diff --git a/MANIFEST.in b/MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,4 +3,4 @@
 include version.txt
 include README.md
 recursive-include swh py.typed
-recursive-include swh/scanner/tests/data/ *.tgz
+recursive-include swh/scanner/tests/data/ *
diff --git a/swh/scanner/cli.py b/swh/scanner/cli.py
--- a/swh/scanner/cli.py
+++ b/swh/scanner/cli.py
@@ -18,7 +18,6 @@
 # All generic config code should reside in swh.core.config
 CONFIG_ENVVAR = "SWH_CONFIG_FILE"
 DEFAULT_CONFIG_PATH = os.path.join(click.get_app_dir("swh"), "global.yml")
-DEFAULT_PATH = os.environ.get(CONFIG_ENVVAR, DEFAULT_CONFIG_PATH)
 
 DEFAULT_CONFIG: Dict[str, Any] = {
     "web-api": {
@@ -57,15 +56,27 @@
 )
 @click.pass_context
 def scanner(ctx, config_file: Optional[str]):
-    if config_file is None and config.config_exists(DEFAULT_PATH):
-        config_file = DEFAULT_PATH
 
-    if config_file is None:
-        conf = DEFAULT_CONFIG
-    else:
-        # read_raw_config do not fail on ENOENT
+    env_config_path = os.environ.get(CONFIG_ENVVAR)
+
+    # read_raw_config do not fail if file does not exist, so check it beforehand
+    # while enforcing loading priority
+    if config_file:
         if not config.config_exists(config_file):
-            raise FileNotFoundError(config_file)
+            raise click.BadParameter(
+                f"File '{config_file}' cannot be opened.", param_hint="--config-file"
+            )
+    elif env_config_path:
+        if not config.config_exists(env_config_path):
+            raise click.BadParameter(
+                f"File '{env_config_path}' cannot be opened.", param_hint=CONFIG_ENVVAR
+            )
+        config_file = env_config_path
+    elif config.config_exists(DEFAULT_CONFIG_PATH):
+        config_file = DEFAULT_CONFIG_PATH
+
+    conf = DEFAULT_CONFIG
+    if config_file is not None:
         conf = config.read_raw_config(config.config_basepath(config_file))
         conf = config.merge_configs(DEFAULT_CONFIG, conf)
 
@@ -108,7 +119,7 @@
 def scan(ctx, root_path, api_url, patterns, out_fmt, interactive):
     """Scan a source code project to discover files and directories already
     present in the archive"""
-    from .scanner import scan
+    import swh.scanner.scanner as scanner
 
     config = ctx.obj["config"]
     if api_url:
@@ -116,7 +127,7 @@
             api_url += "/"
         config["web-api"]["url"] = api_url
 
-    scan(config, root_path, patterns, out_fmt, interactive)
+    scanner.scan(config, root_path, patterns, out_fmt, interactive)
 
 
 def main():
diff --git a/swh/scanner/tests/conftest.py b/swh/scanner/tests/conftest.py
--- a/swh/scanner/tests/conftest.py
+++ b/swh/scanner/tests/conftest.py
@@ -41,8 +41,8 @@
     session.detach()
 
 
-@pytest.fixture(scope="session")
-def temp_folder(tmp_path_factory):
+@pytest.fixture(scope="function")
+def temp_folder(tmp_path):
     """Fixture that generates a temporary folder with the following
     structure:
 
