Use requirements.txt for installing pipy packages

elephant-track · Aug 28, 2024 · c8358a8 · c8358a8
1 parent 5d89a4e
commit c8358a8
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Showing 4 changed files with 18 additions and 313 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -43,21 +43,8 @@ RUN ln -sf /dev/stdout /var/log/nginx/access.log \
 RUN conda install -y -c conda-forge uwsgi
 
 # install pypi packages
-RUN python -m pip install \
-    celery \
-    flask \
-    flask-restx \
-    flask-redis \
-    zarr \
-    filelock \
-    nvsmi \
-    psutil \
-    scikit-image \
-    pika \
-    redis \
-    h5py \
-    tqdm \
-    tensorflow
+COPY requirements.txt /tmp/requirements.txt
+RUN python -m pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
 # RUN pip install memory_profiler line_profiler
 # RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
 

diff --git a/elephant.def b/elephant.def
@@ -6,7 +6,7 @@ From: pytorch/pytorch:2.3.1-cuda12.1-cudnn8-runtime
     ./script /opt/elephant/script
     ./app /app
     ./elephant-core /src/elephant-core
-    ./environment.yml /src/environment.yml
+    ./requirements.txt /src/requirements.txt
 
 %environment
     export UWSGI_UID=$(id -u)
@@ -42,21 +42,7 @@ From: pytorch/pytorch:2.3.1-cuda12.1-cudnn8-runtime
     conda install -y -c conda-forge uwsgi
 
     # install pypi packages
-    python -m pip install \
-    celery \
-    flask \
-    flask-restx \
-    flask-redis \
-    zarr \
-    filelock \
-    nvsmi \
-    psutil \
-    scikit-image \
-    pika \
-    redis \
-    h5py \
-    tqdm \
-    tensorflow
+    python -m pip install -r /src/requirements.txt && rm /src/requirements.txt
 
     # Install and set up RabbbitMQ
     chmod +x /docker/install-rabbitmq.sh && /docker/install-rabbitmq.sh

diff --git a/environment.yml b/environment.yml
diff --git a/requirements.txt b/requirements.txt
@@ -1,12 +1,14 @@
-h5py==2.10.0
-flask==1.1.2
-flask-redis==0.4.0
-pika==1.1.0
-torch==1.4.0
-scikit-learn==0.23.1
-scikit-image==0.17.2
-scipy==1.4.1
-tensorboardX==2.1
-tqdm==4.48.2
-uwsgi==2.0.18
-zarr==2.4.0
+celery~=5.4.0
+Flask~=3.0.3
+flask-restx~=1.3.0
+flask-redis~=0.4.0
+zarr~=2.18.2
+filelock~=3.13.1
+nvsmi~=0.4.2
+psutil~=5.9.0
+scikit-image~=0.24.0
+pika~=1.3.2
+redis~=5.0.8
+h5py~=3.11.0
+tqdm~=4.66.4
+tensorflow~=2.17.0