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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
61 lines
2.9 KiB
Bash
Executable File
61 lines
2.9 KiB
Bash
Executable File
#!/bin/bash
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# Notarize the macOS release artefacts with Apple and staple the ticket where one can be stapled.
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#
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# tools/notarize_macos.sh <jfjoch-viewer-*.dmg | rugnux-*.tar.gz> ...
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#
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# The programs inside must already carry a Developer ID signature with hardened runtime and secure
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# timestamp: configure with -DJFJOCH_MACOS_SIGNING_IDENTITY=<certificate SHA-1> and let cpack produce
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# the artefact (see the top-level CMakeLists.txt). The same certificate signs the .dmg here: the
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# one JFJOCH_MACOS_SIGNING_IDENTITY names, else the Developer ID Application in the keychain. Needs
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# notarytool credentials stored once on the machine, under the profile named by JFJOCH_NOTARY_PROFILE
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# (default jfjoch-notary). On an unattended machine store them in the login keychain file: without
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# --keychain they go into the data-protection keychain, which is unreadable while the screen is
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# locked, and the step then fails with "No Keychain password item found".
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#
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# xcrun notarytool store-credentials jfjoch-notary --apple-id <apple id> --team-id <team id> \
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# --keychain ~/Library/Keychains/login.keychain-db
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#
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# .dmg signed with the same Developer ID, submitted, the ticket stapled to the image.
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# .tar.gz the rugnux binary inside is zipped and submitted; Apple then knows its hash, which is
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# all Gatekeeper needs (a bare executable has nowhere to staple a ticket). The archive is
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# shipped unchanged.
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set -euo pipefail
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profile=${JFJOCH_NOTARY_PROFILE:-jfjoch-notary}
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identity=${JFJOCH_MACOS_SIGNING_IDENTITY:-$(security find-identity -v -p codesigning | sed -n 's/^ *[0-9]*) \([0-9A-F]*\) "Developer ID Application: .*/\1/p' | head -1)}
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if [ -z "$identity" ]; then echo "no Developer ID Application identity in the keychain"; exit 1; fi
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submit() { # submit <file>: wait for Apple's verdict, print the log on rejection
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local out id status
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out=$(xcrun notarytool submit "$1" --keychain-profile "$profile" --wait --output-format plist)
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id=$(echo "$out" | plutil -extract id raw -)
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status=$(echo "$out" | plutil -extract status raw -)
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echo "notarization of $(basename "$1"): $status (submission $id)"
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if [ "$status" != "Accepted" ]; then
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xcrun notarytool log "$id" --keychain-profile "$profile"
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exit 1
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fi
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}
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for file in "$@"; do
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case "$file" in
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*.dmg)
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codesign --force --timestamp --sign "$identity" "$file"
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submit "$file"
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xcrun stapler staple "$file"
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spctl -a -t open --context context:primary-signature -v "$file"
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;;
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*.tar.gz|*.tgz)
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tmp=$(mktemp -d)
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tar xf "$file" -C "$tmp"
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bin=$(find "$tmp" -name rugnux -type f)
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ditto -c -k "$bin" "$tmp/rugnux.zip"
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submit "$tmp/rugnux.zip"
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rm -rf "$tmp"
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;;
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*)
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echo "don't know how to notarize $file"; exit 1
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;;
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esac
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done
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