Update all Rust dependencies

[jdaymude]

I realize it's typically not best practice to update all dependencies in one go, but it's been a while since we checked in on them and there's a handful of feature and security updates we'd benefit from. I have read each explicit dependency's changelog (if one exists), ensured there are no breaking changes, fixed all deprecations, and ran benchmarks which show this PR is performance-netural.

Benchmark 7bd28f7 (this PR) vs. 4989aac (current main) as a baseline

bench_matches/gdb13_1201/nauty
                        time:   [55.423 ms 55.512 ms 55.590 ms]
                        change: [+0.3919% +0.5813% +0.7099%] (p = 0.00 < 0.05)
                        Change within noise threshold.
bench_matches/gdb13_1201/tree-nauty
                        time:   [34.646 ms 34.728 ms 34.785 ms]
                        change: [−2.9632% −2.5590% −2.1703%] (p = 0.00 < 0.05)
                        Performance has improved.
bench_matches/gdb17_200/nauty
                        time:   [202.57 ms 202.67 ms 202.77 ms]
                        change: [+1.1714% +1.2584% +1.3487%] (p = 0.00 < 0.05)
                        Performance has regressed.
bench_matches/gdb17_200/tree-nauty
                        time:   [106.83 ms 106.89 ms 106.94 ms]
                        change: [+0.5232% +0.6041% +0.6890%] (p = 0.00 < 0.05)
                        Change within noise threshold.
bench_matches/checks/nauty
                        time:   [30.111 ms 30.118 ms 30.125 ms]
                        change: [+1.1477% +1.1907% +1.2317%] (p = 0.00 < 0.05)
                        Performance has regressed.
bench_matches/checks/tree-nauty
                        time:   [14.170 ms 14.182 ms 14.192 ms]
                        change: [−1.0248% −0.9564% −0.8845%] (p = 0.00 < 0.05)
                        Change within noise threshold.
bench_matches/coconut_55/nauty
                        time:   [179.22 ms 179.29 ms 179.36 ms]
                        change: [+2.0739% +2.1573% +2.2341%] (p = 0.00 < 0.05)
                        Performance has regressed.
bench_matches/coconut_55/tree-nauty
                        time:   [84.189 ms 84.262 ms 84.331 ms]
                        change: [+0.1978% +0.5263% +0.8783%] (p = 0.00 < 0.05)
                        Change within noise threshold.

bench_bounds/gdb13_1201/no-bounds
                        time:   [60.084 ms 60.527 ms 60.958 ms]
                        change: [−2.3365% −1.3951% −0.4891%] (p = 0.00 < 0.05)
                        Change within noise threshold.
bench_bounds/gdb13_1201/log
                        time:   [59.610 ms 60.196 ms 60.805 ms]
                        change: [−1.6710% −0.5399% +0.6784%] (p = 0.39 > 0.05)
                        No change in performance detected.
bench_bounds/gdb13_1201/int
                        time:   [55.817 ms 56.368 ms 56.946 ms]
                        change: [−3.6602% −2.5518% −1.4043%] (p = 0.00 < 0.05)
                        Performance has improved.
bench_bounds/gdb13_1201/int-vec
                        time:   [53.949 ms 54.375 ms 54.820 ms]
                        change: [−0.2752% +0.7693% +1.8962%] (p = 0.19 > 0.05)
                        No change in performance detected.
bench_bounds/gdb13_1201/int-matchable
                        time:   [54.874 ms 55.304 ms 55.740 ms]
                        change: [−5.0440% −3.9436% −2.7048%] (p = 0.00 < 0.05)
                        Performance has improved.
bench_bounds/gdb17_200/no-bounds
                        time:   [205.90 ms 207.65 ms 209.35 ms]
                        change: [−0.3314% +0.8868% +2.1670%] (p = 0.17 > 0.05)
                        No change in performance detected.
bench_bounds/gdb17_200/log
                        time:   [146.73 ms 147.43 ms 148.18 ms]
                        change: [−0.3318% +0.3433% +1.0174%] (p = 0.35 > 0.05)
                        No change in performance detected.
bench_bounds/gdb17_200/int
                        time:   [49.398 ms 49.629 ms 49.851 ms]
                        change: [+0.3888% +0.9719% +1.6147%] (p = 0.01 < 0.05)
                        Change within noise threshold.
bench_bounds/gdb17_200/int-vec
                        time:   [47.887 ms 48.157 ms 48.417 ms]
                        change: [−0.6920% +0.0465% +0.7971%] (p = 0.91 > 0.05)
                        No change in performance detected.
bench_bounds/gdb17_200/int-matchable
                        time:   [38.255 ms 38.487 ms 38.732 ms]
                        change: [+0.1704% +1.0434% +1.9292%] (p = 0.03 < 0.05)
                        Change within noise threshold.
bench_bounds/checks/no-bounds
                        time:   [157.97 ms 161.12 ms 164.29 ms]
                        change: [−2.6697% +0.1277% +3.1474%] (p = 0.93 > 0.05)
                        No change in performance detected.
bench_bounds/checks/log time:   [94.205 ms 95.374 ms 96.514 ms]
                        change: [−2.4183% −0.8807% +0.6374%] (p = 0.30 > 0.05)
                        No change in performance detected.
bench_bounds/checks/int time:   [10.813 ms 10.867 ms 10.927 ms]
                        change: [−1.1307% −0.1760% +0.6794%] (p = 0.72 > 0.05)
                        No change in performance detected.
bench_bounds/checks/int-vec
                        time:   [7.6954 ms 7.7284 ms 7.7615 ms]
                        change: [−1.4169% −0.2715% +0.8692%] (p = 0.65 > 0.05)
                        No change in performance detected.
bench_bounds/checks/int-matchable
                        time:   [6.1734 ms 6.2036 ms 6.2417 ms]
                        change: [+0.4163% +1.1515% +1.8559%] (p = 0.00 < 0.05)
                        Change within noise threshold.
bench_bounds/coconut_55/no-bounds
                        time:   [1.8255 s 1.8730 s 1.9170 s]
                        change: [−2.7240% +0.6994% +4.4198%] (p = 0.71 > 0.05)
                        No change in performance detected.
bench_bounds/coconut_55/log
                        time:   [1.3284 s 1.3528 s 1.3788 s]
                        change: [+0.0588% +2.7786% +5.8788%] (p = 0.07 > 0.05)
                        No change in performance detected.
bench_bounds/coconut_55/int
                        time:   [127.40 ms 128.67 ms 129.91 ms]
                        change: [−2.4316% −0.9979% +0.5333%] (p = 0.20 > 0.05)
                        No change in performance detected.
bench_bounds/coconut_55/int-vec
                        time:   [112.51 ms 113.80 ms 115.04 ms]
                        change: [−2.6136% −1.1578% +0.3345%] (p = 0.14 > 0.05)
                        No change in performance detected.
bench_bounds/coconut_55/int-matchable
                        time:   [42.930 ms 43.121 ms 43.330 ms]
                        change: [−0.6034% −0.0089% +0.6358%] (p = 0.98 > 0.05)
                        No change in performance detected.

