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Initial release #46

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merged 266 commits into from
Nov 20, 2023
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bf861d1
Add black formatting
BradyPlanden Aug 1, 2023
0fda9f5
Remove duplicate class, typo
BradyPlanden Aug 1, 2023
2bfa33b
Syntax & bug fixes, Updt. optimiser & parameterisation classes
BradyPlanden Aug 1, 2023
d0ac5a4
Initial RMSE optimisation complete, bugfixes, example usage
BradyPlanden Aug 2, 2023
4d12c83
Merge branch 'develop' into Initial_API
BradyPlanden Aug 3, 2023
37c16be
Add PEM holder method, Update example, clean out of date files
BradyPlanden Aug 3, 2023
a8f92d1
Merge pull request #17 from pybop-team/Initial_API
BradyPlanden Aug 3, 2023
282874f
Update LICENSE to BSD 3
BradyPlanden Aug 4, 2023
69c0588
Merge pull request #19 from pybop-team/License
BradyPlanden Aug 4, 2023
5955c94
Progress: Updt. model build structure for parameterisation groups
BradyPlanden Aug 4, 2023
fb082fc
Progress: Add parameter_sets class with model class inclusion
BradyPlanden Aug 5, 2023
d332a3f
Updt. parameterisation for model_build
BradyPlanden Aug 9, 2023
52362fd
Updt parameterisation cls w/ build_model(), set_init_soc(), set_params()
BradyPlanden Aug 9, 2023
57d3025
Non-geometric parameterisation fitting complete, rm simulation class …
BradyPlanden Aug 10, 2023
5df3696
Add optim step method w/ lambda, Add initial test framework w/ nox + …
BradyPlanden Aug 16, 2023
66d5856
Fix test_on_push for nox
BradyPlanden Aug 16, 2023
c0001e5
Updt numpy version requirement, add fail-fast false condition
BradyPlanden Aug 16, 2023
38bddb0
Updt dependancy requirements for python 3.8 support
BradyPlanden Aug 16, 2023
1fb9fac
Updt README w/ build status
BradyPlanden Aug 16, 2023
cc10421
Test icon syntax fix
BradyPlanden Aug 16, 2023
6b7ab48
Updt. x0 to be sampled from priors, Progress: API to list formation
BradyPlanden Aug 17, 2023
d50702e
API change to observation & params definition to type::list
BradyPlanden Aug 17, 2023
ee7fe83
refactor API change for observ. & param class type::list, tests updat…
BradyPlanden Aug 18, 2023
d8b8077
Refactor parameterisation & spm class, Add BaseModel class
BradyPlanden Aug 18, 2023
e3f49c5
Refactor #2 of parameterisation & spm class, Aligned init. parameter …
BradyPlanden Aug 18, 2023
d21249b
Data generation in test methods, debug parameter initilisation proble…
BradyPlanden Aug 18, 2023
4735367
Updt. to default parameter set for a stable & working state
BradyPlanden Aug 18, 2023
3b77733
Merge pull request #20 from pybop-team/test_framework_model_methods
BradyPlanden Aug 18, 2023
9d7181b
Add issue templates
BradyPlanden Aug 19, 2023
d3a4ee6
Merge pull request #22 from pybop-team/issue-templates
BradyPlanden Aug 19, 2023
01ea80e
Syntax fix for issue templates (#23)
BradyPlanden Aug 19, 2023
08e5bce
Updt. README.md w/ allcontributors, Updt. setup.py
BradyPlanden Aug 24, 2023
3950511
Fix links
BradyPlanden Aug 24, 2023
8b08694
Updt. logo size
BradyPlanden Aug 24, 2023
13090a3
Logo crop
BradyPlanden Aug 24, 2023
da9e425
Remove duplicates
BradyPlanden Aug 24, 2023
de800cd
Updt heading structure
BradyPlanden Aug 24, 2023
01ef49d
Upd. commit badge link
BradyPlanden Aug 24, 2023
664d6f3
Remove HMC example
BradyPlanden Aug 24, 2023
9b6e009
Merge pull request #26 from pybop-team/repo-admin
