Merge pull request #369 from oist/develop

Develop

.gitignore

@@ -4,7 +4,8 @@ __pycache__
 .vscode/*
 !.vscode/settings.json
 dist
-./build
+/build
+optinist/frontend
 
 optinist.extensions.yaml
 optinist.namespace.yaml

Dockerfile

@@ -6,7 +6,16 @@ RUN apt-get --allow-releaseinfo-change update && \
     apt-get install --no-install-recommends -y git gcc g++ libgl1 libgl1-mesa-dev && \
     pip3 install --no-cache-dir --upgrade pip && \
     pip3 install --no-cache-dir -r /app/requirements.txt && \
-    pip3 install --no-cache-dir cython==0.29.30 && \
+    pip3 install --no-cache-dir \
+        cython==0.29.30 \
+        holoviews==1.14.9 \
+        ipyparallel==8.4.1 \
+        matplotlib==3.5.2 \
+        opencv-python==4.6.0.66 \
+        scikit-image==0.18.0 \
+        scikit-learn==1.1.1 \
+        tensorflow==2.9.1 && \
+        watershed==2.2.2 \
     pip3 install --no-cache-dir git+https://github.com/flatironinstitute/CaImAn.git@914324989443fac5d481ef32aad4f327701294a8#egg=caiman && \
     apt-get purge git -y && apt-get autoremove -y && apt-get clean && rm -rf /root/.cache/pip/*
 
@@ -28,4 +37,6 @@ COPY main.py /app/main.py
 ENV PATH $PATH:/root/miniconda3/bin
 WORKDIR /app
 EXPOSE 8000
-ENTRYPOINT ["python3", "main.py"]
+
+ENTRYPOINT ["python3", "main.py"]
+CMD ["--host", "0.0.0.0"]

Dockerfile-test

@@ -1,14 +1,13 @@
-FROM python:3.9.7
+FROM python:3.9.7-slim
 
-RUN mkdir /app
-WORKDIR /app
-
-RUN apt-get --allow-releaseinfo-change update
-RUN apt-get install -y git gcc g++ libgl1
+COPY requirements.txt /app/requirements.txt
 
-RUN /usr/local/bin/python -m pip install --upgrade pip
-COPY ./requirements.txt ./
-RUN pip install --no-cache-dir -r requirements.txt
-RUN pip install pytest
+RUN apt-get --allow-releaseinfo-change update && \
+    apt-get install --no-install-recommends -y git gcc g++ libgl1 && \
+    pip3 install --no-cache-dir --upgrade pip && \
+    pip3 install --no-cache-dir -r /app/requirements.txt && \
+    pip3 install --no-cache-dir pytest && \
+    apt-get purge git -y && apt-get autoremove -y && apt-get clean && rm -rf /root/.cache/pip/*
 
-ENTRYPOINT ["python", "-m", "pytest", "-s", "."]
+WORKDIR /app
+ENTRYPOINT ["python3", "-m", "pytest", "-s", "."]

main.py

@@ -3,9 +3,9 @@
 from fastapi.templating import Jinja2Templates
 
 import os
+import argparse
 import uvicorn
 from starlette.middleware.cors import CORSMiddleware
-DIRPATH = os.path.dirname(os.path.abspath(__file__))
 from optinist.routers import (
     files,
     run,
@@ -16,6 +16,8 @@
     experiment,
 )
 
+DIRPATH = os.path.dirname(os.path.abspath(__file__))
+
 app = FastAPI(docs_url="/docs", openapi_url="/openapi")
 app.include_router(algolist.router)
 app.include_router(files.router)
@@ -30,25 +32,29 @@
     allow_origins=["*"],
     allow_credentials=True,
     allow_methods=["*"],
-    allow_headers=["*"]
+    allow_headers=["*"],
 )
 
 app.mount(
     "/static",
     StaticFiles(directory=f"{DIRPATH}/frontend/build/static"),
-    name="static"
+    name="static",
 )
 
 templates = Jinja2Templates(directory=f"{DIRPATH}/frontend/build")
 
+
 @app.get("/")
 async def root(request: Request):
     return templates.TemplateResponse("index.html", {"request": request})
 
 
 def main():
-    uvicorn.run('main:app', port=8000, reload=True)
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--host", type=str, default="127.0.0.1")
+    args = parser.parse_args()
+    uvicorn.run("main:app", host=args.host, port=8000, reload=True)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

optinist/version.py

@@ -3,7 +3,7 @@
 _MINOR = "1"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "0"
+_PATCH = "1"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""

setup.py

@@ -1,11 +1,14 @@
-from setuptools import setup, find_packages, Extension
+import os
+from setuptools import setup, find_packages
+
+here = os.path.abspath(os.path.dirname(__file__))
+exec(open(os.path.join(here, 'optinist', 'version.py')).read())
 
 def _requires_from_file(filepath):
 
     def take_package_name(name):
-        if name.startswith("git+"):
-            _package = name.strip("=")[-1]
-            return f"{_package}"
+        if "snakemake" in name:
+            return f"snakemake @ https://github.com/ShogoAkiyama/snakemake/archive/refs/tags/v7.7.2-post1.zip"
         else:
             return name.strip()
 
@@ -14,7 +17,7 @@ def take_package_name(name):
 
 setup(
     name="optinist",
-    version="0.1.0-6",
+    version=VERSION,
     description="An offline deep reinforcement learning library",
     long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
@@ -34,7 +37,6 @@ def take_package_name(name):
         "Operating System :: MacOS :: MacOS X"
     ],
     install_requires=_requires_from_file('requirements.txt'),
-    dependency_links=["git+https://github.com/ShogoAkiyama/snakemake@main#egg=snakemake"],
     packages=find_packages(exclude=["optinist/tests*"]),
     tests_require=["pytest"],
     zip_safe=False,