diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..57b2ddc --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,50 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: pythonQEPest + +on: + push: + branches: [ "development" ] + pull_request: + branches: [ "development", "release" ] + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-24.04 + strategy: + fail-fast: false + matrix: + python-version: [ "3.12", "3.13", "3.14" ] + + steps: + - uses: actions/checkout@v6 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v6 + with: + python-version: ${{ matrix.python-version }} + + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + version: latest + virtualenvs-create: true + virtualenvs-in-project: true + + - name: Install dependencies + run: | + poetry install --with dev --no-interaction + + - name: Test with pytest (coverage) + run: | + poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 + + - name: Build dist + run: | + poetry build + + - name: Install built wheel and smoke import + run: | + python -m pip install dist/*.whl + python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput(name='smoke', mol_weight=240.2127, log_p=3.2392, hbond_acceptors=5, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1))" diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..64d49ae --- /dev/null +++ b/.gitignore @@ -0,0 +1,216 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[codz] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +# Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# uv.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +# poetry.lock +# poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +# pdm.lock +# pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +# pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# Redis +*.rdb +*.aof +*.pid + +# RabbitMQ +mnesia/ +rabbitmq/ +rabbitmq-data/ + +# ActiveMQ +activemq-data/ + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +# .idea/ + +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ + +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. However, if you prefer, +# you could uncomment the following to ignore the entire vscode folder +# .vscode/ + +# Ruff stuff: +.ruff_cache/ + +# PyPI configuration file +.pypirc + +# Marimo +marimo/_static/ +marimo/_lsp/ +__marimo__/ + +# Streamlit +.streamlit/secrets.toml \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 19af9a4..a7e2f6d 100644 --- a/.pre-commit-config.yaml +++ b/.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 \ No newline at end of file diff --git a/README.md b/README.md index 7210b9c..6e4f552 100644 --- a/README.md +++ b/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): diff --git a/poetry.lock b/poetry.lock index c196542..90ab610 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,15 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. 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+content-hash = "29c0863bfefcb10cd0abfe597cd27281c5e3149ffbbe502e0fed03241e73826c" diff --git a/pyproject.toml b/pyproject.toml index 8a02438..5f25736 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,29 +1,43 @@ -[tool.poetry] +[project] name = "pythonQEPest" -version = "1.1.0" -description = "" -authors = ["Lina "] +version = "1.4.0" +description = "Java QEPest in Python" readme = "README.md" -packages = [ - { include = "pythonQEPest" } -] -[tool.poetry.dependencies] -python = ">=3.9,<3.13" -pydantic = "2.11.7" +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"] + +[project.scripts] +pythonqepest = "pythonQEPest.cli.cli:main" -[tool.poetry.group.dev.dependencies] -pytest = "^8.4.1" -pre-commit = "^4.2.0" -pyinstaller = "^6.15.0" -poethepoet = "^0.36.0" +[project.gui-scripts] +pythonqepest-gui = "pythonQEPest.gui.gui:main" -[tool.poetry.group.ui.dependencies] -pyperclip = "^1.9.0" +[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)", +] [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" \ No newline at end of file +build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py" diff --git a/pythonQEPest/.env.example b/pythonQEPest/.env.example new file mode 100644 index 0000000..63f511b --- /dev/null +++ b/pythonQEPest/.env.example @@ -0,0 +1,4 @@ +LOG_LEVEL="INFO" +LOG_FILE_LOCATION="logs/app.log" + +APP_DEBUG_ENABLE="false" \ No newline at end of file diff --git a/pythonQEPest/__init__.py b/pythonQEPest/__init__.py index e69de29..aff02f2 100644 --- a/pythonQEPest/__init__.py +++ b/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", +] diff --git a/pythonQEPest/cli/__init__.py b/pythonQEPest/cli/__init__.py index e69de29..841f944 100644 --- a/pythonQEPest/cli/__init__.py +++ b/pythonQEPest/cli/__init__.py @@ -0,0 +1,7 @@ +def main(): + from pythonQEPest.cli.cli import main as _main + + return _main() + + +__all__ = ["main"] diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index eb98d32..80a01ca 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -1,47 +1,91 @@ -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 - - -class CLI: - qepest: QEPestMeta | None = None - - def __init__(self, qepest: QEPestMeta): - self.qepest = qepest - - def read_file_and_compute_params(self): - try: - with open(self.qepest.input_file, "r") as file: - lines = file.readlines() - - with open(f"{self.qepest.input_file}.out", "w") as wr: - for index, line in enumerate(lines): - if index == 0: - if get_num_of_cols(line) != self.qepest.col_number: - er = f"Error: Line {index} does not have seven elements." - print(er) - self.qepest.noError = False - break - wr.write("Name QEH QEI QEF\n") - else: - 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] - wr.write( - f"{splitted_line} {self.qepest.qex.qe_h} {self.qepest.qex.qe_i} {self.qepest.qex.qe_f}{chr(10)}" - # chr(10) = \n - ) - else: - er = f"Error: Line {index} does not have seven elements." - print(er) - self.qepest.noError = False - if self.qepest.noError: - print("Computation completed") - else: - print("Finished with errors") - - except FileNotFoundError as e: - self.qepest.noError = False - print(f"Error: can't find : {input}") - print(e) +from __future__ import annotations + +import argparse +import logging +from importlib.metadata import PackageNotFoundError, version +from pathlib import Path +from typing import Sequence + +from pythonQEPest.dto import QEPestFile +from pythonQEPest.services.QEPestFileService import QEPestFileService + +logger = logging.getLogger(__name__) + + +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.out.txt", + help="Path to output tab-separated file with " + + "QEPest descriptors (default: data.txt.out).", + ) + + parser.add_argument( + "-f", + "--format", + default="txt", + help="Format to output file with " + "QEPest (json, txt).", + ) + 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() + + logger.debug("CLI initiated") + logger.info(f"CLI args: {argv}") + + service = QEPestFileService( + qepest=QEPest(), + qepest_file=QEPestFile( + input_file=args.input, output_file=args.output, format=args.format + ), + ) + + service.read_file_and_compute_params() + + return 0 if not service.error else 1 diff --git a/pythonQEPest/config/__init__.py b/pythonQEPest/config/__init__.py new file mode 100644 index 0000000..1f050c1 --- /dev/null +++ b/pythonQEPest/config/__init__.py @@ -0,0 +1,7 @@ +from .qepest_default import qepest_default +from .normalise import normalise_default + +__all__ = [ + "normalise_default", + "qepest_default", +] diff --git a/pythonQEPest/config/normalise.py b/pythonQEPest/config/normalise.py new file mode 100644 index 0000000..666d681 --- /dev/null +++ b/pythonQEPest/config/normalise.py @@ -0,0 +1,12 @@ +normalise_default = { + "herb": (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), + "insect": ( + 78.2919965, + 71.2829691, + 133.9224801, + 331.170104, + 70.5540709, + 193.0023343, + ), + "fung": (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), +} diff --git a/pythonQEPest/config/qepest_default.py b/pythonQEPest/config/qepest_default.py new file mode 100644 index 0000000..93293c7 --- /dev/null +++ b/pythonQEPest/config/qepest_default.py @@ -0,0 +1,26 @@ +qepest_default = { + "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 + ], + "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 + ], + "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 + ], +} diff --git a/pythonQEPest/core/__init__.py b/pythonQEPest/core/__init__.py index e69de29..30b354a 100644 --- a/pythonQEPest/core/__init__.py +++ b/pythonQEPest/core/__init__.py @@ -0,0 +1,7 @@ +from .qepest import QEPest +from .qepest_meta import QEPestMeta + +__all__ = [ + "QEPestMeta", + "QEPest", +] diff --git a/pythonQEPest/core/qepest.py b/pythonQEPest/core/qepest.py index aed1a08..f0716ef 100644 --- a/pythonQEPest/core/qepest.py +++ b/pythonQEPest/core/qepest.py @@ -1,72 +1,126 @@ +import logging import math +from typing import Optional, List + +from pydantic import create_model, BaseModel from pythonQEPest.core.qepest_meta import QEPestMeta -from pythonQEPest.dto.QEPestData import QEPestData from pythonQEPest.dto.QEPestInput import QEPestInput from pythonQEPest.dto.QEPestOutput import QEPestOutput +from pythonQEPest.dto.normalisation.Normaliser import Normaliser from pythonQEPest.helpers.check_nan import check_nan from pythonQEPest.helpers.compute_df import compute_df from pythonQEPest.helpers.get_values_from_line import get_values_from_line -from pythonQEPest.helpers.norm import norm_h, norm_f, norm_i from pythonQEPest.helpers.round_to_4digs import round_to_4digs +logger = logging.getLogger(__name__) + class QEPest(QEPestMeta): + + def __init__(self, *args, **kwargs): + self.coefficients_names = None + self.names = None + + logger.debug("QEPest initialisation") + + logger.info(f"QEPest args: {args}") + logger.info(f"QEPest kwargs: {kwargs}") + + super().