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Merge pull request #20 from RolnickLab/update-makefile-and-default-to-uv
Update makefile and make `uv` project default
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‎.github/workflows/lint.yml‎

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with:
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python-version: '3.11'
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- name: Install Poetry
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- name: Install UV
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run: |
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pip install poetry
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make uv-install-venv
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- name: Cache Poetry virtualenv and dependencies
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- name: Cache UV virtualenv and dependencies
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uses: actions/cache@v4
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with:
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path: |
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~/.cache/pypoetry
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~/.cache/uv
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~/.cache/pip
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key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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restore-keys: |
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poetry-${{ runner.os }}-
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uv-${{ runner.os }}-
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- name: Install dependencies
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run: |

‎.github/workflows/pre-commit.yml‎

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with:
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python-version: '3.11'
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- name: Install Poetry
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- name: Install UV
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run: |
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pip install poetry
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make uv-install-venv
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- name: Cache Poetry virtualenv and dependencies
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- name: Cache UV virtualenv and dependencies
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uses: actions/cache@v4
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with:
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path: |
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~/.cache/pypoetry
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~/.cache/uv
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~/.cache/pip
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key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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restore-keys: |
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poetry-${{ runner.os }}-
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uv-${{ runner.os }}-
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- name: Cache pre-commit
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uses: actions/cache@v4

‎.github/workflows/publish-gh-pages.yml‎

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with:
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python-version: '3.11'
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- name: Install Poetry
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- name: Install UV
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run: |
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pip install poetry
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make uv-install-venv
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- name: Cache Poetry virtualenv and dependencies
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- name: Cache UV virtualenv and dependencies
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uses: actions/cache@v4
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with:
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path: |
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~/.cache/pypoetry
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~/.cache/uv
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~/.cache/pip
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key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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restore-keys: |
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poetry-${{ runner.os }}-
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uv-${{ runner.os }}-
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- name: Install dependencies
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run: |
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make install
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make install-dev
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make install-docs
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- name: Run mkdocs deploy
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run: |

‎.github/workflows/test.yml‎

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with:
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python-version: '3.11'
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- name: Install Poetry
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- name: Install UV
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run: |
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pip install poetry
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make uv-install-venv
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- name: Cache Poetry virtualenv and dependencies
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- name: Cache UV virtualenv and dependencies
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uses: actions/cache@v4
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with:
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path: |
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~/.cache/pypoetry
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~/.cache/uv
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~/.cache/pip
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key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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restore-keys: |
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poetry-${{ runner.os }}-
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uv-${{ runner.os }}-
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- name: Install dependencies
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run: |

‎.make/.bumpversion.toml‎

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[tool.bumpversion]
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current_version = "0.7.1"
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current_version = "1.0.0"
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commit = true
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message = "Makefile version {new_version} released."
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tag = true

‎.make/CHANGES_MAKEFILE.md‎

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______________________________________________________________________
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<!-- (New changes here in list form) -->
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- Fix test targets
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- Move `docs` and `lab` dependency groups as optional groups `[extras]`
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- Add `test-notebooks` target to facilitate running tests using notebooks through the `nbval` library
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- Add configurable `VENV_PATH` to facilitate using virtual environment created outside of the repository
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## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17)
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## [1.2.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.2.0) (2026-01-21)
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______________________________________________________________________
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<!-- (New changes here in list form) -->
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- Add auto-initialization script and corresponding makefile targets
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## [1.1.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.1.0) (2026-01-20)
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______________________________________________________________________
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- Add MkDocs dependencies and skeleton structure for MkDocs pages
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- Add `docs` makefile targets
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- Refactor base package to `src/core` instead of `src/` and improve package structure to follow current python best practices
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- Improve and fix bugs/typos from the conda, poetry and uv targets
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## [1.0.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.0.0) (2025-11-21)
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______________________________________________________________________
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- BREAKING CHANGE - Make default version of project use `uv`
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- Consists of a rework of the `pyproject.toml` file that no longer works with `poetry<2.0.0`
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- Added `poetry python install` functionality to the makefike
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- Refactored `conda` installation to use miniforge and micromamba instead of miniconda
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- Improve determination of build tool and environment by makefile to make experience simpler
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- Refactor target group enablement via `Makefile.variables` file instead of commenting
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out lines in `Makefile`
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- Add link checker to `pre-commit`
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- Refactor tests to reduce duplication
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- Remove target that installed `poetry` inside conda environment
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- Update documentation and README.md
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- Convert to Google docstring format
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## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17)
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______________________________________________________________________
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## [0.7.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.0) (2025-09-10)
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‎.make/Makefile‎

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# files to include.
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########################################################################################
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PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
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MAKEFILE_VERSION := 0.7.1
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MAKEFILE_VERSION := 1.2.0
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BUMP_TOOL := bump-my-version
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BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
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‎.make/README.md‎

