From 508fdd4c26993a05e208e051e95f3740d07371d2 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 16:47:45 -0500
Subject: [PATCH 01/36] feta: add startup dialog

---
 .../_gui_objects/_startup_widget.py           | 166 ++++++++++++++++++
 src/napari_micromanager/main_window.py        |  42 ++++-
 2 files changed, 203 insertions(+), 5 deletions(-)
 create mode 100644 src/napari_micromanager/_gui_objects/_startup_widget.py

diff --git a/src/napari_micromanager/_gui_objects/_startup_widget.py b/src/napari_micromanager/_gui_objects/_startup_widget.py
new file mode 100644
index 00000000..84557e17
--- /dev/null
+++ b/src/napari_micromanager/_gui_objects/_startup_widget.py
@@ -0,0 +1,166 @@
+from __future__ import annotations
+
+import json
+import warnings
+from pathlib import Path
+from typing import cast
+
+from platformdirs import user_config_dir
+from pymmcore_plus import find_micromanager
+from qtpy.QtWidgets import (
+    QComboBox,
+    QDialog,
+    QDialogButtonBox,
+    QFileDialog,
+    QGridLayout,
+    QLabel,
+    QPushButton,
+    QSizePolicy,
+    QWidget,
+)
+
+USER_DIR = Path(user_config_dir("napari_micromanager"))
+USER_CONFIGS_PATHS = USER_DIR / "system_configurations.json"
+FIXED = QSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
+NEW = "New Configuration"
+
+
+class StartupDialog(QDialog):
+    """A dialog to select the MicroManager configuration files."""
+
+    def __init__(self, parent: QWidget | None = None) -> None:
+        super().__init__(parent)
+        self.setWindowTitle("System Configurations")
+
+        # label
+        cfg_lbl = QLabel("Configuration file:")
+        cfg_lbl.setSizePolicy(FIXED)
+
+        # combo box
+        self.cfg_combo = QComboBox()
+        # `AdjustToMinimumContents` is not available in all qtpy backends so using
+        # `AdjustToMinimumContentsLengthWithIcon` instead
+        self.cfg_combo.setSizeAdjustPolicy(
+            QComboBox.SizeAdjustPolicy.AdjustToMinimumContentsLengthWithIcon
+        )
+
+        # browse button
+        self.browse_btn = QPushButton("...")
+        self.browse_btn.setSizePolicy(FIXED)
+        self.browse_btn.clicked.connect(self._on_browse_clicked)
+
+        # Create OK and Cancel buttons
+        button_box = QDialogButtonBox(
+            QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        )
+        button_box.accepted.connect(self.accept)
+        button_box.rejected.connect(self.reject)
+
+        # add widgets to layout
+        wdg_layout = QGridLayout(self)
+        wdg_layout.addWidget(cfg_lbl, 0, 0)
+        wdg_layout.addWidget(self.cfg_combo, 0, 1)
+        wdg_layout.addWidget(self.browse_btn, 0, 2)
+        wdg_layout.addWidget(button_box, 2, 0, 1, 3)
+
+        self._initialize()
+
+    def value(self) -> str:
+        """Return the selected value."""
+        return str(self.cfg_combo.currentText())
+
+    def add_path_to_json(self, path: Path | str) -> None:
+        """Uopdate the json file with the new path."""
+        if isinstance(path, Path):
+            path = str(path)
+
+        # Read the existing data
+        try:
+            with open(USER_CONFIGS_PATHS) as f:
+                data = json.load(f)
+        except json.JSONDecodeError:
+            data = {"paths": []}
+
+        # Append the new path. using insert so we leave the empty string at the end
+        paths = cast(list, data.get("paths", []))
+        paths.insert(0, path)
+
+        # Write the data back to the file
+        with open(USER_CONFIGS_PATHS, "w") as f:
+            json.dump({"paths": paths}, f)
+
+    def _initialize(self) -> None:
+        """Initialize the dialog with the configuration files."""
+        # create USER_CONFIGS_PATHS if it doesn't exist
+        if not USER_CONFIGS_PATHS.exists():
+            USER_DIR.mkdir(parents=True, exist_ok=True)
+            with open(USER_CONFIGS_PATHS, "w") as f:
+                json.dump({"paths": []}, f)
+
+        # get the paths from the json file
+        configs_paths = self._get_config_paths()
+
+        # add the paths to the combo box
+        self.cfg_combo.addItems([*configs_paths, NEW])
+
+        # write the data back to the file
+        with open(USER_CONFIGS_PATHS, "w") as f:
+            json.dump({"paths": configs_paths}, f)
+
+    def _get_config_paths(self) -> list[str]:
+        """Return the paths from the json file.
+
+        If a file stored in the json file doesn't exist, it is removed from the list.
+
+        The method also adds all the .cfg files in the MicroManager folder to the list
+        if they are not already there.
+        """
+        try:
+            with open(USER_CONFIGS_PATHS) as f:
+                data = json.load(f)
+
+            # get path list from json file
+            paths = cast(list, data.get("paths", []))
+
+            # remove any path that doesn't exist
+            for path in paths:
+                if not Path(path).exists():
+                    paths.remove(path)
+
+            # get all the .cfg files in the MicroManager folder
+            cfg_files = self._get_micromanager_cfg_files()
+
+            # add all the .cfg files to the list if they are not already there
+            for cfg in reversed(cfg_files):
+                if str(cfg) not in paths:
+                    # using insert so we leave the empty string at the end
+                    paths.insert(0, str(cfg))
+
+        except json.JSONDecodeError:
+            paths = []
+            warnings.warn("Error reading the json file.", stacklevel=2)
+
+        return paths
+
+    def _get_micromanager_cfg_files(self) -> list[Path]:
+        """Return all the .cfg files in the MicroManager folders."""
+        mm_dir = find_micromanager()
+
+        if mm_dir is None:
+            return []
+
+        cfg_files: list[Path] = []
+        cfg_files.extend(Path(mm_dir).glob("*.cfg"))
+
+        return cfg_files
+
+    def _on_browse_clicked(self) -> None:
+        """Open a file dialog to select a file."""
+        path, _ = QFileDialog.getOpenFileName(
+            self, "Open file", "", "MicroManager files (*.cfg)"
+        )
+        if path:
+            # using insert so we leave the empty string at the end
+            self.cfg_combo.insertItem(0, path)
+            self.cfg_combo.setCurrentText(path)
+            self.add_path_to_json(path)
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 4d3ba523..02512509 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -12,6 +12,7 @@
 from pymmcore_plus import CMMCorePlus
 
