Merge: Enable scikit-fingerprints (#364)

Closes #359

.lockfiles/py310-dev.lock

@@ -103,6 +103,8 @@ cyclonedx-python-lib==7.5.1
     # via pip-audit
 dask==2024.7.1
     # via xyzpy
+datasketch==1.6.5
+    # via scikit-fingerprints
 debugpy==1.8.2
     # via ipykernel
 decorator==5.1.1
@@ -116,6 +118,8 @@ deprecated==1.2.14
     #   opentelemetry-api
     #   opentelemetry-exporter-otlp-proto-grpc
     #   opentelemetry-exporter-otlp-proto-http
+descriptastorus==2.6.1
+    # via scikit-fingerprints
 distlib==0.3.8
     # via virtualenv
 docstring-parser-fork==0.0.9
@@ -126,6 +130,8 @@ docutils==0.21.2
     #   pybtex-docutils
     #   sphinx
     #   sphinxcontrib-bibtex
+e3fp==1.2.5
+    # via scikit-fingerprints
 et-xmlfile==1.1.0
     # via openpyxl
 exceptiongroup==1.2.2
@@ -143,6 +149,7 @@ fastjsonschema==2.20.0
 filelock==3.15.4
     # via
     #   cachecontrol
+    #   huggingface-hub
     #   torch
     #   tox
     #   triton
@@ -160,14 +167,15 @@ fqdn==1.5.1
 fsspec==2024.6.1
     # via
     #   dask
+    #   huggingface-hub
     #   torch
 funcy==1.17
     # via
     #   baybe (pyproject.toml)
     #   funcy-stubs
 funcy-stubs==0.1.1
     # via baybe (pyproject.toml)
-furo==2024.7.18
+furo==2024.8.6
     # via baybe (pyproject.toml)
 future==1.0.0
     # via autograd
@@ -199,6 +207,8 @@ httpcore==1.0.5
     # via httpx
 httpx==0.27.0
     # via jupyterlab
+huggingface-hub==0.25.1
+    # via scikit-fingerprints
 humanfriendly==10.0
     # via coloredlogs
 hypothesis==6.108.4
@@ -228,7 +238,6 @@ ipykernel==6.29.5
     #   jupyter
     #   jupyter-console
     #   jupyterlab
-    #   qtconsole
 ipython==8.26.0
     # via
     #   ipykernel
@@ -256,6 +265,7 @@ jinja2==3.1.4
 joblib==1.4.2
     # via
     #   baybe (pyproject.toml)
+    #   scikit-fingerprints
     #   scikit-learn
     #   xyzpy
 json5==0.9.25
@@ -270,15 +280,14 @@ jsonschema==4.23.0
     #   nbformat
 jsonschema-specifications==2023.12.1
     # via jsonschema
-jupyter==1.0.0
+jupyter==1.1.1
     # via baybe (pyproject.toml)
 jupyter-client==8.6.2
     # via
     #   ipykernel
     #   jupyter-console
     #   jupyter-server
     #   nbclient
-    #   qtconsole
 jupyter-console==6.6.3
     # via jupyter
 jupyter-core==5.7.2
@@ -291,7 +300,6 @@ jupyter-core==5.7.2
     #   nbclient
     #   nbconvert
     #   nbformat
-    #   qtconsole
 jupyter-events==0.10.0
     # via jupyter-server
 jupyter-lsp==2.2.5
@@ -306,7 +314,9 @@ jupyter-server==2.14.2
 jupyter-server-terminals==0.5.3
     # via jupyter-server
 jupyterlab==4.2.4
-    # via notebook
+    # via
+    #   jupyter
+    #   notebook
 jupyterlab-pygments==0.3.0
     # via nbconvert
 jupyterlab-server==2.27.3
@@ -315,7 +325,7 @@ jupyterlab-server==2.27.3
     #   notebook
 jupyterlab-widgets==3.0.11
     # via ipywidgets
-jupytext==1.16.3
+jupytext==1.16.4
     # via baybe (pyproject.toml)
 kiwisolver==1.4.5
     # via matplotlib
@@ -329,6 +339,8 @@ linear-operator==0.5.2
     # via
     #   botorch
     #   gpytorch
+llvmlite==0.43.0
+    # via numba
 locket==1.0.0
     # via partd
 markdown-it-py==3.0.0
@@ -363,8 +375,10 @@ mistune==3.0.2
     # via nbconvert
 mkl==2021.4.0 ; platform_system == 'Windows'
     # via torch
+mmh3==5.0.1
+    # via e3fp
 mordredcommunity==2.0.6
-    # via baybe (pyproject.toml)
+    # via scikit-fingerprints
 mpmath==1.3.0
     # via
     #   botorch
@@ -378,7 +392,7 @@ mypy==1.11.0
     # via baybe (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
-myst-parser==3.0.1
+myst-parser==4.0.0
     # via baybe (pyproject.toml)
 nbclient==0.10.0
     # via nbconvert
@@ -408,19 +422,25 @@ notebook-shim==0.2.4
     # via
     #   jupyterlab
     #   notebook
+numba==0.60.0
+    # via scikit-fingerprints
 numpy==1.26.4
     # via
     #   baybe (pyproject.toml)
     #   altair
     #   autograd
     #   botorch
     #   contourpy
+    #   datasketch
+    #   descriptastorus
+    #   e3fp
     #   formulaic
     #   h5py
     #   lifelines
     #   matplotlib
     #   mordredcommunity
     #   ngboost
+    #   numba
     #   onnx
     #   onnxconverter-common
     #   onnxruntime
@@ -431,6 +451,7 @@ numpy==1.26.4
     #   pydeck
