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Author SHA1 Message Date
duan_jandClaude Fable 5 8843dc7163 Document install verification checklist in careless README 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 11:52:48 +02:00
duan_j 39851ab41b use common cache dir to save disk space and time 2026-08-18 11:17:38 +02:00
duan_j 5daa7cd94e Revert "Split careless into CPU module and careless-gpu using cuda/12.8.1 module" 
This reverts commit 20e69678da.
 2026-08-18 11:14:19 +02:00
duan_j 38ca2271f0 Revert "Drop careless-gpu: the [cuda] pip extra install covers GPU and CPU nodes" 
This reverts commit 5f25c83085.
 2026-08-18 11:14:13 +02:00
duan_jandClaude Fable 5 5f25c83085 Drop careless-gpu: the [cuda] pip extra install covers GPU and CPU nodes 
The installed careless/0.5.4 venv already contains the NVIDIA wheels
([cuda] extra), which need only the node driver and fall back to CPU,
so a separate GPU module and cuda module dep are unnecessary. Revert
careless/build to careless[cuda] to match the actual install.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 11:13:19 +02:00
duan_jandClaude Fable 5 20e69678da Split careless into CPU module and careless-gpu using cuda/12.8.1 module 
careless installs plain careless (CPU). careless-gpu also installs plain
careless but declares cuda/12.8.1 as build_requires/runtime_deps
(jfjoch_viewer pattern) instead of pip-bundling CUDA via the [cuda] extra.
Both builds honor UV_CACHE_DIR to share one download cache.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 11:07:12 +02:00
duan_jandClaude Fable 5 57e6500094 careless: put uv cache under PREFIX, home quota too small for TF wheels 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 10:55:59 +02:00
duan_jandClaude Fable 5 f0724df689 careless: call uv by explicit path, modbuild strips ~/.local/bin from PATH 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 10:54:10 +02:00
duan_jandClaude Fable 5 908e6b9d40 careless: build venv with uv instead of conda (anaconda.com blocked on Ra) 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-18 10:51:44 +02:00
duan_j b4743b72fb test module skill with careless 2026-08-18 10:45:20 +02:00
duan_jandClaude Fable 5 e3b6328f27 Fix module path: /opt/psi/MX, not /etc/psi/MX 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-14 14:47:45 +02:00
duan_jandClaude Fable 5 8fe398eea9 Update READMEs: Pmodules wiki background, unx-mx_adm permissions, build-* propagation notes 
- main README: add Pmodules background from wiki, unx-mx_adm group
  replaces -adm account for updating modules in /etc/psi/MX, and
  how to propagate main to the build-* tutorial branches
- module READMEs: fix titles/paths to match module directories
  (DIALS, jfjoch_viewer), replace -adm login steps with unx-mx_adm note

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-14 14:45:38 +02:00
duan_j 7faa4cac08 Merge branch 'dials' into main (PR #20): add autoPROC module 
# Conflicts:
#	.gitignore
 2026-08-14 14:26:05 +02:00
duan_j fa4b3c694c update module header from Pmodule to Module 2026-08-14 11:47:56 +02:00
duan_j 59d2e03f4c added jfjoch_viewer rc.160, changed 1st line in modulefile from Pmodule to Module to show in the new module 2026-08-14 11:47:56 +02:00
duan_j 392b2eb544 updated README.md 2026-08-14 11:47:56 +02:00
duan_j 90cb0752a0 update DIALS: rememebr to add support to /entry/data/data, see issue in aareproc repo 2026-08-14 11:47:56 +02:00
duan_j 498b607da0 ignore more files 2026-08-14 11:46:55 +02:00
duan_j 8b7e451118 update module header from Pmodule to Module 2026-08-14 11:45:14 +02:00
duan_j 6c5fab11f3 update gitignore 2026-08-14 11:42:30 +02:00
duan_j 38bd4753d3 added jfjoch_viewer rc.160, changed 1st line in modulefile from Pmodule to Module to show in the new module 2026-08-14 11:37:24 +02:00
duan_j 866f44d64d updated README.md 2026-08-12 16:07:29 +02:00
duan_j 7e6e95e758 update DIALS: rememebr to add support to /entry/data/data, see issue in aareproc repo 2026-08-05 09:16:14 +02:00
duan_jandClaude Fable 5 9946b945d1 add autoPROC pmodule 
Scaffold the standard 4-file Pmodule for autoPROC (Global Phasing Ltd.):
build, modulefile, files/config.yaml, README.md. The PSI licence token
(autoPROC/.licence) already existed and is installed into the software tree
at build time.

