python-orfdata (0.52.0+ds1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #1151088).
   * Drop pyensembl-reference-metadata.patch: upstream now handles reference
     strain taxonomy and current PyEnsembl assembly metadata, with regression
     coverage for species, strain and reference validation.
   * Check reference-table text columns with pandas is_string_dtype so the
     schema test works with both pandas 2 and pandas 3 string storage.

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/openvax/orfdata
Upstream-Name: orfdata
Upstream-Contact: OpenVax <https://github.com/openvax/orfdata/issues>
Files-Excluded:
 orfdata.egg-info/*
 tests/data/openprot/*.zip
 tests/data/peptideatlas/atlas_build.tsv.zip

Files: *
Copyright: 2026 OpenVax contributors
License: Apache-2.0

Files: orfdata/data/orf-evidence/*
       orfdata/data/uorf-evidence/*
Copyright: 2025 Leron Kok
           2026 Aaron Wacholder and the community assessment authors
           2026 OpenVax contributors
License: Apache-2.0 and Expat and CC-BY-4.0 and Ensembl
Comment:
 The GENCODE models and HLA mapping/count data are from
 https://github.com/VanHeeschLab/deutsch_kok_et_al_2024 at commit
 b65ae0c09a53e9efe083d806d617581e6139bdde (Expat).
 Community spectrum reviews are from the version 1 dataset at
 https://doi.org/10.6084/m9.figshare.30131869.v1 (CC-BY-4.0).
 Initiation-context sequences are from Ensembl release 101.
 OpenVax selected models, normalized coordinates and source metadata,
 joined peptide observations and reviews, calculated peptide intervals
 and extracted initiation-context sequences. The distributed NOTICE.txt
 and manifest.json files retain attribution, checksums and changes.

Files: orfdata/data/ires/*
Copyright: 2026 Rfam contributors
License: CC0-1.0
Comment:
 Human IRES seed sequences from Rfam 15.1, selected and merged by OpenVax.
 Source attribution and checksums are embedded in the JSON resource.

Files: orfdata/data/viral/*
       tests/data/viral/*
Copyright: NCBI and the submitters of RefSeq NC_001526.4
License: NCBI
Comment:
 OpenVax extracted nine CDS annotations and reference sequences from
 NC_001526.4 and added native and GDC placements. The source record is
 retained in tests/data/viral/NC_001526.4.gb.gz. Attribution, changes and
 checksums are recorded in orfdata/data/viral/NOTICE.md.

Files: tests/data/copy/*
Copyright: 2016 Lawless et al.
License: CC-BY-4.0
Comment:
 Selected supplemental data from https://doi.org/10.1074/mcp.M115.054288.
 GEO RNA data and source metadata are subject to the NCBI terms below.
 OpenVax selected table rows and retained the complete RNA worksheet and
 calibration FASTA; changes and attribution are in NOTICE.md.

Files: tests/data/wang/*
Copyright: 2019 Wang et al.
License: CC-BY-4.0 and Ensembl
Comment:
 Selected source cells from https://doi.org/10.15252/msb.20188503,
 re-encoded as small workbooks by OpenVax, plus Ensembl 83 reference
 records. NOTICE.md and expected.json retain attribution and changes.

Files: tests/data/pfizer/*
       tests/data/kaabinejadian/*
Copyright: 2026 Oziolor et al.
           2026 Kaabinejadian et al.
License: CC0-1.0
Comment:
 Selected numeric data from MassIVE MSV000099729, MSV000099754 and
 MSV000099744, and PRIDE PXD074485, respectively. The original deposits
 are CC0. Original row numbers and source hashes are recorded in the
 fixtures; NOTICE.md or README.md records the selection.

Files: tests/data/pfizer/*/search.fasta
       tests/data/search_reference/dog.fasta
Copyright: UniProt Consortium
License: CC-BY-4.0
Comment:
 Unchanged native UniProt FASTA records selected by OpenVax from
 the deposited search references. See the adjacent NOTICE.md files.

