{bio}[foss/2023a] Monocle3 v1.3.1 w/ R 4.3.2

[verdurin]

(created using eb --new-pr)

[github-actions]

Updated software Monocle3-1.3.1-foss-2023a-R-4.3.2.eb

Diff against Monocle3-1.3.1-foss-2022b-R-4.2.2.eb

easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb

diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
index c19d8aff45..4c6da7d43e 100644
--- a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb
+++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
@@ -7,15 +7,15 @@ versionsuffix = '-R-%(rver)s'
 homepage = 'https://cole-trapnell-lab.github.io/monocle3/'
 description = """ An analysis toolkit for single-cell RNA-seq. """
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
-builddependencies = [('pkgconf', '1.9.3')]  # for textshaping
+builddependencies = [('pkgconf', '1.9.5')]  # for textshaping
 
 dependencies = [
-    ('R', '4.2.2'),
-    ('Python', '3.10.8'),
-    ('R-bundle-Bioconductor', '3.16', versionsuffix),
-    ('GDAL', '3.6.2'),
+    ('R', '4.3.2'),
+    ('Python', '3.11.3'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+    ('GDAL', '3.7.1'),
     ('HarfBuzz', '5.3.1'),  # for textshaping
     ('FriBidi', '1.0.12'),  # for textshaping
 ]

Diff against Monocle3-1.3.1-foss-2022a-R-4.2.1.eb

easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
index 3ca28db9d7..4c6da7d43e 100644
--- a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
@@ -7,16 +7,16 @@ versionsuffix = '-R-%(rver)s'
 homepage = 'https://cole-trapnell-lab.github.io/monocle3/'
 description = """ An analysis toolkit for single-cell RNA-seq. """
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
-builddependencies = [('pkgconf', '1.8.0')]  # for textshaping
+builddependencies = [('pkgconf', '1.9.5')]  # for textshaping
 
 dependencies = [
-    ('R', '4.2.1'),
-    ('Python', '3.10.4'),
-    ('R-bundle-Bioconductor', '3.15', versionsuffix),
-    ('GDAL', '3.5.0'),
-    ('HarfBuzz', '4.2.1'),  # for textshaping
+    ('R', '4.3.2'),
+    ('Python', '3.11.3'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+    ('GDAL', '3.7.1'),
+    ('HarfBuzz', '5.3.1'),  # for textshaping
     ('FriBidi', '1.0.12'),  # for textshaping
 ]
 
@@ -44,27 +44,9 @@ exts_list = [
     ('furrr', '0.3.1', {
         'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'],
     }),
-    ('warp', '0.2.0', {
-        'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'],
-    }),
-    ('rlang', '1.0.6', {
-        'checksums': ['e6973d98a0ea301c0da1eeaa435e9e65d1c3f0b95ed68bdc2d6cb0c610166760'],
-    }),
-    ('vctrs', '0.5.2', {
-        'checksums': ['76bf10243b9b31e23f56ffdaa1677a01767699e2098487f86bd42cb801d8c047'],
-    }),
-    ('slider', '0.3.0', {
-        'checksums': ['bc6a17ba5f0b27c8504a1d04992108470f24fd5662fbea14c300ac75fb02fca1'],
-    }),
-    ('rsample', '1.1.1', {
-        'checksums': ['90d2ae86d27a397ba9d8d010e7dea5c7b86fecbec7e9af273db0c2e8c374b8ba'],
-    }),
     ('RhpcBLASctl', '0.21-247.1', {
         'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'],
     }),
-    ('sf', '1.0-9', {
-        'checksums': ['85c0c71a0a64750281e79aa96e36d13e6285927008b2d37d699e52aba7d8013b'],
-    }),
     ('spdep', '1.2-7', {
         'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'],
     }),
@@ -74,21 +56,6 @@ exts_list = [
     ('speedglm', '0.3-5', {
         'checksums': ['f8663677c10ff324c5639402060ddd2b1a1e917445cb0f8f84e146b85e82bb4b'],
     }),
-    ('uwot', '0.1.14', {
-        'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'],
-    }),
-    ('systemfonts', '1.0.4', {
-        'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'],
-    }),
-    ('textshaping', '0.3.6', {
-        'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'],
-    }),
-    ('ragg', '1.2.5', {
-        'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'],
-    }),
-    ('ggrastr', '1.0.1', {
-        'checksums': ['82d6e90fa38dec85e829f71018532ed5b709a50a585455fc07cb3bae282f5d1f'],
-    }),
     ('leidenbase', '0.1.9', {
         'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}],

Diff against Monocle3-0.2.3-foss-2020b-R-4.0.3.eb

easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb

diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
index fdeb49b42a..4c6da7d43e 100644
--- a/easybuild/easyconfigs/m/Monocle3/Monocle3-0.2.3-foss-2020b-R-4.0.3.eb
+++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2023a-R-4.3.2.eb
@@ -1,20 +1,23 @@
 easyblock = 'Bundle'
 
 name = 'Monocle3'
-local_commit = '4c01d89'
-version = '0.2.3'
+version = '1.3.1'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://cole-trapnell-lab.github.io/monocle3/'
 description = """ An analysis toolkit for single-cell RNA-seq. """
 
