Merge branch 'dev' into feature-default-smiles-and-selfies-tokenizer

CONTRIBUTING.md

@@ -63,6 +63,24 @@ There are several different environments (depending on the black boxes we test).
 
 If you want to run tests in all environments, remove `-e poli-base-py39` and just run `tox`. This might take a while, and several conda envs will be created.
 
+## Bump the version!
+
+Your last commit in your branch should be a bump version.
+
+One of the dev requirements is `bump-my-version`. You should be able to check what the version would be bumped to by running
+
+```bash
+bump-my-version show-bump
+```
+
+For most cases, you'll be bumping `pre_n` in the `dev` branch. You can bump it with
+
+```bash
+bump-my-version bump pre_n
+```
+
+This will modify the relevant files: `pyproject.toml` and `src/poli/__init__.py`.
+
 ## Create a pull request to dev
 
 Once all tests pass and you are ready to share your changes, create a pull request to the `dev` branch.

README.MD

@@ -10,7 +10,7 @@
 | Black box | References | Tests
 |----------|----------|----------|
 |   [Toy continuous functions (e.g. Ackley, Hartmann...)](https://machinelearninglifescience.github.io/poli-docs/using_poli/objective_repository/toy_continuous_problems.html) |  [(Al-Roomi 2015)](https://www.al-roomi.org/benchmarks/unconstrained), [(Surjanovic & Bingham 2013)](https://www.sfu.ca/~ssurjano/optimization.html)  |   [![poli base (dev, conda, python 3.9)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml/badge.svg)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml)  |
-|   Ehrlich functions  |    [(Stanton et al. 2024)](https://arxiv.org/abs/2407.00236)  | [![poli base (dev, conda, python 3.9)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml/badge.svg)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml)
+|   [Ehrlich functions](https://machinelearninglifescience.github.io/poli-docs/using_poli/objective_repository/ehrlich_functions.html)  |    [(Stanton et al. 2024)](https://arxiv.org/abs/2407.00236)  | [![poli base (dev, conda, python 3.9)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml/badge.svg)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-base.yml)
 |   [PMO/GuacaMol benchmark](https://machinelearninglifescience.github.io/poli-docs/#small-molecules)  |   [(Brown et al. 2019)](https://arxiv.org/abs/1811.09621), [(Gao et al. 2022)](https://openreview.net/forum?id=yCZRdI0Y7G), [(Huang et al. 2021)](https://openreview.net/pdf?id=8nvgnORnoWr)  | [![poli tdc (dev, conda, python 3.9)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-tdc-env.yml/badge.svg)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-tdc-env.yml)
 |   [Dockstring](https://machinelearninglifescience.github.io/poli-docs/using_poli/objective_repository/dockstring.html) |  [(García-Ortegón et al. 2022)](https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01334)  | [![poli dockstring (dev, conda, python 3.9)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-dockstring-env.yml/badge.svg)](https://github.com/MachineLearningLifeScience/poli/actions/workflows/python-tox-testing-dockstring-env.yml)
 |   [FoldX stability and SASA](https://machinelearninglifescience.github.io/poli-docs/#proteins)  |   [(Schymkowitz et al. 2005)](https://academic.oup.com/nar/article/33/suppl_2/W382/2505499?login=true) |  -  |

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "poli"
-version = "0.2.1"
+version = "1.0.0.dev2"
 description = "poli, a library of discrete objective functions"
 readme = "README.md"
 authors = [{name="Miguel González-Duque", email="[email protected]"}, {name="Simon Bartels"}]
@@ -28,7 +28,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["black", "tox", "pytest"]
+dev = ["black", "tox", "pytest", "bump-my-version"]
 docs = ["sphinx", "furo"]
 
 [project.urls]
@@ -50,4 +50,47 @@ markers = [
 profile = "black"
 
 [tool.ruff]
-exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]
+exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]
+
+[tool.bumpversion]
+current_version = "1.0.0.dev2"
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        .                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}.{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
+search = 'current_version = "{current_version}"'
+replace = 'current_version = "{new_version}"'
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = false
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[tool.bumpversion.parts.pre_l]
+values = ["dev"]
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "src/poli/__init__.py"
+search = '__version__ = "{current_version}"'
+replace = '__version__ = "{new_version}"'

requirements-dev.txt

@@ -3,4 +3,5 @@ tox
 pytest
 setuptools
 sphinx
-furo
+furo
+bump-my-version

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 name = poli
-version = 0.2.1
-author_email = bartels@di.ku.dk
+version = "1.0.0.dev0"
+author_email = miguel.gonzalez-duque@bio.ku.dk
 description = Protein Objectives Library
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -14,7 +14,7 @@ classifiers =
 package_dir =
     =src
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.8
 include_package_data = True
 
 [options.packages.find]

src/poli/__init__.py

@@ -1,6 +1,6 @@
 """poli, a library for discrete black-box objective functions."""
 
