USE_DOCKER update and Docker build fix (#4)

Co-authored-by: Ludovico Mitchener <ludo@futurehouse.org>

Author: acashmoney

src/fhda/Dockerfile.pinned

@@ -75,8 +75,13 @@ RUN mamba install -c conda-forge -c bioconda -y \
     bioconductor-apeglm=1.24.0
 
 
-COPY requirements.txt .
-RUN mamba install -c conda-forge --file requirements.txt -y
+COPY kernel_requirements.txt .
+
+# Install conda packages first
+RUN mamba install -c conda-forge --file kernel_requirements.txt -y
+
+# Install pip packages
+RUN pip install aiodocker ldp==0.23.0 fhaviary[server]==0.18.1 crow-client==0.3.6
 
 # Certain tools are not easily installable via conda. A common practice for
 # bioinformaticians is to use udocker to run certain heavy duty omics processing

src/fhda/config.py

@@ -1,7 +1,7 @@
 import os
 from pathlib import Path
 
-USE_DOCKER = bool(os.getenv("USE_DOCKER", "false").lower() == "true")
+USE_DOCKER = bool(os.getenv("USE_DOCKER", "true").lower() == "true")
 USE_R = bool(os.getenv("USE_R", "false").lower() == "true")
 NB_ENVIRONMENT_DOCKER_IMAGE = os.getenv(
     "NB_ENVIRONMENT_DOCKER_IMAGE", "futurehouse/bixbench:aviary-notebook-env"

src/fhda/kernel_requirements.txt

@@ -1,12 +1,8 @@
-aiodocker
 anndata==0.11.1
 biopython==1.84
-datasets
 ete3==3.1.3
 gseapy==1.1.4
-fhaviary[server] >= 0.18.0
 keras==3.7.0
-ldp
 jupyter==1.0.0
 matplotlib==3.10.0
 matplotlib-venn==1.1.1
@@ -24,13 +20,3 @@ seaborn==0.13.2
 scikit-learn==1.6.0
 statsmodels==0.14.4
 umap-learn==0.5.7
-aiofiles
-google-auth
-google-cloud-storage
-google-cloud-secret-manager
-google-crc32c
-httpx
-pydantic
-requests
-tqdm
-crow-client