 from ._core_link import CoreViewerLink
+from ._gui_objects._startup_widget import NEW, StartupDialog
 from ._gui_objects._toolbar import MicroManagerToolbar
 
 if TYPE_CHECKING:
@@ -55,12 +56,43 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
+        self._startup = StartupDialog(self.viewer.window._qt_window)
+
+        # if a config is passed, load it
         if config is not None:
-            try:
-                self._mmc.loadSystemConfiguration(config)
-            except FileNotFoundError:
-                # don't crash if the user passed an invalid config
-                warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
+            self._load_system_configuration(config)
+            # add the path to the json file
+            self._startup.add_path_to_json(config)
+            return
+
+        # if no config is passed, show the startup dialog
+        self._center_startup_dialog()
+        if self._startup.exec_():
+            config = self._startup.value()
+            # if the user selected NEW, show the config wizard
+            if config == NEW:
+                ...  # TODO: CONFIG WIZARD
+            else:
+                self._load_system_configuration(config)
+
+    def _load_system_configuration(self, config: str | Path) -> None:
+        """Load a Micro-Manager system configuration file."""
+        try:
+            self._mmc.loadSystemConfiguration(config)
+        except FileNotFoundError:
+            # don't crash if the user passed an invalid config
+            warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
+
+    def _center_startup_dialog(self) -> None:
+        """Center the startup dialog in the viewer window."""
+        self._startup.move(
+            self.viewer.window.qt_viewer.geometry().center()
+            - self._startup.geometry().center()
+        )
+        self._startup.resize(
+            int(self.viewer.window.qt_viewer.geometry().width() / 2),
+            self._startup.sizeHint().height(),
+        )
 
     def _cleanup(self) -> None:
         for signal, slot in self._connections:

