From 25e4855079556bc4bea45f6590e0b77e55690a83 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 13:28:36 -0800 Subject: [PATCH 01/14] Update sklearn to >= 1.5.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index cd5cd0bf..e47a5bce 100644 --- a/setup.cfg +++ b/setup.cfg @@ -41,7 +41,7 @@ install_requires = pandas==2.1.4 requests seaborn==0.13.0 - scikit-learn==1.2.1 + scikit-learn>=1.5.0 sklearn_pandas>=2.0.0 tqdm statsmodels==0.14.0 From 2eccc1f458cf79bd9d1787086a34d4cf986bf264 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 14:44:48 -0800 Subject: [PATCH 02/14] update indices_to_mask import that was changed in sklearn 1.3.0 --- afqinsight/_serial_bagging.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/afqinsight/_serial_bagging.py b/afqinsight/_serial_bagging.py index f9536b0e..24a57a95 100644 --- a/afqinsight/_serial_bagging.py +++ b/afqinsight/_serial_bagging.py @@ -23,7 +23,8 @@ _parallel_predict_regression, ) from sklearn.ensemble._base import _partition_estimators -from sklearn.utils import check_array, check_random_state, indices_to_mask, resample +from sklearn.utils import check_array, check_random_state, resample +from sklearn.utils._mask import indices_to_mask from sklearn.utils.metaestimators import if_delegate_has_method from sklearn.utils.random import sample_without_replacement from sklearn.utils.validation import ( From 9a0b84ec09af206cf37ce19a3c2463a95566fe40 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 14:54:14 -0800 Subject: [PATCH 03/14] change if_delegate_has_method to available_if in metaestimators --- afqinsight/_serial_bagging.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/afqinsight/_serial_bagging.py b/afqinsight/_serial_bagging.py index 24a57a95..c86fb78d 100644 --- a/afqinsight/_serial_bagging.py +++ b/afqinsight/_serial_bagging.py @@ -25,7 +25,7 @@ from sklearn.ensemble._base import _partition_estimators from sklearn.utils import check_array, check_random_state, resample from sklearn.utils._mask import indices_to_mask -from sklearn.utils.metaestimators import if_delegate_has_method +from sklearn.utils.metaestimators import available_if from sklearn.utils.random import sample_without_replacement from sklearn.utils.validation import ( _check_sample_weight, From 5552f24b5664a6d63144be707f19a28e0b6973d9 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 15:07:07 -0800 Subject: [PATCH 04/14] change more if_delegate_has_method --- afqinsight/_serial_bagging.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/afqinsight/_serial_bagging.py b/afqinsight/_serial_bagging.py index c86fb78d..62de2f71 100644 --- a/afqinsight/_serial_bagging.py +++ b/afqinsight/_serial_bagging.py @@ -611,7 +611,7 @@ def predict_log_proba(self, X): else: return np.log(self.predict_proba(X)) - @if_delegate_has_method(delegate="base_estimator") + @available_if(lambda est: hasattr(est.base_estimator, "decision_function")) def decision_function(self, X): """Average of the decision functions of the base classifiers. From 257355d479c7aab6032510adc3e31a8248ad54e0 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:18:13 -0800 Subject: [PATCH 05/14] Fix sklearn to 1.5.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e47a5bce..89d41527 100644 --- a/setup.cfg +++ b/setup.cfg @@ -41,7 +41,7 @@ install_requires = pandas==2.1.4 requests seaborn==0.13.0 - scikit-learn>=1.5.0 + scikit-learn==1.5.2 sklearn_pandas>=2.0.0 tqdm statsmodels==0.14.0 From 0d36bad861f58a7e6a5de94f6eb493b419285c62 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:27:10 -0800 Subject: [PATCH 06/14] Update statsmodels pin from 0.14.0 to 0.14.4 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 89d41527..e28d53bb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -44,7 +44,7 @@ install_requires = scikit-learn==1.5.2 sklearn_pandas>=2.0.0 tqdm - statsmodels==0.14.0 + statsmodels==0.14.4 zip_safe = False include_package_data = True packages = find: From c3f7960459b7af1df753873f1cb5f032d2d55040 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:33:24 -0800 Subject: [PATCH 07/14] Update seaborn pin from 0.13.0 to 0.13.