BradyPlanden Aug 24, 2023
ae61f09
docs: update README.md [skip ci]
allcontributors[bot] Aug 24, 2023
8071ed6
docs: create .all-contributorsrc [skip ci]
allcontributors[bot] Aug 24, 2023
60bfe64
Merge pull request #27 from pybop-team/all-contributors/add-BradyPlanden
BradyPlanden Aug 24, 2023
e111c94
Move all-contributors badge
BradyPlanden Aug 24, 2023
3267403
Updt. README example + grammar
BradyPlanden Sep 8, 2023
1dbd91c
Add init py files
NicolaCourtier Sep 10, 2023
1f4a219
Merge pull request #29 from pybop-team/28-bug-module-not-found
BradyPlanden Sep 12, 2023
936e6a5
docs: update README.md [skip ci]
allcontributors[bot] Sep 12, 2023
9de2ac8
docs: update .all-contributorsrc [skip ci]
allcontributors[bot] Sep 12, 2023
055966c
Merge pull request #31 from pybop-team/all-contributors/add-NicolaCou…
BradyPlanden Sep 12, 2023
aedd14a
docs: update README.md [skip ci]
allcontributors[bot] Sep 12, 2023
a38c67b
docs: update .all-contributorsrc [skip ci]
allcontributors[bot] Sep 12, 2023
72cfb10
Merge pull request #32 from pybop-team/all-contributors/add-davidhowey
BradyPlanden Sep 12, 2023
fd6d52f
docs: update README.md [skip ci]
allcontributors[bot] Sep 12, 2023
6074e97
docs: update .all-contributorsrc [skip ci]
allcontributors[bot] Sep 12, 2023
7b4117f
Merge pull request #34 from pybop-team/all-contributors/add-martinjro…
BradyPlanden Sep 12, 2023
01956aa
__init__.py bugfix for #28
BradyPlanden Sep 13, 2023
0530d11
Add links to PyBaMM
NicolaCourtier Sep 14, 2023
6d20181
Alignment for #28, fix build error
BradyPlanden Sep 14, 2023
0d89b26
Merge pull request #35 from pybop-team/develop
NicolaCourtier Sep 14, 2023
5345a62
Adding CONTRIBUTING.md
BradyPlanden Sep 14, 2023
01f3297
Add codecov to workflow, update noxfile with coverage session
BradyPlanden Sep 14, 2023
b8cef8e
Update installation guide
NicolaCourtier Sep 14, 2023
81b97b9
yaml bugfix
BradyPlanden Sep 15, 2023
609677b
Add cov-report flag
BradyPlanden Sep 15, 2023
b2c5437
Split Nox sessions
BradyPlanden Sep 15, 2023
3c1d3d3
Add codecov badge
BradyPlanden Sep 15, 2023
cf5c50d
bugfix badge
BradyPlanden Sep 15, 2023
58fd600
Update & relax assertations
BradyPlanden Sep 15, 2023
e11781b
Add PR trigger
BradyPlanden Sep 15, 2023
2cdc7e7
Add concurrency cancel trigger
BradyPlanden Sep 15, 2023
1528651
Syntax for concurrency trigger
BradyPlanden Sep 15, 2023
a0cc83c
Grammar, codecov
BradyPlanden Sep 15, 2023
8be3fcd
Merge pull request #37 from pybop-team/30-update-installation
NicolaCourtier Sep 15, 2023
b4b936e
Merge pull request #41 from pybop-team/contributing
BradyPlanden Sep 15, 2023
9e6c5cf
Loosen assertion and shift unit_test bounds
BradyPlanden Sep 15, 2023
62bb422
Merge pull request #40 from pybop-team/codecov
BradyPlanden Sep 15, 2023
38e8339
Update Architecture diagram (#43)
NicolaCourtier Sep 18, 2023
f730427
Add release workflow for pypi + testpypi
BradyPlanden Sep 21, 2023
0086943
Add TestPyPI project hyperlink
BradyPlanden Sep 22, 2023
66507e9
Modify TestPyPI for 'rc' tag dependancy
BradyPlanden Sep 22, 2023
87a28cf
Merge pull request #45 from pybop-team/release-actions
BradyPlanden Sep 22, 2023
1009ee7
Updt readme logo link for PyPI, Add estimation notebook, black format
BradyPlanden Sep 22, 2023
48c44ce
release-action.yaml trigger fix for TestPyPI
BradyPlanden Sep 22, 2023
ed53975
Merge branch 'develop' into readme
BradyPlanden Sep 22, 2023
bc504ea