@@ -58,11 +58,13 @@
             subfile.txt
         }
     """
-    root = tmp_path_factory.getbasetemp()
-    subdir = tmp_path_factory.mktemp("subdir")
-    subsubdir = subdir.joinpath("subsubdir")
+    root = tmp_path
+    subdir = root / "subdir"
+    subdir.mkdir()
+    subsubdir = subdir / "subsubdir"
     subsubdir.mkdir()
-    subdir2 = tmp_path_factory.mktemp("subdir2")
+    subdir2 = root / "subdir2"
+    subdir2.mkdir()
     subfile = root / "subfile.txt"
     subfile.touch()
     filesample = subdir / "filesample.txt"
diff --git a/swh/scanner/tests/data/global.yml b/swh/scanner/tests/data/global.yml
new file mode 100644
--- /dev/null
+++ b/swh/scanner/tests/data/global.yml
@@ -0,0 +1,3 @@
+web-api:
+    url: "https://example.com/api/1"
+    auth-token: "dummy"
diff --git a/swh/scanner/tests/data/global2.yml b/swh/scanner/tests/data/global2.yml
new file mode 100644
--- /dev/null
+++ b/swh/scanner/tests/data/global2.yml
@@ -0,0 +1,3 @@
+web-api:
+    url: "https://example.com/api/2/"
+    auth-token: "dummy2"
diff --git a/swh/scanner/tests/test_cli.py b/swh/scanner/tests/test_cli.py
new file mode 100644
--- /dev/null
+++ b/swh/scanner/tests/test_cli.py
@@ -0,0 +1,121 @@
+# Copyright (C) 2020  The Software Heritage developers
+# See the AUTHORS file at the top-level directory of this distribution
+# License: GNU General Public License version 3, or any later version
+# See top-level LICENSE file for more information
+
+from pathlib import Path
+from unittest.mock import Mock, call
+
+from click.testing import CliRunner
+import pytest
+
+import swh.scanner.cli as cli
+import swh.scanner.scanner as scanner
+
+DATADIR = Path(__file__).absolute().parent / "data"
+CONFIG_PATH_GOOD = str(DATADIR / "global.yml")
+CONFIG_PATH_GOOD2 = str(DATADIR / "global2.yml")  # alternative to global.yml
+ROOTPATH_GOOD = str(DATADIR)
+
+
+@pytest.fixture(scope="function")
+def m_scanner(mocker):
+    """Returns a mock swh.scanner.scanner object with all attributes mocked"""
+    # Customizable mock of scanner module
+    # Fortunately, noop is the default behavior for all methods
+    scanner_mock = Mock(scanner)
+    yield mocker.patch("swh.scanner.scanner", scanner_mock)
+
+
+@pytest.fixture(scope="function")
+def spy_configopen(mocker):
+    """Returns a mock of open builtin scoped to swh.core.config"""
+    yield mocker.patch("swh.core.config.open", wraps=open)
+
+
+@pytest.fixture(scope="function")
+def cli_runner(monkeypatch, tmp_path):
+    """Return a CliRunner with default environment variable SWH_CONFIG_FILE unset"""
+    BAD_CONFIG_PATH = str(tmp_path / "missing")
+    monkeypatch.setattr(cli, "DEFAULT_CONFIG_PATH", BAD_CONFIG_PATH)
+    return CliRunner(env={"SWH_CONFIG_FILE": None})
+
+
+# TEST BEGIN
+
+# For nominal code paths, check that the right config file is loaded
+# scanner is mocked to not run actual scan, config loading is mocked to check its usage
+
+
+def test_smoke(cli_runner):
+    """Break if basic functionality breaks"""
+    res = cli_runner.invoke(cli.scanner, ["scan", "-h"])
+    assert res.exit_code == 0
+
+
+def test_config_path_option_bad(cli_runner, tmp_path):
+    """Test bad option no envvar bad default"""
+    CONFPATH_BAD = str(tmp_path / "missing")
+    res = cli_runner.invoke(cli.scanner, ["-C", CONFPATH_BAD, "scan", ROOTPATH_GOOD])
+    assert res.exit_code != 0
+
+
+def test_default_config_path(cli_runner, m_scanner, spy_configopen, monkeypatch):
+    """Test no option no envvar good default"""
+    monkeypatch.setattr(cli, "DEFAULT_CONFIG_PATH", CONFIG_PATH_GOOD)
