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.env.example

@@ -0,0 +1,6 @@
+# example of file for storing private and user specific environment variables, like keys or system paths
+# rename it to ".env" (excluded from version control by default)
+# .env is loaded by train.py automatically
+# hydra allows you to reference variables in .yaml configs with special syntax: ${oc.env:MY_VAR}
+
+MY_VAR="/home/user/my/system/path"

.github/ISSUE_TEMPLATE/0-bug-report.yaml

@@ -0,0 +1,105 @@
+name: "🐛 Bug Report"
+description: Submit a report to help us reproduce and fix the bug
+title: Title of your bug report
+labels: ["bug"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this bug report 🙏 !
+
+  - type: checkboxes
+    attributes:
+      label: ✅ Code of conduct checklist
+      description: >
+        Before submitting a bug, please make sure you went through the following 
+        steps.
+      options:
+        - label: "🌱 I am using the **_latest version_** of the [code](https://github.com/drprojects/superpoint_transformer/tree/master)."
+          required: true
+        - label: "👩‍💻 I made sure the bug concerns the official [project's codebase](https://github.com/drprojects/superpoint_transformer/tree/master) and not something I coded myself on top of it. (We only provide support for code we wrote and released ourselves)."
+          required: true
+        - label: "🔎 I took appropriate **_time_** to investigate the problem before filing an issue, but am unable to solve it myself."
+          required: true
+        - label: "📙 I **_thoroughly_** went through the [README](https://github.com/drprojects/superpoint_transformer/blob/master/README.md), but could not find the solution there."
+          required: true
+        - label: "📘 I **_thoroughly_** went through the tutorial [slides](media/superpoint_transformer_tutorial.pdf), [notebook](notebooks/superpoint_transformer_tutorial.ipynb), and [video](https://www.youtube.com/watch?v=2qKhpQs9gJw), but could not find the solution there."
+          required: true
+        - label: "📗 I **_thoroughly_** went through the [documentation](https://github.com/drprojects/superpoint_transformer/tree/master/docs), but could not find the solution there."
+          required: true
+        - label: "📜 I went through the **_docstrings_** and **_comments_** in the [source code](https://github.com/drprojects/superpoint_transformer/tree/master) parts relevant to my problem, but could not find the solution there."
+          required: true
+        - label: "👩‍🔧 I searched for [**_similar issues_**](https://github.com/drprojects/superpoint_transformer/issues), but could not find the solution there."
+          required: true
+        - label: "🔎 I made sure my bug is related to the [project's codebase](https://github.com/drprojects/superpoint_transformer/tree/master) and is not in fact a sub-dependency issue (e.g.: FRNN installation issue, PyTorch installation issue, PyTorch Geometric not installed with GPU support, ...)."
+          required: true
+        - label: "⭐ Since I am showing interest in the project, I took the time to give the [repo](https://github.com/drprojects/superpoint_transformer/tree/master) a ⭐ to show support. **Please do, it means a lot to us !**"
+          required: true
+
+  - type: textarea
+    attributes:
+      label: 🐛 Describe the bug
+      description: >
+        Please provide a _**clear and concise**_ description of the issue you
+        are facing. If the code does not behave as anticipated, please describe
+        the expected behavior. Include references to any relevant documentation
+        or related issues.
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: 📜 Log output
+      description: >
+        If relevant, please copy and paste any useful log output. If copying an 
+        error message, make sure you provide the _**full traceback**_. This will
+        be automatically rendered as shell code, so no need for backticks.
+      placeholder: |
+        << Full error message >>
+      render: shell
+
+  - type: textarea
+    attributes:
+      label: 🤖 Steps to reproduce the bug
+      description: >
+        Please provide a _**minimal reproducible example**_ to help us 
+        investigate the bug.
+      placeholder: |
+        A step-by-step recipe for reproducing your bug. Use backticks as shown 
+        below to write and render code snippets. 
+
+        ```python
+        # Some python code to reproduce the problem
+        ```
+
+        ```
+        Some error message you got, with the full traceback.
+        ```
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: 📚 Additional information
+      description: >
+        Please add any additional information that could help us diagnose the
+        problem better. Provide screenshots if applicable. You may attach
+        log files, generated wheel, or any other file that could be helpful.
+
+  - type: textarea
+    attributes:
+      label: 🖥️ Environment
+      description: |
+        Please run the following and paste the output here. This will let us know more about your environment.
+        ```sh
+        curl -OL https://raw.githubusercontent.com/pytorch/pytorch/main/torch/utils/collect_env.py
+        # For security purposes, please check the contents of collect_env.py before running it.
+        python3 collect_env.py
+        ```
+      render: shell
+      placeholder: |
+        << Copy the output of `collect_env.py` here >>
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/1-feature-request.yaml

