ -0,0 +1,29 @@
+# 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 import *
+
+
+class PyViziphant(PythonPackage):
+ """Viziphant is a package for the visualization of the analysis results of electrophysiology data in Python"""
+
+ homepage = "https://viziphant.readthedocs.io/en/latest/"
+ pypi = "viziphant/viziphant-0.1.0.tar.gz"
+
+ # notify when the package is updated.
+ maintainers = ['Moritz-Alexander-Kern']
+
+ version('0.2.0', sha256='044b5c92de169dfafd9665efe2c310e917d2c21980bcc9f560d5c727161f9bd8')
+ version('0.1.0', sha256='8fd56ec8633f799396dc33fbace95d2553bedb17f680a8c0e97f43b3a629bf6c')
+
+ depends_on('py-setuptools', type='build')
+ depends_on('python@3.7:3.10', type=('build', 'run'))
+ depends_on('py-neo@0.9.0:', type=('build', 'run'))
+ depends_on('py-elephant@0.9.0:', type=('build', 'run'))
+ depends_on('py-numpy@1.18.1:', type=('build', 'run'))
+ depends_on('py-quantities@0.12.1:', type=('build', 'run'))
+ depends_on('py-six@1.10.0:', type=('build', 'run'))
+ depends_on('py-matplotlib@3.3.2:', type=('build', 'run'))
+ depends_on('py-seaborn@0.9.0:', type=('build', 'run'))
diff --git a/spack.yaml b/spack.yaml
index 4e967314..6e6a57bd 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -36,6 +36,7 @@ spack:
#- py-ebrains-drive@0.4.0
#- py-vf-client@0.6.3
- py-hbp-archive@1.1.1
+ - py-viziphant
#- py-morphounit@1.0.4
#- py-neurom@1.4.10
#- py-morphio@3.1.1
--
GitLab
From b90f87b277bde9cf79ad748e9a60d6294248c654 Mon Sep 17 00:00:00 2001
From: Moritz-Alexander-Kern <moritz.kern@ymail.com>
Date: Fri, 13 May 2022 17:26:58 +0200
Subject: [PATCH 07/22] fixed variant docs
---
packages/py-elephant/package.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/packages/py-elephant/package.py b/packages/py-elephant/package.py
index 67195d94..984b0a92 100644
--- a/packages/py-elephant/package.py
+++ b/packages/py-elephant/package.py
@@ -38,8 +38,8 @@ class PyElephant(PythonPackage):
depends_on('py-quantities@0.10.1:', type=('build', 'run'), when='@0.3.0:0.4.1')
depends_on('py-scipy@0.14.0:', type=('build', 'run'), when='@0.3.0:0.4.1')
depends_on('py-pandas@0.14.1:', type=('build', 'run'), when='+pandas')
- depends_on('py-numpydoc@0.5:', type=('build', 'run'), when='+doc')
- depends_on('py-sphinx@1.2.2:', type=('build', 'run'), when='+doc')
+ depends_on('py-numpydoc@0.5:', type=('build', 'run'), when='+docs')
+ depends_on('py-sphinx@1.2.2:', type=('build', 'run'), when='+docs')
depends_on('py-pandas@0.18.0:', type=('build', 'run'), when='+extras')
depends_on('py-scikit-learn@0.23.2:', type=('build', 'run'), when='+extras')
depends_on('py-statsmodels@0.12.1:', type=('build', 'run'), when='+extras')
--
GitLab
From d999fda479a4c19ea6de3c014528ae07d921a9b4 Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Thu, 19 May 2022 16:11:19 +0200
Subject: [PATCH 08/22] Update spack.yaml
---
spack.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 0bd507e2..c76f6807 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -28,7 +28,7 @@ spack:
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- - oppulance@2.0-rc1
+ #- oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
- py-cerebrus
--
GitLab
From d496e79f3a92e10d56be60fb15722948a6ef5718 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=20Beltr=C3=A1n?= <daniel.beltran@irbbarcelona.org>
Date: Thu, 19 May 2022 18:43:15 +0200
Subject: [PATCH 09/22] Add new directory
---
packages/biobb-md/.gitkeep | 0
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 packages/biobb-md/.gitkeep
diff --git a/packages/biobb-md/.gitkeep b/packages/biobb-md/.gitkeep
new file mode 100644
index 00000000..e69de29b
--
GitLab
