Code

Bring develop up to date#144

Code

Draft

mosesyhc wants to merge 163 commits intodevelopbandframework/surmise:developfrom mainbandframework/surmise:mainCopy head branch name to clipboard

+4,548-850

Commits

Commits on Jun 26, 2024

• remove transpose attempts to match dimensions

  mosesyhc

  committed
  7fefe4f

  Copy full SHA for 7fefe4f

• updating test suite expected behavior

  mosesyhc

  committed
  79fe3ba

  Copy full SHA for 79fe3ba

Commits on Jun 27, 2024

• include brief introduction and beginner guidance on homepage

  mosesyhc

  committed
  251ed78

  Copy full SHA for 251ed78

• include basic dependencies in description

  mosesyhc

  committed
  c9502e2

  Copy full SHA for c9502e2

• direct to section for pdf users.

  mosesyhc

  committed
  c8d7460

  Copy full SHA for c8d7460

• include jupyter notebook under examples

  mosesyhc

  committed
  7d8fd73

  Copy full SHA for 7d8fd73

• reverting documentation-related push

  mosesyhc

  committed
  78dbdd7

  Copy full SHA for 78dbdd7

Commits on Jun 28, 2024

• simplify optional efficiency code for testing

  mosesyhc

  committed
  c356dc9

  Copy full SHA for c356dc9

• update test suite to improve pcgpwm tests

  mosesyhc

  committed
  16564f7

  Copy full SHA for 16564f7

• include odd spellings in wordlist

  mosesyhc

  committed
  ff4e0e7

  Copy full SHA for ff4e0e7

• remove unintended usage emulator.prediction.rnd() and tests

  mosesyhc

  committed
  88ecd1e

  Copy full SHA for 88ecd1e

• cast to float64 at first encounter

  mosesyhc

  committed
  102f03a

  Copy full SHA for 102f03a

• cast to float64 at first encounter

  mosesyhc

  committed
  c6b91da

  Copy full SHA for c6b91da

• Revert "cast to float64 at first encounter"

