diff --git a/README.md b/README.md index 592d8fe..317e9c5 100755 --- a/README.md +++ b/README.md @@ -20,34 +20,32 @@ A documentation of all features of the *PyGenStability* is available here: https ## Installation - -The wrapper uses Pybind11 https://github.com/pybind/pybind11 and the package can simply be installed by first cloning this repo with +Install the package using [pypi](https://pypi.org/project/PyGenStability/): ``` -git clone --recurse-submodules https://github.com/ImperialCollegeLondon/PyGenStability.git +pip install pygenstability ``` -(if the `--recurse-submodules` has not been used, just do `git submodule update --init --recursive` to fetch the submodule with M. Schaub's code). +Using a fresh python3 virtual environment, e.g. conda, may be recommended to avoid conflicts with other python packages. -Then, to install the package, simply run +By default, the package uses the Louvain algorithm [4] for optimizing generalized Markov Stability. To use the Leiden algorithm [5], install this package with: ``` -pip install . +pip install pygenstability[leiden] ``` -using a fresh `virtualenv` in python3 may be recommended to avoid conflict of python packages. -To use plotly for interactive plots in the browser, install this package with +To plot network partitions using `networkx`, install this package with: ``` -pip install .[plotly] +pip install pygenstability[networkx] ``` -To use a contrib module, with additional tools, run +To use `plotly` for interactive plots in the browser, install this package with: ``` -pip install .[contrib] +pip install pygenstability[plotly] ``` -To install all dependencies, run +To install all dependencies, run: ``` -pip install .[all] +pip install pygenstability[all] ``` ## Using the code diff --git a/docs/index_readme.md b/docs/index_readme.md index 54c75d3..8305e22 100644 --- a/docs/index_readme.md +++ b/docs/index_readme.md @@ -7,34 +7,32 @@ We further provide specific analysis tools to process and analyse the results fr ## Installation - -The wrapper uses Pybind11 https://github.com/pybind/pybind11 and the package can simply be installed by first cloning this repo with +Install the package using [pypi](https://pypi.org/project/PyGenStability/): ``` -git clone --recurse-submodules https://github.com/ImperialCollegeLondon/PyGenStability.git +pip install pygenstability ``` -(if the `--recurse-submodules` has not been used, just do `git submodule update --init --recursive` to fetch the submodule with M. Schaub's code). +Using a fresh python3 virtual environment, e.g. conda, may be recommended to avoid conflicts with other python packages. -Then, to install the package, simply run +By default, the package uses the Louvain algorithm [4] for optimizing generalized Markov Stability. To use the Leiden algorithm [5], install this package with: ``` -pip install . +pip install pygenstability[leiden] ``` -using a fresh `virtualenv` in python3 may be recommended to avoid conflict of python packages. -To use plotly for interactive plots in the browser, install this package with +To plot network partitions using `networkx`, install this package with: ``` -pip install .[plotly] +pip install pygenstability[networkx] ``` -To use a contrib module, with additional tools, run +To use `plotly` for interactive plots in the browser, install this package with: ``` -pip install .[contrib] +pip install pygenstability[plotly] ``` -To install all dependencies, run +To install all dependencies, run: ``` -pip install .[all] +pip install pygenstability[all] ``` ## Using the code