From 062483be24ff765461b4ada1073da32b0e118da0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=20Beltr=C3=A1n?= <daniel.beltran@irbbarcelona.org>
Date: Thu, 19 May 2022 18:49:30 +0200
Subject: [PATCH 10/22] Upload New File
---
packages/biobb-md/package.py | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
create mode 100644 packages/biobb-md/package.py
diff --git a/packages/biobb-md/package.py b/packages/biobb-md/package.py
new file mode 100644
index 00000000..4453fb36
--- /dev/null
+++ b/packages/biobb-md/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class BiobbMd(PythonPackage):
+ """Biobb_md is the Biobb module collection to perform molecular
+ dynamics simulations"""
+
+ # Homepage and download url
+ homepage = "https://github.com/bioexcel/biobb_md"
+ git = 'https://github.com/bioexcel/biobb_md.git'
+
+ # Versions
+ version('3.7.1', branch='master')
+
+ # Dependencies
+ depends_on('biobb-common')
+ depends_on('python@3.7:', type=('build', 'run'))
+ depends_on('gromacs')
--
GitLab
From 080059b491f3d925aca2052c371d8823321dfcf2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Fri, 20 May 2022 12:43:33 +0200
Subject: [PATCH 11/22] Fix oppulance
If starting from scratch the archive file isn't there in do_fetch;
in this case, we can make use of the folder where the freshly
downloaded resources are cloned to.
---
packages/oppulance/package.py | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index ffc1acab..159140c7 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -41,18 +41,23 @@ class Oppulance(Package):
git='https://github.com/electronicvisions/{}'.format(res),
tag=release['tag'],
expand=False,
+ placement=res
)
def do_fetch(self, mirror_only=False):
super(Oppulance, self).do_fetch(mirror_only)
mkdirp(self.stage.source_path)
tar = which('tar')
+ ln = which('ln')
bash = which('bash')
with working_dir(self.stage.source_path):
for key in self.resources:
for res in self.resources[key]:
- tar('xf', res.fetcher.stage.archive_file)
- tar('xf', self.stage.archive_file)
+ if res.fetcher.stage.archive_file:
+ tar('xf', res.fetcher.stage.archive_file)
+ else:
+ # freshly download
+ ln('-sf', res.fetcher.stage.source_path, res.name)
bash('gcc/ci/00_download_prerequisites.sh')
def install(self, spec, prefix):
@@ -60,6 +65,6 @@ class Oppulance(Package):
bash('binutils-gdb/ci/00_build_install.sh')
bash('gcc/ci/01_build_install_freestanding.sh')
bash('newlib/ci/00_build_install.sh')
- bash('oppulance/ci/00_build_install_libstdc++.sh')
+ bash('ci/00_build_install_libstdc++.sh')
mkdirp(spec.prefix)
install_tree('install/.', spec.prefix)
--
GitLab
From a5ea360233fef29b2b7d59e8b025f24b81b166d4 Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Fri, 20 May 2022 13:08:34 +0200
Subject: [PATCH 12/22] Update spack.yaml
---
spack.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index c76f6807..0bd507e2 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -28,7 +28,7 @@ spack:
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- #- oppulance@2.0-rc1
+ - oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
- py-cerebrus
--
GitLab
From 7a8cee0464cd424e2c5edb76291d7dd3d249441e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Fri, 20 May 2022 16:55:53 +0200
Subject: [PATCH 13/22] Fix oppulance: Explicitly depend on modern flex version
---
packages/oppulance/package.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 159140c7..5934d909 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -14,11 +14,10 @@ class Oppulance(Package):
depends_on('gettext')
depends_on('zlib')
depends_on('bison')
- depends_on('flex')
+ depends_on('flex@2.6.4:')
depends_on('m4')
depends_on('texinfo')
depends_on('wget')
- conflicts('flex', when='@2.6.3', msg='Binutils 2.25 for Nux doesn\'t build with flex 2.6.3.')