__init__(*args, **kwargs) + + logger.debug("QEPest initialisation successful") + + def _log_compute_df(self, func, index, lst, data_lst) -> float: + df_result = compute_df(lst[index], *data_lst[index]) + return math.log(func(df_result, index)) + + def get_names(self) -> List[str]: + self.names = [ + n.split("_")[1] for n in dir(self) if n.startswith("coefficient_") + ] + return self.names + + def get_coefficients_names(self) -> List[str]: + self.coefficients_names = [f"coefficient_{name}" for name in self.names] + return self.coefficients_names + def compute_params(self, data_input: QEPestInput) -> QEPestOutput: - self.get_qex_values(get_values_from_line(list(data_input.dict().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: - def log_compute_df(func, index, lst, data_lst) -> float: - df_result = compute_df(lst[index], *data_lst[index]) - return math.log(func(df_result, index)) + def get_qex_values(self, d) -> BaseModel: + names = self.get_names() + + # Coefficients names = ("coefficients_fung, coefficient_herb...) + coefficients_names = self.get_coefficients_names() - qe_h = 0.0 - qe_i = 0.0 - qe_f = 0.0 + if len(coefficients_names) == 0: + raise ValueError( + "No coefficient_ keys, needs to call " + + "initialize_coefficient and workable config to work" + ) + + # coefficients = [{i: getattr(self, i)} for i in coefficients_names] + + # Splitting by _ to get (fung, herb, etc...) to form qe_fung, qe_herb... + # qe_lst = [] + for z in names: + name = f"qe_{z}" + setattr(self, name, 0.0) d_num = len(d) for i in range(d_num): - qe_h += log_compute_df(func=norm_h, index=i, lst=d, data_lst=self.herb) - qe_i += log_compute_df(func=norm_i, index=i, lst=d, data_lst=self.insect) - qe_f += log_compute_df(func=norm_f, index=i, lst=d, data_lst=self.fung) + for name in names: + self.__dict__[f"qe_{name}"] += self._log_compute_df( + func=self.__dict__[f"normaliser_{name}"].norm, + index=i, + lst=d, + data_lst=self.__dict__[f"coefficient_{name}"], + ) q = [ - round_to_4digs(math.exp(qe_h / d_num)), - round_to_4digs(math.exp(qe_i / d_num)), - round_to_4digs(math.exp(qe_f / d_num)), + round_to_4digs(math.exp(self.__dict__[f"qe_{name}"] / d_num)) + for name in names ] result = check_nan(q) - self.qex = QEPestData(qe_h=result[0], qe_i=result[1], qe_f=result[2]) - - def initialize_coefficients(self) -> None: - coefficients = { - '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 - ], - '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 - ], - '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 - ] - } + fields = {f"qe_{name}": (float, 0.0) for name in names} + dynamic_model = create_model("QEPestData", **fields) + self.qex = dynamic_model( + **{f"qe_{names[idx]}": name for idx, name in enumerate(result)} + ) + + return self.qex + + # TODO: Coefficients must be in other class. + # TODO: Ability to provide whatever we want is a good thingy + def initialize_coefficients(self, coefficients: Optional = None) -> None: + logger.debug("QEPest coefficients initialisation") + coefficients = super().initialize_coefficients() + + logger.debug("QEPest coefficients initialisation successful") for category, data in coefficients.items(): - getattr(self, category).extend(data) + setattr(self, f"coefficient_{category}", data) + + logger.info(f"QEPest coefficients initialisation with {coefficients.items()}") + + # TODO: Same with Normalisers + def initialize_normalisers(self, normalisers: Optional = None) -> None: + logger.debug("QEPest normalisers initialisation") + normalisers = super().initialize_normalisers() + + logger.debug("QEPest normalisers initialisation successful") + + for category, data in normalisers.items(): + setattr(self, f"normaliser_{category}", Normaliser(data)) + + logger.info(f"QEPest normalisers initialisation with {normalisers.items()}") + + +if __name__ == "__main__": + qepest = QEPest() + qepest.get_qex_values(1) diff --git a/pythonQEPest/core/qepest_meta.py b/pythonQEPest/core/qepest_meta.py index 18cb882..a808daf 100644 --- a/pythonQEPest/core/qepest_meta.py +++ b/pythonQEPest/core/qepest_meta.py @@ -1,25 +1,20 @@ import os from abc import abstractmethod, ABC -from pythonQEPest.dto import QEPestInput, QEPestOutput, QEPestData +from pydantic import BaseModel +from pythonQEPest.dto import QEPestInput, QEPestOutput -class QEPestMeta(ABC): - def __init__(self, dirname="data.txt"): - self.qex: QEPestData | None = None - self.herb: list[float] = [] - self.insect: list[float] = [] - self.fung: list[float] = [] +class QEPestMeta(ABC): + def __init__(self, *args, **kwargs): + self.qex: BaseModel | None = None self.col_number: int = 7 self.dir: str = os.getcwd() self.initialize_coefficients() - - self.input_file = os.path.join(self.dir, dirname) - - self.noError: bool = True + self.initialize_normalisers() @abstractmethod def compute_params(self, data_input: QEPestInput) -> QEPestOutput: @@ -30,5 +25,17 @@ def get_qex_values(self, d) -> None: pass @abstractmethod - def initialize_coefficients(self) -> None: - pass + def initialize_coefficients(self, coefficients=None) -> None: + if coefficients is None: + from pythonQEPest.config.qepest_default import qepest_default + + coefficients = qepest_default + return coefficients + + @abstractmethod + def initialize_normalisers(self, normalisers=None) -> None: + if normalisers is None: + from pythonQEPest.config.normalise import normalise_default + + normalisers = normalise_default + return normalisers diff --git a/pythonQEPest/dto/QEPestFile.py b/pythonQEPest/dto/QEPestFile.py new file mode 100644 index 0000000..5ccf5c7 --- /dev/null +++ b/pythonQEPest/dto/QEPestFile.py @@ -0,0 +1,33 @@ +from enum import Enum +from typing import Optional + +from pydantic import BaseModel, model_validator + + +class QEPestFormat(Enum): + TXT = "txt" + JSON = "json" + + +class QEPestFile(BaseModel): + input_file: Optional[str] = None + output_file: Optional[str] = None + format: Optional[QEPestFormat] = QEPestFormat.TXT + + model_config = {"arbitrary_types_allowed": True} + + @model_validator(mode="after") + def set_defaults(self): + if self.input_file is None: + self.input_file = "data.txt" + + if self.format is None: + self.format = QEPestFormat.TXT + + formatted_output = self.input_file.replace(".txt", "").replace(".json", "") + if self.format == QEPestFormat.JSON: + self.output_file = f"{formatted_output}.out.json" + else: + self.output_file = f"{formatted_output}.out.txt" + + return self diff --git a/pythonQEPest/dto/QEPestInput.py b/pythonQEPest/dto/QEPestInput.py index b653ad2..0811f26 100644 --- a/pythonQEPest/dto/QEPestInput.py +++ b/pythonQEPest/dto/QEPestInput.py @@ -26,5 +26,5 @@ def from_array(cls, data: Union[list, tuple, set]): hbond_acceptors=int(data[3]), hbond_donors=int(data[4]), rotatable_bonds=int(data[5]), - aromatic_rings=int(data[6]) + aromatic_rings=int(data[6]), ) diff --git a/pythonQEPest/dto/QEPestOutput.py b/pythonQEPest/dto/QEPestOutput.py index cabcfb3..d5415b2 100644 --- a/pythonQEPest/dto/QEPestOutput.py +++ b/pythonQEPest/dto/QEPestOutput.py @@ -1,16 +1,11 @@ -from pydantic import BaseModel +from typing import Optional -from .QEPestData import QEPestData +from pydantic import BaseModel class QEPestOutput(BaseModel): - data: QEPestData - name: str = "" + data: BaseModel + name: Optional[str] = "" def to_array(self) -> list: - return [ - self.name, - self.data.qe_h, - self.data.qe_i, - self.data.qe_f - ] + return [self.name] + list(self.data.model_dump().values()) diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index 363a87c..3db3c11 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1 +1,6 @@ -from . import QEPestData, QEPestInput, QEPestOutput +from pythonQEPest.dto.QEPestData import QEPestData +from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestFile import QEPestFile, QEPestFormat +from pythonQEPest.dto.QEPestOutput import QEPestOutput + +__all__ = ["QEPestOutput", "QEPestData", "QEPestInput", "QEPestFile", "QEPestFormat"] diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficient.py b/pythonQEPest/dto/coefficients/QEPestCoefficient.py new file mode 100644 index 0000000..27c450f --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficient.py @@ -0,0 +1,57 @@ +from pydantic import BaseModel + +from pythonQEPest.dto.coefficients import QEPestCoefficientNumerics + + +class QEPestCoefficient(BaseModel): + name: str + coefficients: QEPestCoefficientNumerics + + def __init__(self, *args, **kwargs): + if args: + if len(args) != 1: + raise ValueError(f"Expected len(args) == 1, got {len(args)}") + + # In case of {"test": [[1,2,3,4],[1,2,3,4],[1,2,3,4]} + if len(args[0]) == 1: + must_be_dict = args[0] + if isinstance(must_be_dict, dict): + key = list(must_be_dict.keys())[0] + coefficients = QEPestCoefficientNumerics(must_be_dict[key]) + super().__init__(name=key, coefficients=coefficients) + + # In case of ["test", [[1,2,3,4],[1,2,3,4],[1,2,3,4]] + elif len(args[0]) == 2: + arr = args[0] + if ( + isinstance(arr, tuple) + or isinstance(arr, set) + or isinstance(arr, list) + ): + name = arr[0] + coefficients = QEPestCoefficientNumerics(arr[1]) + super().__init__(name=name, coefficients=coefficients) + + elif kwargs: + super().