Follows the phenix archetype for the licence-gated install: the snapshot
tarball cannot be wget'd (download needs credentials), so it is staged by
hand in the module dir as autoPROC_snapshot_<date>.tar.gz and unpacked into
PREFIX with --strip-components=1 (xds pattern). Runtime is activated by
sourcing setup.sh via the modulefile.

CCP4 8.0 and XDS are wired as runtime_deps (xds from this repo; ccp4 is a
site module placeholder to confirm with `module avail ccp4`). Adds a
.gitignore guard so the proprietary snapshot is never committed.

Not built locally - to be tested on Ra.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-07-17 18:25:29 +02:00
duan_j de75837b93 add jfjoch_viewer 1.0.0-rc.158 2026-07-13 14:42:57 +02:00
duan_j 9496e65e86 build jfjoch viewer 2026-07-06 15:45:33 +02:00
duan_j eecc7e5c08 compile Xtrapol8 v1.2.8 with phenix 1.21 2026-03-26 17:06:02 +01:00
duan_j 8dbcb20a91 update readme and give solution for unbound variable problem, also including naming convension suggested by Achim 2026-03-26 16:07:58 +01:00
duan_j f3604edfa2 updated XDS version to 20251103 2025-12-21 17:06:27 +01:00
duan_j 977b1f477f Merge pull request 'Changed build to keep the same structure of the installation as the zip archive' (#18) from olex2_v1.5 into main 
Reviewed-on: #18
 2025-11-21 16:00:35 +01:00
agosti_j 838016f473 Changed build to keep the same structure of the installation as the zip archive 2025-11-21 15:56:14 +01:00
duan_j 1b8342f4cc Merge pull request 'Add olex2 v1.5' (#17) from olex2_1.5 into main 
Reviewed-on: #17
 2025-11-21 12:01:12 +01:00
agosti_j f93e5a0ce7 Add olex2 v1.5 2025-11-21 12:01:12 +01:00
duan_j 4f34975e8c Merge pull request 'Add Rosetta v3.15 for x86 and ARM' (#16) from Rosetta_3.15 into main 
Reviewed-on: #16
 2025-11-21 12:00:42 +01:00
duan_j cd979bfb59 Merge branch 'main' into Rosetta_3.15 2025-11-21 12:00:21 +01:00
duan_j 022376c346 added olex2 for MX small molecules 2025-11-19 14:54:54 +01:00
duan_j f5ffae7618 resolved the unsupported dtype issue in DIALS following https://github.com/cctbx/dxtbx/pull/785/files by allowing /entry/data/data 2025-10-28 15:22:47 +01:00
duan_j f4fb1e0fb4 update DIALS to 3.25.0 but has unsupported integer dtype, reported to github page 2025-10-28 14:30:34 +01:00
agosti_j 341814112e Add Rosetta v3.15 for x86 and ARM 2025-10-17 08:55:22 +02:00
duan_j be9e7c48d5 updated xds to stable 202505 version 2025-06-24 11:22:08 +02:00
duan_j e23bb15522 added license to autoPROC frome exisiting module 20240710 2025-05-30 10:49:23 +02:00
duan_j 8429f8cb70 updated xds to 2025 2025-05-30 10:15:19 +02:00
smith_k 45e0d957db Merge branch '6-module-file-for-xds' into 'main' 
add xds/20240724

Closes #6

See merge request Pmodules/mx!7
 2024-07-30 15:40:11 +02:00
ext-smith_m 1cb5815a20 add xds/20240724 2024-07-30 15:18:38 +02:00
assman_g 51d82f2d09 add rosetta 2024-07-24 10:46:42 +02:00
assman_g 599d6240f1 add phenix 2024-07-18 16:06:34 +02:00
assman_g 30c60ca532 add alphafold module 2024-07-18 10:49:35 +02:00
assman_g 6fe7d41d22 add readme 2024-07-18 10:46:02 +02:00
assman_g 887bf03746 add runtime_deps phenix 2024-07-18 10:40:10 +02:00
assman_g 83df4ac041 Merge branch '5-new-pymol-3-0' into 'main' 
Resolve "new pymol 3.0"

Closes #5

See merge request Pmodules/mx!6
 2024-05-27 10:39:45 +02:00