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_GOOD])
+    assert res.exit_code == 0
+    assert spy_configopen.call_args == call(CONFIG_PATH_GOOD)
+    assert m_scanner.scan.call_count == 1
+
+
+def test_root_no_config(cli_runner, m_scanner, spy_configopen):
+    """Test no config = no option no envvar bad default, good root"""
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_GOOD])
+    assert res.exit_code == 0
+    assert spy_configopen.call_count == 0
+    assert m_scanner.scan.call_count == 1
+
+
+def test_root_bad(cli_runner, tmp_path):
+    """Test no option no envvar bad default bad root"""
+    ROOTPATH_BAD = str(tmp_path / "missing")
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_BAD])
+    assert res.exit_code != 0
+
+
+def test_config_path_envvar_good(cli_runner, m_scanner, spy_configopen):
+    """Test no option good envvar bad default good root"""
+    cli_runner.env["SWH_CONFIG_FILE"] = CONFIG_PATH_GOOD
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_GOOD])
+    assert res.exit_code == 0
+    assert spy_configopen.call_args == call(CONFIG_PATH_GOOD)
+    assert m_scanner.scan.call_count == 1
+
+
+def test_config_path_envvar_bad(cli_runner, tmp_path):
+    """Test no option bad envvar bad default good root"""
+    CONFPATH_BAD = str(tmp_path / "missing")
+    cli_runner.env["SWH_CONFIG_FILE"] = CONFPATH_BAD
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_GOOD])
+    assert res.exit_code != 0
+
+
+def test_config_path_option_envvar(cli_runner, m_scanner, spy_configopen):
+    """Test good option good envvar bad default good root
+    Check that option has precedence over envvar"""
+    cli_runner.env["SWH_CONFIG_FILE"] = CONFIG_PATH_GOOD2
+    res = cli_runner.invoke(
+        cli.scanner, ["-C", CONFIG_PATH_GOOD, "scan", ROOTPATH_GOOD]
+    )
+    assert res.exit_code == 0
+    assert spy_configopen.call_args == call(CONFIG_PATH_GOOD)
+    assert m_scanner.scan.call_count == 1
+
+
+def test_api_url_option(cli_runner, m_scanner):
+    """Test no config good root good url"""
+    API_URL = "https://example.com/api/1"  # without trailing "/"
+    res = cli_runner.invoke(cli.scanner, ["scan", ROOTPATH_GOOD, "-u", API_URL])
+    assert res.exit_code == 0
+    assert m_scanner.scan.call_count == 1
diff --git a/swh/scanner/tests/test_model.py b/swh/scanner/tests/test_model.py
--- a/swh/scanner/tests/test_model.py
+++ b/swh/scanner/tests/test_model.py
@@ -57,7 +57,7 @@
     assert len(result) == 6
 
     for path, node_attr in result.items():
-        if path == str(root) + "/subdir0/filesample.txt":
+        if path == str(root) + "/subdir/filesample.txt":
             assert node_attr["known"] is True
         else:
             assert node_attr["known"] is False
diff --git a/swh/scanner/tests/test_plot.py b/swh/scanner/tests/test_plot.py
--- a/swh/scanner/tests/test_plot.py
+++ b/swh/scanner/tests/test_plot.py
@@ -34,8 +34,8 @@
     assert actual_df["known"][1] == 2
 
     # assert subsubdir has correct level information
-    assert actual_df["lev0"][2] == "subdir0"
-    assert actual_df["lev1"][2] == "subdir0/subsubdir"
+    assert actual_df["lev0"][2] == "subdir"
+    assert actual_df["lev1"][2] == "subdir/subsubdir"
 
 
 def test_build_hierarchical_df(temp_folder, example_dirs):
@@ -51,7 +51,7 @@
         actual_df, levels_columns, metrics_columns, root
     )
 
-    assert actual_result["parent"][1] == "subdir0"
+    assert actual_result["parent"][1] == "subdir"
     assert actual_result["contents"][1] == 2
     assert actual_result["id"][5] == root
     assert actual_result["known"][5] == 75