Merge pull request #1 from AllenNeuralDynamics/develop-2

First integration

Author: XX-Yin

.codeocean/datasets.json

@@ -0,0 +1,4 @@
+{
+	"version": 1,
+	"resource_class": "large"
+}

.codeocean/resources.json

@@ -137,3 +137,7 @@ dmypy.json
 
 # MacOs
 **/.DS_Store
+
+.vscode
+code
+data

.gitignore

@@ -0,0 +1,59 @@
+# hash:sha256:ec1b490392664b6c81ea8174f0a6590c12c37d5decefcdd9637b55344c9b0700
+ARG REGISTRY_HOST
+FROM $REGISTRY_HOST/codeocean/c1-vscode:4.20.0-pylint2023.10.1-copilot1.143.601
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG GIT_ASKPASS
+COPY git-askpass /
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends software-properties-common \
+    && add-apt-repository -y ppa:deadsnakes/ppa \
+    && apt-get purge -y --autoremove software-properties-common \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends \
+        build-essential=12.9ubuntu3 \
+        software-properties-common=0.99.22.9 \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN --mount=type=secret,id=git-access-token \
+    GIT_ACCESS_TOKEN="$(cat /run/secrets/git-access-token)" \
+    pip3 install -U --no-cache-dir \
+    aind-analysis-arch-result-access==1.0.0 \
+    aind-mri-utils==0.3.0 \
+    aind-spurious-correlation==0.0.6 \
+    antspyx==0.5.3 \
+    hdmf-zarr==0.11.0 \
+    ipykernel==6.29.5 \
+    jupyter==1.1.1 \
+    matplotlib==3.10.0 \
+    matplotlib-venn==1.1.2 \
+    numpy==2.2.2 \
+    pandas==2.2.3 \
+    pynwb==2.8.3 \
+    scikit-learn==1.6.1 \
+    scipy==1.15.1 \
+    spikeinterface[full]==0.102.2 \
+    statsmodels==0.14.4 \
+    -e git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-basic-analysis.git@5543aa88f3585200e4dc896c1a366de3803c0166#egg=aind-dynamic-foraging-basic-analysis \
+    -e git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-data-utils.git@c2984af731e2d85c250091cfa3cee95c247e5758#egg=aind-dynamic-foraging-data-utils \
+
+RUN pip install git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models.git@update_CTT#egg=aind-dynamic-foraging-models
+
+#ADD "https://github.com/coder/code-server/releases/download/v4.95.3/code-server-4.95.3-linux-amd64.tar.gz" /.code-server/code-server.tar.gz
+	
+#RUN cd /.code-server \
+#    && tar -xvf code-server.tar.gz \
+#    && rm code-server.tar.gz \
+#    && ln -s /.code-server/code-server-4.95.3-linux-amd64/bin/code-server  /usr/bin/code-server
+
+#RUN mkdir -p /.vscode/extensions \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension REditorSupport.R \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension continue.continue \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension ms-python.python \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension ms-toolsai.jupyter \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension reageyao.bioSyntax \
+#    && code-server --extensions-dir="/.vscode/extensions" --install-extension saoudrizwan.claude-dev
+
+COPY postInstall /
+RUN /postInstall

environment/Dockerfile

@@ -0,0 +1,2 @@
+metadata_version: 1
+name: dft-ephys-analysis

metadata/metadata.yml

@@ -0,0 +1 @@
+