Fix missing AutoTapir #2242
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Fix missing AutoTapir #2242
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Pull Request Test Coverage Report for Build 9301554858Warning: This coverage report may be inaccurate.This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.
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yebai
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Jun 3, 2024
* Update README.md * Export adtype `AutoTapir` (#2236) * Export adtype `AutoTapir` * Update Project.toml * Fix missing AutoTapir (#2242) * Update Essential.jl * Update Project.toml * Drop support for ADTypes 0.2 (#2243) ADTypes 0.2 doesn't support AutoTapir yet. * Optimization improvements (#2221) * initial work on interface * Improving the Optimization.jl interface, work in progress * More work on Optimization.jl, still in progress * Add docstrings to Optimisation.jl * Fix OptimizationOptimJL version constraint * Clean up optimisation TODO notes * Relax OptimizationOptimJL version constraints * Simplify optimization imports * Remove commented out code * Small improvements all over in optimisation * Clean up of Optimisation tests * Add a test for OptimizationBBO * Add tests using OptimizationNLopt * Rename/move the optimisation test files The files for Optimisaton.jl and OptimInterface.jl were in the wrong folders: One in `test/optimisation` the other in `test/ext`, but the wrong way around. * Relax compat bounds on OptimizationBBO and OptimizationNLopt * Split a testset to test/optimisation/OptimisationCore.jl * Import AbstractADType from ADTypes, not SciMLBase * Fix Optimization.jl depwarning * Fix seeds in more tests * Merge OptimizationCore into Optimization * In optimisation, rename init_value to initial_params * Optimisation docstring improvements * Code style adjustments in optimisation * Qualify references in optimisation * Simplify creation of ModeResults * Qualified references in optimization tests * Enforce line length in optimization * Simplify optimisation exports * Enforce line legth in Optim.jl interface * Refactor away ModeEstimationProblem * Style and docstring improvements for optimisation * Add := test to optimisation tests. * Clarify comment * Simplify generate_initial_params * Fix doc references * Rename testsets * Refactor check_success * Make initial_params a kwarg * Remove unnecessary type constrain on kwarg * Fix broken reference in tests * Fix bug in generate_initial_params * Fix qualified references in optimisation tests * Add hasstats checks to optimisation tests * Extend OptimizationOptimJL compat to 0.3 Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com> * Change some `import`s to `using` Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> * Change <keyword arguments> to kwargs... in docstrings * Add a two-argument method to OptimLogDensity as callable --------- Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com> * Update Project.toml * CompatHelper: bump compat for OptimizationOptimJL to 0.3 for package test, (keep existing compat) (#2246) Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org> --------- Co-authored-by: Markus Hauru <markus@mhauru.org> Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
mhauru
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Jun 5, 2024
* Remove unused test util function * Refactoring ad and optiminterface tests to modules * Add SelectiveTests.jl * Rework tests CI GA * Switch test CI on Mac back to x64 * Remove coverage from CI. Improve matrix. * Wrap all tests in modules. * Remove unused test utils * Remove GA workflows for DynamicHMC and Numerical * Rename TuringCI GA to Tests * Fix test_args passing in CI * Fix for CI test matrix * Fixes to various test files * Add container.jl to test suite * Fix spacing around * in test includes * Split ad.jl and abstractmcmc.jl tests to separate CI jobs * Alphabetise imports in tests * In tests, use import X over using X: X * Add missing imports to abstractmcmc.jl tests * Add some missing imports to tests * Merge ad_utils.jl to ad.jl in tests * Merge testing_functions.jl into mh.jl in tests * Simplify test_utils Turn all of them into modules or merge them into other files that used to `include` them. * Add missing import to numerical_tests.jl * Update Project.toml (#2244) * Update README.md * Export adtype `AutoTapir` (#2236) * Export adtype `AutoTapir` * Update Project.toml * Fix missing AutoTapir (#2242) * Update Essential.jl * Update Project.toml * Drop support for ADTypes 0.2 (#2243) ADTypes 0.2 doesn't support AutoTapir yet. * Optimization improvements (#2221) * initial work on interface * Improving the Optimization.jl interface, work in progress * More work on Optimization.jl, still in progress * Add docstrings to Optimisation.jl * Fix OptimizationOptimJL version constraint * Clean up optimisation TODO notes * Relax OptimizationOptimJL version constraints * Simplify optimization imports * Remove commented out code * Small improvements all over in optimisation * Clean up of Optimisation tests * Add a test for OptimizationBBO * Add tests using OptimizationNLopt * Rename/move the optimisation test files The files for Optimisaton.jl and OptimInterface.jl were in the wrong folders: One in `test/optimisation` the other in `test/ext`, but the wrong way around. * Relax compat bounds on OptimizationBBO and OptimizationNLopt * Split a testset to test/optimisation/OptimisationCore.jl * Import AbstractADType from ADTypes, not SciMLBase * Fix Optimization.jl depwarning * Fix seeds in more tests * Merge OptimizationCore into Optimization * In optimisation, rename init_value to initial_params * Optimisation docstring improvements * Code style adjustments in optimisation * Qualify references in optimisation * Simplify creation of ModeResults * Qualified references in optimization tests * Enforce line length in optimization * Simplify optimisation exports * Enforce line legth in Optim.jl interface * Refactor away ModeEstimationProblem * Style and docstring improvements for optimisation * Add := test to optimisation tests. * Clarify comment * Simplify generate_initial_params * Fix doc references * Rename testsets * Refactor check_success * Make initial_params a kwarg * Remove unnecessary type constrain on kwarg * Fix broken reference in tests * Fix bug in generate_initial_params * Fix qualified references in optimisation tests * Add hasstats checks to optimisation tests * Extend OptimizationOptimJL compat to 0.3 Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com> * Change some `import`s to `using` Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> * Change <keyword arguments> to kwargs... in docstrings * Add a two-argument method to OptimLogDensity as callable --------- Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com> * Update Project.toml * CompatHelper: bump compat for OptimizationOptimJL to 0.3 for package test, (keep existing compat) (#2246) Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org> --------- Co-authored-by: Markus Hauru <markus@mhauru.org> Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org> * Set fail-fast: false for CI test matrix * Add a step to print matrix variables to tests Action * Fix typo in tests Action * ADTypes v0.2 compatibility for test restructuring (#2253) * Restore compat with ADTypes v0.2. Make AutoTapir export conditional. * Fix AutoTapir export in Essential.jl --------- Co-authored-by: Hong Ge <3279477+yebai@users.noreply.github.com> Co-authored-by: Tor Erlend Fjelde <tor.erlend95@gmail.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
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Follow up of #2236