  Show description for d89fb71
  mosesyhc

  committed
  d89fb71

  Copy full SHA for d89fb71

Commits on Jul 29, 2024

• spellcheck

  mosesyhc

  committed
  6c15c31

  Copy full SHA for 6c15c31

• casting to float64 for calibrator

  mosesyhc

  committed
  a645326

  Copy full SHA for a645326

• reshape to 2d arrays for 1d inputs

  mosesyhc

  committed
  477871a

  Copy full SHA for 477871a

• github action trigger on branch

  mosesyhc

  committed
  5dbda88

  Copy full SHA for 5dbda88

Commits on Jul 31, 2024

• include a description string for trained emulator

  mosesyhc

  committed
  df3403d

  Copy full SHA for df3403d

• pcgp description string

  mosesyhc

  committed
  c4c87c7

  Copy full SHA for c4c87c7

• pcgp update description

  mosesyhc

  committed
  a26a512

  Copy full SHA for a26a512

• pcgpwm descriptions

  mosesyhc

  committed
  c2a0eae

  Copy full SHA for c2a0eae

• indGP descriptions

  mosesyhc

  committed
  b1b9a8b

  Copy full SHA for b1b9a8b

• tests for param_str

  mosesyhc

  committed
  fd3ff2c

  Copy full SHA for fd3ff2c

• pcgpwimpute description

  mosesyhc

  committed
  8c954b2

  Copy full SHA for 8c954b2

• pcsk parameter description

  mosesyhc

  committed
  41a1a67

  Copy full SHA for 41a1a67

• tox coverage to ensure scikit-learn is installed for running pytest

  mosesyhc

  committed
  6818060

  Copy full SHA for 6818060

• including sklearn when tox -e coverage is called

  mosesyhc

  committed
  43f301a

  Copy full SHA for 43f301a

• using tox in github action

  mosesyhc

  committed
  a3a9592

  Copy full SHA for a3a9592

• restrict numpy<2

  mosesyhc

  committed
  8344742

  Copy full SHA for 8344742

• removing py312 as of now

  mosesyhc

  committed
  83466f8

  Copy full SHA for 83466f8

• revert numpy<2

  mosesyhc

  committed
  a92d6fd

  Copy full SHA for a92d6fd

Commits on Aug 1, 2024

• including dill for saving and loading emulators

  mosesyhc

  committed
  37836aa

  Copy full SHA for 37836aa

Commits on Aug 2, 2024

• update to surmise usage reference

  mosesyhc

  committed
  346c0e2

  Copy full SHA for 346c0e2

• do not skip installing package

  mosesyhc

  committed
  2185015

  Copy full SHA for 2185015

• update to bib entry

  mosesyhc

  committed
  fbcb02a

  Copy full SHA for fbcb02a

Commits on Aug 6, 2024

• ignore jupyter cache

  mosesyhc

  committed
  3cc7640

  Copy full SHA for 3cc7640

• cython>=3.0.10 is required for executables to work well with numpy 2.0

  mosesyhc

  committed
  3ab0e8a

  Copy full SHA for 3ab0e8a

Commits on Aug 7, 2024

• additional tests for functional lines

  mosesyhc

  committed
  7a0d180

  Copy full SHA for 7a0d180

• requires theta input in prediction

  mosesyhc

  committed
  84bfcf1

  Copy full SHA for 84bfcf1

• remove transpose attempts to match dimensions

  mosesyhc

  committed
  a2d39d3

  Copy full SHA for a2d39d3

• updating test suite expected behavior

  mosesyhc

  committed
  7e984a0

  Copy full SHA for 7e984a0

• tests for functional lines in calibration

  mosesyhc

  committed
  4469428

  Copy full SHA for 4469428

• remove lpdf from prior if not used in test

  mosesyhc

  committed
  abfe394

  Copy full SHA for abfe394

Commits on Aug 8, 2024

• calibrator and pprediction object saveload.

  mosesyhc

  committed
  870285a

  Copy full SHA for 870285a

• flip exp and log before computing overflow

  mosesyhc

  committed
  573af83

  Copy full SHA for 573af83

• empirical coverage first pass

  mosesyhc

  committed
  2457f8f

  Copy full SHA for 2457f8f

Commits on Aug 9, 2024

• empirical coverage first pass

  mosesyhc

  committed
  043dde9

  Copy full SHA for 043dde9

• include test for empirical coverage

  mosesyhc

  committed
  ae74e60

  Copy full SHA for ae74e60

• storing coverage info in prediction

  mosesyhc

  committed
  4c8e3cd

  Copy full SHA for 4c8e3cd

Commits on Aug 14, 2024

• use (n_theta, n_obs, n_obs) for covariance matrices output

  mosesyhc

  committed
  5c04c58

  Copy full SHA for 5c04c58

• Revert "use (n_theta, n_obs, n_obs) for covariance matrices output"

  Show description for b2d5b21
  mosesyhc

  committed
  b2d5b21

  Copy full SHA for b2d5b21

• return covariance matrices in the format (n_theta, n_obs, n_obs)

  mosesyhc

  committed
  c093bd3

  Copy full SHA for c093bd3

• Merge branch '114-discontinue-matrix-transpose-attempt-to-match-dimensions' of https://github.com/bandframework/surmise into 114-discontinue-matrix-transpose-attempt-to-match-dimensions

  mosesyhc

  committed
  2bb963a

  Copy full SHA for 2bb963a

Commits on Aug 15, 2024

• clean up files after save/load tests

  mosesyhc

  committed
  016501e

  Copy full SHA for 016501e

• clean up files after save/load tests

  mosesyhc

  committed
  dcadfcb

  Copy full SHA for dcadfcb

• Revert "clean up files after save/load tests"

  Show description for 8162982
  mosesyhc

  committed
  8162982

  Copy full SHA for 8162982

Commits on Aug 16, 2024

• py312 and setuptools for distutils

  mosesyhc

  committed
  6d55226

  Copy full SHA for 6d55226

• add py312 back

  mosesyhc

  committed
  334ad56

  Copy full SHA for 334ad56

• Merge pull request #127 from bandframework/123-py312-fails

  Show description for 4680583
  mosesyhc

  authored
  4680583

  Copy full SHA for 4680583

• Update PCGPwM.py

  wildsm

  authored
  f6584dc

  Copy full SHA for f6584dc

• Update PCGPwM.py

  wildsm

  authored
  7c08379

  Copy full SHA for 7c08379

• Update PCGPwM.py

  wildsm

  authored
  fc32738

  Copy full SHA for fc32738

• Update README.rst

  wildsm

  authored
  c44ceca

  Copy full SHA for c44ceca

• minor typo in emulation.py

  mosesyhc

  authored
  a385e6d

  Copy full SHA for a385e6d

Commits on Aug 19, 2024

• update instruction for scikit-learn dependency in running test suite via run-test.sh

  mosesyhc

  committed
  db9484e

  Copy full SHA for db9484e

Commits on Aug 21, 2024

• use install_tox.sh to match with coverage check

  mosesyhc

  committed
  0ebb0d1

  Copy full SHA for 0ebb0d1

• consolidate cast types functions in helper

  mosesyhc

  committed
  e7c9af4

  Copy full SHA for e7c9af4

• consolidate saveloads in helper

  mosesyhc

  committed
  604be2d

  Copy full SHA for 604be2d

• Revert "use install_tox.sh to match with coverage check"