     #   pyro-ppl
     #   rdkit
+    #   scikit-fingerprints
     #   scikit-learn
     #   scikit-learn-extra
     #   scipy
@@ -526,6 +547,7 @@ packaging==24.1
     #   altair
     #   dask
     #   h5netcdf
+    #   huggingface-hub
     #   ipykernel
     #   jupyter-server
     #   jupyterlab
@@ -541,8 +563,6 @@ packaging==24.1
     #   plotly
     #   pyproject-api
     #   pytest
-    #   qtconsole
-    #   qtpy
     #   setuptools-scm
     #   sphinx
     #   streamlit
@@ -556,10 +576,14 @@ pandas==2.2.2
     #   formulaic
     #   hypothesis
     #   lifelines
+    #   pandas-flavor
+    #   scikit-fingerprints
     #   seaborn
     #   streamlit
     #   xarray
     #   xyzpy
+pandas-flavor==0.6.0
+    # via descriptastorus
 pandas-stubs==2.2.2.240603
     # via
     #   baybe (pyproject.toml)
@@ -651,7 +675,6 @@ pygments==2.18.0
     #   ipython
     #   jupyter-console
     #   nbconvert
-    #   qtconsole
     #   rich
     #   sphinx
 pyparsing==3.1.2
@@ -694,6 +717,7 @@ pywinpty==2.0.13 ; os_name == 'nt'
 pyyaml==6.0.1
     # via
     #   dask
+    #   huggingface-hub
     #   jupyter-events
     #   jupytext
     #   myst-parser
@@ -705,15 +729,11 @@ pyzmq==26.0.3
     #   jupyter-client
     #   jupyter-console
     #   jupyter-server
-    #   qtconsole
-qtconsole==5.5.2
-    # via jupyter
-qtpy==2.4.1
-    # via qtconsole
 rdkit==2024.3.3
     # via
-    #   baybe (pyproject.toml)
+    #   descriptastorus
     #   mordredcommunity
+    #   scikit-fingerprints
 referencing==0.35.1
     # via
     #   jsonschema
@@ -722,6 +742,7 @@ referencing==0.35.1
 requests==2.32.3
     # via
     #   cachecontrol
+    #   huggingface-hub
     #   jupyterlab-server
     #   opentelemetry-exporter-otlp-proto-http
     #   pip-audit
@@ -745,11 +766,14 @@ rpds-py==0.19.0
     #   referencing
 ruff==0.5.2
     # via baybe (pyproject.toml)
+scikit-fingerprints==1.9.0
+    # via baybe (pyproject.toml)
 scikit-learn==1.5.1
     # via
     #   baybe (pyproject.toml)
     #   gpytorch
     #   ngboost
+    #   scikit-fingerprints
     #   scikit-learn-extra
     #   skl2onnx
 scikit-learn-extra==0.3.0
@@ -759,13 +783,19 @@ scipy==1.14.0
     #   baybe (pyproject.toml)
     #   autograd-gamma
     #   botorch
+    #   datasketch
+    #   descriptastorus
+    #   e3fp
     #   formulaic
     #   gpytorch
     #   lifelines
     #   linear-operator
     #   ngboost
+    #   scikit-fingerprints
     #   scikit-learn
     #   scikit-learn-extra
+sdaxen-python-utilities==0.1.5
+    # via e3fp
 seaborn==0.13.2
     # via baybe (pyproject.toml)
 send2trash==1.8.3
@@ -787,6 +817,8 @@ six==1.16.0
     #   rfc3339-validator
 skl2onnx==1.17.0
     # via baybe (pyproject.toml)
+smart-open==7.0.5
+    # via e3fp
 smmap==5.0.1
     # via gitdb
 sniffio==1.3.1
@@ -801,7 +833,7 @@ sortedcontainers==2.4.0
     #   hypothesis
 soupsieve==2.5
     # via beautifulsoup4
-sphinx==7.4.7
+sphinx==8.1.3
     # via
     #   baybe (pyproject.toml)
     #   furo
@@ -810,7 +842,7 @@ sphinx==7.4.7
     #   sphinx-basic-ng
     #   sphinx-copybutton
     #   sphinxcontrib-bibtex
-sphinx-autodoc-typehints==2.2.3
+sphinx-autodoc-typehints==2.5.0
     # via baybe (pyproject.toml)
 sphinx-basic-ng==1.0.0b2
     # via furo
@@ -898,8 +930,10 @@ tox-uv==1.9.1
     # via baybe (pyproject.toml)
 tqdm==4.66.4
     # via
+    #   huggingface-hub
     #   ngboost
     #   pyro-ppl
+    #   scikit-fingerprints
     #   xyzpy
 traitlets==5.14.3
     # via
@@ -917,7 +951,6 @@ traitlets==5.14.3
     #   nbclient
     #   nbconvert
     #   nbformat
-    #   qtconsole
 triton==2.3.1 ; python_full_version < '3.12' and platform_machine == 'x86_64' and platform_system == 'Linux'
     # via torch
 typeguard==2.13.3
@@ -939,6 +972,7 @@ typing-extensions==4.12.2
     #   cattrs
     #   formulaic
     #   funcy-stubs
+    #   huggingface-hub
     #   ipython
     #   mypy
     #   opentelemetry-sdk
@@ -977,8 +1011,11 @@ wrapt==1.16.0
     # via
     #   deprecated
     #   formulaic
+    #   smart-open
 xarray==2024.6.0
-    # via xyzpy
+    # via
+    #   pandas-flavor
+    #   xyzpy
 xyzpy==1.2.1
     # via baybe (pyproject.toml)
 zipp==3.19.2