-toolchain = {'name': 'foss', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('pkgconf', '1.9.5')]  # for textshaping
 
 dependencies = [
-    ('R', '4.0.3'),
-    ('Python', '3.8.6'),
-    ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'),
-    ('GDAL', '3.2.1'),
+    ('R', '4.3.2'),
+    ('Python', '3.11.3'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+    ('GDAL', '3.7.1'),
+    ('HarfBuzz', '5.3.1'),  # for textshaping
+    ('FriBidi', '1.0.12'),  # for textshaping
 ]
 
 github_account = 'cole-trapnell-lab'
@@ -35,49 +38,34 @@ exts_list = [
     ('Matrix.utils', '0.9.8', {
         'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'],
     }),
-    ('pbmcapply', '1.5.0', {
-        'checksums': ['df52ed585c0b32ac6180616efd94cd75dd7c5621f5398c0861db2f7b317ba844'],
-    }),
-    ('furrr', '0.2.2', {
-        'checksums': ['e5c10353dc47416eda870d16cf810c576f11bdc9e4c7277f7755581f3824cd4d'],
-    }),
-    ('warp', '0.2.0', {
-        'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'],
-    }),
-    ('slider', '0.1.5', {
-        'checksums': ['93f5801ad81a6e4f7e710666a2ca1530709767d10d171dd6749f91aabae392f4'],
-    }),
-    ('rlang', '0.4.10', {
-        'checksums': ['07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576'],
-    }),
-    ('rsample', '0.0.9', {
-        'checksums': ['4cb4bc9708c9314aecaad703bae5aeffdd533af0bf1273a05042d647fdd61c0f'],
+    ('pbmcapply', '1.5.1', {
+        'checksums': ['7ffc2854a384962f0dd523aa9ef33ce8fc290997206b71b840a49049d87112dd'],
     }),
-    ('RhpcBLASctl', '0.20-137', {
-        'checksums': ['db02cbdad32fc54bc60bb27baf0799e919c09c09710c33bf72c741f93421616f'],
+    ('furrr', '0.3.1', {
+        'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'],
     }),
-    ('sf', '0.9-7', {
-        'checksums': ['4acac2f78badf9d252da5bf377975f984927c14a56a72d9f83d285c0adadae9c'],
+    ('RhpcBLASctl', '0.21-247.1', {
+        'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'],
     }),
-    ('spdep', '1.1-5', {
-        'checksums': ['47cb46cf5cf1f4386eb1b5e4d8541d577d7f2939e74addbdb884ecf2323f6d5d'],
+    ('spdep', '1.2-7', {
+        'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'],
     }),
-    ('speedglm', '0.3-3', {
-        'checksums': ['d065d0ee42fb772760fca8d97ad2aa56cd76b1d9ecb4e97478ec362429e16738'],
+    ('biglm', '0.9-2.1', {
+        'checksums': ['6dcf3c9e7c3f56cdaac94cc0c427f606880467e1e753fe7ea45c10bc44eec947'],
     }),
-    ('uwot', '0.1.10', {
-        'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'],
+    ('speedglm', '0.3-5', {
+        'checksums': ['f8663677c10ff324c5639402060ddd2b1a1e917445cb0f8f84e146b85e82bb4b'],
     }),
-    ('leidenbase', '0.1.2', {
+    ('leidenbase', '0.1.9', {
         'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}],
-        'checksums': ['163f6e8ebc6bd0f6927d1c7e80fe45038eedb07044febb2f8d28459185d367af'],
+        'checksums': ['dd893b13b04d4b943243e7ac8d2ef1850b60d0437b2e4d36a9cff57cd4953f54'],
     }),
     (name, version, {
         'modulename': '%(namelower)s',
         'source_urls': ['https://github.com/%(github_account)s/monocle3/archive'],
-        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}],
-        'checksums': ['fe95f724ff7a8f35cc4c8152865052c3a6d44332485b0626fbc3e1af09c17738'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}],
+        'checksums': ['30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d'],
     }),
 ]
 

[verdurin]

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/a575d54481d75b31826377050f2c56b8 for a full test report.

[verdurin]

@boegelbot please test @ generoso

[boegelbot]

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

PR test command 'EB_PR=21918 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21918 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 14770

Test results coming soon (I hope)...

- notification for comment with ID 2504189875 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/73bb113a8508ccede200214ed7c9517f for a full test report.

[verdurin]

@boegelbot please test @ jsc-zen3

[boegelbot]

@verdurin: 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=21918 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21918 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 5344

Test results coming soon (I hope)...

- notification for comment with ID 2504518831 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/b353779a6c9a5de703aaf516251890c8 for a full test report.