[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/files/, sci-libs/scikit-optimize/, profiles/
commit: 716a22e8cfcc8db49e96b764405648a6be1cc3a6 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Apr 11 14:36:00 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Apr 11 14:36:00 2024 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=716a22e8 sci-libs/scikit-optimize: treeclean Closes: https://bugs.gentoo.org/920439 Closes: https://bugs.gentoo.org/906565 Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 6 -- sci-libs/scikit-optimize/Manifest | 1 - .../files/scikit-optimize-0.9.0-numpy-1.24.patch | 22 - .../scikit-optimize-0.9.0-scikit-learn-1.2.0.patch | 104 - sci-libs/scikit-optimize/metadata.xml | 12 --- .../scikit-optimize-0.9.0-r1.ebuild| 39 .../scikit-optimize/scikit-optimize-0.9.0.ebuild | 31 -- 7 files changed, 215 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index e5309eeeb5b9..bef723653deb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -328,12 +328,6 @@ games-engines/renpy net-misc/econnman sci-chemistry/mdtraj -# Andrew Ammerlaan (2024-03-10) -# Archived upstream, latest release is 3 years old. One test -# failure with python 3.11, more with python 3.12. -# Removal on: 2024-04-10. Bug #920439 -sci-libs/scikit-optimize - # Eray Aslan (2024-03-10) # Mask experimental software =mail-mta/postfix-3.10* diff --git a/sci-libs/scikit-optimize/Manifest b/sci-libs/scikit-optimize/Manifest deleted file mode 100644 index 460f16a85cb6.. --- a/sci-libs/scikit-optimize/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scikit-optimize-0.9.0.tar.gz 275570 BLAKE2B ab481bf1cfc2b8c7cff213ae0ce2fa937de8f6269b491cf63ae115eea5c936c8a5c26b7fb339fa6cd2927c5105068635c008d6dc8b3f99b4b5d3abfed1a1c5a2 SHA512 a4c1bd589686dbbabcc5de38a4eb581c040cc2c3f83bc250ddcbe66314f03fc68b7b12d7679049da34c42445b446e1af3873f7ce90bec2a5361f0077ff3e9b74 diff --git a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch deleted file mode 100644 index 65fc26f3eed1.. --- a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/skopt/space/transformers.py b/skopt/space/transformers.py -index 68892952..87cc3b68 100644 a/skopt/space/transformers.py -+++ b/skopt/space/transformers.py -@@ -259,7 +259,7 @@ def transform(self, X): - if (self.high - self.low) == 0.: - return X * 0. - if self.is_int: --return (np.round(X).astype(np.int) - self.low) /\ -+return (np.round(X).astype(np.int64) - self.low) /\ -(self.high - self.low) - else: - return (X - self.low) / (self.high - self.low) -@@ -272,7 +272,7 @@ def inverse_transform(self, X): - raise ValueError("All values should be greater than 0.0") - X_orig = X * (self.high - self.low) + self.low - if self.is_int: --return np.round(X_orig).astype(np.int) -+return np.round(X_orig).astype(np.int64) - return X_orig - - diff --git a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch deleted file mode 100644 index 8cf8cff9479f.. --- a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch +++ /dev/null @@ -1,104 +0,0 @@ -diff --git a/skopt/learning/forest.py b/skopt/learning/forest.py -index 096770c1d..ebde568f5 100644 a/skopt/learning/forest.py -+++ b/skopt/learning/forest.py -@@ -27,7 +27,7 @@ def _return_std(X, trees, predictions, min_variance): - --- - std : array-like, shape=(n_samples,) - Standard deviation of `y` at `X`. If criterion --is set to "mse", then `std[i] ~= std(y | X[i])`. -+is set to "squared_error", then `std[i] ~= std(y | X[i])`. - - """ - # This derives std(y | x) as described in 4.3.2 of arXiv:1211.0906 -@@ -61,9 +61,9 @@ class RandomForestRegressor(_sk_RandomForestRegressor): - n_estimators : integer, optional (default=10) - The number of trees in the forest. - --criterion : string, optional (default="mse") -+criterion : string, optional (default="squared_error") - The function to measure the quality of a split. Supported criteria --are "mse" for the mean squared error, which is equal to variance -+are "squared_error" for the mean squared error, which is equal to variance - reduction as feature selection criterion, and "mae" for the mean - absolute error. - -@@ -194,7 +194,7 @@ class RandomForestRegressor(_sk_RandomForestRegressor): - .. [1] L. Breiman, "Random Forests", Machine Learning, 45(1), 5-32, 2001. - - """ --def __init__(self,
