Outdated Documentation

[erooke]

As written the current documentation does not line up with the api of this library. Namely there is a bunch of references to the map function being called with nr_cubes and perc_overlap instead of being supplied a cover object. Examples of this:

• The python code on the getting started page
• docs/notebooks/Cancer-demo.ipynb
• docs/notebooks/Confidence-Graphs.ipynb
• docs/notebooks/KeplerMapper-usage-in-Jupyter-Notebook.ipynb
• docs/notebooks/TOR-XGB-TDA.ipynb
• examples/breast-cancer/breast-cancer.ipynb
• examples/cat/cat.ipynb

In addition to the documentation some benchmark code found under tests also has this problem.

There might be more, but I was unable to find them. PR #229 addresses this.

[deargle]

Thanks for this! Will review, but might be a bit before I do.

On Thu, Jun 24, 2021, 7:36 PM Ethan Rooke @.***> wrote:

As written the current documentation does not line up with the api of this library. Namely there is a bunch of references to the map function being called with nr_cubes and perc_overlap instead of being supplied a cover object. Examples of this:

• The python code on the getting started page https://kepler-mapper.scikit-tda.org/en/latest/started.html
• docs/notebooks/Cancer-demo.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/docs/notebooks/Cancer-demo.ipynb
• docs/notebooks/Confidence-Graphs.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/docs/notebooks/Confidence-Graphs.ipynb
• docs/notebooks/KeplerMapper-usage-in-Jupyter-Notebook.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/docs/notebooks/KeplerMapper-usage-in-Jupyter-Notebook.ipynb
• docs/notebooks/TOR-XGB-TDA.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/docs/notebooks/TOR-XGB-TDA.ipynb
• examples/breast-cancer/breast-cancer.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/examples/breast-cancer/breast-cancer.ipynb
• examples/cat/cat.ipynb https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/examples/cat/cat.ipynb

In addition to the documentation some benchmark code found under tests https://github.com/scikit-tda/kepler-mapper/blob/7dc4d0ad3a9020fe51ec7a52995b9593b9090bab/test/benchmarks.py#L40 also has this problem.

There might be more, but I was unable to find them. PR #229 https://github.com/scikit-tda/kepler-mapper/pull/229 addresses this.

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