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Releases: DominikBuchner/BOLDigger3

3.0.1 released

12 Jun 10:02
@DominikBuchner DominikBuchner
3.0.1
febcbd7

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3.0.1 released Latest
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  • bugfix causing the database download to fail due to missing cookies. The download is now initiated with the session instead of urllib.
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3.0.0 released

13 May 05:34
@DominikBuchner DominikBuchner
3.0.0
be93663
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Learn about vigilant mode.

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3.0.0 released
  • the previously monolithic identify workflow has been split into two separate commands: identify and download_db
  • download_db downloads the latest BOLD public data package and converts it to a local DuckDB (.ddb) file
  • BOLDigger3 checks automatically if the local database is already up to date and skips the download if so
  • Requires a valid BOLD account (register at boldsystems.org) — username and password are prompted interactively
  • Credentials are only needed for download_db; identify does not require a login as before
  • identify no has an additional argument pointing at the downloaded database
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2.3.0 released

16 Apr 09:35
@DominikBuchner DominikBuchner
2.3.0
1e06229

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2.3.0 released
  • as BOLD limited the possible number of requests heavily, this is a hotfix to keep BOLDigger3 working.
  • In the meantime I'm already considering a local option for BOLDigger4, so stay tuned.
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2.2.0 released

18 Nov 06:17
@DominikBuchner DominikBuchner
2.2.0
1be5e0d

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2.2.0 released
  • fixed a bug that kept the ID engine stuck at n% whenever one of the request IDs failed to respond. Those request IDs are now being requeued after 15 minutes and downloaded in a second iteration.
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2.1.4 released

14 Aug 05:49
@DominikBuchner DominikBuchner
2.1.4
959fbcc

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2.1.4 released
  • Bugfix that caused the ID engine to no longer work. BOLD keeps on silently changing API commands -.-
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2.1.3 released

13 Aug 09:57
@DominikBuchner DominikBuchner
2.1.3
3577cb3

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2.1.3 released
  • fixed a bug where streaming to excel would result in an overflow
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2.1.2 released

24 Jul 19:19
@DominikBuchner DominikBuchner
2.1.2
7e4f1f2

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2.1.2 released
  • Implemented the % similarity definition by BOLD. The output of BOLDigger now matches the Web Interface perfectly!
  • Fixed a bug where identifying multiple fasta files in the same folder led to an error.
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2.1.1 released

22 Jul 12:02
@DominikBuchner DominikBuchner
2.1.1
7e4f1f2

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2.1.1 released
  • Fixed a bug where the database string led to a different endpoint than the BOLD website
  • There's still some disagreement between the web interface and the downloadable JSONL. I'm in contact with BOLD regarding this matter.
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2.0.2 released

22 Jul 05:43
@DominikBuchner DominikBuchner
2.0.2
88ee5d9

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2.0.2 released
  • bugfix that caused the data cleaning function to fail when taxonomic columns where completly empty.
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2.0.1 released

20 Jul 05:51
@DominikBuchner DominikBuchner
2.0.1
76e9991

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2.0.1 released
  • Fixed a bug, where BOLDigger3 failed when selecting database 2. For unknown reasons BOLD does not return a status when db 2 is used, so the status column has to be updated manually
  • Fixed a bug where BOLDigger3 would crash if only no-matches are returned for a query
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