Removes problem registration from all black boxes

MachineLearningLifeScience · Jul 25, 2024 · 60577ed · 60577ed
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commit 60577ed
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Showing 42 changed files with 6 additions and 496 deletions.
diff --git a/src/poli/objective_repository/albuterol_similarity/register.py b/src/poli/objective_repository/albuterol_similarity/register.py
@@ -213,14 +213,3 @@ def create(
         )
 
         return albuterol_similarity_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        AlbuterolSimilarityProblemFactory(),
-        name="albuterol_similarity",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/aloha/register.py b/src/poli/objective_repository/aloha/register.py
@@ -218,18 +218,3 @@ def create(
         )
 
         return aloha_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    # Once we have created a simple conda enviroment
-    # (see the environment.yml file in this folder),
-    # we can register our problem s.t. it uses
-    # said conda environment.
-    aloha_problem_factory = AlohaProblemFactory()
-    register_problem(
-        aloha_problem_factory,
-        conda_environment_name="poli__base",
-        # force=True
-    )
diff --git a/src/poli/objective_repository/amlodipine_mpo/register.py b/src/poli/objective_repository/amlodipine_mpo/register.py
@@ -208,14 +208,3 @@ def create(
         )
 
         return amlodipine_mpo_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        AmlodipineMPOProblemFactory(),
-        name="amlodipine_mpo",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/celecoxib_rediscovery/register.py b/src/poli/objective_repository/celecoxib_rediscovery/register.py
@@ -211,14 +211,3 @@ def create(
         )
 
         return celecoxib_rediscovery_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        CelecoxibRediscoveryProblemFactory(),
-        name="celecoxib_rediscovery",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/deco_hop/register.py b/src/poli/objective_repository/deco_hop/register.py
@@ -209,14 +209,3 @@ def create(
         )
 
         return deco_hop_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        DecoHopProblemFactory(),
-        name="deco_hop",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/dockstring/register.py b/src/poli/objective_repository/dockstring/register.py
@@ -271,13 +271,3 @@ def create(
         dockstring_problem = Problem(black_box=dockstring_black_box, x0=x0)
 
         return dockstring_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    dockstring_problem_factory = DockstringProblemFactory()
-    register_problem(
-        dockstring_problem_factory,
-        conda_environment_name="poli__dockstring",
-    )
diff --git a/src/poli/objective_repository/drd2_docking/register.py b/src/poli/objective_repository/drd2_docking/register.py
@@ -209,14 +209,3 @@ def create(
         )
 
         return drd2_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        DRD2ProblemFactory(),
-        name="drd2_docking",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/drd3_docking/register.py b/src/poli/objective_repository/drd3_docking/register.py
@@ -17,7 +17,6 @@
 from poli.core.chemistry.tdc_black_box import TDCBlackBox
 from poli.core.problem import Problem
 from poli.core.util.chemistry.string_to_molecule import translate_smiles_to_selfies
-from poli.core.util.isolation.instancing import instance_function_as_isolated_process
 from poli.core.util.seeding import seed_numpy, seed_python
 from poli.objective_repository.drd3_docking.information import drd3_docking_info
 
@@ -178,14 +177,3 @@ def create(
         )
 
         return drd3_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        DRD3ProblemFactory(),
-        name="drd3_docking",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/fexofenadine_mpo/register.py b/src/poli/objective_repository/fexofenadine_mpo/register.py
@@ -206,14 +206,3 @@ def create(
         )
 
         return fexofenadine_mpo_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        FexofenadineMPOProblemFactory(),
-        name="fexofenadine_mpo",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/foldx_rfp_lambo/register.py b/src/poli/objective_repository/foldx_rfp_lambo/register.py
@@ -104,14 +104,3 @@ def create(
         x0 = black_box.inner_function.x0
 
         return Problem(black_box, x0)
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    rfp_problem_factory = FoldXRFPLamboProblemFactory()
-    register_problem(
-        rfp_problem_factory,
-        conda_environment_name="poli__lambo",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/foldx_sasa/register.py b/src/poli/objective_repository/foldx_sasa/register.py
@@ -287,13 +287,3 @@ def create(
 
         problem = Problem(f, x0)
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    foldx_problem_factory = FoldXSASAProblemFactory()
-    register_problem(
-        foldx_problem_factory,
-        conda_environment_name="poli__protein",
-    )
diff --git a/src/poli/objective_repository/foldx_stability/register.py b/src/poli/objective_repository/foldx_stability/register.py
@@ -277,13 +277,3 @@ def create(
         problem = Problem(f, x0)
 
