scikit-survival 0.22.2__cp39-cp39-win_amd64.whl → 0.23.1__cp39-cp39-win_amd64.whl

{scikit_survival-0.22.2.dist-info → scikit_survival-0.23.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-survival
-Version: 0.22.2
+Version: 0.23.1
 Summary: Survival analysis built on top of scikit-learn
 Author-email: Sebastian Pölsterl <sebp@k-d-w.org>
 License: GNU GENERAL PUBLIC LICENSE
@@ -694,13 +694,13 @@ Classifier: Programming Language :: C++
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: COPYING
 Requires-Dist: ecos
@@ -708,20 +708,19 @@ Requires-Dist: joblib
 Requires-Dist: numexpr
 Requires-Dist: numpy
 Requires-Dist: osqp !=0.6.0,!=0.6.1
-Requires-Dist: pandas >=1.0.5
+Requires-Dist: pandas >=1.4.0
 Requires-Dist: scipy >=1.3.2
-Requires-Dist: scikit-learn <1.4,>=1.3.0
-Requires-Dist: importlib-resources >=1.3 ; python_version < "3.9"
+Requires-Dist: scikit-learn <1.6,>=1.4.0
 Provides-Extra: dev
 Requires-Dist: black[jupyter] ; extra == 'dev'
 Requires-Dist: build ; extra == 'dev'
 Requires-Dist: coverage ; extra == 'dev'
-Requires-Dist: cython >=0.29 ; extra == 'dev'
+Requires-Dist: Cython >=3.0.10 ; extra == 'dev'
 Requires-Dist: packaging ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
 Requires-Dist: pytest ; extra == 'dev'
 Requires-Dist: ruff ; extra == 'dev'
-Requires-Dist: setuptools-scm >=6.4 ; extra == 'dev'
+Requires-Dist: setuptools-scm >=8 ; extra == 'dev'
 Requires-Dist: tomli ; extra == 'dev'
 Requires-Dist: tox ; extra == 'dev'
 Provides-Extra: docs
@@ -729,15 +728,15 @@ Requires-Dist: ipython !=8.7.0 ; extra == 'docs'
 Requires-Dist: nbsphinx >=0.9.2 ; extra == 'docs'
 Requires-Dist: docutils ; extra == 'docs'
 Requires-Dist: setuptools-scm ; extra == 'docs'
-Requires-Dist: sphinx ~=6.2.1 ; extra == 'docs'
-Requires-Dist: pydata-sphinx-theme ~=0.13.3 ; extra == 'docs'
+Requires-Dist: sphinx ~=7.3.7 ; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme ~=0.15.2 ; extra == 'docs'
 Requires-Dist: sphinxcontrib-spelling ; extra == 'docs'
-Requires-Dist: sphinx-design ~=0.4.1 ; extra == 'docs'
+Requires-Dist: sphinx-design ~=0.5.0 ; extra == 'docs'
 Requires-Dist: sphinx-copybutton ~=0.5.2 ; extra == 'docs'
 Provides-Extra: nbval
 Requires-Dist: ipykernel ; extra == 'nbval'
 Requires-Dist: ipython !=8.7.0 ; extra == 'nbval'
-Requires-Dist: matplotlib ~=3.6.2 ; extra == 'nbval'
+Requires-Dist: matplotlib ~=3.8.0 ; extra == 'nbval'
 Requires-Dist: nbformat ; extra == 'nbval'
 Requires-Dist: nbval >=0.10.0 ; extra == 'nbval'
 Requires-Dist: seaborn ~=0.11.2 ; extra == 'nbval'
@@ -776,15 +775,15 @@ this unique characteristic of such a dataset into account.
 Requirements
 ============
 
-- Python 3.8 or later
+- Python 3.9 or later
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
-- pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- pandas 1.4.0 or later
+- scikit-learn 1.4 or 1.5
+- scipy
 - C/C++ compiler
 
 ============
@@ -794,7 +793,7 @@ Installation
 The easiest way to install scikit-survival is to use
 `Anaconda <https://www.anaconda.com/distribution/>`_ by running::
 
