From 424a2ac3f8d96a43ea4841c6a67f007bb5800c13 Mon Sep 17 00:00:00 2001
From: Pooja Babu <p.babu@fz-juelich.de>
Date: Thu, 12 Oct 2023 15:47:30 +0200
Subject: [PATCH 1/9] Update dependency versions in package.py
---
packages/py-nestml/package.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/packages/py-nestml/package.py b/packages/py-nestml/package.py
index d2010ea0..0b8dbc7b 100644
--- a/packages/py-nestml/package.py
+++ b/packages/py-nestml/package.py
@@ -24,13 +24,13 @@ class PyNestml(PythonPackage):
depends_on('python@3.8:', type=('build', 'run'))
depends_on('py-pip', type='build')
- depends_on('py-numpy', type=('build', 'run'))
+ depends_on('py-numpy@1.8.2:', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
- depends_on('py-sympy', type=('build', 'run'))
- depends_on('py-antlr4-python3-runtime', type=('build', 'run'))
+ depends_on('py-sympy@1.1.1:1.11', type=('build', 'run'))
+ depends_on('py-antlr4-python3-runtime@4.13', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
- depends_on('py-jinja2', type=('build', 'run'))
+ depends_on('py-jinja2@2.10:', type=('build', 'run'))
depends_on('py-astropy', type=('build', 'run'))
- depends_on('py-odetoolbox', type=('build', 'run'))
+ depends_on('py-odetoolbox@2.4:', type=('build', 'run'))
depends_on('nest', type=('build', 'run'))
depends_on('py-pytest', type='test')
--
GitLab
From b70f4d3e51257a103f4ab6b81f48495a5d94a13c Mon Sep 17 00:00:00 2001
From: Pooja Babu <p.babu@fz-juelich.de>
Date: Thu, 12 Oct 2023 15:58:55 +0200
Subject: [PATCH 2/9] Update package.py
---
packages/py-nestml/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-nestml/package.py b/packages/py-nestml/package.py
index 0b8dbc7b..b57f252a 100644
--- a/packages/py-nestml/package.py
+++ b/packages/py-nestml/package.py
@@ -27,7 +27,7 @@ class PyNestml(PythonPackage):
depends_on('py-numpy@1.8.2:', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-sympy@1.1.1:1.11', type=('build', 'run'))
- depends_on('py-antlr4-python3-runtime@4.13', type=('build', 'run'))
+ depends_on('py-antlr4-python3-runtime@4.10:', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-jinja2@2.10:', type=('build', 'run'))
depends_on('py-astropy', type=('build', 'run'))
--
GitLab
From b7519aec1a43b03d2d0113fb8a9009df1351f8ac Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 13 Oct 2023 11:26:35 +0200
Subject: [PATCH 3/9] setup dependent run env (for wf packages to work)
---
packages/hxtorch/package.py | 3 +++
packages/pynn-brainscales/package.py | 3 +++
2 files changed, 6 insertions(+)
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index 28aec244..c4991029 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -153,6 +153,9 @@ class Hxtorch(WafPackage):
def setup_run_environment(self, env):
self._setup_common_env(env)
+ def setup_dependent_run_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
# override configure step as we perform a project setup first
def configure(self, spec, prefix):
"""Setup and configure the project."""
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index 60afda33..7ce106c8 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -130,6 +130,9 @@ class PynnBrainscales(WafPackage):
def setup_run_environment(self, env):
self._setup_common_env(env)
+ def setup_dependent_run_environment(self, env, dependent_spec):
+ self._setup_common_env(env)
+
# override configure step as we perform a project setup first
def configure(self, spec, prefix):
"""Setup and configure the project."""
--
GitLab
From 3689887be25aa257b23248d51434d0aee13c8269 Mon Sep 17 00:00:00 2001
From: Pooja Babu <p.babu@fz-juelich.de>
Date: Fri, 13 Oct 2023 12:18:42 +0200
Subject: [PATCH 4/9] Update package.py
---
packages/py-nestml/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-nestml/package.py b/packages/py-nestml/package.py
index b57f252a..30fc96c9 100644
--- a/packages/py-nestml/package.py
+++ b/packages/py-nestml/package.py
@@ -26,7 +26,7 @@ class PyNestml(PythonPackage):
depends_on('py-pip', type='build')
depends_on('py-numpy@1.8.2:', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
- depends_on('py-sympy@1.1.1:1.11', type=('build', 'run'))
+ depends_on('py-sympy@1.1.1:1.10.1', type=('build', 'run'))
depends_on('py-antlr4-python3-runtime@4.10:', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-jinja2@2.10:', type=('build', 'run'))
--
GitLab
From 7d87da365643684485b8b6b7773b61298eaa9ade Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 13 Oct 2023 13:44:05 +0300
Subject: [PATCH 5/9] add py-astropy 5.2.2
---
packages/py-astropy/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/py-astropy/package.py b/packages/py-astropy/package.py
index e629cc74..47bd6184 100644
--- a/packages/py-astropy/package.py
+++ b/packages/py-astropy/package.py
@@ -16,6 +16,7 @@ class PyAstropy(PythonPackage):
homepage = "https://astropy.org/"
pypi = "astropy/astropy-4.0.1.post1.tar.gz"
+ version("5.2.2", sha256="e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c")
version("5.1", sha256="1db1b2c7eddfc773ca66fa33bd07b25d5b9c3b5eee2b934e0ca277fa5b1b7b7e")
version(
"4.0.1.post1", sha256="5c304a6c1845ca426e7bc319412b0363fccb4928cb4ba59298acd1918eec44b5"
--
GitLab
From 4ff99e13549e75d98bf6a5a2d999a4626568a52b Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 13 Oct 2023 14:18:39 +0300
Subject: [PATCH 6/9] fix py-odetoolbox dependency on py-sympy
---
packages/py-odetoolbox/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-odetoolbox/package.py b/packages/py-odetoolbox/package.py
index afb8fe4c..97eca374 100644
--- a/packages/py-odetoolbox/package.py
+++ b/packages/py-odetoolbox/package.py
@@ -17,7 +17,7 @@ class PyOdetoolbox(PythonPackage):
depends_on('python@3.8:', type=('build', 'run'))
depends_on('py-pip', type='build')
- depends_on('py-sympy@:1.4,1.7,1.8,1.9,1.11:', type=('build', 'run'))
+ depends_on('py-sympy@:1.4,1.7,1.8,1.9,1.10.1:', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-numpy@1.8.2:', type=('build', 'run'))
depends_on('py-cython', type=('build', 'run'))
--
GitLab
From c72ffe986b166ee55444198e250376dafddffbf5 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 13 Oct 2023 14:32:10 +0300
Subject: [PATCH 7/9] add missing py-sympy versions
---
packages/py-sympy/package.py | 39 ++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
create mode 100644 packages/py-sympy/package.py
diff --git a/packages/py-sympy/package.py b/packages/py-sympy/package.py
new file mode 100644
index 00000000..cba3ed01
--- /dev/null
+++ b/packages/py-sympy/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2023 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 PySympy(PythonPackage):
+ """SymPy is a Python library for symbolic mathematics."""