Merge pull request #48 from pybop-team/readme
BradyPlanden Sep 22, 2023
794d2e8
Updt. contributors section, architecture hyperlink
BradyPlanden Sep 24, 2023
13d41b2
Add version.py functionality
BradyPlanden Sep 25, 2023
e45ae11
python version requries
BradyPlanden Sep 25, 2023
dbcb838
revert python version change
BradyPlanden Sep 25, 2023
2d7ccd6
Merge pull request #49 from pybop-team/readme
BradyPlanden Sep 25, 2023
4d5cd3c
Transfer pybamm model construction methods to BaseModel, Add pybamm S…
BradyPlanden Sep 25, 2023
1e79b47
Add sim method, bugfix data reference in example
BradyPlanden Sep 26, 2023
49b39f1
Add entry logic for sim method, Add SPMe parameterisation testcase
BradyPlanden Sep 26, 2023
bab4b37
Tidy __init__, Updt. model directory names, Updt. BaseModel sim error…
BradyPlanden Sep 26, 2023
6646078
Bump version for initial release
BradyPlanden Oct 2, 2023
99c0095
Updt contributing.md for recommendation on source citation
BradyPlanden Oct 3, 2023
37f512b
Add identified parameters
BradyPlanden Oct 4, 2023
ffc4017
Merge branch 'model-structure' into mle-map
BradyPlanden Oct 6, 2023
a5c8f47
Updt. object tree & directory, Add pints forwardmodel methods
BradyPlanden Oct 6, 2023
9497ff8
Rename model file to base_echem
NicolaCourtier Oct 10, 2023
a05be18
Merge pull request #51 from pybop-team/model-structure
BradyPlanden Oct 10, 2023
653a88d
Initial Pints MLE, Updates to BaseModel for Pints, build()
BradyPlanden Oct 11, 2023
05ec2ce
Merge branch 'develop' into mle-map
BradyPlanden Oct 11, 2023
65ec80d
Update workflow for rename of nox unit session
BradyPlanden Oct 11, 2023
6973479
Merge branch 'mle-map' of https://github.com/pybop-team/PyBOP into ml…
BradyPlanden Oct 11, 2023
e285c42
Remove initial MLE.py, Add black format
BradyPlanden Oct 11, 2023
396a83f
Split Simulate(), Prediction(), Add initial Pints integration
BradyPlanden Oct 13, 2023
22c24cc
Fix tests, black format, update mle example
BradyPlanden Oct 13, 2023
b9751fa
Add pytest marker functionality, updt mle, doc-strings for BaseModel
BradyPlanden Oct 13, 2023
feec21d
Fix coverage session, add tests, Updt model.simulate() args
BradyPlanden Oct 13, 2023
fbe6b4c
ruff & black
BradyPlanden Oct 13, 2023
b66b807
First Repository Clean + Initial model alignment with Pints (#53)
BradyPlanden Oct 13, 2023
f5378c9
docs: update README.md [skip ci]
allcontributors[bot] Oct 13, 2023
468de32
docs: update .all-contributorsrc [skip ci]
allcontributors[bot] Oct 13, 2023
30b72b1
Merge pull request #56 from pybop-team/all-contributors/add-NicolaCou…
BradyPlanden Oct 13, 2023
ce56923
Add prior and parameter_set tests, remove redundant catch in paramete…
BradyPlanden Oct 13, 2023
dccda15
Merge branch 'develop' into pints-integration
BradyPlanden Oct 13, 2023
5168e06
Add periodic tests w/ self-hosted, Updt. dependency install, Updt. wo…
BradyPlanden Oct 23, 2023
393067f
Modify trigger to register workflow
BradyPlanden Oct 23, 2023
c0650e2
Updt trigger, remove style requirement, align nox call
BradyPlanden Oct 23, 2023
bd3b1a3
Add wheel dependency
BradyPlanden Oct 23, 2023
d10804c
Add setuptools dependency
BradyPlanden Oct 23, 2023
60d9a9e
Remove python matrix, 3.10 support only
BradyPlanden Oct 23, 2023
d240399
Updt testing badge for scheduled workflow
BradyPlanden Oct 23, 2023
29eaf3c
Merge pull request #57 from pybop-team/pints-integration
BradyPlanden Oct 24, 2023
e085a7f
