pythonQEPest 2.0.0a3__tar.gz → 2.0.0a4__tar.gz

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 PonyLianna
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 PonyLianna
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonQEPest
-Version: 2.0.0a3
+Version: 2.0.0a4
 Summary: Java QEPest but written in Python
 License-File: LICENSE
 Author: Lina

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/README.md

@@ -1,198 +1,198 @@
-# pythonQEPest
-
-[![pythonQEPest](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml/badge.svg)](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml)
-[![PyPI Version](https://img.shields.io/pypi/v/pythonQEPest)](https://pypi.org/project/pythonQEPest/)
-
-
-Python implementation of QEPest (Quantitative Estimation of Pesticide), a program for scoring molecules as herbicides (QEH), insecticides (QEI), and fungicides (QEF).
-
-Originally published in: [J Cheminform - QEPest](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-014-0042-6)
-Original Program Link is [here](https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-014-0042-6/MediaObjects/13321_2014_42_MOESM2_ESM.zip)  
-
-## Features
-
-- Calculate pesticide scores for herbicidal, insecticidal, and fungicidal activity
-- Command-line interface (CLI)
-- Graphical User Interface (GUI)
-- Support for JSON and TXT output formats
-
-### Pre-built binaries
-
-Download ready-to-use executables from [Releases](https://github.com/PonyLianna/pythonQEPest/releases):
-
-| Platform | Download |
-|----------|----------|
-| Windows CLI | [main.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/main.exe) |
-| Windows GUI | [gui.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/gui.exe) |
-
-
-## Installation
-
-```bash
-pip install pythonQEPest
-```
-
-Or from source:
-
-```bash
-git clone https://github.com/PonyLianna/pythonQEPest.git
-cd pythonQEPest
-poetry install
-```
-
-### With GUI support
-
-```bash
-pip install pythonQEPest[gui]
-# or
-poetry install --extras ui
-```
-
-
-## Quick Start
-
-### CLI
-
-```bash
-pythonqepest -i data.txt -o result.txt
-pythonqepest --input data.txt --format json
-pythonqepest -v  # show version
-```
-
-### GUI
-
-```bash
-pythonqepest-gui
-# or
-python -m pythonQEPest.gui.gui
-```
-
-### Python API
-
-```python
-from pythonQEPest import QEPest, QEPestInput
-
-# Create input data
-qepest = QEPest()
-qepest.initialize_coefficients()
-qepest.initialize_normalisers()
-
-# From individual values
-inp = QEPestInput(
-    name="mol1",
-    mol_weight=240.2127,
-    log_p=3.2392,
-    hbond_acceptors=5,
-    hbond_donors=1,
-    rotatable_bonds=4,
-    aromatic_rings=1
-)
-
-result = qepest.compute_params(inp)
-
-print(result.name)       # mol1
-print(result.data.qe_herb)   # 0.8511
-print(result.data.qe_insect) # 0.5339
-print(result.data.qe_fung)   # 0.6224
-
-# Convert to array
-print(result.to_array())  # ["mol1", 0.6224, 0.8511, 0.5339]
-```
-
-## Input Format
-
-The input file should be a tab-separated text file with the following columns:
-
-| Column | Description |
-|--------|-------------|
-| Name   | Molecule name |
-| MW     | Molecular weight (g/mol) |
-| LogP   | Hydrophobicity (octanol-water partition coefficient) |
-| HBA    | Number of hydrogen bond acceptors |
-| HBD    | Number of hydrogen bond donors |
-| RB     | Number of rotatable bonds |
-| arR    | Number of aromatic rings |
-
-Example `data.txt`:
-
-```
-Name	MW	LogP	HBA	HBD	RB	arR
-mol1	240.2127	3.2392	5	1	4	1
-mol2	249.091	3.0273	3	1	5	1
-mol3	308.354	2.1086	1	0	7	1
-```
-
-## Output Format
-
-### TXT (default output for CLI)
-
-```
-Name	QEF	QEH	QEI
-mol1	0.6224	0.8511	0.5339
-mol2	0.7310	0.9750	0.6913
-```
-
-### JSON
-
-```json
-[
-  {"name": "mol1", "qe_fung": 0.6224, "qe_herb": 0.8511, "qe_insect": 0.5339},
-  {"name": "mol2", "qe_fung": 0.731, "qe_herb": 0.975, "qe_insect": 0.6913}
-]
-```
-
-## Configuration
-
-### Custom Coefficients
-
-```python
-from pythonQEPest import QEPest
-
-custom_coefficients = {
-    "herb": [
-        (70.77, 283.0, 84.97, -1.185),
-        (93.81, 3.077, 1.434, 0.6164),
-        # ... 6 tuples total
-    ],
-    "insect": [...],
-    "fung": [...]
-}
-
-qepest = QEPest(coefficients=custom_coefficients)
-```
-
-### Custom Normalisers
-
-```python
-from pythonQEPest import QEPest
-from pythonQEPest.dto.normalisation.Normaliser import Normaliser
-
-qepest = QEPest(normalisers={"herb": Normaliser(...), ...})
-```
-
-## CLI Options
-
-| Option | Description | Default |
-|--------|-------------|---------|
-| `-i`, `--input` | Input file path | data.txt |
-| `-o`, `--output` | Output file path | data.out.txt |
-| `-f`, `--format` | Output format (json, txt) | txt |
