gemlib 0.9.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (75) hide show
  1. gemlib/__init__.py +9 -0
  2. gemlib/distributions/__init__.py +26 -0
  3. gemlib/distributions/brownian.py +141 -0
  4. gemlib/distributions/categorical2.py +33 -0
  5. gemlib/distributions/continuous_markov.py +371 -0
  6. gemlib/distributions/continuous_time_state_transition_model.py +185 -0
  7. gemlib/distributions/continuous_time_state_transition_model_test.py +289 -0
  8. gemlib/distributions/discrete_markov.py +279 -0
  9. gemlib/distributions/discrete_rejection_sampling.py +149 -0
  10. gemlib/distributions/discrete_time_state_transition_model.py +324 -0
  11. gemlib/distributions/discrete_time_state_transition_model_examples.py +453 -0
  12. gemlib/distributions/discrete_time_state_transition_model_test.py +336 -0
  13. gemlib/distributions/experimental/__init__.py +7 -0
  14. gemlib/distributions/experimental/discrete_approx_cont_state_transition_model.py +194 -0
  15. gemlib/distributions/experimental/state_transition_marginal_model.py +352 -0
  16. gemlib/distributions/hypergeometric.py +144 -0
  17. gemlib/distributions/hypergeometric_sampler.py +103 -0
  18. gemlib/distributions/hypergeometric_test.py +46 -0
  19. gemlib/distributions/kcategorical.py +113 -0
  20. gemlib/distributions/kcategorical_test.py +52 -0
  21. gemlib/distributions/uniform_integer.py +169 -0
  22. gemlib/distributions/uniform_integer_test.py +55 -0
  23. gemlib/mcmc/__init__.py +23 -0
  24. gemlib/mcmc/adaptive_random_walk_metropolis.py +859 -0
  25. gemlib/mcmc/adaptive_random_walk_metropolis_test.py +144 -0
  26. gemlib/mcmc/bb_fixture.pkl +0 -0
  27. gemlib/mcmc/brownian_bridge_kernel.py +291 -0
  28. gemlib/mcmc/brownian_bridge_kernel_test.py +164 -0
  29. gemlib/mcmc/chain_binomial_rippler.py +524 -0
  30. gemlib/mcmc/chain_binomial_rippler_test.py +120 -0
  31. gemlib/mcmc/compound_kernel.py +156 -0
  32. gemlib/mcmc/conftest.py +4 -0
  33. gemlib/mcmc/damped_chain_binomial_rippler.py +840 -0
  34. gemlib/mcmc/discrete_time_state_transition_model/__init__.py +21 -0
  35. gemlib/mcmc/discrete_time_state_transition_model/event_time_proposal.py +275 -0
  36. gemlib/mcmc/discrete_time_state_transition_model/fixtures.py +56 -0
  37. gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_mh.py +258 -0
  38. gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_mh_test.py +108 -0
  39. gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_proposal.py +188 -0
  40. gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_proposal_test.py +33 -0
  41. gemlib/mcmc/discrete_time_state_transition_model/move_events.py +239 -0
  42. gemlib/mcmc/discrete_time_state_transition_model/move_events_test.py +63 -0
  43. gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_mh.py +254 -0
