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Add Inscopix metadata ingestion & update table definitions + make functions #57

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Add Inscopix metadata ingestion & update table definitions + make functions #57

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7cfc720
Update(setup.py) element-interface branch to resolve installation con…
kushalbakshi Jun 18, 2024
589f3d3
Ingest Inscopix metadata
kushalbakshi Jun 27, 2024
63dccf6
Fix(miniscopy.py) TypeError
kushalbakshi Jun 27, 2024
2149c8c
Remove CaImAn install from setup.py
kushalbakshi Jul 1, 2024
2d7418b
Update tables in miniscope schema + update devcontainer for codespaces
kushalbakshi Jul 17, 2024
e9ba34f
Attempt caiman install from dockerfile during devcontainer build
kushalbakshi Jul 17, 2024
715fed7
Clone and install caiman in image build
kushalbakshi Jul 17, 2024
b954899
Install caiman in the devcontainer image
kushalbakshi Jul 17, 2024
dd4a397
Update devcontainer to python 3.10
kushalbakshi Jul 17, 2024
d321be1
Fix(devcontainer.json) imaging -> miniscope
kushalbakshi Jul 17, 2024
b39fe9e
Merge branch 'dev_update_element' of https://github.com/kushalbakshi/…
kushalbakshi Jul 17, 2024
914a55d
Update `PYTHON_VERSION` env
kushalbakshi Jul 17, 2024
46d6d61
Merge branch 'dev_update_element' of https://github.com/kushalbakshi/…
kushalbakshi Jul 17, 2024
2ee2d51
Update element_miniscope/miniscope.py
kushalbakshi Jul 26, 2024
f0de2d1
Update element_miniscope/miniscope.py
kushalbakshi Jul 26, 2024
5494d0f
Update element_miniscope/miniscope.py
kushalbakshi Jul 26, 2024
8d5936e
Update `RecordingInfo` based on code review session
kushalbakshi Jul 26, 2024
0786a24
Update handling timestamps for DAQv4
kushalbakshi Jul 26, 2024
fb2eba9
Fix insert into `Config` part table
kushalbakshi Jul 26, 2024
8dfa957
Add processing method description
kushalbakshi Jul 26, 2024
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12 changes: 7 additions & 5 deletions .devcontainer/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
FROM python:3.10-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f

ENV PATH /usr/local/bin:$PATH
ENV PYTHON_VERSION 3.9.17
ENV PYTHON_VERSION 3.10.13

RUN \
adduser --system --disabled-password --shell /bin/bash vscode && \
Expand Down Expand Up @@ -32,11 +32,13 @@ COPY ./ /tmp/element-miniscope/
RUN \
# pipeline dependencies
apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
pip install numpy Cython && \
pip install --no-cache-dir -e /tmp/element-miniscope[elements,caiman_requirements,caiman] && \
caimanmanager.py install && \
pip install --no-cache-dir -e /tmp/element-miniscope[elements]
RUN cd ./tmp && git clone https://github.com/datajoint/CaImAn.git && cd ./CaImAn && \
pip install -r requirements.txt && pip install -e . && \
caimanmanager install --inplace && cd ~ && \
# clean up
rm -rf /tmp/element-miniscope && \
rm -rf /tmp/CaImAn && \
apt-get clean

ENV DJ_HOST fakeservices.datajoint.io
Expand Down
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