Add pre-commit config and run on repo
BradyPlanden Oct 24, 2023
0f11fb4
Add pre-commit format check
BradyPlanden Oct 25, 2023
5fd104f
Add pre-commit to CONTRIBUTING
BradyPlanden Oct 25, 2023
00403cb
hotfix for model.simulate()
BradyPlanden Oct 25, 2023
3251332
Run example scripts as tests (#65)
NicolaCourtier Oct 25, 2023
019718b
Folder restructure into components of optimisation
NicolaCourtier Oct 25, 2023
25d2f65
Rename optimisation/optimiser objects
NicolaCourtier Oct 25, 2023
7fb11a4
Merge pull request #66 from pybop-team/54-p2-folder-suggestions
BradyPlanden Oct 26, 2023
a6f1a19
Add options to echem_classes, Updt example to show submodel usage
BradyPlanden Oct 26, 2023
dd58d24
black format
BradyPlanden Oct 26, 2023
486e2fc
Add boundary constraints on the prior sampling, bugfix for test asser…
BradyPlanden Oct 26, 2023
ab4ab1d
Add tests for optimisation class, prior bound sampling
BradyPlanden Oct 26, 2023
426baf8
Fix model parameterisation, parameterize tests & add test for incorre…
BradyPlanden Oct 26, 2023
344e85f
Remove commented blacken repo, black format
BradyPlanden Oct 26, 2023
b19f280
Merge pull request #62 from pybop-team/47-add-self-hosted-runner
BradyPlanden Oct 26, 2023
87a619e
Merge branch 'develop' into 58-pre-commit
BradyPlanden Oct 26, 2023
4655f33
Merge pull request #64 from pybop-team/58-pre-commit
BradyPlanden Oct 26, 2023
f5e912c
Merge branch 'develop' into 24-bug-non-default-parameter-sets-arent-i…
BradyPlanden Oct 26, 2023
3b1571e
Add gradient support to BaseModel class, Add Pints gradient descent e…
BradyPlanden Oct 27, 2023
4e06bcc
revert mle parameterisation
BradyPlanden Oct 27, 2023
c840467
Bugfix for BaseModel, reduce grad_descent runtime
BradyPlanden Oct 27, 2023
4df2404
Updt senstitivity inferface in simulateS1(), aligned parameterisation…
BradyPlanden Oct 30, 2023
0dfad2f
ruff fixes, black formatting
BradyPlanden Oct 30, 2023
ad31282
Add citation.cff
BradyPlanden Oct 31, 2023
4465aee
Remove sample DOI
BradyPlanden Oct 31, 2023
2d25ef9
Merge pull request #75 from pybop-team/74-add-citationcff
BradyPlanden Oct 31, 2023
c23be13
Updt. Title
BradyPlanden Oct 31, 2023
d03c21a
refactor for readability
BradyPlanden Oct 31, 2023
6fe2dca
Consistent filenames
NicolaCourtier Oct 31, 2023
80e136b
Consistent formatting
NicolaCourtier Oct 31, 2023
d271733
Update gitattributes and gitignore
NicolaCourtier Oct 31, 2023
0f91bab
Squashed merge of #54
BradyPlanden Oct 31, 2023
a6e59b0
Squashed commit of #54 - optimisation.py changes & dependancies
BradyPlanden Oct 31, 2023
fe5446c
Separate cost and optimiser from optimisation
NicolaCourtier Nov 1, 2023
e4e161d
Squashed commit of #54 - Add Optimisers
BradyPlanden Nov 1, 2023
cee6664
Rename fit_parameters to parameters
NicolaCourtier Nov 1, 2023
6ca9bfb
Separate PyBaMM from BaseModel
NicolaCourtier Nov 1, 2023
05a45d5
Rename opt to optim
NicolaCourtier Nov 1, 2023
79b1907
Updt nlopt initialisation args, Updt default pints method
BradyPlanden Nov 1, 2023
34ffca4
Update parameters
NicolaCourtier Nov 1, 2023
6e67e5e
Add problem class, Add modularity to output of model.simulateS1()
BradyPlanden Nov 1, 2023
d5ae728
Merge remote-tracking branch 'origin/develop-into-54' into 72-add-pin…
BradyPlanden Nov 2, 2023
3b65b02
Add tests for problem class, SciPyMinimize, reduce example/ runtimes,…
BradyPlanden Nov 2, 2023
4d84cb3
Add tests for costs, improve priors and problem tests
