diff --git a/ctapipe/core/tool.py b/ctapipe/core/tool.py
index 8c42930df43..71c8bbd0066 100644
--- a/ctapipe/core/tool.py
+++ b/ctapipe/core/tool.py
@@ -1,21 +1,29 @@
 """Classes to handle configurable command-line user interfaces."""
 import logging
 import logging.config
-import textwrap
-from abc import abstractmethod
-import pathlib
 import os
+import pathlib
 import re
+import textwrap
+from abc import abstractmethod
+from typing import Union
+import yaml
 
-from traitlets import default
-from traitlets.config import Application, Configurable
+try:
+    import tomli as toml
+
+    HAS_TOML = True
+except ImportError:
+    HAS_TOML = False
+
+from traitlets import default, List
+from traitlets.config import Application, Config, Configurable
 
 from .. import __version__ as version
-from .traits import Path, Enum, Bool, Dict
 from . import Provenance
 from .component import Component
-from .logging import create_logging_config, ColoredFormatter, DEFAULT_LOGGING
-
+from .logging import DEFAULT_LOGGING, ColoredFormatter, create_logging_config
+from .traits import Bool, Dict, Enum, Path
 
 __all__ = ["Tool", "ToolConfigurationError"]
 
@@ -119,16 +127,21 @@ def main():
 
     """
 
-    config_file = Path(
-        exists=True,
-        directory_ok=False,
-        allow_none=True,
-        default_value=None,
-        help=(
-            "name of a configuration file with "
-            "parameters to load in addition to "
-            "command-line parameters"
-        ),
+    config_files = List(
+        trait=Path(
+            exists=True,
+            directory_ok=False,
+            allow_none=True,
+            default_value=None,
+            help=(
+                "List of configuration files with parameters to load "
+                "in addition to command-line parameters. "
+                "The order listed is the order of precendence (later config parameters "
+                "overwrite earlier ones), however parameters specified on the "
+                "command line always have the highest precendence. "
+                "Config files may be in JSON, YAML, TOML, or Python format"
+            ),
+        )
     ).tag(config=True)
 
     log_config = Dict(default_value=DEFAULT_LOGGING).tag(config=True)
@@ -158,7 +171,7 @@ def __init__(self, **kwargs):
         # make sure there are some default aliases in all Tools:
         super().__init__(**kwargs)
         aliases = {
-            ("c", "config"): "Tool.config_file",
+            ("c", "config"): "Tool.config_files",
             "log-level": "Tool.log_level",
             ("l", "log-file"): "Tool.log_file",
             "log-file-level": "Tool.log_file_level",
@@ -184,16 +197,19 @@ def __init__(self, **kwargs):
         self.update_logging_config()
 
     def initialize(self, argv=None):
-        """ handle config and any other low-level setup """
+        """handle config and any other low-level setup"""
         self.parse_command_line(argv)
         self.update_logging_config()
 
-        if self.config_file is not None:
-            self.log.debug(f"Loading config from '{self.config_file}'")
+        if self.config_files is not None:
+            self.log.info("Loading config from '%s'", self.config_files)
             try:
-                self.load_config_file(self.config_file)
+                for config_file in self.config_files:
+                    self.load_config_file(config_file)
             except Exception as err:
-                raise ToolConfigurationError(f"Couldn't read config file: {err}")
+                raise ToolConfigurationError(
+                    f"Couldn't read config file: {err} ({type(err)})"
+                ) from err
 
         # ensure command-line takes precedence over config file options:
         self.update_config(self.cli_config)
@@ -201,6 +217,34 @@ def initialize(self, argv=None):
 
         self.log.info(f"ctapipe version {self.version_string}")
 
