Binderising

.github/workflows/test.yaml

@@ -0,0 +1,11 @@
+name: GitHub Actions Demo
+on: [push]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      # - run: python3 -m pip install jupyter-repo2docker
+      # - run: repo2docker --no-run --image-name spline_contour:latest --user-id=1001 --user-name=1001 .
+      # - run: docker run spline_contour:latest pytest --nbmake data.ipynb training.ipynb prediction.ipynb 

Makefile

@@ -0,0 +1,13 @@
+docker.build:
+	docker build . -t spline_contour
+
+docker.test:
+	docker run spline_contour conda run pytest --collect-only --nbmake "data.ipynb" "training.ipynb" "prediction.ipynb"
+
+repo2docker.build:
+	repo2docker --no-run --image-name spline_contour .
+
+# repo2docker.tests:
+
+mamba.build.env:
+	mamba env create -f environment.yml

apt.txt

@@ -0,0 +1 @@
+libgl1-mesa-glx

environment.yml

@@ -0,0 +1,45 @@
+name: splinedist_contour
+channels:
+  - anaconda
+  - pytorch
+  - conda-forge
+  - bioconda
+  - defaults
+  - nvidia
+dependencies:
+  - conda
+  - python
+  - cudatoolkit
+  - pip
+  # - mamba
+  - pytest
+  - tensorflow
+  - tensorflow-gpu
+  - tifffile
+  - nbmake
+  # - nb_conda_kernels
+  - ipykernel
+  - ipywidgets
+  - ipython
+  - numpy
+  - tqdm
+  - scikit-learn
+  - opencv=4.5.0
+  - mesa-libgl-devel-cos7-x86_64
+  - mesa-libgl-cos6-x86_64
+  - libopencv
+  - py-opencv
+  - ipython
+  # - jupyter
+  - nbconvert
+  - matplotlib
+  - scipy
+  - cudnn
+  # - cxx-compilern
+  # - gcc_linux-64
+  # - nvcc_linux-64
+  # - nccl
+  # - nvidia-ml
+  - pip:
+      - stardist
+      - "./"

setup.py

@@ -52,7 +52,7 @@ def build_extension(self, ext):
 common_src = ['stardist/lib/utils.cpp']
 
 setup(
-    name='stardist',
+    name='splinedist',
     version=__version__,
     description='StarDist',
     long_description=long_description,

start

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# # Allow drivers installed by the nvidia-driver-installer to be located
+# export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/nvidia/lib64
+# # Also, utilities like `nvidia-smi` are installed here
+# export PATH=${PATH}:/usr/local/nvidia/bin
+
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${CONDA_PREFIX/lib64}:${CONDA_PREFIX}/lib64/lib:/usr/local/nvidia/lib64
+
+# Also, utilities like `nvidia-smi` are installed here
+export PATH=${PATH}:/usr/local/nvidia/bin
+
+
+exec "$@"