initial commit

.coveragerc

@@ -0,0 +1,11 @@
+[run]
+omit =
+  tests/*
+  setup.py
+  */projects/*
+  */tests/*.py
+  */tools/*.py
+  */tutorials/*.py
+  */config.py
+source =
+  .

.dockerignore

@@ -0,0 +1,19 @@
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+env
+pip-log.txt
+pip-delete-this-directory.txt
+.tox
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+*.log
+.git
+**/*.atommic
+**/*.ckpt

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+
+A clear and concise description of what the bug is.
+
+**Steps/Code to reproduce bug**
+
+Please list *minimal* steps or code snippet for us to be able to reproduce the bug.
+
+A  helpful guide on on how to craft a minimal bug report  http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports.
+
+
+**Expected behavior**
+
+A clear and concise description of what you expected to happen.
+
+**Environment overview (please complete the following information)**
+
+ - Environment location: [Bare-metal, Docker, Cloud(specify cloud provider - AWS, Azure, GCP, Collab)]
+ - Method of ATOMMIC install: [pip install or from source]. Please specify exact commands you used to install.
+ - If method of install is [Docker], provide `docker pull` & `docker run` commands used
+
+**Environment details**
+
+If docker image is used you don't need to specify these.
+Otherwise, please provide:
+- OS version
+- PyTorch version
+- Python version
+
+**Additional context**
+
+Add any other context about the problem here.
+Example: GPU model

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: feature request
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of what you want to happen.
+Provide a code snippet on how new APIs/changes would be used by others.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+# What does this PR do ?
+
+Add a one line overview of what this PR aims to accomplish.
+
+**Collection**: [Note which collection this PR will affect]
+
+# Changelog
+- Add specific line by line info of high level changes in this PR.
+
+# Usage
+* You can potentially add a usage example below
+
+```python
+# Add a code snippet demonstrating how to use this
+```
+
+# Before your PR is "Ready for review"
+**Pre checks**:
+- [ ] Make sure you read and followed [Contributor guidelines](https://github.com/wdika/atommic/blob/main/CONTRIBUTING.md)
+- [ ] Did you write any new necessary tests?
+- [ ] Did you add or update any necessary documentation?
+- [ ] Does the PR affect components that are optional to install? (Ex: Numba, Pynini, Apex etc)
+  - [ ] Reviewer: Does the PR have correct import guards for all optional libraries?
+
+**PR Type**:
+- [ ] New Feature
+- [ ] Bugfix
+- [ ] Documentation
+
+If you haven't finished some of the above items you can still open "Draft" PR.
+
+
+## Who can review?
+
+Anyone in the community is free to review the PR once the checks have passed.
+[Contributor guidelines](https://github.com/wdika/atommic/blob/main/CONTRIBUTING.md) contains specific people who can review PRs to various areas.
+
+# Additional Information
+* Related to # (issue)

.github/labeler.yml

@@ -0,0 +1,32 @@
+MTL:
+- atommic/collections/multitask/**/*
+- docs/source/api/multitask/**/*
+- tests/collections/multitask/**
+
+qMRI:
+- atommic/collections/quantitative/**/*
+- docs/source/api/quantitative/**/*
+- tests/collections/quantitative/**
+
+REC:
+- atommic/collections/reconstruction/**/*
+- docs/source/api/reconstruction/**/*
+- tests/collections/reconstruction/**
+
+SEG:
+- atommic/collections/segmentation/**/*
+- docs/source/api/segmentation/**/*
+- tests/collections/segmentation/**
+
+core:
+- atommic/core/**/*
+- tests/core/**
+
+common:
+- atommic/collections/common/**/*
+
+CI:
+- .github/**/*
+- Jenkinsfile
+- Dockerfile
+- ci.groovy

.github/workflows/changelog-build.yml

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+name: 'Changelog Build (Release)'
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  changelog:
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Required due to the way Git works, without it this action won't be able to find any or the correct tags
+
+      - name: Get Previous tag
+        id: previous_tag
+        # git for-each-ref --sort=-creatordate --format '%(refname)' refs/tags ==> refs/tags/vX.Y.Z in descending order of date
+        # awk 'FNR == 2 {print substr($1, 11, length($1))}') ==> Selects the 2nd tag from the list, then strips the /refs/tags/ part of the tag
+        # set-output name=tag_name:: ==> Takes the clean tag vX.Y.Z and sets it to steps.previous_tag.outputs.tag_name
+        run: |
+          echo "::set-output name=tag_name::$(git for-each-ref --sort=-creatordate --format '%(refname)' refs/tags | awk 'FNR == 2 {print substr($1, 11, length($1))}')"
+          echo ${{ steps.previous_tag.outputs.tag_name }}
+
+      - name: Build Changelog
+        id: github_tag
+        uses: mikepenz/release-changelog-builder-action@v3.3.1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          # Configuration file is setup with filters for domains
+          # owner:repo must point to current repo
+          # fromTag: Auto resolved from historical tag order (previous tag compared to current tag)
+          # toTag: Current tag reference
+          configuration: ".github/workflows/config/changelog-config.json"
+          owner: "wdika"
+          repo: "ATOMMIC"
+          ignorePreReleases: "false"
+          failOnError: "false"
+          fromTag: ${{ steps.previous_tag.outputs.tag_name }}
+          toTag: ${{ github.ref_name }}
+
+      - name: Print Changelog
+        run: |
+          echo "${{steps.github_tag.outputs.changelog}}"
+          echo "--- DONE ---"

.github/workflows/cherry-pick-release-commit.yml

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+name: Create PR to main with cherry-pick from release
+
+on:
+  pull_request_target:
+    branches:
+      - 'r*.*.*'
+    types: ["closed"]
+
+jobs:
+  cherry-pick-release-commit:
+    name: Cherry-pick release commit
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: github-cherry-pick-action v1.0.3
+        uses: carloscastrojumo/github-cherry-pick-action@bb0869df47c27be4ae4c7a2d93d22827aa5a0054
+        with:
+          branch: main
+          labels: |
+            cherry-pick
+          reviewers: |
+            ${{ github.event.pull_request.user.login }}
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/close-inactive-issue-pr.yml

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+name: Stale-Close-Inactive-Issues-PRs
+on:
+  schedule:
+    - cron: "30 1 * * *"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v6
+        with:
+          operations-per-run: 100
+          days-before-issue-stale: 30
+          days-before-issue-close: 7
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for 30 days with no activity. Remove stale label or comment or this will be closed in 7 days."
+          close-issue-message: "This issue was closed because it has been inactive for 7 days since being marked as stale."
+          days-before-pr-stale: 14
+          days-before-pr-close: 7
+          stale-pr-message: "This PR is stale because it has been open for 14 days with no activity. Remove stale label or comment or update or this will be closed in 7 days."
+          close-pr-message: "This PR was closed because it has been inactive for 7 days since being marked as stale."
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main", "[rv][0-9]*",  "gh-pages-src" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '19 1 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        queries: security-and-quality  # security-extended,
+        config-file: ./.github/workflows/config/codeql.yml
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"