Pythondeps (#8)

* include all hippunfold pythondeps, update dockerfile, replace circleci with gh actions

so we can remove these dependencies from the hippunfold repo

note: still WIP

.github/workflows/deploy_docker.yml

@@ -0,0 +1,52 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish Docker image
+
+on: 
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registries:
+    name: Push Docker image to multiple registries
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: |
+            ${{ github.repository }}
+            ghcr.io/${{ github.repository }}
+      
+      - name: Build and push Docker images
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+

Dockerfile

@@ -47,6 +47,14 @@ RUN cd /tmp/JCC-3.10 && python setup.py install && \
 cd /opt && git clone http://github.com/nighres/nighres && cd /opt/nighres && git checkout 1901ce9a9afdfad8e2d66ec09600fbfb9fa0151d && ./build.sh && cd /opt/nighres && pip install . && \
 rm -rf /opt/nighres /tmp/JCC-3.10 /tmp/JCC-3.10.tar.gz
 
+COPY .  /src
+
+ENV SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL True
+RUN pip install --no-cache-dir /src && \
+    apt install -y graphviz && \
+    wget https://imagemagick.org/archive/binaries/magick && \
+    mv magick /usr/bin && chmod a+x /usr/bin/magick
+
 ENV LD_LIBRARY_PATH /opt/itksnap/lib/:/opt/niftyreg-1.3.9/lib:/opt/workbench/libs_linux64:/opt/workbench/libs_linux64_software_opengl:${LD_LIBRARY_PATH}
 ENV PATH /opt/conda/bin:/opt/itksnap/bin/:/opt/niftyreg-1.3.9/bin:/opt/workbench/bin_linux64:/opt/ants-2.3.1-minify:/opt/fsl-5.0.11/bin-minify:$PATH
 

pyproject.toml

@@ -0,0 +1,28 @@
+[tool.poetry]
+name = "autotop_deps"
+version = "0.5.0"
+description = "Dependencies for HippUnfold"
+authors = ["Jordan DeKraker & Ali Khan <[email protected]>"]
+
+[tool.poetry.dependencies]
+python = ">=3.7.1,<3.10"
+batchgenerators = "0.21"
+nnunet-inference-on-cpu-and-gpu = "1.6.6"
+numpy = "1.21.2"
+astropy = "^4.0,<=4.3.1"
+pandas = "^1.2.0,<=1.3.0"
+nibabel = "^3.2.1"
+scipy = "1.7.1"
+nilearn = "^0.8.1"
+seaborn = "^0.11.2"
+scikit-fmm = "^2022.03.26"
+simpleitk = "2.0.2"
+matplotlib = "3.4.2"
+torch = "1.10.0"
+
+
+[tool.poetry.dev-dependencies]
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"