  Show description for e5d41c7
  mosesyhc

  committed
  e5d41c7

  Copy full SHA for e5d41c7

• use install_tox.sh to match with coverage check

  mosesyhc

  committed
  7989f3a

  Copy full SHA for 7989f3a

• resolve path variable

  mosesyhc

  committed
  41eba52

  Copy full SHA for 41eba52

• windows path fix

  mosesyhc

  committed
  fdda0da

  Copy full SHA for fdda0da

• specify bash shell

  mosesyhc

  committed
  e705134

  Copy full SHA for e705134

• simplify documentation

  mosesyhc

  committed
  bd623d4

  Copy full SHA for bd623d4

• remove unnecessary documentation

  mosesyhc

  committed
  17fdde4

  Copy full SHA for 17fdde4

• flake8

  mosesyhc

  committed
  cd6aef7

  Copy full SHA for cd6aef7

• Merge pull request #118 from bandframework/114-discontinue-matrix-transpose-attempt-to-match-dimensions

  Show description for 54d5911
  mosesyhc

  authored
  54d5911

  Copy full SHA for 54d5911

• sphinx, code-block change

  mosesyhc

  committed
  c0f0d8a

  Copy full SHA for c0f0d8a

• Merge branch 'update_test_suite' into v0.3-update

  mosesyhc

  authored
  35171b8

  Copy full SHA for 35171b8

• flake8

  mosesyhc

  committed
  ee433f1

  Copy full SHA for ee433f1

• flake8

  mosesyhc

  committed
  b104e40

  Copy full SHA for b104e40

• Merge pull request #132 from bandframework/v0.3-update

  Show description for 0a645bf
  mosesyhc

  authored
  0a645bf

  Copy full SHA for 0a645bf

• Revert "flake8"

  Show description for 8dbca45
  mosesyhc

  committed
  8dbca45

  Copy full SHA for 8dbca45

• Revert "Merge branch 'update_test_suite' into v0.3-update"

  Show description for 35101ae
  mosesyhc

  committed
  35101ae

  Copy full SHA for 35101ae

• Merge branch 'update_test_suite' of https://github.com/bandframework/surmise into update_test_suite

  mosesyhc

  committed
  f6f1a57

  Copy full SHA for f6f1a57

• Revert "Merge branch 'update_test_suite' of https://github.com/bandframework/surmise into update_test_suite"

  Show description for a7f3e0b
  mosesyhc

  committed
  a7f3e0b

  Copy full SHA for a7f3e0b

Commits on Aug 22, 2024

• bool deprecation

  mosesyhc

  committed
  4c3e0b2

  Copy full SHA for 4c3e0b2

• correct typo

  mosesyhc

  committed
  42a7c37

  Copy full SHA for 42a7c37

• (Issue #134) Try running a "full" test suite outside tox.

  Show description for 5cf24f0
  jared321

  committed
  5cf24f0

  Copy full SHA for 5cf24f0

• Merge branch 'v0.3-update' into update_test_suite

  jared321

  authored
  7be01ef

  Copy full SHA for 7be01ef

• Revert "Merge branch 'v0.3-update' into update_test_suite"

  Show description for 5f4f2d3
  mosesyhc

  committed
  5f4f2d3

  Copy full SHA for 5f4f2d3

• (Issue #125) Nocoverage test should pass fails onto CI build server.

  jared321

  committed
  31a9a65

  Copy full SHA for 31a9a65

• (Issue #125) Install Cython in nocoverage action.

  Show description for 67d5451
  jared321

  committed
  67d5451

  Copy full SHA for 67d5451

Commits on Aug 23, 2024

• rnd and lpdf are not requirements of prediction, and no emu.prediction object is equippped with the functionality.

  mosesyhc

  committed
  9ba81b8

  Copy full SHA for 9ba81b8

• moving command prompt into pytest parameterize

  mosesyhc

  committed
  f84a526

  Copy full SHA for f84a526

• consolidate command prompts into test file.