@@ -0,0 +1,57 @@
+name: "🚀 Feature Request"
+description: Propose a new feature
+title: Title of your feature request
+labels: ["feature"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this feature request report 🙏 !
+
+  - type: checkboxes
+    attributes:
+      label: ✅ Code of conduct checklist
+      description: >
+        Before submitting a feature request, please make sure you went through 
+        the following steps.
+      options:
+        - label: "🌱 I am using the **_latest version_** of the [code](https://github.com/drprojects/superpoint_transformer/tree/master)."
+          required: true
+        - label: "📙 I **_thoroughly_** went through the [README](https://github.com/drprojects/superpoint_transformer/blob/master/README.md), but could not find the feature I need there."
+          required: true
+        - label: "📘 I **_thoroughly_** went through the tutorial [slides](media/superpoint_transformer_tutorial.pdf), [notebook](notebooks/superpoint_transformer_tutorial.ipynb), and [video](https://www.youtube.com/watch?v=2qKhpQs9gJw), but could not find the feature I need there."
+          required: true
+        - label: "📗 I **_thoroughly_** went through the [documentation](https://github.com/drprojects/superpoint_transformer/tree/master/docs), but could not find the feature I need there."
+          required: true
+        - label: "📜 I went through the **_docstrings_** and **_comments_** in the [source code](https://github.com/drprojects/superpoint_transformer/tree/master) parts relevant to my problem, but could not find the feature I need there."
+          required: true
+        - label: "👩‍🔧 I searched for [**_similar issues_**](https://github.com/drprojects/superpoint_transformer/issues), but could not find the feature I need there."
+          required: true
+        - label: "⭐ Since I am showing interest in the project, I took the time to give the [repo](https://github.com/drprojects/superpoint_transformer/tree/master) a ⭐ to show support. **Please do, it means a lot to us !**"
+          required: true
+
+  - type: textarea
+    attributes:
+      label: 🚀 The feature, motivation and pitch
+      description: >
+        A clear and concise description of the feature proposal. Please outline
+        the motivation for the proposal. Is your feature request related to a
+        specific problem ? e.g., *"I'm working on X and would like Y to be 
+        possible"*. If this is related to another GitHub issue, please link here
+        too.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: 🔀 Alternatives
+      description: >
+        A description of any alternative solutions or features you've 
+        considered, if any.
+
+  - type: textarea
+    attributes:
+      label: 📚 Additional context
+      description: >
+        Add any other context or screenshots about the feature request.

.github/ISSUE_TEMPLATE/2-documentation.yaml

@@ -0,0 +1,46 @@
+name: "📚 Typos and Documentation Fixes"
+description: Tell us about how we can improve our documentation
+title: Title of your documentation/typo fix/request
+labels: ["documentation"]
+
+body:
+
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this documentation report 🙏 !
+
+  - type: checkboxes
+    attributes:
+      label: ✅ Code of conduct checklist
+      description: >
+        Before submitting a bug, please make sure you went through the following 
+        steps.
+      options:
+        - label: "🌱 I am using the **_latest version_** of the [code](https://github.com/drprojects/superpoint_transformer/tree/master)."
+          required: true
+        - label: "📙 I went through the [README](https://github.com/drprojects/superpoint_transformer/blob/master/README.md), but could not find the appropriate documentation there."
+          required: true
+        - label: "📘 I went through the tutorial [slides](media/superpoint_transformer_tutorial.pdf), [notebook](notebooks/superpoint_transformer_tutorial.ipynb), and [video](https://www.youtube.com/watch?v=2qKhpQs9gJw), but could not find the appropriate documentation there."
+          required: true
+        - label: "📗 I went through the [documentation](https://github.com/drprojects/superpoint_transformer/tree/master/docs), but could not find the appropriate documentation there."
+          required: true
+        - label: "📜 I went through the **_docstrings_** and **_comments_** in the [source code](https://github.com/drprojects/superpoint_transformer/tree/master) parts relevant to my problem, but could not find the appropriate documentation there."
+          required: true
+        - label: "👩‍🔧 I searched for [**_similar issues_**](https://github.com/drprojects/superpoint_transformer/issues), but could not find the appropriate documentation there."
+          required: true
+        - label: "⭐ Since I am showing interest in the project, I took the time to give the [repo](https://github.com/drprojects/superpoint_transformer/tree/master) a ⭐ to show support. **Please do, it means a lot to us !**"
+          required: true
+
+  - type: textarea
+    attributes:
+      label: 📚 Describe the documentation issue
+      description: |
+        A clear and concise description of the issue.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Suggest a potential alternative/fix
+      description: |
+        Tell us how we could improve the documentation in this regard.

.github/ISSUE_TEMPLATE/3-refactor.yaml

@@ -0,0 +1,28 @@
+name: "🛠 Refactor"
+description: Suggest a code refactor or deprecation
+title: Title of your refactor/deprecation report
+labels: refactor
+
+body:
+
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this refactor report 🙏 !
+
+  - type: textarea
+    attributes:
+      label: 🛠 Proposed Refactor
+      description: |
+        A clear and concise description of the refactor proposal. Please outline
+        the motivation for the proposal. If this is related to another GitHub 
+        issue, please link here too.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Suggest a potential alternative/fix
+      description: |
+        Tell us how we could improve the code in this regard.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yaml

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+blank_issues_enabled: false