-| `-v`, `--version` | Show version | - |
-
-## Development
-
-### Run tests
-
-```bash
-poetry run pytest
-```
-
-### Build
-
-```bash
-# CLI executable
-poetry run poe build-simple
-
-# GUI executable
-poetry run poe build-gui
-```
+# pythonQEPest
+
+[![pythonQEPest](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml/badge.svg)](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml)
+[![PyPI Version](https://img.shields.io/pypi/v/pythonQEPest)](https://pypi.org/project/pythonQEPest/)
+
+
+Python implementation of QEPest (Quantitative Estimation of Pesticide), a program for scoring molecules as herbicides (QEH), insecticides (QEI), and fungicides (QEF).
+
+Originally published in: [J Cheminform - QEPest](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-014-0042-6)
+Original Program Link is [here](https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-014-0042-6/MediaObjects/13321_2014_42_MOESM2_ESM.zip)  
+
+## Features
+
+- Calculate pesticide scores for herbicidal, insecticidal, and fungicidal activity
+- Command-line interface (CLI)
+- Graphical User Interface (GUI)
+- Support for JSON and TXT output formats
+
+### Pre-built binaries
+
+Download ready-to-use executables from [Releases](https://github.com/PonyLianna/pythonQEPest/releases):
+
+| Platform | Download |
+|----------|----------|
+| Windows CLI | [main.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/main.exe) |
+| Windows GUI | [gui.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/gui.exe) |
+
+
+## Installation
+
+```bash
+pip install pythonQEPest
+```
+
+Or from source:
+
+```bash
+git clone https://github.com/PonyLianna/pythonQEPest.git
+cd pythonQEPest
+poetry install
+```
+
+### With GUI support
+
+```bash
+pip install pythonQEPest[gui]
+# or
+poetry install --extras ui
+```
+
+
+## Quick Start
+
+### CLI
+
+```bash
+pythonqepest -i data.txt -o result.txt
+pythonqepest --input data.txt --format json
+pythonqepest -v  # show version
+```
+
+### GUI
+
+```bash
+pythonqepest-gui
+# or
+python -m pythonQEPest.gui.gui
+```
+
+### Python API
+
+```python
+from pythonQEPest import QEPest, QEPestInput
+
+# Create input data
+qepest = QEPest()
+qepest.initialize_coefficients()
+qepest.initialize_normalisers()
+
+# From individual values
+inp = QEPestInput(
+    name="mol1",
+    mol_weight=240.2127,
+    log_p=3.2392,
+    hbond_acceptors=5,
+    hbond_donors=1,
+    rotatable_bonds=4,
+    aromatic_rings=1
+)
+
+result = qepest.compute_params(inp)
+
+print(result.name)       # mol1
+print(result.data.qe_herb)   # 0.8511
+print(result.data.qe_insect) # 0.5339
+print(result.data.qe_fung)   # 0.6224
+
+# Convert to array
+print(result.to_array())  # ["mol1", 0.6224, 0.8511, 0.5339]
+```
+
+## Input Format
+
+The input file should be a tab-separated text file with the following columns:
+
+| Column | Description |
+|--------|-------------|
+| Name   | Molecule name |
+| MW     | Molecular weight (g/mol) |
+| LogP   | Hydrophobicity (octanol-water partition coefficient) |
+| HBA    | Number of hydrogen bond acceptors |
+| HBD    | Number of hydrogen bond donors |
+| RB     | Number of rotatable bonds |
+| arR    | Number of aromatic rings |
+
+Example `data.txt`:
+
+```
+Name	MW	LogP	HBA	HBD	RB	arR
+mol1	240.2127	3.2392	5	1	4	1
+mol2	249.091	3.0273	3	1	5	1
+mol3	308.354	2.1086	1	0	7	1
+```
+
+## Output Format
+
+### TXT (default output for CLI)
+
+```
+Name	QEF	QEH	QEI
+mol1	0.6224	0.8511	0.5339
+mol2	0.7310	0.9750	0.6913
+```
+
+### JSON
+
+```json
+[
+  {"name": "mol1", "qe_fung": 0.6224, "qe_herb": 0.8511, "qe_insect": 0.5339},
+  {"name": "mol2", "qe_fung": 0.731, "qe_herb": 0.975, "qe_insect": 0.6913}
+]
+```
+
+## Configuration
+
+### Custom Coefficients
+
+```python
+from pythonQEPest import QEPest
+
+custom_coefficients = {
+    "herb": [
+        (70.77, 283.0, 84.97, -1.185),
+        (93.81, 3.077, 1.434, 0.6164),
+        # ... 6 tuples total
+    ],
+    "insect": [...],
+    "fung": [...]
+}
+
+qepest = QEPest(coefficients=custom_coefficients)
+```
+
+### Custom Normalisers
+
+```python
+from pythonQEPest import QEPest
+from pythonQEPest.dto.normalisation.Normaliser import Normaliser
+
+qepest = QEPest(normalisers={"herb": Normaliser(...), ...})
+```
+
+## CLI Options
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `-i`, `--input` | Input file path | data.txt |
+| `-o`, `--output` | Output file path | data.out.txt |
+| `-f`, `--format` | Output format (json, txt) | txt |
+| `-v`, `--version` | Show version | - |
+
+## Development
+
+### Run tests
+
+```bash
+poetry run pytest
+```
+
+### Build
+
+```bash
+# CLI executable
+poetry run poe build-simple
+
+# GUI executable
+poetry run poe build-gui
+```

