docs: Small improvements to book by swo · Pull Request #719 · CDCgov/ixa

swo · 2026-02-04T20:33:20Z

Some small changes that make it easier for a new user to run the disease_model example:

Change which dependencies to add, to match https://github.com/CDCgov/ixa/blob/main/docs/book/models/disease_model/Cargo.toml
Use the main branch setup script (so that you get the main branch version of ixa, not release version 0.0.1!)
A typo that broke a suggested command
Some weird whitespace

github-actions · 2026-02-04T20:51:41Z

Benchmark Results

Hyperfine

  Group                  Bench                      Mean [ms]  Min [ms]  Max [ms]       Relative
  ---------------------  ---------------------  -------------  --------  --------  -------------
  large_sir              baseline                   2.9 ± 0.1       2.8       3.2           1.00
  large_sir              ixa                     130.2 ± 17.1     124.7     246.9   45.08 ± 6.02
  large_sir              ixa_no_queries            34.7 ± 0.9      33.2      36.4   12.02 ± 0.40
  periodic_counts_bench  no_periodic_reports        7.2 ± 0.1       7.1       7.5           1.00
  periodic_counts_bench  with_periodic_reports     12.6 ± 0.2      12.4      14.0    1.74 ± 0.04

Criterion

Regressions:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  indexing       query_people_indexed_multi-property                           3.643%    3.319%    3.895%
  indexing       query_people_count_multiple_individually_indexed_properties   1.131%    0.497%    1.537%
  sample_people  sampling_multiple_l_reservoir                                 0.215%    0.141%    0.305%
  large_dataset  bench_query_population_multi_unindexed                        7.202%    6.880%    7.498%
  large_dataset  bench_query_population_multi_indexed                          7.035%    6.612%    7.387%
  large_dataset  bench_query_population_indexed_property                       0.359%    0.131%    0.590%

Improvements:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  indexing       with_query_results_indexed_multi-property                    -3.285%   -3.413%   -3.154%
  indexing       with_query_results_single_indexed_property                   -3.510%   -4.334%   -2.647%
  indexing       query_people_single_indexed_property                         -4.988%   -6.228%   -3.719%
  sample_people  sampling_single_l_reservoir                                  -0.206%   -0.349%   -0.084%
  sample_people  sampling_single_known_length                                 -0.294%   -0.512%   -0.094%
  large_dataset  bench_query_population_derived_property                      -1.267%   -1.381%   -1.139%

Unchanged:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  examples       example-basic-infection                                      -0.008%   -0.591%    0.582%
  examples       example-births-deaths                                        -0.359%   -0.782%    0.135%
  indexing       query_people_count_single_indexed_property                    0.132%   -0.013%    0.352%
  indexing       query_people_count_indexed_multi-property                    -0.262%   -0.483%    0.047%
  indexing       query_people_multiple_individually_indexed_properties        -0.174%   -0.551%    0.086%
  indexing       with_query_results_multiple_individually_indexed_properties  -0.104%   -0.952%    0.687%
  sample_people  sampling_multiple_known_length                                0.068%   -0.022%    0.158%
  large_dataset  bench_query_population_property                               0.345%   -0.000%    0.617%

github-actions · 2026-02-04T20:59:41Z

Benchmark Results

Hyperfine

  Group                  Bench                     Mean [ms]  Min [ms]  Max [ms]       Relative
  ---------------------  ---------------------  ------------  --------  --------  -------------
  periodic_counts_bench  no_periodic_reports       7.4 ± 0.4       7.2       9.7           1.00
  periodic_counts_bench  with_periodic_reports    12.8 ± 1.2      12.4      20.8    1.73 ± 0.19
  large_sir              baseline                  2.9 ± 0.0       2.8       3.0           1.00
  large_sir              ixa                     127.8 ± 1.6     125.1     132.8   44.83 ± 0.91
  large_sir              ixa_no_queries           35.5 ± 1.4      34.0      40.2   12.44 ± 0.52