+    def load_config_file(self, path: Union[str, pathlib.Path]) -> None:
+        """
+        Load a configuration file in one of the supported formats, and merge it with
+        the current config if it exists.
+
+        Parameters
+        ----------
+        path: Union[str, pathlib.Path]
+            config file to load. [yaml, toml, json, py] formats are supported
+        """
+
+        path = pathlib.Path(path)
+
+        if path.suffix in [".yaml", ".yml"]:
+            # do our own YAML loading
+            with open(path, "r") as infile:
+                config = Config(yaml.safe_load(infile))
+            self.update_config(config)
+        elif path.suffix == ".toml" and HAS_TOML:
+            with open(path, "rb") as infile:
+                config = Config(toml.load(infile))
+            self.update_config(config)
+        else:
+            # fall back to traitlets.config.Application's implementation
+            super().load_config_file(str(path))
+
+        Provenance().add_input_file(path, role="Tool Configuration")
+
     def update_logging_config(self):
         """Update the configuration of loggers."""
         cfg = create_logging_config(
@@ -330,11 +374,11 @@ def write_provenance(self):
 
     @property
     def version_string(self):
-        """ a formatted version string with version, release, and git hash"""
+        """a formatted version string with version, release, and git hash"""
         return f"{version}"
 
     def get_current_config(self):
-        """ return the current configuration as a dict (e.g. the values
+        """return the current configuration as a dict (e.g. the values
         of all traits, even if they were not set during configuration)
         """
         conf = {
@@ -350,7 +394,7 @@ def get_current_config(self):
         return conf
 
