From b1bb68bde362ece18f1e5c7a3e488b57c950bc78 Mon Sep 17 00:00:00 2001 From: Vincent Date: Fri, 21 Apr 2023 15:39:31 -0400 Subject: [PATCH 1/5] updates pykilosort --- pykilosort/Dockerfile | 6 +++--- pykilosort/build.sh | 3 ++- pykilosort/push.sh | 3 ++- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/pykilosort/Dockerfile b/pykilosort/Dockerfile index 9e49db7..1e64583 100644 --- a/pykilosort/Dockerfile +++ b/pykilosort/Dockerfile @@ -1,4 +1,4 @@ -FROM nvidia/cuda:10.0-base-ubuntu18.04 +FROM nvidia/cuda:12.1.0-base-ubuntu22.04 LABEL maintainer="Vincent Prevosto " @@ -13,9 +13,9 @@ RUN apt update && \ rm -rf /var/lib/apt/lists/* # install miniconda -ENV MINICONDA_VERSION 4.12.0 +ENV MINICONDA_VERSION 23.1.0-1 ENV CONDA_DIR /home/miniconda3 -ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh" +ENV LATEST_CONDA_SCRIPT "Miniconda3-py310_$MINICONDA_VERSION-Linux-x86_64.sh" RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \ bash ~/miniconda.sh -b -p $CONDA_DIR && \ diff --git a/pykilosort/build.sh b/pykilosort/build.sh index e49eb37..d2c5f68 100755 --- a/pykilosort/build.sh +++ b/pykilosort/build.sh @@ -1,3 +1,4 @@ #!/bin/bash -docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.3 . +# docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.3 . +docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.3 . diff --git a/pykilosort/push.sh b/pykilosort/push.sh index b947473..1a09d89 100644 --- a/pykilosort/push.sh +++ b/pykilosort/push.sh @@ -1,3 +1,4 @@ #!/bin/bash -docker push --all-tags spikeinterface/pykilosort-base +# docker push --all-tags spikeinterface/pykilosort-base +docker push --all-tags wanglabneuro/pykilosort-base \ No newline at end of file From 3f5450e37ba191c3cd700053f5d82d85d9bd79f9 Mon Sep 17 00:00:00 2001 From: Vincent Date: Fri, 26 Jan 2024 18:46:40 -0500 Subject: [PATCH 2/5] updates pykilosort --- pykilosort/Dockerfile | 14 ++++++-------- pykilosort/README.md | 3 +++ pykilosort/build.sh | 8 +++++++- pykilosort/push.sh | 0 4 files changed, 16 insertions(+), 9 deletions(-) mode change 100644 => 100755 pykilosort/push.sh diff --git a/pykilosort/Dockerfile b/pykilosort/Dockerfile index 1e64583..f0cd93e 100644 --- a/pykilosort/Dockerfile +++ b/pykilosort/Dockerfile @@ -1,4 +1,4 @@ -FROM nvidia/cuda:12.1.0-base-ubuntu22.04 +FROM nvidia/cuda:11.5.2-base-ubuntu20.04 LABEL maintainer="Vincent Prevosto " @@ -14,8 +14,9 @@ RUN apt update && \ # install miniconda ENV MINICONDA_VERSION 23.1.0-1 +ENV PY_VERSION py39 ENV CONDA_DIR /home/miniconda3 -ENV LATEST_CONDA_SCRIPT "Miniconda3-py310_$MINICONDA_VERSION-Linux-x86_64.sh" +ENV LATEST_CONDA_SCRIPT "Miniconda3-${PY_VERSION}_$MINICONDA_VERSION-Linux-x86_64.sh" RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \ bash ~/miniconda.sh -b -p $CONDA_DIR && \ @@ -36,7 +37,7 @@ WORKDIR /src/pykilosort # modify env file so that env extends on base RUN sed -i "s/pyks2/base/" pyks2.yml RUN sed -i "s/- spikeinterface//" pyks2.yml -RUN cat pyks2.yml +# RUN cat pyks2.yml # Create environment RUN conda env update --name base --file pyks2.yml --prune @@ -44,10 +45,7 @@ RUN conda env update --name base --file pyks2.yml --prune # Install pykilosort RUN conda install --quiet --yes ipykernel && \ python -m ipykernel install --user --display-name "pyKilosort" && \ - conda develop . + pip install -e . + # conda develop . -# install phylib from master because of read-only bug (https://github.com/cortex-lab/phylib/pull/35) -RUN pip uninstall -y phylib && pip install git+https://github.com/cortex-lab/phylib.git - -#--name pyks2 WORKDIR / diff --git a/pykilosort/README.md b/pykilosort/README.md index 83d3405..3062021 100644 --- a/pykilosort/README.md +++ b/pykilosort/README.md @@ -13,6 +13,9 @@ flags: -v: mounted volumes (directories) --gpus: enables GPU use within container +Check pykilosort version: +docker run --rm -it wanglabneuro/pykilosort-base:latest bash -c "python -c 'import pykilosort; print(pykilosort.