move to src/ based package structure

Author: alpae

pyproject.toml

@@ -33,5 +33,6 @@ requires = ["uv_build>=0.9.14,<0.10.0"]
 build-backend = "uv_build"
 
 [tool.uv.build-backend]
-module-root = "./"
-data = ["omark/assets"]
+module-root = "./src"
+data = ["src/omark/assets"]
+

omark/__init__.py src/omark/__init__.pyomark/__init__.py renamed to src/omark/__init__.py

@@ -17,7 +17,7 @@
 import re
 import jinja2   
 import os
-from omark.utils import LOG
+from .utils import LOG
 
 #This function is called to make sure the input file correspond to OMArk assumption.
 #It return a boolean consisting of whether an errror was detected and print the reason for

omark/assets/summarized_report.txt src/omark/assets/summarized_report.txtomark/assets/summarized_report.txt renamed to src/omark/assets/summarized_report.txt

@@ -17,7 +17,7 @@
 from omamer.hierarchy import get_descendants, get_leaves, get_root_leaf_offsets, get_children
 from tables.exceptions import HDF5ExtError
 import omamer.database
-from omark.utils import LOG
+from .utils import LOG
 import numpy as np
 import tqdm
 

omark/assets/textual_report.txt src/omark/assets/textual_report.txtomark/assets/textual_report.txt renamed to src/omark/assets/textual_report.txt

@@ -15,19 +15,16 @@
         '''
 
 import os
-import omark.files as io
-import omark.species_determination as spd
-import omark.omamer_utils as outils
-import omark.scoring as sc
-import omark.graphics as graph
-from omark.utils import LOG, set_log_level
 import sys
-
-def get_omamer_qscore(omamerfile, dbpath, stordir, taxid=None, contamination= True, original_FASTA_file = None, force = True, isoform_file = None, min_n_species=5, taxonomic_rank= None, extract_conserved_only=True):
+from . import files as io
+from . import species_determination as spd
+from . import omamer_utils as outils
+from . import scoring as sc
+from . import graphics as graph
+from .utils import LOG, set_log_level
 
 
-
-	   
+def get_omamer_qscore(omamerfile, dbpath, stordir, taxid=None, contamination= True, original_FASTA_file = None, force = True, isoform_file = None, min_n_species=5, taxonomic_rank= None, extract_conserved_only=True):
     allres = dict()
 
     basefile = '.'.join(omamerfile.split('/')[-1].split('.')[:-1])