     def _repr_html_(self):
-        """ nice HTML rep, with blue for non-default values"""
+        """nice HTML rep, with blue for non-default values"""
         traits = self.traits()
         name = self.__class__.__name__
         lines = [
@@ -475,7 +519,6 @@ def run_tool(tool: Tool, argv=None, cwd=None):
         # switch to cwd for running and back after
         os.chdir(cwd)
         tool.run(argv or [])
-        return 0
     except SystemExit as e:
         return e.code
     finally:
diff --git a/ctapipe/resources/base_config.yaml b/ctapipe/resources/base_config.yaml
new file mode 100644
index 00000000000..713bf491c74
--- /dev/null
+++ b/ctapipe/resources/base_config.yaml
@@ -0,0 +1,111 @@
+# ==========================================================================
+# ctapipe-process configuration file.
+# version: VERSION
+#
+# This configuration contains a subset of options needed for a basic analysis.
+# Not all possible options are shown. To get a complete list, run:
+#
+#     `ctapipe-process --help-all`
+#
+# ==========================================================================
+
+DataWriter:
+  Contact:
+    # please fill in your contact information here. It will be stored in the
+    # output files as provenance information
+    name: YOUR-NAME-HERE
+    email: YOUREMAIL@EXAMPLE.ORG
+    organization: YOUR-ORGANIZATION
+
+  # options that control what is stored in the output file by default here we
+  # write nothing (can be overridden on the command-line or in subsequent config
+  # files)
+  overwrite: false # do not overwrite existing files
+  write_images: false # store DL1 images
+  write_parameters: false # store DL1 parameters
+  write_stereo_shower: false # store DL2 stereo geometry
+  write_raw_waveforms: false # write R0 waveforms
+  write_waveforms: false # write R1 waveforms
+
+# The CameraCalibrator takes data from R1 or DL0 to DL1a level, applying finer
+# calibration and turning waveforms into images. It is run only if DL1a images
+# do not already exist in the input file.
+CameraCalibrator:
+  # Choose an extractor type from the following possibilities:
+  #'FullWaveformSum', 'FixedWindowSum', 'GlobalPeakWindowSum',
+  #'LocalPeakWindowSum', 'SlidingWindowMaxSum', 'NeighborPeakWindowSum',
+  #'TwoPassWindowSum', 'BaselineSubtractedNeighborPeakWindowSum'
+  #
+  # Note this is a telescope-wise parameter, so can be specified per telescope
+  # if necessary (see below for an example)
+  image_extractor_type: NeighborPeakWindowSum
+
+# The ImageProcessor performs the DL1a-> DL1b (image parameters) transition. It
+# is run only if the parameters `DataWriter.write_image_parameters=True` and the
+# parameters don't already exist in the input file (or if the user forces them
+# to be re-computed using DataWriter.recompute_dl1=True)
+ImageProcessor:
+  # The image cleaner selects pixels which have signal in them and rejects those
+  # without. Options are: 'TailcutsImageCleaner', 'MARSImageCleaner',
+  # 'FACTImageCleaner'
+  image_cleaner_type: TailcutsImageCleaner
+
+  # make sure you include a configuration for the image cleaner you selected
+  # above here. The section named by the image_cleaner_type will be used to
+  # configure it.
+  TailcutsImageCleaner:
+    # the thresholds for this image cleaner must be optimized for the data set
+    # you are analyzing. The defaults may not be correct and should be optimized
+    # for the given use case.
+    #
+    # These are telescope-wise parameters, where the options are patterns
+    # specified in a list in order of precedence, with later options overwriting
+    # earlier ones. Each pattern is a triplet of [scope, key, value], where the
+    # scope can be "type" (matching to the telescope type name) or "id"
+    # (matching a specific telescope ID number). In the case of "type", the key
+    # should be either a telescope type string, or part of one with "*" used as
+    # a wildcard match (e.g. "LST*" would match all LST telescopes). You can
+    # specify a universal default value using "*" as a key. Note that specifying
+    # a single value is equivalent to specifying a one-item list containing
+    # [type, '*', value] .
+    picture_threshold_pe: # top-level threshold in photoelectrons
+      - [type, "LST*", 6.0]
+      - [type, "MST*NectarCam", 8.0]
+      - [type, "MST*FlashCam", 10000] # disabled for now
+      - [type, "SST_ASTRI_CHEC", 4.0]
+    boundary_threshold_pe: # second-level threshold in photoelectrons
+      - [type, "LST*", 3.0]
+      - [type, "MST*NectarCam", 4.0]
+      - [type, "MST*FlashCam", 10000] # disabled for now
+      - [type, "SST_ASTRI_CHEC", 2.0]
+    keep_isolated_pixels: False # If False, pixels with  < min_picture_neighbors are removed.
+    min_picture_neighbors: 2 # Minimum number of neighbors above threshold to consider
+
+  # Choose which images should be parameterized:
+  ImageQualityQuery:
+    # quality critieria should be a list of pairs of [name,
+    # filter_function_string] The filter function should take a single value
+    # which is the image itself, a 1D np.array.
+    quality_criteria:
+      - ["enough_pixels", "lambda im: np.count_nonzero(im) > 2"]
+      - ["enough_charge", "lambda im: im.sum() > 50"]
+
+# The ShowerProcessor performs the DL1 to DL2a (reconstructed shower geometry)
+# transition. It is run only if the parameter DataWriter.write_stereo_shower=True.
+ShowerProcessor:
+  # choose between HillasReconstructor and HillasIntersection (two
+  # implementations of the standard stereo line-intersection method)
+  reconstructor_type: HillasReconstructor
+
+  HillasReconstructor:
+    # Choose which telescope events should be included in the reconstruction.
+    StereoQualityQuery:
+      # the quality criteria here should again be a list of [name,
+      # filter_function_string] pairs, with filter functions that take the set of