  mosesyhc

  committed
  9cda4d1

  Copy full SHA for 9cda4d1

• minor argument missing

  mosesyhc

  committed
  10c939d

  Copy full SHA for 10c939d

• run all tests without -k flag in pytest

  mosesyhc

  committed
  3304f12

  Copy full SHA for 3304f12

• run_full_test_suite can be used without cmdopts

  mosesyhc

  committed
  d2dad6f

  Copy full SHA for d2dad6f

• use tox -e coverage to compile cython code

  mosesyhc

  committed
  80f6f9c

  Copy full SHA for 80f6f9c

• add indGP emulator to test suite

  mosesyhc

  committed
  e22def5

  Copy full SHA for e22def5

• add tests for valid predlpdf in pcgpwm

  mosesyhc

  committed
  ee80997

  Copy full SHA for ee80997

• add tests for PCGPwImpute

  mosesyhc

  committed
  68c79c9

  Copy full SHA for 68c79c9

• reconcile pcgpwImpute lpdf arguments with pcgpwm

  mosesyhc

  committed
  b2fb9a5

  Copy full SHA for b2fb9a5

• include prediction tests for pcgpwimpute

  mosesyhc

  committed
  b358f84

  Copy full SHA for b358f84

• (Issue #125) Add in tox task that tests oldest package versions with 3.9.

  Show description for d51683e
  jared321

  committed
  d51683e

  Copy full SHA for d51683e

• (Issue #125) Try creating oldest versions GH action.

  jared321

  committed
  46cf207

  Copy full SHA for 46cf207

• (Issue #125) Incompatible numpy/scipy versions.

  Show description for 1a9562b
  jared321

  committed
  1a9562b

  Copy full SHA for 1a9562b

• (Issue #125) Swapped last intentional error for a new one.

  Show description for 5f2b26c
  jared321

  committed
  5f2b26c

  Copy full SHA for 5f2b26c

• (Issue #125) Fix up all errors & try more OS.

  Show description for 5b1abe8
  jared321

  committed
  5b1abe8

  Copy full SHA for 5b1abe8

Commits on Aug 27, 2024

• (Issue #125) Run oldest tests on installed Surmise packages.

  Show description for 37deb8e
  jared321

  committed
  37deb8e

  Copy full SHA for 37deb8e

• (Issue #125) Nope. I was wrong. Oldest must run in editable mode.

  Show description for 785e6ab
  jared321

  committed
  785e6ab

  Copy full SHA for 785e6ab

Commits on Aug 28, 2024

• no longer required for test suite.

  mosesyhc

  committed
  1cd5531

  Copy full SHA for 1cd5531

• Merge pull request #135 from bandframework/125Bookends

  Show description for d13f5e6
  jared321

  authored
  d13f5e6

  Copy full SHA for d13f5e6

• Improve language in tox.ini as part of PR review.

  jared321

  committed
  83f9621

  Copy full SHA for 83f9621

Commits on Aug 29, 2024

• Clean GH actions as part of v0.3 review.

  jared321

  committed
  13c57ba

  Copy full SHA for 13c57ba

• Revert to 3.11 but with 3.12 error documented.

  jared321

  committed
  e97538b

  Copy full SHA for e97538b

• Update spelling action's versions.

  jared321

  committed
  95e8cc1

  Copy full SHA for 95e8cc1

• Update two actions for more conservative checks.

  Show description for 37ab867
  jared321

  committed
  37ab867

  Copy full SHA for 37ab867

• correct sentence in readme installation command

  mosesyhc

  committed
  a8b2f27

  Copy full SHA for a8b2f27

• update surmise ver number, remove setup.py, rename contributor doc

  mosesyhc

  committed
  342a27f

  Copy full SHA for 342a27f

• remove doc dependencies in pyproject.toml

  mosesyhc

  committed
  b56e0c3

  Copy full SHA for b56e0c3

• include collaborators and contributors in docs

  mosesyhc

  committed
  0e6e393

  Copy full SHA for 0e6e393

• reintroduce setup.py to resolve Cython extension error

  mosesyhc

  committed
  35500fc

  Copy full SHA for 35500fc

• spellcheck fixes

  mosesyhc

  committed
  c1896c0

  Copy full SHA for c1896c0

• Simplify setup.py.

