From 88786cedd2f39da97eb9ac14890566e957121561 Mon Sep 17 00:00:00 2001
From: ldomide <lia.domide@codemart.ro>
Date: Fri, 19 Apr 2024 12:32:34 +0300
Subject: [PATCH 1/6] Update tvb-* packages to version 2.9
---
packages/py-tvb-contrib/package.py | 7 ++++---
packages/py-tvb-framework/package.py | 14 ++++++--------
packages/py-tvb-library/package.py | 9 ++++-----
packages/py-tvb-storage/package.py | 5 +++--
4 files changed, 17 insertions(+), 18 deletions(-)
diff --git a/packages/py-tvb-contrib/package.py b/packages/py-tvb-contrib/package.py
index 0be799bf..9aabdbaa 100644
--- a/packages/py-tvb-contrib/package.py
+++ b/packages/py-tvb-contrib/package.py
@@ -12,15 +12,16 @@ class PyTvbContrib(PythonPackage):
"""
homepage = "https://www.thevirtualbrain.org/"
- pypi = 'tvb-contrib/tvb-contrib-2.8.2.tar.gz'
+ pypi = 'tvb-contrib/tvb-contrib-2.9.tar.gz'
maintainers = ['dionperd', 'paulapopa', "ldomide"]
+ version('2.9', '64e5f17c46b67c1f92b3cdfb863c7d5e1d97d913b26521a9567735270bb9ad25')
version('2.8.2', 'ff5990e979cf1f87046d7bed2c265f9dec50f9d817abaabdf5df7ec4482b5063')
version('2.8.1', '0b9bc5f837913f1cba007d25ae94c9df51bf43bf19c9fb2af14a90cb6a1e1a66')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:', type=('build', 'run'))
# setup_requires
depends_on('py-pip', type='build')
@@ -36,7 +37,7 @@ class PyTvbContrib(PythonPackage):
depends_on('py-dill', type=('build', 'run'))
# Test dependency
- depends_on('py-pytest@:7.1', type='test')
+ depends_on('py-pytest', type='test')
@run_after('install')
@on_package_attributes(run_tests=True)
diff --git a/packages/py-tvb-framework/package.py b/packages/py-tvb-framework/package.py
index 9d051b60..aa53677a 100644
--- a/packages/py-tvb-framework/package.py
+++ b/packages/py-tvb-framework/package.py
@@ -14,10 +14,11 @@ class PyTvbFramework(PythonPackage):
"""
homepage = "https://www.thevirtualbrain.org/"
- pypi = 'tvb-framework/tvb-framework-2.8.2.tar.gz'
+ pypi = 'tvb-framework/tvb-framework-2.9.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('2.9', '44f102bcfd63a09c9c2af662a004415f2fc64847c0376218011b27fd2bb03848')
version('2.8.2', '00f4bdfc9faccf2df1a95695e231d7d4890cbf5ca7eac0474d52b976a51d91d5')
version('2.8.1.1', '5f858398708453b3ea48de11c4ca1f098fe732738431ed421cc435d9bfc4b6fb')
version('2.7.3.1', 'e1de0df0b8f43a317962b066790a5d724e1e6ae98ee124ad8b977f92aa228877')
@@ -28,7 +29,7 @@ class PyTvbFramework(PythonPackage):
version('2.3', '0f3386135cdbd80bfd7d31f2e056b015a27ff6d081492db16274deed581b0aac')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:', type=('build', 'run'))
# setup_requires
depends_on('py-setuptools', type='build')
@@ -53,7 +54,7 @@ class PyTvbFramework(PythonPackage):
depends_on('py-requests', type=('build', 'run'))
depends_on('py-scikit-learn', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
- # siibra
+ depends_on('py-siibra', type=('build', 'run'))
depends_on('py-simplejson', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
depends_on('py-sqlalchemy', type=('build', 'run'))
@@ -63,9 +64,7 @@ class PyTvbFramework(PythonPackage):
depends_on('py-tvb-storage', type=('build', 'run'))
depends_on('py-werkzeug', type=('build', 'run'))
- # pytest@7.2: does not depend on py-py, which is needed for py-pytest-benchmark@:3 (https://github.com/ionelmc/pytest-benchmark/issues/226)
- # simplest way to address this is to add an upper limit for pytest for now