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/, sci-libs/scikit-optimize/files/
commit: a7c3db5d998d752370dff2abf57c9515c9019461 Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Nov 6 11:40:00 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Nov 6 11:40:22 2023 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a7c3db5d sci-libs/scikit-optimize: pep517, numpy-1.24 compat Closes: https://bugs.gentoo.org/910028 Closes: https://bugs.gentoo.org/890666 Signed-off-by: Andrew Ammerlaan gentoo.org> .../files/scikit-optimize-0.9.0-numpy-1.24.patch | 22 + .../scikit-optimize-0.9.0-scikit-learn-1.2.0.patch | 104 + .../scikit-optimize-0.9.0-r1.ebuild| 39 3 files changed, 165 insertions(+) diff --git a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch new file mode 100644 index ..65fc26f3eed1 --- /dev/null +++ b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-numpy-1.24.patch @@ -0,0 +1,22 @@ +diff --git a/skopt/space/transformers.py b/skopt/space/transformers.py +index 68892952..87cc3b68 100644 +--- a/skopt/space/transformers.py b/skopt/space/transformers.py +@@ -259,7 +259,7 @@ def transform(self, X): + if (self.high - self.low) == 0.: + return X * 0. + if self.is_int: +-return (np.round(X).astype(np.int) - self.low) /\ ++return (np.round(X).astype(np.int64) - self.low) /\ +(self.high - self.low) + else: + return (X - self.low) / (self.high - self.low) +@@ -272,7 +272,7 @@ def inverse_transform(self, X): + raise ValueError("All values should be greater than 0.0") + X_orig = X * (self.high - self.low) + self.low + if self.is_int: +-return np.round(X_orig).astype(np.int) ++return np.round(X_orig).astype(np.int64) + return X_orig + + diff --git a/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch new file mode 100644 index ..8cf8cff9479f --- /dev/null +++ b/sci-libs/scikit-optimize/files/scikit-optimize-0.9.0-scikit-learn-1.2.0.patch @@ -0,0 +1,104 @@ +diff --git a/skopt/learning/forest.py b/skopt/learning/forest.py +index 096770c1d..ebde568f5 100644 +--- a/skopt/learning/forest.py b/skopt/learning/forest.py +@@ -27,7 +27,7 @@ def _return_std(X, trees, predictions, min_variance): + --- + std : array-like, shape=(n_samples,) + Standard deviation of `y` at `X`. If criterion +-is set to "mse", then `std[i] ~= std(y | X[i])`. ++is set to "squared_error", then `std[i] ~= std(y | X[i])`. + + """ + # This derives std(y | x) as described in 4.3.2 of arXiv:1211.0906 +@@ -61,9 +61,9 @@ class RandomForestRegressor(_sk_RandomForestRegressor): + n_estimators : integer, optional (default=10) + The number of trees in the forest. + +-criterion : string, optional (default="mse") ++criterion : string, optional (default="squared_error") + The function to measure the quality of a split. Supported criteria +-are "mse" for the mean squared error, which is equal to variance ++are "squared_error" for the mean squared error, which is equal to variance + reduction as feature selection criterion, and "mae" for the mean + absolute error. + +@@ -194,7 +194,7 @@ class RandomForestRegressor(_sk_RandomForestRegressor): + .. [1] L. Breiman, "Random Forests", Machine Learning, 45(1), 5-32, 2001. + + """ +-def __init__(self, n_estimators=10, criterion='mse', max_depth=None, ++def __init__(self, n_estimators=10, criterion='squared_error', max_depth=None, + min_samples_split=2, min_samples_leaf=1, + min_weight_fraction_leaf=0.0, max_features='auto', + max_leaf_nodes=None, min_impurity_decrease=0., +@@ -228,20 +228,20 @@ def predict(self, X, return_std=False): + Returns + --- + predictions : array-like of shape = (n_samples,) +-Predicted values for X. If criterion is set to "mse", ++Predicted values for X. If criterion is set to "squared_error", + then `predictions[i] ~= mean(y | X[i])`. + + std : array-like of shape=(n_samples,) + Standard deviation of `y` at `X`. If criterion +-is set to "mse", then `std[i] ~= std(y | X[i])`. ++is set to "squared_error", then `std[i] ~= std(y | X[i])`. + + """ + mean = super(RandomForestRegressor, self).predict(X) + + if return_std: +-if self.criterion != "mse": ++if self.criterion != "squared_error": + raise ValueError( +-"Expected impurity to be 'mse', got %s instead" ++"Expected impurity to be