+      # image parameters, `p` (a `ctapipe.containers.ImageParametersContainer`), as
+      # an argument.
+      quality_criteria:
+        - [enough intensity, "lambda p: p.hillas.intensity > 50"]
+        - [Positive width, "lambda p: p.hillas.width.value > 0"]
+        - [enough pixels, "lambda p: p.morphology.num_pixels > 3"]
+        - [not clipped, "lambda p: p.leakage.intensity_width_2 < 0.8"]
diff --git a/ctapipe/tools/tests/resources/image_modification_config.json b/ctapipe/resources/image_modification_config.json
similarity index 100%
rename from ctapipe/tools/tests/resources/image_modification_config.json
rename to ctapipe/resources/image_modification_config.json
diff --git a/ctapipe/tools/tests/resources/stage1_config.json b/ctapipe/resources/stage1_config.json
similarity index 100%
rename from ctapipe/tools/tests/resources/stage1_config.json
rename to ctapipe/resources/stage1_config.json
diff --git a/ctapipe/resources/stage1_config.toml b/ctapipe/resources/stage1_config.toml
new file mode 100644
index 00000000000..4a2b1740233
--- /dev/null
+++ b/ctapipe/resources/stage1_config.toml
@@ -0,0 +1,55 @@
+[DataWriter.Contact]
+# please fill in your contact information here. It will be stored in the
+# output files as provenance information
+name = "YOUR-NAME-HERE"
+email = "YOUREMAIL@EXAMPLE.ORG"
+organization = "YOUR-ORGANIZATION"
+
+[DataWriter]
+# options that control what is stored in the output file
+overwrite = false
+write_images = true
+write_parameters = true
+write_stereo_shower = false
+write_mono_shower = false
+transform_image = true
+transform_peak_time = true
+
+[CameraCalibrator]
+image_extractor_type = "NeighborPeakWindowSum"
+
+[ImageProcessor]
+image_cleaner_type = "TailcutsImageCleaner"
+
+
+
+[ImageProcessor.TailcutsImageCleaner]
+picture_threshold_pe = [
+    [ "type", "*", 10.0,],
+    [ "type", "LST_LST_LSTCam", 5.0,],
+    [ "type", "MST_MST_NectarCam", 5.0,],
+    [ "type", "SST_ASTRI_CHEC", 3.0,],
+]
+boundary_threshold_pe = [
+    [ "type", "*", 5.0,],
+    [ "type", "LST_LST_LSTCam", 2.5,],
+    [ "type", "MST_MST_NectarCam", 2.5,],
+    [ "type", "SST_ASTRI_CHEC", 1.5,],
+]
+min_picture_neighbors = [ [ "type", "*", 2,],]
+
+[ImageProcessor.ImageQualityQuery]
+# These specify which images should be parameterized:
+quality_criteria = [
+    [ "enough_pixels", "lambda im: np.count_nonzero(im) > 2",],
+    [ "enough_charge", "lambda im: im.sum() > 50",]
+]
+
+[ShowerProcessor.ShowerQualityQuery]
+# These specify criteria for telescopes that should be included in stereo
+# reconstruction:
+quality_criteria = [
+    [ "enough intensity", "lambda p: p.hillas.intensity > 50",],
+    [ "Positive width", "lambda p: p.hillas.width.value > 0",],
+    [ "enough pixels", "lambda p: p.morphology.num_pixels > 3",],
+]
diff --git a/ctapipe/resources/stage1_config.yaml b/ctapipe/resources/stage1_config.yaml
new file mode 100644
index 00000000000..77bac36c3c7
--- /dev/null
+++ b/ctapipe/resources/stage1_config.yaml
@@ -0,0 +1,15 @@
+# ======================================================================
+# ctapipe-process configuration file.
+# version: VERSION
+#
+# Perform Stage 1 Processing
+#
+# This configuration enables options needed for Rx to DL1b (image parameters)
+# ======================================================================
+#
+#  Make sure you first include `--config base_config.yaml` before including this file
+
+DataWriter:
+  write_images: true
+  write_parameters: true
+  write_stereo_shower: false
diff --git a/ctapipe/tools/tests/resources/stage2_config.json b/ctapipe/resources/stage2_config.json
similarity index 100%
rename from ctapipe/tools/tests/resources/stage2_config.json
rename to ctapipe/resources/stage2_config.json
diff --git a/ctapipe/resources/stage2_config.yaml b/ctapipe/resources/stage2_config.yaml
new file mode 100644
index 00000000000..00ae9725b94
--- /dev/null
+++ b/ctapipe/resources/stage2_config.yaml
@@ -0,0 +1,16 @@
+# ======================================================================
+# ctapipe-process configuration file.
+# version: VERSION
+#
+# Perform Stage 2 Processing
+#
+# This configuration enables options needed for Rx to DL2a (shower
+# reconstruction) But not including any image parameters
+# ======================================================================
+#
+#  Make sure you first include `--config base_config.yaml` before including this file
+
+DataWriter:
+  write_images: false
+  write_parameters: false
+  write_stereo_shower: true
diff --git a/ctapipe/tools/tests/resources/training_config.json b/ctapipe/resources/training_config.json
similarity index 100%
rename from ctapipe/tools/tests/resources/training_config.json
rename to ctapipe/resources/training_config.json
diff --git a/ctapipe/resources/training_config.yaml b/ctapipe/resources/training_config.yaml
new file mode 100644
index 00000000000..3258342407f
--- /dev/null
+++ b/ctapipe/resources/training_config.yaml
@@ -0,0 +1,17 @@
+# ======================================================================
+# ctapipe-process configuration file.
+# version: VERSION
+#
+# Perform Stage 1 and Stage 2a processing to generate features needed for
+# training machine learning algorithms.
+#
+#  Note that here write_images is disabled by default (to avoid very large
+# files), however for training deep learning algorithms, it should be turned on.
+# ======================================================================
+#
+#  Make sure you first include `--config base_config.yaml` before including this file
+
+DataWriter:
+  write_images: false
+  write_parameters: true
+  write_stereo_shower: true
diff --git a/ctapipe/tools/quickstart.py b/ctapipe/tools/quickstart.py
index 678c5978b36..a4c2446ec67 100644
--- a/ctapipe/tools/quickstart.py
+++ b/ctapipe/tools/quickstart.py
@@ -14,7 +14,12 @@
 