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e28d53bb..06188479 100644 --- a/setup.cfg +++ b/setup.cfg @@ -40,7 +40,7 @@ install_requires = numpy==1.23.5 pandas==2.1.4 requests - seaborn==0.13.0 + seaborn==0.13.2 scikit-learn==1.5.2 sklearn_pandas>=2.0.0 tqdm From 555c321497230680ccd3cdedbbb693c2275324e5 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:37:50 -0800 Subject: [PATCH 08/14] Update pandas pin from 2.1.4 to 2.2.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 06188479..58a6e54f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -38,7 +38,7 @@ install_requires = matplotlib<3.9 groupyr>=0.3.4 numpy==1.23.5 - pandas==2.1.4 + pandas==2.2.3 requests seaborn==0.13.2 scikit-learn==1.5.2 From 2a340b94eb0104d3b8a4c36029b994df258e6d31 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:47:51 -0800 Subject: [PATCH 09/14] Update matplotlib pin from <3.9 to 3.9.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 58a6e54f..b30a135b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -35,7 +35,7 @@ python_requires = >=3.10 install_requires = scipy==1.13.1 dipy>=1.0.0 - matplotlib<3.9 + matplotlib==3.9.3 groupyr>=0.3.4 numpy==1.23.5 pandas==2.2.3 From 0ed6477c3861bc5e5467dc0163550afd20eccc51 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 16:53:03 -0800 Subject: [PATCH 10/14] Update scipy pin from 1.3.1 to 1.4.1 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b30a135b..1b3f5202 100644 --- a/setup.cfg +++ b/setup.cfg @@ -33,7 +33,7 @@ setup_requires = setuptools_scm python_requires = >=3.10 install_requires = - scipy==1.13.1 + scipy==1.14.1 dipy>=1.0.0 matplotlib==3.9.3 groupyr>=0.3.4 From d0c414884c129c9a0d9e8a9d373ce474b46c06e9 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 17:01:06 -0800 Subject: [PATCH 11/14] Update dipy pin from 1.0.0 to 1.9.0 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 1b3f5202..c8be5a60 100644 --- a/setup.cfg +++ b/setup.cfg @@ -34,7 +34,7 @@ setup_requires = python_requires = >=3.10 install_requires = scipy==1.14.1 - dipy>=1.0.0 + dipy==1.9.0 matplotlib==3.9.3 groupyr>=0.3.4 numpy==1.23.5 From 6fd1e5cd1d37c34817b22c6209567b8157a9004c Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 17:06:38 -0800 Subject: [PATCH 12/14] Update numpy pin from 1.23.5 to 2.1.3 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index c8be5a60..4ba765a0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -37,7 +37,7 @@ install_requires = dipy==1.9.0 matplotlib==3.9.3 groupyr>=0.3.4 - numpy==1.23.5 + numpy==2.1.3 pandas==2.2.3 requests seaborn==0.13.2 From 4417b470c22f4aaab3520d4736c863eea4efb754 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 17:08:50 -0800 Subject: [PATCH 13/14] Update numpy pin from 1.23.5 to 1.26.4, numpy >= 2 breaking change --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 4ba765a0..93b8a131 100644 --- a/setup.cfg +++ b/setup.cfg @@ -37,7 +37,7 @@ install_requires = dipy==1.9.0 matplotlib==3.9.3 groupyr>=0.3.4 - numpy==2.1.3 + numpy==1.26.4 pandas==2.2.3 requests seaborn==0.13.2 From d557b04fada3c884e08ea57ecba6111d7e9cc8d7 Mon Sep 17 00:00:00 2001 From: Howard Chiu <137316255+chiuhoward@users.noreply.github.com> Date: Wed, 4 Dec 2024 17:20:45 -0800 Subject: [PATCH 14/14] Update references to richford to tractometry in contributing.md --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index fb09e31c..5d39ed25 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -31,7 +31,7 @@ You can contribute in many ways: ### Report Bugs -Report bugs at . +Report bugs at . If you are reporting a bug, please include: @@ -64,7 +64,7 @@ articles, and such. ### Submit Feedback The best way to send feedback is to file an issue at -. +. If you are proposing a feature: