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Upgrade to ndarray 0.16 #371

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Upgrade to ndarray 0.16 #371

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f3a14ac
Bump ndarray version to 0.16
relf Jan 29, 2025
2f39681
Bump ndarray-linalg version to 0.17
relf Jan 29, 2025
3ae5153
Bump ndarray-stats version to 0.6
relf Jan 29, 2025
5e5ac3a
Bump ndarray-rand version to 0.15
relf Jan 29, 2025
e6cbae2
Unpin ndarray-csv
relf Jan 29, 2025
a4f4586
Bump approx version to 0.5
relf Jan 29, 2025
473db70
Bump linfa-linalg version to 0.2
relf Jan 29, 2025
10c5405
Unpin sprs
relf Jan 29, 2025
2389ee6
Fix forgotten bumps
relf Jan 29, 2025
0abb174
Fix deprecated into_shape()
relf Jan 29, 2025
b48b20e
Fix deprecated into_raw_vec()
relf Jan 29, 2025
70bee1d
Fix deprecated into_shape()
relf Jan 29, 2025
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10 changes: 5 additions & 5 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,11 @@ serde = ["serde_crate", "ndarray/serde"]
[dependencies]
num-traits = "0.2"
rand = { version = "0.8", features = ["small_rng"] }
approx = "0.4"
approx = "0.5"

ndarray = { version = "0.15", features = ["approx"] }
ndarray-linalg = { version = "0.16", optional = true }
sprs = { version = "=0.11.1", default-features = false }
ndarray = { version = "0.16", features = ["approx"] }
ndarray-linalg = { version = "0.17", optional = true }
sprs = { version = "0.11", default-features = false }

thiserror = "1.0"

Expand All @@ -56,7 +56,7 @@ default-features = false
features = ["std", "derive"]

[dev-dependencies]
ndarray-rand = "0.14"
ndarray-rand = "0.15"
linfa-datasets = { path = "datasets", features = [
"winequality",
"iris",
Expand Down
10 changes: 6 additions & 4 deletions algorithms/linfa-bayes/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,14 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15" , features = ["approx"]}
ndarray-stats = "0.5"
ndarray = { version = "0.16", features = ["approx"] }
ndarray-stats = "0.6"
thiserror = "1.0"

linfa = { version = "0.7.1", path = "../.." }

[dev-dependencies]
approx = "0.4"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = ["winequality"] }
approx = "0.5"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"winequality",
] }
16 changes: 8 additions & 8 deletions algorithms/linfa-clustering/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,11 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15", features = ["rayon", "approx"] }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-linalg = { version = "0.16", optional = true }
ndarray-rand = "0.14"
ndarray-stats = "0.5"
ndarray = { version = "0.16", features = ["rayon", "approx"] }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-linalg = { version = "0.17", optional = true }
ndarray-rand = "0.15"
ndarray-stats = "0.6"
num-traits = "0.2"
rand_xoshiro = "0.6"
space = "0.12"
Expand All @@ -50,14 +50,14 @@ linfa-nn = { version = "0.7.1", path = "../linfa-nn" }
noisy_float = "0.2.0"

[dev-dependencies]
ndarray-npy = { version = "0.8", default-features = false }
ndarray-npy = { version = "0.9", default-features = false }
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"generate",
] }
criterion = "0.4.0"
serde_json = "1"
approx = "0.4"
lax = "0.15.0"
approx = "0.5"
lax = "0.17.0"
linfa = { version = "0.7.1", path = "../..", features = ["benchmarks"] }

[[bench]]
Expand Down
2 changes: 1 addition & 1 deletion algorithms/linfa-clustering/src/gaussian_mixture/algorithm.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -390,7 +390,7 @@ impl<F: Float> GaussianMixtureModel<F> {
let n_clusters = matrix_chol.shape()[0];
let log_diags = &matrix_chol
.to_owned()
.into_shape((n_clusters, n_features * n_features))
.into_shape_with_order((n_clusters, n_features * n_features))
.unwrap()
.slice(s![.., ..; n_features+1])
.to_owned()
Expand Down
10 changes: 5 additions & 5 deletions algorithms/linfa-elasticnet/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,12 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15", features = ["approx"] }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-linalg = { version = "0.16", optional = true }
ndarray = { version = "0.16", features = ["approx"] }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-linalg = { version = "0.17", optional = true }

num-traits = "0.2"
approx = "0.4"
approx = "0.5"
thiserror = "1.0"

linfa = { version = "0.7.1", path = "../.." }
Expand All @@ -44,5 +44,5 @@ linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"diabetes",
"linnerud",
] }
ndarray-rand = "0.14"
ndarray-rand = "0.15"
rand_xoshiro = "0.6"
4 changes: 2 additions & 2 deletions algorithms/linfa-ftrl/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ version = "1.0"
features = ["derive"]

[dependencies]
ndarray = { version = "0.15.4", features = ["serde"] }
ndarray = { version = "0.16", features = ["serde"] }
ndarray-rand = "0.14.0"
argmin = { version = "0.9.0", default-features = false }
argmin-math = { version = "0.3", features = ["ndarray_v0_15-nolinalg"] }
Expand All @@ -36,7 +36,7 @@ linfa = { version = "0.7.1", path = "../.." }

[dev-dependencies]
criterion = "0.4.0"
approx = "0.4"
approx = "0.5"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"winequality",
] }
Expand Down
16 changes: 12 additions & 4 deletions algorithms/linfa-hierarchical/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,17 @@ license = "MIT OR Apache-2.0"
repository = "https://github.com/rust-ml/linfa"
readme = "README.md"

keywords = ["hierachical", "agglomerative", "clustering", "machine-learning", "linfa"]
keywords = [
"hierachical",
"agglomerative",
"clustering",
"machine-learning",
"linfa",
]
categories = ["algorithms", "mathematics", "science"]

[dependencies]
ndarray = { version = "0.15" }
ndarray = { version = "0.16" }
kodama = "0.2"
thiserror = "1.0.25"

Expand All @@ -23,5 +29,7 @@ linfa-kernel = { version = "0.7.1", path = "../linfa-kernel" }

[dev-dependencies]
rand = "0.8"
ndarray-rand = "0.14"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = ["iris"] }
ndarray-rand = "0.15"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"iris",
] }
12 changes: 6 additions & 6 deletions algorithms/linfa-ica/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,19 +25,19 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15" }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-linalg = { version = "0.16", optional = true }
ndarray-rand = "0.14"
ndarray-stats = "0.5"
ndarray = { version = "0.16" }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-linalg = { version = "0.17", optional = true }
ndarray-rand = "0.15"
ndarray-stats = "0.6"
num-traits = "0.2"
rand_xoshiro = "0.6"
thiserror = "1.0"

linfa = { version = "0.7.1", path = "../.." }

[dev-dependencies]
ndarray-npy = { version = "0.8", default-features = false }
ndarray-npy = { version = "0.9", default-features = false }
paste = "1.0"
criterion = "0.4.0"
linfa = { version = "0.7.1", path = "../..", features = ["benchmarks"] }
Expand Down
4 changes: 2 additions & 2 deletions algorithms/linfa-kernel/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = "0.15"
ndarray = "0.16"
num-traits = "0.2"
sprs = { version = "=0.11.1", default-features = false }
sprs = { version = "0.11", default-features = false }

