diff --git a/.gitignore b/.gitignore
index 3815d553..70d616a3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
+tox.ini
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/.travis.yml b/.travis.yml
index eefc834b..fa99e4d8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -65,6 +65,6 @@ install:
   - pip freeze
   - printenv
 script:
-  - $TRAVISCMD tox -vv -e $TOXENV -- $TOTEST
+  - $TRAVISCMD tox -c tox-pyenv.ini -e $TOXENV -- $TOTEST
 after_success:
   - codecov
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index b7127071..b9657c6c 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -90,7 +90,15 @@ to see the available make targets. If you cannot use ``make``, but want to use
 
     $ tox -av
 
-to see a list of tox environments and a description.
+to see a list of tox environments and a description. For the initial
+configuration of tox environments, you may have to run
+
+.. code-block:: console
+
+    $ tox -e bootstrap
+
+in order to set up the ``tox.ini`` configuration file.
+
 
 If you are a member of the `qucontrol organization`_, there is no need to fork
 ``krotov`` - you can directly pull and push to ``git@github.com:qucontrol/krotov.git``.
@@ -128,7 +136,8 @@ that you may run into occasional binary incompatibilities between conda packages
    If you want to use `conda`, you must use the ``tox-conda.ini`` configuration
    file. That is, run all ``make`` comands as e.g.
    ``make TOXINI=tox-conda.ini test`` and ``tox`` commands as e.g.
-   ``tox -c tox-conda.ini -e py35-test,py36-test,py37-test``
+   ``tox -c tox-conda.ini -e py35-test,py36-test,py37-test``. Alternatively,
+   make ``tox-conda.ini`` the default by copying it to ``tox.ini``.
 
 .. _pyenv: https://github.com/pyenv/pyenv
 .. _pyenv-win: https://github.com/pyenv-win/pyenv-win
@@ -258,7 +267,7 @@ Testing
 
 The Krotov package includes a full test-suite using pytest_. We strive for a `test coverage`_ above 90%.
 
-From a checkout of the ``krotov`` repository, assuming conda_ is installed, you can use
+From a checkout of the ``krotov`` repository, you can use
 
 .. code-block:: console
 
@@ -315,8 +324,9 @@ requirements. These hooks are managed through the `pre-commit framework`_.
 
 .. warning::
    After cloning the ``krotov`` repository, you should run
-   ``make bootstrap``, or ``tox -e run-cmd -- pre-commit install``
-   from within the project root folder.
+   ``make bootstrap``, ``tox -e bootstrap``, or ``python scripts/bootstrap.py``
+   from within the project root folder. These set up ``tox``, and the
+   pre-commit hooks
 
 .. _pre-commit framework: https://pre-commit.com
 
@@ -373,8 +383,7 @@ Also see :ref:`math-in-example-notebooks`.
 
 You may use the BibTeX_ plugin for citations.
 
-At any point, from a checkout of the ``krotov`` repository (and
-assuming you have conda_ installed), you may run
+At any point, from a checkout of the ``krotov`` repository, you may run
 
 .. code-block:: console
 
diff --git a/Makefile b/Makefile
index 53f21662..5b10f65c 100644
--- a/Makefile
+++ b/Makefile
@@ -22,53 +22,33 @@ e.g. with `make TOXINI=tox-conda.ini test` You may also run `tox` directly. See
 endef
 export PRINT_HELP_PYSCRIPT
 
-define BOOTSTRAP_PYSCRIPT
-import sys
-import os
-from textwrap import dedent
-try:
-    import tox
-    TOXINI = os.environ.get('TOXINI', 'tox.ini')
-    if not os.path.isfile(".git/hooks/pre-commit"):
-        print("bootstrapping pre-commit hook")
-        cmdline = ['-c', TOXINI, '-e', 'run-cmd', '--', 'pre-commit', 'install']
-        print("tox " + " ".join(cmdline))
-        tox.cmdline(cmdline)
-except ImportError:
-    print(dedent("""
-    tox is not available. See https://tox.readthedocs.io for installation
-    instructions.
-    """))
-    sys.exit(1)
-endef
-export BOOTSTRAP_PYSCRIPT
 
 help:  ## show this help
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
 
 bootstrap: ## verify that tox is available and pre-commit hooks are active
-	@TOXINI="$(TOXINI)" python -c "$$BOOTSTRAP_PYSCRIPT"
+	python scripts/bootstrap.py
 
-clean: ## remove all build, test, coverage, and Python artifacts, as well as environments
+clean: bootstrap ## remove all build, test, coverage, and Python artifacts, as well as environments
 	$(TOX) -e clean
 
-clean-build: ## remove build artifacts
+clean-build: bootstrap ## remove build artifacts
 	$(TOX) -e clean-build
 
-clean-tests: ## remove test and coverage artifacts
+clean-tests: bootstrap ## remove test and coverage artifacts
 	$(TOX) -e clean-tests
 
