{bio}[foss/2023b] Mustache v1.3.3, hic-straw v1.3.1, cooler v0.10.2, multiprocess v0.70.16 by pavelToman · Pull Request #21783 · easybuilders/easybuild-easyconfigs

pavelToman · 2024-11-04T18:18:24Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#442
requires dill-0.3.8 from:

…-foss-2023b.eb, cooler-0.10.2-foss-2023b.eb, multiprocess-0.70.16-gfbf-2023b.eb

boegel · 2024-11-08T10:50:27Z

I've opened a separate PR for dill, so once that's merged this one should be ready to go:

{data}[GCCcore/13.2.0] dill v0.3.8 #21808

…asyconfigs into 20241104191820_new_pr_mustache-hic133

github-actions · 2024-11-08T12:28:06Z

Updated software `cooler-0.10.2-foss-2023b.eb`

Diff against cooler-0.10.2-foss-2023a.eb

easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb
index 57091228de..f092666e99 100644
--- a/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb
@@ -7,18 +7,21 @@ homepage = 'https://open2c.github.io/cooler'
 description = """Cooler is a support library for a storage format, also called cooler, used to store
  genomic interaction data of any size, such as Hi-C contact matrices."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 builddependencies = [
     ('hatchling', '1.18.0'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('h5py', '3.9.0'),
-    ('PyYAML', '6.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
+    ('PyYAML', '6.0.1'),
     ('pyfaidx', '0.8.1.1'),
+    ('dill', '0.3.8'),
+    ('multiprocess', '0.70.16'),
 ]
 
 use_pip = True
@@ -27,17 +30,11 @@ exts_list = [
     ('asciitree', '0.3.3', {
         'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'],
     }),
-    ('toolz', '0.12.0', {
-        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    ('toolz', '1.0.0', {
+        'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'],
     }),
-    ('cytoolz', '0.12.3', {
-        'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'],
-    }),
-    ('dill', '0.3.8', {
-        'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'],
-    }),
-    ('multiprocess', '0.70.16', {
-        'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'],
+    ('cytoolz', '1.0.0', {
+        'checksums': ['eb453b30182152f9917a5189b7d99046b6ce90cdf8aeb0feff4b2683e600defd'],
     }),
     (name, version, {
         'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'],

Diff against cooler-0.9.1-foss-2022a.eb

easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb
index 75afbccdba..f092666e99 100644
--- a/easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/cooler/cooler-0.10.2-foss-2023b.eb
@@ -1,46 +1,43 @@
 easyblock = 'PythonBundle'
 
 name = 'cooler'
-version = '0.9.1'
+version = '0.10.2'
 
 homepage = 'https://open2c.github.io/cooler'
 description = """Cooler is a support library for a storage format, also called cooler, used to store
  genomic interaction data of any size, such as Hi-C contact matrices."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('h5py', '3.7.0'),
-    ('PyYAML', '6.0'),
-    ('pyfaidx', '0.7.1'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
+    ('PyYAML', '6.0.1'),
+    ('pyfaidx', '0.8.1.1'),
+    ('dill', '0.3.8'),
+    ('multiprocess', '0.70.16'),
 ]
 
 use_pip = True
 
 exts_list = [
-    # cooler 0.9.1 requires setuptools >= 64.0
-    ('setuptools', '67.2.0', {
-        'checksums': ['b440ee5f7e607bb8c9de15259dba2583dd41a38879a7abc1d43a71c59524da48'],
-    }),
     ('asciitree', '0.3.3', {
         'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'],
     }),
-    ('toolz', '0.12.0', {
-        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
-    }),
-    ('cytoolz', '0.12.1', {
-        'checksums': ['fc33909397481c90de3cec831bfb88d97e220dc91939d996920202f184b4648e'],
-    }),
-    ('dill', '0.3.6', {
-        'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'],
+    ('toolz', '1.0.0', {
+        'checksums': ['2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02'],
     }),
-    ('multiprocess', '0.70.14', {
-        'checksums': ['3eddafc12f2260d27ae03fe6069b12570ab4764ab59a75e81624fac453fbf46a'],
+    ('cytoolz', '1.0.0', {
+        'checksums': ['eb453b30182152f9917a5189b7d99046b6ce90cdf8aeb0feff4b2683e600defd'],
     }),
     (name, version, {
-        'checksums': ['e29ee54797c71c5e3af520772e32d664e7fd09318f15c318777dd62125b15731'],
+        'checksums': ['3780a2e69b2ec89882dfc2775de5d9b54ccb79569dc5f042b4851599388112dc'],
     }),
 ]

Updated software `hic-straw-1.3.1-foss-2023b.eb`

Diff against hic-straw-1.3.1-foss-2022a.eb

easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2022a.eb b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb
index e713ea6337..4a9b159e99 100644
--- a/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/h/hic-straw/hic-straw-1.3.1-foss-2023b.eb
@@ -6,28 +6,24 @@ version = '1.3.1'
 homepage = 'https://github.com/aidenlab/straw'
 description = "Straw is a library which allows rapid streaming of contact data from .hic files."
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['fb0f878127f6b1d096303c67793477c83fddf3f4a1a8e29a9d92952634989876']
 
-builddependencies = [('pybind11', '2.9.2')]
+builddependencies = [('pybind11', '2.11.1')]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('cURL', '7.83.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('cURL', '8.3.0'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 download_dep_fail = True
 
-sanity_check_paths = {
-    'files': [],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
 options = {'modulename': 'hicstraw'}
 
 moduleclass = 'bio'