BradyPlanden Nov 2, 2023
b7dca7e
Add additional cost function tests
BradyPlanden Nov 2, 2023
e98d840
+ black format
BradyPlanden Nov 2, 2023
fd11fca
Update tests
BradyPlanden Nov 2, 2023
326666a
Updt default SciPyMinimize Method, Reduce assert on prior tests
BradyPlanden Nov 2, 2023
d595cb0
Change rtol assert to atol
BradyPlanden Nov 2, 2023
3a58bcd
Updt costs exception catches and tests
BradyPlanden Nov 2, 2023
39dcaeb
standardise case in __init__, Updt. optimisation parameter dict forma…
BradyPlanden Nov 3, 2023
e77c5a2
Merge pull request #80 from pybop-team/72-54-restructure-and-add-pint…
BradyPlanden Nov 3, 2023
f104e62
Merge remote-tracking branch 'origin/develop' into 67-bug-pybamm-subm…
BradyPlanden Nov 3, 2023
346931f
Merge pull request #68 from pybop-team/67-bug-pybamm-submodels-arent-…
BradyPlanden Nov 3, 2023
1aa77bd
Merge origin/develop, updt. bound limiting to parameter class
BradyPlanden Nov 3, 2023
f672d6e
restore rmse_estimation script parameter bounds
BradyPlanden Nov 3, 2023
fbde169
Updt num_samples and bounds for test_optimisation
BradyPlanden Nov 3, 2023
490b86a
Merge pull request #70 from pybop-team/69-bug-prior-sampling-outside-…
BradyPlanden Nov 3, 2023
a6d00e8
Merge origin/develop, Updt. pytest parameterisations for test_paramet…
BradyPlanden Nov 3, 2023
2637230
Merge pull request #71 from pybop-team/24-bug-non-default-parameter-s…
BradyPlanden Nov 3, 2023
8c66077
Add ruff format, jupyter notebook support, fix exception in base_para…
BradyPlanden Nov 3, 2023
8dc572e
Merge pull request #84 from pybop-team/83-ruff-format-to-pre-commit
BradyPlanden Nov 6, 2023
df79b9a
Split optimisation class, Updt cost classes, Updt problem class for a…
BradyPlanden Nov 6, 2023
d7baa5d
chore: update pre-commit hooks
pre-commit-ci[bot] Nov 6, 2023
ff0f323
Merge pull request #85 from pybop-team/pre-commit-ci-update-config
BradyPlanden Nov 6, 2023
76ba992
Additions for init. pints implementation, rework cost function implem…
BradyPlanden Nov 7, 2023
bb79dda
Pints controller options, example Updts, current function input bugfix
BradyPlanden Nov 7, 2023
99457db
Updt readme + contributing
BradyPlanden Nov 7, 2023
433940f
Updt. optimisation class, signal defintion in problem class, examples…
BradyPlanden Nov 8, 2023
cccdca3
Updt. Fig1 size, new example
BradyPlanden Nov 8, 2023
225964b
Pints integration structure change, Inherit pints.optimisers, merging…
BradyPlanden Nov 8, 2023
17ccfbe
Add Pints requirements to optimiser & optimisation class
BradyPlanden Nov 9, 2023
f063786
Move example code
NicolaCourtier Nov 9, 2023
cc2fc86
Finialise optimisation class for multi-backend, Add CMAES optimiser, …
BradyPlanden Nov 9, 2023
2f1abcd
Update text
NicolaCourtier Nov 9, 2023
bf350ee
Rename SPM_example to spm_example
NicolaCourtier Nov 9, 2023
edf4b15
Fix braces
NicolaCourtier Nov 9, 2023
f41d426
Switch show to draw so scripts run to the end
NicolaCourtier Nov 9, 2023
a3b3149
Fix bugs and small changes added during development
BradyPlanden Nov 9, 2023
0edf919
chore: update pre-commit hooks
pre-commit-ci[bot] Nov 13, 2023
45d1254
Merge pull request #94 from pybop-team/pre-commit-ci-update-config
BradyPlanden Nov 14, 2023
cc6ba0f
Udt. Cost base class, add optimisation evolution log, updt. parameter…
BradyPlanden Nov 15, 2023
077dad7
style: pre-commit fixes
pre-commit-ci[bot] Nov 15, 2023
1e1f911
Updt tests, iters limit on examples, refact optimiser construction, r…