bench_memoize/gdb13_1201/no-memoize
                        time:   [43.860 ms 44.177 ms 44.476 ms]
                        change: [−0.5233% +0.2064% +1.0248%] (p = 0.64 > 0.05)
                        No change in performance detected.
bench_memoize/gdb13_1201/nauty-index
                        time:   [60.122 ms 60.671 ms 61.183 ms]
                        change: [−1.0227% +0.3269% +1.6008%] (p = 0.63 > 0.05)
                        No change in performance detected.
bench_memoize/gdb13_1201/tree-nauty-index
                        time:   [57.703 ms 58.101 ms 58.499 ms]
                        change: [−0.2185% +0.8118% +1.8349%] (p = 0.14 > 0.05)
                        No change in performance detected.
bench_memoize/gdb17_200/no-memoize
                        time:   [23.917 ms 23.989 ms 24.107 ms]
                        change: [−2.7861% +1.0154% +5.3886%] (p = 0.64 > 0.05)
                        No change in performance detected.
bench_memoize/gdb17_200/nauty-index
                        time:   [40.837 ms 41.016 ms 41.184 ms]
                        change: [−0.5814% +0.1324% +0.8347%] (p = 0.72 > 0.05)
                        No change in performance detected.
bench_memoize/gdb17_200/tree-nauty-index
                        time:   [38.274 ms 38.502 ms 38.745 ms]
                        change: [+0.0500% +0.8521% +1.7436%] (p = 0.07 > 0.05)
                        No change in performance detected.
bench_memoize/checks/no-memoize
                        time:   [4.1886 ms 4.2295 ms 4.2677 ms]
                        change: [−0.0703% +0.9190% +1.9527%] (p = 0.07 > 0.05)
                        No change in performance detected.
bench_memoize/checks/nauty-index
                        time:   [7.0216 ms 7.0503 ms 7.0803 ms]
                        change: [−0.3499% +0.2591% +0.9501%] (p = 0.45 > 0.05)
                        No change in performance detected.
bench_memoize/checks/tree-nauty-index
                        time:   [6.1511 ms 6.2006 ms 6.2615 ms]
                        change: [−0.0050% +1.3439% +2.7620%] (p = 0.08 > 0.05)
                        No change in performance detected.
bench_memoize/coconut_55/no-memoize
                        time:   [33.539 ms 33.655 ms 33.790 ms]
                        change: [−2.8986% −1.2576% +0.2728%] (p = 0.15 > 0.05)
                        No change in performance detected.
bench_memoize/coconut_55/nauty-index
                        time:   [47.548 ms 47.841 ms 48.184 ms]
                        change: [−0.1447% +0.6206% +1.4971%] (p = 0.14 > 0.05)
                        No change in performance detected.
bench_memoize/coconut_55/tree-nauty-index
                        time:   [42.801 ms 42.946 ms 43.114 ms]
                        change: [−0.6143% −0.1038% +0.4358%] (p = 0.70 > 0.05)
                        No change in performance detected.

Fixes:

• https://github.com/DaymudeLab/assembly-theory/security/dependabot/1
• https://github.com/DaymudeLab/assembly-theory/security/dependabot/24
• https://github.com/DaymudeLab/assembly-theory/security/dependabot/25

[AgentElement]

Thanks!