Merge pull request #11 from ecrl/dev

Readthedocs API documentation

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

@@ -11,13 +11,11 @@
 Future plans for GraphChem include:
 - Robust hyper-parameter and model architecture tuning runtimes
 - Molecule visualization via RDKit
-- Extensive automated testing
 
 # Installation:
 
 ### Prerequisites:
-- Have Python 3.8+ installed
-- Have [RDKit](https://www.rdkit.org/docs/Install.html) installed (using Conda environments is highly recommended)
+- Have Python 3.11+ installed
 
 ### Method 1: pip
 ```
@@ -31,11 +29,15 @@ $ cd graphchem
 $ python setup.py install
 ```
 
-If any errors occur when installing dependencies, namely with PyTorch or torch-geometric, visit their installation pages and follow the installation instructions: [PyTorch](https://pytorch.org/get-started/locally/), [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html)
+If any errors occur when installing dependencies, namely with RDKit, PyTorch, or torch-geometric, visit their installation pages and follow the installation instructions: [RDKit](https://www.rdkit.org/docs/Install.html), [PyTorch](https://pytorch.org/get-started/locally/), [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html)
 
 # Usage:
 
-API documentation is coming in the future! In the meantime, take a look at some [examples](https://github.com/ecrl/GraphChem/tree/master/examples).
+WIP
+
+# Examples
+
+To view some examples of how GraphChem can be used, head over to our [examples](https://github.com/ecrl/graphchem/tree/master/examples) folder on GitHub.
 
 # Contributing, Reporting Issues and Other Support:
 

azure-pipelines.yml

@@ -0,0 +1,26 @@
+# Python package
+# Create and test a Python package on multiple Python versions.
+# Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:
+# https://docs.microsoft.com/azure/devops/pipelines/languages/python
+
+trigger:
+- master
+
+pool:
+  vmImage: 'ubuntu-latest'
+
+steps:
+- task: UsePythonVersion@0
+  inputs:
+    versionSpec: '3.11'
+    architecture: 'x64'
+
+- script: |
+    python -m pip install --upgrade pip setuptools wheel
+    python setup.py install
+  displayName: 'Install dependencies'
+
+- script: |
+    cd tests
+    python test_all.py
+  displayName: 'Unit testing'

docs/api_data.md

@@ -0,0 +1,7 @@
+# graphchem.data
+
+::: graphchem.data.MoleculeGraph
+    handler: python
+
+::: graphchem.data.MoleculeDataset
+    handler: python

docs/api_datasets.md

@@ -0,0 +1,16 @@
+# graphchem.datasets
+
+::: graphchem.datasets.load_cn
+    handler: python
+
+::: graphchem.datasets.load_lhv
+    handler: python
+
+::: graphchem.datasets.load_mon
+    handler: python
+
+::: graphchem.datasets.load_ron
+    handler: python
+
+::: graphchem.datasets.load_ysi
+    handler: python

docs/api_nn.md

@@ -0,0 +1,4 @@
+# graphchem.nn
+
+::: graphchem.nn.MoleculeGCN
+    handler: python

docs/api_preprocessing.md

@@ -0,0 +1,16 @@
+# graphchem.preprocessing
+
+::: graphchem.preprocessing.MoleculeEncoder
+    handler: python
+
+::: graphchem.preprocessing.Tokenizer
+    handler: python
+
+::: graphchem.preprocessing.atom_to_str
+    handler: python
+
+::: graphchem.preprocessing.bond_to_str
+    handler: python
+
+::: graphchem.preprocessing.get_ring_size
+    handler: python