releases = [
{
--
GitLab
From 3c72d4be6726ba868bb032a0ba84b778265d422b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 24 May 2022 10:30:33 +0200
Subject: [PATCH 14/22] Fix py-torch: Enable tensorpipe
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Importing torch yields an ImportError caused by some mismatch between
build options (distributed is enabled, but tensorpipe is not →
this seems unsupported → enable tensorpipe).
Related to: https://support.humanbrainproject.eu/#ticket/zoom/14319
---
spack.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 0bd507e2..2c92e597 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -43,7 +43,7 @@ spack:
- py-hippounit@1.3.6
- py-efel@4.0.4
- py-hbp-neuromorphic-platform@0.10.1
- - py-torch~cuda~rocm~valgrind~mkldnn~mpi~gloo~tensorpipe~onnx_ml@1.9.1 ^protobuf@:3.17.999
+ - py-torch~cuda~rocm~valgrind~mkldnn~mpi~gloo+tensorpipe~onnx_ml@1.9.1 ^protobuf@:3.17.999
- py-lfpy@2.2.6
#- biobb-common
# demo for codejam12
--
GitLab
From 166bead25dda3837059de06874f9310a0e4fb660 Mon Sep 17 00:00:00 2001
From: EtienneCmb <e.combrisson@gmail.com>
Date: Tue, 24 May 2022 13:15:33 +0200
Subject: [PATCH 15/22] Initial commit for adding Frites
---
packages/py-frites/package.py | 61 +++++++++++++++++++++++++++++++++++
1 file changed, 61 insertions(+)
create mode 100644 packages/py-frites/package.py
diff --git a/packages/py-frites/package.py b/packages/py-frites/package.py
new file mode 100644
index 00000000..33622ed8
--- /dev/null
+++ b/packages/py-frites/package.py
@@ -0,0 +1,61 @@
+# 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)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack. We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+# spack install py-frites
+#
+# You can edit this file again by typing:
+#
+# spack edit py-frites
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack import *
+
+
+class PyFrites(PythonPackage):
+ """Frites is a Python toolbox for assessing information-based measures on
+ human and animal neurophysiological data (M/EEG, Intracranial)."""
+
+ # FIXME: Add a proper url for your package's homepage here.
+ homepage = "https://brainets.github.io/frites/"
+ pypi = "frites/frites-0.4.2.tar.gz"
+
+ # FIXME: Add a list of GitHub accounts to
+ # notify when the package is updated.
+ # maintainers = ['github_user1', 'github_user2']
+
+ version('0.4.2', sha256='5da63f6f91515ff0dbed0252a75fcbdeade4311bfd28d08cd644c89c85e6ac5a')
+
+ # FIXME: Only add the python/pip/wheel dependencies if you need specific versions
+ # or need to change the dependency type. Generic python/pip/wheel dependencies are
+ # added implicity by the PythonPackage base class.
+ depends_on('python@3.7:', type=('build', 'run'))
+ # depends_on('py-pip@X.Y:', type='build')
+ # depends_on('py-wheel@X.Y:', type='build')
+
+ # FIXME: Add a build backend, usually defined in pyproject.toml. If no such file
+ # exists, use setuptools.
+ depends_on('py-setuptools', type='build')
+ # depends_on('py-flit-core', type='build')
+ # depends_on('py-poetry-core', type='build')
+
+ # FIXME: Add additional dependencies if required.
