Adds an exception for when foldx is not found #165
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miguelgondu
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* Allows mutations to be lowercase, and adds regression tests * Adds test to the foldx interface * Adds eager reparation when a FoldX black box is created (#85) * Adds eager reparation when a FoldX black box is created * Adds a flag for eager repairing, removes gcc from dependencies * Refactors examples, and cleans old ones (#87) * Implements dockstring as a black box function (#89) * Implements dockstring as a black box function * Adds tests for dockstring, fixes bug when converting to SELFIES * Adds citations for TDC and Dockstring * Adding continuous toy examples (#91) * Scaffolds the continuous problems * Lints the files defining the continuous objective functions * Updates requirements for setuptools * Adds a simple example of how to use the toy continuous problems * Adds toy examples, includes a slow fixture for pytest, adds it to the dev ini of tox * Adds a parametrized test for all possible toy continuous objectives * Renames the objective tests accordingly * The (first) great documentation PR (#95) * Adds documentation to most core files * Documents the rest of the core modules, starts documenting the objective repostories * Adds documentation for some objective functions * 96 add a gfp vae surrogate modeling task (#97) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main --------- * Implements a way to embed continuous problems in higher dimensions (#98) * Adds Styblinsky-Tang objective to continuous problems (#99) * cleaned up a bit, removed global variable * Updates the data by adding the relevant assets for gfp-cbas * Adds evaluation budgets and number-of-evaluations tracking (#102) * Adds an evaluation budget that can be strictly enforced * Adds 'optional' to the docs * Hotfix: evaluation in the aloha problem didn't work for batches * Builds automatic documentation of the API (#103) * Scaffolds automatic documentation of the API * Adds links to class implementations * Removes colons from attribute, raises, returns titles in docstrings * Fixes a colon in docstrings, to follow numpy standards * Adds documentation to the core module * Adds documentation to the objective factory module * Documents the objective script * Documents most functions inside the objective repository * Documents the remaining objective functions inside the repository * Adds several packages to the mock imports of autodoc * Removes the autogenerated rst files from git tracking * 96 add a gfp vae surrogate modeling task (#105) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main * added cbas module with assets and wrapper classes * restructure vae asset location * updated vae location * added SequenceGP model (Listgarten) and persisted assets * add Cbas GP npy files --------- * add npy assets to setup.cfg , cleanup rebase mistakes (#106) * 108 cbas available problem factory only returns gp (#109) * add problem factories, register multiple sub objectives --------- * Adds a test of `force_isolation` (#110) * Adds a test of force isolation * Updates the aloha environment to run on dev branch instead of master * Adds an environment yaml for basic chemistry objectives (#111) * Adds an environment yaml for basic objectives * Adds chemistry-related requirements * Removes biopython from the new requirements * Installs poli from the dev branch instead of master (#112) * Updates envs to install from dev instead of master * Modifies the poli installation for some environments, adds dependencies to installing * Moves required arguments to the top of objective factories (#114) * Moves required arguments to the top of objective factories * Moves the documentation of toy continuous objectives kwargs * Small improvements on chemistry and foldx black boxes (#115) * removes alphabet from chemistry boxes, defaults to 1 in foldx batch size * Changes an error message to reflect changes * added LamBO repo as dependency * ensured that base candidates are always among the first given sequences * adhering to coding standard * Adds immediate feedback on create using prints (#120) * remove CBas imports from __init__ (#123) * Allows flat inputs (i.e. `[b,]` instead of `[b, L]`) to black-boxes (#125) * Re-implements the logic of alignment in the abstract black box call * Implements an alignment input checker * Removes drd3 from TDC from the latest test * Removes lambo-related test until we can automatically install it * Adds `__repr__` and `__str__` to core objects (#127) * Implements str and repr dunder methods for black boxes and problem setups * Adds str and repr methods for the process warpper and observers * Foldx5 no longer needs a `rotabase.txt` file (#128) * Removes dependence on rotabase.txt file from foldx interface * Adds backwards compatibility, copying the rotabase file if users have it * Removes commented-out check of rotabase file * Minor fixes to the `foldx_rfp_lambo` black box. (#130) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * 132 problem factories fixed size initial dataset rfp and gfp (#133) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * 132 problem factories fixed size initial dataset rfp and gfp (#135) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * bugfix: default number of starting points is number of provided files if n_starting_points is None create fails * 136 gfp cbas factory create has no problem type (#137) * added problem_type parameter to factory create * black * Cleans the readme of drd3 docking, and fixes the env name (#140) * add unique flag: drop duplicate AA sequences, correct init seq selection (#142) * 139 create dedicated rfp foldx stability sasa and revert foldx stability sasa (#143) * add RFP specific stability_sasa objective * revert foldx_stability_and_sasa to rfp independent state, no n_starting * add rfp_stability_and_sasa to module import * Bugfix: parallelization flag in `foldx` now changes batch size accordingly. (#138) * Foldx parallelization now infers the appropriate batch size from the number of workers * Updates the readme to reflect the change in kwargs of getproblem * Removing the output from `foldx` w. a flag (#145) * Adds a verbose flag to foldx interface and black boxes * Adds a test for verbose output, and adds the verbose flag to the factories * the broadcasting behavior of numpy must have changed with a new version -- now we are getting the right predictions * Adding the relevant citations (#146) * Adds a table with the relevant references to cite per black box * Updates readme, removing unnecessary text * Updates citation * Renames the workflow for the website (#147) * Adds automatic installation of `lambo` (#134) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * Downloads files from LaMBO's repo automatically * Only downloads PDB folders that are not there yet * Refactors the code, implementing a function for downloading assets * merges dev * Moves the warning to the black boxes --------- Co-authored-by: Richard Michael <[email protected]> * Lints using black==24.1.1 (#153) * fix GFP problem, define singular WT start, remove redundant prob type (#152) * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong * Lints using black==24.1.1 * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong --------- * BUGFIX update minimum at iteration (#154) Currently min_hd is not set correctly. * 155 gfp provide problem type on factory create (#156) * GFPCBas factory set problem_type on create, default gp * linting * 158 gfpcbas elbo objective misspecified (#159) * format ifix inputs * optimize neg. ELBO by minimization --------- Co-authored-by: Richard Michael <[email protected]> * Implements a new interface for `create` (#161) * Implements a new interface for create * Updates the example in the readme * Updates the examples to the new interface * Adds a test of multiple observer registration (#162) * Updates readme with link to docs * Allows for creating black boxes without instancing problem factories (#163) * scaffolds the change that would allow us to create black boxes alone * Starts re-implementing the interface to return problems, solves tests for white noise * Modifies the external instancing of black box functions * Prototypes a new way of isolating complicated black box functions * Implements a way to isolate logic that's not dependent on abstract black boxes * Fixes instancing of drd3, at the cost of instancing dockstring. * Fixes registration s.t. functions and problems have separate entries in the config * Updates white noise to the new problem interface * Adapts foldx rfp lambo to the new interface * Modifies registration s.t. we no longer need to instantiate beforehand * Adapts foldx_sasa to the new interface * Adapts foldx stability to the new interface * Adapts foldx stability and sasa to the new interface * Adapts gfp_cbas to the new api * Adapts gfp select to the new interface * Adapts penalized logp to the new interface * Adapts rasp to the new interface * Adapts rdkit logp to the new interface * Adapts qed to the new interface * Adapts the rfp problem to the new interface * Adapts SA to the new interface * Removes the previous way of importing black boxes * Adapts SMB to the new interface * Adds toy continuous problems to the roster, tests all the black box functions * Updates tests to the new interface * Updates environments inside tox ini= * Updates the basic environment for forceful isolation * Updates examples to the new interface, fixes a bug on termination of isolated functions * Adds more docs examples to tests * Adds poli lambo env to tox * Adds a (slow) test for rasp's example * Updates readme to the new interface * Fixes a couple of bugs on negative and multiobjective black boxes (#164) * Adds an exception for when foldx is not found (#165) * hot-fixes the CI for master branch * hot-fix: removes lambo from master CI * hot-fix: since we lack the space, decided to test on dev only --------- Co-authored-by: Richard Michael <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Richard Michael <[email protected]>