- depends_on('py-pytest@:7.1', type='test')
+ depends_on('py-pytest', type='test')
depends_on('py-pytest-benchmark', type='test')
depends_on('py-pytest-mock', type='test')
depends_on('py-beautifulsoup4', type='test')
@@ -74,5 +73,4 @@ class PyTvbFramework(PythonPackage):
@on_package_attributes(run_tests=True)
def install_test(self):
pytest = which('pytest')
- pytest('--ignore', 'tvb/tests/framework/adapters/creators/siibra_base_test.py',
- '--ignore', 'tvb/tests/framework/adapters/creators/siibra_creator_test.py')
+ pytest()
diff --git a/packages/py-tvb-library/package.py b/packages/py-tvb-library/package.py
index ea9407bb..68786c67 100644
--- a/packages/py-tvb-library/package.py
+++ b/packages/py-tvb-library/package.py
@@ -14,10 +14,11 @@ class PyTvbLibrary(PythonPackage):
"""
homepage = "https://www.thevirtualbrain.org/"
- pypi = 'tvb-library/tvb-library-2.8.2.tar.gz'
+ pypi = 'tvb-library/tvb-library-2.9.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('2.9', '0a65fa3d803ef8da3d69a0f27a13e40b79876ee6d5b627c34d0c9fc5c12697e6')
version('2.8.2', '4222dadbecce53b29e2141801b1ca8eb99c4595ace6c7d0469f7e0a41d3f384a')
version('2.8.1', 'be130b10e7e176d503709afd211ae728f45d4e8b4a6082c6f6fcfbc1be990d0c')
version('2.8', '49624cc8ca0673f8590227a9246ea2ffa855ef7a4242235ce85263ff6f3db7c8')
@@ -31,7 +32,7 @@ class PyTvbLibrary(PythonPackage):
version('2.3', '0595f2eca95e5ed4c7a1c88425914cc71d0ea7a9f4ec575b6a315ca2408ea801')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:', type=('build', 'run'))
# setup_requires
depends_on('py-setuptools', type='build')
@@ -55,9 +56,7 @@ class PyTvbLibrary(PythonPackage):
depends_on('py-tvb-data', type=('run', 'test'))
depends_on('py-tvb-gdist', type=('run', 'test'))
- # pytest@7.2: does not depend on py-py, which is needed for py-pytest-benchmark@:3 (https://github.com/ionelmc/pytest-benchmark/issues/226)
- # simplest way to address this is to add an upper limit for pytest for now
- depends_on('py-pytest@:7.1', type='test')
+ depends_on('py-pytest', type='test')
depends_on('py-h5py', type='test')
depends_on('py-pytest-benchmark', type='test')
depends_on('py-pytest-xdist', type='test')
diff --git a/packages/py-tvb-storage/package.py b/packages/py-tvb-storage/package.py
index dbf0660a..d25e7690 100644
--- a/packages/py-tvb-storage/package.py
+++ b/packages/py-tvb-storage/package.py
@@ -14,10 +14,11 @@ class PyTvbStorage(PythonPackage):
"""
homepage = "https://www.thevirtualbrain.org/"
- pypi = 'tvb-storage/tvb-storage-2.8.1.tar.gz'
+ pypi = 'tvb-storage/tvb-storage-2.9.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('2.9', 'b64ac69a1ffee3ed18664d60012511d0d37c2205c1c2ee1030b442d23fbfbe52')
version('2.8.1', '4bbfd65ab1e150cf28a8206bcf5e30a8a092293b108b1bbb3365e6675f6d8837')
version('2.7.3', '7f8b4d60313003e3c2b5b2f370f0a3a33ea5b22fde8b3f428eee7f2874673e4f')
version('2.7.2', '501443ceb9f6374922a024b07ef09138f826fd0deaa69883c63dd0dff34fb16c')
@@ -27,7 +28,7 @@ class PyTvbStorage(PythonPackage):
version('2.3', 'e10bb40a486771703ba2776555ea5a453e619b07f10e4dea0d347043dee8f54b')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:', type=('build', 'run'))
# setup_requires
depends_on('py-setuptools', type='build')
--
GitLab
From 32760f76f15623db196cc4c1804e21191706f232 Mon Sep 17 00:00:00 2001
From: ldomide <lia.domide@codemart.ro>
Date: Fri, 19 Apr 2024 12:37:08 +0300