__version__)'" + ### Test Download Neuropixel 1.0 data to your data directory: https://catalystneuro.github.io/spike-sorting-hackathon/datasets/datasets.html#allen-institute-example (see also https://github.com/int-brain-lab/pykilosort/tree/ibl_prod/examples, although apparently not up to date) diff --git a/pykilosort/build.sh b/pykilosort/build.sh index d2c5f68..f6b296e 100755 --- a/pykilosort/build.sh +++ b/pykilosort/build.sh @@ -1,4 +1,10 @@ #!/bin/bash # docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.3 . -docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.3 . +# docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.3 . +# docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.4.7_cuda-11.3.1 . +docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.4.7_cuda-11.5.2 . + +# version info +# 01/21/2024 - IBL 1.4.7 CUDA 11.3.1 Ubuntu 20.04 +# 01/21/2024 - IBL 1.4.7 CUDA 11.5.2 Ubuntu 20.04 \ No newline at end of file diff --git a/pykilosort/push.sh b/pykilosort/push.sh old mode 100644 new mode 100755 From 6a624345b5dc0ff08501ff22e1937da5a5f8b26f Mon Sep 17 00:00:00 2001 From: Vincent Date: Thu, 1 Feb 2024 12:56:45 -0500 Subject: [PATCH 3/5] for PR --- pykilosort/build.sh | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/pykilosort/build.sh b/pykilosort/build.sh index d17db60..4b8dc24 100755 --- a/pykilosort/build.sh +++ b/pykilosort/build.sh @@ -1,9 +1,6 @@ #!/bin/bash -# docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.3 . -# docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.3 . -# docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.4.7_cuda-11.3.1 . -docker build -t wanglabneuro/pykilosort-base:latest -t wanglabneuro/pykilosort-base:ibl-1.4.7_cuda-11.5.2 . +docker build -t spikeinterface/pykilosort-base:latest -t spikeinterface/pykilosort-base:ibl-1.4.7_cuda-11.5.2 . # version info # 01/21/2024 - IBL 1.4.7 CUDA 11.3.1 Ubuntu 20.04 From 976c62bad2f06f0a63cc5a0ca8e31a1d007003a2 Mon Sep 17 00:00:00 2001 From: Vincent Date: Thu, 1 Feb 2024 13:00:53 -0500 Subject: [PATCH 4/5] updates rm for PR --- pykilosort/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pykilosort/README.md b/pykilosort/README.md index 3062021..a9f8944 100644 --- a/pykilosort/README.md +++ b/pykilosort/README.md @@ -14,7 +14,7 @@ flags: --gpus: enables GPU use within container Check pykilosort version: -docker run --rm -it wanglabneuro/pykilosort-base:latest bash -c "python -c 'import pykilosort; print(pykilosort.__version__)'" +docker run --rm -it spikeinterface/pykilosort-base:latest bash -c "python -c 'import pykilosort; print(pykilosort.__version__)'" ### Test Download Neuropixel 1.0 data to your data directory: https://catalystneuro.github.io/spike-sorting-hackathon/datasets/datasets.html#allen-institute-example From bf200dc41498f9b639da0a2cd8b03922e2b1e70f Mon Sep 17 00:00:00 2001 From: Vincent Date: Thu, 1 Feb 2024 13:02:26 -0500 Subject: [PATCH 5/5] updates push.sh for PR --- pykilosort/push.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pykilosort/push.sh b/pykilosort/push.sh index 1a09d89..52bc325 100755 --- a/pykilosort/push.sh +++ b/pykilosort/push.sh @@ -1,4 +1,3 @@ #!/bin/bash -# docker push --all-tags spikeinterface/pykilosort-base -docker push --all-tags wanglabneuro/pykilosort-base \ No newline at end of file +docker push --all-tags spikeinterface/pykilosort-base \ No newline at end of file