miguelgondu
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Mar 12, 2024
* Allows mutations to be lowercase, and adds regression tests * Adds test to the foldx interface * Adds eager reparation when a FoldX black box is created (#85) * Adds eager reparation when a FoldX black box is created * Adds a flag for eager repairing, removes gcc from dependencies * Refactors examples, and cleans old ones (#87) * Implements dockstring as a black box function (#89) * Implements dockstring as a black box function * Adds tests for dockstring, fixes bug when converting to SELFIES * Adds citations for TDC and Dockstring * Adding continuous toy examples (#91) * Scaffolds the continuous problems * Lints the files defining the continuous objective functions * Updates requirements for setuptools * Adds a simple example of how to use the toy continuous problems * Adds toy examples, includes a slow fixture for pytest, adds it to the dev ini of tox * Adds a parametrized test for all possible toy continuous objectives * Renames the objective tests accordingly * The (first) great documentation PR (#95) * Adds documentation to most core files * Documents the rest of the core modules, starts documenting the objective repostories * Adds documentation for some objective functions * 96 add a gfp vae surrogate modeling task (#97) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main --------- * Implements a way to embed continuous problems in higher dimensions (#98) * Adds Styblinsky-Tang objective to continuous problems (#99) * cleaned up a bit, removed global variable * Updates the data by adding the relevant assets for gfp-cbas * Adds evaluation budgets and number-of-evaluations tracking (#102) * Adds an evaluation budget that can be strictly enforced * Adds 'optional' to the docs * Hotfix: evaluation in the aloha problem didn't work for batches * Builds automatic documentation of the API (#103) * Scaffolds automatic documentation of the API * Adds links to class implementations * Removes colons from attribute, raises, returns titles in docstrings * Fixes a colon in docstrings, to follow numpy standards * Adds documentation to the core module * Adds documentation to the objective factory module * Documents the objective script * Documents most functions inside the objective repository * Documents the remaining objective functions inside the repository * Adds several packages to the mock imports of autodoc * Removes the autogenerated rst files from git tracking * 96 add a gfp vae surrogate modeling task (#105) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main * added cbas module with assets and wrapper classes * restructure vae asset location * updated vae location * added SequenceGP model (Listgarten) and persisted assets * add Cbas GP npy files --------- * add npy assets to setup.cfg , cleanup rebase mistakes (#106) * 108 cbas available problem factory only returns gp (#109) * add problem factories, register multiple sub objectives --------- * Adds a test of `force_isolation` (#110) * Adds a test of force isolation * Updates the aloha environment to run on dev branch instead of master * Adds an environment yaml for basic chemistry objectives (#111) * Adds an environment yaml for basic objectives * Adds chemistry-related requirements * Removes biopython from the new requirements * Installs poli from the dev branch instead of master (#112) * Updates envs to install from dev instead of master * Modifies the poli installation for some environments, adds dependencies to installing * Moves required arguments to the top of objective factories (#114) * Moves required arguments to the top of objective factories * Moves the documentation of toy continuous objectives kwargs * Small improvements on chemistry and foldx black boxes (#115) * removes alphabet from chemistry boxes, defaults to 1 in foldx batch size * Changes an error message to reflect changes * added LamBO repo as dependency * ensured that base candidates are always among the first given sequences * adhering to coding standard * Adds immediate feedback on create using prints (#120) * remove CBas imports from __init__ (#123) * Allows