From f5ee942827371bfb891843ff48c2cc84dab8e99e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 15:21:15 +0200 Subject: [PATCH 01/10] adding easyconfigs: netcdf4-python-1.6.4-foss-2023a.eb --- .../netcdf4-python-1.6.4-foss-2023a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb new file mode 100644 index 00000000000..58f5790b23e --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.4' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('netCDF', '4.9.2'), + ('cURL', '8.0.1'), + ('mpi4py', '3.1.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netCDF4-1.6.4.tar.gz': '66da6542cbc7a6045cd1d979397dfd5a3f6c880c76d52b8f98bb108c82ee8c6e'}, + {'netcdf4-python-1.1.8-avoid-diskless-test.patch': + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'}, + {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch': + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From e5428bd469652fa177eeb5281eebbd2f3ead880d Mon Sep 17 00:00:00 2001 From: Jessie Hernandez Date: Fri, 18 Aug 2023 13:50:35 +0200 Subject: [PATCH 02/10] Adding easyconfigs: libedit-20210910-GCCcore-10.3.0 --- .../libedit-20210910-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..42ee25b2a47 --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20210910' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['6792a6a992050762edcca28ff3318cdb7de37dccf7bc30db59fcd7017eed13c5'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' From ba6e76c9bcf01e8f886e98040fc75e78437822d2 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 5 Oct 2023 11:21:17 +0200 Subject: [PATCH 03/10] adding easyconfigs: rasterstats-0.19.0-foss-2022a.eb --- .../rasterstats-0.19.0-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb new file mode 100644 index 00000000000..d9d69d4e77b --- /dev/null +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'rasterstats' +version = '0.19.0' + +homepage = 'https://github.com/perrygeo/python-rasterstats' +description = "rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('Fiona', '1.8.21'), + ('rasterio', '1.3.4'), +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.1', { + 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + (name, version, { + 'checksums': ['066c44feb6f3936804a0c79d112271fa5bf5de0d5058823ab5c1e0047ab7bbbc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From e962a0c0848b5b14f4f1a3582fd1023b10dc94a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 16:22:19 +0200 Subject: [PATCH 04/10] adding easyconfigs: imutils-0.5.4-fosscuda-2020b.eb --- .../i/imutils/imutils-0.5.4-fosscuda-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb new file mode 100644 index 00000000000..0c948731f6f --- /dev/null +++ b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imutils' +version = '0.5.4' + +homepage = 'https://github.com/jrosebr1/imutils' +description = """A series of convenience functions to make basic image processing operations such as translation, +rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['03827a9fca8b5c540305c0844a62591cf35a0caec199cb0f2f0a4a0fb15d8f24'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('OpenCV', '4.5.1', '-contrib'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' From c85ed46b05ab625dee5df4d9b5da7be293fd9171 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 5 Oct 2023 16:40:56 +0200 Subject: [PATCH 05/10] Update easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb index d9d69d4e77b..f235adbb6a0 100644 --- a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -22,9 +22,6 @@ exts_list = [ ('affine', '2.3.1', { 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], }), - ('click', '8.1.3', { - 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], - }), ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], }), From 1665e3f9514ccb145bcec5deea21558dbe535193 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 5 Oct 2023 16:41:03 +0200 Subject: [PATCH 06/10] Update easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb index f235adbb6a0..a2c9fc437b6 100644 --- a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -25,9 +25,6 @@ exts_list = [ ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], }), - ('simplejson', '3.17.6', { - 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], - }), (name, version, { 'checksums': ['066c44feb6f3936804a0c79d112271fa5bf5de0d5058823ab5c1e0047ab7bbbc'], }), From 7ed522cd35f3ac8bfee1a3bd310fcdac3cecd9c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:25:41 +0200 Subject: [PATCH 07/10] adding easyconfigs: uncertainties-3.1.7-foss-2021b.eb --- .../uncertainties-3.1.7-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb new file mode 100644 index 00000000000..21ad86a60e7 --- /dev/null +++ b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'uncertainties' +version = '3.1.7' + +homepage = 'http://uncertainties-python-package.readthedocs.io' +description = """Transparent calculations with uncertainties on the quantities involved (aka error propagation); + fast calculation of derivatives""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 5e64829e2cdddef87958799dbd3646d947cfa24a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:54:11 +0200 Subject: [PATCH 08/10] add ridge extension to R 4.2.2 --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 598a3d2bb3e..5c533ecb998 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3666,6 +3666,9 @@ exts_list = [ ('flextable', '0.9.2', { 'checksums': ['bccd53919ae58f1d26c4a8ee42da1f5e0b7333f8b4ee295b380ed256069f923d'], }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), ] moduleclass = 'lang' From 1e3870559532eae0c41f6adb17f21b66519f73f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 23:08:03 +0200 Subject: [PATCH 09/10] adding easyconfigs: ArviZ-0.16.1-foss-2023a.eb, h5netcdf-1.2.0-foss-2023a.eb, xarray-2023.9.0-gfbf-2023a.eb --- .../a/ArviZ/ArviZ-0.16.1-foss-2023a.eb | 35 +++++++++++++++++++ .../h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb | 28 +++++++++++++++ .../x/xarray/xarray-2023.9.0-gfbf-2023a.eb | 28 +++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb new file mode 100644 index 00000000000..af5291fdab6 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.16.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.4'), + ('xarray', '2023.9.0'), + ('matplotlib', '3.7.2'), + ('h5netcdf', '1.2.0'), +] + +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.6.0', { + 'sources': ['xarray_einstats-%(version)s.tar.gz'], + 'checksums': ['ace90601505cfbe2d374762e674557ed14e1725b024823372f7ef9fd237effad'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['35bab9072f66f5a8204d2a71911d09ce05056c177f1a780de53efa2714c27575'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb new file mode 100644 index 00000000000..311855957b7 --- /dev/null +++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'h5netcdf' +version = '1.2.0' + +homepage = 'https://h5netcdf.org/' +description = """A Python interface for the netCDF4 file-format that reads and writes local or +remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata +netCDF library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('h5py', '3.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['7f6b2733bde06ea2575b79a6450d9bd5c38918ff4cb2a355bf22bbe8c86c6bcf'], + 'preinstallopts': """sed -i 's/^dynamic = .*/version = "%(version)s"/g' pyproject.toml && """, + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb new file mode 100644 index 00000000000..fefb271482f --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2023.9.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['271955c05dc626dad37791a7807d920aaf9c64cac71d03b45ec7e402cc646603'], + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + }), +] + +moduleclass = 'data' From c1be8140469f183bf4fb1a0da9f70b84a79a92fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 23:10:20 +0200 Subject: [PATCH 10/10] {math}[gfbf/2023a] PyTensor v2.17.1 --- .../p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb new file mode 100644 index 00000000000..5ae101c343e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'PyTensor' +version = '2.17.1' + +homepage = 'https://github.com/pymc-devs/pytensor' +description = "Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cons', '0.4.6', { + 'checksums': ['669fe9d5ee916d5e42b9cac6acc911df803d04f2e945c1604982a04d27a29b47'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('etuples', '0.3.9', { + 'checksums': ['a474e586683d8ba8d842ba29305005ceed1c08371a4b4b0e0e232527137e5ea3'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('logical-unification', '0.4.6', { + 'checksums': ['908435123f8a106fa4dcf9bf1b75c7beb309fa2bbecf277868af8f1c212650a0'], + 'modulename': 'unification', + }), + ('miniKanren', '1.0.3', { + 'checksums': ['1ec8bdb01144ad5e8752c7c297fb8a122db920f859276d25a72d164e998d7f6e'], + 'modulename': 'kanren', + }), + (name, version, { + 'sources': ['pytensor-%(version)s.tar.gz'], + 'checksums': ['64855a453b945c52d674086f1d160a35e910efbf13693dfaf0c39e92d474a851'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytensor-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math'