BradyPlanden Nov 15, 2023
53f6c72
style: pre-commit fixes
pre-commit-ci[bot] Nov 15, 2023
8f7f4fa
Add tests, remove redundant method from optimisation, add try-except …
BradyPlanden Nov 16, 2023
3c556cf
Merge branch '72-add-pints-optimisation-methods' of https://github.co…
BradyPlanden Nov 16, 2023
11d5e60
Update notebook for API changes
BradyPlanden Nov 16, 2023
881ab84
Add BaseModel tests
BradyPlanden Nov 16, 2023
bfde78a
style: pre-commit fixes
pre-commit-ci[bot] Nov 16, 2023
1119914
Add Optimisation.max_evalutions(), Add halting tests for Optimisation
BradyPlanden Nov 16, 2023
2c7e744
Merge pull request #88 from pybop-team/72-add-pints-optimisation-methods
BradyPlanden Nov 16, 2023
f3ab37f
Merge branch 'develop' into 86-bug-update-readmemd
BradyPlanden Nov 16, 2023
62ce466
Merge pull request #97 from pybop-team/develop
NicolaCourtier Nov 16, 2023
2d52079
Update rmse-estimisation.ipynb
NicolaCourtier Nov 17, 2023
7047af7
Turn off f_guessed for performance assertion
BradyPlanden Nov 17, 2023
8846725
tighten parameter bounds
BradyPlanden Nov 17, 2023
4604f11
Updt. notebook name
BradyPlanden Nov 17, 2023
7bc92d9
Split-model, add solved state
BradyPlanden Nov 17, 2023
8002a27
Merge pull request #96 from pybop-team/87-add-workflow-for-daily-test…
BradyPlanden Nov 17, 2023
f159296
Update pytest flags and usage
BradyPlanden Nov 17, 2023
283ccd0
Updt example name, links in readme, and phrasing
BradyPlanden Nov 17, 2023
1906f8d
Add colab badge
BradyPlanden Nov 17, 2023
9529456
Add jupyter notebook nox session and scheduled tests
BradyPlanden Nov 17, 2023
e0cdb75
Add checks on early termination of simulation
NicolaCourtier Nov 17, 2023
16b2fbf
Revert "Add checks on early termination of simulation"
NicolaCourtier Nov 17, 2023
790bb47
Return Infinity if simulation terminates early (#99)
NicolaCourtier Nov 17, 2023
15076ff
Merge branch 'develop' into 102-bug-github-pybopcmaes-tests-are-faili…
BradyPlanden Nov 17, 2023
3523f20
Updt max iterations for convergance, rename test method
BradyPlanden Nov 17, 2023
f67c810
Pass x0, bounds and n_parameters into Cost (#101)
NicolaCourtier Nov 17, 2023
4dc8a3d
Update CONTRIBUTING.md
NicolaCourtier Nov 17, 2023
500fc68
Update README.md
NicolaCourtier Nov 17, 2023
c8bd36c
Merge pull request #95 from pybop-team/86-bug-update-readmemd
BradyPlanden Nov 17, 2023
0c7d566
Merge branch 'develop' into 102-bug-github-pybopcmaes-tests-are-faili…
BradyPlanden Nov 20, 2023
d2b1d17
Updt CMAES with pints.RectangularBoundaries
BradyPlanden Nov 20, 2023
ec2f863
Refactor x0 sampling w/o bound clashes, reduce test_parameterisation …
BradyPlanden Nov 20, 2023
c82b85b
Updt. tests, grad descent boundaries
BradyPlanden Nov 20, 2023
854e1ec
Remove PintsBoundaries class as not required
BradyPlanden Nov 20, 2023
a66be81
Restore simple f_guessed test
BradyPlanden Nov 20, 2023
3437b95
Bounds message for GradDescent, Add hyperparameter for parameter boun…
BradyPlanden Nov 20, 2023
355bbda
Merge pull request #105 from pybop-team/102-bug-github-pybopcmaes-tes…
BradyPlanden Nov 20, 2023
dc6c6de
Merge branch 'develop' into 87-add-workflow-for-daily-testing-of-jupy…
BradyPlanden Nov 20, 2023
652de22
Merge pull request #103 from pybop-team/87-add-workflow-for-daily-tes…
BradyPlanden Nov 20, 2023
dd88872
bump to v23.11
BradyPlanden Nov 20, 2023
