Merge branch 'main' into Rosetta_3.15

DIALS/.licence

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+# Paul Scherrer Institute, Macromolecular Crystallography
+ 3938465545 2992269931 2851646202 2685600639 2346109776 3745393523

DIALS/README.md

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+XDS
+
+Step 1: login with your -adm account
+
+```
+kinit xxxx_x-adm
+aklog
+```
+
+Step 2: load the latest Pmodules package
+
+```
+module use unstable
+module load Pmodules/2.0.0
+```
+
+Step 3: go into DIALS directory, update config.yaml to add newest release version and build module with that release name
+
+```
+cd DIALS
+vi files/config.yaml
+./build 3.25.0
+```
+
+Step 4: confirm that the module loads as expected 
+
+PS:
+Unsupported dtype issue is resolved by changing modules/dxtbx/src/dxtbx/format/FormatNXmx.py
+allowing the return of also /entry/data/data to the handle:
+https://github.com/dials/dials/issues/3033

DIALS/build

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+#!/usr/bin/env modbuild
+
+
+pbuild::prep() { :; }
+
+pbuild::configure() { :; }
+
+pbuild::compile() { :; }
+
+pbuild::install() {
+    cd "${PREFIX}"
+    wget https://dials.diamond.ac.uk/diamond_builds/dials-linux-x86_64-conda3.tar.xz
+    tar -xJf dials-linux-x86_64-conda3.tar.xz
+    cd dials-installer-dev
+    ./install --prefix=$PREFIX
+    cd "${PREFIX}"
+    rm dials-linux-x86_64-conda3.tar.xz
+    rm -r dials-installer-dev
+    ln -s dials-dev20251026 dials-v3-25-0
+}

DIALS/files/config.yaml

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+---
+format: 1
+DIALS:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: stable
+  versions:
+    3.25.0:
+      config:
+        relstage: unstable

DIALS/modulefile

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+#%Module1.0
+
+module-whatis	        "DIALS: Diffraction Integration for Advanced Light Sources"
+module-url		"https://dials.github.io/"
+module-license	        "DIALS license"
+module-maintainer       "Jiaxin Duan <jiaxin.duan@psi.ch>"
+
+module-help	"
+X-ray crystallography for structural biology has benefited greatly from a number of advances in recent years including high performance pixel array detectors, new beamlines capable of delivering micron and sub-micron focus and new light sources such as X-FELs. The DIALS project is a collaborative endeavour to develop new diffraction integration software to meet the data analysis requirements presented by these recent advances. There are three end goals: to develop an extensible framework for the development of algorithms to analyse X-ray diffraction data; the implementation of algorithms within this framework and finally a set of user facing tools using these algorithms to allow integration of data from diffraction experiments on synchrotron and free electron sources.
+
+License : https://dials.github.io/license.html
+"
+
+puts stdout "source $PREFIX/dials-v3-25-0/dials_env.sh;"

olex2/README.md

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+XDS
+
+Step 1: login with your -adm account
+
+```
+[smith_k@ra-l-005 xds]$ kinit smith_k-adm
+[smith_k@ra-l-005 xds]$ aklog
+```
+
+Step 2: load the latest Pmodules package
+
+```
+module use unstable
+module load Pmodules/2.0.0
+```
+
+Step 3: go into olex2 directory, update config.yaml to add newest release version and build module with that release name (e.g. below is for 1.5)
+
+```
+cd olex2
+vi files/config.yaml
+./build 1.5
+```
+
+Step 4: confirm that the module loads as expected 

olex2/build

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+#!/usr/bin/env modbuild
+
+
+pbuild::prep() { :; }
+
+pbuild::configure() { :; }
+
+pbuild::compile() { :; }
+
+pbuild::install() {
+    #wget --no-check-certificate https://xds.mr.mpg.de/XDS-gfortran_Linux_x86_64.tar.gz
+    mkdir -p "${PREFIX}/bin"
+    cd "${PREFIX}/bin"
+    unzip "${BUILDBLOCK_DIR}/Olex2Linux64.zip"
+}

olex2/files/config.yaml

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+---
+format: 1
+olex2:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: stable
+  versions:
+    1.5:
+      config:
+        relstage: stable

olex2/modulefile

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+#%Pmodule
+
+module-whatis       "OlexSys Ltd is a scientific software company providing State of the Art Crystallographic Software as well as the best Laboratory Chemicals Management there is."
+module-url          "https://www.olexsys.org/categories/installation/"
+module-license      "Olex2 is completely free to use for anyone. There is no catch here – whether you are in industry, academia or a student, it’s free!"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help     "
+Olex2 is open source – all our code is available for you to look at, check and – hopefully!
+"
+
+setenv          Olex2                     $PREFIX/bin