update autogmm-joss

.devops/README.md

@@ -0,0 +1,26 @@
+# Continuous Integration for `graspologic`
+
+Microsoft requires - and it's simply good policy - that we run continuous scans
+of our builds checking for any accidental commits of credentials, as well as 
+keeping track of all of our dependencies, looking for security issues as well 
+as any legal concerns.
+
+However, using Azure DevOps for our entire build restricts visibility into the
+steps we require be completed for a viable build.  This makes processing
+PRs a Microsoft-first process, instead of enabling our wonderful contributing
+community to be able to see the actual build failures as they occur, instead of
+relying on a Microsoft employee to convey the error conditions to them.
+
+To achieve this, we broke our CI process into two primary processes:
+1. Community build (via Github Actions)
+2. Compliance and security build (via Azure DevOps)
+
+We want to ensure we're up front about all our processes, so these build specification
+files are committed into the repository for community inspection.
+
+Of the steps included in `Compliance and Security` (Component Governance and Credential Scan),
+the only part that should be possible to fail a build is Credential Scan. 
+
+Unfortunately, this will require an approved Microsoft employee to determine the actual
+feedback around it, but hopefully this isolation of black box failures to an individual
+task will help mitigate most problems.

.devops/scan-and-register.yml

@@ -0,0 +1,25 @@
+jobs:
+  - job: cred_scan
+    displayName: Credential Scan
+    pool:
+      vmImage: "windows-latest"
+    steps:
+      - task: CredScan@3
+        displayName: 'Run CredScan'
+        inputs:
+          outputFormat: sarif
+          debugMode: false
+  - job: component_governance
+    displayName: Component Governance
+    pool:
+      vmImage: "ubuntu-latest"
+    steps:
+      - task: UsePythonVersion@0
+        inputs:
+          versionSpec: '3.8'
+      - script: |
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          pip freeze > requirements.txt
+      - task: ms.vss-governance-buildtask.governance-build-task-component-detection.ComponentGovernanceComponentDetection@0
+        displayName: 'Component Detection'

.github/CODEOWNERS

@@ -0,0 +1,16 @@
+# graspologic package
+# /graspologic/align @alyakin314 @bdpedigo
+# /graspologic/cluster @bdpedigo @j1c
+# /graspologic/datasets @bdpedigo
+# /graspologic/embed @j1c @bdpedigo
+# /graspologic/inference @alyakin314 @bdpedigo
+# /graspologic/match @asaadeldin11 @bdpedigo
+# /graspologic/models @bdpedigo @j1c
+# /graspologic/pipeline @j1c @bdpedigo
+# /graspologic/plot @j1c @bdpedigo
+# /graspologic/subgraph @j1c
+# /graspologic/utils/ @j1c @bdpedigo
+
+# tutorials
+
+# tests

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Bug reports help us improve!  Thanks for submitting yours!
+title: "[BUG] "
+labels: bug
+assignees: ''
+
+---
+
+## Expected Behavior
+Tell us what should happen
+
+## Actual Behavior
+Tell us what happens instead
+
+## Example Code
+Please see [How to create a Minimal, Reproducible example](https://stackoverflow.com/help/minimal-reproducible-example) for some guidance on creating the best possible example of the problem
+```python
+
+```
+
+## Full Traceback
+```pytb
+Paste the full traceback in case there is an exception
+
+```
+
+## Your Environment
+* Python version:
+* graspologic version:
+
+## Additional Details
+Any other contextual information you might feel is important.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,2 @@
+blank_issues_enabled: false
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,24 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+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.
+
+## Describe alternatives you've considered
+A clear and concise description of any alternative solutions or features you've considered.
+
+## Provide references (if applicable)
+If your feature request is related to a published algorithm/idea, please provide links to 
+any relevant articles or webpages.
+
+## Additional context
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/usage-question.md

@@ -0,0 +1,10 @@
+---
+name: Usage Question
+about: Ask us a question about graspologic and graphs!
+title: "[Question]"
+labels: question
+assignees: ''
+
+---
+
+This is our forum for asking whatever network question you'd like!  No need to feel shy - we're happy to talk about graphs!

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 <!--
 Thanks for contributing a pull request! Please ensure you have taken a look at
-the contribution guidelines: https://github.com/neurodata/graspy/blob/master/CONTRIBUTING.md#pull-request-checklist
+the contribution guidelines: https://github.com/microsoft/graspologic/blob/dev/CONTRIBUTING.md
 -->
 
 #### Reference Issues/PRs
@@ -11,9 +11,6 @@ you resolved, so that they will automatically be closed when your pull request
 is merged. See https://github.com/blog/1506-closing-issues-via-pull-requests
 -->
 
-
-#### What does this implement/fix? Explain your changes.
-
+#### What does this implement/fix? Briefly explain your changes.
 
 #### Any other comments?
-

.github/build/set_version.py

@@ -0,0 +1,25 @@
+
+"""
+Build script that will check some environment variables set by Github during build.
+See: https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables#default-environment-variables
+If the branch is master or dev, it will generate the appropriate content for version.txt. If it isn't, it returns nothing.  Note that the version.txt file is set by bash, not by this file.
+"""
+
+import os
+from graspologic.version.version import __semver
+
+ref_key = "GITHUB_REF"
+run_id_key = "GITHUB_RUN_ID"
+prerelease_ref = "refs/heads/dev"
+release_ref = "refs/heads/main"
+publish_refs = [prerelease_ref, release_ref]
+
+environ = os.environ
+
+if ref_key in environ and run_id_key in environ:
+    ref = environ[ref_key]
+    run_id = environ[run_id_key]
+    if ref == prerelease_ref:
+        print(f"{__semver}.dev{run_id}")
+    elif ref == release_ref:
+        print(f"{__semver}")

.github/workflows/build.yml

@@ -0,0 +1,105 @@
+name: graspologic CI
+on: [push, pull_request]
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - name: "Run Documentation Generation"
+        run: |
+          sudo apt install pandoc
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          sphinx-build -W -a docs/ docs/_build/html
+  code-format-check:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - name: Run Format Check
+        run: |
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          black --check --diff ./graspologic ./tests
+  mypy-type-check:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - name: "[Optional] Run Type Validation Checks"
+        run: |
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          mypy ./graspologic
+  test-coverage:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - name: Run Test Coverage
+        run: |
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          python -m pytest --co --cov=graspologic
+  unit-and-doc-test:
+    runs-on: ${{matrix.os}}
+    continue-on-error: true
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python_version: [3.6, 3.7, 3.8]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{matrix.python_version}}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{matrix.python_version}}
+      - name: Run Unit Tests and Doctests
+        run: |
+          pip install -U pip setuptools
+          pip install -r requirements.txt
+          pytest tests  # note: should be pytest graspologic tests, but we're skipping doctests for now and re-enabling them in another PR
+  publish:
+    runs-on: ubuntu-latest
+    needs: [build-documentation, code-format-check, unit-and-doc-test]
+    if: github.ref=='refs/heads/main' || github.ref=='refs/heads/dev'
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel twine
+          pip install -r requirements.txt
+      - name: Materialize Fixed Version
+        run: |
+          python .github/build/set_version.py > graspologic/version/version.txt
+          cat graspologic/version/version.txt
+      - name: Build with setuptools
+        run: |
+          python setup.py build sdist
+      - name: Publish with twine
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          twine upload dist/*

.gitignore

@@ -121,3 +121,5 @@ docs/bpedigo/ase_clustering.py
 notebooks/bpedigo
 
 *.DS_Store
+.idea
+*.iml