docs: change order in readme (#294) (#321)

* Order change in readme
* Fixed readme order
* Added venv changes
* Readme changes

Co-authored-by: Shivang Bagri <[email protected]>

README.md

@@ -28,17 +28,68 @@ The ga4gh/vrs-python repo embeds the ga4gh/vrs repo as a git submodule, and
 therefore each ga4gh.vrs package on PyPi embeds a particular version of VRS. The
 correspondences between the packages may be summarized as:
 
-| vrs-python branch | vrs branch |
-| --- | --- |
-| [main](https://github.com/ga4gh/vrs-python/tree/main) | [main](https://github.com/ga4gh/vrs/tree/main) |
-| [0.6](https://github.com/ga4gh/vrs-python/tree/0.6) | [1.1](https://github.com/ga4gh/vrs/tree/1.1) |
-| [0.7](https://github.com/ga4gh/vrs-python/tree/0.7) | [1.2](https://github.com/ga4gh/vrs/tree/1.2) |
-| [0.8](https://github.com/ga4gh/vrs-python/tree/0.8) | [1.3](https://github.com/ga4gh/vrs/tree/1.3) |
-| [0.9](https://github.com/ga4gh/vrs-python/tree/0.9) | [metaschema-update](https://github.com/ga4gh/vrs/tree/metaschema-update) |
+| vrs-python branch                                     | vrs branch                                                               |
+| ----------------------------------------------------- | ------------------------------------------------------------------------ |
+| [main](https://github.com/ga4gh/vrs-python/tree/main) | [main](https://github.com/ga4gh/vrs/tree/main)                           |
+| [0.6](https://github.com/ga4gh/vrs-python/tree/0.6)   | [1.1](https://github.com/ga4gh/vrs/tree/1.1)                             |
+| [0.7](https://github.com/ga4gh/vrs-python/tree/0.7)   | [1.2](https://github.com/ga4gh/vrs/tree/1.2)                             |
+| [0.8](https://github.com/ga4gh/vrs-python/tree/0.8)   | [1.3](https://github.com/ga4gh/vrs/tree/1.3)                             |
+| [0.9](https://github.com/ga4gh/vrs-python/tree/0.9)   | [metaschema-update](https://github.com/ga4gh/vrs/tree/metaschema-update) |
 
 ⚠ **Developers: See the development section below for recommendations for using submodules
 gracefully (and without causing problems for others!).**
 
+# Pre-requisite
+
+[Python 3.10](https://www.python.org/downloads/release/python-3100/)
+
+# Development
+
+## Submodules!
+
+vrs-python embeds vrs as a submodule. When checking out vrs-python and switching
+branches, it is important to make sure that the submodule tracks vrs-python
+correctly. The recommended way to do this is `git config --global submodule.recurse true`. **If you don't set submodule.recurse, developers and
+reviewers must be extremely careful to not accidentally upgrade or downgrade
+schemas with respect to vrs-python.**
+
+Alternatively, see `misc/githooks/`.
+
+## Installing for development
+
+Fork the repo at https://github.com/ga4gh/vrs-python/ .
+
+    $ git clone --recurse-submodules [email protected]:YOUR_GITHUB_ID/vrs-python.git
+    $ cd vrs-python
+    $ make devready
+
+Activate the virtual environment (if not already) :
+
+    $ source venv/3.10/bin/activate
+
+## Pre-commit
+
+We use [pre-commit](https://pre-commit.com/) to check code style.
+
+Before first commit, run:
+
+    $ pre-commit install
+
+## Testing
+
+This package implements typical unit tests for ga4gh.core and ga4gh.vrs. This
+package also implements the compliance tests from vrs (vrs/validation) in the
+tests/validation/ directory.
+
+    $ make test
+
+## Developing VRS (the schema) too
+
+If you want to develop the VRS schema in conjunction with vrs-python, the
+recommended approach for most users is to fork and clone the `ga4gh/vrs` repo,
+then set the `VRS_SCHEMA_DIR` environment variable to use an alternative schema
+location.
+
 # Installation
 
 ## Installing with pip
@@ -104,7 +155,6 @@ Here are some things to try.
 
 Once installed as described above, type
 
-    $ source venv/3.10/bin/activate
     $ jupyter notebook --notebook-dir notebooks/
 
 The following jupyter extensions are recommended but not required
@@ -129,39 +179,11 @@ We have created a public [`VRS-demo-notebooks`](https://app.terra.bio/#workspace
 **4. Select the Jupyter Kernel**: In a notebook, click `Select Kernel` at the top right. Select the option where the path is `venv/3.10/bin/python3`. See [here](https://code.visualstudio.com/docs/datascience/jupyter-kernel-management) for more information on managing Jupyter Kernels in VS Code.
 **5. Run the Notebook**: After selecting the kernel you can now run the notebook.
 
-# Development
-
-## Submodules!
-
-vrs-python embeds vrs as a submodule. When checking out vrs-python and switching
-branches, it is important to make sure that the submodule tracks vrs-python
-correctly. The recommended way to do this is `git config --global submodule.recurse true`. **If you don't set submodule.recurse, developers and
-reviewers must be extremely careful to not accidentally upgrade or downgrade
-schemas with respect to vrs-python.**
-
-Alternatively, see `misc/githooks/`.
-
-## Installing for development
-
-Fork the repo at https://github.com/ga4gh/vrs-python/ .
-
-    $ git clone --recurse-submodules [email protected]:YOUR_GITHUB_ID/vrs-python.git
-    $ cd vrs-python
-    $ make devready
-
-## Testing
-
-This package implements typical unit tests for ga4gh.core and ga4gh.vrs. This
-package also implements the compliance tests from vrs (vrs/validation) in the
-tests/validation/ directory.
-
-    $ make test
-
 # Security Note (from the GA4GH Security Team)
 
 A stand-alone security review has been performed on the specification itself.
 This implementation is offered as-is, and without any security guarantees. It
 will need an independent security review before it can be considered ready for
 use in security-critical applications. If you integrate this code into your
 application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security
-audit.
+audit.