Merge branch 'dev'

.Dockerfile

@@ -0,0 +1,30 @@
+FROM tiangolo/uvicorn-gunicorn-fastapi:python3.11-slim
+LABEL authors="Nathan Sheffield"
+
+# RUN apt-get update -y && \
+#     apt-get install -y libpq-dev && \  # for postgres backend
+#     apt-get install -y gcc && \
+#     apt-get install -y wget && \
+#     apt-get install -y libcurl4 && \
+# cpp compiler required for hsnwlib
+
+# RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed -P /usr/local/bin
+# RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedIntersect -P /usr/local/bin
+# RUN chmod 755 /usr/local/bin/bigBedToBed /usr/local/bin/bedIntersect
+
+RUN pip install --upgrade pip
+# Install CPU-only pytorch, eliminating huge nvidia dependencies
+RUN pip install torch==2.1.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+RUN pip install https://github.com/pepkit/pipestat/archive/refs/heads/dev.zip
+
+RUN pip install sqlmodel  # to be removed after https://github.com/pepkit/pipestat/issues/117 
+RUN pip install psycopg2-binary  # to be removed after https://github.com/pepkit/pipestat/issues/117 
+RUN pip install "pydantic>=1.10.7,<2.0.0"  # to be removed after https://github.com/pepkit/pipestat/issues/117 
+
+
+COPY . /app
+RUN pip install -r requirements/requirements-all.txt
+RUN pip install .
+
+# RUN pip install --upgrade "tokenizers>=0.14,<0.15"  # to be removed after https://github.com/databio/bbconf/issues/35
+# RUN pip install --upgrade "biocframe==0.4.1"  # https://github.com/BiocPy/GenomicRanges/issues/41

README.md

@@ -48,10 +48,15 @@ This will start the server, which will listen on [http://0.0.0.0:8000](http:/0.0
 
 ### Building container
 
+- Primary container: `docker build -t databio/bedhost -f .Dockerfile .`
+- Test container: `docker build -t databio/bedhost:dev -f test.Dockerfile .`
+
 ```console
 docker build -t databio/bedhost:dev -f dev.Dockerfile .
 ```
 
+
+
 ### Running container for development
 
 The container will need to have access to two different directories:

test.Dockerfile

@@ -16,7 +16,7 @@ RUN pip install --upgrade pip
 # Install CPU-only pytorch, eliminating huge nvidia dependencies
 RUN pip install torch==2.1.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
 RUN pip install https://github.com/pepkit/pipestat/archive/refs/heads/dev.zip
-RUN pip install https://github.com/databio/bbconf/archive/refs/heads/dev.zip#
+#RUN pip install https://github.com/databio/bbconf/archive/refs/heads/dev.zip
 
 RUN pip install sentence_transformers  # to be removed after https://github.com/databio/bbconf/issues/35
 RUN pip install psycopg2-binary  # to be removed after https://github.com/pepkit/pipestat/issues/117