docs/index.md

@@ -0,0 +1,46 @@
+# GraphChem Documentation
+
+[![UML Energy & Combustion Research Laboratory](https://sites.uml.edu/hunter-mack/files/2021/11/ECRL_final.png)](http://faculty.uml.edu/Hunter_Mack/)
+
+[![GitHub version](https://badge.fury.io/gh/ecrl%2FGraphChem.svg)](https://badge.fury.io/gh/ecrl%2FGraphChem)
+[![PyPI version](https://badge.fury.io/py/graphchem.svg)](https://badge.fury.io/py/graphchem)
+[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ecrl/GraphChem/master/LICENSE.txt)
+
+**GraphChem** is an open source Python package for constructing graph-based machine learning models with a focus on fuel property prediction. 
+
+Future plans for GraphChem include:
+
+- Robust hyper-parameter and model architecture tuning runtimes
+
+- Molecule visualization via RDKit
+
+# Installation:
+
+### Prerequisites:
+- Have Python 3.11+ installed
+
+### Method 1: pip
+```
+$ pip install graphchem
+```
+
+### Method 2: From Source
+```
+$ git clone https://github.com/ecrl/graphchem
+$ cd graphchem
+$ python setup.py install
+```
+
+If any errors occur when installing dependencies, namely with RDKit, PyTorch, or torch-geometric, visit their installation pages and follow the installation instructions: [RDKit](https://www.rdkit.org/docs/Install.html), [PyTorch](https://pytorch.org/get-started/locally/), [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html)
+
+# Examples
+
+To view some examples of how GraphChem can be used, head over to our [examples](https://github.com/ecrl/graphchem/tree/master/examples) folder on GitHub.
+
+# Contributing, Reporting Issues and Other Support:
+
+To contribute to GraphChem, make a pull request. Contributions should include tests for new features added, as well as extensive documentation.
+
+To report problems with the software or feature requests, file an issue. When reporting problems, include information such as error messages, your OS/environment and Python version.
+
+For additional support/questions, contact Travis Kessler (Travis_Kessler@student.uml.edu).