CHANGELOG.md

@@ -10,8 +10,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Example for a traditional mixture
 
 ### Changed
+- `SubstanceParameter` encodings are now computed exclusively with the
+  `scikit-fingerprints` package, granting access to all fingerprints available therein
 - Example for slot-based mixtures has been revised and grouped together with the new 
   traditional mixture example
+- Memory caching is now non-verbose
 
 ### Deprecations
 - Passing a dataframe via the `data` argument to `Objective.transform` is no longer
@@ -21,6 +24,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `get_transform_parameters` has been replaced with `get_transform_objects`
 - Passing a dataframe via the `data` argument to `Target.transform` is no longer
   possible. The data must now be passed as a series as first positional argument.
+- `SubstanceEncoding` value `MORGAN_FP`. As a replacement, `ECFP` with 1024 bits and
+  radius of 4 can be used.
+- `SubstanceEncoding` value `RDKIT`. As a replacement, `RDKIT2DDESCRIPTORS` can be used.
 
 ## [0.11.3] - 2024-11-06
 ### Fixed

CONTRIBUTORS.md

@@ -25,4 +25,6 @@
 - Di Jin (Merck Life Science KGaA, Darmstadt, Germany):\
   Cardinality constraints
 - Julian Streibel (Merck Life Science KGaA, Darmstadt, Germany):\
-  Bernoulli multi-armed bandit and Thompson sampling
+  Bernoulli multi-armed bandit and Thompson sampling
+- Karin Hrovatin (Merck KGaA, Darmstadt, Germany):\
+  `scikit-fingerprints` support