Merge pull request #28 from LuxImagingAI/update

v0.2.0
LuxImagingAI · May 23, 2024 · 3e52339 · 3e52339
2 parents f1f1db9 + b747da2
commit 3e52339
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,7 @@
+Dockerfile
+build
+.github
+CHANGELOG.md
+README.md
+DBSegment.egg-info
+build
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -0,0 +1,46 @@
+name: ci
+
+on: 
+  push:
+    branches:
+      - "main"
+      - "development"
+    # tags:
+    #   - '*'
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v4
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: imagingai/$REPOSITORY_NAME
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -0,0 +1,34 @@
+# 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.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12.3'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,6 @@
+build/
+models/
+input/
+output/
+
+DBSegment/.DS_Store
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,17 @@
+This changelog follows the Semantic Versioning convention (version 2.0.0)
+
+# Changelog
+
+## 23.05.24
+
+### Added
+- Dockerfile
+- Github action for publishing on docker
+- Github action for publishing on pypi
+
+### Changed
+- updated dependencies
+- replaced nnUNet code by dependency
+
+### Removed
+- most of the dependencies could be removed
diff --git a/DBSegment.egg-info/PKG-INFO b/DBSegment.egg-info/PKG-INFO
diff --git a/DBSegment.egg-info/SOURCES.txt b/DBSegment.egg-info/SOURCES.txt
diff --git a/DBSegment.egg-info/dependency_links.txt b/DBSegment.egg-info/dependency_links.txt
diff --git a/DBSegment.egg-info/entry_points.txt b/DBSegment.egg-info/entry_points.txt
diff --git a/DBSegment.egg-info/requires.txt b/DBSegment.egg-info/requires.txt
diff --git a/DBSegment.egg-info/top_level.txt b/DBSegment.egg-info/top_level.txt
diff --git a/DBSegment/.DS_Store b/DBSegment/.DS_Store
diff --git a/DBSegment/DBSegment.py b/DBSegment/DBSegment.py
@@ -9,7 +9,6 @@
 import requests
 import zipfile
 import argparse
-import torch
 import SimpleITK as sitk
 import warnings
 import platform
@@ -129,11 +128,11 @@ def enablePrint():
 
 blockPrint()
 
-import DBSegment.nnunet
-from DBSegment.nnunet.inference.predict import predict_from_folder
-from DBSegment.nnunet.paths import default_plans_identifier, network_training_output_dir, default_cascade_trainer, default_trainer
+import nnunet
+from nnunet.inference.predict import predict_from_folder
+from nnunet.paths import default_plans_identifier, network_training_output_dir, default_cascade_trainer, default_trainer
 from batchgenerators.utilities.file_and_folder_operations import join, isdir
-from DBSegment.nnunet.utilities.task_name_id_conversion import convert_id_to_task_name
+from nnunet.utilities.task_name_id_conversion import convert_id_to_task_name
 enablePrint()
 
 

diff --git a/DBSegment/nnunet/.DS_Store b/DBSegment/nnunet/.DS_Store
diff --git a/DBSegment/nnunet/__init__.py b/DBSegment/nnunet/__init__.py
diff --git a/DBSegment/nnunet/configuration.py b/DBSegment/nnunet/configuration.py
diff --git a/DBSegment/nnunet/dataset_conversion/Task017_BeyondCranialVaultAbdominalOrganSegmentation.py b/DBSegment/nnunet/dataset_conversion/Task017_BeyondCranialVaultAbdominalOrganSegmentation.py
diff --git a/DBSegment/nnunet/dataset_conversion/Task024_Promise2012.py b/DBSegment/nnunet/dataset_conversion/Task024_Promise2012.py