  44. gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_mh_test.py +28 -0
  45. gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_proposal.py +150 -0
  46. gemlib/mcmc/discrete_time_state_transition_model/util.py +9 -0
  47. gemlib/mcmc/experimental/__init__.py +0 -0
  48. gemlib/mcmc/experimental/composable_kernel.py +270 -0
  49. gemlib/mcmc/experimental/discrete_time_state_transition_model/__init__.py +1 -0
  50. gemlib/mcmc/experimental/discrete_time_state_transition_model/left_censored_events_mh.py +149 -0
  51. gemlib/mcmc/experimental/discrete_time_state_transition_model/move_events.py +71 -0
  52. gemlib/mcmc/experimental/discrete_time_state_transition_model/move_events_test.py +48 -0
  53. gemlib/mcmc/experimental/discrete_time_state_transition_model/right_censored_events_mh.py +89 -0
  54. gemlib/mcmc/experimental/discrete_time_state_transition_model/right_censored_events_mh_test.py +28 -0
  55. gemlib/mcmc/experimental/hmc.py +111 -0
  56. gemlib/mcmc/experimental/hmc_test.py +61 -0
  57. gemlib/mcmc/experimental/mcmc_base.py +33 -0
  58. gemlib/mcmc/experimental/mcmc_sampler.py +94 -0
  59. gemlib/mcmc/experimental/mcmc_sampler_test.py +44 -0
  60. gemlib/mcmc/experimental/multi_scan.py +53 -0
  61. gemlib/mcmc/experimental/multi_scan_test.py +71 -0
  62. gemlib/mcmc/experimental/random_walk_metropolis.py +107 -0
  63. gemlib/mcmc/experimental/random_walk_metropolis_test.py +214 -0
  64. gemlib/mcmc/experimental/test_util.py +49 -0
  65. gemlib/mcmc/gibbs_kernel.py +505 -0
  66. gemlib/mcmc/gibbs_kernel_test.py +212 -0
  67. gemlib/mcmc/h5_posterior.py +77 -0
  68. gemlib/mcmc/multi_scan_kernel.py +59 -0
  69. gemlib/mcmc/zarr_posterior.py +132 -0
  70. gemlib/util.py +117 -0
  71. gemlib/util_test.py +75 -0
  72. gemlib-0.9.2.dist-info/LICENSE +21 -0
  73. gemlib-0.9.2.dist-info/METADATA +19 -0
  74. gemlib-0.9.2.dist-info/RECORD +75 -0
  75. gemlib-0.9.2.dist-info/WHEEL +4 -0
gemlib-0.9.2.dist-info/METADATA ADDED
@@ -0,0 +1,19 @@
1
+ Metadata-Version: 2.1
2
+ Name: gemlib
3
+ Version: 0.9.2
4
+ Summary: GEMlib scientific compute library for epidemic modelling
5
+ Home-page: http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib
6
+ Author: Chris Jewell
7
+ Author-email: c.jewell@lancaster.ac.uk
8
+ Requires-Python: >=3.9.0,<3.12.0
9
+ Classifier: Programming Language :: Python :: 3
10
+ Classifier: Programming Language :: Python :: 3.9
11
+ Classifier: Programming Language :: Python :: 3.10
12
+ Classifier: Programming Language :: Python :: 3.11
13
+ Requires-Dist: scipy (>=1.12.0,<2.0.0)
14
+ Requires-Dist: sphinx-book-theme (>=1.1.3,<2.0.0)
15
+ Requires-Dist: tensorflow (>=2.15.0,<2.16.0) ; sys_platform == "linux"
16
+ Requires-Dist: tensorflow-cpu (>=2.15.0,<2.16.0) ; sys_platform == "darwin"
17
+ Requires-Dist: tensorflow-intel (>=2.15.0,<2.16.0) ; sys_platform == "win32"
