WorkingVersion_2

For setuptools the following changes were made:
bin-folder was renamed to bamsurgeon, as the bin-folder naming can cause issues. Furthermore, all files within bin/bamsurgeon were transferred to bamsurgeon (formerly "bin"), as files need to be on PATH. In addition, setuptools writes a automatic script file calling a main function without arguments. Therefore, the main or run functions was renamed and a submain-function was used, which is called by main and can take arguments. The test-command on original github works in the folder, where the test-files lay by calling

addsv -p 1 -v test_data/test_sv.txt -f test_data/testregion_realign.bam -r test_data/Homo_sapiens_chr22_assembly19.fasta -o test_data/testregion_sv_mut.bam --aligner mem --keepsecondary --seed 1234 --inslib test_data/test_inslib.fa

instead

python3 -O bin/addsv.py -p 1 -v test_data/test_sv.txt -f test_data/testregion_realign.bam -r test_data/Homo_sapiens_chr22_assembly19.fasta -o test_data/testregion_sv_mut.bam --aligner mem --keepsecondary --seed 1234 --inslib test_data/test_inslib.fa

test2

Modified setuptools: deleted srcm-part

test1

using setuptools instead hatchling

Pyproject-Test

Release including pyproject-toml to test pip installation

WorkingVersion_1

For setuptools the following changes were made:
bin-folder was renamed to bamsurgeon, as the bin-folder naming can cause issues. Furthermore, all files within bin/bamsurgeon were transferred to bamsurgeon (formerly "bin"), as files need to be on PATH. In addition, setuptools writes a automatic script file calling a main function without arguments. Therefore, the main or run functions was renamed and a submain-function was used, which is called by main and can take arguments. The test-command on original github works in the folder, where the test-files lay by calling

addsv -p 1 -v test_data/test_sv.txt -f test_data/testregion_realign.bam -r test_data/Homo_sapiens_chr22_assembly19.fasta -o test_data/testregion_sv_mut.bam --aligner mem --keepsecondary --seed 1234 --inslib test_data/test_inslib.fa

instead

python3 -O bin/addsv.py -p 1 -v test_data/test_sv.txt -f test_data/testregion_realign.bam -r test_data/Homo_sapiens_chr22_assembly19.fasta -o test_data/testregion_sv_mut.bam --aligner mem --keepsecondary --seed 1234 --inslib test_data/test_inslib.fa