From ae1b04e698029cd7387b311fdf519a25997d3774 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Mon, 15 Jun 2026 18:44:22 +0200 Subject: [PATCH] TurnerLab 001636: pin numpy to 2.0.2 (match Colab runtime) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Colab 2026.04 ships numpy 2.0.2 on Python 3.12; the notebooks pinned 2.2.6, forcing an in-kernel numpy upgrade (and restart) on Colab. Nothing in the dependency graph requires >2.0 — numba 0.65.1, the tightest constraint, allows numpy>=1.22,<2.5 — so 2.0.2 resolves cleanly with the full jax/numba/nemos/pynapple GLM stack unchanged. Edits the numpy pin only (install cells + environment.yml); the rest of the Colab-matched lock is untouched. All four notebooks verified end-to-end via .github/scripts/run_notebook.py (ok: true): turner_m1_glm, turner_m1_peth, turner_m1_usage, antidromic_detection_tutorial. Co-Authored-By: Claude Opus 4.8 (1M context) --- .../TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb | 2 +- 001636/TurnerLab/motor_cortex/environment.yml | 2 +- 001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb | 2 +- 001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb | 2 +- 001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb index 512d9f80..800dd8d0 100644 --- a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb +++ b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb @@ -148,7 +148,7 @@ " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.2.6\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/environment.yml b/001636/TurnerLab/motor_cortex/environment.yml index 57381571..e52a9f19 100644 --- a/001636/TurnerLab/motor_cortex/environment.yml +++ b/001636/TurnerLab/motor_cortex/environment.yml @@ -14,7 +14,7 @@ dependencies: - matplotlib==3.10.8 - nemos==0.2.6 - optimistix==0.0.11 - - numpy==2.2.6 + - numpy==2.0.2 - pandas==2.3.3 - pynapple==0.10.3 - pynwb==3.1.3 diff --git a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb index dccf9d9f..d61122d7 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb @@ -148,7 +148,7 @@ " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.2.6\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb index 683f71a3..b7f4f9b9 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb @@ -148,7 +148,7 @@ " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.2.6\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb index c2c5dbf2..ffc98011 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb @@ -148,7 +148,7 @@ " \"notebook-shim==0.2.4\" \\\n", " \"numba==0.65.1\" \\\n", " \"numcodecs==0.15.1\" \\\n", - " \"numpy==2.2.6\" \\\n", + " \"numpy==2.0.2\" \\\n", " \"nwbinspector==0.7.1\" \\\n", " \"opt-einsum==3.4.0\" \\\n", " \"optax==0.2.8\" \\\n",