 __all__ = ["QuickStartTool"]
 
-CONFIGS_TO_WRITE = ["stage1_config.json", "stage2_config.json", "training_config.json"]
+CONFIGS_TO_WRITE = [
+    "base_config.yaml",
+    "stage1_config.yaml",
+    "stage2_config.yaml",
+    "training_config.yaml",
+]
 
 README_TEXT = f"""
 ctapipe working directory
@@ -23,19 +28,25 @@
 This working directory contains some example configuration files that are useful
 for processing data with `ctapipe-process`. These include:
 
-- stage1_config.json:  generate DL1 data from lower data levels
-- stage2_config.json:  generate DL2 shower geometry from DL1 or lower levels
-- training_config.json: generate both DL1 parameter and DL2 shower geometry data
+- base_config.yaml: standard configuration options, to be included always
 
-You can modify these to change the output,  and run ctapipe using:
+In addition several sub-configurations to be included after base_config.yaml
+
+- stage1_config.yaml: generate DL1 data from lower data levels
+- stage2_config.yaml: generate DL2 shower geometry from DL1 or lower levels
+- training_config.yaml: generate both DL1 parameter and DL2 shower geometry
+      data, useful for training ML algorithms
+
+You can modify these to change the output, and run ctapipe by including both the
+base config plus one additional configuration using:
 
 ```
-ctapipe-process --config <CONFIG> --input <EVENTS FILE> --output <OUTPUT FILE>
+ctapipe-process --config base_config.yaml --config <CONFIG> --input <EVENTS FILE> --output <OUTPUT FILE>
 ``` 
 
-Where <EVENTS FILE> is any ctapipe-readable event file at a lower or equal data
-level to the one requested to be produced, and <CONFIG> is one of the
-configuration files generated by `ctapipe-quickstart`.
+Where <CONFIG> is one of the non-base configs above, <EVENTS FILE> is any
+ctapipe-readable event file at a lower or equal data level to the one requested
+to be produced.
 