-  conda install -c sebp scikit-survival
+  conda install -c conda-forge scikit-survival
 
 Alternatively, you can install scikit-survival from source
 following `this guide <https://scikit-survival.readthedocs.io/en/stable/install.html#from-source>`_.
@@ -867,7 +866,7 @@ Please cite the following paper if you are using **scikit-survival**.
   :alt: codecov
 
 .. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
-   :target: https://www.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=sebp/scikit-survival&amp;utm_campaign=Badge_Grade
+   :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
    :alt: Codacy Badge
 
 .. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest

{scikit_survival-0.22.2.dist-info → scikit_survival-0.23.1.dist-info}/RECORD

@@ -1,18 +1,18 @@
 sksurv/__init__.py,sha256=ylL6ChkAkHWnuIFWG5lky_d_ZNFfukUUt5tU0HVJfgo,3710
-sksurv/base.py,sha256=4T5WgwWl4sPO3HvlfLZ1dm5CN5ZPcnaVOfvJYG08YIc,3735
-sksurv/column.py,sha256=KuzS4ayH5VWvT13n_7S7uafNI2VqQsMSJxKlMC95V9w,7028
+sksurv/base.py,sha256=0HXvIivawJMsby7UxnLUFOKbKvurrJEM0KrMIYmqyBU,3801
+sksurv/column.py,sha256=hojN9vVDw2ka5LRueyc3f1g12AjwuzSIiPqGP5js2Nk,6670
 sksurv/compare.py,sha256=WbJb2NFXMncgkcrNKq3Xgo5YqW_klgkDkKJc219aJiw,4212
 sksurv/exceptions.py,sha256=WopRsYNia5MQTvvVXL3U_nf418t29pplfBz6HFtmt1M,819
 sksurv/functions.py,sha256=x63NGGVQVqtFiEG-wXW569q1U_kKJFwbOb9-8BcfpaM,3780
-sksurv/metrics.py,sha256=fT-PLqo4THSuBJC1jo4FiMjwXgUgIReTxVcaoJYZ6Yo,38409
-sksurv/nonparametric.py,sha256=e1ESEJFL-3pHGXquXLKcp8h7ATyHxXerfAuY_3MruGo,19353
+sksurv/metrics.py,sha256=rAA_UmN-ddNm52OE3pcixZcfg_XKFig7CeQ2eQw7ArI,38379
+sksurv/nonparametric.py,sha256=aZo5tXkv8a6Fup7NKZzSqW9GEtpCfwk82B2RCWvD0QI,19339
 sksurv/preprocessing.py,sha256=WGrL3ngfskFuMqdMxr7Dkw5Bj8NWij_xZuLRqDdz5Eo,5315
-sksurv/testing.py,sha256=n85UI7pniFfd0A20RB2R1DjC_DMIfbQdGxDxtGRQ8Fs,4180
+sksurv/testing.py,sha256=9qoUAeRfp3tb4Zg7oCHkBS0DJXkIuxdflRLoV7NEfek,4403
 sksurv/util.py,sha256=S8GnCvsaOUqjbzFXQylXCUnQSfoy057H8FQ4XidYqgI,12276
 sksurv/bintrees/__init__.py,sha256=z0GwaTPCzww2H2aXF28ubppw0Oc4umNTAlFAKu1VBJc,742
-sksurv/bintrees/_binarytrees.cp39-win_amd64.pyd,sha256=9XA4wgZDGGgRqC1XYg3AA2v8cqnAOgQCdJAjc1P3H10,68608
+sksurv/bintrees/_binarytrees.cp39-win_amd64.pyd,sha256=30uo_DC-lbLBObTEFnzmE7Xxe4IvZ1VSWVJtwcl-Ghw,68608
 sksurv/datasets/__init__.py,sha256=ZIU1vPRhO2CYpTf-Lbr64S73JkR1CAP7aVBO_wGHHAY,313
-sksurv/datasets/base.py,sha256=bVSE6Eg1HLvQZwxLhc5IxZtQOEJaag6RYIroaLBtbfI,15234
+sksurv/datasets/base.py,sha256=l4xiUUNkYbY-JhpU2En6Kr7AZ29cb-KVUxS6SL-RxAk,15126