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This folder contains the base makefile targets.
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5-
It should not be modified outside the [Template's repository](https://github.com/RolnickLab/lab-advanced-template).
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The project uses a Makefile to automate most operations. If `make` is available on your
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machine there's a good chance this will work.
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## The Makefiles
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The following Makefile files should not be modified, but can be consulted:
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- [Makefile](../Makefile) : Entrypoint of the makefile utilities.
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- [base.make](base.make) : Shared utilities, project agnostic.
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- [conda.make](conda.make) : Conda related targets.
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- [lint.make](lint.make) : Linting and formatting related targets.
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- [poetry.make](poetry.make) : Poetry related targets.
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- [manager.make](manager.make) : Manages which group to include based on Makefile variables.
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- [test.make](test.make) : Test related targets.
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- [uv.make](uv.make) : UV related targets.
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The following Makefile files are project or user specific and can be modified by
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project users:
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- [Makefile.variables](../Makefile.variables) : Shared project variables.
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- In this file, you can activate or deactivate target groups, and configure
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settings according to your project's needs.
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- [Makefile.targets](../Makefile.targets) : Shared project targets.
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- [Makefile.private](../Makefile.private.example) : User specific variables and targets.
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- This file is ignored by git and should never be committed, as it can also contain
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secrets. You can override project configurations for local requirements, as
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well as personal preferences.
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- You can create your own version locally by copying from
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[Makefile.private.example](../Makefile.private.example)
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## Basic Information
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The different targets and their description can be examined by executing the command:
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![](img/make_targets.png)
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If there is a problem with the contents of these targets, please open an
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issue [here](https://github.com/RolnickLab/lab-advanced-template/issues).
@@ -25,5 +59,5 @@ essentially bash scripts to test the different makefile targets.
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These should only be run when modifying the makefiles inside the
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[Template's repository](https://github.com/RolnickLab/lab-advanced-template).
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They should never be run in a project implemented from the template, as they could cause
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side effects to your project.
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They should **never** be run in a project implemented from the template, as they could
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cause side effects to your project.

