Update docs on installation, widget; update Readme and Makefile

Makefile

@@ -56,7 +56,7 @@ test-ci-github: lint-deps lint pre-commit ci-github-deps test-deps test-ci
 
 .PHONY: publish-deps
 publish-deps:
-	@$(PYTHON3) -m pip install -e .'[packaging]' --use-pep517
+	@$(PYTHON3) -m pip install -e .[packaging] --use-pep517
 
 .PHONY: build-dist
 build-dist: publish-deps clean
@@ -75,21 +75,21 @@ publish-to-pypi: publish-deps build-dist
 
 .PHONY: version-deps
 version-deps:
-	@$(PYTHON3) -m pip install .'[releases]' --use-pep517
+	@$(PYTHON3) -m pip install .[releases] --use-pep517
 
 
 ### Documentation
 
 .PHONY: docs-deps
 docs-deps:
-	@$(PYTHON3) -m pip install .'[documentation]' --use-pep517
+	@$(PYTHON3) -m pip install .[documentation] --use-pep517
 
 
 ## Tutorials
 
 .PHONY: tutorial-deps
 tutorial-deps:
-	@$(PYTHON3) -m pip install .'[tutorials]' .'[widget]' --use-pep517
+	@$(PYTHON3) -m pip install .[tutorials] .[widget] --use-pep517
 
 .PHONY: tutorials
 tutorials:
@@ -116,16 +116,16 @@ ci-github-deps:
 
 .PHONY: lint-deps
 lint-deps:
-	@$(PYTHON3) -m pip install .'[lint]' --use-pep517
+	@$(PYTHON3) -m pip install .[lint] --use-pep517
 
 .PHONY: format-deps
 format-deps:
-	@$(PYTHON3) -m pip install .'[format]' --use-pep517
+	@$(PYTHON3) -m pip install .[format] --use-pep517
 
 .PHONY: test-deps
 test-deps:
-	@$(PYTHON3) -m pip install .'[testing]' --use-pep517
+	@$(PYTHON3) -m pip install .[testing] --use-pep517
 
 .PHONY: all-deps
 all-deps:
-	@$(PYTHON3) -m pip install .'[all]' --use-pep517
+	@$(PYTHON3) -m pip install .[all] --use-pep517

README.md

@@ -150,8 +150,8 @@ conda activate venv-hnx
 
 
 ```shell
-virtualenv env-hnx
-source env-hnx/bin/activate
+virtualenv venv-hnx
+source venv-hnx/bin/activate
 ```
 
 
@@ -190,19 +190,11 @@ Ensure that you have [git](https://git-scm.com/book/en/v2/Getting-Started-Instal
 ```shell
 git clone https://github.com/pnnl/HyperNetX.git
 cd HyperNetX
+make venv
+source venv-hnx/bin/activate
 pip install .
 ```
 
-Post-Installation Actions
-=========================
-
-Running Tests
--------------
-
-```shell
-python -m pytest
-```
-
 Development
 ===========
 
@@ -213,10 +205,13 @@ Install an editable version
 pip install -e .
 ```
 
-Install an editable version with access to jupyter notebooks
-------------------------------------------------------------
+Install an editable version with supported applications
+-------------------------------------------------------
 
 ```shell
+pip install -e .['all']
+
+# for zsh users
 pip install -e .'[all]'
 ```
 
@@ -226,7 +221,7 @@ Install support for testing
 > ℹ️ **NOTE:** This project has a pytest configuration file named 'pytest.ini'. By default, pytest will use those configuration settings to run tests.
 
 ```shell
-pip install .'[testing]'
+make test-deps
 
 # run tests
 python -m pytest
@@ -243,20 +238,14 @@ Install support for tutorials
 -----------------------------
 
 ``` shell
-pip install .'[tutorials]'
+make tutorial-deps
+
+# open Jupyter notebooks in a browser
+make tutorials
 ```
 
-Install support for documentation
----------------------------------
 
-```shell
-pip install .'[documentation]'
-cd docs
 
-## This will generate the documentation in /docs/build/
-## Open them in your browser with docs/build/html/index.html
-make html
-```
 
 
 Code Quality
@@ -269,7 +258,7 @@ HyperNetX uses a number of tools to maintain code quality:
 Before using these tools, ensure that you install Pylint in your environment:
 
 ```shell
-pip install .'[lint]'
+make lint-deps
 ```
 
 
@@ -299,6 +288,7 @@ For more information on configuration, see https://pylint.pycqa.org/en/latest/us
 
 
 ```shell
+make format-deps
 black hypernetx
 ```
 
@@ -309,19 +299,20 @@ Build and view documentation locally
 ---------------------------
 
 ```
+make docs-deps
 cd docs
 make html
 open docs/build/html/index.html
 ```
 
 Editing documentation
 ----------------------
-NOTE: make sure you install the required dependencies using: `make docs-deps`
 
 When editing documentation, you can auto-rebuild the documentation locally so that you can view your document changes
 live on the browser without having to rebuild every time you have a change.
 
 ```
+make docs-deps
 cd docs
 make livehtml
 ```

docs/source/classes/classes.rst

@@ -4,14 +4,6 @@ classes package
 Submodules
 ----------
 
-classes.entity module
----------------------
-
-.. automodule:: classes.entity
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 classes.entityset module
 ------------------------
 

docs/source/install.rst

@@ -26,21 +26,21 @@ Create a virtual environment
 Using Anaconda
 *************************
 
