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lots of changes #48

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lots of changes #48

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fface9a
Update Alliance genome URL and delay in UI test
nuin Jun 4, 2024
969904f
Add new SGD test configuration file
nuin Jun 5, 2024
32e63e6
Add new test case and refine UI testing
nuin Jun 20, 2024
94c1895
changes on test
nuin Aug 2, 2024
194ec4b
Refactor imports and remove unused route53_check
nuin Oct 23, 2024
7fc3a98
Refactor FASTA validation and add DB list function.
nuin Oct 23, 2024
6814042
Update dependencies and packages in poetry.lock
nuin Oct 23, 2024
60dcdea
Add needs_parse_seqids function and integrate with makeblastdb
nuin Oct 23, 2024
e3ab993
Add FASTA file processing and database creation functions
nuin Oct 23, 2024
96dc177
Add mod-based MD5 check conditionality and reformat process_entry
nuin Oct 23, 2024
f974ca9
Refactor FTP/HTTP file handling and format output strings
nuin Oct 23, 2024
bfc45d4
Add keep-files option to retain FASTA files after processing
nuin Oct 23, 2024
fc9a1fc
Refactor utils and create_blast_db, remove keep_files option
nuin Oct 23, 2024
75eaefd
Simplify utils.py functions and clean up create_blast_db.py imports
nuin Oct 23, 2024
5c3cd07
Refactor utils and create_blast_db for better readability
nuin Oct 23, 2024
0039210
Merge branch 'main' into more_tests
nuin Oct 23, 2024
d7d9f40
Enhance logging and file handling in utility functions
nuin Oct 23, 2024
2428d3d
Add support for FASTA file cleanup after processing
nuin Oct 23, 2024
86960d0
Add genome browser mapping function.
nuin Oct 23, 2024
32f329b
Refactor logging and progress display
nuin Oct 23, 2024
3a57502
Enhance logging and user feedback; refactor file operations
nuin Oct 23, 2024
e1361df
Add functions to copy config files and update genome browser map
nuin Oct 23, 2024
42f5d29
Refactor genome browser mapping & handle makeblastdb errors
nuin Oct 23, 2024
6859a5f
Remove extra blank lines in test files
nuin Oct 23, 2024
61a01b4
Enhance genome browser map logging and error handling
nuin Oct 23, 2024
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1,643 changes: 854 additions & 789 deletions poetry.lock
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3 changes: 1 addition & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,14 @@ authors = ["Adam Wright, Paulo Nuin and the Alliance of Genome Resources"]
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
python = "^3.9"
rich = "^13.5.2"
click = "^8.1.6"
requests = "^2.31.0"
tqdm = "^4.65.0"
wget = "^3.2"
pyyaml = "^6.0.1"
boto3 = "^1.28.46"
biopython = "^1.81"
py-fasta-validator = "^0.6"
python-dotenv = "^1.0.0"
slack-sdk = "^3.23.0"
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