Remove linter action redundancies

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
+{
+	"name": "py4dstem-dev",
+	"image": "mcr.microsoft.com/vscode/devcontainers/miniconda:0-3",
+	// "build": { 
+	// 	"context": "..",
+	// 	"dockerfile": "Dockerfile"
+	// },
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": []
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "/opt/conda/bin/conda init && /opt/conda/bin/pip install -e /workspaces/py4DSTEM/ && /opt/conda/bin/pip install ipython ipykernel jupyter",
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"python.defaultInterpreterPath": "/opt/conda/bin/python",
+				"python.analysis.autoFormatStrings": true,
+				"python.analysis.completeFunctionParens": true,
+				"ruff.showNotifications": "onWarning",
+				"workbench.colorTheme": "Monokai",
+				// "editor.defaultFormatter": "ms-python.black-formatter",
+				"editor.fontFamily": "Menlo, Monaco, 'Courier New', monospace",
+				"editor.bracketPairColorization.enabled": true,
+				"editor.guides.bracketPairs": "active",
+				"editor.minimap.renderCharacters": false,
+				"editor.minimap.autohide": true,
+				"editor.minimap.scale": 2,
+				"[python]": {
+					"editor.defaultFormatter": "ms-python.black-formatter",
+					"editor.codeActionsOnSave": {
+						"source.organizeImports": false
+					}
+				}
+			},
+			"extensions": [
+				"ms-python.python",
+				"donjayamanne.python-extension-pack",
+				"ms-python.vscode-pylance",
+				"ms-toolsai.jupyter",
+				"GitHub.codespaces",
+				"ms-azuretools.vscode-docker",
+				"DavidAnson.vscode-markdownlint",
+                "ms-vsliveshare.vsliveshare",
+				"charliermarsh.ruff",
+				"eamodio.gitlens",
+				"ms-python.black-formatter"
+			]
+		}
+	}
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.flake8

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+[flake8]
+extend-ignore:
+    E114,
+    E115,
+    E116,
+    E201,
+    E202,
+    E203,
+    E204,
+    E231,
+    E265,
+    E266,
+    E303,
+    E402,
+    E501,
+
+

.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/scripts/update_version.py

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+"""
+Script to update the patch version number of the py4DSTEM package.
+"""
+
+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].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/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: ["3.9", "3.10", "3.11", "3.12"]
+                # 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_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: ["3.9", "3.10", "3.11", "3.12"]
+                #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: ["3.9", "3.12"]
+                # 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: Lint with super-linter@v5-slim
+
+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: super-linter/super-linter/slim@v5 # updated to latest slim as quicker to download 
+        env:
+          VALIDATE_ALL_CODEBASE: false # only check changes
+          VALIDATE_PYTHON_FLAKE8: true # lint with flake8
+          DEFAULT_BRANCH: "dev" # set default branch to dev
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # for github things
+          # FILTER_REGEX_EXCLUDE: .*test/.* # exclude test dirs
+          FILTER_REGEX_EXCLUDE: .*__init__.py/.* # exclude test dirs
+          FILTER_REGEX_INCLUDE: .*py4DSTEM/.* # only look for py4DSTEM
+          LINTER_RULES_PATH: / # set toplevel dir as the path to look for rules
+          PYTHON_FLAKE8_CONFIG_FILE: .flake8 # set specific config file