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PR validation testing [Do not merge] #1

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6f699f7
Built basic framework for seq retrieval component
mluypaert Mar 6, 2024
33396e2
Updated input params to match single sequence retrieval and added inp…
mluypaert Mar 7, 2024
14090ac
Added code for basic (+ strand) seq retrieval
mluypaert Mar 7, 2024
29c4dff
Refactored faidx to enable more broad seq functions import
mluypaert Mar 7, 2024
048b9f1
Added support for correct negative strand sequence retrieval (and cha…
mluypaert Mar 7, 2024
26fc878
Added additional python pysam and biopython package installation depe…
mluypaert Mar 7, 2024
3965c48
Updated fasta_file option to support remote URLs
mluypaert Mar 8, 2024
0d2400b
Added Make targets for easy python dependency installation
mluypaert Mar 8, 2024
a759e4d
Sorted python requirements alphabetically
mluypaert Mar 8, 2024
47d62a9
Minor docstring update
mluypaert Mar 8, 2024
50ced5c
Added option to reuse local cache
mluypaert Mar 8, 2024
44dbe05
Prevent reads of partial streamed file after interrupts
mluypaert Mar 8, 2024
3228d45
Refactor to improve code readability
mluypaert Mar 11, 2024
bde10e2
Minor refactor to improve code readability
mluypaert Mar 11, 2024
78d4c63
Unused import cleanup
mluypaert Mar 12, 2024
fee42df
Added framework for PR validation through GH actions
mluypaert Mar 12, 2024
b628658
Added python type testing + included in PR validation
mluypaert Mar 12, 2024
d02d0ab
Python type checking bugfix
mluypaert Mar 12, 2024
51fa3aa
Added main app dependencies as dependency for type testing
mluypaert Mar 12, 2024
4fae5a7
Fixed typing errors reported by mypy
mluypaert Mar 12, 2024
4e25e6f
Updated GH actions runner to current Ubuntu LTS (22.04)
mluypaert Mar 12, 2024
b5e4a98
GH actions checkout version bump (to deprecate node.js v16 usage)
mluypaert Mar 12, 2024
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Unused import cleanup
mluypaert committed Mar 12, 2024

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commit 78d4c639396a3e811492bbb01503def8430bf4a2
1 change: 0 additions & 1 deletion pipeline/seq_retrieval/src/main.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import click
import json
from os import path

import data_mover.data_file_mover as data_file_mover
from seq_region import SeqRegion, chain_seq_region_seqs