‎.make/base.make‎

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# Please report bugs to francis.pelletier@mila.quebec
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########################################################################################
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.DEFAULT_GOAL := help
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# Basic variables
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PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
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MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
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SHELL := /usr/bin/env bash
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BUMP_TOOL := bump-my-version
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MAKEFILE_VERSION := 0.7.1
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MAKEFILE_VERSION := 1.2.0
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DOCKER_COMPOSE ?= docker compose
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AUTO_INSTALL ?=
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CONDA_ENVIRONMENT ?=
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CONDA_YES_OPTION ?=
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# Default environment to install package
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# Can be overridden in Makefile.private file
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DEFAULT_INSTALL_ENV ?=
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DEFAULT_POETRY_INSTALL_ENV ?=
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# Colors
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_SECTION := \033[1m\033[34m
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_TARGET := \033[36m
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_NORMAL := \033[0m
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.DEFAULT_GOAL := help
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# Default variables (if Makefile.variables is missing)
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APP_VERSION := 0.0.0
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APPLICATION_NAME := src
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PYTHON_VERSION := 3.12
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DEFAULT_INSTALL_ENV := uv
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DEFAULT_BUILD_TOOL := uv
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TARGET_GROUPS := lint,test
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CONDA_ENVIRONMENT := src-env
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# Targets Colors
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_ESC := $(shell printf '\033')
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_SECTION := $(_ESC)[1m\033[34m
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_BLUE := $(_ESC)[1m\033[34m
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_TARGET := $(_ESC)[1m\033[36m
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_CYAN := $(_ESC)[36m
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_NORMAL := $(_ESC)[0m
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_WARNING := $(_ESC)[1;39;41m
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WARNING := $(_WARNING) -- WARNING -- $(_NORMAL)
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# Project and Private variables and targets import to override variables for local
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# This is to make sure, sometimes the Makefile includes don't work.
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-include Makefile.variables
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-include Makefile.private
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contains = $(if $(findstring $(1),$(2)),true)
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not_in = $(if $(findstring $(1),$(2)),,true)
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INSTALL_ENV_IS_VENV := $(call contains,venv,$(DEFAULT_INSTALL_ENV))
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INSTALL_ENV_IS_UV := $(call contains,uv,$(DEFAULT_INSTALL_ENV))
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INSTALL_ENV_IS_POETRY := $(call contains,poetry,$(DEFAULT_INSTALL_ENV))
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INSTALL_ENV_IS_CONDA := $(call contains,conda,$(DEFAULT_INSTALL_ENV))
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BUILD_TOOL_IS_UV := $(call contains,uv,$(DEFAULT_BUILD_TOOL))
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BUILD_TOOL_IS_POETRY := $(call contains,poetry,$(DEFAULT_BUILD_TOOL))
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CONDA_CONFLICT := $(and $(INSTALL_ENV_IS_CONDA),$(BUILD_TOOL_IS_UV))
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UV_CONFLICT := $(and $(INSTALL_ENV_IS_POETRY),$(BUILD_TOOL_IS_UV))
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POETRY_CONFLICT := $(and $(INSTALL_ENV_IS_UV),$(BUILD_TOOL_IS_POETRY))
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PLEASE_FIX_CONFLICT_MSG := Please fix the conflict in your [Makefile.variables] and/or [Makefile.private] file(s)
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IS_MAKEFILE_VARIABLES_MISSING := $(call not_in,Makefile.variables,$(MAKEFILE_LIST))
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PLEASE_FIX_MISSING_FILE := Please consider adding a [Makefile.variables] file to your project - See lab-advanced-template for more info
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TAG_WARN := $(_WARNING) -- WARNING -- $(_NORMAL)
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check_configs = $(if $($(1)), \
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$(info ) \
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$(info $(TAG_WARN) $(2)) \
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$(info $(PLEASE_FIX_CONFLICT_MSG)) \
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$(info ) \
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)
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check_files = $(if $($(1)), \
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$(info ) \
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$(info $(TAG_WARN) $(2)) \
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$(info $(PLEASE_FIX_MISSING_FILE)) \
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$(info ) \
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)
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# Config Checks
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# These run immediately when you type 'make'
93+
$(call check_configs,CONDA_CONFLICT,'conda' environment is enabled while using 'uv')
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$(call check_configs,UV_CONFLICT,'poetry' environment is enabled while using 'uv')
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$(call check_configs,POETRY_CONFLICT,'uv' environment is enabled while using 'poetry')
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$(call check_files,IS_MAKEFILE_VARIABLES_MISSING,The configuration file 'Makefile.variables' is missing - Using default values)
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## -- Initialization targets ---------------------------------------------------------------------------------------- ##
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.PHONY: project-init
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project-init: ## Initialize the project from the template - Only run once!
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@python3 $(PROJECT_PATH).make/scripts/auto_init_script.py
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.PHONY: project-init-dry-run
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project-init-dry: ## Test run: no changes will be made - Initialize the project from the template
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@python3 $(PROJECT_PATH).make/scripts/auto_init_script.py --dry
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## -- Informative targets ------------------------------------------------------------------------------------------- ##
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.PHONY: info
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info: ## Get project configuration info
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@echo ""
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@echo -e "$(_BLUE)--- Configuration Status ---$(_NORMAL)"
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@echo ""
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@echo -e "$(_CYAN)Application Name$(_NORMAL) : $(APPLICATION_NAME)"
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@echo -e "$(_CYAN)Application version$(_NORMAL) : $(APP_VERSION)"
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@echo -e "$(_CYAN)Application Root$(_NORMAL) : [$(PROJECT_PATH)]"
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@echo -e "$(_CYAN)Application package$(_NORMAL) : [$(PROJECT_PATH)src/$(APPLICATION_NAME)]"
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@echo -e "$(_CYAN)Environment manager$(_NORMAL) : $(DEFAULT_INSTALL_ENV)"
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@echo -e "$(_CYAN)Build tool$(_NORMAL) : $(DEFAULT_BUILD_TOOL)"
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@echo -e "$(_CYAN)Python version$(_NORMAL) : $(PYTHON_VERSION)"
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@echo -e "$(_CYAN)Active makefile targets$(_NORMAL) : [$(TARGET_GROUPS)]"
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@echo -e "$(_CYAN)Makefile version$(_NORMAL) : $(MAKEFILE_VERSION)"
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.PHONY: all
48128
all: help
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79159
.PHONY: version
80160
version: ## display current version
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@echo "version: $(APP_VERSION)"
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@echo -e "$(_CYAN)Application version$(_NORMAL) : $(APP_VERSION)"
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@echo -e "$(_CYAN)Makefile version$(_NORMAL) : $(MAKEFILE_VERSION)"
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## -- Virtualenv targets -------------------------------------------------------------------------------------------- ##
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.PHONY: bump-major
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bump-major: ## Bump application major version <X.0.0>
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$(BUMP_TOOL) bump $(BUMP_ARGS) major
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@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) major
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.PHONY: bump-minor
144225
bump-minor: ## Bump application minor version <0.X.0>
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$(BUMP_TOOL) bump $(BUMP_ARGS) minor
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@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) minor
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.PHONY: bump-patch
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bump-patch: ## Bump application patch version <0.0.X>
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$(BUMP_TOOL) bump $(BUMP_ARGS) patch
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@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) patch
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