RolnickLab · f-PLT · Jan 19, 2026 · Jan 19, 2026 · Jan 29, 2026 · Jan 29, 2026
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -19,19 +19,19 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install Poetry
+      - name: Install UV
         run: |
-          pip install poetry
+          make uv-install-venv
 
-      - name: Cache Poetry virtualenv and dependencies
+      - name: Cache UV virtualenv and dependencies
         uses: actions/cache@v4
         with:
           path: |
-            ~/.cache/pypoetry
+            ~/.cache/uv
             ~/.cache/pip
-          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
-            poetry-${{ runner.os }}-
+            uv-${{ runner.os }}-
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -19,19 +19,19 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install Poetry
+      - name: Install UV
         run: |
-          pip install poetry
+          make uv-install-venv
 
-      - name: Cache Poetry virtualenv and dependencies
+      - name: Cache UV virtualenv and dependencies
         uses: actions/cache@v4
         with:
           path: |
-            ~/.cache/pypoetry
+            ~/.cache/uv
             ~/.cache/pip
-          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
-            poetry-${{ runner.os }}-
+            uv-${{ runner.os }}-
 
       - name: Cache pre-commit
         uses: actions/cache@v4

diff --git a/.github/workflows/publish-gh-pages.yml b/.github/workflows/publish-gh-pages.yml
@@ -27,23 +27,24 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install Poetry
+      - name: Install UV
         run: |
-          pip install poetry
+          make uv-install-venv
 
-      - name: Cache Poetry virtualenv and dependencies
+      - name: Cache UV virtualenv and dependencies
         uses: actions/cache@v4
         with:
           path: |
-            ~/.cache/pypoetry
+            ~/.cache/uv
             ~/.cache/pip
-          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
-            poetry-${{ runner.os }}-
+            uv-${{ runner.os }}-
 
       - name: Install dependencies
         run: |
-          make install
+          make install-dev
+          make install-docs
 
       - name: Run mkdocs deploy
         run: |

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -19,19 +19,19 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install Poetry
+      - name: Install UV
         run: |
-          pip install poetry
+          make uv-install-venv
 
-      - name: Cache Poetry virtualenv and dependencies
+      - name: Cache UV virtualenv and dependencies
         uses: actions/cache@v4
         with:
           path: |
-            ~/.cache/pypoetry
+            ~/.cache/uv
             ~/.cache/pip
-          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: uv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
           restore-keys: |
-            poetry-${{ runner.os }}-
+            uv-${{ runner.os }}-
 
       - name: Install dependencies
         run: |

diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.7.1"
+current_version = "1.0.0"
 commit = true
 message = "Makefile version {new_version} released."
 tag = true

diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md
@@ -6,11 +6,41 @@ ______________________________________________________________________
 
 <!-- (New changes here in list form) -->
 
-## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17)
+## [1.2.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.2.0) (2026-01-21)
 
 ______________________________________________________________________
 
-<!-- (New changes here in list form) -->
+- Add auto-initialization script and corresponding makefile targets
+
+## [1.1.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.1.0) (2026-01-20)
+
+______________________________________________________________________
+
+- Add MkDocs dependencies and skeleton structure for MkDocs pages
+- Add `docs` makefile targets
+- Refactor base package to `src/core` instead of `src/` and improve package structure to follow current python best practices
+- Improve and fix bugs/typos from the conda, poetry and uv targets
+
+## [1.0.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-1.0.0) (2025-11-21)
+
+______________________________________________________________________
+
+- BREAKING CHANGE - Make default version of project use `uv`
+    - Consists of a rework of the `pyproject.toml` file that no longer works with `poetry<2.0.0`
+- Added `poetry python install` functionality to the makefike
+- Refactored `conda` installation to use miniforge and micromamba instead of miniconda
+- Improve determination of build tool and environment by makefile to make experience simpler
+- Refactor target group enablement via `Makefile.variables` file instead of commenting
+    out lines in `Makefile`
+- Add link checker to `pre-commit`
+- Refactor tests to reduce duplication
+- Remove target that installed `poetry` inside conda environment
+- Update documentation and README.md
+- Convert to Google docstring format
+
+## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17)
+
+______________________________________________________________________
 
 ## [0.7.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.0) (2025-09-10)
 

diff --git a/.make/Makefile b/.make/Makefile
@@ -10,7 +10,7 @@
 # files to include.
 ########################################################################################
 PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
-MAKEFILE_VERSION := 0.7.1
+MAKEFILE_VERSION := 1.2.0
 BUMP_TOOL := bump-my-version
 BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml
 

diff --git a/.make/README.md b/.make/README.md
@@ -2,7 +2,41 @@
 
 This folder contains the base makefile targets.
 