flat inputs (i.e. `[b,]` instead of `[b, L]`) to black-boxes (#125) * Re-implements the logic of alignment in the abstract black box call * Implements an alignment input checker * Removes drd3 from TDC from the latest test * Removes lambo-related test until we can automatically install it * Adds `__repr__` and `__str__` to core objects (#127) * Implements str and repr dunder methods for black boxes and problem setups * Adds str and repr methods for the process warpper and observers * Foldx5 no longer needs a `rotabase.txt` file (#128) * Removes dependence on rotabase.txt file from foldx interface * Adds backwards compatibility, copying the rotabase file if users have it * Removes commented-out check of rotabase file * Minor fixes to the `foldx_rfp_lambo` black box. (#130) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * 132 problem factories fixed size initial dataset rfp and gfp (#133) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * 132 problem factories fixed size initial dataset rfp and gfp (#135) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * bugfix: default number of starting points is number of provided files if n_starting_points is None create fails * 136 gfp cbas factory create has no problem type (#137) * added problem_type parameter to factory create * black * Cleans the readme of drd3 docking, and fixes the env name (#140) * add unique flag: drop duplicate AA sequences, correct init seq selection (#142) * 139 create dedicated rfp foldx stability sasa and revert foldx stability sasa (#143) * add RFP specific stability_sasa objective * revert foldx_stability_and_sasa to rfp independent state, no n_starting * add rfp_stability_and_sasa to module import * Bugfix: parallelization flag in `foldx` now changes batch size accordingly. (#138) * Foldx parallelization now infers the appropriate batch size from the number of workers * Updates the readme to reflect the change in kwargs of getproblem * Removing the output from `foldx` w. a flag (#145) * Adds a verbose flag to foldx interface and black boxes * Adds a test for verbose output, and adds the verbose flag to the factories * the broadcasting behavior of numpy must have changed with a new version -- now we are getting the right predictions * Adding the relevant citations (#146) * Adds a table with the relevant references to cite per black box * Updates readme, removing unnecessary text * Updates citation * Renames the workflow for the website (#147) * Adds automatic installation of `lambo` (#134) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * Downloads files from LaMBO's repo automatically * Only downloads PDB folders that are not there yet * Refactors the code, implementing a function for downloading assets * merges dev * Moves the warning to the black boxes --------- * Lints using black==24.1.1 (#153) * fix GFP problem, define singular WT start, remove redundant prob type (#152) * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong * Lints using black==24.1.1 * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong --------- * BUGFIX update minimum at iteration (#154) Currently min_hd is not set correctly. * 155 gfp provide problem type on factory create (#156) * GFPCBas factory set problem_type on create, default gp * linting * 158 gfpcbas elbo objective misspecified (#159) * format ifix inputs * optimize neg. ELBO by minimization --------- * Implements a new interface for `create` (#161) * Implements a new interface for create * Updates the example in the readme * Updates the examples to the new interface * Adds a test of multiple observer registration (#162) * Updates readme with link to docs * Allows for creating black boxes without instancing problem factories (#163) * scaffolds the change that would allow us to create black boxes alone * Starts re-implementing the interface to return problems, solves tests for white noise * Modifies the external instancing of black box functions * Prototypes a new way of isolating complicated black box functions * Implements a way to isolate logic that's not dependent on abstract black boxes * Fixes instancing of drd3, at the cost of instancing dockstring. * Fixes registration s.t. functions and problems have separate entries in the config * Updates white noise to the new problem interface * Adapts foldx rfp lambo to the new interface * Modifies registration s.t. we no longer need to instantiate beforehand * Adapts foldx_sasa to the new interface * Adapts foldx stability to the new interface * Adapts foldx stability and sasa to the new interface * Adapts gfp_cbas to the new api * Adapts gfp select to the new interface * Adapts penalized logp to the new interface * Adapts rasp to the new interface * Adapts rdkit logp to the new interface * Adapts