Write benchmarks

README.md

@@ -2,17 +2,18 @@
 [![Build Status](https://dev.azure.com/cwzou/mongo-rdkit/_apis/build/status/rdkit.mongo-rdkit?branchName=master)](https://dev.azure.com/cwzou/mongo-rdkit/_build/latest?definitionId=1&branchName=master)
 
 <a href="https://github.com/rdkit/mongo-rdkit">Mongo-rdkit</a> is an integration between MongoDB, 
-a NoSQL database platform, and RDKit, a collection of chemoinformatics and machine-learning software.
+a NoSQL database platform, and RDKit, a collection of cheminformatics and machine-learning software.
 This package contains tools to create and manipulate a chemically-intelligent database, as well as
 methods for high-performance searches on the database that leverage native MongoDB features.
 
 Useful links: 
 * [BSD License](https://github.com/rdkit/mongo-rdkit/blob/master/LICENSE) - a business friendly license for open-source.
-* [Jupyter Notebooks](https://github.com/rdkit/mongo-rdkit/tree/master/docs) - resources for getting started.
+* [Jupyter Notebooks](https://github.com/rdkit/mongo-rdkit/tree/master/docs) - walkthroughs for main functionality.
+* [Testing Guide](https://github.com/rdkit/mongo-rdkit/blob/master/docs/testing.md) - walkthrough of running `mongordkit` tests.
 
 ## Documentation
 Jupyter Notebooks and resources for getting started in the [docs](https://github.com/rdkit/mongo-rdkit/tree/master/docs) 
-folder on GitHub
+folder on GitHub.
 
 ## Installation
 As the package is not officially configured with a setup.py file or pushed onto PyPi, these are working install instructions.
@@ -43,9 +44,43 @@ echo $PYTHONPATH
 You can now `import mongordkit` in your Python interpreter or run all tests using the `pytest` command.
 
 ### Windows:
+Similarly, ensure that `conda` has been added to `PATH`.
 
+Clone the repository into your desired directory and navigate into it.
 
+Create a conda environment called mongo_rdkit that includes dependencies:
+```
+conda env create --quiet --force --file env.yml
+```
+Activate this conda environment: 
+```
+call activate mongo_rdkit
+```
+Check that you are able to import mongordkit:
+```
+python -c "import mongordkit"
+```
+If this fails, you may need to add the current directory manually to `PYTHONPATH`:
+```
+set PYTHONPATH=%PYTHONPATH%;C:.
+```
+You can now use `mongordkit` in your interpreter and run tests using `python -m pytest`.
+## Package Contents
+### Modules
+`mongordkit` contains two main modules, each of which contains a variety of importable methods and classes.
+`Database` contains functionality for writing and registering data. `Search` contains functionality for setting up and performing
+substructure and similarity search. Detailed walkthroughs can be found in the notebooks, listed below.
+
+### Notebooks
+- **Creating and Writing to MongoDB**: documentation and demos for creating and modifying mongo-rdkit databases.
+- **Similarity and Substructure Search**: documentation and demos for similarity and substructure search.
+- **Similarity Benchmarking**: documentation for reproducing similarity benchmarking.
+- **Substructure Benchmarking**: documentation for reproducing substructure benchmarking.
 
+### Configuration
+- **azure_pipelines.yml**: CI/CD pipeline configurations.
+- **conftest.py**: `pytest` configurations.
+- **env.yml**: required dependencies.
 
 ## License
 Code released under the BSD License.