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+## What does this PR do?
+
+<!--
+Please include a summary of the change and which issue is fixed.
+Please also include relevant motivation and context.
+List any dependencies that are required for this change.
+List all the breaking changes introduced by this pull request.
+-->
+
+Fixes #\<issue_number>
+
+## Before submitting
+
+- [ ] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?
+- [ ] Did you make sure your **PR does only one thing**, instead of bundling different changes together?
+- [ ] Did you list all the **breaking changes** introduced by this pull request?
+- [ ] Did you **test your PR locally** with `pytest` command?
+- [ ] Did you **run pre-commit hooks** with `pre-commit run -a` command?
+
+## Did you have fun?
+
+Make sure you had fun coding 🙃

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    ignore:
+      - dependency-name: "pytorch-lightning"
+        update-types: ["version-update:semver-patch"]
+      - dependency-name: "torchmetrics"
+        update-types: ["version-update:semver-patch"]

.github/workflows/code-quality-main.yaml

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+# Same as `code-quality-pr.yaml` but triggered on commit to main branch
+# and runs on all files (instead of only the changed ones)
+
+name: Code Quality Main
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3

.github/workflows/code-quality-pr.yaml

@@ -0,0 +1,36 @@
+# This workflow finds which files were changed, prints them,
+# and runs `pre-commit` on those files.
+
+# Inspired by the sktime library:
+# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
+
+name: Code Quality PR
+
+on:
+  pull_request:
+    branches: [main, "release/*"]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Find modified files
+        id: file_changes
+        uses: trilom/file-changes-action@v1.2.4
+        with:
+          output: " "
+
+      - name: List modified files
+        run: echo '${{ steps.file_changes.outputs.files}}'
+
+      - name: Run pre-commits
+        uses: pre-commit/action@v2.0.3
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}

.github/workflows/test.yml

@@ -0,0 +1,104 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, "release/*"]
+
+jobs:
+  run_tests:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    timeout-minutes: 10
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install sh
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  run_tests_windows:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-latest"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    timeout-minutes: 10
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  # upload code coverage report
+  code-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install pytest-cov[toml]
+          pip install sh
+
+      - name: Run tests and collect coverage
+        run: pytest --cov src # NEEDS TO BE UPDATED WHEN CHANGING THE NAME OF "src" FOLDER
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3

.gitignore

@@ -0,0 +1,169 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### VisualStudioCode
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+**/.vscode
+
+# JetBrains
+.idea/
+
+# Data & Models
+*.h5
+*.tar
+*.tar.gz
+
+# Lightning-Hydra-Template
+configs/local/default.yaml
+data/
+logs/
+.env
+.autoenv
+
+
+# Superpoint Transformer project
+.idea
+src/dependencies/parallel_cut_pursuit
+src/dependencies/grid_graph
+src/dependencies/FRNN
+src/dependencies/point_geometric_features
+src/dependencies/
+*.pyc
+*DS_Store*
+*.vscode
+*.so
+*.cmake
+*__pycache__*
+*.ipynb*
+notebooks/*

.pre-commit-config.yaml

@@ -0,0 +1,122 @@
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      # list of supported hooks: https://pre-commit.com/hooks.html
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: debug-statements
+      - id: detect-private-key
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-case-conflict
+      - id: check-added-large-files
+
+  # python code formatting
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+        args: [--line-length, "99"]
+
+  # python import sorting
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+  # python upgrading syntax to newer version
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.32.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  # python docstring formatting
+  - repo: https://github.com/myint/docformatter
+    rev: v1.4
+    hooks:
+      - id: docformatter
+        args: [--in-place, --wrap-summaries=99, --wrap-descriptions=99]
+
+  # python check (PEP8), programming errors and code complexity
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args:
+          [
+            "--extend-ignore",
+            "E203,E402,E501,F401,F841",
+            "--exclude",
+            "logs/*,data/*",
+          ]
+
+  # python security linter
+  - repo: https://github.com/PyCQA/bandit
+    rev: "1.7.1"
+    hooks:
+      - id: bandit
+        args: ["-s", "B101"]
+
+  # yaml formatting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+        types: [yaml]
+
+  # shell scripts linter
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.8.0.4
+    hooks:
+      - id: shellcheck
+
+  # md formatting
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.14
+    hooks:
+      - id: mdformat
+        args: ["--number"]
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-tables
+          - mdformat_frontmatter
+          # - mdformat-toc
+          # - mdformat-black
+
+  # word spelling linter
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        args:
+          - --skip=logs/**,data/**,*.ipynb
+          # - --ignore-words-list=abc,def
+
+  # jupyter notebook cell output clearing
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.5.0
+    hooks:
+      - id: nbstripout
+
+  # jupyter notebook linting
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.4.0
+    hooks:
+      - id: nbqa-black
+        args: ["--line-length=99"]
+      - id: nbqa-isort
+        args: ["--profile=black"]
+      - id: nbqa-flake8
+        args:
+          [
+            "--extend-ignore=E203,E402,E501,F401,F841",
+            "--exclude=logs/*,data/*",
+          ]

.project-root

@@ -0,0 +1,2 @@
+# this file is required for inferring the project root directory
+# do not delete