qed to the new interface * Adapts the rfp problem to the new interface * Adapts SA to the new interface * Removes the previous way of importing black boxes * Adapts SMB to the new interface * Adds toy continuous problems to the roster, tests all the black box functions * Updates tests to the new interface * Updates environments inside tox ini= * Updates the basic environment for forceful isolation * Updates examples to the new interface, fixes a bug on termination of isolated functions * Adds more docs examples to tests * Adds poli lambo env to tox * Adds a (slow) test for rasp's example * Updates readme to the new interface * Fixes a couple of bugs on negative and multiobjective black boxes (#164) * Adds an exception for when foldx is not found (#165) * hot-fixes the CI for master branch * hot-fix: removes lambo from master CI * hot-fix: since we lack the space, decided to test on dev only --------- Co-authored-by: Richard Michael <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Richard Michael <[email protected]>
miguelgondu
added a commit
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Jun 6, 2024
* changes-of-poli-in-master * Allows mutations to be lowercase, and adds regression tests * Adds test to the foldx interface * Adds eager reparation when a FoldX black box is created (#85) * Adds eager reparation when a FoldX black box is created * Adds a flag for eager repairing, removes gcc from dependencies * Refactors examples, and cleans old ones (#87) * Implements dockstring as a black box function (#89) * Implements dockstring as a black box function * Adds tests for dockstring, fixes bug when converting to SELFIES * Adds citations for TDC and Dockstring * Adding continuous toy examples (#91) * Scaffolds the continuous problems * Lints the files defining the continuous objective functions * Updates requirements for setuptools * Adds a simple example of how to use the toy continuous problems * Adds toy examples, includes a slow fixture for pytest, adds it to the dev ini of tox * Adds a parametrized test for all possible toy continuous objectives * Renames the objective tests accordingly * The (first) great documentation PR (#95) * Adds documentation to most core files * Documents the rest of the core modules, starts documenting the objective repostories * Adds documentation for some objective functions * 96 add a gfp vae surrogate modeling task (#97) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main --------- * Implements a way to embed continuous problems in higher dimensions (#98) * Adds Styblinsky-Tang objective to continuous problems (#99) * cleaned up a bit, removed global variable * Updates the data by adding the relevant assets for gfp-cbas * Adds evaluation budgets and number-of-evaluations tracking (#102) * Adds an evaluation budget that can be strictly enforced * Adds 'optional' to the docs * Hotfix: evaluation in the aloha problem didn't work for batches * Builds automatic documentation of the API (#103) * Scaffolds automatic documentation of the API * Adds links to class implementations * Removes colons from attribute, raises, returns titles in docstrings * Fixes a colon in docstrings, to follow numpy standards * Adds documentation to the core module * Adds documentation to the objective factory module * Documents the objective script * Documents most functions inside the objective repository * Documents the remaining objective functions inside the repository * Adds several packages to the mock imports of autodoc * Removes the autogenerated rst files from git tracking * 96 add a gfp vae surrogate modeling task (#105) * added cbas module with assets and wrapper classes * added factory init * cleanup wrapper main * added cbas module with assets and wrapper classes * restructure vae asset location * updated vae location * added SequenceGP model (Listgarten) and persisted assets * add Cbas GP npy files --------- * add npy assets to setup.cfg , cleanup rebase mistakes (#106) * 108 cbas available problem factory only returns gp (#109) * add problem factories, register multiple sub objectives --------- * Adds a test of `force_isolation` (#110) * Adds a test of force isolation * Updates the aloha environment to run on dev branch instead of master * Adds an environment yaml for basic chemistry objectives (#111) * Adds an environment yaml for basic objectives * Adds chemistry-related requirements * Removes biopython from the new requirements * Installs poli from the dev branch instead of master (#112) * Updates envs to install from dev instead of master * Modifies the poli installation for some environments, adds dependencies to installing * Moves required arguments to the top of objective factories (#114) * Moves required arguments to the top of objective