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Commit e4049f83 authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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Merge branch 'backports-ebrains-23-06' into 'ebrains-23-06' 

Backports for ebrains 23 06

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!458
parents 31d5bb1b 7ce8bc77
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1 merge request!458Backports for ebrains 23 06
Pipeline #26084 waiting for manual action with stage
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.gitlab-ci.yml
+ 5
− 2
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......@@ -242,7 +242,7 @@ sync-gitlab-spack-instance:
- read-write
image: $GITLAB_BUILD_ENV_DOCKER_IMAGE
variables:
SPACK_NFS_ENV: ebrains-runner-build
SPACK_NFS_ENV: $CI_COMMIT_BRANCH
SPACK_PATH: $SPACK_PATH_GITLAB
SPACK_USER_CACHE_PATH: $SPACK_PATH/spack/.spack
SPACK_USER_CONFIG_PATH: $SPACK_PATH/spack/.spack
......@@ -283,6 +283,9 @@ sync-gitlab-spack-instance:
- spack env activate $SPACK_NFS_ENV
- spack install -y -j2 --fresh --test root
- spack reindex
# create kernel spec, so that the environment can be used in gitlab CI jobs
- RELEASE_NAME=$(case $CI_COMMIT_BRANCH in experimental_rel) echo ebrains-experimental;; ebrains*) echo ${CI_COMMIT_BRANCH:0:10}.${CI_COMMIT_BRANCH:11};; *) echo $CI_COMMIT_BRANCH;; esac);
- . create_JupyterLab_kernel.sh $SPACK_PATH_GITLAB $SPACK_NFS_ENV $RELEASE_NAME /mnt/ebrains_env
after_script:
- mkdir spack_logs
- |
......@@ -305,5 +308,5 @@ sync-gitlab-spack-instance:
- spack_logs
when: always
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /technical-coordination/
- if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_NAMESPACE =~ /technical-coordination/
when: manual
create_JupyterLab_kernel.sh
+ 2
− 0
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......@@ -28,6 +28,8 @@ EOF
# (2) append the necessary env variables for spack env and tools
cat $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh >> $KERNEL_PATH/bin/env.sh
# also copy the script so that it can be used independently:
cp $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh $KERNEL_PATH/bin/
# (3) also add the user's .local locations to allow package installation at runtime,
# and the location of python modules installed in the base docker Collab image
......
packages/biobb-analysis/package.py
+ 3
− 1
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......@@ -7,12 +7,14 @@ class BiobbAnalysis(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_analysis"
git = 'https://github.com/bioexcel/biobb_analysis.git'
url = 'https://github.com/bioexcel/biobb_analysis/archive/refs/tags/v4.0.1.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('4.0.1', branch='master')
version('master', branch='master')
version('4.0.1', sha256='3d7190d0cae6af42b2e7c0ecf073930a609b699ef311e8b74afc1634958e09b0')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
......
packages/biobb-chemistry/package.py
+ 3
− 1
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......@@ -7,12 +7,14 @@ class BiobbChemistry(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_chemistry"
git = 'https://github.com/bioexcel/biobb_chemistry.git'
url = 'https://github.com/bioexcel/biobb_chemistry/archive/refs/tags/v4.0.0.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='40f65b4a93dff24e19995265e41fd6821f5ac2f35199d938f1d00fa035883e64')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
......
packages/biobb-common/package.py
+ 3
− 1
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......@@ -6,12 +6,14 @@ class BiobbCommon(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_common"
git = 'https://github.com/bioexcel/biobb_common.git'
url = 'https://github.com/bioexcel/biobb_common/archive/refs/tags/v4.0.0.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='fff990dce42ded2af3d587567dbf5321b1498f12f24d04d62003f9869d6eb8fe')
# Dependencies
depends_on('py-setuptools')
......
packages/biobb-gromacs/package.py
+ 4
− 2
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......@@ -7,9 +7,11 @@ class BiobbGromacs(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_gromacs"
git = 'https://github.com/bioexcel/biobb_gromacs.git'
url = 'https://github.com/bioexcel/biobb_gromacs/archive/refs/tags/v4.0.0.tar.gz'
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='87f9079ec8b72ff43cd1b388a06fee5b1f64bb4080ffab110941f3c6d155ef0b')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
......@@ -18,7 +20,7 @@ class BiobbGromacs(PythonPackage):
# 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(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
# Test
@run_after('install')
......
packages/biobb-io/package.py
+ 3
− 1
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......@@ -7,9 +7,11 @@ class BiobbIo(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_io"
git = 'https://github.com/bioexcel/biobb_io.git'
url = 'https://github.com/bioexcel/biobb_io/archive/refs/tags/v4.0.0.tar.gz'
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='600a30f14b1a0e21f57775ba1be695e1595f5702237415fe90d7c531b5a0408a')
# Dependencies
depends_on('biobb-common')
......
packages/biobb-model/package.py
+ 4
− 2
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......@@ -7,9 +7,11 @@ class BiobbModel(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_model"
git = 'https://github.com/bioexcel/biobb_model.git'
url = 'https://github.com/bioexcel/biobb_model/archive/refs/tags/v4.0.0.tar.gz'
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='92387725b7ccd3f40d18c1d3e30a6169ca4204ba498ac72e25c9e701b1a89d91')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
......@@ -18,7 +20,7 @@ class BiobbModel(PythonPackage):
# 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(" 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 "
......
packages/biobb-structure-checking/package.py
+ 3
− 1
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......@@ -8,9 +8,11 @@ class BiobbStructureChecking(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_structure_checking"
git = 'https://github.com/bioexcel/biobb_structure_checking.git'
url = 'https://github.com/bioexcel/biobb_structure_checking/archive/refs/tags/v3.12.1.tar.gz'
# Versions
version('3.12.1', branch='master')
version('master', branch='master')
version('3.12.1', sha256='ef3e6fe5f7763e534c91fac00bf873c3d88bcca18be7a63c63608dceb36f3d40')
# Dependencies
depends_on('py-setuptools')
......
packages/biobb-structure-utils/package.py
+ 4
− 2
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......@@ -7,9 +7,11 @@ class BiobbStructureUtils(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_structure_utils"
git = 'https://github.com/bioexcel/biobb_structure_utils.git'
url = 'https://github.com/bioexcel/biobb_structure_utils/archive/refs/tags/v4.0.0.tar.gz'
# Versions
version('4.0.0', branch='master')
version('master', branch='master')
version('4.0.0', sha256='f328eee2166631e1cc514118eb41187620c358c8024431ce2a0b0e4547692c47')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
......@@ -18,7 +20,7 @@ class BiobbStructureUtils(PythonPackage):
# 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(" 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 "
......
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