-    >>> conda create -n env-hnx python=3.8 -y
-    >>> conda activate env-hnx
+    >>> conda create -n venv-hnx python=3.8 -y
+    >>> conda activate venv-hnx
 
 Using venv
 *************************
 
     >>> python -m venv venv-hnx
-    >>> source env-hnx/bin/activate
+    >>> source venv-hnx/bin/activate
 
 
 Using virtualenv
 *************************
 
-    >>> virtualenv env-hnx
-    >>> source env-hnx/bin/activate
+    >>> virtualenv venv-hnx
+    >>> source venv-hnx/bin/activate
 
 
 For Windows Users
@@ -66,6 +66,15 @@ Installing from PyPi
 
     >>> pip install hypernetx
 
+If you want to use supported applications built upon HyperNetX (e.g. ``hypernetx.algorithms.hypergraph_modularity`` or
+``hypernetx.algorithms.contagion``), you can install HyperNetX with those supported applications by using
+the following command:
+
+    >>> pip install hypernetx[all]
+
+If you are using zsh as your shell, use single quotation marks around the square brackets:
+
+    >>> pip install hypernetx'[all]'
 
 Installing from Source
 *************************
@@ -74,43 +83,14 @@ Ensure that you have ``git`` installed.
 
     >>> git clone https://github.com/pnnl/HyperNetX.git
     >>> cd HyperNetX
-    >>> pip install -e .['all']
-
-If you are using zsh as your shell, ensure that the single quotation marks are placed outside the square brackets:
-
-    >>> pip install -e .'[all]'
+    >>> make venv
+    >>> source venv-hnx/bin/activate
+    >>> pip install .
 
 
 Post-Installation Actions
 ##########################
 
-Running Tests
-**************
-
-To run all the tests, ensure that you first install the testing dependencies:
-
-    >>> pip install -e .['testing']
-
-Then try running all the tests:
-
-    >>> python -m pytest
-
-
-Dependencies for some Submodules
-********************************
-
-Two submodules in the library, ``hypernetx.algorithms.hypergraph_modularity`` and ``hypernetx.algorithms.contagion``,
-require some additional dependencies. If you want to use those submodules, you will need to install those dependencies.
-
-For ``hypernetx.algorithms.hypergraph_modularity``, install the following:
-
-    >>> pip install 'igraph>=0.10.4'
-
-For ``hypernetx.algorithms.contagion``, install the following:
-
-    >>> pip install 'celluloid>=0.2.0'
-
-
 Interact with HyperNetX in a REPL
 ********************************************
 
@@ -130,22 +110,29 @@ Ensure that your environment is activated and that you run ``python`` on your te
 Other Actions if installed from source
 ********************************************
 
-Ensure that you are at the root of the source directory before running any of the following commands:
+If you have installed HyperNetX from source, you can perform additional actions such as viewing the provided Jupyter notebooks
+or building the documentation locally.
+
+Ensure that you have activated your virtual environment and are at the root of the source directory before running any of the following commands:
+
 
 Viewing jupyter notebooks
 --------------------------
 
 The following command will automatically open the notebooks in a browser.
 
-    >>> jupyter-notebook tutorials
+    >>> make tutorial-deps
+    >>> make tutorials
 
 
 Building documentation
 -----------------------
 
 The following commands will build and open a local version of the documentation in a browser:
 
-    >>> make build-docs
-    >>> open docs/build/index.html
+    >>> make docs-deps
+    >>> cd docs
+    >>> make html
+    >>> open build/index.html
 
 

docs/source/widget.rst

@@ -30,10 +30,16 @@ HyperNetXWidget is currently in beta and will only work on Jupyter Notebook 6.5.
 but support for Jupyter Lab is in planning.
 
 In addition, HyperNetXWidget must be installed using the `Anaconda platform <https://www.anaconda.com/>`_ so that the
-widget can render on Jupyter notebook. It is highly recommended to use the base environment provided by Anaconda because
-Anaconda's package management system, `conda`, will resolve dependencies when HyperNetX and HyperNetXWidget are
-installed. For more information on `conda` environments, please see `their documentation here.
-<https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment>`_
+widget can render on Jupyter notebook.
+
+For users with inexperience with Jupyter and Anaconda, it is highly recommended to use the base environment of Anaconda so
+that the widget works seamlessly and out-of-the box on Jupyter Notebook. The widget does not work on Jupyter Lab.
+
+If users want to create a custom environment instead of using the base environment provided by Anaconda, then users
+will need to do additional configuration on Jupyter and the kernel to ensure that the widget works.
+Specifically, users will need to set the Kernel to use a custom environment. For a guide on how to do this, please
+read and follow this guide: `How to add your Conda environment to your jupyter notebook in just 4 steps <https://medium.com/@nrk25693/how-to-add-your-conda-environment-to-your-jupyter-notebook-in-just-4-steps-abeab8b8d084>`_.
+
 
 **Do not use python's built-in venv module or virtualenv to create a virtual environment; the widget will not render on
 Jupyter notebook.**
@@ -91,12 +97,6 @@ following screenshot as an example:
    :align: center
 
 
-|
-| For more information on setting the environment in Jupyter notebook, see
-  `How to add your Conda environment to your jupyter notebook in just 4 steps.
-  <https://medium.com/@nrk25693/how-to-add-your-conda-environment-to-your-jupyter-notebook-in-just-4-steps-abeab8b8d084>`_
-
-
 Using the Tool
 --------------