Add airspeed velocity benchmarks

[nawtrey]

Changes

• Add asv configuration file

• Add two benchmark files: bench_diagrams.py for benchmarking functions in diagrams.py and
  bench_calculations.py for benchmarking
  functions in calculations.py

• Add requirements_dev.txt for easy installation of required packages for
  asv benchmarking and testing with
  pytest. Will eventually be used in CI.

• Related to CI: Add Airspeed Velocity benchmarking to CI #108

Description

As discussed in #108, we are adding some benchmarks for easy performance comparison between commits.

To run the benchmarks locally, simply run asv run from the kda/benchmarks directory. Running on this commit gave me the following results:

Output for local run

$ asv run
Couldn't load asv.plugins._mamba_helpers because
No module named 'conda'
▒ Creating environments
▒ Discovering benchmarks
▒▒ Uninstalling from conda-py3.9-pip+networkx-pip+numpy-pip+pytest-pip+sympy
▒▒ Building 254155f8 <issue_108_add_asv> for conda-py3.9-pip+networkx-pip+numpy-pip+pytest-pip+sympy
▒▒ Installing 254155f8 <issue_108_add_asv> into conda-py3.9-pip+networkx-pip+numpy-pip+pytest-pip+sympy
▒ Running 10 total benchmarks (1 commits * 1 environments * 10 benchmarks)
[ 0.00%] ▒ For kda commit 254155f8 <issue_108_add_asv>:
[ 0.00%] ▒▒ Benchmarking conda-py3.9-pip+networkx-pip+numpy-pip+pytest-pip+sympy
[10.00%] ▒▒▒ Running (bench_calculations.Sigma.time_calc_sigma--)..
[30.00%] ▒▒▒ Running (bench_diagrams.DirectionalDiagrams.time_generate_directional_diagrams--)...
[55.00%] ▒▒▒ bench_calculations.Sigma.peakmem_calc_sigma                    ok
[55.00%] ▒▒▒ ============== ======= =======
             --              output_strings
             -------------- ---------------
                 graph        True   False
             ============== ======= =======
                3-state      70.4M   70.3M
              Hill-5-state   70.4M    70M
              Hill-8-state   70.7M   70.9M
              EmrE-8-state   73.3M   73.4M
             ============== ======= =======

[60.00%] ▒▒▒ bench_calculations.Sigma.time_calc_sigma                       ok
[60.00%] ▒▒▒ ============== ============ ============
             --                   output_strings
             -------------- -------------------------
                 graph          True        False
             ============== ============ ============
                3-state      73.6~20us     58.7~8us
              Hill-5-state   531~200us    552~100us
              Hill-8-state   6.68▒0.7ms   6.41▒0.3ms
              EmrE-8-state    40.8▒1ms    50.7▒10ms
             ============== ============ ============

[65.00%] ▒▒▒ ...ulations.StateProbs.peakmem_calc_state_probs                ok
[65.00%] ▒▒▒ ============== ======= =======
             --              output_strings
             -------------- ---------------
                 graph        True   False
             ============== ======= =======
                3-state      72.3M   70.5M
              Hill-5-state   72.4M   70.6M
              Hill-8-state    75M     71M
              EmrE-8-state    81M    73.3M
             ============== ======= =======

[70.00%] ▒▒▒ ...alculations.StateProbs.time_calc_state_probs                ok
[70.00%] ▒▒▒ ============== ============ ============
             --                   output_strings
             -------------- -------------------------
                 graph          True        False
             ============== ============ ============
                3-state      3.60▒0.9ms   1.43▒0.2ms
              Hill-5-state    14.9▒1ms    6.87▒0.4ms
              Hill-8-state    653▒40ms     63.3▒9ms
              EmrE-8-state   11.0▒0.1s     418▒20ms
             ============== ============ ============

[75.00%] ▒▒▒ ...agrams.peakmem_generate_directional_diagrams                ok
[75.00%] ▒▒▒ ============== ======= =======
             --               return_edges
             -------------- ---------------
                 graph        True   False
             ============== ======= =======
                3-state      70.2M   70.3M
              Hill-5-state   70.4M   70.8M
              Hill-8-state   70.8M   76.2M
              EmrE-8-state   73.4M    109M
             ============== ======= =======

[80.00%] ▒▒▒ ...lDiagrams.time_generate_directional_diagrams                ok
[80.00%] ▒▒▒ ============== ============= =============
             --                     return_edges
             -------------- ---------------------------
                 graph           True         False
             ============== ============= =============
                3-state      1.17▒0.01ms   1.52▒0.01ms
              Hill-5-state    6.29▒0.1ms   9.05▒0.05ms
              Hill-8-state    53.6▒0.5ms     89.2▒3ms
              EmrE-8-state     388▒30ms      684▒50ms
             ============== ============= =============

[85.00%] ▒▒▒ ....FluxDiagrams.peakmem_generate_flux_diagrams                ok
[85.00%] ▒▒▒ ============== =======
                 graph
             -------------- -------
                3-state      70.6M
              Hill-5-state   70.8M
              Hill-8-state   71.3M
              EmrE-8-state   76.5M
             ============== =======

[90.00%] ▒▒▒ ...ams.FluxDiagrams.time_generate_flux_diagrams                ok
[90.00%] ▒▒▒ ============== ============
                 graph
             -------------- ------------
                3-state       859~20us
              Hill-5-state   2.64▒0.6ms
              Hill-8-state    24.7▒4ms
              EmrE-8-state    157▒1ms
             ============== ============

[95.00%] ▒▒▒ ...alDiagrams.peakmem_generate_partial_diagrams                ok
[95.00%] ▒▒▒ ============== ======= =======
             --               return_edges
             -------------- ---------------
                 graph        True   False
             ============== ======= =======
                3-state      70.2M   70.3M
              Hill-5-state   70.2M   70.4M
              Hill-8-state   70.5M   70.8M
              EmrE-8-state   70.3M    73M
             ============== ======= =======

[100.00%] ▒▒▒ ...rtialDiagrams.time_generate_partial_diagrams                ok
[100.00%] ▒▒▒ ============== ============ =============
              --                    return_edges
              -------------- --------------------------
                  graph          True         False
              ============== ============ =============
                 3-state       246~8us       234~7us
               Hill-5-state    494~7us       469~2us
               Hill-8-state   3.00▒0.2ms   2.77▒0.06ms
               EmrE-8-state   17.7▒0.1ms     17.9▒2ms
              ============== ============ =============

The 10 benchmarks are parameterized over different graphs starting from the simple 3-state model to the 8-state EmrE model to give a reasonable range for comparison.

[nawtrey]

Alright, I think this is a healthy starting point for benchmarking KDA functions and all benchmarks are working as intended locally. Merging.