 Details about all configuration options can be found by running:
 
@@ -127,12 +138,13 @@ def setup(self):
             "YOUR-NAME-HERE": self.contact_name,
             "YOUREMAIL@EXAMPLE.ORG": self.contact_email,
             "YOUR-ORGANIZATION": self.contact_organization,
+            "VERSION": VERSION,
         }
 
     def start(self):
 
         for filename in CONFIGS_TO_WRITE:
-            config = files("ctapipe.tools.tests").joinpath("resources", filename)
+            config = files("ctapipe").joinpath("resources", filename)
             destination = self.workdir / filename
 
             if destination.exists():
@@ -156,7 +168,7 @@ def finish(self):
 
 
 def main():
-    """ run the tool"""
+    """run the tool"""
     tool = QuickStartTool()
     tool.run()
 
diff --git a/ctapipe/tools/tests/test_merge.py b/ctapipe/tools/tests/test_merge.py
index c1d2408006c..446bff21afe 100644
--- a/ctapipe/tools/tests/test_merge.py
+++ b/ctapipe/tools/tests/test_merge.py
@@ -18,7 +18,7 @@
 
 
 def run_stage1(input_path, cwd, output_path=None):
-    config = files("ctapipe.tools.tests").joinpath("resources", "stage1_config.json")
+    config = files("ctapipe").joinpath("resources", "stage1_config.json")
 
     if output_path is None:
         output_path = Path(
diff --git a/ctapipe/tools/tests/test_process.py b/ctapipe/tools/tests/test_process.py
index f3eef639ab3..d8f1a4b88ec 100644
--- a/ctapipe/tools/tests/test_process.py
+++ b/ctapipe/tools/tests/test_process.py
@@ -22,13 +22,56 @@
 
 
 def resource_file(filename):
-    return files("ctapipe.tools.tests").joinpath("resources", filename)
+    return files("ctapipe").joinpath("resources", filename)
+
+
+@pytest.mark.parametrize(
+    "config_files",
+    [
+        ("base_config.yaml", "stage1_config.yaml"),
+        ("stage1_config.toml",),
+        ("stage1_config.json",),
+    ],
+)
+def test_read_yaml_toml_json_config(dl1_image_file, config_files):
+    """check that we can read multiple formats of config file"""
+    tool = ProcessorTool()
 
+    for config_base in config_files:
+        config = resource_file(config_base)
+        tool.load_config_file(config)
 
-def test_stage_1_dl1(tmp_path, dl1_image_file, dl1_parameters_file):
-    """  check simtel to DL1 conversion """
+    tool.config.EventSource.input_url = dl1_image_file
+    tool.config.DataWriter.overwrite = True
+    tool.setup()
+    assert (
+        tool.get_current_config()["ProcessorTool"]["DataWriter"]["contact_info"].name
+        == "YOUR-NAME-HERE"
+    )
+
+
+def test_multiple_configs(dl1_image_file):
+    """ensure a config file loaded later overwrites keys from an earlier one"""
+    tool = ProcessorTool()
+
+    tool.load_config_file(resource_file("base_config.yaml"))
+    tool.load_config_file(resource_file("stage2_config.yaml"))
 
+    tool.config.EventSource.input_url = dl1_image_file
+    tool.config.DataWriter.overwrite = True
+    tool.setup()
+
+    # ensure the overwriting works (base config has this option disabled)
+    assert (
+        tool.get_current_config()["ProcessorTool"]["DataWriter"]["write_stereo_shower"]
+        == True
+    )
+
+
+def test_stage_1_dl1(tmp_path, dl1_image_file, dl1_parameters_file):
+    """check simtel to DL1 conversion"""
     config = resource_file("stage1_config.json")
+
     # DL1A file as input
     dl1b_from_dl1a_file = tmp_path / "dl1b_fromdl1a.dl1.h5"
     assert (
@@ -102,7 +145,7 @@ def test_stage1_datalevels(tmp_path):
     """test the dl1 tool on a file not providing r1, dl0 or dl1a"""
 
     class DummyEventSource(EventSource):
-        """ for testing """
+        """for testing"""
 