Criterion

Regressions:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  examples       example-basic-infection                                       1.967%    1.530%    2.355%
  indexing       with_query_results_indexed_multi-property                     0.262%    0.035%    0.508%
  indexing       query_people_count_single_indexed_property                   14.768%   14.668%   14.844%
  indexing       query_people_single_indexed_property                          8.008%    6.617%    9.435%
  indexing       query_people_count_multiple_individually_indexed_properties   3.293%    2.949%    3.733%
  sample_people  sampling_multiple_known_length                                0.489%    0.306%    0.645%
  sample_people  sampling_single_l_reservoir                                   0.406%    0.331%    0.496%
  large_dataset  bench_query_population_property                               1.633%    1.380%    1.849%
  large_dataset  bench_query_population_multi_unindexed                        0.913%    0.608%    1.430%
  large_dataset  bench_query_population_indexed_property                       0.832%    0.520%    1.103%

Improvements:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  indexing       with_query_results_single_indexed_property                   -0.900%   -1.424%   -0.299%
  indexing       query_people_multiple_individually_indexed_properties        -1.708%   -1.937%   -1.364%
  indexing       with_query_results_multiple_individually_indexed_properties  -0.489%   -0.567%   -0.411%
  indexing       query_people_indexed_multi-property                          -6.103%   -6.335%   -5.841%
  sample_people  sampling_multiple_l_reservoir                                -0.442%   -0.550%   -0.336%

Unchanged:
  Group          Bench                                                         Change  CI Lower  CI Upper
  -------------  -----------------------------------------------------------  -------  --------  --------
  examples       example-births-deaths                                         0.009%   -0.090%    0.116%
  indexing       query_people_count_indexed_multi-property                     0.062%   -0.201%    0.419%
  sample_people  sampling_single_known_length                                 -0.066%   -0.334%    0.198%
  large_dataset  bench_query_population_derived_property                       0.266%   -0.018%    0.591%
  large_dataset  bench_query_population_multi_indexed                          0.576%   -0.142%    1.078%

github-actions · 2026-02-13T17:05:44Z

Benchmark Results

Hyperfine

| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|:---|---:|---:|---:|---:|
| `large_sir::baseline` | 2.4 ± 0.1 | 2.3 | 2.7 | 1.00 |
| `large_sir::entities` | 10.2 ± 0.2 | 10.0 | 11.3 | 4.33 ± 0.21 |

Criterion

Regressions:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  indexing                               query_people_count_single_indexed_property_entities                1.921%    1.272%    2.569%
  large_dataset                          bench_query_population_property_entities                           0.434%    0.007%    0.937%
  sampling                               sampling_single_known_length_entities                              2.682%    2.153%    3.256%
  sampling                               sampling_multiple_known_length_entities                            0.538%    0.380%    0.691%
  sample_entity_whole_population         10000                                                              0.525%    0.259%    0.923%

Improvements:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  indexing                               with_query_results_multiple_individually_indexed_properties_enti  -0.302%   -0.492%   -0.118%
  indexing                               query_people_multiple_individually_indexed_properties_entities    -0.284%   -0.350%   -0.223%
  indexing                               query_people_count_indexed_multi-property_entities                -0.929%   -1.199%   -0.496%
  indexing                               query_people_count_multiple_individually_indexed_properties_enti  -1.167%   -1.246%   -1.094%
  indexing                               query_people_single_indexed_property_entities                     -0.244%   -0.337%   -0.153%
  large_dataset                          bench_query_population_derived_property_entities                  -1.885%   -2.162%   -1.492%
  large_dataset                          bench_query_population_multi_unindexed_entities                   -0.460%   -0.903%   -0.119%
  large_dataset                          bench_query_population_indexed_property_entities                  -6.137%   -9.225%   -3.596%
  sampling                               sampling_multiple_l_reservoir_entities                            -1.734%   -1.815%   -1.630%
  sampling                               sampling_single_l_reservoir_entities                              -3.797%   -3.875%   -3.726%

Unchanged:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  sample_entity_single_property_indexed  10000                                                              0.408%   -0.765%    1.242%
  sample_entity_single_property_indexed  100000                                                             0.268%   -0.211%    0.626%
  sample_entity_single_property_indexed  1000                                                              -0.567%   -1.225%    0.054%
  indexing                               with_query_results_indexed_multi-property_entities                 0.622%   -0.106%    1.251%
  indexing                               query_people_indexed_multi-property_entities                      -0.304%   -0.854%    0.154%
  indexing                               with_query_results_single_indexed_property_entities               -0.170%   -0.650%    0.152%
  sample_entity_multi_property_indexed   10000                                                              0.003%   -0.515%    0.322%
  sample_entity_multi_property_indexed   100000                                                            -0.065%   -0.699%    0.446%
  sample_entity_multi_property_indexed   1000                                                              -0.074%   -0.690%    0.307%
  large_dataset                          bench_filter_indexed_entity                                       -2.144%  -11.321%    8.460%
  large_dataset                          bench_filter_unindexed_entity                                     -0.873%   -3.970%    2.257%
  large_dataset                          bench_match_entity                                                -0.170%   -0.726%    0.215%
  large_dataset                          bench_query_population_multi_indexed_entities                     -0.004%   -0.613%    0.582%
  sample_entity_whole_population         100000                                                             0.181%   -0.110%    0.408%
  sample_entity_whole_population         1000                                                               0.174%   -0.010%    0.390%