 sksurv/datasets/data/GBSG2.arff,sha256=oX_UM7Qy841xBOArXBkUPLzIxNTvdtIJqpxXsqGGw9Q,26904
 sksurv/datasets/data/actg320.arff,sha256=BwIq5q_i_75G2rPFQ6TjO0bsiR8MwA6wPouG-SX7TUo,46615
 sksurv/datasets/data/breast_cancer_GSE7390-metastasis.arff,sha256=1dNSJczfgZOjp4Ya0SKREreyGorzWd-rm1ryihwIAck,265026
@@ -20,18 +20,18 @@ sksurv/datasets/data/flchain.arff,sha256=4LVUyEe-45ozaWPy0VkN-1js_MNsKw1gs2E-JRy
 sksurv/datasets/data/veteran.arff,sha256=LxZtbmq4I82rcB24JeJTYRtlgwPc3vM2OX5hg-q7xTw,5408
 sksurv/datasets/data/whas500.arff,sha256=dvqRzx-nwgSVJZxNVE2zelnt7l3xgzFtMucB7Wux574,28292
 sksurv/ensemble/__init__.py,sha256=aBjRTFm8UE5sTew292-qcplLUCc6owAfY6osWlj-VSM,193
-sksurv/ensemble/_coxph_loss.cp39-win_amd64.pyd,sha256=ANUWXm78pndwaxVrnTlejslJYRYBl4XAnqpXm_mFwUE,149504
-sksurv/ensemble/boosting.py,sha256=nILMMJQnJ46psx3apcrwnOV5EZ2AKNkx7FAdTSz7iwo,53672
-sksurv/ensemble/forest.py,sha256=gBxayDinoqMq_3ymwUvJVaKP4ghPTUo5hlli0TSPx5Q,35289
-sksurv/ensemble/survival_loss.py,sha256=kQOjF_kZQ_ilrHP9ogp4ZqeBM27gRfUk084_-zRuiTo,6515
+sksurv/ensemble/_coxph_loss.cp39-win_amd64.pyd,sha256=J0X-IVzklB5uO9pN4YQGqd7W_2Uraz_YrK4nLDz4484,151040
+sksurv/ensemble/boosting.py,sha256=T2DWIPGMK9S_BX9dIuhnptH3v2P5jfCv_d-wXR0l3zE,63690
+sksurv/ensemble/forest.py,sha256=su6MFuBhD2mMM6SAAq8_ixEv4i7kYm40gcBdNeXmw14,36330
+sksurv/ensemble/survival_loss.py,sha256=v3tSou5t1YY6lBydAZYZ66DLqAirvRhErqW1dZYrTWE,6093
 sksurv/io/__init__.py,sha256=dalzZGTrvekCM8wwsB636rg1dwDkQtDWaBOw7TpHr5U,94
 sksurv/io/arffread.py,sha256=47rFxaZuavV0cbFUrZ_NjSmSByWXqkwZ4MkpFK4jw_w,1897
 sksurv/io/arffwrite.py,sha256=Dkvnr_zz4i23xGPDTwxTAOOggbL1GxtgSi1em6kVp0Q,4609
 sksurv/kernels/__init__.py,sha256=R1if2sVd_0_f6LniIGUR0tipIfzRKpzgGYnvrVZZvHM,78
-sksurv/kernels/_clinical_kernel.cp39-win_amd64.pyd,sha256=wGlEGxNrmzjTtoh3ldE9uEKCbdULSFbMZqugCCiY_sw,156160
-sksurv/kernels/clinical.py,sha256=tkc-usSB9wn6KMmNi45F992r9wX4mKNXEEKSvfJX_Mk,10910
+sksurv/kernels/_clinical_kernel.cp39-win_amd64.pyd,sha256=XscUnLBFhTgd3Iac8bl3Jtn4cFToU27T2n8LEbl7JcQ,157696
+sksurv/kernels/clinical.py,sha256=kVAMx95rgrerfvGlmuNgW4hc3HojTruKoNnhuaeLkGw,11046
 sksurv/linear_model/__init__.py,sha256=dO6Mr3wXk6Q-KQEuhpdgMeY3ji8ZVdgC-SeSRnrJdmw,155
-sksurv/linear_model/_coxnet.cp39-win_amd64.pyd,sha256=BtD7k2kt7fZ79Ne_KHN9t85mVqDzYg1tfPQyNH8fehQ,91136
+sksurv/linear_model/_coxnet.cp39-win_amd64.pyd,sha256=zNBEO3bpUAyawI-X6NN-sfd8lQElEWKfIktbk3Ml3tI,92672
 sksurv/linear_model/aft.py,sha256=oWtLF-WCCrdmjJtb9e91SHA-be_IQPTf7Kf9VWoXQB8,7616
 sksurv/linear_model/coxnet.py,sha256=ZJAsJImSoGCL6HJ9uXQdph8sDLAZakcIvMuzRy28F4M,20727
 sksurv/linear_model/coxph.py,sha256=PeYw7I_EHSgV3kriUnEhJg6CIdISkFk9ewlzijHC8Nw,21475
