Fix divide-by-zero, deprecation, and futurewarnings

[erooke]

Currently the test suite generates a handful of warnings. These include:

• Deprecation warnings for np.float and np.int
• Future warnings about AffinityPropogation api changes
• Division by 0 warnings
• Invalid division (0 / 0) warnings This pull request aims to fix these warnings. It changes all occurences of np.int and np.float to int and float respectively, adds randomstate=0 to AffinityPropogation to keep previous behavior, and silences division by 0 errors as the behavior x / 0 = inf seems to be the expect behavior where they arose. It does not fix the invalid division error as I don't understand the function which raises that warning well enough to tell if NaN is expected behavior or if the data has to be cleansed somehow.

[codecov[bot]]

Codecov Report

Merging #236 (d056782) into master (eb4ba35) will increase coverage by 0.04%. The diff coverage is 50.00%.

@@            Coverage Diff             @@
##           master     #236      +/-   ##
==========================================
+ Coverage   80.27%   80.32%   +0.04%     
==========================================
  Files          11       11              
  Lines         862      864       +2     
  Branches      189      189              
==========================================
+ Hits          692      694       +2     
  Misses        138      138              
  Partials       32       32              

Impacted Files	Coverage Δ
kmapper/plotlyviz.py	48.17% <48.17%> (ø)
kmapper/cover.py	88.54% <100.00%> (+0.12%)	:arrow_up:
kmapper/visuals.py	85.58% <100.00%> (+0.06%)	:arrow_up:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update eb4ba35...d056782. Read the comment docs.

[deargle]

Thanks for this. Docs are currently acting funny right now -- plotlyviz stuff not displaying, I suspect due to sphinx v4 vs v3 -- after that is fixed, I'll look to this.

On Wed, Oct 6, 2021, 7:35 PM codecov[bot] @.***> wrote:

Codecov https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda Report

Merging #236 https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda (d056782 https://github.com/scikit-tda/kepler-mapper/commit/d05678218248364cdc8b00d7bc93af372cfc3416) into master https://codecov.io/gh/scikit-tda/kepler-mapper/commit/eb4ba352e3310bd54fdbf21ff7a303cccd97484e?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda (eb4ba35 https://github.com/scikit-tda/kepler-mapper/commit/eb4ba352e3310bd54fdbf21ff7a303cccd97484e) will increase coverage by 0.04%. The diff coverage is 50.00%.

[image: Impacted file tree graph] https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda

@@ Coverage Diff @@

master #236 +/-

==========================================

• Coverage 80.27% 80.32% +0.04%

==========================================

Files 11 11

Lines 862 864 +2

Branches 189 189

==========================================

• Hits 692 694 +2

  Misses 138 138

  Partials 32 32

Impacted Files https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda Coverage Δ kmapper/plotlyviz.py https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda#diff-a21hcHBlci9wbG90bHl2aXoucHk= 48.17% <48.17%> (ø) kmapper/cover.py https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda#diff-a21hcHBlci9jb3Zlci5weQ== 88.54% <100.00%> (+0.12%) ⬆️ kmapper/visuals.py https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda#diff-a21hcHBlci92aXN1YWxzLnB5 85.58% <100.00%> (+0.06%) ⬆️

Continue to review full report at Codecov https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda .

Legend - Click here to learn more https://docs.codecov.io/docs/codecov-delta?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda Δ = absolute (impact), ø = not affected, ? = missing data Powered by Codecov https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=footer&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda. Last update eb4ba35...d056782 https://codecov.io/gh/scikit-tda/kepler-mapper/pull/236?src=pr&el=lastupdated&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda. Read the comment docs https://docs.codecov.io/docs/pull-request-comments?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scikit-tda .

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[deargle]

Cool, thanks. I wonder why plotlyviz had not-unix line endings...

Can you make any future PRs off of not-master branches? It's okay for this one.

[erooke]

Can you make any future PRs off of not-master branches? It's okay for this one.

Sure, is there a particular branch you would like me to use?

[deargle]

Oh, you know what, I totally misread it. I thought this was coming from your fork's master branch. Long day, sorry. PRs against this repo's master is preferred, as you've been doing.