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Update from makefile project
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10 files changed

+42
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‎.make/.bumpversion.toml‎

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@@ -1,5 +1,5 @@
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[tool.bumpversion]
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current_version = "0.7.0"
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current_version = "0.7.1"
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commit = true
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message = "Makefile version {new_version} released."
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tag = true
@@ -12,18 +12,18 @@ serialize = [
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[[tool.bumpversion.files]]
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filename = "CHANGES_MAKEFILE.md"
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search = '''
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[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
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## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
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______________________________________________________________________
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'''
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replace = '''
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[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
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## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest)
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______________________________________________________________________
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<!-- (New changes here in list form) -->
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[{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
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## [{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d})
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______________________________________________________________________
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'''

‎.make/CHANGES_MAKEFILE.md‎

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@@ -6,6 +6,12 @@ ______________________________________________________________________
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<!-- (New changes here in list form) -->
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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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<!-- (New changes here in list form) -->
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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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@@ -10,7 +10,7 @@
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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 := 0.7.0
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MAKEFILE_VERSION := 0.7.1
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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/base.make‎

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Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ 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 := 0.7.0
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MAKEFILE_VERSION := 0.7.1
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DOCKER_COMPOSE ?= docker compose
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AUTO_INSTALL ?=
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‎.make/lint.make‎

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Original file line numberDiff line numberDiff line change
@@ -2,36 +2,36 @@
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.PHONY: check-lint
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check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint)
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$(ENV_COMMAND_TOOL) run nox -s check
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$(ENV_COMMAND_TOOL) nox -s check
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.PHONY: check-pylint
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check-pylint: ## Check code with pylint
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$(ENV_COMMAND_TOOL) run nox -s pylint
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$(ENV_COMMAND_TOOL) nox -s pylint
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.PHONY: check-complexity
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check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe
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$(ENV_COMMAND_TOOL) run nox -s complexity
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$(ENV_COMMAND_TOOL) nox -s complexity
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.PHONY: fix-lint
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fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter)
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$(ENV_COMMAND_TOOL) run nox -s fix
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$(ENV_COMMAND_TOOL) nox -s fix
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.PHONY: markdown-lint
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markdown-lint: ## Fix markdown linting using mdformat
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$(ENV_COMMAND_TOOL) run nox -s mdformat
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$(ENV_COMMAND_TOOL) nox -s mdformat
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.PHONY: precommit
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precommit: ## Run Pre-commit on all files manually
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$(ENV_COMMAND_TOOL) run nox -s precommit
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$(ENV_COMMAND_TOOL) nox -s precommit
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.PHONY: ruff
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ruff: ## Run the ruff linter
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$(ENV_COMMAND_TOOL) run nox -s ruff-lint
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$(ENV_COMMAND_TOOL) nox -s ruff-lint
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.PHONY: ruff-fix
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ruff-fix: ## Run the ruff linter and fix automatically fixable errors
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$(ENV_COMMAND_TOOL) run nox -s ruff-fix
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$(ENV_COMMAND_TOOL) nox -s ruff-fix
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.PHONY: ruff-format
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ruff-format: ## Run the ruff code formatter
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$(ENV_COMMAND_TOOL) run nox -s ruff-format
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$(ENV_COMMAND_TOOL) nox -s ruff-format

‎.make/poetry.make‎

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@@ -3,7 +3,7 @@
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-include Makefile.variables
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-include Makefile.private
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ENV_COMMAND_TOOL := poetry
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ENV_COMMAND_TOOL := poetry run
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## -- Poetry targets ------------------------------------------------------------------------------------------------ ##
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‎.make/test.make‎

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Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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.PHONY: test
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test: ## Run all tests
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$(ENV_COMMAND_TOOL) run nox -s test
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$(ENV_COMMAND_TOOL) nox -s test
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TEST_ARGS ?=
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MARKER_TEST_ARGS = -m "$(TEST_ARGS)"
@@ -12,7 +12,7 @@ CUSTOM_TEST_ARGS = "$(TEST_ARGS)"
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.PHONY: test-marker
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test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="<marker>"
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@if [ -n "$(TEST_ARGS)" ]; then \
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$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
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$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(MARKER_TEST_ARGS); \
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else \
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echo "" ; \
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echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
@@ -23,7 +23,7 @@ test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="
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.PHONY: test-specific
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test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="<name-of-test>"
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@if [ -n "$(TEST_ARGS)" ]; then \
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$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
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$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \
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else \
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echo "" ; \
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echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \
@@ -35,7 +35,7 @@ test-specific: ## Run specific tests using the -k option. Ex. make test-specific
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.PHONY: test-custom
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test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'"
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@if [ -n "$(TEST_ARGS)" ]; then \
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$(ENV_COMMAND_TOOL) run nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
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$(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \
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else \
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echo "" ; \
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echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \

‎.make/uv.make‎

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@@ -2,7 +2,7 @@
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# This is to make sure, sometimes the Makefile includes don't work.
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## -- UV targets ------------------------------------------------------------------------------------------------ ##
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ENV_COMMAND_TOOL := uv
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ENV_COMMAND_TOOL := uv run
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.PHONY: uv-install-auto
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uv-install-auto:
@@ -292,7 +292,7 @@ install-precommit: install-dev ## Install the pre-commit hooks (also installs de
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echo "Pre-commit hook found"; \
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else \
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echo "Pre-commit hook not found, proceeding to configure it"; \
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$(ENV_COMMAND_TOOL) run pre-commit install; \
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$(ENV_COMMAND_TOOL) pre-commit install; \
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fi;
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.PHONY: install-dev

‎Makefile.private.example‎

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## Private variables
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19-
# If you use a different Conda tool, say `micromamba`, or if you use a different alias
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# CONDA_TOOL := <YOU_CONDA_TOOL_IF_DIFFERENT_FROM_CONDA>
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DOCKER_COMPOSE := docker compose
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# Some targets use this variable. A 'false' value will ask user to confirm some steps.
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# a 'true' value will automatically install/remove without asking beforehand.
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# Most, but not all install/remove targets use this variable. A 'false' value will ask
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# users to confirm some steps. A 'true' value will automatically install/remove without
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# asking beforehand.
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AUTO_INSTALL := false
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# The default environment to use. The choices are as follow: [venv, poetry, conda]
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# The default environment where Poetry will be installed. The choices are as follow: [venv, conda]
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# If this is not set, the makefile will ask the user where they want to install Poetry
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DEFAULT_POETRY_INSTALL_ENV := venv
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#DEFAULT_POETRY_INSTALL_ENV := venv
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# This variable is to enable the '-y' flag when newer version of conda is available.
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# The default Mila conda module does not allow this flag; leave blanks or commented out
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#CONDA_YES_OPTION := -y
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# If you use a different Conda tool, say `micromamba`, or if you use a different alias
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# CONDA_TOOL := <YOU_CONDA_TOOL_IF_DIFFERENT_FROM_CONDA>
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DOCKER_COMPOSE := docker compose
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## -- Private targets ------------------------------------------------------------------------------------------------##
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‎Makefile.targets‎

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.PHONY: test-notebooks
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test-notebooks: ## Execute test notebooks using pytest and nbval
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nox -s test_nb
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$(ENV_COMMAND_TOOL) nox -s test_nb

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