-__author__ = "Simon Bartels & Miguel González-Duque (MLLS)"
+__version__ = "1.0.0.dev2"
 from .core.util.isolation.instancing import instance_function_as_isolated_process
 
 # from .core import get_problems

src/poli/core/abstract_benchmark.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import List, Union
 
 from poli.core.abstract_problem_factory import AbstractProblemFactory
@@ -46,6 +48,8 @@ def info(self) -> str:
     @property
     def problem_names(self) -> List[str]:
         return [
-            problem_factory.get_setup_information().name
+            problem_factory.__module__.replace(
+                "poli.objective_repository.", ""
+            ).replace(".register", "")
             for problem_factory in self.problem_factories
         ]

src/poli/core/abstract_black_box.py

@@ -105,15 +105,14 @@ def __init__(
 
         self.batch_size = batch_size
 
-    @staticmethod
-    def get_black_box_info() -> BlackBoxInformation:
+    def get_black_box_info(self) -> BlackBoxInformation:
         raise NotImplementedError(
             "Black box information must be implemented in subclasses."
         )
 
     @property
     def info(self) -> BlackBoxInformation:
-        return self.__class__.get_black_box_info()
+        return self.get_black_box_info()
 
     def set_observer(self, observer: AbstractObserver):
         """

src/poli/core/abstract_problem_factory.py

@@ -1,6 +1,5 @@
 """This module implements the abstract problem factory."""
 
-from poli.core.black_box_information import BlackBoxInformation
 from poli.core.problem import Problem
 
 
@@ -11,12 +10,7 @@ class MetaProblemFactory(type):
     """
 
     def __repr__(cls) -> str:
-        try:
-            problem_info = cls().get_setup_information()
-        except NotImplementedError:
-            return f"<{cls.__name__}()>"
-
-        return f"<{cls.__name__}(L={problem_info.max_sequence_length})>"
+        return f"<{cls.__name__}()>"
 
     def __str__(cls) -> str:
         return f"{cls.__name__}"
@@ -30,28 +24,10 @@ class AbstractProblemFactory(metaclass=MetaProblemFactory):
 
     Methods
     -------
-    get_setup_information:
-        Returns the setup information for the problem.
     create:
         Creates a problem instance with the specified parameters.
     """
 
-    def get_setup_information(self) -> BlackBoxInformation:
-        """
-        Returns the setup information for the problem.
-
-        Returns
-        --------
-        problem_info: BlackBoxInformation
-            Information for the problem (e.g. whether it is discrete, deterministic...).
-
-        Raises
-        -------
-        NotImplementedError:
-            This method is abstract and must be implemented by subclasses.
-        """
-        raise NotImplementedError("abstract method")
-
     def create(
         self,
         seed: int = None,
@@ -90,4 +66,6 @@ def create(
             NotImplementedError: This method is abstract and must be implemented by subclasses.
 
         """
-        raise NotImplementedError("abstract method")
+        raise NotImplementedError(
+            "Abstract method create() must be implemented by subclasses."
+        )

src/poli/core/chemistry/environment.yml

@@ -19,7 +19,7 @@ dependencies:
     - cachetools
     - rdkit
     - selfies
-    - pytdc==0.4.7
+    - pytdc
     - pyscreener
     - colorama
     - configparse

src/poli/core/proteins/foldx_black_box.py

@@ -18,7 +18,7 @@
 from uuid import uuid4
 
 from poli.core.abstract_black_box import AbstractBlackBox
-from poli.core.problem_setup_information import ProblemSetupInformation
+from poli.core.black_box_information import BlackBoxInformation
 from poli.core.util.proteins.foldx import FoldxInterface
 from poli.core.util.proteins.pdb_parsing import (
     parse_pdb_as_residue_strings,
@@ -85,7 +85,7 @@ class FoldxBlackBox(AbstractBlackBox):
 
     def __init__(
         self,
-        info: ProblemSetupInformation = None,
+        info: BlackBoxInformation = None,
         batch_size: int = None,
         parallelize: bool = False,
         num_workers: int = None,