18
+ Requires-Dist: tensorflow-probability (>=0.23.0,<0.24.0)
19
+ Project-URL: Repository, http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib
gemlib-0.9.2.dist-info/RECORD ADDED
@@ -0,0 +1,75 @@
1
+ gemlib/__init__.py,sha256=dJJM0sATv7585wF5sOlC-NIaqFdTORZqGY_GbPRQ8Pk,228
2
+ gemlib/distributions/__init__.py,sha256=TrrHM9ZAH24eLif8Rc9Rte_eZKkNbis1txHmxPpQcUQ,921
3
+ gemlib/distributions/brownian.py,sha256=uBsZ3bzif2ensLUe2R7veErW0mWPZD7ixrJ2frCtHdA,4550
4
+ gemlib/distributions/categorical2.py,sha256=tqmjrRFL35lKBj5YGhNzZxyol61_qwIGYdiK0sXrO9Y,1237
5
+ gemlib/distributions/continuous_markov.py,sha256=bGLv25_uxQK0ODTlOiiWQeEOFUU3ODkplFKRB3B481E,12787
6
+ gemlib/distributions/continuous_time_state_transition_model.py,sha256=6h41JiKOK0CGwzij7VhzCIBheXEPkwJlt8eWTym0vrs,6480
7
+ gemlib/distributions/continuous_time_state_transition_model_test.py,sha256=aOW3_Sn49g9Tpwpm6XPckIqpedkH0wC-4Al9wZFOc2Y,8147
8
+ gemlib/distributions/discrete_markov.py,sha256=5ejYaYJO65MvGhl9dFJTo7NZefGKkdINUxt1ofcVl8o,10390
9
+ gemlib/distributions/discrete_rejection_sampling.py,sha256=_SBwaxsKyw5M7nJauuVCsMZuFP1UEtr14QaynuSauS0,5707
10
+ gemlib/distributions/discrete_time_state_transition_model.py,sha256=oCALsg9v4eGr7CP4m2tK6GMeNXKhTqdLuV28hmks1dw,11509
11
+ gemlib/distributions/discrete_time_state_transition_model_examples.py,sha256=uNnFKQzAmOAwCYAcauQK_yZ08BIPeqP9p4Tk2j2FmVY,11360
12
+ gemlib/distributions/discrete_time_state_transition_model_test.py,sha256=NY2xLu1Dk837_CsjbdKTd9fj_WYyPYbkfqZM4QPWRgc,11678
13
+ gemlib/distributions/experimental/__init__.py,sha256=4aJCVEs-2Tn7IyGiSUYyg5zu-4AaAbWEoUemrdgXOIs,247
14
+ gemlib/distributions/experimental/discrete_approx_cont_state_transition_model.py,sha256=AoCNxBnlGfpUAMuSkAcnsvZ_-RJGgLC_Z-4jy4ipHQ8,6808
15
+ gemlib/distributions/experimental/state_transition_marginal_model.py,sha256=RcIfDwe6-Dy43Dc8Sf3jdSMMX9QEpCidEeDUIFcZl24,13249
16
+ gemlib/distributions/hypergeometric.py,sha256=neJg3M_Twab5mZHP-rHKDyyHh5GcOf9He87PGy54ECU,4173
17
+ gemlib/distributions/hypergeometric_sampler.py,sha256=v3RywBkOD2G2zQ0Y7asklVQyNQ_QMQirQYTz8nETe3s,3486
18
+ gemlib/distributions/hypergeometric_test.py,sha256=4ueqZ4Ug-y2q2iwgxRH093RB23xu1RMllN5ji4NCRrA,1433
19
+ gemlib/distributions/kcategorical.py,sha256=QhFm-NnoelwG7Ycs6wY2UYnhyIHHUBkukLR07gxzhSM,3960
20
+ gemlib/distributions/kcategorical_test.py,sha256=YWtf5vg-APyeYuQGuaTN_XpWxwjEhh-ju0S2bbjZW_A,1795
21
+ gemlib/distributions/uniform_integer.py,sha256=Rg3dbxORq-cECQfgXfFgeKBwKPnbOYy4bSs4cT5yzLo,5655
22
+ gemlib/distributions/uniform_integer_test.py,sha256=TssHFLBV3cXqQx6Xgbjric6dvB7BYBJzQ5vGHHaP7Rw,1931
23
+ gemlib/mcmc/__init__.py,sha256=UvBnhNPY3KkM8r-3-2flJLKYLiIuTCsrj7h6kmbWozA,722
24
+ gemlib/mcmc/adaptive_random_walk_metropolis.py,sha256=5Ab3CoacKqjsqxsf8qYD_suCr0-gYcSMJXYdp3xJZDU,31516
25