github-actions · 2026-02-13T17:14:12Z

Benchmark Results

Hyperfine

| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|:---|---:|---:|---:|---:|
| `large_sir::baseline` | 3.0 ± 0.1 | 2.9 | 3.7 | 1.00 |
| `large_sir::entities` | 13.1 ± 1.2 | 12.6 | 19.4 | 4.32 ± 0.42 |

Criterion

Regressions:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  indexing                               with_query_results_multiple_individually_indexed_properties_enti   1.205%    0.976%    1.538%
  indexing                               query_people_indexed_multi-property_entities                       0.498%    0.194%    0.796%
  large_dataset                          bench_match_entity                                                 2.963%    2.495%    3.418%
  large_dataset                          bench_query_population_multi_indexed_entities                      0.944%    0.226%    2.011%
  large_dataset                          bench_query_population_multi_unindexed_entities                    0.293%    0.063%    0.510%
  large_dataset                          bench_query_population_indexed_property_entities                   4.062%    3.295%    5.108%
  sampling                               sampling_single_l_reservoir_entities                               2.420%    2.234%    2.615%
  sampling                               sampling_single_known_length_entities                              1.133%    0.701%    1.650%

Improvements:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  sample_entity_single_property_indexed  10000                                                             -2.707%   -3.127%   -2.365%
  sample_entity_single_property_indexed  100000                                                            -0.536%   -0.878%   -0.022%
  sample_entity_single_property_indexed  1000                                                              -3.902%   -4.831%   -3.300%
  indexing                               with_query_results_indexed_multi-property_entities                -1.923%   -4.038%   -0.223%
  indexing                               with_query_results_single_indexed_property_entities               -0.763%   -1.277%   -0.268%
  indexing                               query_people_multiple_individually_indexed_properties_entities    -1.377%   -2.918%   -0.204%
  indexing                               query_people_count_multiple_individually_indexed_properties_enti  -1.271%   -1.415%   -1.150%
  indexing                               query_people_single_indexed_property_entities                     -1.171%   -1.275%   -1.011%
  sample_entity_multi_property_indexed   10000                                                             -1.643%   -2.161%   -1.005%
  sample_entity_multi_property_indexed   100000                                                            -2.474%   -3.379%   -1.776%
  sample_entity_multi_property_indexed   1000                                                              -4.322%   -4.681%   -3.827%
  large_dataset                          bench_filter_unindexed_entity                                     -7.294%  -11.419%   -2.858%
  sampling                               sampling_multiple_l_reservoir_entities                            -0.576%   -0.736%   -0.428%
  sample_entity_whole_population         10000                                                             -2.406%   -2.838%   -2.011%
  sample_entity_whole_population         100000                                                            -1.234%   -1.832%   -0.548%
  sample_entity_whole_population         1000                                                              -4.497%   -5.226%   -3.932%

Unchanged:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  indexing                               query_people_count_single_indexed_property_entities               -0.615%   -1.031%    0.038%
  indexing                               query_people_count_indexed_multi-property_entities                -0.537%   -1.309%    0.040%
  large_dataset                          bench_filter_indexed_entity                                       -1.270%  -13.692%   12.723%
  large_dataset                          bench_query_population_property_entities                          -0.214%   -0.659%    0.127%
  large_dataset                          bench_query_population_derived_property_entities                   0.022%   -0.205%    0.243%
  sampling                               sampling_multiple_known_length_entities                           -0.017%   -0.072%    0.036%

github-actions · 2026-02-13T17:36:29Z

Benchmark Results

Hyperfine

| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|:---|---:|---:|---:|---:|
| `large_sir::baseline` | 3.1 ± 0.1 | 2.9 | 3.9 | 1.00 |
| `large_sir::entities` | 12.7 ± 0.4 | 12.4 | 14.1 | 4.18 ± 0.23 |

