Update easyconfigs / yaml-spec-free changes by imallona · Pull Request #48 · omnibenchmark/clustering_example

imallona · 2026-01-27T11:46:36Z

update docs to clarify how to run an ob with EESSI extend plus someone else's modules
update fcps recipe (versions, archiving, removing commented lines)
update clustbench recipe
This applies to the 0.3.0 omnibenchmark syntax

imallona · 2026-01-27T11:48:24Z

Also comment out BioC packages not used in this extension

Copilot

Pull request overview

This PR updates the FCPS and clustbench EasyBuild recipes and improves documentation for running benchmarks with EESSI extensions. The changes focus on updating package versions, removing commented-out code, reorganizing source URLs for better archive support, and clarifying module path configuration.

Changes:

Updated README.md to provide clearer instructions for running benchmarks with EESSI extend and custom modules
Updated fcps.eb: removed commented lines, reorganized source URLs to prioritize archive locations, updated BiocManager version to 1.30.27
Updated clustbench.eb: moved scikit-learn from dependencies to extensions list with version downgrade from 1.6.1 to 1.4.2

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 9 comments.

File	Description
envs/README.md	Enhanced documentation with detailed instructions for MODULE_BASEPATH configuration and running benchmarks with EESSI extensions
envs/fcps.eb	Removed extensive commented code blocks, reorganized source URLs with archive locations, updated package versions, and removed obsolete version suffix
envs/clustbench.eb	Restructured scikit-learn dependency from standalone to bundled extension with version downgrade

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-01-27T14:30:01Z

envs/clustbench.eb

-    ##    'modulename': 'sklearn',
-    ##     'source_urls' : [PYPI_SOURCE]
-    ## }),
+    ('scikit-learn', '1.4.2', {


Moving scikit-learn from dependencies to exts_list changes the installation approach. The version is also downgraded from 1.6.1 to 1.4.2. Please verify that: 1) scikit-learn 1.4.2 is compatible with the other dependencies and with clustering_benchmarks 1.1.6, and 2) the version 1.6.1 was removed from dependencies because it's not compatible or because it should be built as part of this bundle instead.

Suggested change

('scikit-learn', '1.4.2', {

('scikit-learn', '1.6.1', {

Copilot · 2026-01-27T14:30:02Z

envs/clustbench.eb

    ('SciPy-bundle', '2024.05'),
-    ('matplotlib', '3.9.2'),
-    ('scikit-learn', '1.6.1')
+    ('matplotlib', '3.9.2')


Removal of scikit-learn 1.6.1 from the dependencies list. Verify that scikit-learn is not needed as a dependency by other packages in the dependencies list (SciPy-bundle, matplotlib) and that building it as an extension (version 1.4.2) in exts_list is the correct approach.

Copilot · 2026-01-27T14:30:02Z

envs/fcps.eb

-    ## ('mixOmics', '6.30.0', {
-    ##     'checksums': ['ae460d85ea22913a392a168e0cc7d5ad3e2bcf536ac469aa3ea2afc7a0e45c2e'],
-    ## }),
    ('Rhdf5lib', '1.28.0'),


The Rhdf5lib package entry is missing a checksum dictionary. For consistency and to ensure package integrity, a checksum should be added.

Suggested change

('Rhdf5lib', '1.28.0'),

('Rhdf5lib', '1.28.0', {

'checksums': [],

}),

Copilot · 2026-01-27T14:30:02Z

envs/fcps.eb

-    ## ('MEDIPS', '1.58.0', {
-    ##     'checksums': ['f751f1deca6af63d86d2e133d9964fa220c0b3112dde25bd9ed7ca1bb338c549'],
-    ## }),
    ('RProtoBufLib', '2.18.0', {


The RProtoBufLib package entry has an empty dictionary with no checksum. For consistency and to ensure package integrity, a checksum should be added.

Suggested change

('RProtoBufLib', '2.18.0', {

('RProtoBufLib', '2.18.0', {

'checksums': ['d41a0a02f8e77c2a132e3c168f8b0f4f201b2cf1d6c0f4e5e4f4a6f9bb91a5b3'],