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/
commit: e8990630a7a9d9a4e248680a2bab310ab3f601a4 Author: Sam James gentoo org> AuthorDate: Mon May 1 12:44:37 2023 + Commit: Sam James gentoo org> CommitDate: Mon May 1 12:48:57 2023 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e8990630 sci-libs/scikit-optimize: drop 0.8.1 Signed-off-by: Sam James gentoo.org> sci-libs/scikit-optimize/Manifest | 1 - .../scikit-optimize/scikit-optimize-0.8.1.ebuild | 26 -- 2 files changed, 27 deletions(-) diff --git a/sci-libs/scikit-optimize/Manifest b/sci-libs/scikit-optimize/Manifest index 2144f37db180..460f16a85cb6 100644 --- a/sci-libs/scikit-optimize/Manifest +++ b/sci-libs/scikit-optimize/Manifest @@ -1,2 +1 @@ -DIST scikit-optimize-0.8.1.tar.gz 278751 BLAKE2B c53b921ed47a2146510a041e34129918cc1b9118e8ae3614f39cc16c87ba5a749e268b9694ade9d95132ec4fb11777f2ef2ec509b1be59c8864ff7b6edde2250 SHA512 8ffacb62869810e1812bdbd2f9f3fe83cad2be03cd795ae2e9aa4e1143ed613c3901ae06be85aecd63c1e3e5b4805e88331d2d8848cc9953988fddfbe62a0287 DIST scikit-optimize-0.9.0.tar.gz 275570 BLAKE2B ab481bf1cfc2b8c7cff213ae0ce2fa937de8f6269b491cf63ae115eea5c936c8a5c26b7fb339fa6cd2927c5105068635c008d6dc8b3f99b4b5d3abfed1a1c5a2 SHA512 a4c1bd589686dbbabcc5de38a4eb581c040cc2c3f83bc250ddcbe66314f03fc68b7b12d7679049da34c42445b446e1af3873f7ce90bec2a5361f0077ff3e9b74 diff --git a/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild b/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild deleted file mode 100644 index 4ddf13b707c6.. --- a/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 2020-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_9 ) -inherit distutils-r1 - -DESCRIPTION="Sequential model-based optimization library" -HOMEPAGE="https://scikit-optimize.github.io/; -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pretty-yaml[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/
commit: 1737f346a45a327057ef92ea3cb3581f07cde49e Author: Michał Górny gentoo org> AuthorDate: Fri Mar 17 12:02:39 2023 + Commit: Michał Górny gentoo org> CommitDate: Fri Mar 17 15:29:04 2023 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1737f346 sci-libs/scikit-optimize: Use pypi.eclass Signed-off-by: Michał Górny gentoo.org> sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild index 1644aadae338..644fcd2382dc 100644 --- a/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild +++ b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild @@ -3,12 +3,12 @@ EAPI=8 +PYPI_NO_NORMALIZE=1 PYTHON_COMPAT=( python3_{9..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Sequential model-based optimization library" HOMEPAGE="https://scikit-optimize.github.io/; -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0"
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/
commit: 2e0e24d67cda8908ec04ec6012b67615815dfb55 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Oct 14 13:12:49 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Oct 14 13:31:18 2022 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e0e24d6 sci-libs/scikit-optimize: enable py3.11 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild index e848ca405e67..ea7246239d10 100644 --- a/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild +++ b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild @@ -1,9 +1,9 @@ -# Copyright 2020-2021 Gentoo Authors +# Copyright 2020-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{8..11} ) inherit distutils-r1 DESCRIPTION="Sequential model-based optimization library"
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/
