From c1b940ca5a9eedbb0279977007439d928dc39b3c Mon Sep 17 00:00:00 2001 From: Josh Carmichael Date: Tue, 25 Nov 2025 10:28:24 -0500 Subject: [PATCH 1/3] bump numpy>=1.25.0 --- environment-accelerate.yml | 2 +- environment-default.yml | 2 +- environment-intel.yml | 2 +- environment-openblas.yml | 2 +- environment-win64.yml | 2 +- pyproject.toml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/environment-accelerate.yml b/environment-accelerate.yml index 5248c3a953..0ff8097e49 100644 --- a/environment-accelerate.yml +++ b/environment-accelerate.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy=1.24.1 + - numpy>=1.25.0 - scipy=1.10.1 - scikit-learn - scikit-image diff --git a/environment-default.yml b/environment-default.yml index f827ec55bc..2bcd3bc0ea 100644 --- a/environment-default.yml +++ b/environment-default.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy=1.23.5 + - numpy>=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-intel.yml b/environment-intel.yml index 840dd92f76..98c5feee7e 100644 --- a/environment-intel.yml +++ b/environment-intel.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy=1.23.5 + - numpy>=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-openblas.yml b/environment-openblas.yml index 088035f88d..41f761c696 100644 --- a/environment-openblas.yml +++ b/environment-openblas.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy=1.23.5 + - numpy>=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-win64.yml b/environment-win64.yml index 34ca5d9fa6..62e55ceda9 100644 --- a/environment-win64.yml +++ b/environment-win64.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy=1.23.5 + - numpy>=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/pyproject.toml b/pyproject.toml index 8a7696dcb9..2e132d8e1e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "joblib", "matplotlib >= 3.2.0", "mrcfile", - "numpy>=1.21.5", + "numpy>=1.25.0", "packaging", "pooch>=1.7.0", "pillow", From bf2b626dad6de2e684dc4111307af7612452ecb8 Mon Sep 17 00:00:00 2001 From: Josh Carmichael Date: Mon, 1 Dec 2025 09:11:27 -0500 Subject: [PATCH 2/3] pin env*.yml np version --- environment-accelerate.yml | 2 +- environment-default.yml | 2 +- environment-intel.yml | 2 +- environment-openblas.yml | 2 +- environment-win64.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/environment-accelerate.yml b/environment-accelerate.yml index 0ff8097e49..18a1c73204 100644 --- a/environment-accelerate.yml +++ b/environment-accelerate.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy>=1.25.0 + - numpy=1.25.0 - scipy=1.10.1 - scikit-learn - scikit-image diff --git a/environment-default.yml b/environment-default.yml index 2bcd3bc0ea..274292c723 100644 --- a/environment-default.yml +++ b/environment-default.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy>=1.25.0 + - numpy=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-intel.yml b/environment-intel.yml index 98c5feee7e..c302df2846 100644 --- a/environment-intel.yml +++ b/environment-intel.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy>=1.25.0 + - numpy=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-openblas.yml b/environment-openblas.yml index 41f761c696..4a216b9d9c 100644 --- a/environment-openblas.yml +++ b/environment-openblas.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy>=1.25.0 + - numpy=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image diff --git a/environment-win64.yml b/environment-win64.yml index 62e55ceda9..aa5d969e8c 100644 --- a/environment-win64.yml +++ b/environment-win64.yml @@ -7,7 +7,7 @@ channels: dependencies: - pip - python=3.9 - - numpy>=1.25.0 + - numpy=1.25.0 - scipy=1.9.3 - scikit-learn - scikit-image From c0c2485a0542c32516cd037fd3214e5c9ece5d25 Mon Sep 17 00:00:00 2001 From: Josh Carmichael Date: Mon, 1 Dec 2025 13:46:04 -0500 Subject: [PATCH 3/3] bump scipy accel envs --- environment-accelerate.yml | 2 +- environment-default.yml | 2 +- environment-intel.yml | 2 +- environment-openblas.yml | 2 +- environment-win64.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/environment-accelerate.yml b/environment-accelerate.yml index 18a1c73204..5738909d7d 100644 --- a/environment-accelerate.yml +++ b/environment-accelerate.yml @@ -8,7 +8,7 @@ dependencies: - pip - python=3.9 - numpy=1.25.0 - - scipy=1.10.1 + - scipy=1.13.1 - scikit-learn - scikit-image - libblas=*=*accelerate diff --git a/environment-default.yml b/environment-default.yml index 274292c723..2b1d542fd6 100644 --- a/environment-default.yml +++ b/environment-default.yml @@ -8,6 +8,6 @@ dependencies: - pip - python=3.9 - numpy=1.25.0 - - scipy=1.9.3 + - scipy=1.13.1 - scikit-learn - scikit-image diff --git a/environment-intel.yml b/environment-intel.yml index c302df2846..3295ff934a 100644 --- a/environment-intel.yml +++ b/environment-intel.yml @@ -8,7 +8,7 @@ dependencies: - pip - python=3.9 - numpy=1.25.0 - - scipy=1.9.3 + - scipy=1.13.1 - scikit-learn - scikit-image - mkl_fft diff --git a/environment-openblas.yml b/environment-openblas.yml index 4a216b9d9c..04f80266be 100644 --- a/environment-openblas.yml +++ b/environment-openblas.yml @@ -8,7 +8,7 @@ dependencies: - pip - python=3.9 - numpy=1.25.0 - - scipy=1.9.3 + - scipy=1.13.1 - scikit-learn - scikit-image - libblas=*=*openblas diff --git a/environment-win64.yml b/environment-win64.yml index aa5d969e8c..ea9ed840f6 100644 --- a/environment-win64.yml +++ b/environment-win64.yml @@ -8,7 +8,7 @@ dependencies: - pip - python=3.9 - numpy=1.25.0 - - scipy=1.9.3 + - scipy=1.13.1 - scikit-learn - scikit-image - mkl=2024.1.* # possible regression impacts eig solver in later versions up to 2025.0