Criterion

Regressions:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  indexing                               query_people_indexed_multi-property_entities                      15.104%   14.873%   15.339%
  indexing                               with_query_results_single_indexed_property_entities                0.626%    0.184%    1.318%
  indexing                               query_people_count_multiple_individually_indexed_properties_enti   0.197%    0.046%    0.346%
  indexing                               query_people_single_indexed_property_entities                     14.649%   11.310%   17.658%
  large_dataset                          bench_query_population_derived_property_entities                   3.099%    2.454%    3.680%
  sampling                               sampling_multiple_l_reservoir_entities                             0.847%    0.685%    1.030%
  sampling                               sampling_single_l_reservoir_entities                               0.566%    0.305%    0.767%
  sampling                               sampling_single_known_length_entities                              0.901%    0.639%    1.191%
  sampling                               sampling_multiple_known_length_entities                            0.362%    0.276%    0.438%

Improvements:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  sample_entity_single_property_indexed  1000                                                              -0.384%   -0.849%   -0.079%
  indexing                               with_query_results_multiple_individually_indexed_properties_enti  -1.407%   -1.664%   -1.134%
  sample_entity_multi_property_indexed   10000                                                             -0.412%   -0.827%   -0.125%
  sample_entity_multi_property_indexed   1000                                                              -0.792%   -1.315%   -0.386%
  large_dataset                          bench_query_population_property_entities                          -5.504%   -7.034%   -3.968%
  large_dataset                          bench_match_entity                                                -4.315%   -4.528%   -4.114%
  large_dataset                          bench_query_population_multi_unindexed_entities                   -3.044%   -4.597%   -1.505%
  sample_entity_whole_population         10000                                                             -2.934%   -3.181%   -2.680%
  sample_entity_whole_population         100000                                                            -0.688%   -0.990%   -0.414%
  sample_entity_whole_population         1000                                                              -4.571%   -4.895%   -4.312%

Unchanged:
  Group                                  Bench                                                              Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  -------  --------  --------
  sample_entity_single_property_indexed  10000                                                              0.182%   -0.445%    0.971%
  sample_entity_single_property_indexed  100000                                                            -0.192%   -0.763%    0.427%
  indexing                               query_people_count_single_indexed_property_entities               -0.098%   -0.334%    0.137%
  indexing                               with_query_results_indexed_multi-property_entities                -0.036%   -0.567%    0.461%
  indexing                               query_people_multiple_individually_indexed_properties_entities    -0.155%   -0.428%    0.109%
  indexing                               query_people_count_indexed_multi-property_entities                -0.156%   -0.785%    0.355%
  sample_entity_multi_property_indexed   100000                                                            -0.261%   -0.750%    0.269%
  large_dataset                          bench_filter_indexed_entity                                        0.178%  -11.640%   14.964%
  large_dataset                          bench_filter_unindexed_entity                                     -0.013%   -4.566%    4.746%
  large_dataset                          bench_query_population_multi_indexed_entities                      0.111%   -0.446%    0.677%
  large_dataset                          bench_query_population_indexed_property_entities                  -0.052%   -0.567%    0.448%

github-actions · 2026-02-13T17:46:13Z

Benchmark Results

Hyperfine

| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|:---|---:|---:|---:|---:|
| `large_sir::baseline` | 3.0 ± 0.1 | 2.9 | 3.2 | 1.00 |
| `large_sir::entities` | 12.7 ± 0.1 | 12.5 | 13.1 | 4.23 ± 0.10 |

Criterion

Regressions:
  Group                                  Bench                                                               Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  --------  --------  --------
  sample_entity_single_property_indexed  1000                                                                2.710%    0.707%    5.257%
  sample_entity_multi_property_indexed   10000                                                               1.649%    1.249%    2.055%
  sample_entity_multi_property_indexed   100000                                                              1.741%    1.404%    2.086%
  sample_entity_multi_property_indexed   1000                                                                1.929%    1.378%    2.478%
  large_dataset                          bench_query_population_property_entities                           30.149%   29.459%   30.717%
  large_dataset                          bench_query_population_derived_property_entities                    1.272%    0.904%    1.587%
  sampling                               sampling_single_known_length_entities                               0.936%    0.335%    1.522%