Subject: [PATCH 2/6] Update tvb 3rd party dependencies with new versions
---
packages/py-bct/package.py | 3 ++-
packages/py-flask-restx/package.py | 3 ++-
packages/py-formencode/package.py | 3 ++-
packages/py-lems/package.py | 3 ++-
packages/py-pyaescrypt/package.py | 3 ++-
5 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/packages/py-bct/package.py b/packages/py-bct/package.py
index bfa61d91..1d1472ab 100644
--- a/packages/py-bct/package.py
+++ b/packages/py-bct/package.py
@@ -12,10 +12,11 @@ class PyBct(PythonPackage):
"""
homepage = "https://pypi.org/project/bctpy/"
- pypi = 'bctpy/bctpy-0.6.0.tar.gz'
+ pypi = 'bctpy/bctpy-0.6.1.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('0.6.1', '9c47757596ce386e226353a16ab94e6071a4d3b8acf6c7b2623b45d9e0c5d1a0')
version('0.6.0', '36392049ec5a2ccae75a0cf89b21838fda41a351c31fe6c6622cfcff1c997933')
# python_requires
diff --git a/packages/py-flask-restx/package.py b/packages/py-flask-restx/package.py
index f6bcc060..171f1039 100644
--- a/packages/py-flask-restx/package.py
+++ b/packages/py-flask-restx/package.py
@@ -12,10 +12,11 @@ class PyFlaskRestx(PythonPackage):
"""
homepage = "https://pypi.org/project/flask-restx"
- pypi = 'flask-restx/flask-restx-1.0.5.tar.gz'
+ pypi = 'flask-restx/flask-restx-1.3.0.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('1.3.0', '4f3d3fa7b6191fcc715b18c201a12cd875176f92ba4acc61626ccfd571ee1728')
version('1.0.5', 'e23dc4ff24869c92faa719b7a58be1203ed741275ff32c9f03d0ab56ed01546c')
# python_requires
diff --git a/packages/py-formencode/package.py b/packages/py-formencode/package.py
index 5557e1f6..f78e0e63 100644
--- a/packages/py-formencode/package.py
+++ b/packages/py-formencode/package.py
@@ -12,10 +12,11 @@ class PyFormencode(PythonPackage):
"""
homepage = "https://pypi.org/project/FormEncode"
- pypi = 'FormEncode/FormEncode-2.0.1.tar.gz'
+ pypi = 'FormEncode/FormEncode-2.1.0.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('2.1.0', 'eb74d223078a28cf015fa88966c6e34f2d18d75127318d65c144bed9afc4263f')
version('2.0.1', '8f2974112c2557839d5bae8b76490104c03830785d923abbdef148bf3f710035')
version('2.0.0', 'f2eb92297417eb64e4aa8e368783a5ac1311e385d4f3ff3a181090608ea83711')
diff --git a/packages/py-lems/package.py b/packages/py-lems/package.py
index 12ec0d3c..456c8676 100644
--- a/packages/py-lems/package.py
+++ b/packages/py-lems/package.py
@@ -12,10 +12,11 @@ class PyLems(PythonPackage):
"""
homepage = "https://pypi.org/project/PyLEMS/"
- pypi = 'PyLEMS/PyLEMS-0.6.0.tar.gz'
+ pypi = 'PyLEMS/PyLEMS-0.6.7.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('0.6.7', 'b82b66dbe51206b6c3db915651aadfeb6e8eeb5a95d3114ca8b97725f2fafce6')
version('0.6.0', '809cb1186be18fc0390f9656677847d3a2666cfae816ed82897cc91dfdfa8a1c')
# python_requires
diff --git a/packages/py-pyaescrypt/package.py b/packages/py-pyaescrypt/package.py
index a50fdc18..d0b38eb1 100644
--- a/packages/py-pyaescrypt/package.py
+++ b/packages/py-pyaescrypt/package.py
@@ -12,10 +12,11 @@ class PyPyaescrypt(PythonPackage):
"""
homepage = "https://pypi.org/project/pyAesCrypt"
- pypi = 'pyAesCrypt/pyAesCrypt-6.0.0.tar.gz'
+ pypi = 'pyAesCrypt/pyAesCrypt-6.1.1.tar.gz'
maintainers = ['paulapopa', 'ldomide']
+ version('6.1.1', '6bf8f97c03ec0e42008da911ac25e523f11f160f684d5f2bc9579ce501be9eae')
version('6.0.0', 'a26731960fb24b80bd3c77dbff781cab20e77715906699837f73c9fcb2f44a57')