linfa = { version = "0.7.1", path = "../.." }
linfa-nn = { version = "0.7.1", path = "../linfa-nn" }
8 changes: 4 additions & 4 deletions algorithms/linfa-linear/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,9 +29,9 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15", features = ["approx"] }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-linalg = { version = "0.16", optional = true }
ndarray = { version = "0.16", features = ["approx"] }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-linalg = { version = "0.17", optional = true }
num-traits = "0.2"
argmin = { version = "0.9.0", default-features = false }
argmin-math = { version = "0.3", features = ["ndarray_v0_15-nolinalg"] }
Expand All @@ -43,7 +43,7 @@ linfa = { version = "0.7.1", path = "../.." }
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"diabetes",
] }
approx = "0.4"
approx = "0.5"
criterion = "0.4.0"
statrs = "0.16.0"
linfa = { version = "0.7.1", path = "../..", features = ["benchmarks"] }
Expand Down
4 changes: 2 additions & 2 deletions algorithms/linfa-logistic/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ optional = true
version = "1.0"

[dependencies]
ndarray = { version = "0.15", features = ["approx"] }
ndarray = { version = "0.16", features = ["approx"] }
ndarray-stats = "0.5.0"
num-traits = "0.2"
argmin = { version = "0.9.0", default-features = false }
Expand All @@ -34,7 +34,7 @@ thiserror = "1.0"
linfa = { version = "0.7.1", path = "../.." }

[dev-dependencies]
approx = "0.4"
approx = "0.5"
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"winequality",
] }
Expand Down
13 changes: 8 additions & 5 deletions algorithms/linfa-logistic/src/lib.rs
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Expand Up @@ -476,9 +476,9 @@ fn logistic_loss<F: Float, A: Data<Elem = F>>(
) -> F {
let n_features = x.shape()[1];
let (params, intercept) = convert_params(n_features, w);
let yz = x.dot(&params.into_shape((params.len(), 1)).unwrap()) + intercept;
let yz = x.dot(&params.into_shape_with_order((params.len(), 1)).unwrap()) + intercept;
let len = yz.len();
let mut yz = yz.into_shape(len).unwrap() * y;
let mut yz = yz.into_shape_with_order(len).unwrap() * y;
yz.mapv_inplace(log_logistic);
-yz.sum() + F::cast(0.5) * alpha * params.dot(&params)
}
Expand All @@ -492,9 +492,9 @@ fn logistic_grad<F: Float, A: Data<Elem = F>>(
) -> Array1<F> {
let n_features = x.shape()[1];
let (params, intercept) = convert_params(n_features, w);
let yz = x.dot(&params.into_shape((params.len(), 1)).unwrap()) + intercept;
let yz = x.dot(&params.into_shape_with_order((params.len(), 1)).unwrap()) + intercept;
let len = yz.len();
let mut yz = yz.into_shape(len).unwrap() * y;
let mut yz = yz.into_shape_with_order(len).unwrap() * y;
yz.mapv_inplace(logistic);
yz -= F::one();
yz *= y;
Expand Down Expand Up @@ -523,7 +523,10 @@ fn multi_logistic_prob_params<'a, F: Float, A: Data<Elem = F>>(
let h = x.dot(&params) + intercept;
// This computes `H - log(sum(exp(H)))`, which is equal to
// `log(softmax(H)) = log(exp(H) / sum(exp(H)))`
let log_prob = &h - log_sum_exp(&h, Axis(1)).into_shape((h.nrows(), 1)).unwrap();
let log_prob = &h
- log_sum_exp(&h, Axis(1))
.into_shape_with_order((h.nrows(), 1))
.unwrap();
(log_prob, params)
}

Expand Down
8 changes: 4 additions & 4 deletions algorithms/linfa-nn/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15", features = ["approx"]}
ndarray-stats = "0.5"
ndarray = { version = "0.16", features = ["approx"] }
ndarray-stats = "0.6"
num-traits = "0.2.0"
noisy_float = "0.2.0"
order-stat = "0.1.3"
Expand All @@ -36,10 +36,10 @@ kdtree = "0.6.0"
linfa = { version = "0.7.1", path = "../.." }

[dev-dependencies]
approx = "0.4"
approx = "0.5"
criterion = "0.4.0"
rand_xoshiro = "0.6"
ndarray-rand = "0.14"
ndarray-rand = "0.15"
linfa = { version = "0.7.1", path = "../..", features = ["benchmarks"] }

