Diskdetection refactor

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is, 
+
+**To Reproduce**
+Steps to reproduce the behavior, please be as general as possible, and ideally recreate a minimal reproducible example:
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+
+**py4DSTEM version** 
+It can be accessed by running `py4DSTEM.__version__`
+**Python version**
+It can be accessed using `sys.version`
+**Operating system** 
+Windows, Mac (Intel or ARM), Linux (Distro)
+
+**GPU**
+If GPU related please provide:
+- CUDA driver - It can be accessed by: `nvidia-smi`
+- Cupy Version - It can be accessed by `cupy.__version__`
+
+**Screenshots**
+If applicable, could you add screenshots to help explain your problem?
+
+
+**Additional context**
+Please feel free to add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. 
+
+**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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/linters/.flake8

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+[flake8]
+select: "F402,F404,F812,F823,F831,F821,F822,E112,E113,E901,E902,E999"

.github/scripts/update_version.py

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+"""
+Script to update the patch version number of the py4DSTEM package.
+Author: Tara Mishra (Quantumstud)
+"""
+
+version_file_path = "py4DSTEM/version.py"
+
+with open(version_file_path, "r") as f:
+    lines = f.readlines()
+
+line_split = lines[0].split(".")
+patch_number = line_split[2].split("'")[0]
+
+# Increment patch number
+patch_number = str(int(patch_number) + 1) + "'"
+
+
+new_line = line_split[0] + "." + line_split[1] + "." + patch_number
+
+with open(version_file_path, "w") as f:
+    f.write(new_line)

.github/workflows/black.yml

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+name: Check code style
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.github/workflows/build-flake.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Check module can be imported
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test that the module imports
+      run: |
+        pip install .
+        python -c "import py4DSTEM; print(py4DSTEM.__version__)"

.github/workflows/check_install_dev.yml

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+name: Install Checker Dev
+on: 
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+jobs:
+
+    test-python-os-versions:
+        name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} on ${{ matrix.architecture }}
+        continue-on-error: ${{ matrix.allow_failure }}
+        runs-on: ${{ matrix.runs-on }}
+        strategy:
+            fail-fast: false
+            matrix:
+                allow_failure: [false]
+                runs-on: [ubuntu-latest]
+                architecture: [x86_64]
+                python-version: ["3.10", "3.11",]
+                # Currently no public runners available for this but this or arm64 should work next time
+                # include:
+                #     - python-version: "3.10"
+                #       architecture: [aarch64]
+                #       runs-on: macos-latest
+                #       allow_failure: true
+        steps:
+            - uses: actions/checkout@v3
+
+            - name: Setup Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v4
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install repo
+              run: |
+                python -m pip install .
+            - name: Check installation
+              run: |
+                python -c "import py4DSTEM; print(py4DSTEM.__version__)"
+            # - name: Check machine arch
+            #   run: |
+            #     python -c "import platform; print(platform.machine())"

.github/workflows/check_install_main.yml

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+name: Install Checker Main
+on: 
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+jobs:
+
+    test-python-os-versions:
+        name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} on ${{ matrix.architecture }}
+        continue-on-error: ${{ matrix.allow_failure }}
+        runs-on: ${{ matrix.runs-on }}
+        strategy:
+            fail-fast: false
+            matrix:
+                allow_failure: [false]
+                runs-on: [ubuntu-latest, windows-latest, macos-latest]
+                architecture: [x86_64]
+                python-version: ["3.10", "3.11",]
+                include:
+                    - python-version: "3.12.0-beta.4"
+                      runs-on: ubuntu-latest
+                      allow_failure: true
+                # Currently no public runners available for this but this or arm64 should work next time
+                # include:
+                #     - python-version: "3.10"
+                #       architecture: [aarch64]
+                #       runs-on: macos-latest
+                #       allow_failure: true
+        steps:
+            - uses: actions/checkout@v3
+
+            - name: Setup Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v4
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install repo
+              run: |
+                python -m pip install .
+            - name: Check installation
+              run: |
+                python -c "import py4DSTEM; print(py4DSTEM.__version__)"
+            - name: Check machine arch
+              run: |
+                python -c "import platform; print(platform.machine())"

.github/workflows/check_install_quick.yml

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+name: Install Checker Quick
+on: 
+  push:
+    branches-ignore:
+      - main
+      - dev
+  pull_request:
+    branches-ignore:
+      - main
+      - dev
+jobs:
+
+    test-python-os-versions:
+        name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} on ${{ matrix.architecture }}
+        continue-on-error: ${{ matrix.allow_failure }}
+        runs-on: ${{ matrix.runs-on }}
+        strategy:
+            fail-fast: false
+            matrix:
+                allow_failure: [false]
+                runs-on: [ubuntu-latest] 
+                architecture: [x86_64]
+                python-version: ["3.10"]
+                # Currently no public runners available for this but this or arm64 should work next time
+                # include:
+                #     - python-version: "3.10"
+                #       architecture: [aarch64]
+                #       runs-on: macos-latest
+                #       allow_failure: true
+        steps:
+            - uses: actions/checkout@v3
+
+            - name: Setup Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v4
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install repo
+              run: |
+                python -m pip install .
+            - name: Check installation
+              run: |
+                python -c "import py4DSTEM; print(py4DSTEM.__version__)"
+            # - name: Check machine arch
+            #   run: |
+            #     python -c "import platform; print(platform.machine())"

.github/workflows/linter.yml

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+name: Check for errors with flake8
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+
+jobs:
+  run-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          # Full git history is needed to get a proper list of changed files within `super-linter`
+          fetch-depth: 0
+
+      - name: Lint Code Base
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          VALIDATE_PYTHON_FLAKE8: true
+          DEFAULT_BRANCH: "dev"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pypi_upload.yml

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+# Action to check the version of the package and upload it to PyPI
+# if the version is higher than the one on PyPI
+# Author: @quantumstud
+name: PyPI Upload
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  update_version:
+    runs-on: ubuntu-latest
+    name: Check if version.py is changed and update if the version.py is not changed
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0        
+          token: ${{ secrets.GH_ACTION_VERSION_UPDATE }}      
+      - name: Get changed files
+        id: changed-files-specific
+        uses: tj-actions/changed-files@v32
+        with:
+          files: |
+            py4DSTEM/version.py
+      - name: Running if py4DSTEM/version.py file is not changed
+        if: steps.changed-files-specific.outputs.any_changed == 'false'
+        run: |
+          echo "Version file not changed, running script to change the version file."
+          #git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
+          python .github/scripts/update_version.py
+          git config --global user.email "ben.savitzky@gmail.com"
+          git config --global user.name "bsavitzky"
+          git commit -a -m "Auto-update version number (GH Action)"
+          git push origin main
+  sync_with_dev:
+    needs: update_version
+    runs-on: ubuntu-latest
+    name: Sync main with dev
+    steps:
+      - name: Sync main with dev
+        uses: actions/checkout@v3
+        with:
+          ref: dev
+          fetch-depth: 0
+          token: ${{ secrets.GH_ACTION_VERSION_UPDATE }}
+      - run: |
+          # set strategy to default merge
+          git config pull.rebase false
+          git config --global user.email "ben.savitzky@gmail.com"
+          git config --global user.name "bsavitzky"
+          git pull origin main --commit --no-edit
+          git push origin dev
+  deploy:
+    needs: sync_with_dev
+    runs-on: ubuntu-latest
+    name: Deploy to PyPI
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: dev
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - 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:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+