add tutorial "How to turn ancient calendar sources into absolute dates"#6957
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add tutorial "How to turn ancient calendar sources into absolute dates"#6957jnussbaum wants to merge 6 commits into
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Replace the skeleton placeholders with the domain logic and concrete, data-verified parameter values for the lunar-chronology workflow: - Anchor the worked example on Senwosret III (12th Dynasty); the 1240/1900 line cuts bracket the ~1900-1748 BCE window. - Explain the -2-day rule and express search terms as -i -P regexes (1 peret\s+5\b, 2 shemou\s+18\b, 1 shemou\s+7\b), each verified to match the data file; preceding/trailing context set to 0. - Explain that the descending sort on column 3 (deltaT) orders the candidates chronologically, and document the 15-row result. - Add the Gautschy 2011 reference to tutorial.bib. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add an @online entry for the gautschy.ch lunar-data page and reference it from the data-download paragraph and the -2-day quote box. Remove the unused gtn-website example entry from the bibliography. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
In BibTeX/LaTeX a bare ~ is a non-breaking space, which the GTN bibliography parser decodes to U+00A0 and then URL-encodes to %C2%A0, breaking the link. Encoding the tilde as %7E keeps the URL correct everywhere it is cited. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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🚫 [GTN Lint] <GTN:027> reported by reviewdog 🐶
This workflow is missing a test, which is now mandatory. Please see the FAQ on how to add tests to your workflows.
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| {"a_galaxy_workflow": "true", "annotation": "This workflow extracts possible absolute dates of preserved ancient lunar observations (first / last sighting of the Moon). ", "comments": [], "creator": [{"class": "Person", "identifier": "https://orcid.org/0000-0002-5470-8720", "name": "Rita Gautschy"}], "format-version": "0.1", "name": "Analysis of a sequence of ancient lunar data (imported from uploaded file)", "readme": "This workflow can be used for the analysis of a sequence of preserved lunar data, namely first or last visibilities of the Moon after or before New Moon. In many cultures this event announced the beginning of a new (lunar) month. Sequences of preserved lunar data can help to retrieve absolute dates for ancient rulers, e.g. Egyptian pharaohs.\n\nThe input data - calculations of first or last visibility of the Moon - must be in tabular format. Since the original file contains four millennia, cutting it down to the historically reasonable time range for a ruler may be useful. To achieve that, a number of lines are removed from the beginning (Tool: Remove beginning of a file) and the end (Tool: Select first lines from a dataset) of the input file.\n\nThen the successive search for the preserved lunar dates can begin (Tool: Search in textfiles (grep)). As a next step the results of the individual searches need to be concatenated (Tool: Concatenate multiple datasets or collections). \n\nTo eliminate duplicates, the output of the previous step needs to be cleaned and only unique values kept (Tool: Unique occurrences of each record).\n\nFinally, the data need to be sorted chronologically (Tool: Sort data in ascending or descending order). \n\nThe result is a text file containing all remaining viable dating options for the preserved lunar dates in other calendars (Egyptian civil calendar in the original example).", "report": {"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"}, "steps": {"0": {"annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "", "name": "Thebenletzte.tsv"}], "label": "Thebenletzte.tsv", 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🚫 [GTN Lint] <GTN:046> reported by reviewdog 🐶
Please do not include an # Introduction section, it is unnecessary here, just start directly into your text. The first paragraph that is seen by our infrastructure will automatically be shown in a few places as an abstract.
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TODO: Describe your changes here..