255 implement set of dms experiment results as static optimization problems (#300)

* setup GB1 structure

* setup TprbB structure

* init isolated functions, RasP copy

* add GB1 black box and isolation

* add TrpB black-box and isolation

* add tests DMS repository

* add tox, add pytest marker

* fix ruff checks import

* add imports

* bump version DEV

* correct load dms and return indexing

* correct WT loading with b, dim

* fix dms df string indexing

* correct test AA override

* added poli-dms to tox ini list of envs

* make ValueErrors more verbose

* cleanup docstring, missing raises

* bump version

---------

Co-authored-by: Richard Michael <[email protected]>

Author: RMichae1

CITATION.cff

@@ -8,6 +8,6 @@ authors:
 - family-names: "Michael"
   given-names: "Richard"
 title: "poli: a libary of discrete sequence objectives"
-version: 1.1.1
+version: 1.2.0
 date-released: 2024-01-23
 url: "https://github.com/MachineLearningLifeScience/poli"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "poli-core"
-version = "1.1.1"
+version = "1.2.0"
 description = "poli, a library of discrete objective functions"
 readme = "README.md"
 authors = [{name="Miguel González-Duque", email="[email protected]"}, {name="Simon Bartels", email="[email protected]"}]
@@ -42,6 +42,9 @@ protein = [
     "python-levenshtein",
     "pdb-tools",
 ]
+dms = [
+    "pandas",
+]
 ehrlich = [
     "pytorch-holo",
 ]
@@ -78,6 +81,7 @@ markers = [
     "poli__rmf: marks tests that run in poli__rmf environment",
     "poli__rosetta_energy: marks tests that run in poli__rosetta_energy",
     "poli__ehrlich_holo: marks tests that run in poli__ehrlich_holo environment",
+    "poli__dms: marks tests that run in poli__dms environment",
     "unmarked: All other tests, which usually run in the base environment",
 ]
 
@@ -88,7 +92,7 @@ profile = "black"
 exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]
 
 [tool.bumpversion]
-current_version = "1.1.1"
+current_version = "1.2.0"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = poli-core
-version = "1.1.1"
+version = "1.2.0"
 author = Miguel González-Duque
 author_email = [email protected]
 description = A library of discrete objective functions

src/poli/__init__.py

@@ -1,6 +1,6 @@
 """poli, a library for discrete black-box objective functions."""
 
-__version__ = "1.1.1"
+__version__ = "1.2.0"
 from .core.util.isolation.instancing import instance_function_as_isolated_process
 
 # from .core import get_problems

src/poli/objective_repository/__init__.py

@@ -13,6 +13,8 @@
     CelecoxibRediscoveryProblemFactory,
 )
 from .deco_hop.register import DecoHopBlackBox, DecoHopProblemFactory
+from .dms_gb1.register import DMSGB1BlackBox, DMSGB1ProblemFactory
+from .dms_trpb.register import DMSTrpBBlackBox, DMSTrpBProblemFactory
 from .dockstring.register import DockstringBlackBox, DockstringProblemFactory
 from .drd2_docking.register import DRD2BlackBox, DRD2ProblemFactory
 from .drd3_docking.register import DRD3BlackBox, DRD3ProblemFactory
@@ -126,6 +128,8 @@
     "aloha": AlohaProblemFactory,
     "ehrlich": EhrlichProblemFactory,
     "ehrlich_holo": EhrlichHoloProblemFactory,
+    "dms_gb1": DMSGB1ProblemFactory,
+    "dms_trpb": DMSTrpBProblemFactory,
     "dockstring": DockstringProblemFactory,
     "drd3_docking": DRD3ProblemFactory,
     "foldx_rfp_lambo": FoldXRFPLamboProblemFactory,
@@ -175,6 +179,8 @@
     "aloha": AlohaBlackBox,
     "ehrlich": EhrlichBlackBox,
     "ehrlich_holo": EhrlichHoloBlackBox,
+    "dms_gb1": DMSGB1BlackBox,
+    "dms_trpb": DMSTrpBBlackBox,
     "dockstring": DockstringBlackBox,
     "drd3_docking": DRD3BlackBox,
     "foldx_rfp_lambo": FoldXRFPLamboBlackBox,