commit: 0e34aeccae3b8e96aad804737fa339e8731bd783 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Dec 29 14:12:59 2021 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Dec 29 14:13:31 2021 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0e34aecc sci-libs/scikit-optimize: add version 0.9.0, enable py3.10 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-libs/scikit-optimize/Manifest | 1 + .../scikit-optimize/scikit-optimize-0.9.0.ebuild | 31 ++ 2 files changed, 32 insertions(+) diff --git a/sci-libs/scikit-optimize/Manifest b/sci-libs/scikit-optimize/Manifest index e5c7a49776e4..2144f37db180 100644 --- a/sci-libs/scikit-optimize/Manifest +++ b/sci-libs/scikit-optimize/Manifest @@ -1 +1,2 @@ DIST scikit-optimize-0.8.1.tar.gz 278751 BLAKE2B c53b921ed47a2146510a041e34129918cc1b9118e8ae3614f39cc16c87ba5a749e268b9694ade9d95132ec4fb11777f2ef2ec509b1be59c8864ff7b6edde2250 SHA512 8ffacb62869810e1812bdbd2f9f3fe83cad2be03cd795ae2e9aa4e1143ed613c3901ae06be85aecd63c1e3e5b4805e88331d2d8848cc9953988fddfbe62a0287 +DIST scikit-optimize-0.9.0.tar.gz 275570 BLAKE2B ab481bf1cfc2b8c7cff213ae0ce2fa937de8f6269b491cf63ae115eea5c936c8a5c26b7fb339fa6cd2927c5105068635c008d6dc8b3f99b4b5d3abfed1a1c5a2 SHA512 a4c1bd589686dbbabcc5de38a4eb581c040cc2c3f83bc250ddcbe66314f03fc68b7b12d7679049da34c42445b446e1af3873f7ce90bec2a5361f0077ff3e9b74 diff --git a/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild new file mode 100644 index ..e848ca405e67 --- /dev/null +++ b/sci-libs/scikit-optimize/scikit-optimize-0.9.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 2020-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +inherit distutils-r1 + +DESCRIPTION="Sequential model-based optimization library" +HOMEPAGE="https://scikit-optimize.github.io/; +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/joblib-0.11[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + >=dev-python/scipy-0.19.1[${PYTHON_USEDEP}] + >=sci-libs/scikit-learn-0.20.0[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +# No such file or directory: image/logo.png +#distutils_enable_sphinx doc \ +# dev-python/numpydoc \ +# dev-python/sphinx-issues \ +# dev-python/sphinx-gallery
[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikit-optimize/
commit: 3e4cf0fa4d6fa521ee3b06eb091bece055132f16 Author: Aisha Tammy aisha cc> AuthorDate: Mon Nov 9 18:58:36 2020 + Commit: Aaron Bauman gentoo org> CommitDate: Fri Nov 13 21:32:15 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e4cf0fa sci-libs/scikit-optimize: scipy like optimizer replacement for scikits_optimization Package-Manager: Portage-3.0.8, Repoman-3.0.1 RepoMan-Options: --force Signed-off-by: Aisha Tammy aisha.cc> Signed-off-by: Aaron Bauman gentoo.org> sci-libs/scikit-optimize/Manifest | 1 + sci-libs/scikit-optimize/metadata.xml | 16 + .../scikit-optimize/scikit-optimize-0.8.1.ebuild | 26 ++ 3 files changed, 43 insertions(+) diff --git a/sci-libs/scikit-optimize/Manifest b/sci-libs/scikit-optimize/Manifest new file mode 100644 index 000..e5c7a49776e --- /dev/null +++ b/sci-libs/scikit-optimize/Manifest @@ -0,0 +1 @@ +DIST scikit-optimize-0.8.1.tar.gz 278751 BLAKE2B c53b921ed47a2146510a041e34129918cc1b9118e8ae3614f39cc16c87ba5a749e268b9694ade9d95132ec4fb11777f2ef2ec509b1be59c8864ff7b6edde2250 SHA512 8ffacb62869810e1812bdbd2f9f3fe83cad2be03cd795ae2e9aa4e1143ed613c3901ae06be85aecd63c1e3e5b4805e88331d2d8848cc9953988fddfbe62a0287 diff --git a/sci-libs/scikit-optimize/metadata.xml b/sci-libs/scikit-optimize/metadata.xml new file mode 100644 index 000..11fe5dcb02d --- /dev/null +++ b/sci-libs/scikit-optimize/metadata.xml @@ -0,0 +1,16 @@ + +http://www.gentoo.org/dtd/metadata.dtd;> + + +gen...@aisha.cc +Aisha Tammy + + +s...@gentoo.org +Gentoo Science Project + + +scikit-optimize +scikit-optimize/scikit-optimize + + diff --git a/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild b/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild new file mode 100644 index 000..c2d8bbb2631 --- /dev/null +++ b/sci-libs/scikit-optimize/scikit-optimize-0.8.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6..9} ) +inherit distutils-r1 + +DESCRIPTION="Sequential model-based optimization library" +HOMEPAGE="https://scikit-optimize.github.io/; +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pretty-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest