Reorganize

.gitignore

@@ -0,0 +1,139 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+#ignore lightning_logs folder anywhere in source tree
+lightning_logs/
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+.pytest_cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# DS Store:
+.DS_Store
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# DS Store
+.DS_Store
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Pycharm settings
+.idea
+*.iml
+*.iws
+*.ipr
+
+# Ignore Sublime Text settings
+*.sublime-workspace
+*.sublime-project
+
+# vim swap
+*.swp
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# PyTorch Lightning logs
+lightning_logs/
+**/lightning_logs/
+
+# profraw files from LLVM? Unclear exactly what triggers this
+# There are reports this comes from LLVM profiling, but also Xcode 9.
+*profraw
+
+# In-tree generated files
+*/_version.py
+*/*/_version.py
+
+# Cookiecutter-CMS Test Artifacts
+/tests/CI_files

comsia.py → pycomisa/comsia.py

@@ -1,13 +1,15 @@
-from src.DataLoader import DataLoader
-from src.MoleculeAligner import MoleculeAligner
-from src.MolecularGridCalculator import MolecularGridCalculator
-from src.MolecularFieldCalculator import MolecularFieldCalculator
-from src.MolecularVisualizer import MolecularVisualizer
-from src.PLSAnalysis import PLSAnalysis
-from src.ContourPlotVisualizer import ContourPlotVisualizer
+from pycomisa.src.DataLoader import DataLoader
+from pycomisa.src.MoleculeAligner import MoleculeAligner
+from pycomisa.src.MolecularGridCalculator import MolecularGridCalculator
+from pycomisa.src.MolecularFieldCalculator import MolecularFieldCalculator
+from pycomisa.src.MolecularVisualizer import MolecularVisualizer
+from pycomisa.src.PLSAnalysis import PLSAnalysis
+from pycomisa.src.ContourPlotVisualizer import ContourPlotVisualizer
 import os
 import argparse
-from datetime import datetime 
+from datetime import datetime
+
+
 data_loader = DataLoader()
 aligner = MoleculeAligner()
 field_calculator = MolecularFieldCalculator()
@@ -27,7 +29,7 @@
 }
 
 
-def main(input_file, sdf_activity, predict_file, grid_resolution, grid_padding, num_components, column_filter, visualization, fields):
+def run_comisa(input_file, sdf_activity, predict_file, grid_resolution, grid_padding, num_components, column_filter, visualization, fields):
     # Create the directory system for results
     current_time = datetime.now()
     directory_name = current_time.strftime("%Y-%m-%d_%H-%M-%S")
@@ -159,10 +161,13 @@ def create_parser():
 
     return parser
 
-if __name__ == "__main__":
+def main():
     parser = create_parser()
     args = parser.parse_args()
 
-    main(args.train_file, args.sdf_activity, args.predict_file,
-         args.grid_resolution, args.grid_padding, args.num_components, 
+    run_comisa(args.train_file, args.sdf_activity, args.predict_file,
+         args.grid_resolution, args.grid_padding, args.num_components,
          args.column_filter, not args.disable_visualization, args.fields)
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -0,0 +1,84 @@
+[build-system]
+requires = ["setuptools>=61.0", "versioningit~=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pycomisa"
+description = "A short description of the project (less than one line)."
+dynamic = ["version"]
+readme = "README.md"
+license = { text = "MIT" }
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.10"
+
+# Declare any run-time dependencies that should be installed with the package.
+dependencies = [
+    "numpy",
+    "pyvista",
+    "pandas",
+    "rdkit",
+    "scikit-learn",
+    "matplotlib",
+    "seaborn",
+    "pubchempy"
+
+]
+
+[project.urls]
+
+[project.optional-dependencies]
+test = [
+  "pytest>=6.1.2",
+]
+
+[project.scripts]
+pycomisa = "pycomisa.comsia:main"
+
+[tool.setuptools]
+# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
+#
+# As of version 0.971, mypy does not support type checking of installed zipped
+# packages (because it does not actually import the Python packages).
+# We declare the package not-zip-safe so that our type hints are also available
+# when checking client code that uses our (installed) package.
+# Ref:
+# https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561
+zip-safe = false
+# Let setuptools discover the package in the current directory,
+# but be explicit about non-Python files.
+# See also:
+#   https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
+# Note that behavior is currently evolving with respect to how to interpret the
+# "data" and "tests" subdirectories. As of setuptools 63, both are automatically
+# included if namespaces is true (default), even if the package is named explicitly
+# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered
+# recursively because of its __init__.py file, but the data subdirectory is excluded
+# with include-package-data = false and namespaces = false.
+include-package-data = true
+[tool.setuptools.packages.find]
+namespaces = true
+where = ["."]
+
+[tool.setuptools.package-data]
+"pycomisa.tests" = ["**"]
+
+
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.vcs]
+# The method key:
+method = "git"  # <- The method name
+# Parameters to pass to the method:
+match = ["*"]
+default-tag = "0.0.0"
+