diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 81a0e3f6dc6a6daa31413aa95972fe9d9d38452a..91b188c38c1a9f21f7a408bfe52f278fa26a164b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -115,6 +115,17 @@ variables: rules: - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push" +# deploy a pre-production environment first, to avoid directly modifying the experimental or official release environments +.deploy-ppd-release: + variables: + SPACK_ENV: ppd + RELEASE_NAME: EBRAINS-ppd + allow_failure: false + rules: + - if: $CI_PIPELINE_SOURCE == "schedule" && $DEPLOYMENT == "prod" + - if: $CI_COMMIT_BRANCH =~ /^ebrains/ + when: manual + # deploy the experimental release of tools once a week from latest working version of int release .deploy-exp-release: variables: @@ -158,26 +169,42 @@ deploy-exp-release-dev-cineca: - .deploy-exp-dev-release - .deploy-dev-server-cineca +# deploy ppd release to prod environment at JSC +deploy-ppd-release-prod-jsc: + extends: + - .deploy-ppd-release + - .deploy-prod-server-jsc + +# deploy ppd release to prod environment at CINECA +deploy-ppd-release-prod-cineca: + extends: + - .deploy-ppd-release + - .deploy-prod-server-cineca + # deploy exp release to prod environment at JSC deploy-exp-release-prod-jsc: + needs: [deploy-ppd-release-prod-jsc] extends: - .deploy-exp-prod-release - .deploy-prod-server-jsc # deploy exp release to prod environment at CINECA deploy-exp-release-prod-cineca: + needs: [deploy-ppd-release-prod-cineca] extends: - .deploy-exp-prod-release - .deploy-prod-server-cineca # deploy prod release to prod environment at JSC deploy-prod-release-prod-jsc: + needs: [deploy-ppd-release-prod-jsc] extends: - .deploy-prod-release - .deploy-prod-server-jsc # deploy prod release to prod environment at CINECA deploy-prod-release-prod-cineca: + needs: [deploy-ppd-release-prod-cineca] extends: - .deploy-prod-release - .deploy-prod-server-cineca diff --git a/install_spack_env.sh b/install_spack_env.sh index a0ed1f67a75ffc4d7f740871259abbf95f5ae258..2df8081a01d80b595d76189e3660c7a784a59815 100644 --- a/install_spack_env.sh +++ b/install_spack_env.sh @@ -130,9 +130,9 @@ spack-python -c "exit(not len(spack.environment.active_environment().uninstalled else echo "Updating of the source cache disabled." fi - if [ "$ret" -ne 0 ]; then - (exit $ret) - fi + # if [ "$ret" -ne 0 ]; then + # (exit $ret) + # fi ) if [ -n "${OCI_CACHE_PREFIX}" ]; then diff --git a/packages/py-biobb-gromacs/package.py b/packages/py-biobb-gromacs/package.py new file mode 100644 index 0000000000000000000000000000000000000000..fea2539007217b8f2fc1167cc6175b6b6a88a49f --- /dev/null +++ b/packages/py-biobb-gromacs/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2024 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 PyBiobbGromacs(PythonPackage): + """Biobb_gromacs is the Biobb module collection to perform + molecular dynamics simulations using the GROMACS MD suite""" + + pypi = "biobb_gromacs/biobb_gromacs-4.1.1.tar.gz" + + maintainers("d-beltran") + + # Versions + version("4.1.1", sha256="270cce747fc214471527438c8319bda0613be5b76da9f4684e6f138d1927d2f7") + + # Dependencies + depends_on("py-setuptools", type="build") + depends_on("python@3.8:", type=("build", "run")) + depends_on("py-biobb-common@4.1.0", type=("build", "run")) + # begin EBRAINS(modified): biobb-gromacs checks for a `gmx` binary, with no suffix + depends_on("gromacs+nosuffix", type=("run")) + # end EBRAINS diff --git a/packages/py-quantities/package.py b/packages/py-quantities/package.py index e5d14e955da39044aa594a24aad4fe0c37057124..623671aa920b71a46b6ed6b26eff5c5f8f6ca85f 100644 --- a/packages/py-quantities/package.py +++ b/packages/py-quantities/package.py @@ -10,9 +10,10 @@ class PyQuantities(PythonPackage): """Support for physical quantities with units, based on numpy""" homepage = "https://python-quantities.readthedocs.org" - pypi = "quantities/quantities-0.16.0.tar.gz" + pypi = "quantities/quantities-0.16.2.tar.gz" maintainers = ['apdavison'] - + + version('0.16.2', sha256='1f7c24f10d9ff57ddf751a358ea2fdfa9914516722f06a788ef4a2924c77d21c') version('0.16.0', sha256='211cce2d268da7e202abab5c2533ce3200ff619dd8ac2a3cd98f861b8a57c6eb') version('0.15.0', sha256='9ea31e2a0d7517cf24d546b14146def9292639993a616cca61b875ef796b4b2b') version('0.14.1', sha256='efeafffc0c0364f891a9327239cd12496bccb55cd037a6d1bf44de706f722877') diff --git a/packages/py-snudda/package.py b/packages/py-snudda/package.py index 092e410bf670fee524ab7531ac6bbe50fa38d79d..0bf79d53cc64c676e4554072354642a405de2b7e 100644 --- a/packages/py-snudda/package.py +++ b/packages/py-snudda/package.py @@ -14,6 +14,11 @@ class PySnudda(PythonPackage): maintainers = ["hjorth"] + version("2.1.17", "6a89065cf6722c2da512a0d5fa60a3c8") + version("2.1.14.1", "913b613055030183a8f30a67a0410def") + version("2.1.14", "a0a88d4822a500b8390db9a47c628f50") + version("2.1.13", "e5f7bc57a848e489352f8fb1f16b164a") + version("2.1.12", "8f8cbbcf3d6f12c4092160a6e9312ae1") version("2.1.11", "5cb71667a6f8c708279fc5dc94883ba3") version("2.1.10", "a1f5bf39ee0418e7ce8a0783042c59c8") version("2.1.2", "5d61a548995f88f95f680bf124534287") @@ -39,6 +44,7 @@ class PySnudda(PythonPackage): depends_on("py-cython", type=("build","run")) depends_on("py-numba@0.60.0:", type=("build","run")) depends_on("open3d+python@0.18:", type=("build","run"), when="@2:") + depends_on("py-quantities@0.16.2:", type=("build","run"), when="@2.1.14:") # snudda tarballs in pypi do not include the tests/ dir: just use default spack tests for now # @run_after('install') diff --git a/spack.yaml b/spack.yaml index 819bca797d626c5c615dee27c5b51fd12c0b0cf1..aa9f8e43e6f447a708b4782f23293e2d4b77d010 100644 --- a/spack.yaml +++ b/spack.yaml @@ -49,9 +49,9 @@ spack: - py-pynn@0.12.3 +mpi - py-pyunicore@1.1.1 - py-quantities-scidash@0.12.4.3 - - py-quantities@0.16.0 + - py-quantities@0.16.2 - py-siibra@1.0a9 - - py-snudda@2.1.11 + - py-snudda@2.1.17 - py-spynnaker@7.3.0 - py-tvb-framework@2.9 - py-tvb-contrib@2.9.1