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Commits on Sep 4, 2024

• fixing function call in uniprot

  codyheiser

  committed
  b807c55

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Commits on Nov 2, 2023

• Merge pull request #267 from bnymnsen/master

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  deeenes

  authored
  8bbc1e4

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Commits on Nov 1, 2023

• `unichem` url update

  bnymnsen

  authored
  da49e11

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Commits on Oct 30, 2023

• add missing import to `uniprot`

  bnymnsen

  authored
  decb3bf

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• `string` url update

  bnymnsen

  authored
  023fb51

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Commits on Oct 13, 2023

• `inputs` biogrid and intact url update

  ervau

  committed
  b0916d5

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• `inputs.string` new version url update

  ervau

  committed
  a565074

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Commits on Oct 5, 2023

• Bump version: 0.15.12 → 0.15.13

  deeenes

  committed
  2f7192d

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• `orthology.translate_df`: forward properly `kwargs`

  deeenes

  committed
  bccbaef

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• `ProteinOrthology.translate_df`: fixed access to `source` attr

  deeenes

  committed
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Commits on Sep 29, 2023

• Bump version: 0.15.11 → 0.15.12

  deeenes

  committed
  b928609

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• `Mapper`: uniprot idmapping: remove version information from ensembl IDs

  deeenes

  committed
  183e2e8

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• `Mapper`: uniprot idmapping: addressed IO operation on closed file error

  deeenes

  committed
  5896335

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• fixed `UniprotListMapping.possible`

  deeenes

  committed
  ccb1fcb

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• updated imports of `inputs.uniprot(|_db)`

  deeenes

  committed
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• `Mapper.which_table` uses `MappingInput.possible`

  deeenes

  committed
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• `MappingInput.possible` classmethod: tells if its possible to translate between the given ID pair

  deeenes

  committed
  cc8e5fb

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• `taxonomy`: fixed bug introduced in ccae9ed that compromised to ensembl translation

  deeenes

  committed
  76a2366

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• fixed `force_sets` option in `common.swap_dict`

  deeenes

  committed
  efa073f

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• split off db related parts from `inputs.uniprot` into `inputs.uniprot_db`

  deeenes

  committed
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• `uniprot.idmapping_idtypes`: metadata & allowed ID types in the idmapping api

  deeenes

  committed
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Commits on Sep 28, 2023

• Bump version: 0.15.10 → 0.15.11

  deeenes

  committed
  0995796

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• poetry update + security related version constraints in dependencies

  deeenes

  committed
  af64c86

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• Bump version: 0.15.9 → 0.15.10

  deeenes

  committed
  8da4e53

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• Merge branch 'pr264'

  deeenes

  committed
  3122e66

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• do taxonomy processing in `inputs`, do not import `taxonomy` in `resources.data_formats`

  deeenes

  committed
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• `inputs.trrust`: use `utils.taxonomy`

  deeenes

  committed
  4580fbc

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• `taxonomy`: some NCBI taxons have multiple common names; selecting the shortest when translating to common name

  deeenes

  committed
  ccae9ed

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• updated Orthology section in book

  deeenes

  committed
  8df8c8c

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• some more docstring updates in `utils.orthology`

  deeenes

  committed
  993d105

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• Bump version: 0.15.8 → 0.15.9

  deeenes

  committed
  6051e8f

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• renaming `utils.homology` to `utils.orthology` + same for all similar class or function names

  deeenes

  committed
  9174921

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• `utils.homology`: major refactoring (name and design changes) + OMA is a new (and default) backend

  deeenes

  committed
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• `common.first_value`: return first non-None value

  deeenes

  committed
  d0df2e0

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• `utils.seq`: use `inputs.uniprot` (removed old API client from `swissprot_seq`)

  deeenes

  committed
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