+ gemlib/mcmc/adaptive_random_walk_metropolis_test.py,sha256=VPejlQlHbuELBDaGCRlAnsA5oFCnIRVkPwGVcFIcZ4s,4638
26
+ gemlib/mcmc/bb_fixture.pkl,sha256=7WUYpB4B4mC5Zts2Dd5Dny1QaW1NhpqUx_xDl7I68yk,1946
27
+ gemlib/mcmc/brownian_bridge_kernel.py,sha256=PHGF6O4poZwnbiHVJUE69qjMOHhhtAieoU09-eai7Eg,11075
28
+ gemlib/mcmc/brownian_bridge_kernel_test.py,sha256=WJx6f-WysUGST4z6cCWtewvC5nVAtAjhnqZbh14pYzE,4631
29
+ gemlib/mcmc/chain_binomial_rippler.py,sha256=FyXKbt4K66-Ug_liKOFA3fvPcOaSiQAC1tAxw8rFTKU,17518
30
+ gemlib/mcmc/chain_binomial_rippler_test.py,sha256=jS4WeOi-IG9tG-XGIQUIK5xTfoxJaxwSvS8RmA48XZw,3630
31
+ gemlib/mcmc/compound_kernel.py,sha256=Wktmpnd_A4eLzOiVEDqdfUy_2AgWmz1ktNPN4I5hTmY,5285
32
+ gemlib/mcmc/conftest.py,sha256=vmiIdJGecbp9ACebqKKHEzIpQuFE4PAjxYRH_lAsBCw,33
33
+ gemlib/mcmc/damped_chain_binomial_rippler.py,sha256=02BeU29nDufiYhT6937nI8oBspm1c1npOHQogXzKtho,27833
34
+ gemlib/mcmc/discrete_time_state_transition_model/__init__.py,sha256=oIvFbtyYwrM20VnGrsTLW_D46QkZ024D7Ce6aYM9bbY,707
35
+ gemlib/mcmc/discrete_time_state_transition_model/event_time_proposal.py,sha256=RMjJqPXDBTQWJsfaV61ak5n4qYOq980M7YbnvUSFA1Y,9665
36
+ gemlib/mcmc/discrete_time_state_transition_model/fixtures.py,sha256=8PCLgwecFxIxeWMZ2Zq6vS5rHZLndTqNtGxfjZtn7Ak,1396
37
+ gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_mh.py,sha256=Z6Hstu-PdUDj7jIhZxgrlzwMHvDYj_hfSeC-LgCsVME,8703
38
+ gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_mh_test.py,sha256=-qyXog3LCYD6nT-_sRMeTCmQLunkK9Pksn2CkJxawKs,3143
39
+ gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_proposal.py,sha256=UVMgWUdDNJD1gFdc066JKuX4lxKpjw_AdQMrbLFdxvM,7378
40
+ gemlib/mcmc/discrete_time_state_transition_model/left_censored_events_proposal_test.py,sha256=YoGo3N2g97XHteaiwaKJ1h0kTKASjmeWpkV6JwOibOY,925
41
+ gemlib/mcmc/discrete_time_state_transition_model/move_events.py,sha256=UGUqAfsfMWYAF6FN2KIwmIaDB9gKyQqor6nE0hO6Ju8,8363
42
+ gemlib/mcmc/discrete_time_state_transition_model/move_events_test.py,sha256=3mcVpOAzAK_-yAPp2-7bW31XOXXbOZSYATydnys1xxY,1544
43
+ gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_mh.py,sha256=5i7o5erDuOWb-GBp9a5FwiXMW-EFZ2y0QsW3IMFLSI0,9192
44
+ gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_mh_test.py,sha256=wKiyZepjzUTisgGO5ovgTjW4q6SRdKUd1ak3rDLOgmY,616
45
+ gemlib/mcmc/discrete_time_state_transition_model/right_censored_events_proposal.py,sha256=vUHM0ygKpfrt5bkH1mX6T1GGi825sBZiGT8FtDmuZgE,4715
46
+ gemlib/mcmc/discrete_time_state_transition_model/util.py,sha256=SpwiYX19GlOYBBAZaHrBiuYLV28v9_RGB35BCI4sqbw,181
47
+ gemlib/mcmc/experimental/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
48
+ gemlib/mcmc/experimental/composable_kernel.py,sha256=C_kkpr-BUprm08qQ-MX3kPHOqE9dRYP1DBgP5csoYlA,8295
49
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/__init__.py,sha256=GLodHZc_XktXVMEQIGT4ECHMyaLNSU8m2fuX5aZpWZY,61