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/pyproject.toml

@@ -1,46 +1,46 @@
-[project]
-name = "pythonQEPest"
-version = "2.0.0a3"
-description = "Java QEPest but written in Python"
-readme = "README.md"
-requires-python = ">=3.12,<3.15"
-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"]
-rdkit = ["rdkit (>=2024.3.1,<2026.0.0)"]
-
-[project.scripts]
-pythonqepest = "pythonQEPest.cli.cli:main"
-
-[project.gui-scripts]
-pythonqepest-gui = "pythonQEPest.gui.gui:main"
-
-[tool.poetry]
-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)",
-    "pytest-cov (>=7.0.0,<8.0.0)",
-    "twine (>=6.2.0,<7.0.0)",
-]
-
-[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"
-build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py"
-publish-pypi = "twine upload --repository pythonQEPest dist/*"
+[project]
+name = "pythonQEPest"
+version = "2.0.0a4"
+description = "Java QEPest but written in Python"
+readme = "README.md"
+requires-python = ">=3.12,<3.15"
+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"]
+rdkit = ["rdkit (>=2024.3.1,<2026.0.0)"]
+
+[project.scripts]
+pythonqepest = "pythonQEPest.cli.cli:main"
+
+[project.gui-scripts]
+pythonqepest-gui = "pythonQEPest.gui.gui:main"
+
+[tool.poetry]
+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)",
+    "pytest-cov (>=7.0.0,<8.0.0)",
+    "twine (>=6.2.0,<7.0.0)",
+]
+
+[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"
+build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py"
+publish-pypi = "twine upload --repository pythonQEPest dist/*"

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/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"

{pythonqepest-2.0.0a3 → pythonqepest-2.0.0a4}/pythonQEPest/__init__.py

@@ -1,11 +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",
-]
+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-2.0.0a3 → pythonqepest-2.0.0a4}/pythonQEPest/cli/__init__.py

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