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58 changes: 58 additions & 0 deletions .all-contributorsrc
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{
"files": [
"README.md"
],
"imageSize": 100,
"commit": false,
"commitType": "docs",
"commitConvention": "angular",
"contributors": [
{
"login": "BradyPlanden",
"name": "Brady Planden",
"avatar_url": "https://avatars.githubusercontent.com/u/55357039?v=4",
"profile": "http://bradyplanden.github.io",
"contributions": [
"infra",
"test",
"code",
"example"
]
},
{
"login": "NicolaCourtier",
"name": "NicolaCourtier",
"avatar_url": "https://avatars.githubusercontent.com/u/45851982?v=4",
"profile": "https://github.com/NicolaCourtier",
"contributions": [
"code"
]
},
{
"login": "davidhowey",
"name": "David Howey",
"avatar_url": "https://avatars.githubusercontent.com/u/2247552?v=4",
"profile": "http://howey.eng.ox.ac.uk",
"contributions": [
"ideas",
"mentoring"
]
},
{
"login": "martinjrobins",
"name": "Martin Robinson",
"avatar_url": "https://avatars.githubusercontent.com/u/1148404?v=4",
"profile": "http://www.rse.ox.ac.uk",
"contributions": [
"ideas",
"mentoring"
]
}
],
"contributorsPerLine": 7,
"skipCi": true,
"repoType": "github",
"repoHost": "https://github.com",
"projectName": "PyBOP",
"projectOwner": "pybop-team"
}
37 changes: 37 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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name: Bug Report
description: Create a bug report
title: "[Bug]: "
labels: ["bug"]
body:
- type: markdown
attributes:
value: |
Thanks for filling out this report to help us improve!
- type: input
id: python-version
attributes:
label: Python Version
description: What python version are you using?
placeholder: python version
validations:
required: true
- type: textarea
id: bug-description
attributes:
label: Describe the bug
description: A clear and concise description of the bug.
validations:
required: true
- type: textarea
id: reproduce
attributes:
label: Steps to reproduce the behaviour
description: Tell us how to reproduce this behaviour. Please try to include a [Minimum Workable Example](https://stackoverflow.com/help/minimal-reproducible-example)
validations:
required: true
- type: textarea
id: logs
attributes:
label: Relevant log output
description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
render: shell
30 changes: 30 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.yml
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name: Feature request
description: Suggest a feature
labels: ["enhancement"]
body:
- type: markdown
attributes:
value: |
Thanks for filling out this report to help us improve!
- type: textarea
id: feature
attributes:
label: Feature description
description: Describe the feature you'd like.
validations:
required: true
- type: textarea
id: motivation
attributes:
label: Motivation
description: Please enter the motivation for this feature i.e (problem, performance, etc).
- type: textarea
id: possible-implementation
attributes:
label: Possible implementation
description: Please enter any possible implementation for this feature.
- type: textarea
id: context
attributes:
label: Additional context
description: Add any additional context about the feature request.
110 changes: 110 additions & 0 deletions .github/workflows/release-action.yaml
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name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI

on: push

jobs:
build:
name: Build distribution 📦
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.8"
- name: Install pypa/build
run: >-
python3 -m
pip install
build
--user
- name: Build a binary wheel and a source tarball
run: python3 -m build
- name: Store the distribution packages
uses: actions/upload-artifact@v3
with:
name: python-package-distributions
path: dist/

publish-to-pypi:
name: >-
Publish Python 🐍 distribution 📦 to PyPI
if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
needs:
- build
runs-on: ubuntu-latest
environment:
name: pypi
url: https://pypi.org/p/pybop
permissions:
id-token: write # IMPORTANT: mandatory for trusted publishing

steps:
- name: Download all the dists
uses: actions/download-artifact@v3
with:
name: python-package-distributions
path: dist/
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1

github-release:
name: >-
Sign the Python 🐍 distribution 📦 with Sigstore
and upload them to GitHub Release
needs:
- publish-to-pypi
runs-on: ubuntu-latest

permissions:
contents: write # IMPORTANT: mandatory for making GitHub Releases
id-token: write # IMPORTANT: mandatory for sigstore

steps:
- name: Download all the dists
uses: actions/download-artifact@v3
with:
name: python-package-distributions
path: dist/
- name: Sign the dists with Sigstore
uses: sigstore/gh-action-sigstore-python@v1.2.3
with:
inputs: >-
./dist/*.tar.gz
./dist/*.whl
- name: Upload artifact signatures to GitHub Release
env:
GITHUB_TOKEN: ${{ github.token }}
# Upload to GitHub Release using the `gh` CLI.
# `dist/` contains the built packages, and the
# sigstore-produced signatures and certificates.
run: >-
gh release upload
'${{ github.ref_name }}' dist/**
--repo '${{ github.repository }}'

publish-to-testpypi:
name: Publish Python 🐍 distribution 📦 to TestPyPI
if: contains(github.ref, 'rc') # only publish to TestPyPI for rc tags
needs:
- build
runs-on: ubuntu-latest

environment:
name: testpypi
url: https://test.pypi.org/project/pybop/

permissions:
id-token: write # IMPORTANT: mandatory for trusted publishing

steps:
- name: Download all the dists
uses: actions/download-artifact@v3
with:
name: python-package-distributions
path: dist/
- name: Publish distribution 📦 to TestPyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
repository-url: https://test.pypi.org/legacy/
69 changes: 69 additions & 0 deletions .github/workflows/test_on_push.yaml
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name: PyBOP

on:
push:
workflow_dispatch:
pull_request:

concurrency:
# github.workflow: name of the workflow, so that we don't cancel other workflows
# github.event.pull_request.number || github.ref: pull request number or branch name if not a pull request
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
# Cancel in-progress runs when a new workflow with the same group name is triggered
# This avoids workflow runs on both pushes and PRs
cancel-in-progress: true

jobs:
build:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]

steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade pip nox
pip install -e .
- name: Unit tests with nox
run: |
nox -s unit_test

# Runs only on Ubuntu with Python 3.11
check_coverage:
runs-on: ubuntu-latest
strategy:
fail-fast: false
name: Coverage tests (ubuntu-latest / Python 3.11)

steps:
- name: Check out PyBOP repository
uses: actions/checkout@v4
- name: Set up Python 3.11
id: setup-python
uses: actions/setup-python@v4
with:
python-version: 3.11
cache: 'pip'
cache-dependency-path: setup.py

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade pip nox
pip install -e .

- name: Run unit tests for Ubuntu with Python 3.11 and generate coverage report
run: nox -s coverage

- name: Upload coverage report
uses: codecov/codecov-action@v3
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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