__init__(**kwargs) + else: + raise ValueError( + "No name and coefficients provided. Please provide either a " + + "name and coefficients tuple or keyword arguments." + ) + + +if __name__ == "__main__": + # Example usage + coefficients = QEPestCoefficient( + mw=[0.1, 0.2, 0.3, 0.4], + logp=[0.1, 0.2, 0.3, 0.4], + hba=[0.1, 0.2, 0.3, 0.4], + hbd=[0.1, 0.2, 0.3, 0.4], + rb=[0.1, 0.2, 0.3, 0.4], + ar=[0.1, 0.2, 0.3, 0.4], + ) + print(coefficients) + + coefficients_alternative = QEPestCoefficient([[0.1, 0.2, 0.3, 0.4] * 6]) + print(coefficients_alternative) diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficientList.py b/pythonQEPest/dto/coefficients/QEPestCoefficientList.py new file mode 100644 index 0000000..4975a5d --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficientList.py @@ -0,0 +1,29 @@ +from typing import Optional, List + +from pydantic import BaseModel + +from pythonQEPest.dto.coefficients import QEPestCoefficient + + +class QEPestCoefficientList(BaseModel): + name: Optional[str] + named_coefficients: List[QEPestCoefficient] + + # TODO: Done all the cases and make some sort of docs here, pls + def __init__(self, *args, **kwargs): + if args: + named_coeff = args[0] + if len(named_coeff) == 1: + pass + elif len(named_coeff) > 1: + if isinstance(named_coeff, dict): + lst = [QEPestCoefficient({i: z}) for i, z in named_coeff.items()] + super().__init__(name="generic", named_coefficients=lst) + + elif kwargs: + super().__init__(**kwargs) + else: + raise ValueError( + "No name and coefficients provided. Please provide either a " + + "name and coefficients tuple or keyword arguments." + ) diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py b/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py new file mode 100644 index 0000000..8c51224 --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py @@ -0,0 +1,44 @@ +from pydantic import BaseModel + +CoefficientTuple = tuple[float, float, float, float] + + +class QEPestCoefficientNumerics(BaseModel): + mw: CoefficientTuple + logp: CoefficientTuple + hba: CoefficientTuple + hbd: CoefficientTuple + rb: CoefficientTuple + ar: CoefficientTuple + + def __init__(self, *args, **kwargs): + if args: + # In case of [[1,2,3,4],[1,2,3,4],[1,2,3,4]] + # I don't want it to be a pain to init D: + if len(args) != 1: + raise ValueError( + f"Expected a single list of coefficients, got {len(args)}" + ) + + coefficients = args[0] + if len(coefficients) != 6: + raise ValueError( + "Expected list with structure [[1,2,3,4,5,6], ", + "[1,2,3,4,5,6], [1,...] ...] got ", + f"{len(coefficients)} and {coefficients}", + ) + + coefficients_mapped = { + field: coefficients[i] + for i, field in enumerate(["mw", "logp", "hba", "hbd", "rb", "ar"]) + } + super().__init__(**coefficients_mapped) + + elif kwargs: + super().__init__(**kwargs) + + else: + raise ValueError( + "No coefficients provided. Please provide either a ", + "list of coefficient tuples or keyword arguments.", + ) diff --git a/pythonQEPest/dto/coefficients/__init__.py b/pythonQEPest/dto/coefficients/__init__.py new file mode 100644 index 0000000..94e829f --- /dev/null +++ b/pythonQEPest/dto/coefficients/__init__.py @@ -0,0 +1,7 @@ +from pythonQEPest.dto.coefficients.QEPestCoefficientNumerics import ( + QEPestCoefficientNumerics, +) +from pythonQEPest.dto.coefficients.QEPestCoefficient import QEPestCoefficient +from pythonQEPest.dto.coefficients.QEPestCoefficientList import QEPestCoefficientList + +__all__ = ["QEPestCoefficientNumerics", "QEPestCoefficient", "QEPestCoefficientList"] diff --git a/pythonQEPest/dto/normalisation/Normaliser.py b/pythonQEPest/dto/normalisation/Normaliser.py new file mode 100644 index 0000000..ace3606 --- /dev/null +++ b/pythonQEPest/dto/normalisation/Normaliser.py @@ -0,0 +1,16 @@ +from typing import Union + + +class Normaliser: + def __init__(self, arr: Union[tuple, list]): + # if len(arr) != 6: + # raise ValueError(f"Array must be exact length of 6. Given: {len(arr)}") + + self.arr = arr + + def norm(self, d: Union[int, float], descr: int) -> float: + if descr > len(self.arr): + raise KeyError(f"Out of array. {descr} > {len(self.arr)}") + + max_val = self.arr[int(descr)] + return d / max_val if max_val != 0 else 0.0 diff --git a/pythonQEPest/dto/normalisation/__init__.py b/pythonQEPest/dto/normalisation/__init__.py new file mode 100644 index 0000000..3c2db34 --- /dev/null +++ b/pythonQEPest/dto/normalisation/__init__.py @@ -0,0 +1,3 @@ +from pythonQEPest.dto.normalisation.Normaliser import Normaliser + +__all__ = ["Normaliser"] diff --git a/pythonQEPest/gui/__init__.py b/pythonQEPest/gui/__init__.py index e69de29..23e3466 100644 --- a/pythonQEPest/gui/__init__.py +++ b/pythonQEPest/gui/__init__.py @@ -0,0 +1,7 @@ +def main(): + from pythonQEPest.gui.gui import main as _main + + return _main() + + +__all__ = ["main"] diff --git a/pythonQEPest/gui/actions/__init__.py b/pythonQEPest/gui/actions/__init__.py index e7e4c32..47fdc62 100644 --- a/pythonQEPest/gui/actions/__init__.py +++ b/pythonQEPest/gui/actions/__init__.py @@ -1,3 +1,9 @@ from pythonQEPest.gui.actions.action_clicks import GUIActionsClicks from pythonQEPest.gui.actions.actions_crud import GUIActionsCRUD from pythonQEPest.gui.actions.actions_other import GUIActionsOther + +__all__ = [ + "GUIActionsClicks", + "GUIActionsCRUD", + "GUIActionsOther", +] diff --git a/pythonQEPest/gui/actions/action_clicks.py b/pythonQEPest/gui/actions/action_clicks.py index 10425e0..b302e38 100644 --- a/pythonQEPest/gui/actions/action_clicks.py +++ b/pythonQEPest/gui/actions/action_clicks.py @@ -30,11 +30,12 @@ def resize_columns(self, event): if not col: return - col_index = int(col.replace('#', '')) - 1 - col_id = widget['columns'][col_index] + col_index = int(col.replace("#", "")) - 1 + col_id = widget["columns"][col_index] max_width = max( - [len(str(widget.set(k, col_id))) for k in widget.get_children('')] + [len(col_id)] + [len(str(widget.set(k, col_id))) for k in widget.get_children("")] + + [len(col_id)] ) pixel_width = max_width * 8 diff --git a/pythonQEPest/gui/actions/actions_crud.py b/pythonQEPest/gui/actions/actions_crud.py index 6c78fb9..a23a5d3 100644 --- a/pythonQEPest/gui/actions/actions_crud.py +++ b/pythonQEPest/gui/actions/actions_crud.py @@ -1,6 +1,9 @@ from tkinter import messagebox, ttk -import pyperclip +try: + import pyperclip +except ImportError: + pyperclip = None from pythonQEPest.gui.elements.EditWindow import EditWindow from pythonQEPest.gui.utility.DataManager import DataManager @@ -33,22 +36,45 @@ def copy_selected(self, *args, **kwargs): rows_text = [] if selected_data_tree: - rows_text.append('\t'.join(map(str, ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR")))) + rows_text.append( + "\t".join( + map(str, ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR")) + ) + ) for item in selected_data_tree: - values = self.data_tree.item(item, 'values')[1:] - rows_text.append('\t'.join(map(str, values))) + values = self.data_tree.item(item, "values")[1:] + rows_text.append("\t".join(map(str, values))) if selected_result_tree: - rows_text.append('\t'.join(map(str, ("ID", "Name", "QEH", "QEI", "QEF")))) + rows_text.append("\t".join(map(str, ("ID", "Name", "QEH", "QEI", "QEF")))) for item in selected_result_tree: - values = self.result_tree.item(item, 'values')[1:] - rows_text.append('\t'.join(map(str, values))) + values = self.result_tree.item(item, "values")[1:] + rows_text.append("\t".join(map(str, values))) + + data_str = "\n".join(rows_text) + + if not pyperclip: + messagebox.showerror( + "Error", + "pyperclip module is not installed. Install it with command" + + "'pip install .[gui]' or 'poetry install --with ui'" + + "to enable copy functionality.", + ) + return - data_str = '\n'.join(rows_text) pyperclip.copy(data_str) messagebox.showinfo("Copied", "Data copied to clipboard.") def paste_entries(self, *args, **kwargs): + if not pyperclip: + messagebox.showerror( + "Error", + "pyperclip module is not installed. Install it with command" + + "'pip install .[gui]' or 'poetry install --with ui'" + + "to enable copy functionality.", + ) + return + clipboard_text = pyperclip.paste() if not clipboard_text.strip(): messagebox.showwarning("Clipboard is empty", "Copy the text first.") @@ -58,16 +84,19 @@ def paste_entries(self, *args, **kwargs): count_added = 0 for line in lines: - parts = line.strip().split('\t') + parts = line.strip().split("\t") if len(parts) == 7: idx = self.index self.data_manager.add_file((idx, *parts)) - self.data_tree.insert('', 'end', values=(idx, *parts)) + self.data_tree.insert("", "end", values=(idx, *parts)) count_added += 1 self.index += 1 if count_added: - messagebox.showinfo("Inserted", f"Inserted {count_added} entries. Don't forget to process the data.") + messagebox.showinfo( + "Inserted", + f"Inserted {count_added} entries. Don't forget to process the data.", + ) def delete_selected(self, *args, **kwargs): selected = self.data_tree.selection() @@ -77,7 +106,7 @@ def delete_selected(self, *args, **kwargs): idxs_to_remove = [] for item in selected: - values = self.data_tree.item(item, 'values') + values = self.data_tree.item(item, "values") idx_to_remove = int(values[0]) idxs_to_remove.append(idx_to_remove) @@ -92,7 +121,7 @@ def delete_selected(self, *args, **kwargs): messagebox.showinfo("Deleted", "The selected records have been deleted.") if not self.data_manager: - self.save_button.config(state='disabled') + self.save_button.config(state="disabled") def clear_everything(self, *args, **kwargs): self.data_manager.clear_file() diff --git a/pythonQEPest/gui/actions/actions_other.py b/pythonQEPest/gui/actions/actions_other.py index 7be276b..d7df8a3 100644 --- a/pythonQEPest/gui/actions/actions_other.py +++ b/pythonQEPest/gui/actions/actions_other.py @@ -15,22 +15,26 @@ def __init__(self, root, data_tree, result_tree, save_button, qepest): self.qepest = qepest def load_file(self): - file_path = filedialog.askopenfilename(filetypes=[("Text files", "*.txt"), ("CSV files", "*.csv")]) + file_path = filedialog.askopenfilename( + filetypes=[("Text files", "*.txt"), ("CSV files", "*.csv")] + ) if not file_path: return try: - with open(file_path, 'r', encoding='utf-8') as file: + with open(file_path, "r", encoding="utf-8") as file: self.data_manager.clear_file() self.data_tree.delete(*self.data_tree.get_children()) for idx, line in enumerate(file): - parts = line.strip().split('\t') + parts = line.strip().split("\t") if len(parts) == 7: self.data_manager.add_file((idx, *parts)) - self.data_tree.insert('', 'end', values=(idx, *parts)) + self.data_tree.insert("", "end", values=(idx, *parts)) - messagebox.showinfo("File uploaded", f"Loaded {len(self.data_manager.file_data)} rows.") + messagebox.showinfo( + "File uploaded", f"Loaded {len(self.data_manager.file_data)} rows." + ) except Exception as e: messagebox.showerror("Loading error", str(e)) @@ -41,10 +45,12 @@ def add_entry(self): form.grab_set() entries = {} - fields = ['Name', 'MW', 'LogP', 'HBA', 'HBD', 'RB', 'arR'] + fields = ["Name", "MW", "LogP", "HBA", "HBD", "RB", "arR"] for idx, field in enumerate(fields): - tk.Label(form, text=field).grid(row=idx, column=0, padx=5, pady=5, sticky='e') + tk.Label(form, text=field).grid( + row=idx, column=0, padx=5, pady=5, sticky="e" + ) entry = tk.Entry(form) entry.grid(row=idx, column=1, padx=5, pady=5) entries[field] = entry @@ -60,11 +66,16 @@ def submit(): idx = len(self.data_manager.file_data) self.data_manager.add_file((idx, *values)) - self.data_tree.insert('', 'end', values=(idx, *values)) + self.data_tree.insert("", "end", values=(idx, *values)) form.destroy() - messagebox.showinfo("Added", "The entry has been added. Process the data to update the result.") + messagebox.showinfo( + "Added", + "The entry has been added. Process the data to update the result.", + ) - tk.Button(form, text="Add", command=submit).grid(row=len(fields), column=0, columnspan=2, pady=10) + tk.Button(form, text="Add", command=submit).grid( + row=len(fields), column=0, columnspan=2, pady=10 + ) form.wait_window() @@ -78,29 +89,36 @@ def process_data(self): for row in self.data_manager.file_data: try: - result_row = [row[0], *self.qepest.compute_params(QEPestInput.from_array(row[1:])).to_array()] + result_row = [ + row[0], + *self.qepest.compute_params( + QEPestInput.from_array(row[1:]) + ).to_array(), + ] except ValueError as e: messagebox.showwarning("Warning!", f"Line number: {row[0]}\n{str(e)}") continue self.data_manager.add_result(result_row) - self.result_tree.insert('', 'end', values=result_row) + self.result_tree.insert("", "end", values=result_row) - self.save_button.config(state='normal') + self.save_button.config(state="normal") def save_result(self): if not self.data_manager.result_data: messagebox.showwarning("No result", "Process the data first.") return - save_path = filedialog.asksaveasfilename(defaultextension='.txt', filetypes=[("Text files", "*.txt")]) + save_path = filedialog.asksaveasfilename( + defaultextension=".txt", filetypes=[("Text files", "*.txt")] + ) if not save_path: return try: - with open(save_path, 'w', encoding='utf-8') as file: + with open(save_path, "w", encoding="utf-8") as file: file.write("Name\tQEH\tQEI\tQEF\n") for row in self.data_manager.result_data: - file.write('\t'.join(map(str, row)) + '\n') + file.write("\t".join(map(str, row)) + "\n") messagebox.showinfo("Saved", f"The result is saved in: {save_path}") diff --git a/pythonQEPest/gui/elements/ButtonsFrame.py b/pythonQEPest/gui/elements/ButtonsFrame.py index d87180b..ceca759 100644 --- a/pythonQEPest/gui/elements/ButtonsFrame.py +++ b/pythonQEPest/gui/elements/ButtonsFrame.py @@ -1,11 +1,16 @@ from tkinter import Frame, Button +try: + import pyperclip +except ImportError: + pyperclip = None + class ButtonsFrame(Frame): def __init__(self, root, *args, **kwargs): super().__init__(root, *args, **kwargs) - self.pack(anchor='w', fill='x', pady=5) + self.pack(anchor="w", fill="x", pady=5) # TODO: select_file must have an option for CSV self.select_file_button = Button(self, text="Select File") @@ -19,15 +24,20 @@ def __init__(self, root, *args, **kwargs): self.clear_button = Button(self, text="Clear Data") def set_actions(self, actions_crud, actions_other): - self.select_file_button.pack(side='left', padx=(10, 4)) - self.add_entry_button.pack(side='left', padx=4) - self.edit_entry_button.pack(side='left', padx=4) - self.delete_selected_button.pack(side='left', padx=4) - self.copy_button.pack(side='left', padx=4) - self.paste_button.pack(side='left', padx=4) - - self.process_data_button.pack(side='right', padx=(4, 10)) - self.clear_button.pack(side='right', padx=4) + self.select_file_button.pack(side="left", padx=(10, 4)) + self.add_entry_button.pack(side="left", padx=4) + self.edit_entry_button.pack(side="left", padx=4) + self.delete_selected_button.pack(side="left", padx=4) + + if not pyperclip: + self.copy_button.config(state="disabled") + self.paste_button.config(state="disabled") + + self.copy_button.pack(side="left", padx=4) + self.paste_button.pack(side="left", padx=4) + + self.process_data_button.pack(side="right", padx=(4, 10)) + self.clear_button.pack(side="right", padx=4) self.select_file_button.config(command=actions_other.load_file) self.add_entry_button.config(command=actions_other.add_entry) diff --git a/pythonQEPest/gui/elements/DataTree.py b/pythonQEPest/gui/elements/DataTree.py index ab5ed3c..346de71 100644 --- a/pythonQEPest/gui/elements/DataTree.py +++ b/pythonQEPest/gui/elements/DataTree.py @@ -3,19 +3,19 @@ class DataTree(Treeview): def __init__(self, root, *args, **kwargs): - columns = ('ID', 'Name', 'MW', 'LogP', 'HBA', 'HBD', 'RB', 'arR') - super().__init__(root, columns=columns, show='headings', *args, **kwargs) + columns = ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR") + super().__init__(root, *args, columns=columns, show="headings", **kwargs) for col in columns: self.heading(col, text=col) - self.pack(padx=10, pady=10, fill='both', expand=True) + self.pack(padx=10, pady=10, fill="both", expand=True) def set_actions(self, sort_column, actions_clicks): - for col in self['columns']: - self.heading(col, - text=col, - command=lambda _col=col: sort_column(self, _col, False)) + for col in self["columns"]: + self.heading( + col, text=col, command=lambda _col=col: sort_column(self, _col, False) + ) self.bind("", actions_clicks.on_treeview_click_left) self.bind("", actions_clicks.on_treeview_click_right) diff --git a/pythonQEPest/gui/elements/EditWindow.py b/pythonQEPest/gui/elements/EditWindow.py index d671e7f..36a8a94 100644 --- a/pythonQEPest/gui/elements/EditWindow.py +++ b/pythonQEPest/gui/elements/EditWindow.py @@ -6,25 +6,27 @@ class EditWindow(tk.Toplevel): def __init__(self, tree: Treeview, child_tree: Treeview, item_id, *args, **kwargs): - super().__init__(master=tree, *args, **kwargs) + super().__init__(*args, master=tree, **kwargs) self.title("Edit Entry") # self.geometry("200x300") self.data_manager = DataManager() - values = tree.item(item_id, 'values') + values = tree.item(item_id, "values") old_id = values[0] entries = [] - columns = tree['columns'] + columns = tree["columns"] self.grid_columnconfigure(0, weight=0) self.grid_columnconfigure(1, weight=3) self.resizable(True, False) for idx, col in enumerate(columns): - tk.Label(self, text=col).grid(row=idx, column=0, padx=5, pady=5, sticky='ew') + tk.Label(self, text=col).grid( + row=idx, column=0, padx=5, pady=5, sticky="ew" + ) entry = tk.Entry(self) entry.insert(0, values[idx]) entry.grid(row=idx, column=1, padx=(5, 5), pady=5, sticky="ew") @@ -34,7 +36,7 @@ def save_changes() -> None: new_values = [entry.get() for entry in entries] if child_tree.exists(item_id): - new_child_values = list(child_tree.item(item_id, 'values')) + new_child_values = list(child_tree.item(item_id, "values")) if new_child_values[0] != new_values[0]: new_child_values[0] = new_values[0] child_tree.item(item_id, values=new_child_values) @@ -46,12 +48,16 @@ def save_changes() -> None: update_file_data(new_values) def update_file_data(values: list) -> None: - element = list(filter(lambda x: str(x[0]) == str(old_id), self.data_manager.file_data))[0] + element = list( + filter(lambda x: str(x[0]) == str(old_id), self.data_manager.file_data) + )[0] if element: self.data_manager.update_file(index=element[0], new_entry=values) self.destroy() - tk.Button(self, text="Save", command=save_changes).grid(row=len(columns), column=0, columnspan=2, pady=10) + tk.Button(self, text="Save", command=save_changes).grid( + row=len(columns), column=0, columnspan=2, pady=10 + ) self.grab_set() self.wait_window() diff --git a/pythonQEPest/gui/elements/ResultTree.py b/pythonQEPest/gui/elements/ResultTree.py index d9b940e..843911f 100644 --- a/pythonQEPest/gui/elements/ResultTree.py +++ b/pythonQEPest/gui/elements/ResultTree.py @@ -3,16 +3,18 @@ class ResultTree(Treeview): def __init__(self, root, *args, **kwargs): - columns = ('ID', 'Name', 'QEH', 'QEI', 'QEF') - super().__init__(root, columns=columns, show='headings', *args, **kwargs) + columns = ("ID", "Name", "QEH", "QEI", "QEF") + super().