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export to ecotaxa format#101

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joefutrelle merged 5 commits into
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ecotaxa_export
Jul 2, 2025
Merged

export to ecotaxa format#101
joefutrelle merged 5 commits into
masterfrom
ecotaxa_export

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@joefutrelle
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Provides a to_ecotaxa function that produces a compressed archive of an IFCB bin containing pngs and necessary metadata for import into ecotaxa or ecotaxa-compatible tools such as morphocluster.

@joefutrelle joefutrelle requested a review from Copilot July 1, 2025 18:54
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Pull Request Overview

Adds a new to_ecotaxa function that generates a ZIP archive containing PNG images and a TSV metadata file for import into EcoTaxa or compatible tools.

  • Introduces to_ecotaxa in ifcb/data/export.py to export images and metadata.
  • Writes image files and assembles a TSV metadata file with manual header/type rows.
  • Uses pandas and BytesIO to build and write the TSV into the ZIP.
Comments suppressed due to low confidence (3)

ifcb/data/export.py:10

  • [nitpick] The parameter name b is ambiguous; consider renaming it to something more descriptive like bin_obj or ifcb_bin to clarify its purpose.
def to_ecotaxa(b, zip_path=None):

ifcb/data/export.py:10

  • Add a docstring for to_ecotaxa to explain its parameters, behavior, and the format of the resulting ZIP archive.
def to_ecotaxa(b, zip_path=None):

ifcb/data/export.py:10

  • A new export function was added without any accompanying tests; consider adding unit tests to verify ZIP contents and TSV formatting.
def to_ecotaxa(b, zip_path=None):

Comment thread ifcb/data/export.py Outdated
Comment thread ifcb/data/export.py Outdated
Comment thread ifcb/data/export.py
joefutrelle and others added 3 commits July 1, 2025 14:56
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@joefutrelle joefutrelle requested a review from johnwaalsh July 2, 2025 10:50
Comment thread ifcb/data/export.py
@joefutrelle joefutrelle merged commit 541c848 into master Jul 2, 2025
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@joefutrelle joefutrelle deleted the ecotaxa_export branch July 2, 2025 18:44
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3 participants