-It should not be modified outside the [Template's repository](https://github.com/RolnickLab/lab-advanced-template).
+The project uses a Makefile to automate most operations. If `make` is available on your
+machine there's a good chance this will work.
+
+## The Makefiles
+
+The following Makefile files should not be modified, but can be consulted:
+
+- [Makefile](../Makefile) : Entrypoint of the makefile utilities.
+- [base.make](base.make) : Shared utilities, project agnostic.
+- [conda.make](conda.make) : Conda related targets.
+- [lint.make](lint.make) : Linting and formatting related targets.
+- [poetry.make](poetry.make) : Poetry related targets.
+- [manager.make](manager.make) : Manages which group to include based on Makefile variables.
+- [test.make](test.make) : Test related targets.
+- [uv.make](uv.make) : UV related targets.
+
+The following Makefile files are project or user specific and can be modified by
+project users:
+
+- [Makefile.variables](../Makefile.variables) : Shared project variables.
+    - In this file, you can activate or deactivate target groups, and configure
+        settings according to your project's needs.
+- [Makefile.targets](../Makefile.targets) : Shared project targets.
+- [Makefile.private](../Makefile.private.example) : User specific variables and targets.
+    - This file is ignored by git and should never be committed, as it can also contain
+        secrets. You can override project configurations for local requirements, as
+        well as personal preferences.
+    - You can create your own version locally by copying from
+        [Makefile.private.example](../Makefile.private.example)
+
+## Basic Information
+
+The different targets and their description can be examined by executing the command:
+
+![](img/make_targets.png)
 
 If there is a problem with the contents of these targets, please open an
 issue [here](https://github.com/RolnickLab/lab-advanced-template/issues).
@@ -25,5 +59,5 @@ essentially bash scripts to test the different makefile targets.
 These should only be run when modifying the makefiles inside the
 [Template's repository](https://github.com/RolnickLab/lab-advanced-template).
 
-They should never be run in a project implemented from the template, as they could cause
-side effects to your project.
+They should **never** be run in a project implemented from the template, as they could
+cause side effects to your project.
diff --git a/.make/base.make b/.make/base.make
@@ -11,12 +11,14 @@
 # Please report bugs to francis.pelletier@mila.quebec
 ########################################################################################
 
+.DEFAULT_GOAL := help
+
 # Basic variables
 PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))
 SHELL := /usr/bin/env bash
 BUMP_TOOL := bump-my-version
-MAKEFILE_VERSION := 0.7.1
+MAKEFILE_VERSION := 1.2.0
 DOCKER_COMPOSE ?= docker compose
 AUTO_INSTALL ?=
 
@@ -26,24 +28,102 @@ CONDA_TOOL := conda
 CONDA_ENVIRONMENT ?=
 CONDA_YES_OPTION ?=
 
-# Default environment to install package
-# Can be overridden in Makefile.private file
-DEFAULT_INSTALL_ENV ?=
-DEFAULT_POETRY_INSTALL_ENV ?=
-
-# Colors
-_SECTION := \033[1m\033[34m
-_TARGET  := \033[36m
-_NORMAL  := \033[0m
-
-.DEFAULT_GOAL := help
+# Default variables (if Makefile.variables is missing)
+APP_VERSION := 0.0.0
+APPLICATION_NAME := src
+PYTHON_VERSION := 3.12
+DEFAULT_INSTALL_ENV := uv
+DEFAULT_BUILD_TOOL := uv
+TARGET_GROUPS := lint,test
+CONDA_ENVIRONMENT := src-env
+
+# Targets Colors
+_ESC := $(shell printf '\033')
+_SECTION := $(_ESC)[1m\033[34m
+_BLUE := $(_ESC)[1m\033[34m
+_TARGET  := $(_ESC)[1m\033[36m
+_CYAN := $(_ESC)[36m
+_NORMAL  := $(_ESC)[0m
+_WARNING := $(_ESC)[1;39;41m
+
+WARNING := $(_WARNING) -- WARNING -- $(_NORMAL)
 
