diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e826c8acf5d2bc062bd56a08d32a083ea801ac93..85bc2cfe30d39fb31e4f9f3f1018b65356607321 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -64,7 +64,7 @@ doc:
     - install_silx
     - install_tomoscan
     - python -m pip install pytest-cov
-    - python -m pip install .[full]
+    - python -m pip install -e .[full]
   script:
     - python -m pytest --cov-config=.coveragerc --cov=nxtomomill nxtomomill/
 
diff --git a/nxtomomill/app/test/test_dxfile2nx_app.py b/nxtomomill/app/test/test_dxfile2nx_app.py
new file mode 100644
index 0000000000000000000000000000000000000000..258b5f6a5b30790c2b999aad7e2b8dc6c912fb5f
--- /dev/null
+++ b/nxtomomill/app/test/test_dxfile2nx_app.py
@@ -0,0 +1,63 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+"""
+test the dxfile2nx application
+"""
+
+__authors__ = [
+    "H. Payno",
+]
+__license__ = "MIT"
+__date__ = "30/08/2021"
+
+
+import tempfile
+from nxtomomill.test.utils.dxfile import MockDxFile
+import os
+import subprocess
+
+
+def test_dxfile2nx_application():
+    """test nxtomomill dxfile2nx input_file output_file"""
+    with tempfile.TemporaryDirectory() as folder:
+        dx_file_path = os.path.join(folder, "dxfile.dx")
+        nx_file_path = os.path.join(folder, "dxfile.nx")
+        n_projections = 50
+        n_darks = 2
+        n_flats = 4
+
+        mock = MockDxFile(
+            file_path=dx_file_path,
+            n_projection=n_projections,
+            n_darks=n_darks,
+            n_flats=n_flats,
+        )
+        assert not os.path.exists(nx_file_path), "outputfile exists already"
+        process = subprocess.Popen(
+            ["nxtomomill", "dxfile2nx", dx_file_path, nx_file_path]
+        )
+        stdout, stderr = process.communicate()
+        assert os.path.exists(nx_file_path), "outputfile doesn't exists"
diff --git a/nxtomomill/app/test/test_edf2nx_app.py b/nxtomomill/app/test/test_edf2nx_app.py
new file mode 100644
index 0000000000000000000000000000000000000000..bdc2b33860813a6a4eccf60916bece27fb600890
--- /dev/null
+++ b/nxtomomill/app/test/test_edf2nx_app.py
@@ -0,0 +1,58 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+"""
+test the edf2nx application
+"""
+
+__authors__ = [
+    "H. Payno",
+]
+__license__ = "MIT"
+__date__ = "30/08/2021"
+
+
+import tempfile
+from tomoscan.esrf.mock import MockEDF
+import os
+import subprocess
+
+
+def test_edf2nx_application():
+    """test nxtomomill edf2nx input_file output_file"""
+    with tempfile.TemporaryDirectory() as folder:
+        edf_acq_path = os.path.join(folder, "acquisition")
+        n_proj = 10
+        MockEDF(
+            scan_path=edf_acq_path,
+            n_radio=n_proj,
+            n_ini_radio=n_proj,
+        )
+        output_file = os.path.join(edf_acq_path, "nexus_file.nx")
+
+        assert not os.path.exists(output_file), "output_file exists already"
+        process = subprocess.Popen(["nxtomomill", "edf2nx", edf_acq_path, output_file])
+        stdout, stderr = process.communicate()
+        assert os.path.exists(output_file), "output_file doesn't exists"
diff --git a/nxtomomill/app/test/test_h52nx_app.py b/nxtomomill/app/test/test_h52nx_app.py
new file mode 100644
index 0000000000000000000000000000000000000000..13a9bd4faf2ee21179819b9d1d6f5c637067cf51
--- /dev/null
+++ b/nxtomomill/app/test/test_h52nx_app.py
@@ -0,0 +1,65 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+"""
+test the h52nx application
+"""
+
+__authors__ = [
+    "H. Payno",
+]
+__license__ = "MIT"
+__date__ = "30/08/2021"
+
+
+import tempfile
+from nxtomomill.test.utils.bliss import MockBlissAcquisition
+import os
+import subprocess
+
+
+def test_h52nx_application():
+    """test nxtomomill h52nx input_file output_file --single-file"""
+    with tempfile.TemporaryDirectory() as folder:
+        nx_file_path = os.path.join(folder, "acquisition.nx")
+
+        bliss_mock = MockBlissAcquisition(
+            n_sample=2,
+            n_sequence=1,
+            n_scan_per_sequence=10,
+            n_darks=5,
+            n_flats=5,
+            with_nx_detector_attr=True,
+            output_dir=folder,
+            detector_name="pcolinux",
+        )
+
+        h5_file_path = bliss_mock.samples[0].sample_file
+        assert not os.path.exists(nx_file_path), "outputfile exists already"
+        process = subprocess.Popen(
+            ["nxtomomill", "h52nx", h5_file_path, nx_file_path, "--single-file"]
+        )
+        stdout, stderr = process.communicate()
+        assert os.path.exists(nx_file_path), "outputfile doesn't exists"
diff --git a/nxtomomill/app/test/test_patch_nx_app.py b/nxtomomill/app/test/test_patch_nx_app.py
new file mode 100644
index 0000000000000000000000000000000000000000..b88981f1350f97646280f3d3ce425e4cb2b6390d
--- /dev/null
+++ b/nxtomomill/app/test/test_patch_nx_app.py
@@ -0,0 +1,72 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+"""
+test the patch-nx application
+"""
+
+__authors__ = [
+    "H. Payno",
+]
+__license__ = "MIT"
+__date__ = "30/08/2021"
+
+
+import tempfile
+from tomoscan.esrf.mock import MockHDF5
+import h5py
+import os
+import subprocess
+
+
+def test_patch_nx_application():
+    """test nxtomomill patch-nx input_file entry --invalid-frames XX:YY"""
+
+    with tempfile.TemporaryDirectory() as folder:
+        nx_path = os.path.join(folder, "nexus_file.nx")
+        dim = 55
+        nproj = 20
+        scan = MockHDF5(
+            scan_path=nx_path,
+            n_proj=nproj,
+            n_ini_proj=nproj,
+            create_ini_dark=False,
+            create_ini_ref=False,
+            create_final_ref=False,
+            dim=dim,
+        ).scan
+        process = subprocess.Popen(
+            [
+                "nxtomomill",
+                "patch-nx",
+                scan.master_file,
+                "entry",
+                "--invalid-frames",
+                "0:12",
+            ]
+        )
+        stdout, stderr = process.communicate()
+        scan.clear_caches()
+        assert len(scan.projections) == 8, "Scan is expected to have 8 projections now"