         @staticmethod
         def is_compatible(file_path):
@@ -157,7 +200,7 @@ def _generator(self):
 
 
 def test_stage_2_from_simtel(tmp_path):
-    """ check we can go to DL2 geometry from simtel file """
+    """check we can go to DL2 geometry from simtel file"""
     config = resource_file("stage2_config.json")
     output = tmp_path / "test_stage2_from_simtel.DL2.h5"
 
@@ -182,7 +225,7 @@ def test_stage_2_from_simtel(tmp_path):
 
 
 def test_stage_2_from_dl1_images(tmp_path, dl1_image_file):
-    """ check we can go to DL2 geometry from DL1 images """
+    """check we can go to DL2 geometry from DL1 images"""
     config = resource_file("stage2_config.json")
     output = tmp_path / "test_stage2_from_dl1image.DL2.h5"
 
@@ -206,7 +249,7 @@ def test_stage_2_from_dl1_images(tmp_path, dl1_image_file):
 
 
 def test_stage_2_from_dl1_params(tmp_path, dl1_parameters_file):
-    """ check we can go to DL2 geometry from DL1 parameters """
+    """check we can go to DL2 geometry from DL1 parameters"""
 
     config = resource_file("stage2_config.json")
     output = tmp_path / "test_stage2_from_dl1param.DL2.h5"
@@ -231,7 +274,7 @@ def test_stage_2_from_dl1_params(tmp_path, dl1_parameters_file):
 
 
 def test_training_from_simtel(tmp_path):
-    """ check we can write both dl1 and dl2 info (e.g. for training input) """
+    """check we can write both dl1 and dl2 info (e.g. for training input)"""
 
     config = resource_file("training_config.json")
     output = tmp_path / "test_training.DL1DL2.h5"
@@ -288,9 +331,11 @@ def test_image_modifications(tmp_path, dl1_image_file):
     assert modified_images["image"].sum() / unmodified_images["image"].sum() > 1.5
 
 
-@pytest.mark.parametrize("filename", CONFIGS_TO_WRITE)
+@pytest.mark.parametrize(
+    "filename", ["base_config.yaml", "stage1_config.json", "stage1_config.toml"]
+)
 def test_quickstart_templates(filename):
-    """ ensure template configs have an appropriate placeholder for the contact info """
+    """ensure template configs have an appropriate placeholder for the contact info"""
     config = resource_file(filename)
     text = config.read_text()
 
@@ -300,7 +345,7 @@ def test_quickstart_templates(filename):
 
 
 def test_quickstart(tmp_path):
-    """ ensure quickstart tool generates expected output """
+    """ensure quickstart tool generates expected output"""
 
     tool = QuickStartTool()
     run_tool(
diff --git a/environment.yml b/environment.yml
index 243ad6dd119..610818ace63 100644
--- a/environment.yml
+++ b/environment.yml
@@ -36,6 +36,7 @@ dependencies:
   - sphinx=3.5
   - sphinx-automodapi
   - sphinx_rtd_theme
+  - tomli
   - tqdm
   - traitlets
   - vitables
diff --git a/setup.py b/setup.py
index 298ed9d56d6..202d55827b2 100755
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,12 @@
     "ctapipe-fileinfo = ctapipe.tools.fileinfo:main",
     "ctapipe-quickstart = ctapipe.tools.quickstart:main",
 ]
-tests_require = ["pytest", "pandas>=0.24.0", "importlib_resources;python_version<'3.9'"]
+tests_require = [
+    "pytest",
+    "pandas>=0.24.0",
+    "importlib_resources;python_version<'3.9'",
+    "tomli",
+]
 docs_require = [
     "sphinx_rtd_theme",
     "sphinx_automodapi",
@@ -57,6 +62,7 @@
         "setuptools_scm>=3.4",
         "importlib_resources;python_version<'3.9'",
         "jinja2~=3.0.2",  # for sphinx 3.5, update when moving to 4.x
+        "pyyaml>=5.1",
     ],
     # here are optional dependencies (as "tag" : "dependency spec")
     extras_require={