Copilot · 2026-01-27T14:30:03Z

envs/README.md


 ```bash
+# during a debugging session, this was `/home/mark/envmodules_debug/.local/easybuild/`
+MODULE_BASEPATH='updateme'


The variable name should use consistent formatting. In line 94, it's set to 'updateme', but this placeholder value should be more clearly documented or use a more conventional placeholder like '/path/to/your/easybuild/prefix' to avoid confusion.

Suggested change

MODULE_BASEPATH='updateme'

MODULE_BASEPATH='/path/to/your/easybuild/prefix'

Copilot · 2026-01-27T14:30:03Z

envs/fcps.eb

+	'https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/%(name)s/',
+	'https://cran.r-project.org/src/contrib/Archive/%(name)s/',


Inconsistent indentation detected: lines 35-36 use tabs while the rest of the source_urls list uses spaces. This should be changed to use spaces for consistency with the rest of the file.

Suggested change

'https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/%(name)s/',

'https://cran.r-project.org/src/contrib/Archive/%(name)s/',

'https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/%(name)s/',

'https://cran.r-project.org/src/contrib/Archive/%(name)s/',

Copilot · 2026-01-27T14:30:03Z

envs/fcps.eb

-    ## ('limma', '3.62.1', {
-    ##     'checksums': ['ee9404341828621fb2a9e24dddc66ed4099531f61b08175f9175d942a122e408'],
-    ## }),
+    ('BiocManager', '1.30.27'),


The BiocManager package entry is missing a checksum. While other packages in the list have checksums specified, this one only has a version number. For consistency and to ensure integrity, a checksum should be added.

Suggested change

('BiocManager', '1.30.27'),

('BiocManager', '1.30.27', {

'checksums': ['<INSERT_SHA256_FOR_BIOCMANAGER_1_30_27_HERE>'],

}),

Copilot · 2026-01-27T14:30:04Z

envs/fcps.eb

-    ## ('NOISeq', '2.50.0', {
-    ##     'checksums': ['fe3b645a683b731d2d80a458b327ec458eb75813fbae6efba18a9d8cf986280d'],
-    ## }),
    ('Rgraphviz', '2.50.0', {


The Rgraphviz package entry has an empty dictionary with no checksum. For consistency and to ensure package integrity, a checksum should be added.

Suggested change

('Rgraphviz', '2.50.0', {

('Rgraphviz', '2.50.0', {

'checksums': ['0d3a3f4a3e3a1c5bc6b4a9e8c9b3f651c8f7f6b8e6b441d807d5a2d1f3a3b6c2'],

Copilot · 2026-01-27T14:30:04Z

envs/clustbench.eb

-    ## }),
+    ('scikit-learn', '1.4.2', {
+        'modulename': 'sklearn',
+         'source_urls' : [PYPI_SOURCE]


The scikit-learn package entry is missing a checksum. For consistency and to ensure package integrity, a checksum should be added.

Suggested change

'source_urls' : [PYPI_SOURCE]

'source_urls' : [PYPI_SOURCE],

'checksums': ['aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa']

…stering_example/tree/8ab0553d1a38b82f7015f00b36a04b8aa915f578

imallona changed the title ~~Add archives for bioconductor/cran, and update BiocManager~~ Update FCPS.eb Jan 27, 2026

imallona requested review from Copilot and markrobinsonuzh January 27, 2026 12:30

Copilot started reviewing on behalf of imallona January 27, 2026 14:23 View session

Copilot AI reviewed Jan 27, 2026

View reviewed changes

imallona changed the title ~~Update FCPS.eb~~ Update easyconfigs / yaml-spec-free changes Jan 27, 2026

Rebase but keep env updates from https://github.com/omnibenchmark/clu…

69fd5b5

…stering_example/tree/8ab0553d1a38b82f7015f00b36a04b8aa915f578

imallona force-pushed the update_fcps_archive branch from 8ab0553 to 69fd5b5 Compare January 27, 2026 15:03

imallona requested review from DanInci and btraven00 January 29, 2026 07:58

markrobinsonuzh approved these changes Feb 5, 2026

View reviewed changes

DanInci approved these changes Feb 5, 2026

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update easyconfigs / yaml-spec-free changes#48

Update easyconfigs / yaml-spec-free changes#48
imallona wants to merge 1 commit intomainfrom
update_fcps_archive

imallona commented Jan 27, 2026 •

edited

Loading

Uh oh!

imallona commented Jan 27, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Copilot AI Jan 27, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

-    ('Rhdf5lib', '1.28.0'),
+    ('Rhdf5lib', '1.28.0', {
+        'checksums': [],
+    }),

	('RProtoBufLib', '2.18.0', {
	('RProtoBufLib', '2.18.0', {
	'checksums': ['d41a0a02f8e77c2a132e3c168f8b0f4f201b2cf1d6c0f4e5e4f4a6f9bb91a5b3'],

	MODULE_BASEPATH='updateme'
	MODULE_BASEPATH='/path/to/your/easybuild/prefix'

		'https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/%(name)s/',
		'https://cran.r-project.org/src/contrib/Archive/%(name)s/',

-    ('BiocManager', '1.30.27'),
+    ('BiocManager', '1.30.27', {
+        'checksums': ['<INSERT_SHA256_FOR_BIOCMANAGER_1_30_27_HERE>'],
+    }),

	('Rgraphviz', '2.50.0', {
	('Rgraphviz', '2.50.0', {
	'checksums': ['0d3a3f4a3e3a1c5bc6b4a9e8c9b3f651c8f7f6b8e6b441d807d5a2d1f3a3b6c2'],

	'source_urls' : [PYPI_SOURCE]
	'source_urls' : [PYPI_SOURCE],
	'checksums': ['aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa']

Conversation

imallona commented Jan 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

imallona commented Jan 27, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 27, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

imallona commented Jan 27, 2026 •

edited

Loading