@@ -40,16 +40,16 @@ sksurv/meta/base.py,sha256=AdhIkZi9PvucZ3B2lhhFQpQbwp8EUCDUVOiaev_UsX8,1472
 sksurv/meta/ensemble_selection.py,sha256=NTXzq6xvwL5IwdxyjNVkPOgzU_9lzdsyFKCq0YbdOXo,24673
 sksurv/meta/stacking.py,sha256=md3ZKYYlS23YKbbLjWZqtPRSJYAHfLzN9RlC5RgzYEQ,12629
 sksurv/svm/__init__.py,sha256=CSceYEcBPGKRcJZ4R0u7DzwictGln_weLIsbt2i5xeU,339
-sksurv/svm/_minlip.cp39-win_amd64.pyd,sha256=jug6DXgJCOh1wnm3veapsArORog8z8uUIJ3E6rr5KRQ,154112
-sksurv/svm/_prsvm.cp39-win_amd64.pyd,sha256=DgnoVLTlPRCPVURltwq5KvVx4Jp3yknvCrI8iOEQeRo,151552
-sksurv/svm/minlip.py,sha256=9wPgWblOUe_fVx9xKeaSPT0FaZ3rC6T6Z9Aj5oH2S48,22443
+sksurv/svm/_minlip.cp39-win_amd64.pyd,sha256=h-Cjf1Q_Sg1Y6FYa_Z0uUU1usZ1VrlxEJQoFIvfPlIE,155136
+sksurv/svm/_prsvm.cp39-win_amd64.pyd,sha256=F97QXz0njJ2Bvzeu1EaEEK_HxhTIolIKq2xgunLP6cA,153088
+sksurv/svm/minlip.py,sha256=Elej96P4s6jMNCbGIbNm4ehWI3ew9o2IyF5tfZuTEqg,22416
 sksurv/svm/naive_survival_svm.py,sha256=D6l8ctlpyUPBhcMlF_6KJq9d_tq1Xmtb9w--n8pGcfM,8209
-sksurv/svm/survival_svm.py,sha256=LeZWBZ8kCcbiQwgDVLp34wOcGkBMJHgliTDgsfF6Wts,44793
-sksurv/tree/__init__.py,sha256=XkegoaxZZQK3QFhME1RarbR7tFIEO-qSYsiPCveHszg,46
-sksurv/tree/_criterion.cp39-win_amd64.pyd,sha256=DtFY3h7n1mXbSCSTxbAP2a-OA2COo7FSwbOJg2jHP5o,172032
-sksurv/tree/tree.py,sha256=j6GkRDshPXPv95zQVCVN1cZKJ8A_xHkIWqFfnXthTvc,26000
-scikit_survival-0.22.2.dist-info/COPYING,sha256=Czg9WmPaZE9ijZnDOXbqZIftiaqlnwsyV5kt6sEXHms,35821
-scikit_survival-0.22.2.dist-info/METADATA,sha256=H6USeZIakYzD3UDSN1Cs1_gNkrG7afVJRnM-YGgNv4k,49964
-scikit_survival-0.22.2.dist-info/WHEEL,sha256=GZFS91_ufm4WrNPBaFVPB9MvOXR6bMZQhPcZRRTN5YM,100
-scikit_survival-0.22.2.dist-info/top_level.txt,sha256=fPkcFA-XQGbwnD_ZXOvaOWmSd34Qezr26Mn99nYPvAg,7
-scikit_survival-0.22.2.dist-info/RECORD,,
+sksurv/svm/survival_svm.py,sha256=oGac8mWlDOlZPRoK1MmbcigKUq2bWPw1Uc8vYSsSlwI,44730
+sksurv/tree/__init__.py,sha256=ozb0fhURX-lpiSiHZd0DMnjkqhC0XOC2CTZq0hEZLPw,65
+sksurv/tree/_criterion.cp39-win_amd64.pyd,sha256=oWNiyb9ApRWoIBvOaXGl2E5f-zHQDwAhoqMdTPaVLDM,173056
+sksurv/tree/tree.py,sha256=PPkqq8jDeAHCd9L283-SLCk7lTBfH-HObTOuOXOvqHs,27248
+scikit_survival-0.23.1.dist-info/COPYING,sha256=Czg9WmPaZE9ijZnDOXbqZIftiaqlnwsyV5kt6sEXHms,35821
+scikit_survival-0.23.1.dist-info/METADATA,sha256=alYA45glhQaH9X_MzelejmubVqXGWVaPiiMPqRa6Yns,49841
+scikit_survival-0.23.1.dist-info/WHEEL,sha256=zq3MnTB53_Huh0eFGROKhLNn5cmUbG6gUFCG6-LWXTY,99
+scikit_survival-0.23.1.dist-info/top_level.txt,sha256=fPkcFA-XQGbwnD_ZXOvaOWmSd34Qezr26Mn99nYPvAg,7
+scikit_survival-0.23.1.dist-info/RECORD,,

