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Commit 088e000d authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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feat(biobb): align packages with Spack upstream

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3 merge requests!651create new experimental release,!650update spack version to v0.23.1,!633update spack version to v0.23.0
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packages/biobb-common/package.py deleted 100644 → 0
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# 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 import *
class BiobbCommon(PythonPackage):
"""Biobb_common is the base package required to use the biobb packages"""
# 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('master', branch='master')
version('4.0.0', sha256='fff990dce42ded2af3d587567dbf5321b1498f12f24d04d62003f9869d6eb8fe')
# Dependencies
depends_on('py-setuptools')
depends_on('python@3.8:', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
# Custom patch to enable python 3.10.8 for this package
def patch(self):
filter_file(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_common')
packages/biobb-gromacs/package.py deleted 100644 → 0
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− 37
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# 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 import *
class BiobbGromacs(PythonPackage):
"""Biobb_gromacs is the Biobb module collection to perform molecular
dynamics simulations using Gromacs"""
# 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'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('4.0.0', sha256='87f9079ec8b72ff43cd1b388a06fee5b1f64bb4080ffab110941f3c6d155ef0b')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('biobb-common')
depends_on('gromacs')
# 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")
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_gromacs')
packages/biobb-io/package.py deleted 100644 → 0
+ 0
− 42
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# 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 import *
class BiobbIo(PythonPackage):
"""Biobb_io is the Biobb module collection to fetch data to be
consumed by the rest of the Biobb building blocks"""
# 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'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('4.0.0', sha256='600a30f14b1a0e21f57775ba1be695e1595f5702237415fe90d7c531b5a0408a')
# Dependencies
depends_on('biobb-common')
depends_on('python@3.8:', type=('build', 'run'))
# 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(
"'Programming Language :: Python :: 3.9'",
"'Programming Language :: Python :: 3.9',\r\n "
"'Programming Language :: Python :: 3.10'",
"setup.py",
)
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_io')
packages/biobb-model/package.py deleted 100644 → 0
+ 0
− 43
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# 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 import *
class BiobbModel(PythonPackage):
"""Biobb_model is the Biobb module collection to check and model 3d structures,
create mutations or reconstruct missing atoms"""
# 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'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('4.0.0', sha256='92387725b7ccd3f40d18c1d3e30a6169ca4204ba498ac72e25c9e701b1a89d91')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('biobb-common')
depends_on('biobb-structure-checking')
# 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(
"'Programming Language :: Python :: 3.9'",
"'Programming Language :: Python :: 3.9',\r\n "
"'Programming Language :: Python :: 3.10'",
"setup.py",
)
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_model')
packages/biobb-structure-checking/package.py deleted 100644 → 0
+ 0
− 36
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# 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 import *
class BiobbStructureChecking(PythonPackage):
"""Biobb_structure_checking performs a checking of the quality of a
3D structure intended to facilitate the setup of molecular dynamics
simulation of protein or nucleic acids systems"""
# 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'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('3.12.1', sha256='ef3e6fe5f7763e534c91fac00bf873c3d88bcca18be7a63c63608dceb36f3d40')
# Dependencies
depends_on('py-setuptools')
depends_on('python@3.8:', type=('build', 'run'))
depends_on('py-psutil', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_structure_checking')
packages/biobb-structure-utils/package.py deleted 100644 → 0
+ 0
− 43
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# 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 import *
class BiobbStructureUtils(PythonPackage):
"""Biobb_structure_utils is the Biobb module collection to modify
or extract information from a PDB structure file."""
# 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'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('4.0.0', sha256='f328eee2166631e1cc514118eb41187620c358c8024431ce2a0b0e4547692c47')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('biobb-common')
depends_on('biobb-structure-checking')
# 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(
"'Programming Language :: Python :: 3.9'",
"'Programming Language :: Python :: 3.9',\r\n "
"'Programming Language :: Python :: 3.10'",
"setup.py",
)
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import biobb_structure_utils')
packages/biobb-analysis/package.py → packages/py-biobb-analysis/package.py
+ 2
− 2
View file @ 088e000d
......@@ -5,7 +5,7 @@
from spack import *
class BiobbAnalysis(PythonPackage):
class PyBiobbAnalysis(PythonPackage):
"""Biobb_analysis is the Biobb module collection to perform analysis
of molecular dynamics simulations"""
......@@ -23,7 +23,7 @@ class BiobbAnalysis(PythonPackage):
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('biobb-common')
depends_on('py-biobb-common')
depends_on('gromacs')
depends_on('ambertools')
......
packages/biobb-chemistry/package.py → packages/py-biobb-chemistry/package.py
+ 2
− 2
View file @ 088e000d
......@@ -5,7 +5,7 @@
from spack import *
class BiobbChemistry(PythonPackage):
class PyBiobbChemistry(PythonPackage):
"""Biobb_chemistry is the Biobb module collection to perform chemistry
over molecular dynamics simulations."""
......@@ -23,7 +23,7 @@ class BiobbChemistry(PythonPackage):
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('biobb-common')
depends_on('py-biobb-common')
depends_on('openbabel')
depends_on('ambertools')
depends_on('acpype')
......
spack.yaml
+ 8
− 8
View file @ 088e000d
......@@ -4,14 +4,14 @@ spack:
specs:
# EBRAINS tools
- arbor@0.9.0 +python +mpi
- biobb-analysis@4.0.1
- biobb-chemistry@4.0.0
- biobb-common@4.0.0
- biobb-gromacs@4.0.0
- biobb-io@4.0.0
- biobb-model@4.0.0
- biobb-structure-checking@3.12.1
- biobb-structure-utils@4.0.0
- py-biobb-analysis@4.0.1
- py-biobb-chemistry@4.0.0
- py-biobb-common@4.1.0
- py-biobb-gromacs@4.1.1
- py-biobb-io@4.1.0
- py-biobb-model@4.1.0
- py-biobb-structure-checking@3.13.4
- py-biobb-structure-utils@4.1.0
- hxtorch@9.0-a8
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
......
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