Merge pull request #17 from MorganCThomas/packaging

Improved for packaging

Author: MorganCThomas

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.3.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

.ruff.toml

@@ -0,0 +1,61 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.8
+target-version = "py38"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+select = ["E4", "E7", "E9", "F", "I"]
+ignore = []
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"

README.md

@@ -3,22 +3,19 @@
 This repo contains code for a SMILES-based recurrent neural network used for *de novo* molecule generation with several  reinforcement learning algorithms available for molecule optimization. This was written to be used in conjunction with [MolScore](https://github.com/MorganCThomas/MolScore) - although any other scoring function can also be used.
 
 ## Installation
-First setup a conda environment with the correct requirements.
+This code can be installed via pip.
 
 ```
-conda env create -f environment.yml
+pip install smiles-rnn
 ```
 
-Or to update a prexisting environment.
+Or via cloning this repository and setting up an environment with mamba.
 
 ```
-conda env update --name myenv --file environment.yml
-```
-
-The package can also be installed into the conda evironment.
-
-```
-python setup.py install  # if you plan to make changes use 'develop' instead of 'install'
+git clone https://github.com/MorganCThomas/SMILES-RNN.git
+cd SMILES-RNN
+mamba env create -f environment.yml
+pip install ./
 ```
 
 ## Usage