From 8070b9faef9c46ca5f9dd47da695c91efc8510d7 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 16:55:16 -0500
Subject: [PATCH 02/36] feat: add wizard

---
 src/napari_micromanager/main_window.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 02512509..321d468f 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -10,6 +10,7 @@
 import napari.layers
 import napari.viewer
 from pymmcore_plus import CMMCorePlus
+from pymmcore_widgets import ConfigWizard
 
 from ._core_link import CoreViewerLink
 from ._gui_objects._startup_widget import NEW, StartupDialog
@@ -71,7 +72,10 @@ def __init__(
             config = self._startup.value()
             # if the user selected NEW, show the config wizard
             if config == NEW:
-                ...  # TODO: CONFIG WIZARD
+                # TODO: subclass to load the new cfg if created and to add it to the
+                # json file. instead of show() should use exec_() and check the return
+                self._cfg_wizard = ConfigWizard(parent=self.viewer.window._qt_window)
+                self._cfg_wizard.show()
             else:
                 self._load_system_configuration(config)
 

From ca6a053e66589f088663b59423b70ead1f159a1c Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 16:58:44 -0500
Subject: [PATCH 03/36] fix: _handle_system_configuration

---
 src/napari_micromanager/main_window.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 321d468f..ef96302e 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -57,19 +57,23 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        self._startup = StartupDialog(self.viewer.window._qt_window)
-
         # if a config is passed, load it
+        self._handle_system_configuration(config)
+
+    def _handle_system_configuration(self, config: str | Path | None) -> None:
+        """Handle the system configuration file. If None, show the startup dialog."""
+        startup = StartupDialog(self.viewer.window._qt_window)
+
         if config is not None:
             self._load_system_configuration(config)
             # add the path to the json file
-            self._startup.add_path_to_json(config)
+            startup.add_path_to_json(config)
             return
 
         # if no config is passed, show the startup dialog
         self._center_startup_dialog()
-        if self._startup.exec_():
-            config = self._startup.value()
+        if startup.exec_():
+            config = startup.value()
             # if the user selected NEW, show the config wizard
             if config == NEW:
                 # TODO: subclass to load the new cfg if created and to add it to the

From 9d0e5393b57061c02d32296cb854bb06711c66c1 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 17:00:24 -0500
Subject: [PATCH 04/36] fix: _center_dialog_in_viewer

---
 src/napari_micromanager/main_window.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index ef96302e..b2968ca5 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -20,6 +20,7 @@
     from pathlib import Path
 
     from pymmcore_plus.core.events._protocol import PSignalInstance
+    from qtpy.QtWidgets import QDialog
 
 
 # this is very verbose
@@ -71,7 +72,7 @@ def _handle_system_configuration(self, config: str | Path | None) -> None:
             return
 
         # if no config is passed, show the startup dialog
-        self._center_startup_dialog()
+        self._center_dialog_in_viewer(startup)
         if startup.exec_():
             config = startup.value()
             # if the user selected NEW, show the config wizard
@@ -91,15 +92,15 @@ def _load_system_configuration(self, config: str | Path) -> None:
             # don't crash if the user passed an invalid config
             warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
 
-    def _center_startup_dialog(self) -> None:
-        """Center the startup dialog in the viewer window."""
-        self._startup.move(
+    def _center_dialog_in_viewer(self, startup: QDialog) -> None:
+        """Center the dialog in the viewer window."""
+        startup.move(
             self.viewer.window.qt_viewer.geometry().center()
-            - self._startup.geometry().center()
+            - startup.geometry().center()
         )
-        self._startup.resize(
+        startup.resize(
             int(self.viewer.window.qt_viewer.geometry().width() / 2),
-            self._startup.sizeHint().height(),
+            startup.sizeHint().height(),
         )
 
     def _cleanup(self) -> None:

From dc129b27958da05b4e25928b1da13af7b41cf121 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 17:01:43 -0500
Subject: [PATCH 05/36] fix: add_path_to_json

---
 src/napari_micromanager/_gui_objects/_startup_widget.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_widget.py b/src/napari_micromanager/_gui_objects/_startup_widget.py
index 84557e17..6772851a 100644
--- a/src/napari_micromanager/_gui_objects/_startup_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_widget.py
@@ -83,7 +83,8 @@ def add_path_to_json(self, path: Path | str) -> None:
 