__init__(root, *args, columns=columns, show="headings", **kwargs) for col in columns: self.heading(col, text=col) - self.pack(padx=10, pady=10, fill='both', expand=True) + self.pack(padx=10, pady=10, fill="both", expand=True) def set_actions(self, sort_column, actions_clicks): - for col in self['columns']: - self.heading(col, text=col, command=lambda _col=col: sort_column(self, _col, False)) + for col in self["columns"]: + self.heading( + col, text=col, command=lambda _col=col: sort_column(self, _col, False) + ) self.bind("", actions_clicks.on_treeview_click_left) self.bind("", actions_clicks.on_treeview_click_right) diff --git a/pythonQEPest/gui/elements/SaveButton.py b/pythonQEPest/gui/elements/SaveButton.py index 35c42f3..ec30efd 100644 --- a/pythonQEPest/gui/elements/SaveButton.py +++ b/pythonQEPest/gui/elements/SaveButton.py @@ -3,8 +3,8 @@ class SaveButton(Button): def __init__(self, root, *args, **kwargs): - super().__init__(root, text="Save Results", state='disabled', *args, **kwargs) - self.pack(padx=10, pady=10, side='right') + super().__init__(root, *args, text="Save Results", state="disabled", **kwargs) + self.pack(padx=10, pady=10, side="right") def set_actions(self, actions_other): self.config(command=actions_other.save_result) diff --git a/pythonQEPest/gui/elements/__init__.py b/pythonQEPest/gui/elements/__init__.py index bdd240f..67e44da 100644 --- a/pythonQEPest/gui/elements/__init__.py +++ b/pythonQEPest/gui/elements/__init__.py @@ -1 +1,17 @@ -from pythonQEPest.gui.elements import ResultTree, DataTree, ButtonsFrame, Menu, SaveButton, EditWindow +from pythonQEPest.gui.elements import ( + ResultTree, + DataTree, + ButtonsFrame, + Menu, + SaveButton, + EditWindow, +) + +__all__ = [ + "ResultTree", + "DataTree", + "ButtonsFrame", + "Menu", + "SaveButton", + "EditWindow", +] diff --git a/pythonQEPest/gui/gui.py b/pythonQEPest/gui/gui.py index 33e31cc..d172cfb 100644 --- a/pythonQEPest/gui/gui.py +++ b/pythonQEPest/gui/gui.py @@ -1,5 +1,14 @@ import tkinter as tk +from dotenv import load_dotenv + +from pythonQEPest.logger import init_logger + +try: + import pyperclip +except ImportError: + pyperclip = None + from pythonQEPest.gui.actions import GUIActionsCRUD from pythonQEPest.gui.actions import GUIActionsClicks from pythonQEPest.gui.actions import GUIActionsOther @@ -11,35 +20,47 @@ from pythonQEPest.gui.gui_meta import QEPestMeta +# TODO: Outdated. Must be dynamic class GUI(QEPestMeta): def treeview_sort_column(self, treeview, col, reverse): - l = [(treeview.set(k, col), k) for k in treeview.get_children('')] + treeview_lst = [(treeview.set(k, col), k) for k in treeview.get_children("")] try: - l.sort(key=lambda t: float(t[0]), reverse=reverse) + treeview_lst.sort(key=lambda t: float(t[0]), reverse=reverse) except ValueError: - l.sort(key=lambda t: t[0], reverse=reverse) + treeview_lst.sort(key=lambda t: t[0], reverse=reverse) - for index, (val, k) in enumerate(l): - treeview.move(k, '', index) + for index, (_, k) in enumerate(treeview_lst): + treeview.move(k, "", index) - treeview.heading(col, command=lambda: self.treeview_sort_column(treeview, col, not reverse)) + treeview.heading( + col, command=lambda: self.treeview_sort_column(treeview, col, not reverse) + ) def build_gui(self): self.file_data = [] self.index = 0 - self.buttons_frame = ButtonsFrame(root=root) - self.data_tree = DataTree(root=root) - self.result_tree = ResultTree(root=root) - self.save_button = SaveButton(root=root) - self.menu = Menu(root=root) + self.buttons_frame = ButtonsFrame(root=self.root) + self.data_tree = DataTree(root=self.root) + self.result_tree = ResultTree(root=self.root) + self.save_button = SaveButton(root=self.root) + self.menu = Menu(root=self.root) self.actions_clicks = GUIActionsClicks(menu=self.menu) - self.actions_crud = GUIActionsCRUD(data_tree=self.data_tree, result_tree=self.result_tree, - save_button=self.save_button, index=self.index) + self.actions_crud = GUIActionsCRUD( + data_tree=self.data_tree, + result_tree=self.result_tree, + save_button=self.save_button, + index=self.index, + ) - self.actions_other = GUIActionsOther(data_tree=self.data_tree, result_tree=self.result_tree, qepest=self.qepest, - root=self.root, save_button=self.save_button) + self.actions_other = GUIActionsOther( + data_tree=self.data_tree, + result_tree=self.result_tree, + qepest=self.qepest, + root=self.root, + save_button=self.save_button, + ) self.buttons_frame.set_actions(self.actions_crud, self.actions_other) self.data_tree.set_actions(self.treeview_sort_column, self.actions_clicks) @@ -47,11 +68,20 @@ def build_gui(self): self.save_button.set_actions(self.actions_other) self.menu.set_actions(self.actions_crud) - root.bind('', self.actions_crud.paste_entries) - root.bind('', self.actions_crud.copy_selected) + if pyperclip: + self.root.bind("", self.actions_crud.paste_entries) + self.root.bind("", self.actions_crud.copy_selected) -if __name__ == '__main__': +def main() -> int: + load_dotenv() + init_logger() + root = tk.Tk() - app = GUI(root) + GUI(root) root.mainloop() + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/pythonQEPest/gui/utility/__init__.py b/pythonQEPest/gui/utility/__init__.py index bf52550..48dc389 100644 --- a/pythonQEPest/gui/utility/__init__.py +++ b/pythonQEPest/gui/utility/__init__.py @@ -1 +1,6 @@ from pythonQEPest.gui.utility import DataManager, DataManagerMeta + +__all__ = [ + "DataManager", + "DataManagerMeta", +] diff --git a/pythonQEPest/helpers/__init__.py b/pythonQEPest/helpers/__init__.py index 752f0f0..ae7b2f4 100644 --- a/pythonQEPest/helpers/__init__.py +++ b/pythonQEPest/helpers/__init__.py @@ -1 +1,17 @@ -from . import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm, compute_df +from pythonQEPest.helpers.check_nan import check_nan +from pythonQEPest.helpers.compute_df import compute_df +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 pythonQEPest.helpers.norm import norm_h, norm_f, norm_i +from pythonQEPest.helpers.round_to_4digs import round_to_4digs + +__all__ = [ + "check_nan", + "compute_df", + "get_num_of_cols", + "get_values_from_line", + "norm_h", + "norm_f", + "norm_i", + "round_to_4digs", +] diff --git a/pythonQEPest/helpers/norm.py b/pythonQEPest/helpers/norm.py index 4786b1d..74dd865 100644 --- a/pythonQEPest/helpers/norm.py +++ b/pythonQEPest/helpers/norm.py @@ -10,12 +10,24 @@ def norm(arr: Union[list, tuple], d: Union[int, float], descr: int) -> float: def norm_h(d: Union[int, float], descr: int) -> float: - return norm((69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), d, descr) + return norm( + (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), + d, + descr, + ) def norm_i(d: Union[int, float], descr: int) -> float: - return norm((78.2919965, 71.2829691, 133.9224801, 331.170104, 70.5540709, 193.0023343), d, descr) + return norm( + (78.2919965, 71.2829691, 133.9224801, 331.170104, 70.5540709, 193.0023343), + d, + descr, + ) def norm_f(d: Union[int, float], descr: int) -> float: - return norm((53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), d, descr) + return norm( + (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), + d, + descr, + ) diff --git a/pythonQEPest/logger.py b/pythonQEPest/logger.py new file mode 100644 index 0000000..575b247 --- /dev/null +++ b/pythonQEPest/logger.py @@ -0,0 +1,58 @@ +import logging +import os +from logging.handlers import RotatingFileHandler +from pathlib import Path + + +def init_logger() -> None: + # If debug mode is enabled, we want to log everything, otherwise we can skip logging + if os.getenv("APP_DEBUG_ENABLE", "true").lower() == "false": + return + + root_logger = logging.getLogger("pythonQEPest") + + log_file: str = os.getenv("LOG_FILE_LOCATION", "logs/app.log") + level = os.getenv("LOG_LEVEL", "INFO").upper() + + match level: + case "DEBUG": + level = logging.DEBUG + case "INFO": + level = logging.INFO + case "WARNING": + level = logging.WARNING + case "ERROR": + level = logging.ERROR + case _: + level = logging.INFO + + if root_logger.handlers: + return + + log_path = Path(log_file) + log_path.parent.mkdir(parents=True, exist_ok=True) + + formatter = logging.Formatter( + fmt="%(asctime)s %(levelname)s %(name)s: %(message)s", + datefmt="%Y-%m-%d %H:%M:%S", + ) + + file_handler = RotatingFileHandler( + log_path, + maxBytes=1_000_000, + backupCount=3, + encoding="utf-8", + ) + file_handler.setLevel(level) + file_handler.setFormatter(formatter) + + console_handler = logging.StreamHandler() + console_handler.setLevel(level) + console_handler.setFormatter(formatter) + + root_logger.setLevel(level) + root_logger.addHandler(file_handler) + root_logger.addHandler(console_handler) + + root_logger.info("Logger started Successfully") + root_logger.info(f"Level: {level}") diff --git a/pythonQEPest/main.py b/pythonQEPest/main.py index e0940f5..72f17cd 100644 --- a/pythonQEPest/main.py +++ b/pythonQEPest/main.py @@ -1,5 +1,4 @@ -from pythonQEPest.cli.cli import CLI -from pythonQEPest.core.qepest import QEPest +from pythonQEPest.cli.cli import main if __name__ == "__main__": - cli = CLI(qepest=QEPest()).read_file_and_compute_params() + raise SystemExit(main()) diff --git a/pythonQEPest/services/QEPestFileService.py b/pythonQEPest/services/QEPestFileService.py new file mode 100644 index 0000000..2796b2e --- /dev/null +++ b/pythonQEPest/services/QEPestFileService.py @@ -0,0 +1,66 @@ +import logging +import json + +from pythonQEPest.core import QEPestMeta +from pythonQEPest.dto import QEPestFile +from pythonQEPest.dto.QEPestFile import QEPestFormat +from pythonQEPest.helpers.get_values_from_line import get_values_from_line +from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols + +logger = logging.getLogger(__name__) + + +class QEPestFileService: + + def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile): + self.qepest = qepest + self.qepest_file = qepest_file + self.error = False + + def _write_txt_line(self, line: str, file) -> None: + splitted_line = line.split("\t")[0] + qex_headers = " ".join(self.qepest.qex.model_dump().keys()) + qex_values = " ".join(str(x) for x in self.qepest.qex.model_dump().values()) + + file.write(f"Name {qex_headers.upper()}\n") + file.write(f"{splitted_line} {qex_values}\n") + + def _write_json_line(self, line: str, file) -> None: + splitted_line = line.split("\t")[0] + data = {"name": splitted_line, **self.qepest.qex.model_dump()} + file.write(json.dumps(data) + "\n") + + def read_file_and_compute_params(self) -> None: + try: + with open(self.qepest_file.input_file, "r") as f: + lines = f.readlines() + + with open(self.qepest_file.output_file, "w") as wr: + for index, line in enumerate(lines): + if get_num_of_cols(line) != self.qepest.col_number: + logger.error( + f"Error: Line {index} does not have the " + "expected number of columns." + ) + self.error = True + break + + if index == 0: + continue + + d_values = get_values_from_line(line.split("\t")) + self.qepest.get_qex_values(d_values) + + if self.qepest_file.format == QEPestFormat.TXT: + self._write_txt_line(line, wr) + else: + self._write_json_line(line, wr) + + if not self.error: + logger.info("Computation completed") + else: + logger.warning("Finished with errors") + + except FileNotFoundError: + self.error = True + logger.error(f"Error: can't find: {self.qepest_file.input_file}") diff --git a/pythonQEPest/services/__init__.py b/pythonQEPest/services/__init__.py new file mode 100644 index 0000000..7df49da --- /dev/null +++ b/pythonQEPest/services/__init__.py @@ -0,0 +1,3 @@ +from pythonQEPest.services.QEPestFileService import QEPestFileService + +__all__ = ["QEPestFileService"] diff --git a/requirements.txt b/requirements.txt index d8fdb55..09d940e 100644 Binary files a/requirements.txt and b/requirements.txt differ diff --git a/tests/cli/__init__.py b/tests/cli/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py new file mode 100644 index 0000000..da70cc9 --- /dev/null +++ b/tests/cli/test_cli_contract.py @@ -0,0 +1,101 @@ +import pytest + +from pythonQEPest.cli.cli import main + + +class TestCLIContract: + def test_cli_help_exits_with_zero(self, monkeypatch): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + with pytest.raises(SystemExit) as exc: + main(["--help"]) + assert exc.value.code == 0 + + def test_cli_version_exits_with_zero(self, monkeypatch): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + with pytest.raises(SystemExit) as exc: + main(["--version"]) + assert exc.value.code == 0 + + def test_cli_runs_with_explicit_input_file(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.out.txt" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main(["--input", str(data_file), "--output", str(output_file)]) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + assert output_file.name == "input.out.txt" + assert ( + output_text == "Name QE_FUNG QE_HERB QE_INSECT\nmol1 0.6224 0.8511 0.5339\n" + ) + + def test_cli_runs_with_explicit_input_file_format(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.out.txt" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main( + ["--input", str(data_file), "--output", str(output_file), "--format=txt"] + ) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + + assert output_file.name == "input.out.txt" + assert isinstance(output_text, str) + + assert ( + output_text == "Name QE_FUNG QE_HERB QE_INSECT\nmol1 0.6224 0.8511 0.5339\n" + ) + + def test_cli_runs_with_input_file_format(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.out.json" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main(["--input", str(data_file), "--format=json"]) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + + assert output_file.name == "input.out.json" + assert isinstance(output_text, str) + + import json + + assert json.loads(output_text) == { + "name": "mol1", + "qe_fung": 0.6224, + "qe_herb": 0.8511, + "qe_insect": 0.5339, + } diff --git a/tests/config/__init__.py b/tests/config/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/config/test_coefficients.py b/tests/config/test_coefficients.py new file mode 100644 index 0000000..7f564a3 --- /dev/null +++ b/tests/config/test_coefficients.py @@ -0,0 +1,369 @@ +from pythonQEPest.dto.coefficients import ( + QEPestCoefficient, + QEPestCoefficientNumerics, + QEPestCoefficientList, +) + + +class TestQEPestCoefficients: + def test_qepest_coefficient_numerics_strict(self): + qep_coeff_num = QEPestCoefficientNumerics( + mw=(0.1, 0.2, 0.3, 0.4), + logp=(0.1, 0.2, 0.3, 0.4), + hba=(0.1, 0.2, 0.3, 0.4), + hbd=(0.1, 0.2, 0.3, 0.4), + rb=(0.1, 0.2, 0.3, 0.4), + ar=(0.1, 0.2, 0.3, 0.4), + ) + + assert qep_coeff_num.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficient_numerics_unstrict(self): + qep_coeff_num = QEPestCoefficientNumerics([[0.1, 0.2, 0.3, 0.4]] * 6) + + assert qep_coeff_num.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_strict(self): + coefficients_name = "herb" + coefficients_dict = [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ] + qep_coeff = QEPestCoefficient( + name=coefficients_name, + coefficients=QEPestCoefficientNumerics(coefficients_dict), + ) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_unstrict(self): + coefficients_dict = { + "herb": [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ] + } + qep_coeff = QEPestCoefficient(coefficients_dict) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_unstrict_chaos(self): + coefficients_dict = [ + "herb", + [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ], + ] + + qep_coeff = QEPestCoefficient(coefficients_dict) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_lst_basic(self): + coefficients_dict = { + "test1": [ + (0.1, 0.2, 0.3, 0.4), # mwI + (0.1, 0.2, 0.3, 0.4), # logpI + (0.1, 0.2, 0.3, 0.4), # hbaI + (0.1, 0.2, 0.3, 0.4), # hbdI + (0.1, 0.2, 0.3, 0.4), # rbI + (0.1, 0.2, 0.3, 0.4), # arRCI + ], + "test2": [ + (0.1, 0.2, 0.3, 0.4), # mwF + (0.1, 0.2, 0.3, 0.4), # logpF + (0.1, 0.2, 0.3, 0.4), # hbaF + (0.1, 0.2, 0.3, 0.4), # hbdF + (0.1, 0.2, 0.3, 0.4), # rbF + (0.1, 0.2, 0.3, 0.4), # arRCF + ], + } + + qep_coeff_lst = QEPestCoefficientList(coefficients_dict) + + assert qep_coeff_lst.name == "generic" + assert qep_coeff_lst.named_coefficients is not None + + assert len(qep_coeff_lst.named_coefficients) == 2 + + assert qep_coeff_lst.named_coefficients[0].name == "test1" + + assert qep_coeff_lst.named_coefficients[0].coefficients.mw == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.logp == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hba == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hbd == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.rb == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.ar == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + + assert qep_coeff_lst.named_coefficients[1].name == "test2" + + assert qep_coeff_lst.named_coefficients[1].coefficients.mw == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.logp == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hba == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hbd == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.rb == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.ar == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + + def test_qepest_coefficients_lst_w_import(self): + from pythonQEPest.config.qepest_default import qepest_default + + qep_coeff_lst = QEPestCoefficientList(qepest_default) + + assert qep_coeff_lst.name == "generic" + assert qep_coeff_lst.named_coefficients is not None + + assert len(qep_coeff_lst.named_coefficients) == 3 + + assert qep_coeff_lst.named_coefficients[0].name == "herb" + + assert qep_coeff_lst.named_coefficients[0].coefficients.mw == ( + 70.77, + 283.0, + 84.97, + -1.185, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.logp == ( + 93.81, + 3.077, + 1.434, + 0.6164, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hba == ( + 117.6, + 2.409, + 1.567, + 7.155, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hbd == ( + 233.4, + 0.4535, + -1.48, + 4.47, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.rb == ( + 84.7, + 4.758, + -2.423, + 5.437, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.ar == ( + 301.8, + 1.101, + 0.8869, + -22.81, + ) + + assert qep_coeff_lst.named_coefficients[1].name == "insect" + + assert qep_coeff_lst.named_coefficients[1].coefficients.mw == ( + 76.38, + 298.3, + 83.64, + 1.912, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.logp == ( + 74.27, + 4.555, + -2.193, + -2.987, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hba == ( + 139.4, + 1.363, + 1.283, + 0.5341, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hbd == ( + 670.6, + -1.163, + 0.7856, + 0.7951, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.rb == ( + 65.49, + 6.219, + -2.448, + 5.318, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.ar == ( + 287.5, + 0.305, + 1.554, + -88.64, + ) + + assert qep_coeff_lst.named_coefficients[2].name == "fung" + + assert qep_coeff_lst.named_coefficients[2].coefficients.mw == ( + 51.03, + 314.2, + -56.31, + 2.342, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.logp == ( + 50.73, + 3.674, + -1.238, + 2.067, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.hba == ( + 73.79, + 1.841, + 1.326, + 0.5158, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.hbd == ( + 164.7, + -0.9762, + -2.027, + 1.384, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.rb == ( + 40.91, + 1.822, + 2.582, + 0.6235, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.ar == ( + 134.4, + 0.8383, + 1.347, + -31.17, + ) + + def test_qepest_default_coefficients(self): + from pythonQEPest.config.qepest_default import qepest_default + + assert "fung" in qepest_default + assert "herb" in qepest_default + assert "insect" in qepest_default + + coefficients = { + "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 + ], + "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 + ], + "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 + ], + } + + assert qepest_default == coefficients diff --git a/tests/config/test_normalisation.py b/tests/config/test_normalisation.py new file mode 100644 index 0000000..88350bd --- /dev/null +++ b/tests/config/test_normalisation.py @@ -0,0 +1,36 @@ +class TestQEPestNormalisation: + def test_qepest_default_coefficients(self): + from pythonQEPest.config.normalise import normalise_default + + assert "fung" in normalise_default + assert "herb" in normalise_default + assert "insect" in normalise_default + + normalise = { + "herb": ( + 69.5849922, + 94.4228257, + 120.4572352, + 228.1589796, + 89.7012502, + 276.9634213, + ), + "insect": ( + 78.2919965, + 71.2829691, + 133.9224801, + 331.170104, + 70.5540709, + 193.0023343, + ), + "fung": ( + 53.3719946, + 52.773116, + 73.7976536, + 144.9887053, + 41.4385926, + 102.3024319, + ), + } + + assert normalise_default == normalise diff --git a/tests/core/test_qepest.py b/tests/core/test_qepest.py index 6eef0c2..eb7fc46 100644 --- a/tests/core/test_qepest.py +++ b/tests/core/test_qepest.py @@ -2,9 +2,8 @@ import pytest from pydantic import ValidationError - from pythonQEPest.core.qepest import QEPest -from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto import QEPestInput class TestQEPest: @@ -17,88 +16,112 @@ def make_input(self, name="test", mw=120.5, logp=3.1, hba=2, hbd=1, rb=4, ar=1): hbond_acceptors=hba, hbond_donors=hbd, rotatable_bonds=rb, - aromatic_rings=ar + aromatic_rings=ar, ) def test_qepest_compute_params_basic(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + + qepest.initialize_coefficients() + qepest.initialize_normalisers() + inp = self.make_input() - result = qep.compute_params(inp) + result = qepest.compute_params(inp) + assert hasattr(result, "data") - assert hasattr(result.data, "qe_f") - assert hasattr(result.data, "qe_h") - assert hasattr(result.data, "qe_i") - assert math.isfinite(result.data.qe_h) - assert math.isfinite(result.data.qe_i) - assert math.isfinite(result.data.qe_f) + assert hasattr(result.data, "qe_fung") + assert hasattr(result.data, "qe_herb") + assert hasattr(result.data, "qe_insect") + + assert math.isfinite(result.data.qe_herb) + assert math.isfinite(result.data.qe_insect) + assert math.isfinite(result.data.qe_fung) + assert hasattr(result, "name") assert result.name == inp.name def test_qepest_zero_input(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + inp = self.make_input(mw=0, logp=0, hba=0, hbd=0, rb=0, ar=0) + with pytest.raises(ValueError): - qep.compute_params(inp) + qepest.compute_params(inp) def test_qepest_multiple_names(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + for i in range(3): name = f"test_{i}" inp = self.make_input(name=name) - result = qep.compute_params(inp) + result = qepest.compute_params(inp) assert result.name == name def test_qepest_nan_protection(self): - qep = QEPest() - qep.initialize_coefficients() - with pytest.raises(ValidationError): - self.make_input(mw=float('nan'), logp=float('nan'), hba=float('nan'), - hbd=float('nan'), rb=float('nan'), ar=float('nan')) + # qepest = QEPest() + with pytest.raises(ValidationError): + self.make_input( + mw=float("nan"), + logp=float("nan"), + hba=float("nan"), + hbd=float("nan"), + rb=float("nan"), + ar=float("nan"), + ) def test_qepest_compare_with_original(self): - qep = QEPest() + qepest = QEPest() - result = qep.compute_params( - self.make_input("mol1", 240.2127, 3.2392, 5, 1, 4, 1)) + result = qepest.compute_params( + self.make_input("mol1", 240.2127, 3.2392, 5, 1, 4, 1) + ) assert result.name == "mol1" - assert result.data.qe_h == 0.8511 - assert result.data.qe_i == 0.5339 - assert result.data.qe_f == 0.6224 - assert result.to_array() == ["mol1", 0.8511, 0.5339, 0.6224] + assert result.data.qe_herb == 0.8511 + assert result.data.qe_insect == 0.5339 + assert result.data.qe_fung == 0.6224 - result = qep.compute_params( - self.make_input("mol2", 249.091, 3.0273, 3, 1, 5, 1)) + assert result.to_array() == ["mol1", 0.6224, 0.8511, 0.5339] + + result = qepest.compute_params( + self.make_input("mol2", 249.091, 3.0273, 3, 1, 5, 1) + ) assert result.name == "mol2" - assert result.data.qe_h == 0.975 - assert result.data.qe_i == 0.6913 - assert result.data.qe_f == 0.731 - assert result.to_array() == ["mol2", 0.975, 0.6913, 0.731] - result = qep.compute_params( - self.make_input("mol3", 308.354, 2.1086, 1, 0, 7, 1)) + assert result.data.qe_herb == 0.975 + assert result.data.qe_insect == 0.6913 + assert result.data.qe_fung == 0.731 + + assert result.to_array() == ["mol2", 0.731, 0.975, 0.6913] + + result = qepest.compute_params( + self.make_input("mol3", 308.354, 2.1086, 1, 0, 7, 1) + ) assert result.name == "mol3" - assert result.data.qe_h == 0.798 - assert result.data.qe_i == 0.9018 - assert result.data.qe_f == 0.732 - assert result.to_array() == ["mol3", 0.798, 0.9018, 0.732] - result = qep.compute_params( - self.make_input("mol4", 360.444, 4.0137, 3, 0, 8, 0)) + assert result.data.qe_herb == 0.798 + assert result.data.qe_insect == 0.9018 + assert result.data.qe_fung == 0.732 + + assert result.to_array() == ["mol3", 0.732, 0.798, 0.9018] + + result = qepest.compute_params( + self.make_input("mol4", 360.444, 4.0137, 3, 0, 8, 0) + ) assert result.name == "mol4" - assert result.data.qe_h == 0.5839 - assert result.data.qe_i == 0.8382 - assert result.data.qe_f == 0.6594 - assert result.to_array() == ["mol4", 0.5839, 0.8382, 0.6594] + assert result.data.qe_herb == 0.5839 + assert result.data.qe_insect == 0.8382 + assert result.data.qe_fung == 0.6594 + + assert result.to_array() == ["mol4", 0.6594, 0.5839, 0.8382] - result = qep.compute_params( - self.make_input("mol5", 295.335, 4.9335, 2, 0, 1, 1)) + result = qepest.compute_params( + self.make_input("mol5", 295.335, 4.9335, 2, 0, 1, 1) + ) assert result.name == "mol5" - assert result.data.qe_h == 0.8099 - assert result.data.qe_i == 0.8118 - assert result.data.qe_f == 0.8742 - assert result.to_array() == ["mol5", 0.8099, 0.8118, 0.8742] + assert result.data.qe_herb == 0.8099 + assert result.data.qe_insect == 0.8118 + assert result.data.qe_fung == 0.8742 + + assert result.to_array() == ["mol5", 0.8742, 0.8099, 0.8118] diff --git a/tests/dto/test_norm.py b/tests/dto/test_norm.py new file mode 100644 index 0000000..2125c1a --- /dev/null +++ b/tests/dto/test_norm.py @@ -0,0 +1,74 @@ +import pytest + +from pythonQEPest.dto.normalisation.Normaliser import Normaliser + +# from pythonQEPest.helpers.norm import norm_i, norm_h, norm, norm_f + + +class TestNorm: + def test_norm_basic(self): + arr = [10, 20, 30] + d = 20 + + normaliser = Normaliser(arr) + + assert normaliser.norm(d, 1) == 1.0 + assert normaliser.norm(d, 2) == 20 / 30 + assert normaliser.norm(d, 0) == 2.0 + + def test_norm_zero_div(self): + arr = [10, 0, 30] + d = 5 + + normaliser = Normaliser(arr) + + assert normaliser.norm(d, 1) == 0.0 + + def test_norm_out_of_range(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + with pytest.raises(KeyError): + normaliser.norm(2, 5) + + def test_norm_negative_descr(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + + assert normaliser.norm(2, -1) == 2 / 3 + + def test_norm_h(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["herb"]) + + assert normaliser.norm(69.5849922, 0) == 1.0 + assert normaliser.norm(0, 2) == 0.0 + assert pytest.approx(normaliser.norm(60, 1), rel=1e-6) == 60 / 94.4228257 + + def test_norm_i(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["insect"]) + + assert normaliser.norm(78.2919965, 0) == 1.0 + assert normaliser.norm(0, 3) == 0.0 + assert pytest.approx(normaliser.norm(66, 1), rel=1e-6) == 66 / 71.2829691 + + def test_norm_f(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["fung"]) + + assert normaliser.norm(53.3719946, 0) == 1.0 + assert normaliser.norm(0, 5) == 0.0 + assert pytest.approx(normaliser.norm(70, 2), rel=1e-6) == 70 / 73.7976536 + + def test_norm_invalid_descr_type(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + + with pytest.raises(TypeError): + normaliser.norm(1, "not_an_int") diff --git a/tests/dto/test_qepest_file.py b/tests/dto/test_qepest_file.py new file mode 100644 index 0000000..67a4bc6 --- /dev/null +++ b/tests/dto/test_qepest_file.py @@ -0,0 +1,41 @@ +class TestQEPestFile: + def _import_qepest_file(self): + try: + from pythonQEPest.dto import QEPestFile + except ImportError: + QEPestFile = None + + return QEPestFile + + def test_qepest_file_import(self): + QEPestFile = self._import_qepest_file() + + assert ( + QEPestFile is not None + ), "QEPestFile should be importable from pythonQEPest.dto" + + def test_qepest_file_standard(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile( + input_file="input_example.txt", output_file="output_example.txt" + ) + + assert qepest_output_file.input_file == "input_example.txt" + assert qepest_output_file.output_file == "input_example.out.txt" + + def test_qepest_file_with_no_output_file(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile(input_file="input1.txt") + + assert qepest_output_file.input_file == "input1.txt" + assert qepest_output_file.output_file == "input1.out.txt" + + def