Fixes

.github/workflows/python-package.yml

@@ -7,7 +7,8 @@ on:
   push:
     branches: [ "development" ]
   pull_request:
-    branches: [ "development" , "release" ]
+    branches: [ "development", "release" ]
+  workflow_dispatch:
 
 jobs:
   build:
@@ -16,30 +17,40 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: [ "3.10", "3.11", "3.12" ]
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install poetry
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install poetry
-
-    - name: Install dependencies
-      run: |
-        poetry install
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        poetry run poe test
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry
+
+      - name: Install dependencies
+        run: |
+          poetry install --with dev
+
+      # - name: Lint with flake8
+      #   run: |
+      #     # stop the build if there are Python syntax errors or undefined names
+      #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest (coverage)
+        run: |
+          poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40
+
+      - name: Build dist
+        run: |
+          poetry build
+
+      - name: Install built wheel and smoke import
+        run: |
+          python -m pip install dist/*.whl
+          python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput(name='smoke', mol_weight=240.2127, log_p=3.2392, hbond_acceptors=5, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1))"

.pre-commit-config.yaml

@@ -8,6 +8,7 @@ repos:
         pass_filenames: false
         files: \.py$
         exclude: ^tests/data/
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -17,3 +18,27 @@ repos:
         files: \.py$
       - id: check-yaml
         files: \.ya?ml$
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.13
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - flake8-bugbear
+          - flake8-comprehensions
+        args:
+          - --max-line-length=88
+          - --extend-ignore=E203,W503

README.md

@@ -13,7 +13,7 @@ The rewritten version of Java QEPest. Made by PonyLianna (https://github.com/Pon
 You can use a .exe version (which you can find at https://github.com/PonyLianna/pythonQEPest/releases)
 or run it by yourself.
 
-To be able to do it you'll need `Python >3.12 + pip3` (https://www.python.org/downloads/)
+To be able to do it you'll need `Python >3.10 + pip3` (https://www.python.org/downloads/)
 
 Further installation (I skip venv here):
 

pyproject.toml

@@ -1,37 +1,42 @@
 [project]
 name = "pythonQEPest"
-version = "1.1.2"
+version = "1.1.4"
 description = "The rewritten version of Java QEPest"
 readme = "README.md"
 requires-python = ">=3.10,<3.13"
-authors = [
-    { name = "Lina", email = "knocker767@gmail.com" }
-]
-dependencies = [
-    "pydantic==2.12.5",
-    "python-dotenv>=1.2.1,<2.0.0"
-]
+authors = [{ name = "Lina", email = "knocker767@gmail.com" }]
+dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0"]
 
 [project.optional-dependencies]
 gui = ["pyperclip>=1.11.0,<2.0.0"]
 
+[project.scripts]
+pythonqepest = "pythonQEPest.cli.cli:main"
+
+[project.gui-scripts]
+pythonqepest-gui = "pythonQEPest.gui.gui:main"
+
 [tool.poetry]
-packages = [
-    { include = "pythonQEPest" }
-]
+packages = [{ include = "pythonQEPest" }]
 
 [dependency-groups]
 dev = [
     "pytest (>=9.0.0)",
     "pre-commit (>=4.3.0,<5.0.0)",
     "pyinstaller (>=6.18.0,<7.0.0)",
-    "poethepoet[poetry_plugin] (>=0.39.0)"
+    "poethepoet[poetry_plugin] (>=0.39.0)",
+    "pytest-cov (>=7.0.0,<8.0.0)",
 ]
 
 [build-system]
 requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"]
 build-backend = "poetry.core.masonry.api"
 
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503"]
+exclude = [".venv", ".git", "__pycache__", "build", "dist"]
+
 [tool.poe.tasks]
 test = "pytest"
 build-simple = "pyinstaller --onefile pythonQEPest/main.py"

pythonQEPest/.env.example

@@ -1,4 +1,4 @@
-LOG_LEVEL = "INFO"
-LOG_FILE_LOCATION = "logs/app.log"
+LOG_LEVEL="INFO"
+LOG_FILE_LOCATION="logs/app.log"
 
-APP_DEBUG_ENABLE = "false"
+APP_DEBUG_ENABLE="false"

pythonQEPest/__init__.py

@@ -0,0 +1,11 @@
+from pythonQEPest.core import QEPest
+from pythonQEPest.dto import QEPestData
+from pythonQEPest.dto import QEPestInput
+from pythonQEPest.dto import QEPestOutput
+
+__all__ = [
+    "QEPest",
+    "QEPestData",
+    "QEPestInput",
+    "QEPestOutput",
+]

pythonQEPest/cli/__init__.py

@@ -0,0 +1,7 @@
+def main():
+    from pythonQEPest.cli.cli import main as _main
+
+    return _main()
+
+
+__all__ = ["main"]

pythonQEPest/cli/cli.py

@@ -1,24 +1,32 @@
-from pythonQEPest.core.qepest_meta import QEPestMeta
-from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols
-from pythonQEPest.helpers.get_values_from_line import get_values_from_line
+from __future__ import annotations
+
+import argparse
 import logging
+from importlib.metadata import PackageNotFoundError, version
+from pathlib import Path
+from typing import Sequence
 
+from pythonQEPest.core import QEPestMeta
+from pythonQEPest.dto import QEPestFile
+from pythonQEPest.helpers import get_num_of_cols
+from pythonQEPest.helpers.get_values_from_line import get_values_from_line
 
 logger = logging.getLogger(__name__)
 
 
 class CLI:
     qepest: QEPestMeta | None = None
 
-    def __init__(self, qepest: QEPestMeta):
+    def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile):
         self.qepest = qepest
+        self.qepest_file = qepest_file
 
     def read_file_and_compute_params(self):
         try:
-            with open(self.qepest.input_file, "r") as file:
+            with open(self.qepest_file.input_file, "r") as file:
                 lines = file.readlines()
 
