[WIP] 141 add dicom loader

.github/workflows/pythonapp.yml

@@ -1,6 +1,6 @@
 name: Lint
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   flake8-py3:

.gitignore

@@ -103,7 +103,7 @@ venv.bak/
 # mypy
 .mypy_cache/
 examples/scd_lvsegs.npz
-.temp/
+temp/
 .idea/
 
 *~

.gitlab-ci.yml

@@ -1,20 +1,34 @@
 stages:
-    - build
+  - build
+  - coverage
 
-.base_template : &BASE
-   script:
-   - nvidia-smi
-   - export CUDA_DEVICE_ORDER=PCI_BUS_ID
-   - export CUDA_VISIBLE_DEVICES=0,1
-   - python -m pip install --upgrade pip
-   - pip uninstall -y torch torchvision
-   - pip install -r requirements.txt
-   # - pip list
-   - ./runtests.sh --net
-   - echo "Done with runtests.sh"
+full integration:
+  stage: build
+  script:
+  - nvidia-smi
+  - export CUDA_DEVICE_ORDER=PCI_BUS_ID
+  - export CUDA_VISIBLE_DEVICES=0,1
+  - python -m pip install --upgrade pip
+  - pip uninstall -y torch torchvision
+  - pip install -q -r requirements.txt
+  - ./runtests.sh --net
+  - echo "Done with runtests.sh --net"
+  tags:
+  - test
 
-build-ci-test:
-    stage: build
-    tags:
-    - test
-    <<: *BASE
+coverage test:
+  stage: coverage
+  only:
+    - master
+    - ci-stages
+  script:
+  - nvidia-smi
+  - export CUDA_DEVICE_ORDER=PCI_BUS_ID
+  - export CUDA_VISIBLE_DEVICES=0,1
+  - python -m pip install --upgrade pip
+  - pip uninstall -y torch torchvision
+  - pip install -q -r requirements.txt
+  - pip list
+  - ./runtests.sh --coverage
+  tags:
+  - test

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/source/conf.py
 
 # Build documentation with MkDocs
 #mkdocs:

CONTRIBUTING.md

@@ -57,6 +57,15 @@ License information: all source code files should start with this paragraph:
 
 ```
 
+### Building the documentation
+To build documentation via Sphinx in`docs/` folder:
+```bash
+cd docs/
+make html
+```
+The above commands build html documentation. Type `make help` for all supported formats,
+type `make clean` to remove the current build files.
+
 ## Unit testing
 MONAI tests are located under `tests/`.
 

Dockerfile

@@ -0,0 +1,35 @@
+# Copyright 2020 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:19.10-py3
+
+FROM ${PYTORCH_IMAGE} as base
+RUN apt-get update
+
+WORKDIR /opt/monai
+COPY . .
+
+ENV PYTHONPATH=$PYTHONPATH:/opt/monai
+ENV PATH=/opt/tools:$PATH
+
+RUN python -m pip install -U pip
+# remove preintalls
+RUN python -m pip uninstall -y torch torchvision
+# install dependencies
+RUN python -m pip install -r requirements.txt
+
+
+# NGC Client
+WORKDIR /opt/tools
+RUN wget -q https://ngc.nvidia.com/downloads/ngccli_cat_linux.zip && \
+    unzip ngccli_cat_linux.zip && chmod u+x ngc && \
+    rm -rf ngccli_cat_linux.zip ngc.md5
+WORKDIR /opt/monai