test_qepest_file_with_no_input_file(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile() + + assert qepest_output_file.input_file == "data.txt" + assert qepest_output_file.output_file == "data.out.txt" diff --git a/tests/dto/test_qepest_input.py b/tests/dto/test_qepest_input.py index 937406c..f2ca35b 100644 --- a/tests/dto/test_qepest_input.py +++ b/tests/dto/test_qepest_input.py @@ -26,9 +26,15 @@ def test_qepest_input(self): assert qepest_input.aromatic_rings == 0 def test_qepest_input_with_changing(self): - qepest_input = QEPestInput(name=self.name, mol_weight=self.mol_weight, log_p=self.log_p, - hbond_acceptors=self.hbond_acceptors, hbond_donors=self.hbond_donors, - rotatable_bonds=self.rotatable_bonds, aromatic_rings=self.aromatic_rings) + qepest_input = QEPestInput( + name=self.name, + mol_weight=self.mol_weight, + log_p=self.log_p, + hbond_acceptors=self.hbond_acceptors, + hbond_donors=self.hbond_donors, + rotatable_bonds=self.rotatable_bonds, + aromatic_rings=self.aromatic_rings, + ) assert qepest_input.name == self.name @@ -42,8 +48,15 @@ def test_qepest_input_with_changing(self): assert qepest_input.aromatic_rings == self.aromatic_rings def test_qepest_output_functions(self): - arr = (self.name, self.mol_weight, self.log_p, self.hbond_acceptors, - self.hbond_donors, self.rotatable_bonds, self.aromatic_rings) + arr = ( + self.name, + self.mol_weight, + self.log_p, + self.hbond_acceptors, + self.hbond_donors, + self.rotatable_bonds, + self.aromatic_rings, + ) qepest_input = QEPestInput.from_array(arr) diff --git a/tests/dto/test_qepest_output.py b/tests/dto/test_qepest_output.py index 72b0b0e..c34c955 100644 --- a/tests/dto/test_qepest_output.py +++ b/tests/dto/test_qepest_output.py @@ -21,7 +21,9 @@ def test_qepest_output_with_changing(self): qepest_data = QEPestData(qe_h=self.qe_h, qe_i=self.qe_i, qe_f=self.qe_f) qepest_output = QEPestOutput(name=self.name, data=qepest_data) - new_qepest_data = QEPestData(qe_h=self.new_qe_h, qe_i=self.new_qe_i, qe_f=self.new_qe_f) + new_qepest_data = QEPestData( + qe_h=self.new_qe_h, qe_i=self.new_qe_i, qe_f=self.new_qe_f + ) qepest_output.name = self.new_name qepest_output.data = new_qepest_data diff --git a/tests/gui/__init__.py b/tests/gui/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/gui/test_gui_smoke.py b/tests/gui/test_gui_smoke.py new file mode 100644 index 0000000..734fd98 --- /dev/null +++ b/tests/gui/test_gui_smoke.py @@ -0,0 +1,19 @@ +import os +import tkinter as tk + +import pytest + +from pythonQEPest.gui.gui import GUI + + +@pytest.mark.skipif( + os.name != "nt", + reason="Tkinter GUI smoke test is enabled only on Windows by default.", +) +def test_gui_smoke_creation(): + root = tk.Tk() + root.withdraw() + + GUI(root) + + root.destroy() diff --git a/tests/helpers/test_check_nan.py b/tests/helpers/test_check_nan.py index 189dba1..fc6e4f3 100644 --- a/tests/helpers/test_check_nan.py +++ b/tests/helpers/test_check_nan.py @@ -5,10 +5,22 @@ class TestCheckNAN: lst_good = [0.0, 0.1, 0.2] - lst_bad = [math.nan, float('nan'), 0.0] + lst_bad = [math.nan, float("nan"), 0.0] lst_bad_result = [0.0, 0.0, 0.0] lst_strange = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1, -45.43, math.nan, float("inf")] - lst_strange_result = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1, -45.43, 0.0, float("inf")] + lst_strange_result = [ + 0.0, + 0.1, + 0.2, + 0.3, + 0.4, + 0.5, + 0.6, + 1, + -45.43, + 0.0, + float("inf"), + ] def test_check_nan(self): result = check_nan(self.lst_good) diff --git a/tests/helpers/test_norm.py b/tests/helpers/test_norm.py deleted file mode 100644 index 6e1ebd3..0000000 --- a/tests/helpers/test_norm.py +++ /dev/null @@ -1,47 +0,0 @@ -import pytest - -from pythonQEPest.helpers.norm import norm_i, norm_h, norm, norm_f - - -class TestNorm: - def test_norm_basic(self): - arr = [10, 20, 30] - d = 20 - - assert norm(arr, d, 1) == 1.0 - assert norm(arr, d, 2) == 20 / 30 - assert norm(arr, d, 0) == 2.0 - - def test_norm_zero_div(self): - arr = [10, 0, 30] - d = 5 - assert norm(arr, d, 1) == 0.0 - - def test_norm_out_of_range(self): - arr = [1, 2, 3] - with pytest.raises(KeyError): - norm(arr, 2, 5) - - def test_norm_negative_descr(self): - arr = [1, 2, 3] - assert norm(arr, 2, -1) == 2 / 3 - - def test_norm_h(self): - assert norm_h(69.5849922, 0) == 1.0 - assert norm_h(0, 2) == 0.0 - assert pytest.approx(norm_h(60, 1), rel=1e-6) == 60 / 94.4228257 - - def test_norm_i(self): - assert norm_i(78.2919965, 0) == 1.0 - assert norm_i(0, 3) == 0.0 - assert pytest.approx(norm_i(66, 1), rel=1e-6) == 66 / 71.2829691 - - def test_norm_f(self): - assert norm_f(53.3719946, 0) == 1.0 - assert norm_f(0, 5) == 0.0 - assert pytest.approx(norm_f(70, 2), rel=1e-6) == 70 / 73.7976536 - - def test_norm_invalid_descr_type(self): - arr = [1, 2, 3] - with pytest.raises(TypeError): - norm(arr, 1, "not_an_int") diff --git a/tests/logger/__init__.py b/tests/logger/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py new file mode 100644 index 0000000..2685094 --- /dev/null +++ b/tests/logger/test_logging.py @@ -0,0 +1,119 @@ +import logging +from pathlib import Path + +from pythonQEPest.logger import init_logger + + +# TODO: Locations must be temporary +class TestLogger: + def _reset_logger(self): + logger = logging.getLogger("pythonQEPest") + for h in list(logger.handlers): + logger.removeHandler(h) + h.close() + logger.setLevel(logging.NOTSET) + return logger + + def test_logger_initialization(self): + self._reset_logger() + try: + init_logger() + assert True # If no exception is raised, the test passes + except Exception as e: + raise AssertionError(f"Logger initialization failed with exception: {e}") + + def test_default_configuration(self, monkeypatch): + self._reset_logger() + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + monkeypatch.delenv("LOG_LEVEL", raising=False) + monkeypatch.delenv("APP_DEBUG_ENABLE", raising=False) + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert logger.level == logging.INFO + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename).as_posix().endswith("/logs/app.log") + ), "Default LOG_FILE_LOCATION should be logs/app.log" + + def test_logger_levels(self, monkeypatch): + def _logger_levels(monkeypatch, level: str, assert_level): + self._reset_logger() + + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.setenv("LOG_LEVEL", level) + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert logger.level == assert_level + + """ Logger levels testing""" + _logger_levels(monkeypatch, level="DEBUG", assert_level=logging.DEBUG) + _logger_levels(monkeypatch, level="INFO", assert_level=logging.INFO) + _logger_levels(monkeypatch, level="WARNING", assert_level=logging.WARNING) + _logger_levels(monkeypatch, level="ERROR", assert_level=logging.ERROR) + _logger_levels(monkeypatch, level="", assert_level=logging.INFO) + + def test_file_location(self, monkeypatch): + """LOG_FILE_LOCATION testing""" + + # Test with custom LOG_FILE_LOCATION + self._reset_logger() + + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.setenv("LOG_FILE_LOCATION", "test_logs/app.log") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] + + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename) + .as_posix() + .endswith("/test_logs/app.log") + ), "File handler should use LOG_FILE_LOCATION" + + # Test with default LOG_FILE_LOCATION + self._reset_logger() + + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + + init_logger() + + logger = logging.getLogger("pythonQEPest") + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] + + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename).as_posix().endswith("/logs/app.log") + ), "File handler should use LOG_FILE_LOCATION" + + def test_debug_option(self, monkeypatch): + """Debug switch testing""" + self._reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) == 0 + + self._reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) != 0 diff --git a/tests/public_api/__init__.py b/tests/public_api/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py new file mode 100644 index 0000000..9880604 --- /dev/null +++ b/tests/public_api/test_import_contract.py @@ -0,0 +1,61 @@ +import pytest +from pydantic import BaseModel + +from pythonQEPest import QEPest, QEPestData, QEPestInput, QEPestOutput + + +class TestPublicAPI: + def test_public_api_symbols_are_importable(self): + assert QEPest is not None + assert QEPestInput is not None + assert QEPestOutput is not None + assert QEPestData is not None + + def test_public_api_compute_smoke(self): + model = QEPest() + payload = QEPestInput( + name="mol1", + mol_weight=308.354, + log_p=2.1086, + hbond_acceptors=2, + hbond_donors=1, + rotatable_bonds=4, + aromatic_rings=1, + ) + + result = model.compute_params(payload) + + assert isinstance(result, QEPestOutput) + assert isinstance(result.data, BaseModel) + + assert result.name == "mol1" + assert result.data.model_dump() == { + "qe_herb": 0.9357, + "qe_insect": 0.7146, + "qe_fung": 0.8022, + } + + @pytest.mark.skip(reason="Need to find optional approach") + def test_helpers_imports(self): + try: + from pythonQEPest.helpers import ( + check_nan, + get_values_from_line, + get_num_of_cols, + round_to_4digs, + norm_h, + norm_f, + norm_i, + compute_df, + ) + + assert check_nan is not None + assert get_values_from_line is not None + assert get_num_of_cols is not None + assert round_to_4digs is not None + assert norm_h is not None + assert norm_f is not None + assert norm_i is not None + assert compute_df is not None + except ImportError as er: + raise AssertionError(f"Failed to import helper functions: {er}")