  Show description for 5342e65
  jared321

  committed
  5342e65

  Copy full SHA for 5342e65

• clarify saveload functions in emulator and calibrator and check type

  mosesyhc

  committed
  0608007

  Copy full SHA for 0608007

• replace assertions with if statements and error raising, include clean up code if failure

  mosesyhc

  committed
  7b46464

  Copy full SHA for 7b46464

• include matplotlib requirement in examples documentation

  mosesyhc

  committed
  7a188c7

  Copy full SHA for 7a188c7

• use of matrixmatching is employed in Example3, include warning for mismatch coverage computation

  mosesyhc

  committed
  96c7468

  Copy full SHA for 96c7468

• Merge pull request #138 from bandframework/example3_test

  Show description for be9acca
  mosesyhc

  authored
  be9acca

  Copy full SHA for be9acca

• Merge pull request #136 from bandframework/saveload_fix

  Show description for a600f43
  mosesyhc

  authored
  a600f43

  Copy full SHA for a600f43

• Merge branch 'v0.3-update' of https://github.com/bandframework/surmise into v0.3-update

  mosesyhc

  committed
  ccffc1a

  Copy full SHA for ccffc1a

• flake8

  mosesyhc

  committed
  974eb9e

  Copy full SHA for 974eb9e

Commits on Sep 3, 2024

• consolidating object loading code to helper.

  mosesyhc

  committed
  2619127

  Copy full SHA for 2619127

Commits on Sep 4, 2024

• update test instruction in README

  mosesyhc

  committed
  2e39c6f

  Copy full SHA for 2e39c6f

• expand description in doc

  mosesyhc

  committed
  f8f731f

  Copy full SHA for f8f731f

• move programming details under examples and tutorial in readme

  mosesyhc

  committed
  71b8bf1

  Copy full SHA for 71b8bf1

• include new reference

  mosesyhc

  committed
  c0d8d37

  Copy full SHA for c0d8d37

• correct sphinx error and shorten section title

  mosesyhc

  committed
  30080e3

  Copy full SHA for 30080e3

• partial correction for bibentry rendering

  mosesyhc

  committed
  fd02099

  Copy full SHA for fd02099

• include instruction to upgrade pip before installation

  mosesyhc

  committed
  7db8d27

  Copy full SHA for 7db8d27

• allow non-blocking figures, specify dynamic filepaths, avoid plot warnings

  mosesyhc

  committed
  6257312

  Copy full SHA for 6257312

• add the surmise colab notebook as .py for testing

  mosesyhc

  committed
  54f975a

  Copy full SHA for 54f975a

• (Issue #131) Try fixing broken RTD build.

  jared321

  committed
  e6f7e34

  Copy full SHA for e6f7e34

• converting block strings in usage tutorial to literal strings in example.

  mosesyhc

  committed
  58a0f20

  Copy full SHA for 58a0f20

• Merge branch 'v0.3-update' of https://github.com/bandframework/surmise into v0.3-update

  mosesyhc

  committed
  9268598

  Copy full SHA for 9268598

• bibentries standardization, and urls

  mosesyhc

  committed
  fdda188

  Copy full SHA for fdda188

• include cython language_level specification

  mosesyhc

  committed
  cd2c938

  Copy full SHA for cd2c938

Commits on Sep 5, 2024

• add new reference to use cases

  mosesyhc

  committed
  692ac4f

  Copy full SHA for 692ac4f

• add notebook version of tutorial

  mosesyhc

  committed
  41fd3a6

  Copy full SHA for 41fd3a6

Commits on Sep 9, 2024

• include test directory for pytest command in README

  mosesyhc

  committed
  c819975

  Copy full SHA for c819975

Commits on Sep 10, 2024

• Merge pull request #121 from bandframework/v0.3-update

  Show description for 7b242aa
  mosesyhc

  authored
  7b242aa

  Copy full SHA for 7b242aa

Commits on Sep 11, 2024

• update emails in pyproject.toml, SUPPORT

  mosesyhc

  committed
  932a8b5

  Copy full SHA for 932a8b5

• SDK review

  mosesyhc

  committed
  56463b7

  Copy full SHA for 56463b7

• add names in spellcheck list.

  mosesyhc

  committed
  5f02f01

  Copy full SHA for 5f02f01

• Merge pull request #140 from bandframework/sdk-contact-update

  Show description for 2d56372
  mosesyhc

  authored
  2d56372

  Copy full SHA for 2d56372

Commits on Sep 12, 2024

• update publish action to fix bug for pypa/cibuildwheel<2.16.5

  mosesyhc

  committed
  d2813ac

  Copy full SHA for d2813ac

• Merge pull request #141 from bandframework/patch-publish-action

  Show description for da45d64
  mosesyhc

  authored
  da45d64

  Copy full SHA for da45d64

• patch os runner version

  mosesyhc

  committed
  d6f9844

  Copy full SHA for d6f9844

• update os versions to latest, and include most recent 2 macos

  mosesyhc

  committed
  d111e29

  Copy full SHA for d111e29

• Merge pull request #142 from bandframework/patch-publish-action

  Show description for a40f755
  mosesyhc

  authored
  a40f755

  Copy full SHA for a40f755