Nic-Ma · Nic-Ma · Feb 1, 2021 · Dec 17, 2020 · Dec 17, 2020 · Dec 17, 2020
diff --git a/.deepsource.toml b/.deepsource.toml
@@ -0,0 +1,27 @@
+version = 1
+
+test_patterns = ["tests/**"]
+
+exclude_patterns = [
+    "monai/_version.py",
+    "versioneer.py"
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+
+[[analyzers]]
+name = "test-coverage"
+enabled = true
+
+[[analyzers]]
+name = "docker"
+enabled = true
+
+[[analyzers]]
+name = "shell"
+enabled = true
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,12 @@
+# Ignore the following files/folders during docker build
+
+__pycache__/
+docs/
+
+.coverage
+.readthedocs.yml
+*.md
+*.toml
+
+!README.md
+
diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml
@@ -0,0 +1,20 @@
+name: cleanup-workflow
+
+on:
+  workflow_run:
+    workflows:
+      - "build"
+    types: ["requested"]
+
+jobs:
+  cancel-duplicated-workflow:
+    name: "Cancel duplicated workflow"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: potiuk/cancel-workflow-runs@953e057dc81d3458935a18d1184c386b0f6b5738 # tested
+        name: "Cancel duplicate workflows"
+        with:
+          cancelMode: allDuplicates
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sourceRunId: ${{ github.event.workflow_run.id }}
+          skipEventTypes: '["schedule"]'
diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -56,11 +56,12 @@ jobs:
   cron-docker:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
-      image: docker://projectmonai/monai:latest
+      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - name: Run tests report coverage
+      # The docker image process has done the compilation.  BUILD_MONAI=1 may not be necessary.
       run: |
         cd /opt/monai
         nvidia-smi

diff --git a/.github/workflows/setupapp.yml b/.github/workflows/setupapp.yml
@@ -149,11 +149,17 @@ jobs:
         ref: master
     - name: docker_build
       run: |
+        # build and run original docker image for local registry
         docker build -t localhost:5000/local_monai:latest -f Dockerfile .
         docker push localhost:5000/local_monai:latest
+        # build once more w/ tag "latest": remove flake package as it is not needed on hub.docker.com
         sed -i '/flake/d' requirements-dev.txt
         docker build -t projectmonai/monai:latest -f Dockerfile .
-        docker login -u projectmonai -p ${{ secrets.DOCKER_PW }}
+        # also push as tag "dockerhub" to local registry
+        docker image tag projectmonai/monai:latest localhost:5000/local_monai:dockerhub
+        docker push localhost:5000/local_monai:dockerhub
+        # distribute as always w/ tag "latest" to hub.docker.com
+        echo "${{ secrets.DOCKER_PW }}" | docker login -u projectmonai --password-stdin
         docker push projectmonai/monai:latest
         docker logout
 

diff --git a/.github/workflows/weekly-preview.yml b/.github/workflows/weekly-preview.yml
@@ -6,6 +6,7 @@ on:
 
 jobs:
   packaging:
+    if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
@@ -24,12 +25,16 @@ jobs:
         sed -i 's/name\ =\ monai$/name\ =\ monai-weekly/g' setup.cfg
         echo "__commit_id__ = \"$HEAD_COMMIT_ID\"" >> monai/__init__.py
         git diff setup.cfg monai/__init__.py
-        # build tar.gz and wheel
         git config user.name "CI Builder"
-        git config user.email "monai.miccai2019@gmail.com"
+        git config user.email "monai.contact@gmail.com"
         git add setup.cfg monai/__init__.py
         git commit -m "Weekly build at $HEAD_COMMIT_ID"
-        git tag 0.5.dev$(date +'%y%U')
+        export YEAR_WEEK=$(date +'%y%U')
+        echo "Year week for tag is ${YEAR_WEEK}"
+        if ! [[ $YEAR_WEEK =~ ^[0-9]{4}$ ]] ; then echo "Wrong 'year week' format.  Should be 4 digits."; exit 1 ; fi
+        git tag "0.5.dev${YEAR_WEEK}"
+        git log -1
+        git tag --list
         python setup.py sdist bdist_wheel
 
     - name: Publish to PyPI

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -32,6 +32,8 @@ _Pull request early_
 
 We encourage you to create pull requests early. It helps us track the contributions under development, whether they are ready to be merged or not. Change your pull request's title to begin with `[WIP]` until it is ready for formal review.
 
+Please note that, as per PyTorch, MONAI uses American English spelling. This means classes and variables should be: normali**z**e, visuali**z**e, colo~~u~~r, etc.
+
 ### Preparing pull requests
 To ensure the code quality, MONAI relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort)),
 static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.
@@ -58,7 +60,7 @@ pip install -U -r requirements-dev.txt  # install the latest tools
 
 License information: all source code files should start with this paragraph:
 ```
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 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
@@ -71,6 +73,13 @@ License information: all source code files should start with this paragraph:
 
 ```
 
+##### Exporting modules
+
+If you intend for any variables/functions/classes to be available outside of the file with the edited functionality, then:
+
+- Create or append to the `__all__` variable (in the file in which functionality has been added), and
+- Add to the `__init__.py` file.
+
 #### Unit testing
 MONAI tests are located under `tests/`.
 