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    foldx_problem_factory = FoldXStabilityProblemFactory()
-    register_problem(
-        foldx_problem_factory,
-        conda_environment_name="poli__protein",
-    )
diff --git a/src/poli/objective_repository/foldx_stability_and_sasa/register.py b/src/poli/objective_repository/foldx_stability_and_sasa/register.py
@@ -291,13 +291,3 @@ def create(
 
         problem = Problem(f, x0)
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    foldx_problem_factory = FoldXStabilityAndSASAProblemFactory()
-    register_problem(
-        foldx_problem_factory,
-        conda_environment_name="poli__protein",
-    )
diff --git a/src/poli/objective_repository/gfp_cbas/register.py b/src/poli/objective_repository/gfp_cbas/register.py
@@ -148,28 +148,3 @@ def create(
         problem = Problem(f, x0)
 
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    gfp_problem_factory = GFPCBasProblemFactory()
-    register_problem(
-        gfp_problem_factory,
-        conda_environment_name="poli__protein_cbas",
-    )
-    # NOTE: default problem is GP problem
-    gfp_problem_factory.create(seed=12)
-    # instantiate different types of CBas problems:
-    gfp_problem_factory_vae = GFPCBasProblemFactory(problem_type="vae")
-    register_problem(
-        gfp_problem_factory_vae,
-        conda_environment_name="poli__protein_cbas",
-    )
-    gfp_problem_factory_vae.create(seed=12, problem_type="vae")
-    gfp_problem_factory_elbo = GFPCBasProblemFactory(problem_type="elbo")
-    register_problem(
-        gfp_problem_factory_elbo,
-        conda_environment_name="poli__protein_cbas",
-    )
-    gfp_problem_factory_elbo.create(seed=12, problem_type="elbo")
diff --git a/src/poli/objective_repository/gfp_select/register.py b/src/poli/objective_repository/gfp_select/register.py
@@ -1,5 +1,3 @@
-from typing import Tuple
-
 import numpy as np
 
 from poli.core.abstract_black_box import AbstractBlackBox
@@ -91,13 +89,3 @@ def create(
         problem = Problem(f, x0)
 
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    gfp_problem_factory = GFPSelectionProblemFactory()
-    register_problem(
-        gfp_problem_factory,
-        conda_environment_name="poli__protein_cbas",
-    )
diff --git a/src/poli/objective_repository/gsk3_beta/register.py b/src/poli/objective_repository/gsk3_beta/register.py
@@ -226,14 +226,3 @@ def create(
         )
 
         return gsk3_beta_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        GSK3BetaProblemFactory(),
-        name="gs3_beta",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/isomer_c7h8n2o2/register.py b/src/poli/objective_repository/isomer_c7h8n2o2/register.py
@@ -206,14 +206,3 @@ def create(
         )
 
         return isomer_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        IsomerC7H8N2O2ProblemFactory(),
-        name="isomer_c7h8n2o2",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/isomer_c9h10n2o2pf2cl/register.py b/src/poli/objective_repository/isomer_c9h10n2o2pf2cl/register.py
@@ -211,14 +211,3 @@ def create(
         )
 
         return isomer_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        IsomerC9H10N2O2PF2ClProblemFactory(),
-        name="isomer_c9h10n2o2pf2cl",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/jnk3/register.py b/src/poli/objective_repository/jnk3/register.py
@@ -222,14 +222,3 @@ def create(
         )
 
         return jnk3_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        JNK3ProblemFactory(),
-        name="jnk3",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/median_1/register.py b/src/poli/objective_repository/median_1/register.py
@@ -205,14 +205,3 @@ def create(
         )
 
         return median_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        Median1ProblemFactory(),
-        name="median_1",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/median_2/register.py b/src/poli/objective_repository/median_2/register.py
@@ -204,14 +204,3 @@ def create(
         )
 
         return median_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        Median2ProblemFactory(),
-        name="median_2",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/mestranol_similarity/register.py b/src/poli/objective_repository/mestranol_similarity/register.py
@@ -211,14 +211,3 @@ def create(
         )
 
         return mestranol_similarity_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        MestranolSimilarityProblemFactory(),
-        name="mestranol_similarity",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/osimetrinib_mpo/register.py b/src/poli/objective_repository/osimetrinib_mpo/register.py
@@ -205,14 +205,3 @@ def create(
         )
 
         return osimetrinib_mpo_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        OsimetrinibMPOProblemFactory(),
-        name="osimetrinib_mpo",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )
diff --git a/src/poli/objective_repository/penalized_logp_lambo/register.py b/src/poli/objective_repository/penalized_logp_lambo/register.py
@@ -140,12 +140,3 @@ def create(
         problem = Problem(f, x0)
 
         return problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        PenalizedLogPLamboProblemFactory(),
-        conda_environment_name="poli__lambo",
-    )
diff --git a/src/poli/objective_repository/perindopril_mpo/register.py b/src/poli/objective_repository/perindopril_mpo/register.py
@@ -204,14 +204,3 @@ def create(
         )
 
         return perindopril_mpo_problem
-
-
-if __name__ == "__main__":
-    from poli.core.registry import register_problem
-
-    register_problem(
-        PerindoprilMPOProblemFactory(),
-        name="perindopril_mpo",
-        conda_environment_name="poli__tdc",
-        force=True,
-    )