# python_requires
--
GitLab
From 263d739d122138826df8bafee3a04a2f0dc1104c Mon Sep 17 00:00:00 2001
From: ldomide <lia.domide@codemart.ro>
Date: Fri, 19 Apr 2024 12:52:54 +0300
Subject: [PATCH 3/6] py-bct release 0.6.1 is incomplete (missing tar.gz from
Pypi)
---
packages/py-bct/package.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/packages/py-bct/package.py b/packages/py-bct/package.py
index 1d1472ab..bfa61d91 100644
--- a/packages/py-bct/package.py
+++ b/packages/py-bct/package.py
@@ -12,11 +12,10 @@ class PyBct(PythonPackage):
"""
homepage = "https://pypi.org/project/bctpy/"
- pypi = 'bctpy/bctpy-0.6.1.tar.gz'
+ pypi = 'bctpy/bctpy-0.6.0.tar.gz'
maintainers = ['paulapopa', 'ldomide']
- version('0.6.1', '9c47757596ce386e226353a16ab94e6071a4d3b8acf6c7b2623b45d9e0c5d1a0')
version('0.6.0', '36392049ec5a2ccae75a0cf89b21838fda41a351c31fe6c6622cfcff1c997933')
# python_requires
--
GitLab
From 7b4196b1363c96dfdec2172f0977604345cfea4f Mon Sep 17 00:00:00 2001
From: ldomide <lia.domide@codemart.ro>
Date: Fri, 19 Apr 2024 14:15:59 +0300
Subject: [PATCH 4/6] tvb-framework depends on the latest siibra
---
packages/py-tvb-framework/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-tvb-framework/package.py b/packages/py-tvb-framework/package.py
index aa53677a..0d8c7ac1 100644
--- a/packages/py-tvb-framework/package.py
+++ b/packages/py-tvb-framework/package.py
@@ -54,7 +54,7 @@ class PyTvbFramework(PythonPackage):
depends_on('py-requests', type=('build', 'run'))
depends_on('py-scikit-learn', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
- depends_on('py-siibra', type=('build', 'run'))
+ depends_on('py-siibra@1.0:', type=('build', 'run'))
depends_on('py-simplejson', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
depends_on('py-sqlalchemy', type=('build', 'run'))
--
GitLab
From 3a9b3e28e2b8220e3fb4625bbbb8cd8cbf3d1627 Mon Sep 17 00:00:00 2001
From: ldomide <lia.domide@codemart.ro>
Date: Fri, 19 Apr 2024 14:53:48 +0300
Subject: [PATCH 5/6] keep siibra tests as ignored
---
packages/py-tvb-framework/package.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/packages/py-tvb-framework/package.py b/packages/py-tvb-framework/package.py
index 0d8c7ac1..764ba19a 100644
--- a/packages/py-tvb-framework/package.py
+++ b/packages/py-tvb-framework/package.py
@@ -73,4 +73,6 @@ class PyTvbFramework(PythonPackage):
@on_package_attributes(run_tests=True)
def install_test(self):
pytest = which('pytest')
- pytest()
+ pytest('--ignore', 'tvb/tests/framework/adapters/creators/siibra_base_test.py',
+ '--ignore', 'tvb/tests/framework/adapters/creators/siibra_creator_test.py')
+
--
GitLab
From ad788bb88cfb310953f6932be8d5b4dd04d90123 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 19 Apr 2024 19:43:17 +0300
Subject: [PATCH 6/6] enable new versions
---
spack.yaml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/spack.yaml b/spack.yaml
index 5644d3f7..4dc8dedc 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -46,13 +46,13 @@ spack:
- py-siibra@1.0a9
- py-snudda@2.0.1
- py-spynnaker@7.0.0
- - py-tvb-contrib@2.8.2
+ - py-tvb-contrib@2.9
- py-tvb-data@2.8
- - py-tvb-framework@2.8.2
+ - py-tvb-framework@2.9
- py-tvb-gdist@2.2
- - py-tvb-library@2.8.2
+ - py-tvb-library@2.9
- py-tvb-multiscale@2.1.0.ebrains
- - py-tvb-storage@2.8.1
+ - py-tvb-storage@2.9
- py-viziphant@0.4.0
- pynn-brainscales@8.0-a4
- r-rgsl@0.1.1
--
GitLab