docs/requirements.txt

@@ -0,0 +1,2 @@
+mkdocs-material
+mkdocstrings-python

examples/comparison/schweidtmann_test.csv

@@ -0,0 +1,76 @@
+Compounds, SMILES,Meas DCN,Meas MON,Meas RON
+δ-undecalactone,CCCCCCC1CCCC(=O)O1,48.6,n.a.,n.a.
+"3,4,4-Trimethyl-2-pentene", C/C=C(\C)C(C)(C)C,n.a.,86.1,103.0
+"2,3-Dimethyl-2-pentene", CCC(C)=C(C)C,n.a.,80.0,97.5
+2-methyl furan, Cc1ccco1,9.0,86.0,103.0
+Methylcyclopropane, CC1CC1,n.a.,81.2,102.5
+"1,2-dimethylbenzene", Cc1ccccc1C,8.3,100.0,105.0
+furan, c1ccoc1,7.0,91.6,108.6
+4-Methyl-2-pentene (trans), C/C=C/C(C)C,n.a.,82.6,98.0
+"2,3-Dimethyl-2-hexene", CCCC(C)=C(C)C,n.a.,79.3,93.1
+"4,4-Dimethyl-2-pentene (trans)", C/C=C/C(C)(C)C,n.a.,90.9,105.3
+"2,2-Dimethyloctane", CCCCCCC(C)(C)C,n.a.,46.0,49.0
+methyl erucate, CCCCCCCC/C=C\CCCCCCCCCCCC(=O)OC,74.2,n.a.,n.a.
+3-Ethyl-1-pentene, C=CC(CC)CC,n.a.,81.6,95.6
+Sec-Butylcyclohexane, CCC(C)C1CCCCC1,n.a.,55.2,51.0
+aceticacid-2-methylpropylester, CC(=O)OCC(C)C,n.a.,112.3,108.7
+menthone, CC1CCC(C(C)C)C(=O)C1,20.6,n.a.,n.a.
+4-Methylcyclohexene, CC1CC=CCC1,n.a.,67.0,84.1
+tetrahydrofuran, C1CCOC1,21.9,64.8,72.9
+2-Octene, C/C=C\CCCCC,n.a.,56.5,56.3
+1-decene, C=CCCCCCCCC,49.1,n.a.,n.a.
+methyl-9-decenoate, C=CCCCCCCCC(=O)OC,38.3,n.a.,n.a.
+"1,3-Dimethylcyclohexane (trans)", C[C@H]1CCC[C@H](C)C1,n.a.,64.2,66.9
+1-Methylcyclohexene, CC1=CCCCC1,n.a.,72.1,89.2
+2-Phenylpentane, CCCC(C)c1ccccc1,n.a.,92.1,103.5
+2-octanone, CCCCCCC(C)=O,36.6,n.a.,n.a.
+n-Propylbenzene, CCCc1ccccc1,n.a.,98.7,101.5
+3-Ethylhexane, CCCC(CC)CC,n.a.,52.4,33.5
+2-heptanol, CCCCCC(C)O,25.0,n.a.,n.a.
+"2,2-dimethylbutane", CCC(C)(C)C,24.4,93.4,91.8
+"1,2,3-Trimethylcyclohexane (cis, trans, cis)", CC1[C@@H](C)CCC[C@H]1C,n.a.,81.0,83.4
+4-methoxybenzaldehyde, COc1ccc(C=O)cc1,25.8,n.a.,n.a.
+iso-Butylbenzene, CC(C)Cc1ccccc1,n.a.,98.0,111.4
+geraniol, CC(C)=CCC/C(C)=C/CO,19.3,n.a.,n.a.
+trans-3-octene, CC/C=C/CCCC,34.0,n.a.,n.a.
+dipropylene glycol monomethyl ether, COC(C)COC(C)CO,43.9,n.a.,n.a.
+2-methylpropanoicacidmethylester, COC(=O)C(C)C,n.a.,104.7,103.6
+"1,5-Hexadiene", C=CCCC=C,n.a.,37.6,71.1
+dibutyl ether, CCCCOCCCC,115.4,n.a.,n.a.
+1-Methyl-4-isopropylbenzene, Cc1ccc(C(C)C)cc1,n.a.,97.7,101.4
+tert-Butylbenzene, CC(C)(C)c1ccccc1,n.a.,107.4,115.5
+"3,3-Dimethyl-1-pentene", C=CC(C)(C)CC,n.a.,86.1,103.5
+4-ethyl guaiacol, CCc1ccc(OC)c(O)c1,19.6,n.a.,n.a.
+butanal, CCCC=O,41.1,n.a.,n.a.
+"1,4-Diethylbenzene", CCc1ccc(CC)cc1,n.a.,95.2,106.0
+"2,5-Dimethyl-3-hexene (cis)", CC(C)/C=C\C(C)C,n.a.,87.4,104.0
+3-methyl-2-butanone, CC(=O)C(C)C,n.a.,102.2,108.9
+"1,3,5triisopropylbenzene", CC(C)c1cc(C(C)C)cc(C(C)C)c1,2.8,n.a.,n.a.
+"2,2,3-Trimethylpentane", CCC(C)C(C)(C)C,n.a.,99.9,109.6
+ocimene, C=C/C(C)=C/C=C/C(C)C,28.0,n.a.,n.a.
+1-Methyl-2-ethylbenzene, CCc1ccccc1C,n.a.,92.1,102.5
+"2,2-Dimethyl-3-hexene (cis)", CC/C=C\C(C)(C)C,n.a.,88.0,106.7
+2-Methyl-1-pentene, C=C(C)CCC,n.a.,81.5,94.2
+6-Methyl-1-heptene, C=CCCCC(C)C,n.a.,62.6,63.6
+1-Methyl-2-n-propylcyclohexane (trans), CCC[C@@H]1CCCC[C@H]1C,n.a.,38.8,29.4
+2-methylheptane, CCCCCC(C)C,49.8,23.0,20.7
+dodecyl vinyl ether, C=COCCCCCCCCCCCC,101.7,n.a.,n.a.
+"1,1,3-Trimethylcyclohexane", CC1CCCC(C)(C)C1,n.a.,82.6,81.3
+2-Methyl-2-pentene, CCC=C(C)C,n.a.,83.0,97.8
+"1,4-dimethylbenzene", Cc1ccc(C)cc1,6.2,101.2,103.4
+Methyl-2-methylbutanoate, CCC(C)C(=O)OC,n.a.,99.1,110.5
+"3,3-Dimethylhexane", CCCC(C)(C)CC,n.a.,83.4,75.5
+methyl α-linolenate, CC/C=C\C/C=C\C/C=C\CCCCCCCC(=O)OC,22.7,n.a.,n.a.
+n-pentanol, CCCCCO,n.a.,74.0,78.0
+1-Methyl-3-n-propylbenzene, CCCc1cccc(C)c1,n.a.,100.5,111.9
+propylene glycol monomethyl ether acetate, COCC(C)OC(C)=O,24.0,n.a.,n.a.
+4-Octene (trans), CCC/C=C/CCC,n.a.,74.3,73.3
+6-undecanone, CCCCCC(=O)CCCCC,49.0,n.a.,n.a.
+methyl caproate, CCCCCC(=O)OC,24.6,n.a.,n.a.
+"1,2,3,4-Tetramethylbenzene", Cc1ccc(C)c(C)c1C,n.a.,100.3,105.3
+"2,4-Hexadiene", C/C=C\C=C\C,n.a.,80.7,97.1
+4-nonanone, CCCCCC(=O)CCC,43.0,n.a.,n.a.
+n-butylbenzene, CCCCc1ccccc1,12.5,94.4,104.4
+Allylcyclopentane, C=CCC1CCCC1,n.a.,45.6,52.1
+diisobutylether, CC(C)COCC(C)C,59.7,n.a.,n.a.
+β-citronellol, CC(C)=CCCC(C)CCO,25.6,n.a.,n.a.