-clean-venvs: ## remove tox virtual environments
+clean-venvs: bootstrap ## remove tox virtual environments
 	$(TOX) -e clean-venv
 
-clean-docs: ## remove documentation artifacts
+clean-docs: bootstrap ## remove documentation artifacts
 	$(TOX) -e clean-docs
 
-flake8-check: ## check style with flake8
+flake8-check: bootstrap ## check style with flake8
 	$(TOX) -e run-flake8
 
-pylint-check: ## check style with pylint
+pylint-check: bootstrap ## check style with pylint
 	$(TOX) -e run-pylint
 
 test: bootstrap ## run tests for current stable Python release
diff --git a/scripts/bootstrap.py b/scripts/bootstrap.py
new file mode 100755
index 00000000..02e4d30f
--- /dev/null
+++ b/scripts/bootstrap.py
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+"""Bootstrap script for setting up tox and pre-commit hooks
+
+This scripts is called either by any invocation of the Makefile, or by the tox
+configuration in setup.cvg, if there is no tox.ini.
+
+It sets up the main tox.ini file and the pre-commit hooks.
+"""
+import os
+import pathlib
+import shutil
+import sys
+
+
+_TOX_ERR_MSG = r'''
+tox is not available. See https://tox.readthedocs.io for installation
+instructions.
+'''
+
+
+def main(argv=None):
+    """Main function"""
+    if argv is None:
+        argv = sys.argv
+    root = pathlib.Path(__file__).parent.parent
+
+    # 1. Bootstrap the tox.ini file
+    if not (root / 'tox.ini').is_file():
+        tox_ini = os.environ.get('TOXINI', 'tox-pyenv.ini')
+        if not (root / tox_ini).is_file():
+            tox_ini = 'tox-pyenv.ini'
+        tox_src = root / tox_ini
+        tox_dst = root / "tox.ini"
+        print("Copying %s to %s" % (tox_src, tox_dst))
+        shutil.copyfile(tox_src, tox_dst)
+
+    # 2. Ensure tox is installed
+    try:
+        import tox
+    except ImportError:
+        print(_TOX_ERR_MSG)
+        sys.exit(1)
+
+    # 3. Ensure pre-commit hooks are installed
+    if not (root / ".git" / "hooks" / "pre-commit").is_file():
+        # we're using the tox.ini environments that we got from step 1
+        print("bootstrapping pre-commit hook")
+        cmdline = ['-e', 'run-cmd', '--', 'pre-commit', 'install']
+        print("tox " + " ".join(cmdline))
+        tox.cmdline(cmdline)
+
+
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/setup.cfg b/setup.cfg
index 7a05001b..fbdb1502 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -29,3 +29,16 @@ use_parentheses = True
 multi_line_output = 3
 include_trailing_comma = True
 skip = src/krotov/__init__.py
+
+[tox:tox]
+minversion = 3.7
+envlist = bootstrap
+
+[testenv:bootstrap]
+description = "Configure tox"
+whitelist_externals =
+    python
+skip_install = True
+deps = tox
+commands =
+    python scripts/bootstrap.py
diff --git a/tox-conda.ini b/tox-conda.ini
index 1a4eb240..a632d47a 100644
--- a/tox-conda.ini
+++ b/tox-conda.ini
@@ -10,7 +10,7 @@ envdir = {toxworkdir}/.tox
 [testenv]
 basepython =
     # current "stable" python
-    py37,run,docs,coverage: python3.7
+    py37,run,docs,coverage,clean,bootstrap: python3.7
     # older pythons
     py36: python3.6
     py35: python3.5
@@ -58,6 +58,17 @@ commands =
     sphinx-build . _build {posargs:--color}
 
 
+[testenv:bootstrap]
+description = "Configure tox"
+envdir = {toxworkdir}/bootstrap
+deps = tox
+conda_deps =
+skip_install = True
+commands_pre =
+commands =
+    python scripts/bootstrap.py
+
+
 [testenv:clean]
 description = "Clean up"
 envdir = {toxworkdir}/clean_
diff --git a/tox.ini b/tox-pyenv.ini
similarity index 95%
rename from tox.ini
rename to tox-pyenv.ini
index be080da8..40078584 100644
--- a/tox.ini
+++ b/tox-pyenv.ini
@@ -9,7 +9,7 @@ envdir = {toxworkdir}/.tox
 [testenv]
 basepython =
     # current "stable" python
-    py37,run,docs,coverage,clean: python3.7
+    py37,run,docs,coverage,clean,bootstrap: python3.7
     # older pythons
     py36: python3.6
     py35: python3.5
@@ -63,6 +63,16 @@ commands =
     sphinx-build . _build {posargs:--color}
 
 
+[testenv:bootstrap]
+description = "Configure tox"
+envdir = {toxworkdir}/bootstrap
+deps = tox
+skip_install = True
+commands_pre =
+commands =
+    python scripts/bootstrap.py
+
+
 [testenv:clean]
 description = "Clean up"
 envdir = {toxworkdir}/clean_