+ depends_on('py-numpy', type=('build', 'run'))
+ depends_on('py-scipy', type=('build', 'run'))
+ depends_on('py-mne', type=('build', 'run'))
+ depends_on('py-joblib', type=('build', 'run'))
+ depends_on('py-xarray', type=('build', 'run'))
+ depends_on('py-netcdf4', type=('build', 'run'))
+ depends_on('py-h5netcdf', type=('build', 'run'))
+ depends_on('py-scikit-learn', type=('build', 'run'))
--
GitLab
From 082c414dc6a481aa0e3dfa8a0e420df0c9b370ba Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Tue, 24 May 2022 18:16:28 +0200
Subject: [PATCH 16/22] Update spack.yaml
---
spack.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 0bd507e2..c76f6807 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -28,7 +28,7 @@ spack:
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
- - oppulance@2.0-rc1
+ #- oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
- py-cerebrus
--
GitLab
From 647a522eec735747a564032adb10c900340193da Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Tue, 24 May 2022 18:23:18 +0200
Subject: [PATCH 17/22] Add py-lazyarray in response to MR !84
---
spack.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/spack.yaml b/spack.yaml
index c76f6807..08f3acdd 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -15,6 +15,7 @@ spack:
- py-seaborn
- py-matplotlib
- py-nameparser
+ - py-lazyarray
#- py-version-query
# EBRAINS simulators
- nest@3.3 +python +gsl +mpi
--
GitLab
From b4775b666494f130b865d21223caf111b016af3c Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 25 May 2022 16:44:30 +0200
Subject: [PATCH 18/22] Update spack.yaml
---
spack.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/spack.yaml b/spack.yaml
index 692bebdf..571a2ca0 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -29,6 +29,7 @@ spack:
- py-formencode
- tvb-framework ^binutils+ld+gold
- pynn-brainscales@2.0-rc1 ^log4cxx@0.10.0 ^googletest@1.11.0:+gmock
+ - py-neo
#- oppulance@2.0-rc1
#- py-cerebstats
#- py-cerebunit
--
GitLab
From ecc4505ff32d07917c4f29766233250fed043e7f Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Thu, 26 May 2022 14:08:51 +0000
Subject: [PATCH 19/22] updates in track_spack_releases
---
operations/track_spack_releases.xlsx | Bin 10958 -> 10959 bytes
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/operations/track_spack_releases.xlsx b/operations/track_spack_releases.xlsx
index f4a99b2b76ef0c995c6332e437bd8573a2f2c6c9..4f6f87f8155cb580a66489fc44c8b64db035dc45 100644
GIT binary patch
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--
GitLab
From c0272c30cb994f289191dcc282cf59a57920c5be Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Thu, 26 May 2022 16:36:27 +0200
Subject: [PATCH 20/22] Update spack.yaml
---
spack.yaml | 1 +
1 file changed, 1 insertion(+)
diff --git a/spack.yaml b/spack.yaml
index 6a13c7c5..55228eb9 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -50,6 +50,7 @@ spack:
- py-torch~cuda~rocm~valgrind~mkldnn~mpi~gloo~tensorpipe~onnx_ml@1.9.1 ^protobuf@:3.17.999
- py-lfpy@2.2.6
- py-elephant
+ - py-frites
#- biobb-common
# demo for codejam12
#- funniest1022
--
GitLab
From 04e913518f10bffef812b5279c4d36d76e83cd0d Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 27 May 2022 11:48:33 +0200
Subject: [PATCH 21/22] Update spack.yaml
---
spack.yaml | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 2ea80450..55e5f250 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -51,7 +51,8 @@ spack:
- py-lfpy@2.2.6
- py-elephant
- py-frites
- #- biobb-common
+ - biobb-common
+ - biobb-md
# demo for codejam12
#- funniest1022
concretization: together
--
GitLab
From 11bd33f54127cc55d9e178d420a2fc2fdec0fe6f Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 27 May 2022 13:18:07 +0200
Subject: [PATCH 22/22] Update spack.yaml
---
spack.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/spack.yaml b/spack.yaml
index 55e5f250..dd0c326c 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -51,8 +51,8 @@ spack:
- py-lfpy@2.2.6
- py-elephant
- py-frites
- - biobb-common
- - biobb-md
+ #- biobb-common
+ #- biobb-md
# demo for codejam12
#- funniest1022
concretization: together
--
GitLab