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faster install, new packages
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stsievert committed Apr 11, 2021
1 parent e32947c commit 6bab90f
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19 changes: 3 additions & 16 deletions Dockerfile
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FROM continuumio/miniconda3:4.7.12
FROM continuumio/miniconda3:4.9.2

RUN apt-get update
RUN apt-get install -y gcc cmake g++
RUN conda -V

# from https://hub.docker.com/r/daskdev/dask/dockerfile
RUN pip install --ignore-installed PyYAML
RUN conda install --yes \
-c conda-forge \
python==3.8 \
python-blosc \
cytoolz \
dask==2.20.0 \
lz4 \
nomkl \
numpy==1.18.1 \
pandas==1.0.1 \
tini==0.18.0

RUN pip install --ignore-installed PyYAML
COPY salmon.yml /salmon/salmon.yml
RUN conda env update --file /salmon/salmon.yml --prefix $(which python)/../..
RUN pip install --ignore-installed PyYAML

# to view Dask dashboard
RUN pip install jupyter-server-proxy
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14 changes: 9 additions & 5 deletions salmon.yml
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Expand Up @@ -5,21 +5,25 @@ channels:
- pytorch
- anaconda
dependencies:
- python==3.7.* # skorch doesn't officialy support 3.8 yet
- Cython
- numba
- python>=3.7.0
- pip
- numpy>=1.18.0
- scipy
- pandas>=1.0.1
- Cython
- numba
- scikit-learn
- pip
- nomkl
- dask>=2.30.0
- distributed>=2.30.0
- lz4
- python-blosc
- tini==0.18.0
- cytoolz
- ujson
- msgpack-python>=1.0.0 # some issues w/ FORTE
- msgpack-numpy # some issues w/ FORTE
- pytorch==1.4.* # skorch doesn't support 1.5 yet
- pytorch
- cpuonly
- nb_conda_kernels
- pip:
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -13,7 +13,7 @@
description="Efficient crowdsourcing of triplet queries",
author="Scott Sievert",
author_email="dev@stsievert.com",
url="https://stsievert.com/salmon",
url="https://docs.stsievert.com/salmon",
packages=["salmon"],
# install_requires=requirements,
)

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