Merge branch 'dials' into main (PR #20): add autoPROC module

# Conflicts:
#	.gitignore

autoPROC/README.md

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+# autoPROC
+
+autoPROC (Global Phasing Ltd.) is an automated pipeline for integrating and scaling
+macromolecular crystallography diffraction data. It is licence-gated: the PSI licence
+token is committed as `autoPROC/.licence` and installed into the software tree at build
+time. CCP4 8.0 and XDS are hard runtime requirements and are pulled in as module
+dependencies.
+
+## Build on Ra
+
+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: stage the licence-gated snapshot. Download it from Global Phasing (needs
+credentials, so `wget` in the build script will not work) and save it in this module
+directory named by its snapshot date. Do NOT commit it (it is proprietary and large;
+`.gitignore` already excludes `autoPROC_snapshot_*.tar.gz`).
+
+```
+cd autoPROC
+# e.g. save the download as autoPROC_snapshot_20240710.tar.gz here
+```
+
+Step 4: edit `files/config.yaml` to add the real snapshot date as the version, and
+confirm the `ccp4` dependency coordinates for this cluster:
+
+```
+module avail ccp4          # adjust ccp4/8.0 in runtime_deps if the name/version differs
+vi files/config.yaml
+```
+
+Step 5: build (installs to `/opt/psi/MX/autoPROC/<date>`)
+
+```
+./build 20240710
+```
+
+Step 6: confirm the module loads and autoPROC is licensed
+
+```
+module use MX unstable
+module load autoPROC/20240710
+process -h
+```
+
+## Assumptions to verify on the first real build
+
+- The snapshot tarball has a single top-level directory, so `tar --strip-components=1`
+  puts `setup.sh` directly at `$PREFIX/setup.sh`. If the layout differs, adjust the
+  strip level in `build`.
+- autoPROC reads its licence from the software home, i.e. `$autoPROC_home/.licence`,
+  which equals `$PREFIX/.licence` after the strip. `build` copies `.licence` there.
+- If loading the module fails with `... : unbound variable` (setup.sh under `set -u`),
+  add `puts stdout "set +x nounset"` before the `source` line in `modulefile` (same fix
+  used for phenix).
+- There is no `ccp4` module in this repo; `runtime_deps` references a site CCP4 module.
+  Set the exact name/version from `module avail ccp4`.

autoPROC/build

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+#!/usr/bin/env modbuild
+
+
+pbuild::prep() { :; }
+
+pbuild::configure() { :; }
+
+pbuild::compile() { :; }
+
+pbuild::install() {
+    # autoPROC is licence-gated: the Global Phasing snapshot cannot be wget'd
+    # (download needs credentials), so stage it in this module dir first as
+    # autoPROC_snapshot_<version>.tar.gz, then unpack into $PREFIX. Not committed to git.
+    mkdir -p "${PREFIX}"
+    cd "${PREFIX}"
+    tar -xf "${BUILDBLOCK_DIR}/autoPROC_snapshot_${V}.tar.gz" --strip-components=1
+
+    # Install the PSI licence token at the software home so autoPROC is activated.
+    cp "${BUILDBLOCK_DIR}/.licence" "${PREFIX}/.licence"
+}

autoPROC/files/config.yaml

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+---
+format: 1
+autoPROC:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+  versions:
+    20240710:
+      config:
+        relstage: unstable
+        # XDS = in-repo module; CCP4 = site module, confirm name with `module avail ccp4`.
+        runtime_deps: [xds/20251103, ccp4/8.0]

autoPROC/modulefile

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+#%Module1.0
+
+module-whatis       "autoPROC: automated data processing for macromolecular crystallography"
+module-url          "https://www.globalphasing.com/autoproc/"
+module-license      "Global Phasing Ltd. proprietary licence"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help "
+autoPROC (Global Phasing Ltd.) is an automated pipeline for integrating and scaling
+macromolecular crystallography diffraction data. It wraps XDS, CCP4 and other tools and
+requires a valid Global Phasing licence plus CCP4 8.0 and XDS at runtime (both pulled in
+as module dependencies).
+"
+
+# autoPROC is activated by sourcing its setup script (sets autoPROC_home, PATH, etc.).
+puts stdout "source $PREFIX/setup.sh;"