 # Project and Private variables and targets import to override variables for local
 # This is to make sure, sometimes the Makefile includes don't work.
 -include Makefile.variables
 -include Makefile.private
+
+contains = $(if $(findstring $(1),$(2)),true)
+not_in = $(if $(findstring $(1),$(2)),,true)
+
+INSTALL_ENV_IS_VENV := $(call contains,venv,$(DEFAULT_INSTALL_ENV))
+INSTALL_ENV_IS_UV := $(call contains,uv,$(DEFAULT_INSTALL_ENV))
+INSTALL_ENV_IS_POETRY := $(call contains,poetry,$(DEFAULT_INSTALL_ENV))
+INSTALL_ENV_IS_CONDA := $(call contains,conda,$(DEFAULT_INSTALL_ENV))
+
+BUILD_TOOL_IS_UV := $(call contains,uv,$(DEFAULT_BUILD_TOOL))
+BUILD_TOOL_IS_POETRY := $(call contains,poetry,$(DEFAULT_BUILD_TOOL))
+
+CONDA_CONFLICT := $(and $(INSTALL_ENV_IS_CONDA),$(BUILD_TOOL_IS_UV))
+UV_CONFLICT := $(and $(INSTALL_ENV_IS_POETRY),$(BUILD_TOOL_IS_UV))
+POETRY_CONFLICT := $(and $(INSTALL_ENV_IS_UV),$(BUILD_TOOL_IS_POETRY))
+PLEASE_FIX_CONFLICT_MSG := Please fix the conflict in your [Makefile.variables] and/or [Makefile.private] file(s)
+
+IS_MAKEFILE_VARIABLES_MISSING := $(call not_in,Makefile.variables,$(MAKEFILE_LIST))
+PLEASE_FIX_MISSING_FILE := Please consider adding a [Makefile.variables] file to your project - See lab-advanced-template for more info
+
+TAG_WARN  := $(_WARNING) -- WARNING -- $(_NORMAL)
+
+check_configs = $(if $($(1)), \
+    $(info ) \
+    $(info $(TAG_WARN) $(2)) \
+    $(info $(PLEASE_FIX_CONFLICT_MSG)) \
+    $(info ) \
+)
+
+check_files = $(if $($(1)), \
+    $(info ) \
+    $(info $(TAG_WARN) $(2)) \
+    $(info $(PLEASE_FIX_MISSING_FILE)) \
+    $(info ) \
+)
+
+# Config Checks
+# These run immediately when you type 'make'
+$(call check_configs,CONDA_CONFLICT,'conda' environment is enabled while using 'uv')
+$(call check_configs,UV_CONFLICT,'poetry' environment is enabled while using 'uv')
+$(call check_configs,POETRY_CONFLICT,'uv' environment is enabled while using 'poetry')
+$(call check_files,IS_MAKEFILE_VARIABLES_MISSING,The configuration file 'Makefile.variables' is missing - Using default values)
+
+
+## -- Initialization targets ---------------------------------------------------------------------------------------- ##
+.PHONY: project-init
+project-init: ## Initialize the project from the template - Only run once!
+	@python3 $(PROJECT_PATH).make/scripts/auto_init_script.py
+
+.PHONY: project-init-dry-run
+project-init-dry: ## Test run: no changes will be made - Initialize the project from the template
+	@python3 $(PROJECT_PATH).make/scripts/auto_init_script.py --dry
+
+
 ## -- Informative targets ------------------------------------------------------------------------------------------- ##
 
+.PHONY: info
+info: ## Get project configuration info
+	@echo ""
+	@echo -e "$(_BLUE)--- Configuration Status ---$(_NORMAL)"
+	@echo ""
+	@echo -e "$(_CYAN)Application Name$(_NORMAL)         : $(APPLICATION_NAME)"
+	@echo -e "$(_CYAN)Application version$(_NORMAL)      : $(APP_VERSION)"
+	@echo -e "$(_CYAN)Application Root$(_NORMAL)         : [$(PROJECT_PATH)]"
+	@echo -e "$(_CYAN)Application package$(_NORMAL)      : [$(PROJECT_PATH)src/$(APPLICATION_NAME)]"
+	@echo -e "$(_CYAN)Environment manager$(_NORMAL)      : $(DEFAULT_INSTALL_ENV)"
+	@echo -e "$(_CYAN)Build tool$(_NORMAL)               : $(DEFAULT_BUILD_TOOL)"
+	@echo -e "$(_CYAN)Python version$(_NORMAL)           : $(PYTHON_VERSION)"
+	@echo -e "$(_CYAN)Active makefile targets$(_NORMAL)  : [$(TARGET_GROUPS)]"
+	@echo -e "$(_CYAN)Makefile version$(_NORMAL)         : $(MAKEFILE_VERSION)"
+
+
 .PHONY: all
 all: help
 
@@ -78,11 +158,13 @@ targets: help
 
 .PHONY: version
 version: ## display current version
-	@echo "version: $(APP_VERSION)"
+	@echo -e "$(_CYAN)Application version$(_NORMAL)  : $(APP_VERSION)"
+	@echo -e "$(_CYAN)Makefile version$(_NORMAL)     : $(MAKEFILE_VERSION)"
 
 ## -- Virtualenv targets -------------------------------------------------------------------------------------------- ##
 
-VENV_PATH := $(PROJECT_PATH).venv
+DEFAULT_VENV_PATH := $(PROJECT_PATH).venv
+VENV_PATH := $(DEFAULT_VENV_PATH)
 VENV_ACTIVATE := $(VENV_PATH)/bin/activate
 
 .PHONY: venv-create
@@ -138,15 +220,15 @@ dry: ## Add the dry target for a preview of changes; ex. 'make bump-major dry'
 
 .PHONY: bump-major
 bump-major: ## Bump application major version  <X.0.0>
-	$(BUMP_TOOL) bump $(BUMP_ARGS) major
+	@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) major
 
 .PHONY: bump-minor
 bump-minor: ## Bump application minor version  <0.X.0>
-	$(BUMP_TOOL) bump $(BUMP_ARGS) minor
+	@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) minor
 
 .PHONY: bump-patch
 bump-patch: ## Bump application patch version  <0.0.X>
-	$(BUMP_TOOL) bump $(BUMP_ARGS) patch
+	@$(ENV_COMMAND_TOOL) $(BUMP_TOOL) bump $(BUMP_ARGS) patch