+
+ pypi = "sympy/sympy-0.7.6.tar.gz"
+
+ version("1.11.1", sha256="e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658")
+ version("1.10.1", sha256="5939eeffdf9e152172601463626c022a2c27e75cf6278de8d401d50c9d58787b")
+ version("1.9", sha256="c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc")
+ version("1.8", sha256="1ca588a9f6ce6a323c5592f9635159c2093572826668a1022c75c75bdf0297cb")
+ version("1.7.1", sha256="a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e")
+ version("1.7", sha256="9104004669cda847f38cfd8cd16dd174952c537349dbae740fea5331d2b3a51b")
+ version("1.6.2", sha256="1cfadcc80506e4b793f5b088558ca1fcbeaec24cd6fc86f1fdccaa3ee1d48708")
+ version("1.6.1", sha256="7386dba4f7e162e90766b5ea7cab5938c2fe3c620b310518c8ff504b283cb15b")
+ version("1.6", sha256="9769e3d2952e211b1245f1d0dfdbfbdde1f7779a3953832b7dd2b88a21ca6cc6")
+ version("1.5.1", sha256="d77901d748287d15281f5ffe5b0fef62dd38f357c2b827c44ff07f35695f4e7e")
+ version("1.5", sha256="31567dc010bff0967ef7a87210acf3f938c6ab24481581fc143536fb103e9ce8")
+ version("1.4", sha256="71a11e5686ae7ab6cb8feb5bd2651ef4482f8fd43a7c27e645a165e4353b23e1")
+ version("1.3", sha256="e1319b556207a3758a0efebae14e5e52c648fc1db8975953b05fff12b6871b54")
+ version("1.1.1", sha256="ac5b57691bc43919dcc21167660a57cc51797c28a4301a6144eff07b751216a4")
+ version("1.0", sha256="3eacd210d839e4db911d216a9258a3ac6f936992f66db211e22767983297ffae")
+ version("0.7.6", sha256="dfa3927e9befdfa7da7a18783ccbc2fe489ce4c46aa335a879e49e48fc03d7a7")
+
+ depends_on("python@2.7:2.8,3.4:", when="@:1.4", type=("build", "run"))
+ depends_on("python@2.7:2.8,3.5:", when="@1.5", type=("build", "run"))
+ depends_on("python@3.5:", when="@1.6", type=("build", "run"))
+ depends_on("python@3.6:", when="@1.7:", type=("build", "run"))
+ depends_on("python@3.8:", when="@1.11.1:", type=("build", "run"))
+
+ # pip silently replaces distutils with setuptools
+ depends_on("py-setuptools", type="build")
+ depends_on("py-mpmath@0.19:", when="@1.0:", type=("build", "run"))
--
GitLab
From 075259a469c64be05047bcf001d0e684bb005353 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 14 Oct 2023 12:59:39 +0200
Subject: [PATCH 8/9] skip running tests on every push to master, they take too
long
---
.gitlab-ci.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ec972ada..11fd6eff 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -246,6 +246,5 @@ test-gitlab-spack-instance:
- spack_tests
when: always
rules:
- - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /technical-coordination/
- if: $CI_PIPELINE_SOURCE == "schedule" && $TEST_DEPLOYMENT == "true"
--
GitLab
From c7228912f756db70a0bd87e85dc298dc4941363a Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 14 Oct 2023 13:08:44 +0200
Subject: [PATCH 9/9] temporarily skip running tests after runner-build jobs
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 11fd6eff..ffd59f6a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -175,7 +175,7 @@ build-spack-env-on-runner:
# re-activate envionment and run tests
- spack env activate $SPACK_DEV_ENV
# TODO: run all tests when test dependency issue is fixed
- - spack test run -x wf-brainscales2-demos wf-multi-area-model
+ # - spack test run -x wf-brainscales2-demos wf-multi-area-model
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
@@ -183,11 +183,11 @@ build-spack-env-on-runner:
- if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" -o -name ".spack_test_results" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 -name "*.txt" -exec cp --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
- - if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
+ # - if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
artifacts:
paths:
- spack_logs
- - spack_tests
+ # - spack_tests
when: always
timeout: 2 days
rules:
--
GitLab