First commit

.flake8

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+[flake8]
+max-line-length = 120
+extend-ignore = E203

.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.
+
+**To Reproduce**
+A clear and concise description on how to reproduce the problem.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment**
+dlup version:
+How installed:
+Python version:
+Operating System:
+
+**Additional context**
+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: 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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+Fixes #{issue number}

.github/workflows/precommit_checks.yml

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+# This action is triggered when a pull request review is submitted.
+# It will run precommit checks only when the pull request is approved.
+# Reference: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#running-a-workflow-when-a-pull-request-is-approved
+
+name: Run Precommit Checks on PR Approval
+
+on:
+    workflow_dispatch:
+    push:
+        branches:
+          - main
+    pull_request_review:
+        types: [submitted]
+
+jobs:
+    # This job runs the precommit checks on the changed files.
+    run_precommit_checks:
+
+        # Ensures the job only runs when the PR review state is "approved".
+        if: github.event.review.state == 'approved'
+        runs-on: ubuntu-22.04
+
+        steps:
+            # Checkout the repository to the GitHub Actions runner.
+            - name: Checkout Repository
+              uses: actions/checkout@v4
+
+            # Set up the desired Python environment.
+            - name: Setup Python Environment
+              uses: actions/setup-python@v4
+              with:
+                python-version: '3.10.13'
+                cache: 'pip'
+
+            # Install the required dependencies for local repos in the precommit hooks
+            - name: Install Dependencies
+              run: pip install -r .github/workflows/requirements.txt
+
+            # Determine which python files have changed in the PR.
+            - name: Get Changed Files
+              id: changed-files
+              uses: tj-actions/changed-files@v36
+              with:
+                files: '*.py'
+
+            # Run the precommit hooks only on the changed files.
+            - name: Execute Precommit Hooks on Changed Files in PR
+              uses: pre-commit/action@v3.0.0
+              with:
+                extra_args: --files ${{ steps.changed-files.outputs.all_changed_files }}

.github/workflows/requirements.txt

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+pylint==2.17.5
+mypy==1.5.1
+numpy==1.25.2

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# CMake
+CMakeCache.txt
+CMakeFiles
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/
+
+# Output of tests
+dlup/preprocessors/tests/data/test_output
+
+# OS files
+.DS_Store
+
+
+tools/logs
+config/machine_settings/*
+!config/machine_settings/example.yaml

.mypy.ini

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+[mypy]
+plugins = numpy.typing.mypy_plugin
+
+[mypy-h5py.*]
+ignore_missing_imports = True
+
+[mypy-pytorch_lightning.*]
+ignore_missing_imports = True
+
+[mypy-torchvision.*]
+ignore_missing_imports = True
+
+[mypy-torchmetrics.*]
+ignore_missing_imports = True
+
+[mypy-scipy.ndimage.*]
+ignore_missing_imports = True
+
+[mypy-kornia.*]
+ignore_missing_imports = True
+
+[mypy-shapely.*]
+ignore_missing_imports = True
+
+[mypy-tqdm.*]
+ignore_missing_imports = True
+
+[mypy-cv2.*]
+ignore_missing_imports = True
+
+; shouldn't this be in types-Pillow?
+[mypy-PIL.*]
+ignore_missing_imports = True
+
+# TODO: This needs to be fixed obviously
+[mypy-dlup.*]
+ignore_errors = True

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    # Ignore the configuration files
+    hooks:
+    -   id: flake8
+        exclude: ^docs/
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+-   repo: local # Use pylint from local environment as it requires to import packages
+    hooks:
+    -   id: mypy
+        name: mypy
+        entry: mypy
+        language: system
+        types: [python]
+        args: ["ahcore", "--strict"]
+-   repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+    -   id: detect-secrets
+- repo: local  # Use pylint from local environment as it requires to import packages
+  hooks:
+    - id: pylint
+      name: pylint
+      entry: pylint
+      language: system
+      types: [python]
+      args:
+        [
+          "-rn", # Only display messages
+          "-sn", # Don't display the score
+          "--errors-only"  # Only show the errors
+        ]