From 18289aa7c7bf24d2fc3eac7f565b2772ffa0b88f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 19 Jun 2024 10:33:58 +0200 Subject: [PATCH 1/5] adding easyconfigs: OpenForceField-Toolkit-0.16.0-foss-2023a.eb --- ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb new file mode 100644 index 00000000000..3ef84650f5e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'OpenForceField-Toolkit' +version = '0.16.0' + +homepage = 'https://github.com/openforcefield/openff-toolkit' +description = """The Open Force Field Toolkit provides implementations of the SMIRNOFF format, +parameterization engine, and other tools.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('poetry', '1.5.1')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('typing-extensions', '4.9.0'), + ('pydantic', '2.5.3'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('PyYAML', '6.0'), + ('RDKit', '2024.03.3'), + ('MDTraj', '1.9.9'), + ('JupyterNotebook', '7.0.2'), + ('AmberTools', '23.6'), + ('Pint', '0.23'), + ('nglview', '3.1.2'), +] + +use_pip = True + +exts_list = [ + ('qcelemental', '0.26.0', { + 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('apsw', '3.46.0.0', { + 'checksums': ['e128ccaab511f9a7fc48be6414f99a9197f83a69624d8ba40c1ca241bdef418e'], + }), + ('zstandard', '0.18.0', { + 'checksums': ['0ac0357a0d985b4ff31a854744040d7b5754385d1f98f7145c30e02c6865cb6f'], + }), + ('qcportal', '0.55', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f6eb86d6ace4ae6a71bbd8e2ee054305aff2c1da0198a3741b0d589c572a31b3'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cachetools', '5.3.3', { + 'checksums': ['ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('bson', '0.5.10', { + 'checksums': ['d6511b2ab051139a9123c184de1a04227262173ad593429d21e443d6462d6590'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('intermol', '0.1.2', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], + }), + ('SMIRNOFF99Frosst', '1.1.0', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], + }), + ('SMIRNOFF-Plugins', '2024.01.0', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], + }), + ('OpenForceField-ForceFields', '2024.04.0', { + 'modulename': 'openforcefields', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], + }), + ('OpenForceField-Amber-FF-Ports', '0.0.4', { + 'modulename': 'openff.amber_ff_ports', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], + }), + ('OpenForceField-Utilities', '0.1.12', { + 'modulename': 'openff.utilities', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], + }), + ('OpenForceField-Units', '0.2.2', { + 'modulename': 'openff.units', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], + }), + ('OpenForceField-NAGL-Models', '0.2.0', { + 'modulename': 'openff.nagl_models', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], + 'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'], + }), + ('OpenForceField-Models', '0.1.2', { + 'modulename': 'openff.models', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], + }), + ('OpenForceField-Interchange', '0.3.27', { + 'modulename': 'openff.interchange', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], + }), + (name, version, { + 'modulename': 'openff.toolkit', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'], + }), +] + +sanity_check_commands = [ + "python -c 'from openff.toolkit import Molecule, Topology, ForceField'", + "python -c 'from openff.interchange import Interchange'", + "python -c 'from openff.units import unit'", + "python -c 'from openff.interchange.components.mdconfig import MDConfig'", + "python -c 'from openff.interchange.models import TopologyKey'", + "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", +] + +sanity_pip_check = True + +moduleclass = 'bio' From f3d65d25392fe06b1b61e404747111869e8d495a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 19 Jul 2024 12:51:00 +0200 Subject: [PATCH 2/5] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index 3ef84650f5e..effa0f88656 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -28,8 +28,6 @@ dependencies = [ ('nglview', '3.1.2'), ] -use_pip = True - exts_list = [ ('qcelemental', '0.26.0', { 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], @@ -139,6 +137,7 @@ sanity_check_commands = [ "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", ] +use_pip = True sanity_pip_check = True moduleclass = 'bio' From b94bb4c5b8df22f68a6b0cdbb75b09b4806520e5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 19 Jul 2024 12:56:25 +0200 Subject: [PATCH 3/5] fix checksum of toolkit --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index effa0f88656..a656f10d6ab 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -28,6 +28,8 @@ dependencies = [ ('nglview', '3.1.2'), ] +use_pip = True + exts_list = [ ('qcelemental', '0.26.0', { 'checksums': ['a14e8510cdbfda645ef1461c1afd02efb599311733dbba5f83fcd1d6168a6ddd'], @@ -124,7 +126,7 @@ exts_list = [ 'modulename': 'openff.toolkit', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], - 'checksums': ['1c1aa2ac9fff7c1613168531884da4ade53cbe21069022c999996d7effd2474c'], + 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], }), ] @@ -137,7 +139,6 @@ sanity_check_commands = [ "python -c 'from openff.toolkit.typing.engines.smirnoff import ForceField'", ] -use_pip = True sanity_pip_check = True moduleclass = 'bio' From 48d40dcb19b97cda7ef44f0fb5685c19068a91e7 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 19 Jul 2024 14:40:22 +0200 Subject: [PATCH 4/5] Update OpenForceField-Toolkit-0.16.0-foss-2023a.eb fix whitespace --- .../OpenForceField-Toolkit-0.16.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index a656f10d6ab..06e5075f674 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -8,7 +8,7 @@ description = """The Open Force Field Toolkit provides implementations of the SM parameterization engine, and other tools.""" toolchain = {'name': 'foss', 'version': '2023a'} - + builddependencies = [('poetry', '1.5.1')] dependencies = [ ('Python', '3.11.3'), From 31713d5c7756cfa95c339420a64b2c2111d8b369 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Aug 2024 16:38:41 +0200 Subject: [PATCH 5/5] update checksum openff-nagl + change to sources --- ...penForceField-Toolkit-0.16.0-foss-2023a.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb index 06e5075f674..f323c61f065 100644 --- a/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/OpenForceField-Toolkit/OpenForceField-Toolkit-0.16.0-foss-2023a.eb @@ -66,66 +66,66 @@ exts_list = [ 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], }), ('intermol', '0.1.2', { - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/shirtsgroup/InterMol/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['a3065133ba16585a5db3807466a36242d191156525c33079cf46a97cedcfe835'], }), ('SMIRNOFF99Frosst', '1.1.0', { - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/smirnoff99Frosst/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['940c4ed3cd720e746549a3335f10b7b0d9047a67bc216ad45dd875be5c8ec467'], }), ('SMIRNOFF-Plugins', '2024.01.0', { - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/smirnoff-plugins/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['8ba4dbc6ed320f06f30bf42e8f70399bc3818becd668990693b51ddca183ff74'], }), ('OpenForceField-ForceFields', '2024.04.0', { 'modulename': 'openforcefields', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-forcefields/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['fc7094cdb74bf9f0ed665dfc716cc62c5a37def3fc7e852adeae0ae4b60169c7'], }), ('OpenForceField-Amber-FF-Ports', '0.0.4', { 'modulename': 'openff.amber_ff_ports', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-amber-ff-ports/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['dbf2d1ccce06b0627b1eccae7e227ad800ff1cbac3e869344de265b178cc0207'], }), ('OpenForceField-Utilities', '0.1.12', { 'modulename': 'openff.utilities', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-utilities/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['92882c5b87b40bdb4ee1e8c84c0ecc0fc83f26eaf3e3befde41bfdcf93d75dea'], }), ('OpenForceField-Units', '0.2.2', { 'modulename': 'openff.units', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-units/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['532746534c1937938580d5cfe98f414aff9bfbcc66970e115a88a38f6d5a2581'], }), ('OpenForceField-NAGL-Models', '0.2.0', { 'modulename': 'openff.nagl_models', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-nagl-models/archive/'], - 'checksums': ['df8e7ee980aa7ea99559759258a16e3aaa362245f5b7c32f9c25fb226eaee222'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['5ccc55d7f0fcd24577796fd8b2bfd85b035ee8060e441c1f7dfc6f1949b9dee5'], }), ('OpenForceField-Models', '0.1.2', { 'modulename': 'openff.models', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-models/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['cf2aa7ef467721f141149e4ce96134db390b27012f09996c4442a3fad2371653'], }), ('OpenForceField-Interchange', '0.3.27', { 'modulename': 'openff.interchange', - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-interchange/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['6b44ba8a89921b3843a5f9fc41dc4f8a0c784ba12221e3ea0fb8c1b01a10cf2e'], }), (name, version, { 'modulename': 'openff.toolkit', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/openforcefield/openff-toolkit/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['70a81e914e86efd933819a5db05fc4400dcd23e12ad29398fdad46f2765b5634'], }), ]