Update documentation and readme

Makefile

@@ -13,18 +13,19 @@ venv: clean-venv
 clean-venv:
 	rm -rf $(VENV)
 
-.PHONY: install-reqs
-install-reqs:
-	pip install --upgrade pip
+.PHONY: install
+install:
+	@$(PYTHON3) -m pip install --upgrade pip
+	@$(PYTHON3) -m pip install -e .
 	@$(PYTHON3) -m pip install -r requirements.txt
-	pip install pytest pytest-cov decorator
 
 ## Environment using Poetry
 
 .PHONY: develop
 develop: clean-poetry-env
-	poetry install --all-extras --with test
 	poetry shell
+	poetry install --with test
+
 
 .PHONY: requirements.txt
 requirements.txt:

README.md

@@ -190,29 +190,71 @@ 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
+
+# Create a virtual environment
 make venv
 source venv-hnx/bin/activate
-pip install .
+
+# install required dependencies
+make install
 ```
 
 Development
 ===========
 
 Install an editable version
----------------------------
-
 ```
 pip install -e .
 ```
 
-Install an editable version with supported applications
--------------------------------------------------------
+Install additional dependencies to support testing and jupyter notebooks:
+```
+pip install -r requirements.txt
+```
 
-```shell
-pip install -e .['all']
+You can also install all these requirements in one Make target:
+
+```
+make install
+```
+
+Poetry
+======
 
-# for zsh users
-pip install -e .'[all]'
+This library uses [Poetry](https://python-poetry.org/docs/) to manage dependencies and packaging. Poetry can also be
+used to manage your environment for development.
+
+Prerequisites
+-------------
+
+* [Install Poetry](https://python-poetry.org/docs/#installation)
+
+
+Configure Poetry
+----------------
+
+[Configure your Poetry](https://python-poetry.org/docs/configuration/) to create the virtual environment in your project directory:
+```
+poetry config virtualenvs.in-project true
+
+# check the poetry configuration
+poetry config --list
+```
+
+Set up virtual environment
+----------------------------
+
+Create and activate a virtual environment.
+```
+poetry shell
+```
+
+NOTE: If you plan to use Poetry to manage your virtual environment, you can activate the virtual environment
+using poerty: `poetry shell`. Another option is to directly
+
+Install required dependencies and HyperNetX in editable mode.
+```
+poetry install
 ```
 
 Install support for testing
@@ -221,7 +263,7 @@ 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
-make test-deps
+poetry install --with test
 
 # run tests
 python -m pytest
@@ -237,17 +279,13 @@ open htmlcov/index.html
 Install support for tutorials
 -----------------------------
 
-``` shell
-make tutorial-deps
+```
+poetry install --with tutorials
 
 # open Jupyter notebooks in a browser
 make tutorials
 ```
 
-
-
-
-
 Code Quality
 ------------
 HyperNetX uses a number of tools to maintain code quality:
@@ -257,12 +295,12 @@ HyperNetX uses a number of tools to maintain code quality:
 
 Before using these tools, ensure that you install Pylint in your environment:
 
-```shell
-make lint-deps
+```
+poetry install --with lint
 ```
 
-
-### Pylint
+Pylint
+------
 
 [Pylint](https://pylint.pycqa.org/en/latest/index.html) is a static code analyzer for Python-based projects. From the [Pylint docs](https://pylint.pycqa.org/en/latest/index.html#what-is-pylint):
 
@@ -282,37 +320,31 @@ pylint hypernetx --output=pylint-results.txt
 
 For more information on configuration, see https://pylint.pycqa.org/en/latest/user_guide/configuration/index.html
 
-### Black
-
+Black
+-----
 [Black](https://black.readthedocs.io/en/stable/) is a PEP 8 compliant formatter for Python-based project. This tool is highly opinionated about how Python should be formatted and will automagically reformat your code.
 
