commit 9cee33c405dd529267074c93ce33b1b239df4745
Author: asreva <ivan.sievering@epfl.ch>
Date:   Fri May 1 09:24:14 2026 +0200

    Initial commit

diff --git a/.gitattributes b/.gitattributes
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+++ b/.gitattributes
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+# By default, normalize line endings
+* text=auto
+
+# Force Windows batch files to use CRLF
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf
+*.{ics,[iI][cC][sS]} text eol=crlf
+
+# Force Unix bash files to use LF
+*.sh text eol=lf
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
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+++ b/.github/workflows/tests.yml
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+name: Run tests
+
+on: [push]
+
+jobs:
+
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    env:
+      PIP_ROOT_USER_ACTION: ignore
+      UV_LINK_MODE: copy
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+        uv sync --locked
+
+    - name: Check format with ruff
+      run: |
+        uv run ruff format --check
+
+    - name: Check code linting with ruff
+      run: |
+        uv run ruff check
diff --git a/.gitignore b/.gitignore
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+++ b/.gitignore
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+# Python cache
+*.pyc
+.ipynb_checkpoints/
+*.egg-info/
+
+# IDE settings
+.vscode/
+.idea/
+
+# OSX-specific
+.DS_Store
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
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--- /dev/null
+++ b/.gitlab-ci.yml
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+stages:
+- test
+
+run-tests:
+  stage: test
+  image: python:3.12
+  variables:
+    PIP_ROOT_USER_ACTION: ignore
+    UV_LINK_MODE: copy
+  before_script:
+  - python -m pip install --upgrade pip
+  - pip install uv
+  - uv sync --locked
+  script:
+  - uv run ruff format --check
+  - uv run ruff check
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
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+++ b/.pre-commit-config.yaml
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+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-added-large-files
+    args: ["--maxkb=2000"]
+  - id: check-case-conflict
+  - id: check-illegal-windows-names
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-symlinks
+  - id: check-toml
+  - id: check-xml
+  - id: check-yaml
+  - id: destroyed-symlinks
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.0
+  hooks:
+    - id: ruff-check
+      args: [ --fix ]
+    - id: ruff-format
+- repo: https://github.com/astral-sh/uv-pre-commit
+  rev: 0.10.2
+  hooks:
+    - id: uv-lock
+    - id: uv-export
diff --git a/.python-version b/.python-version
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index 0000000..e4fba21
--- /dev/null
+++ b/.python-version
@@ -0,0 +1 @@
+3.12
diff --git a/README.md b/README.md
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+++ b/README.md
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+# river-annotation-tool
+
+This project is made using [this template](https://github.com/SwissDataScienceCenter/innovation-cookiecutter).
+Next steps include:
+
+ - [x] Create project from the Cookiecutter template.
+ - [ ] Create a virtual environment to work in an isolated Python installation.
+ - [ ] Install [pre-commit](https://pre-commit.com/) hooks.
+ - [ ] Keep either [`.gitlab-ci.yml`](https://docs.gitlab.com/ee/ci/yaml/gitlab_ci_yaml.html) or [`.github/`](https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python), according to your Git hosting platform.
+ - [ ] Update `authors` and `description`, in `pyproject.toml`.
+ - [ ] Add development and installation dependencies in `pyproject.toml`, with permissive version constraints.
+ - [ ] Add a `LICENSE` file, if applicable. This is *highly recommended* if the project is open source.
+ - [ ] Add a [`CITATION.cff`](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), to ease citation of your work.
+ - [ ] Replace this `README.md` with a proper one. Among others, it must explain the overall context, the installation instructions, a quick start guide, and a repository structure description.
+
+
+## Getting started
+
+In order to use [pre-commit](https://pre-commit.com/) hooks, they need to be registered:
+
+```sh
+pre-commit install
+```
+
+It is a good practice to manually invoke hooks after installation, just in case:
+
+```sh
+pre-commit run --all-files
+```
+
+During development, install pinned dependencies in your virtual environment, including the module itself in [editable mode](https://setuptools.pypa.io/en/latest/userguide/development_mode.html), using:
+
+```sh
+uv sync
+```
+
+New dependencies can be added using [`uv add`](https://docs.astral.sh/uv/concepts/projects/dependencies/) (or `uv add --dev` for development dependencies), or by manually configuring `pyproject.toml` and using [`uv lock && uv sync`](https://docs.astral.sh/uv/concepts/projects/sync/).
diff --git a/data/.gitkeep b/data/.gitkeep
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index 0000000..e69de29
diff --git a/notebooks/.gitkeep b/notebooks/.gitkeep
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index 0000000..e69de29
diff --git a/pyproject.toml b/pyproject.toml
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+++ b/pyproject.toml
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+[build-system]
+requires = ["setuptools>=61.0.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "river_annotation_tool"
+authors = [
+    # TODO configure authors
+    # { name = "Jane Smith", email = "jane.smith@example.com" },
+    # { name = "John Doe", email = "john.doe@example.com" },
+]
+description = ""
+readme = "README.md"
+requires-python = "~=3.12.0"
+dependencies = [
+    # TODO configure install dependencies
+]
+dynamic = ["version"]
+
+[dependency-groups]
+dev = [
+    "notebook~=7.5",
+    "pre-commit~=4.5",
+    "ruff==0.15.0",
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "river_annotation_tool.__version__"}
+
+[tool.ruff]
+target-version = "py312"
+line-length = 88
+
+[tool.ruff.lint]
+extend-select = ["B", "I", "RUF1", "UP", "W"]
+
+[tool.ruff.lint.isort]
+lines-after-imports = 2
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]
diff --git a/requirements.txt b/requirements.txt
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+++ b/requirements.txt
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+# This file will be autogenerated from pyproject.toml
diff --git a/src/river_annotation_tool/__init__.py b/src/river_annotation_tool/__init__.py
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+++ b/src/river_annotation_tool/__init__.py
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+__version__ = "0.1.0"
diff --git a/uv.lock b/uv.lock
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+++ b/uv.lock
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+# This file will be autogenerated from pyproject.toml
+version = 1
+requires-python = "~=3.12.0"