Updated software `multiprocess-0.70.16-gfbf-2023b.eb`

Diff against multiprocess-0.70.15-gfbf-2022b.eb

easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb
index 2bac0d9bfe..956b6c8610 100644
--- a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb
@@ -1,20 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'multiprocess'
-version = '0.70.15'
+version = '0.70.16'
 
 homepage = 'https://github.com/uqfoundation/multiprocess'
 description = "better multiprocessing and multithreading in python"
 
-toolchain = {'name': 'gfbf', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e']
+checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1']
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('dill', '0.3.7'),
-    ('Arrow', '11.0.0'),  # if needed rebuild --from-pr 19758
+    ('Python', '3.11.5'),
+    ('dill', '0.3.8'),
+    ('Arrow', '16.1.0'),
 ]
 
 download_dep_fail = True

Diff against multiprocess-0.70.15-gfbf-2023a.eb

easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb
index 631ec9aa69..956b6c8610 100644
--- a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023b.eb
@@ -1,20 +1,20 @@
 easyblock = 'PythonPackage'
 
 name = 'multiprocess'
-version = '0.70.15'
+version = '0.70.16'
 
 homepage = 'https://github.com/uqfoundation/multiprocess'
 description = "better multiprocessing and multithreading in python"
 
-toolchain = {'name': 'gfbf', 'version': '2023a'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e']
+checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1']
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('dill', '0.3.7'),
-    ('Arrow', '14.0.1'),  # if needed rebuild --from-pr 19758
+    ('Python', '3.11.5'),
+    ('dill', '0.3.8'),
+    ('Arrow', '16.1.0'),
 ]
 
 download_dep_fail = True

pavelToman · 2024-11-08T12:30:05Z

@boegelbot please test @ generoso

boegelbot · 2024-11-08T12:30:09Z

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=21783 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21783 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14664

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-08T12:37:19Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/d4b9ae7439fefa54e27d376f36a35775 for a full test report.

easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb

boegel · 2024-11-08T12:48:58Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3103.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/7fd9b2691650de8bce4ed0defde7dea1 for a full test report.

pavelToman · 2024-11-08T12:53:10Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-08T13:00:15Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21783 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21783 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5232

Test results coming soon (I hope)...

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easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb

boegel · 2024-11-08T13:05:03Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3103.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/e74a6851fec8be1fef678aee0f977ba9 for a full test report.

boegelbot · 2024-11-08T13:09:29Z

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 5 (4 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/1bc4c5bd0bb1c3452e1a563e8a531d2e for a full test report.

boegel · 2024-11-08T14:30:40Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-08T14:40:09Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21783 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21783 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5236

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-11-08T14:44:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/3e5b05a7f79d72eff44c2dc032acf20a for a full test report.

boegel · 2024-11-08T14:57:10Z

Going in, thanks @pavelToman!

adding easyconfigs: mustache-hic-1.3.3-foss-2023b.eb, hic-straw-1.3.1…

7b99beb

…-foss-2023b.eb, cooler-0.10.2-foss-2023b.eb, multiprocess-0.70.16-gfbf-2023b.eb

pavelToman mentioned this pull request Nov 4, 2024

Mustache vscentrum/vsc-software-stack#442

Closed

10 tasks

boegel mentioned this pull request Nov 8, 2024

{devel}[foss/2023b] TensorFlow v2.15.1, Bazel v6.3.1, flatbuffers-python v23.5.26, ml_dtypes v0.4.0 #21169

Merged

2 tasks

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

fd3ea92

…asyconfigs into 20241104191820_new_pr_mustache-hic133

github-actions bot added new update labels Nov 8, 2024

boegel added this to the 4.x milestone Nov 8, 2024

boegel requested changes Nov 8, 2024

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easybuild/easyconfigs/m/mustache-hic/mustache-hic-1.3.3-foss-2023b.eb Outdated Show resolved Hide resolved

update naming of mustache

fa3f2c9

boegel changed the title ~~{bio}[foss/2023b] mustache-hic v1.3.3, hic-straw v1.3.1, cooler v0.10.2, ...~~ {bio}[foss/2023b] Mustache v1.3.3, hic-straw v1.3.1, cooler v0.10.2, ... Nov 8, 2024

boegel changed the title ~~{bio}[foss/2023b] Mustache v1.3.3, hic-straw v1.3.1, cooler v0.10.2, ...~~ {bio}[foss/2023b] Mustache v1.3.3, hic-straw v1.3.1, cooler v0.10.2, multiprocess v0.70.16 Nov 8, 2024

boegel requested changes Nov 8, 2024

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easybuild/easyconfigs/m/Mustache/Mustache-1.3.3-foss-2023b.eb Show resolved Hide resolved

add custom source URL for Mustache

5fd37e0

boegel approved these changes Nov 8, 2024

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boegel modified the milestones: 4.x, release after 4.9.4 Nov 8, 2024

boegel merged commit 5fa3db9 into easybuilders:develop Nov 8, 2024

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

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Updated software cooler-0.10.2-foss-2023b.eb

Updated software hic-straw-1.3.1-foss-2023b.eb

Updated software multiprocess-0.70.16-gfbf-2023b.eb

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pavelToman commented Nov 4, 2024 •

edited by boegel

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Updated software `cooler-0.10.2-foss-2023b.eb`

Updated software `hic-straw-1.3.1-foss-2023b.eb`

Updated software `multiprocess-0.70.16-gfbf-2023b.eb`