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 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
@@ -11,10 +11,11 @@
 
 ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:20.10-py3
 
-FROM ${PYTORCH_IMAGE} as base
+FROM ${PYTORCH_IMAGE}
+
+LABEL maintainer="[email protected]"
 
 WORKDIR /opt/monai
-ENV PATH=/opt/tools:$PATH
 
 # install full deps
 COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
@@ -23,13 +24,24 @@ RUN cp /tmp/requirements.txt /tmp/req.bak \
   && python -m pip install --no-cache-dir --use-feature=2020-resolver -r /tmp/requirements-dev.txt
 
 # compile ext and remove temp files
-COPY . .
+# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)
+# please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache
+# this or anything below it and always will build from at most here; one file change leads to no caching from here on...
+
+COPY LICENSE setup.py setup.cfg versioneer.py runtests.sh .gitignore .gitattributes README.md MANIFEST.in ./
+COPY tests ./tests
+COPY monai ./monai
+COPY .git ./.git
 RUN BUILD_MONAI=1 FORCE_CUDA=1 python setup.py develop \
   && rm -rf build __pycache__
 
 # NGC Client
 WORKDIR /opt/tools
-RUN wget -q https://ngc.nvidia.com/downloads/ngccli_cat_linux.zip && \
+ARG NGC_CLI_URI="https://ngc.nvidia.com/downloads/ngccli_cat_linux.zip"
+RUN wget -q ${NGC_CLI_URI} && \
     unzip ngccli_cat_linux.zip && chmod u+x ngc && \
+    md5sum -c ngc.md5 && \
     rm -rf ngccli_cat_linux.zip ngc.md5
+# append /opt/tools to runtime path for NGC CLI to be accessible from all file system locations
+ENV PATH=${PATH}:/opt/tools
 WORKDIR /opt/monai
diff --git a/README.md b/README.md
@@ -29,23 +29,14 @@ Its ambitions are:
 
 
 ## Installation
-To install [the current release](https://pypi.org/project/monai/):
-```bash
-pip install monai
-```
 
-To install from the source code repository:
+To install [the current release](https://pypi.org/project/monai/), you can simply run:
+
 ```bash
-pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
+pip install monai
 ```
 
-Alternatively, pre-built Docker image is available via [DockerHub](https://hub.docker.com/r/projectmonai/monai):
-  ```bash
-  # with docker v19.03+
-  docker run --gpus all --rm -ti --ipc=host projectmonai/monai:latest
-  ```
-
-For more details, please refer to [the installation guide](https://docs.monai.io/en/latest/installation.html).
+For other installation methods (using the master branch, using Docker, etc.), please refer to [the installation guide](https://docs.monai.io/en/latest/installation.html).
 
 ## Getting Started
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,7 +22,7 @@
 
 # -- Project information -----------------------------------------------------
 project = "MONAI"
-copyright = "2020 MONAI Consortium"
+copyright = "2020 - 2021 MONAI Consortium"
 author = "MONAI Contributors"
 
 # The full version, including alpha/beta/rc tags

diff --git a/docs/source/data.rst b/docs/source/data.rst
@@ -63,6 +63,11 @@ Generic Interfaces
   :members:
   :special-members: __getitem__
 
+`ImageDataset`
+~~~~~~~~~~~~~~
+.. autoclass:: ImageDataset
+  :members:
+  :special-members: __getitem__
 
 Patch-based dataset
 -------------------
@@ -104,11 +109,6 @@ PILReader
 Nifti format handling
 ---------------------
 
-Reading
-~~~~~~~
-.. autoclass:: monai.data.NiftiDataset
-  :members:
-
 Writing Nifti
 ~~~~~~~~~~~~~
 .. autoclass:: monai.data.NiftiSaver

diff --git a/docs/source/handlers.rst b/docs/source/handlers.rst
@@ -16,12 +16,25 @@ Model checkpoint saver
 .. autoclass:: CheckpointSaver
   :members:
 
+
+Metrics saver
+-------------
+.. autoclass:: MetricsSaver
+    :members:
+
+
 CSV saver
 ---------
 .. autoclass:: ClassificationSaver
     :members:
 
 
+Iteration Metric
+----------------
+.. autoclass:: IterationMetric
+    :members:
+
+
 Mean Dice metrics handler
 -------------------------
 .. autoclass:: MeanDice

diff --git a/docs/source/highlights.md b/docs/source/highlights.md
@@ -39,7 +39,7 @@ There is a rich set of transforms in six categories: Crop & Pad, Intensity, IO,
 ### 2. Medical specific transforms
 MONAI aims at providing a comprehensive medical image specific
 transformations. These currently include, for example:
-- `LoadNifti`:  Load Nifti format file from provided path
+- `LoadImage`:  Load medical specific formats file from provided path
 - `Spacing`:  Resample input image into the specified `pixdim`
 - `Orientation`: Change the image's orientation into the specified `axcodes`
 - `RandGaussianNoise`: Perturb image intensities by adding statistical noises