[[bench]]
Expand Down
12 changes: 6 additions & 6 deletions algorithms/linfa-pls/Cargo.toml
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Expand Up @@ -25,11 +25,11 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15" }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-linalg = { version = "0.16", optional = true }
ndarray-stats = "0.5"
ndarray-rand = "0.14"
ndarray = { version = "0.16" }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-linalg = { version = "0.17", optional = true }
ndarray-stats = "0.6"
ndarray-rand = "0.15"
num-traits = "0.2"
paste = "1.0"
thiserror = "1.0"
Expand All @@ -40,7 +40,7 @@ linfa = { version = "0.7.1", path = "../..", features = ["benchmarks"] }
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"linnerud",
] }
approx = "0.4"
approx = "0.5"
rand_xoshiro = "0.6"
criterion = "0.4.0"
statrs = "0.16.0"
Expand Down
14 changes: 7 additions & 7 deletions algorithms/linfa-preprocessing/Cargo.toml
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Expand Up @@ -19,17 +19,17 @@ serde = ["serde_crate", "ndarray/serde", "serde_regex"]

[dependencies]
linfa = { version = "0.7.1", path = "../.." }
ndarray = { version = "0.15", features = ["approx"] }
ndarray-linalg = { version = "0.16", optional = true }
linfa-linalg = { version = "0.1", default-features = false }
ndarray-stats = "0.5"
ndarray = { version = "0.16", features = ["approx"] }
ndarray-linalg = { version = "0.17", optional = true }
linfa-linalg = { version = "0.2", default-features = false }
ndarray-stats = "0.6"
thiserror = "1.0"
approx = { version = "0.4" }
ndarray-rand = { version = "0.14" }
approx = "0.5"
ndarray-rand = "0.15"
unicode-normalization = "0.1.8"
regex = "1.4.5"
encoding = "0.2"
sprs = { version = "=0.11.1", default-features = false }
sprs = { version = "0.11", default-features = false }

serde_regex = { version = "1.1", optional = true }

Expand Down
14 changes: 7 additions & 7 deletions algorithms/linfa-reduction/Cargo.toml
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Expand Up @@ -34,25 +34,25 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15", features = ["approx"] }
linfa-linalg = { version = "0.1" }
ndarray-linalg = { version = "0.16", optional = true }
ndarray-rand = "0.14"
ndarray = { version = "0.16", features = ["approx"] }
linfa-linalg = { version = "0.2" }
ndarray-linalg = { version = "0.17", optional = true }
ndarray-rand = "0.15"
num-traits = "0.2"
thiserror = "1.0"
rand = { version = "0.8", features = ["small_rng"] }

linfa = { version = "0.7.1", path = "../.." }
linfa-kernel = { version = "0.7.1", path = "../linfa-kernel" }
sprs = "=0.11.1"
sprs = { version = "0.11" }
rand_xoshiro = "0.6.0"

[dev-dependencies]
ndarray-npy = { version = "0.8", default-features = false }
ndarray-npy = { version = "0.9", default-features = false }
linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"iris",
"generate",
] }
approx = { version = "0.4" }
approx = "0.5"
mnist = { version = "0.6.0", features = ["download"] }
linfa-trees = { version = "0.7.1", path = "../linfa-trees" }
6 changes: 3 additions & 3 deletions algorithms/linfa-svm/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ default-features = false
features = ["std", "derive"]

[dependencies]
ndarray = { version = "0.15" }
ndarray-rand = "0.14"
ndarray = { version = "0.16" }
ndarray-rand = "0.15"
num-traits = "0.2"
thiserror = "1.0"

Expand All @@ -38,4 +38,4 @@ linfa-datasets = { version = "0.7.1", path = "../../datasets", features = [
"diabetes",
] }
rand_xoshiro = "0.6"
approx = "0.4"
approx = "0.5"
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