Code

Release 0.1.8#114

Code

Merged

twomagpi merged 132 commits intomasterukhsa-collaboration/pygom:masterfrom devukhsa-collaboration/pygom:devCopy head branch name to clipboardAug 5, 2024

+9,255-31,080

Commits

Commits on Apr 26, 2024

• Add missing space bar

  j-c-gibson

  committed
  fbf3991

Commits on Apr 30, 2024

• Change introduction structure

  j-c-gibson

  committed
  0e7642f

Commits on May 30, 2024

• Fix multiplication assignment bug

  j-c-gibson

  committed
  c0939ab

• Fix to get unroll to work when denominators are present in ODEs

  j-c-gibson

  committed
  0a5fc17

• Make SimulateOde main class by giving it both stochastic and deterministic solvers

  j-c-gibson

  committed
  59998c5

• Add some SimulateOde objects, currently they are only DeterministicOde. In future, SimulateOde might be only necessary class.

  j-c-gibson

  committed
  bf75f3c

• Fix bugs in NormalLoss and PoissonLoss declarations

  j-c-gibson

  committed
  b2ddcfc

• Intro edits

  j-c-gibson

  committed
  61a7dfe

• ODE solving and simulation edits

  j-c-gibson

  committed
  5246fc1

• Parameter fitting edits

  j-c-gibson

  committed
  ed58a1c

• Generate synthetic epi data for doc examples

  j-c-gibson

  committed
  23b4403

• Pygom analytical features edits

  j-c-gibson

  committed
  faa0a40

• Model specification edits

  j-c-gibson

  committed
  7574242

• Tidying up files a bit

  j-c-gibson

  committed
  790a7dc

Commits on Jun 4, 2024

• Remove redundant doc folder

  j-c-gibson

  committed
  07143ac

• Update readme

  j-c-gibson

  committed
  35d4e4e

• Clean up readme rst bugs

  j-c-gibson

  committed
  94b336c

• Readme bullet points

  j-c-gibson

  committed
  941eae1

• Change README from rst to md

  j-c-gibson

  committed
  7b3021b

• More README edits

  j-c-gibson

  committed
  5ebe701

• Even more README edits

  j-c-gibson

  committed
  d5f7189

• Further minor README edits

  j-c-gibson

  committed
  ea67a42

• Try to fix failed workflow

  j-c-gibson

  committed
  a283f42

Commits on Jun 5, 2024

• Finishing touches

  j-c-gibson

  committed
  acd270b

Commits on Jun 6, 2024

• Add forgotten files and undo R0 test edits which were crashing test cases

  j-c-gibson

  committed
  8a7c464

Commits on Jun 11, 2024

• Update README.md

  Show description for 707755c
  j-c-gibson

  authored
  707755c

Commits on Jun 19, 2024

• Update setup.py

  wardo5

  authored
  0c82e64

Commits on Jun 20, 2024

• Fix numpy version and Inf deprecation

  j-c-gibson

  committed
  f582b04

• Merge remote-tracking branch 'origin/feature/c99-enabled' into feature/prep-doc

  j-c-gibson

  committed
  5c7ad82

• Numpy >=2.0 requires python >=3.9. Also add 3.12 to tests.

  j-c-gibson

  committed
  2ec2dc3

Commits on Jun 21, 2024

• Remove DeterministicOde class from common models

  j-c-gibson

  committed
  7c6d233

• More doc tweaks

  j-c-gibson

  committed
  9d02f2d

• Other file to get rid of DeterministicOde from common models

  j-c-gibson

  committed
  abd4c12

• Define function to avoid DRY violation

  j-c-gibson

  committed
  b97d589

Commits on Jun 26, 2024

• Add a try-except for newer versions of scipy that have renamed the simps function

  twomagpi

  committed
  2f05282

Commits on Jul 8, 2024

• draft time dependent params section

  j-c-gibson

  committed
  7df31b0

Commits on Jul 12, 2024

• Fix some minor warnings in doc building

  twomagpi

  committed
  d0c8045

• Updates to the documentation.

  twomagpi

  committed
  100434d

Commits on Jul 19, 2024

• Test tau leap step size algorithm

  j-c-gibson

  committed
  f4623c1

Commits on Jul 30, 2024

• Fix bug in tau leap algorithm

  j-c-gibson

  committed
  b4d3a67

• Polish common models doc section and some underlying code too

  j-c-gibson

  committed
  4780f58

Commits on Jul 31, 2024

• update tests to replect SIR common models changes

  j-c-gibson

  committed
  e4a8484

• separate unrolling and plotting functions

  j-c-gibson

  committed
  789b079

• more updated tests

  j-c-gibson

  committed
  fe8faf8

• documentation, mainly common model examples

  j-c-gibson

  committed
  6664cb8

• More docs stuff

  j-c-gibson

  committed
  41d4115

• Manually add Tom's simps fix

  j-c-gibson

  committed
  7c1b874

• Module affected by splitting of unrolling module

  j-c-gibson

  committed
  180e02b

• fix docstring

  j-c-gibson

  committed
  20f6e5c

• Edit existing and add new common models

  j-c-gibson

  committed
  24770da

• numpy >2 was causing error, see if this remedies it

  j-c-gibson

  committed
  1efd8a9

• Set numpy back >=2.0.0

  j-c-gibson

  committed
  d061328

• get_A should return A if it already exists

  j-c-gibson

  committed
  4d8a78e

• unroll now working again

  j-c-gibson

  committed
  aeb32d2

Commits on Aug 1, 2024

• update README

  j-c-gibson

  committed
  7670e22

• setup.py might be deprecated for python 3.12

  j-c-gibson

  authored
  29fb091

• Merge branch 'feature/prep-doc' of https://github.com/ukhsa-collaboration/pygom into feature/prep-doc

  j-c-gibson

  committed
  31ae4a4

• Merging doc update branch

  twomagpi

  committed
  e5821b4

• one term missing in equations

  j-c-gibson

  committed
  e70df4f

Commits on Aug 2, 2024

• Remove requirements needed only for documentation from the main requirements file.

  twomagpi

  committed
  53e7eb1

• Update the bib file to remove duplicate publisher.

  twomagpi

  committed
  51112c6

• and one last error in the ABC notebook

  j-c-gibson

  committed
  d44b9d1

• Adjust the readme to show how to install the requirements via conda.

  twomagpi

  committed
  8eeb9b3

• Merge branch 'feature/prep-doc' of github.com:ukhsa-collaboration/pygom into feature/prep-doc

  twomagpi

  committed
  e6b861f

• First test of actions building wheels.

  twomagpi

  committed
  2bc23ca

• Add the requirements to the build environment.

  twomagpi

  committed
  f5f8525

• Without MacOS, can't test locally.

  twomagpi

  committed
  909d9d3

• Make the wheel building match the testing.

  twomagpi

  committed
  74658e4

• Restructure to use a pyproject.toml file.

  twomagpi

  committed
  f6bd33a

• Additional tidying and ensuring git is used for versions again.

  twomagpi

  committed
  550e5a2

• Missing a comma

  twomagpi

  committed
  58e7dc1

• Change the command to run the test suite.

  twomagpi

  committed
  ec55fa5

• Make sure we have PyGOM installed.

  twomagpi

  committed
  5992ea5

• Fix the YML file

  twomagpi

  committed
  dc76233

• Set the anylinux base and only build wheels for 3.9 up

  twomagpi

  committed
  e12fd25

• Restrict the python versions the wheels are built for.

  twomagpi

  committed
  8076f9f

• Remove the version file option.

  twomagpi

  committed
  add68c3

• Can we get away with a lower version of numpy (so we can build anylinux wheels)?

  twomagpi

  committed
  9d3accc

• Can we get away with a lower version of scipy (so we can build anylinux wheels)?

  twomagpi

  committed
  77e7c0c

• Windows only wheels?

  twomagpi

  committed
  9043981

• Simplified CI, omitted wheel building.

  twomagpi

  committed
  b729579

Commits on Aug 3, 2024

• Retry manylinux wheel building

  twomagpi

  committed
  bb39b98

• Use openblas?

  twomagpi

  committed
  8e84a67

• Do we need the runtimes too?

  twomagpi

  committed
  f85908d

• Try to only build amd64 wheels on Windows?

  twomagpi

  committed
  53d6ed7

• Be more specific about what versons on what OS

  twomagpi

  committed
  ad99e3d

• Try a differnt way to provide blas

  

  Thomas Finnie

  committed
  2608179

• Wilth better escaping

  

  Thomas Finnie

  committed
  8474c33

• Actually specify the blas version.

  

  Thomas Finnie

  committed
  f88369f

• Now install our own BLAS

  

  Thomas Finnie

  committed
  ab78470

• Does it work with a pip install?

  

  Thomas Finnie

  committed
  2670b05

• make pip perfer a binary

  

  Thomas Finnie

  committed
  76d62df

• Is this because we have too high a scipy version specified?

  

  Thomas Finnie

  committed
  f1995c4

• Need to specify in the build section too.

  

  Thomas Finnie

  committed
  f53b48a

• Revert to pkgconfig

  

  Thomas Finnie

  committed
  c59f5b0

• Set a version of scipy that manylinux wheels exist for.

  

  Thomas Finnie

  committed
  d9d12c6

• Can we get a scipy wheel inside the container?

  

  Thomas Finnie

  committed
  a5a1619

• Do we only get one line?

  

  Thomas Finnie

  committed
  49ed763

• With pip only

  

  Thomas Finnie

  committed
  dc8c20c

• Return to suppling our own Blas

  

  Thomas Finnie

  committed
  f57b052

• Ensure the python versions targetted in the CI translate to CIBW

  

  Thomas Finnie

  committed
  64af40e

• Correct the CI variables

  

  Thomas Finnie

  committed
  21fa9ac

• Drop wheel building for Python 3.9 on Linux

  

  Thomas Finnie

  committed
  74c9ff0

• Fix the python versions for windows wheels

  

  Thomas Finnie

  committed
  a58a8ed

• A bit of testing for the wheels

  

  Thomas Finnie

  committed
  1f3e6aa

• Fix the missing comma

  

  Thomas Finnie

  committed
  1ab70b2

• Tidy the CI and pyproject scripts

  

  Thomas Finnie

  committed
  003c6db

• Tidy the CI more and add src distributions & pypi

  

  Thomas Finnie

  committed
  7954fd4

• Unbreak the pyproject file

  

  Thomas Finnie

  committed
  00519ff

• Attempt to fix version numbering.

  twomagpi

  committed
  e5e2d7c

• Change the git repo fetch depth to fix version number in CI.

  

  Thomas Finnie

  committed
  20a20f4

• Fix the YML syntax

  

  Thomas Finnie

  committed
  109fa9c

• In both places

  

  Thomas Finnie

  committed
  dd2ccf4

• Don't forget the "with:" in the syntax!

  

  Thomas Finnie

  committed
  de46605

• Include tags in the fetch.

  

  Thomas Finnie

  committed
  1c69dc6

Commits on Aug 5, 2024

• Merge branch 'dev' into feature/prep-doc

  twomagpi

  authored
  20a2b10

• Merge pull request #111 from ukhsa-collaboration/feature/prep-doc

  Show description for d8c52bf
  twomagpi

  authored
  d8c52bf

• Fix the horrible default PR template to make it fit the repo better.

  

  Thomas Finnie

  committed
  81c164f

• Update the doc building action

  

  Thomas Finnie

  committed
  a70fca0

• Update the book buiding to separate dev and master

  

  Thomas Finnie

  committed
  3089346

• Merge pull request #112 from ukhsa-collaboration/feature/build_wheels

  Show description for 5f4592d
  j-c-gibson

  authored
  5f4592d

• The version of Python needs to be a string to separate 3.1 from 3.10.

  

  Thomas Finnie

  committed
  e200345

• Update so that dev branch pushes end up with an upload to pypi testing

  

  Thomas Finnie

  committed
  9db03c7

• Merge pull request #113 from ukhsa-collaboration/feature/build_wheels

  Show description for 721f940
  j-c-gibson

  authored
  721f940

• Merge branch 'master' of github.com:ukhsa-collaboration/pygom into dev

  

  Thomas Finnie

  committed
  92b5f59

• Update readme for new release.

  

  Thomas Finnie

  committed
  3d5a7f6

• Fix versioning for dev commits to test.pypi.org

  

  Thomas Finnie

  committed
  d7148d5

• Fix metadata

  

  Thomas Finnie

  committed
  d19a68c

• The update needs to happen _inside_ the manylinux build container.

  

  Thomas Finnie

  committed
  d54499b

• Disable of local version also needs to hapen for source distro

  

  Thomas Finnie

  committed
  ad2727e

• Newlines do not work within the CIBW env varible

  

  Thomas Finnie

  committed
  7697464

• Account for the different behaviour of echo on Windows and Linux

  

  Thomas Finnie

  committed
  3995597