factories * Moves the documentation of toy continuous objectives kwargs * Small improvements on chemistry and foldx black boxes (#115) * removes alphabet from chemistry boxes, defaults to 1 in foldx batch size * Changes an error message to reflect changes * added LamBO repo as dependency * ensured that base candidates are always among the first given sequences * adhering to coding standard * Adds immediate feedback on create using prints (#120) * remove CBas imports from __init__ (#123) * Allows flat inputs (i.e. `[b,]` instead of `[b, L]`) to black-boxes (#125) * Re-implements the logic of alignment in the abstract black box call * Implements an alignment input checker * Removes drd3 from TDC from the latest test * Removes lambo-related test until we can automatically install it * Adds `__repr__` and `__str__` to core objects (#127) * Implements str and repr dunder methods for black boxes and problem setups * Adds str and repr methods for the process warpper and observers * Foldx5 no longer needs a `rotabase.txt` file (#128) * Removes dependence on rotabase.txt file from foldx interface * Adds backwards compatibility, copying the rotabase file if users have it * Removes commented-out check of rotabase file * Minor fixes to the `foldx_rfp_lambo` black box. (#130) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * 132 problem factories fixed size initial dataset rfp and gfp (#133) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * 132 problem factories fixed size initial dataset rfp and gfp (#135) * add n_starting_points to GFP problem * add n_starting_points, loading pareto front PDBs is minimum, add strict evluation option for Errors on mismatch * add GFP problem type * bugfix: default number of starting points is number of provided files if n_starting_points is None create fails * 136 gfp cbas factory create has no problem type (#137) * added problem_type parameter to factory create * black * Cleans the readme of drd3 docking, and fixes the env name (#140) * add unique flag: drop duplicate AA sequences, correct init seq selection (#142) * 139 create dedicated rfp foldx stability sasa and revert foldx stability sasa (#143) * add RFP specific stability_sasa objective * revert foldx_stability_and_sasa to rfp independent state, no n_starting * add rfp_stability_and_sasa to module import * Bugfix: parallelization flag in `foldx` now changes batch size accordingly. (#138) * Foldx parallelization now infers the appropriate batch size from the number of workers * Updates the readme to reflect the change in kwargs of getproblem * Removing the output from `foldx` w. a flag (#145) * Adds a verbose flag to foldx interface and black boxes * Adds a test for verbose output, and adds the verbose flag to the factories * the broadcasting behavior of numpy must have changed with a new version -- now we are getting the right predictions * Adding the relevant citations (#146) * Adds a table with the relevant references to cite per black box * Updates readme, removing unnecessary text * Updates citation * Renames the workflow for the website (#147) * Adds automatic installation of `lambo` (#134) * add verbose error, if FoldX fails the Lambo foldx_manager fails silently * Modifies the x0 and the black box of foldx rfp lambo, adds a basic test of evaluation * Adds a skip if lambo is not installed * Downloads files from LaMBO's repo automatically * Only downloads PDB folders that are not there yet * Refactors the code, implementing a function for downloading assets * merges dev * Moves the warning to the black boxes --------- * Lints using black==24.1.1 (#153) * fix GFP problem, define singular WT start, remove redundant prob type (#152) * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong * Lints using black==24.1.1 * fix GFP problem, define singular WT start, remove redundant prob type ELBO working * add missing GFP asset, oracle predictiong --------- * BUGFIX update minimum at iteration (#154) Currently min_hd is not set correctly. * 155 gfp provide problem type on factory create (#156) * GFPCBas factory set problem_type on create, default gp * linting * 158 gfpcbas elbo objective misspecified (#159) * format ifix inputs * optimize neg. ELBO by minimization --------- * Implements a new interface for `create` (#161) * Implements a new interface for create * Updates the example in the readme * Updates the examples to the new interface * Adds a test of multiple observer registration (#162) * Updates readme with link to docs * Allows for creating black boxes without instancing problem factories (#163) * scaffolds the change that would allow us to create black boxes alone * Starts re-implementing the interface to return problems, solves tests for white noise * Modifies the external