{scikit_survival-0.22.2.dist-info → scikit_survival-0.23.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (75.3.0)
 Root-Is-Purelib: false
 Tag: cp39-cp39-win_amd64
 

sksurv/base.py

@@ -98,3 +98,6 @@ class SurvivalAnalysisMixin:
 
         result = concordance_index_censored(y[name_event], y[name_time], risk_score)
         return result[0]
+
+    def _more_tags(self):
+        return {"requires_y": True}

sksurv/column.py

@@ -64,18 +64,8 @@ def standardize(table, with_std=True):
         Table with numeric columns normalized.
         Categorical columns in the input table remain unchanged.
     """
-    if isinstance(table, pd.DataFrame):
-        cat_columns = table.select_dtypes(include=["category"]).columns
-    else:
-        cat_columns = []
-
     new_frame = _apply_along_column(table, standardize_column, with_std=with_std)
 
-    # work around for apply converting category dtype to object
-    # https://github.com/pydata/pandas/issues/9573
-    for col in cat_columns:
-        new_frame[col] = table[col].copy()
-
     return new_frame
 
 
@@ -199,7 +189,7 @@ def categorical_to_numeric(table):
             except ValueError:
                 classes = column.dropna().unique()
                 classes.sort(kind="mergesort")
-                nc = column.replace(classes, np.arange(classes.shape[0], dtype=np.int64))
+                nc = column.map(dict(zip(classes, range(classes.shape[0]))))
             return nc
         if column.dtype == bool:
             return column.astype(np.int64)

sksurv/datasets/base.py

@@ -1,4 +1,3 @@
-import sys
 import warnings
 
 import numpy as np
@@ -22,10 +21,8 @@ __all__ = [
 
 
 def _get_data_path(name):
-    if sys.version_info >= (3, 9):
-        from importlib.resources import files
-    else:
-        from importlib_resources import files
+    from importlib.resources import files
+
     return files(__package__) / "data" / name