refactoring for additional speed improvements

[plusk01]

these changes are API breaking

further speed improvements over (#3) are found by improving the use of sparsity (i.e., only populating the upper triangle) and by limiting the amount of data that is copied.

note: this PR leaves matlab bindings broken for now

Sparse and avoiding mat-vec multiplies (#3)

Benchmarking over 20 trials


Benchmarking ρ = 90% [██████████████████████████████████████████████████] 100% [00m:56s]               

+-------+---------+----------------+-------------------+---------------+------------+
| ρ [%] | # assoc |  affinity [ms] | dense clique [ms] | precision [%] | recall [%] |
+-------+---------+----------------+-------------------+---------------+------------+
| 0     | 64      |   0.52  ±  0.9 |      0.07  ±  0.0 | 100           | 89         |
| 0     | 256     |   1.41  ±  0.4 |      0.92  ±  0.2 | 100           | 89         |
| 0     | 512     |   5.30  ±  0.3 |      3.62  ±  0.8 | 100           | 89         |
| 0     | 1024    |  42.30  ±  1.7 |      9.63  ±  1.5 | 100           | 89         |
| 0     | 2048    | 174.11  ±  9.8 |     47.51  ±  9.4 | 100           | 89         |
+-------+---------+----------------+-------------------+---------------+------------+
| 20    | 64      |   0.25  ±  0.0 |      0.24  ±  0.0 | 100           | 89         |
| 20    | 256     |   1.18  ±  0.1 |      3.89  ±  0.8 | 100           | 89         |
| 20    | 512     |   5.10  ±  0.3 |     15.27  ±  2.5 | 99            | 89         |
| 20    | 1024    |  23.18  ±  2.5 |     54.81  ± 11.1 | 99            | 89         |
| 20    | 2048    | 133.73  ± 12.5 |    345.16  ± 77.3 | 99            | 89         |
+-------+---------+----------------+-------------------+---------------+------------+
| 40    | 64      |   5.34  ±  5.6 |      0.25  ±  0.0 | 100           | 89         |
| 40    | 256     |   1.04  ±  0.1 |      3.36  ±  0.7 | 99            | 89         |
| 40    | 512     |   4.22  ±  0.4 |     12.42  ±  1.5 | 100           | 89         |
| 40    | 1024    |  21.38  ±  3.6 |     48.93  ± 11.1 | 99            | 89         |
| 40    | 2048    |  92.75  ±  4.5 |    264.75  ± 55.5 | 99            | 89         |
+-------+---------+----------------+-------------------+---------------+------------+
| 80    | 64      |   0.37  ±  0.6 |      0.16  ±  0.0 | 99            | 91         |
| 80    | 256     |   0.86  ±  0.1 |      1.71  ±  0.2 | 100           | 90         |
| 80    | 512     |   3.46  ±  0.3 |      7.44  ±  1.7 | 99            | 89         |
| 80    | 1024    |  15.76  ±  0.4 |     23.73  ±  3.6 | 99            | 89         |
| 80    | 2048    |  63.44  ±  4.6 |    113.56  ± 28.4 | 99            | 89         |
+-------+---------+----------------+-------------------+---------------+------------+
| 90    | 64      |   0.23  ±  0.0 |      0.17  ±  0.0 | 99            | 91         |
| 90    | 256     |   0.86  ±  0.1 |      1.64  ±  0.2 | 99            | 90         |
| 90    | 512     |   3.22  ±  0.4 |      6.25  ±  1.0 | 99            | 90         |
| 90    | 1024    |  15.01  ±  0.5 |     21.29  ±  2.9 | 99            | 90         |
| 90    | 2048    |  61.48  ±  3.3 |     93.10  ± 13.6 | 99            | 90         |
+-------+---------+----------------+-------------------+---------------+------------+

this version

Benchmarking over 20 trials


Benchmarking ρ = 90% [██████████████████████████████████████████████████] 100% [00m:46s]               

+-------+---------+---------------+-------------------+---------------+------------+
| ρ [%] | # assoc | affinity [ms] | dense clique [ms] | precision [%] | recall [%] |
+-------+---------+---------------+-------------------+---------------+------------+
| 0     | 64      |  0.29  ±  0.3 |      0.07  ±  0.0 | 100           | 89         |
| 0     | 256     |  0.88  ±  0.1 |      0.79  ±  0.2 | 100           | 89         |
| 0     | 512     |  3.42  ±  0.3 |      3.18  ±  1.1 | 100           | 89         |
| 0     | 1024    | 16.52  ±  1.2 |     11.79  ±  4.5 | 100           | 89         |
| 0     | 2048    | 73.97  ±  2.5 |     44.81  ± 20.4 | 100           | 89         |
+-------+---------+---------------+-------------------+---------------+------------+
| 20    | 64      |  0.81  ±  2.6 |      0.21  ±  0.0 | 100           | 89         |
| 20    | 256     |  0.88  ±  0.1 |      3.15  ±  0.7 | 100           | 89         |
| 20    | 512     |  3.63  ±  0.4 |     13.58  ±  2.3 | 100           | 89         |
| 20    | 1024    | 16.22  ±  0.3 |     40.62  ± 10.0 | 99            | 89         |
| 20    | 2048    | 69.55  ±  4.3 |    235.73  ± 50.8 | 99            | 89         |
+-------+---------+---------------+-------------------+---------------+------------+
| 40    | 64      |  0.22  ±  0.0 |      0.20  ±  0.0 | 100           | 89         |
| 40    | 256     |  0.86  ±  0.1 |      2.49  ±  0.3 | 99            | 89         |
| 40    | 512     |  3.49  ±  0.4 |     11.55  ±  2.3 | 100           | 89         |
| 40    | 1024    | 15.40  ±  0.4 |     39.22  ±  8.8 | 100           | 89         |
| 40    | 2048    | 57.30  ±  2.6 |    187.87  ± 50.2 | 99            | 89         |
+-------+---------+---------------+-------------------+---------------+------------+
| 80    | 64      |  0.22  ±  0.0 |      0.14  ±  0.0 | 100           | 91         |
| 80    | 256     |  0.83  ±  0.1 |      1.50  ±  0.2 | 99            | 90         |
| 80    | 512     |  3.10  ±  0.3 |      5.81  ±  1.0 | 99            | 89         |
| 80    | 1024    | 15.39  ±  3.1 |     23.94  ±  6.1 | 99            | 89         |
| 80    | 2048    | 53.72  ±  1.4 |     86.29  ± 20.8 | 99            | 89         |
+-------+---------+---------------+-------------------+---------------+------------+
| 90    | 64      |  0.22  ±  0.0 |      0.16  ±  0.0 | 100           | 92         |
| 90    | 256     |  0.98  ±  0.8 |      1.48  ±  0.2 | 99            | 89         |
| 90    | 512     |  3.43  ±  1.1 |      5.57  ±  1.0 | 99            | 91         |
| 90    | 1024    | 14.61  ±  1.2 |     21.31  ±  2.4 | 99            | 90         |
| 90    | 2048    | 53.18  ±  1.8 |     83.43  ± 15.7 | 99            | 90         |
+-------+---------+---------------+-------------------+---------------+------------+