 
 ```shell
-make format-deps
 black hypernetx
 ```
 
 Documentation
-===============
+-------------
 
-Build and view documentation locally
----------------------------
+Build and view documentation locally:
 
 ```
-make docs-deps
+poetry install --with docs
 cd docs
 make html
 open docs/build/html/index.html
 ```
 
-Editing documentation
-----------------------
-
 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
 ```
@@ -353,15 +385,15 @@ gh run list --workflow=ci.yml --repo pnnl/HyperNetX
 
 
 Versioning
-----------
+==========
 
 This project uses [`commitizen`](https://github.com/commitizen-tools/commitizen) to manage versioning.
 The files where "version" will be updated are listed in the '.cz.toml' file. To create a new version and the associated tag,
 run the following commands:
 
 ```shell
 # Install commitizen tool to environment
-make version-deps
+pip install commitizen
 
 # Updates version; values for '--increment' can be MAJOR, MINOR, or PATCH
 # Autocreates a tag and commit for the updated version

docs/source/install.rst

@@ -2,10 +2,6 @@
 Installing HyperNetX
 ********************
 
-
-Installation
-############
-
 The recommended installation method for most users is to create a virtual environment
 and install HyperNetX from PyPi.
 
@@ -56,43 +52,39 @@ To deactivate your environment, use:
     >>> .\env-hnx\Scripts\deactivate
 
 
-Installing Hypernetx
-####################
+Installation
+############
 
 Regardless of how you install HyperNetX, ensure that your environment is activated and that you are running Python >=3.8.
 
 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]'
+    >>> pip install igraph celluloid
 
 Installing from Source
-*************************
+**********************
 
 Ensure that you have ``git`` installed.
 
     >>> git clone https://github.com/pnnl/HyperNetX.git
     >>> cd HyperNetX
     >>> make venv
     >>> source venv-hnx/bin/activate
-    >>> pip install .
+    >>> make install
 
 
 Post-Installation Actions
-##########################
+#########################
 
 Interact with HyperNetX in a REPL
-********************************************
+*********************************
 
 Ensure that your environment is activated and that you run ``python`` on your terminal to open a REPL:
 
@@ -108,7 +100,7 @@ Ensure that your environment is activated and that you run ``python`` on your te
 
 
 Other Actions if installed from source
-********************************************
+**************************************
 
 If you have installed HyperNetX from source, you can perform additional actions such as viewing the provided Jupyter notebooks
 or building the documentation locally.
@@ -121,7 +113,6 @@ Viewing jupyter notebooks
 
 The following command will automatically open the notebooks in a browser.
 
-    >>> make tutorial-deps
     >>> make tutorials
 
 
@@ -130,9 +121,7 @@ Building documentation
 
 The following commands will build and open a local version of the documentation in a browser:
 
-    >>> make docs-deps
+    >>> pip install sphinx sphinx-autobuild sphinx-rtd-theme sphinx-copybutton
     >>> cd docs
     >>> make html
     >>> open build/index.html
-
-

pyproject.toml

@@ -26,9 +26,11 @@ python = "^3.8,<3.12"
 networkx = "^2.2"
 pandas = "^1.5.3"
 scikit-learn = "^1.3.2"
+
+[tool.poetry.group.algorithms.dependencies]
+decorator = "^5.1.1"
 celluloid = "^0.2.0"
 igraph = "^0.11.4"
-decorator = "^5.1.1"
 
 [tool.poetry.group.widget]
 optional = true

requirements.txt

@@ -35,6 +35,7 @@ h11==0.14.0
 hnxwidget==0.1.1b3
 httpcore==1.0.5
 httpx==0.27.0
+-e git+ssh://git@stash.pnnl.gov:7999/hyp/hypernetx.git@70360f14748f8f66188a04179d741201452e389a#egg=hypernetx
 idna==3.6
 igraph==0.11.4
 iniconfig==2.0.0
@@ -74,7 +75,7 @@ matplotlib-inline==0.1.6
 mistune==3.0.2
 nbclient==0.6.8
 nbconvert==7.16.3
-nbformat==5.10.3
+nbformat==5.10.4
 nbmake==1.5.3
 nest-asyncio==1.6.0
 networkx==2.8.8