50
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/left_censored_events_mh.py,sha256=0DntTaJPiSelPpMGCWJv8QHXZo9jD3ArZ5LPivT4Uv4,4511
51
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/move_events.py,sha256=UKyi1-07ky6zeJtbpOcDqsu-V-5NCmVIBsB284dY5to,2155
52
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/move_events_test.py,sha256=n6a01XsupWNkx4XjzFgmGfvQLn6Hh4ImvD7YksLokUc,1179
53
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/right_censored_events_mh.py,sha256=RqyiEX3woSudMPMgaRlwG16G41apFnXlyXBAvncO5u4,2721
54
+ gemlib/mcmc/experimental/discrete_time_state_transition_model/right_censored_events_mh_test.py,sha256=LL-sqvYq505VUZfmfGdCjb55p3yQI9YEDHuFl1OTsFY,711
55
+ gemlib/mcmc/experimental/hmc.py,sha256=1vdHKDwRh4AMGbKJDRc4qxYp326Tf-WCM9W0uoHqX_U,3385
56
+ gemlib/mcmc/experimental/hmc_test.py,sha256=dg1wm8sex_z-NDCFApW4k927f2HJLFJKvoe75rFAK-w,1620
57
+ gemlib/mcmc/experimental/mcmc_base.py,sha256=0IgPIydpOUb01NrV6R2ju_97skzcpRcsJgIh02GJwXw,736
58
+ gemlib/mcmc/experimental/mcmc_sampler.py,sha256=PEdQh3P1nAOSR5gSoG-7GR5Q1WUVRSh6Whp_uXpOy1A,2450
59
+ gemlib/mcmc/experimental/mcmc_sampler_test.py,sha256=YoQHjU9nA6b-XsF12p4U-X0lbOI3b_bfZhDzRDerbMY,949
60
+ gemlib/mcmc/experimental/multi_scan.py,sha256=oAYOPkYogtpJ5v6eLoGjdVxBn65cBbjQ_nFX9kWr9uY,1547
61
+ gemlib/mcmc/experimental/multi_scan_test.py,sha256=yTuOnAI6NrxABLUeg4LJQk3sCJd6ssWAmO-Zt1LSnE0,1737
62
+ gemlib/mcmc/experimental/random_walk_metropolis.py,sha256=97blKbDHH79CE-qK-51UpXS7LfURtPzl5zbA_oRCy0U,3157
63
+ gemlib/mcmc/experimental/random_walk_metropolis_test.py,sha256=vUVyyFlki2cc6DL2uWveXV0WKPW_sW9Aaqd-7zQXztg,5375
64
+ gemlib/mcmc/experimental/test_util.py,sha256=_eEBsGL0IDd4Jj_QqXSiYOq8a73nWi4WcSLEmBk2IqE,1392
65
+ gemlib/mcmc/gibbs_kernel.py,sha256=ZHU2ODK_l8znAZ_w9ZcLr58x9fzNVUG5KUxJu5SjG-Q,16769
66
+ gemlib/mcmc/gibbs_kernel_test.py,sha256=-j9SVA21dzgN-3QWCWlEFSuwn75jyXF1gc7FwiGStME,7313
67
+ gemlib/mcmc/h5_posterior.py,sha256=uypd51NM3dhums9Qxb8WCaC-YdLlDva4fLWU0J3afWQ,2478
68
+ gemlib/mcmc/multi_scan_kernel.py,sha256=40mcNj1dMMrHSHeqHfhNf1XXMjxT2P-z8P7Onmh9POs,1813
69
+ gemlib/mcmc/zarr_posterior.py,sha256=McYkkFWM-6n63ykAD3Y_ihCxTVh7Ej_ixPxc6YcT1xY,4440
70
+ gemlib/util.py,sha256=C6i1RpWW9o2lvBdESTbEXvPxJk5zwUk37RWNhX3kBmw,3409
71
+ gemlib/util_test.py,sha256=11PJC8PZxFmnOBr_EjWlIeuzhijzbF5D03qolb2oSDk,1833
72
+ gemlib-0.9.2.dist-info/LICENSE,sha256=lJBt4qzi_t9MjmMB3IgsCBhA3gFVFJM6jHP0rebB6p8,1095
73
+ gemlib-0.9.2.dist-info/METADATA,sha256=mtnllbj8bkpbBNcn-MxoYivnIa_TI25-NJWC1I9HyF8,907
74
+ gemlib-0.9.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
75
+ gemlib-0.9.2.dist-info/RECORD,,
gemlib-0.9.2.dist-info/WHEEL ADDED
@@ -0,0 +1,4 @@
1
+ Wheel-Version: 1.0
2
+ Generator: poetry-core 1.9.0
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any