Add notebook on persistent homology of undirected and directed graphs…

…, fix bugs with homology_dimensions in FlagserPersistence, fix #92, bump pyflagser version (#462)

* Add notebook on persistent homology of undirected and directed graphs

* Fix errors with use of homology_dimensions kwarg in FlagserPersistence

- Implementation was incorrect in cases where minimum in homology_dimensions is greater than 1
- Implementation would crash whenever `flagser_weighted` does not return a list of size self._max_homology_dimension + 1 - self._min_homology_dimension, as can happen with small graphs

* Fix #92

Document removal of one infinite bar in simplicial transformers

* Polish up classifying_shapes notebook

* Upload clique complex filtration images

* Add SVGs for directed flag complex illustration

* Implement some of @lewtun's suggestions for classifying shapes notebook

* Add general persistence diagram discussion to vietoris_rips_quickstart.ipynb

* Fix VR notebook and add explanation of homology_dimensions parameter

* Bump pyflagser version required by giotto-tda

* Improve docs for VietorisRipsPersistence by explaining how precomputed input is handled

README.rst

@@ -67,7 +67,7 @@ The latest stable version of ``giotto-tda`` requires:
 - SciPy (>= 1.5.0)
 - joblib (>= 0.16.0)
 - scikit-learn (>= 0.23.1)
-- pyflagser (>= 0.4.0)
+- pyflagser (>= 0.4.1)
 - python-igraph (>= 0.8.2)
 - plotly (>= 4.8.2)
 - ipywidgets (>= 7.5.1)

doc/installation.rst

@@ -8,26 +8,26 @@ Installation
 Dependencies
 ************
 
-The latest stable version of giotto-tda requires:
+The latest stable version of ``giotto-tda`` requires:
 
 - Python (>= 3.6)
 - NumPy (>= 1.19.1)
 - SciPy (>= 1.5.0)
 - joblib (>= 0.16.0)
 - scikit-learn (>= 0.23.1)
-- pyflagser (>= 0.4.0)
+- pyflagser (>= 0.4.1)
 - python-igraph (>= 0.8.2)
 - plotly (>= 4.8.2)
 - ipywidgets (>= 7.5.1)
 
-To run the examples, jupyter is required.
+To run the examples, ``jupyter`` is required.
 
 
 *****************
 User installation
 *****************
 
-The simplest way to install giotto-tda is using ``pip``   ::
+The simplest way to install ``giotto-tda`` is using ``pip``   ::
 
     python -m pip install -U giotto-tda
 
@@ -39,10 +39,10 @@ bug fixes can be installed by running   ::
 
     python -m pip install -U giotto-tda-nightly
 
-The main difference between giotto-tda-nightly and the developer installation (see the section
+The main difference between ``giotto-tda-nightly`` and the developer installation (see the section
 on contributing, below) is that the former is shipped with pre-compiled wheels (similarly to the stable
 release) and hence does not require any C++ dependencies. As the main library module is called ``gtda`` in
-both the stable and nightly versions, giotto-tda and giotto-tda-nightly should not be installed in
+both the stable and nightly versions, ``giotto-tda`` and ``giotto-tda-nightly`` should not be installed in
 the same environment.
 
 **********************
@@ -51,7 +51,7 @@ Developer installation
 
 .. _dev_installation:
 
-Installing both the PyPI release and source of giotto-tda in the same environment is not recommended since it is
+Installing both the PyPI release and source of ``giotto-tda`` in the same environment is not recommended since it is
 known to cause conflicts with the C++ bindings.
 
 The developer installation requires three important C++ dependencies:
@@ -97,44 +97,43 @@ is as follows:
 Boost
 -----
 
-Some users are experiencing some issue when installation `boost` on Windows. To help them resolve this issue, we customized a little bit the detection of `boost` library.
-To install boost on windows, we (maintainers of giotto-tda) recommend 3 options:
+Some users have been experiencing issues when installing Boost on Windows. To help them resolve them, we customized a little bit the detection of Boost.
+To install Boost on Windows, we recommend 3 options:
 
 - Pre-built binaries,
 - Directly from source,
-- Use an already installed boost version that fulfills `giotto-tda` requirements.
+- Use an already installed Boost version that fulfills ``giotto-tda`` requirements.
 
 Pre-built binaries
 ------------------
 
-Boost propose for windows pre-built binaries to ease the installation of boost
-in your system. In the
-`website <https://sourceforge.net/projects/boost/files/boost-binaries/>`_, you'll have access to all versions of boost. At the time of writing
-this documentation, the most recent version of boost is `1.72.0`. If you go
-into the folder, you'll find different executables - choose the version
-corresponding to your system (32, 64 bits). In our case, we downloaded `boost_1_72_0-msvc-14.2-64.exe`.
-Follow the installation instructions, and when prompted to specify the folder to install boost, go for `C:\\local\\`.
+For Windows, Boost propose pre-built binaries to ease the installation in your system. In the
+`website <https://sourceforge.net/projects/boost/files/boost-binaries/>`_, you'll have access to all versions of Boost.
+At the time of writing this documentation, the most recent version of Boost is `1.72.0`. If you go into the folder,
+you'll find different executables - choose the version corresponding to your system (32, 64 bits). In our case, we
+downloaded `boost_1_72_0-msvc-14.2-64.exe`. Follow the installation instructions, and when prompted to specify the
+folder to install Boost, go for `C:\\local\\`.
 
 Source code
 -----------
 
-Boost proposes to `download <https://www.boost.org/users/download/>`_ directly the source code of boost.
+Boost proposes to `download <https://www.boost.org/users/download/>`_ directly the Boost source code.
 You can choose from different sources (compressed in `.7z` or `.zip`).
 Download one and uncompress it in `C:\\local\\`, so you should have something like `C:\\local\\boost_x_y_z\\<boost_files>`.
 
-Already installed boost version
+Already installed Boost version
 -------------------------------
 
-If by some obscure reason, you have boost installed in your system but the installation procedure cannot find it (can happen, no control on cmake ...).
-You can help the installation script by adding the path to your installation in the following place `gtda\\cmake\\HelperBoost.cmake`.
+If, for some obscure reason, you have Boost installed in your system but the installation procedure cannot find it (can happen, no control on cmake ...).
+You can help the installation script by adding the path to your installation in the following place: `gtda\\cmake\\HelperBoost.cmake`.
 In `HelperBoost.cmake` file, line 7, you can add your path between the quotation marks, e.g.::
 
    list(APPEND BOOST_ROOT "C:\\<path_to_your_boost_installation>").
 
 Troubleshooting
 ---------------
 
-If you need to understand where the compiler tries to look for ``boost`` headers,
+If you need to understand where the compiler tries to look for Boost headers,
 you can install ``giotto-tda`` with::
 
    python -m pip install -e . -v
@@ -144,7 +143,7 @@ Then you can look at the output for lines starting with::
    Boost_INCLUDE_DIR: <path>
    Boost_INCLUDE_DIRS: <path>
 
-Also, if you have installed different versions of ``boost`` in the process of trying to instal ``giotto-tda``,
+Also, if you have installed different versions of Boost in the process of trying to install ``giotto-tda``,
 make sure to clear CMake cache entries::
 
     rm -rf build/