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docs: update, add example, small fixes - #30

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eseiler merged 5 commits into
OpenMS:masterfrom
eseiler:docs/readme-example
Nov 5, 2026
Merged

eseiler merged 5 commits into
OpenMS:masterfrom
eseiler:docs/readme-example

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@eseiler eseiler commented Nov 5, 2026

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eseiler and others added 5 commits November 5, 2026 16:28
The log is a 10,000 line sample of the SeqAn version check log with
randomized IP addresses and timestamps, including the timestamps embedded
in test_version_check requests. Calls from the same day and addresses from
the same /16 network stay grouped, so that merging of calls and cluster
detection behave as on real data.

output_seqan is the result of running scripts/run.sh on this log.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The top-level README still described removed scripts and a PDF report.
Describe the current workflow and add scripts/README.md for the individual
steps, configuration, data sources and output. Rewrite docker/README.md for
the published image and the compose-based build.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The Dockerfile copies the requirement files from an additional build
context that is defined in compose.yaml. A plain docker build does not know
this context, and the workflow has been failing since 1feabab.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
scripts/data_processing/py/config.py was a symlink to
scripts/config/config.py that nothing imported.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The country code of Namibia is NA, which read.table parsed as a missing
value, so drop_na() removed these rows. Do not treat any string in the
geolocations as missing. Empty coordinates are still missing values, because
they are in numeric columns.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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@eseiler
eseiler merged commit 6a1a3e8 into OpenMS:master Nov 5, 2026
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@eseiler
eseiler deleted the docs/readme-example branch November 5, 2026 16:00
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