-            with open(f"{self.qepest.input_file}.out", "w") as wr:
+            with open(self.qepest_file.output_file, "w") as wr:
                 for index, line in enumerate(lines):
                     if index == 0:
                         if get_num_of_cols(line) != self.qepest.col_number:
@@ -31,9 +39,11 @@ def read_file_and_compute_params(self):
                         if get_num_of_cols(line) == self.qepest.col_number:
                             d_values = get_values_from_line(line.split("\t"))
                             self.qepest.get_qex_values(d_values)
-                            splitted_line = line.split('\t')[0]
+                            splitted_line = line.split("\t")[0]
                             wr.write(
-                                f"{splitted_line} {self.qepest.qex.qe_h} {self.qepest.qex.qe_i} {self.qepest.qex.qe_f}{chr(10)}"
+                                f"{splitted_line} {self.qepest.qex.qe_h} "
+                                + f"{self.qepest.qex.qe_i} {self.qepest.qex.qe_f}"
+                                + f"{chr(10)}"
                             )
                         else:
                             er = f"Error: Line {index} does not have seven elements."
@@ -46,5 +56,71 @@ def read_file_and_compute_params(self):
 
         except FileNotFoundError as e:
             self.qepest.noError = False
-            logger.error("Error: can't find : %s", input)
+            logger.error("Error: can't find : %s", self.qepest_file.input_file)
             logger.exception(e)
+
+
+def _resolve_package_version() -> str:
+    try:
+        return version("pythonQEPest")
+    except PackageNotFoundError:
+        pass
+
+    try:
+        import tomllib  # py3.11+
+
+        pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
+        data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
+        return data["project"]["version"]
+    except Exception:
+        return "0+unknown"
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="pythonqepest",
+        description="Compute QEPest scores from a tab-separated input file.",
+    )
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"%(prog)s {_resolve_package_version()}",
+        help="Show program's version number.",
+    )
+    parser.add_argument(
+        "-i",
+        "--input",
+        default="data.txt",
+        help="Path to input tab-separated file with "
+        + "QEPest descriptors (default: data.txt).",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        default="data.txt.out",
+        help="Path to output tab-separated file with "
+        + "QEPest descriptors (default: data.txt.out).",
+    )
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    from dotenv import load_dotenv
+
+    from pythonQEPest.core.qepest import QEPest
+    from pythonQEPest.logger import init_logger
+
+    args = build_parser().parse_args(argv)
+
+    load_dotenv()
+    init_logger()
+
+    cli = CLI(
+        qepest=QEPest(),
+        qepest_file=QEPestFile(input_file=args.input, output_file=args.output),
+    )
+    cli.read_file_and_compute_params()
+
+    return 0 if cli.qepest and cli.qepest.noError else 1

pythonQEPest/core/__init__.py

@@ -1,5 +1,5 @@
-from .qepest_meta import QEPestMeta
 from .qepest import QEPest
+from .qepest_meta import QEPestMeta
 
 __all__ = [
     "QEPestMeta",

pythonQEPest/core/qepest.py

@@ -13,7 +13,9 @@
 
 class QEPest(QEPestMeta):
     def compute_params(self, data_input: QEPestInput) -> QEPestOutput:
-        self.get_qex_values(get_values_from_line(list(data_input.model_dump().values())))
+        self.get_qex_values(
+            get_values_from_line(list(data_input.model_dump().values()))
+        )
         return QEPestOutput(data=self.qex, name=data_input.name)
 
     def get_qex_values(self, d) -> None:
@@ -42,30 +44,30 @@ def log_compute_df(func, index, lst, data_lst) -> float:
 
     def initialize_coefficients(self) -> None:
         coefficients = {
-            'herb': [
+            "herb": [
                 (70.77, 283.0, 84.97, -1.185),  # mwH
                 (93.81, 3.077, 1.434, 0.6164),  # logpH
                 (117.6, 2.409, 1.567, 7.155),  # hbaH
                 (233.4, 0.4535, -1.48, 4.47),  # hbdH
                 (84.7, 4.758, -2.423, 5.437),  # rbH
-                (301.8, 1.101, 0.8869, -22.81)  # arRCH
+                (301.8, 1.101, 0.8869, -22.81),  # arRCH
             ],
-            'insect': [
+            "insect": [
                 (76.38, 298.3, 83.64, 1.912),  # mwI
                 (74.27, 4.555, -2.193, -2.987),  # logpI
                 (139.4, 1.363, 1.283, 0.5341),  # hbaI
                 (670.6, -1.163, 0.7856, 0.7951),  # hbdI
                 (65.49, 6.219, -2.448, 5.318),  # rbI
-                (287.5, 0.305, 1.554, -88.64)  # arRCI
+                (287.5, 0.305, 1.554, -88.64),  # arRCI
             ],
-            'fung': [
+            "fung": [
                 (51.03, 314.2, -56.31, 2.342),  # mwF
                 (50.73, 3.674, -1.238, 2.067),  # logpF
                 (73.79, 1.841, 1.326, 0.5158),  # hbaF
                 (164.7, -0.9762, -2.027, 1.384),  # hbdF
                 (40.91, 1.822, 2.582, 0.6235),  # rbF
-                (134.4, 0.8383, 1.347, -31.17)  # arRCF
-            ]
+                (134.4, 0.8383, 1.347, -31.17),  # arRCF
+            ],
         }
 
         for category, data in coefficients.items():