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Remove curation table + update tutorial & devcontainer #58

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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
a393a38
Create `no_curation` module
kushalbakshi Jul 18, 2024
b566fd9
Update with changes from code review and testing
kushalbakshi Jul 29, 2024
80845ef
Apply Black formatting
kushalbakshi Jul 29, 2024
9afedbb
Update element_miniscope/miniscope_no_curation.py
kushalbakshi Jul 29, 2024
e5358cb
Remove updated `key_source` for `Processing` table
kushalbakshi Jul 29, 2024
42c52bd
Update foreign key reference in `miniscope_report`
kushalbakshi Jul 31, 2024
05b36a7
Fix(miniscope_no_curation.py) session directory handling in `infer_ou…
kushalbakshi Aug 1, 2024
1603fb7
Remove input hash generation in `Processing`
kushalbakshi Aug 5, 2024
0fdd66f
Remove redundant `as_posix()` for output_dir
kushalbakshi Aug 5, 2024
52fae0f
Change `Curation` to `ProcessingTask` in `get_loader_result()`
kushalbakshi Aug 9, 2024
a7d6b9c
`insert()` -> `insert1() for MotionCorrection.Summary
kushalbakshi Aug 9, 2024
0a4ecdc
Fix fluo_channel -> fluorescence_channel
kushalbakshi Aug 12, 2024
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12 changes: 7 additions & 5 deletions .devcontainer/Dockerfile
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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