instancing of black box functions * Prototypes a new way of isolating complicated black box functions * Implements a way to isolate logic that's not dependent on abstract black boxes * Fixes instancing of drd3, at the cost of instancing dockstring. * Fixes registration s.t. functions and problems have separate entries in the config * Updates white noise to the new problem interface * Adapts foldx rfp lambo to the new interface * Modifies registration s.t. we no longer need to instantiate beforehand * Adapts foldx_sasa to the new interface * Adapts foldx stability to the new interface * Adapts foldx stability and sasa to the new interface * Adapts gfp_cbas to the new api * Adapts gfp select to the new interface * Adapts penalized logp to the new interface * Adapts rasp to the new interface * Adapts rdkit logp to the new interface * Adapts qed to the new interface * Adapts the rfp problem to the new interface * Adapts SA to the new interface * Removes the previous way of importing black boxes * Adapts SMB to the new interface * Adds toy continuous problems to the roster, tests all the black box functions * Updates tests to the new interface * Updates environments inside tox ini= * Updates the basic environment for forceful isolation * Updates examples to the new interface, fixes a bug on termination of isolated functions * Adds more docs examples to tests * Adds poli lambo env to tox * Adds a (slow) test for rasp's example * Updates readme to the new interface * Fixes a couple of bugs on negative and multiobjective black boxes (#164) * Adds an exception for when foldx is not found (#165) * hot-fixes the CI for master branch * hot-fix: removes lambo from master CI * hot-fix: since we lack the space, decided to test on dev only --------- Co-authored-by: Richard Michael <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Richard Michael <[email protected]> * Updates the SMB black box to be discrete instead of continuous (#175) * Adds the Hartmann6D objective to toy problems (#177) * Adds the Branin toy function (#178) * Adds slurm scripts to gitignore * Adding the remaining PMO tasks (#180) * Adds GSK3Beta, including tests * Implements an isolation for all TDC black boxes, adds DRD2 * Adds JNK3, lacks testing until tdc is fixed * Implements an abstract black box for TDC to reduce code duplication * Adds Celecoxib rediscovery * Adds Thiothixene rediscovery * Adds troglitazone rediscovery * Adds albuterol similarity * Adds mestranol similarity * amlodipine_mpo * Adds Fexofenadine MPO * Adds the remaining MPO tasks * Forgot about Zaleplon MPO * Adds the two Hop tasks * Adds the two isomer tasks * Adds the median tasks * Adds the Valsartan SMARTS task * Changes the environment creation for poli tdc * Updates the poli tdc env to have laxer restrictions on biopython and pandas * Polishes the docstrings for the new black boxes * Adds citing information to remaining black boxes * Polishes the update and guacamol tests * Adds benchmarks (#181) * Adds a benchmarks feature, starting with guacamol, pmo and toy functions * Adds two more benchmarks for embedded functions * Adds an x0 for all toy objectives * Adds documentation to PMO, GuacaMol and toy continuous benchmarks * Adds an example of running a benchmark * Fixes the bounds in toy continuous problems * Adds Levy and Rosenbrock test functions (#182) * Hotfix: removes shifted sphere from the 2d list * Fixes the solution length for shifted sphere * Makes new functions maximizable * Adds problem names as property of benchmarks * Fixes a bug: logp and qed are discrete objectives, adds a shortcut to black boxes (#183) * Abstracts away isolated function imports (#185) * Instances the inner function inside every black-box call for FoldX, adds utility for abstracting away isolated function instantiation * Uses the new isolation interface for all isolate-able black boxes (except RFP) * Removes unused imports * Removes unused import from TDC black box, removes inner_function attribute in foldx stability * fix RFPFoldXStabilityAndSASA create, eliminate inner_function (#189) * add negate flag to invert negative GP predictions for max objectives (#191) * Adds a warning when the user is not setting an observer properly (#192) * Adds a warning when the user is not setting an observer properly * Self is not available in 3.9 * Missed a space in the warning * Hotfix: gfp cbas should be installing from dev branch * Implements a multi-observer (#194) * Allows other values than NaN for unplayable levels in SMB (#196) --------- Co-authored-by: Richard Michael <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Simon Bartels <[email protected]> Co-authored-by: Richard Michael <[email protected]>
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Closes #124