Files: tests/data/ingolia/*
       tests/data/regions/*
       tests/data/pfizer_rna/*
Copyright: 2009 Ingolia et al.
           2026 Oziolor et al.
License: NCBI
Comment:
 Factual slices from GEO GSE13750 and GSE325522/GSE325523/GSE325525.
 The Pfizer sample workbook is a newly encoded container of factual
 sample rows; the original article supplement is not redistributed.
 Ensembl annotation slices retain the Ensembl terms below.
 NOTICE.md and fixture manifests record sources and transformations.

Files: tests/data/ncorf_mammals/S3.xlsx
       tests/data/riborf/SD3.xlsx
Copyright: 2025 Chang et al.
           2024 Yang et al.
License: CC-BY-4.0
Comment:
 Selected supplemental rows from https://doi.org/10.7554/eLife.109128
 and https://doi.org/10.1038/s41467-024-46240-9, respectively.
 OpenVax re-encoded the selected rows; adjacent README.md files retain
 source attribution and document the selections.

Files: tests/data/ncorf_mammals/*.bed
       tests/data/ncorf_mammals/*.pep.fa
Copyright: 2025 Chang et al.
License: Expat
Comment:
 Selected ORFs from https://github.com/gxelab/ncorf_mammals at commit
 9a7baa318fd53f4faf7fa8fe0030e1e2b0d44ee0 (MIT License).

Files: tests/data/references/*.json
       tests/data/*/ensembl*.gz
       tests/data/ncorf_mammals/*ensembl*.gz
       tests/data/riborf/*ensembl*.gz
       tests/data/pfizer_rna/*annotation.gtf.gz
       tests/data/wang/annotation.gtf.gz
Copyright: Ensembl/EMBL-EBI and the original data contributors
License: Ensembl
Comment:
 Small canonical sequence and annotation slices; source URLs and checksums
 are retained in the fixtures and adjacent README.md or NOTICE.md files.
 The reference JSON files also contain source facts and OpenVax metadata.

Files: debian/*
Copyright: 2026 Steffen Moeller <moeller@debian.org>
License: Apache-2.0

License: Apache-2.0
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
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 See the License for the specific language governing permissions and
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Comment:
 On Debian systems, the complete text of the Apache version 2.0 license
 can be found in "/usr/share/common-licenses/Apache-2.0".

License: Expat
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
 in the Software without restriction, including without limitation the rights
 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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 THE SOFTWARE.

License: CC-BY-4.0
 On Debian systems, the complete text of the Creative Commons Attribution
 4.0 International license can be found in
 "/usr/share/common-licenses/CC-BY-4.0".

License: CC0-1.0
 On Debian systems, the complete text of the Creative Commons CC0 1.0
 Universal license can be found in "/usr/share/common-licenses/CC0-1.0".

License: Ensembl
 Ensembl imposes no restrictions on access to, or use of, the data provided
 and the software used to analyse and present it. Ensembl data generated by
 members of the project are available without restriction.
Comment:
 https://www.ensembl.org/info/about/legal/disclaimer.html

License: NCBI
 Databases of molecular data on the NCBI Web site include such examples
 as nucleotide sequences (GenBank), protein sequences, macromolecular
 structures, molecular variation, gene expression, and mapping data. They
 are designed to provide and encourage access within the scientific
 community to sources of current and comprehensive information. Therefore,
 NCBI itself places no restrictions on the use or distribution of the
 data contained therein. Nor do we accept data when the submitter has
 requested restrictions on reuse or redistribution. However, some
 submitters of the original data (or the country of origin of such data)
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 all or a portion of the data (that has been submitted). NCBI is not in
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 no transfer of rights from submitters to NCBI, NCBI has no rights to
 transfer to a third party. Therefore, NCBI cannot provide comment or
 unrestricted permission concerning the use, copying, or distribution
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Comment:
 https://www.ncbi.nlm.nih.gov/home/about/policies/