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removed legacy metadata (closes #219)
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.gitignore

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@@ -6,3 +6,5 @@ build/
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dist/
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*.pyc
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.DS_Store
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.coverage
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htmlcov

docs/metadata.md

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@@ -276,24 +276,13 @@ so that now ``n.metadata`` would be a dict,
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with entries ``n.metadata["slim_id"]`` and ``n.metadata["is_null"]`` and ``n.metadata["genome_type"]``.
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Annotation should be done with tskit methods (e.g., ``packset_metadata``).
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For now, the old-style metadata is still available:
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passing the argument ``legacy_metadata=True`` to {meth}`load`
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will produce a tree sequence whose metadata is just as before,
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and so all previously-written scripts that depend on metadata processing should work, unchanged.
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Restating this:
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.. note::
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:::{note}
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To make an script that relied on previous metadata parsing work,
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it should suffice to add `legacy_metadata=True` to calls producing
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SlimTreeSequences, e.g., replacing ``pyslim.load("file.trees")`` with
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``pyslim.load("file.trees", legacy_metadata=True)``, and
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``ts.simplify(nodes)`` with
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``pyslim.SlimTreeSequence(ts.simplify(nodes), legacy_metadata=True)``.
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If this fails, please file an issue on github.
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:::
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Until pyslim version 0.600, the old-style metadata was still available,
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but this functionality has been removed.
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Here are more detailed notes on how to migrate a script from the legacy
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metadata handling.
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metadata handling. If you run into issues, please ask (open a discussion on github).
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**1.** Use top-level metadata instead of ``slim_provenance``:
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previously, information about the model type and the time counter (generation)

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