Improvements:
  Group                                  Bench                                                               Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  --------  --------  --------
  indexing                               with_query_results_multiple_individually_indexed_properties_enti   -2.780%   -3.014%   -2.559%
  indexing                               query_people_count_single_indexed_property_entities               -19.950%  -20.086%  -19.790%
  indexing                               with_query_results_indexed_multi-property_entities                 -7.543%   -8.128%   -6.995%
  indexing                               query_people_indexed_multi-property_entities                       -6.717%   -7.093%   -6.340%
  indexing                               with_query_results_single_indexed_property_entities               -26.681%  -26.847%  -26.503%
  indexing                               query_people_multiple_individually_indexed_properties_entities     -2.753%   -3.032%   -2.495%
  indexing                               query_people_count_indexed_multi-property_entities                -12.325%  -12.710%  -11.884%
  indexing                               query_people_count_multiple_individually_indexed_properties_enti   -3.109%   -3.292%   -2.923%
  indexing                               query_people_single_indexed_property_entities                     -24.644%  -24.959%  -24.163%
  large_dataset                          bench_query_population_multi_indexed_entities                      -4.936%   -5.581%   -4.509%
  large_dataset                          bench_query_population_multi_unindexed_entities                    -3.029%   -4.558%   -1.835%
  large_dataset                          bench_query_population_indexed_property_entities                   -0.572%   -0.933%   -0.132%
  sampling                               sampling_multiple_l_reservoir_entities                             -2.304%   -2.507%   -2.113%
  sampling                               sampling_single_l_reservoir_entities                               -0.623%   -0.798%   -0.431%
  sample_entity_whole_population         10000                                                              -1.959%   -2.534%   -1.405%
  sample_entity_whole_population         100000                                                             -2.157%   -2.641%   -1.780%

Unchanged:
  Group                                  Bench                                                               Change  CI Lower  CI Upper
  -------------------------------------  ----------------------------------------------------------------  --------  --------  --------
  sample_entity_single_property_indexed  10000                                                               0.020%   -0.420%    0.360%
  sample_entity_single_property_indexed  100000                                                              0.498%   -0.054%    1.015%
  large_dataset                          bench_filter_indexed_entity                                         0.538%  -12.083%   14.383%
  large_dataset                          bench_filter_unindexed_entity                                      -0.404%   -5.171%    4.544%
  large_dataset                          bench_match_entity                                                 -0.076%   -0.334%    0.203%
  sampling                               sampling_multiple_known_length_entities                             0.027%   -0.027%    0.084%
  sample_entity_whole_population         1000                                                               -0.394%   -0.740%    0.026%

swo mentioned this pull request Feb 4, 2026

ixa book questions/complaints #721

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swo force-pushed the swo_where_is_the_crab branch from 843eb64 to 2e0efe5 Compare February 4, 2026 20:43

swo changed the title ~~Put the logo in the book~~ docs: Put the logo in the book Feb 4, 2026

swo changed the title ~~docs: Put the logo in the book~~ docs: Small improvements to book Feb 4, 2026

swo marked this pull request as draft February 4, 2026 21:26

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swo force-pushed the swo_where_is_the_crab branch from e164acb to 0a81054 Compare February 13, 2026 16:47

docs: small typo and whitespace

4c48517

swo force-pushed the swo_where_is_the_crab branch from 0a81054 to 4c48517 Compare February 13, 2026 16:55

docs: fix dependencies

f35d257

swo marked this pull request as ready for review February 13, 2026 17:19

swo requested a review from RobertJacobsonCDC February 13, 2026 17:19

docs: use main branch setup script

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docs: Small improvements to book#719

docs: Small improvements to book#719
swo wants to merge 3 commits intomainfrom
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swo commented Feb 4, 2026 •

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Benchmark Results

Hyperfine

Criterion

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Benchmark Results

Hyperfine

Criterion

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github-actions bot commented Feb 13, 2026

Benchmark Results

Hyperfine

Criterion

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github-actions bot commented Feb 13, 2026

Benchmark Results

Hyperfine

Criterion

Uh oh!

github-actions bot commented Feb 13, 2026

Benchmark Results

Hyperfine

Criterion

Uh oh!

github-actions bot commented Feb 13, 2026

Benchmark Results

Hyperfine

Criterion

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swo commented Feb 4, 2026 •

edited

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