Fix installation

Author: Karo555

pyproject.toml

@@ -5,25 +5,26 @@ build-backend = "setuptools.build_meta"
 [tool.black]
 line-length = 88
 
-[metadata]
-name = needleman-wunsch
-version = 0.1.0
-description = Needleman-Wunsch
-license = MIT
+[project]
+name = "needleman-wunsch"
+version = "0.1.0"
+description = "Needleman-Wunsch"
+license = {text = "MIT"}
+dependencies = [
+    "matplotlib",
+]
 
+[project.optional-dependencies]
+html = ["jinja2"]
+pdf = ["reportlab"]
 
-[options]
-package_dir = 
-    = src
-packages = find:
+[tool.setuptools]
+package-dir = {"" = "src"}
+packages = {find = {where = ["src"]}}
 
-[options.packages.find]
-where = src
+[project.scripts]
+needleman-wunsch = "aligner.cli:main"
 
-[options.entry_points]
-controle_scripts = 
-    needleman-wunsch = aligner.cli:main
-
-[mypy]
-mypy_path = src
-ignore_missing_imports = True
+[tool.mypy]
+mypy_path = "src"
+ignore_missing_imports = true

src/aligner/cli.py

@@ -2,14 +2,14 @@
 import os
 from aligner.html_report import format_html_report
 from typing import Optional
-from src.aligner.plot import plot_matrix
+from aligner.plot import plot_matrix
 from aligner.pdf_report import write_pdf
-from src.aligner.core import (
+from aligner.core import (
     build_score_matrix,
     traceback as single_traceback,
     trace_all_paths,
 )
-from src.aligner.io import (
+from aligner.io import (
     create_output_dict,
     format_multi_report,
     format_report,
@@ -169,6 +169,9 @@ def main():
 
     if args.output:
         write_report(args.output, report_text)
+    else:
+        # Print report to console when no output file is specified
+        print(report_text)
 
     if args.json_out:
         data = create_output_dict(

src/aligner/core.py

@@ -1,5 +1,5 @@
 from typing import List, Tuple
-from src.aligner.models import Sequence
+from aligner.models import Sequence
 
 
 def build_score_matrix(

src/aligner/io.py

@@ -1,7 +1,6 @@
 import csv
 import json
 from typing import Dict, List, Tuple
-from src.aligner.models import Sequence
 from aligner.models import Sequence