         # Append the new path. using insert so we leave the empty string at the end
         paths = cast(list, data.get("paths", []))
-        paths.insert(0, path)
+        if path not in paths:
+            paths.insert(0, path)
 
         # Write the data back to the file
         with open(USER_CONFIGS_PATHS, "w") as f:

From b04006e96bcc7d18dc36c8e6fb5715b6917558e7 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 20:41:50 -0500
Subject: [PATCH 06/36] fix: rename

---
 .../_gui_objects/_startup_widget.py                  |  2 +-
 src/napari_micromanager/main_window.py               | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_widget.py b/src/napari_micromanager/_gui_objects/_startup_widget.py
index 6772851a..98d00bd5 100644
--- a/src/napari_micromanager/_gui_objects/_startup_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_widget.py
@@ -25,7 +25,7 @@
 NEW = "New Configuration"
 
 
-class StartupDialog(QDialog):
+class ConfigurationsDialog(QDialog):
     """A dialog to select the MicroManager configuration files."""
 
     def __init__(self, parent: QWidget | None = None) -> None:
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index b2968ca5..c94c1df1 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -13,7 +13,7 @@
 from pymmcore_widgets import ConfigWizard
 
 from ._core_link import CoreViewerLink
-from ._gui_objects._startup_widget import NEW, StartupDialog
+from ._gui_objects._startup_widget import NEW, ConfigurationsDialog
 from ._gui_objects._toolbar import MicroManagerToolbar
 
 if TYPE_CHECKING:
@@ -63,18 +63,18 @@ def __init__(
 
     def _handle_system_configuration(self, config: str | Path | None) -> None:
         """Handle the system configuration file. If None, show the startup dialog."""
-        startup = StartupDialog(self.viewer.window._qt_window)
+        config_dialog = ConfigurationsDialog(self.viewer.window._qt_window)
 
         if config is not None:
             self._load_system_configuration(config)
             # add the path to the json file
-            startup.add_path_to_json(config)
+            config_dialog.add_path_to_json(config)
             return
 
         # if no config is passed, show the startup dialog
-        self._center_dialog_in_viewer(startup)
-        if startup.exec_():
-            config = startup.value()
+        self._center_dialog_in_viewer(config_dialog)
+        if config_dialog.exec_():
+            config = config_dialog.value()
             # if the user selected NEW, show the config wizard
             if config == NEW:
                 # TODO: subclass to load the new cfg if created and to add it to the

From 1ec8c21150512ee763e90ebe5516ca67ac7dfd54 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 20:44:41 -0500
Subject: [PATCH 07/36] fix: move config_dialog

---
 src/napari_micromanager/main_window.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index c94c1df1..16512c96 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -58,23 +58,23 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
+        self.config_dialog = ConfigurationsDialog(self.viewer.window._qt_window)
+
         # if a config is passed, load it
         self._handle_system_configuration(config)
 
     def _handle_system_configuration(self, config: str | Path | None) -> None:
         """Handle the system configuration file. If None, show the startup dialog."""
-        config_dialog = ConfigurationsDialog(self.viewer.window._qt_window)
-
         if config is not None:
             self._load_system_configuration(config)
             # add the path to the json file
-            config_dialog.add_path_to_json(config)
+            self.config_dialog.add_path_to_json(config)
             return
 
         # if no config is passed, show the startup dialog
-        self._center_dialog_in_viewer(config_dialog)
-        if config_dialog.exec_():
-            config = config_dialog.value()
+        self._center_dialog_in_viewer(self.config_dialog)
+        if self.config_dialog.exec_():
+            config = self.config_dialog.value()
             # if the user selected NEW, show the config wizard
             if config == NEW:
                 # TODO: subclass to load the new cfg if created and to add it to the

From 31762b4ac9cafdf3aa2fe625f0b00e5dfff2cfbd Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 20:45:31 -0500
Subject: [PATCH 08/36] fix: rename

---
 .../_gui_objects/_startup_widget.py                  |  2 +-
 src/napari_micromanager/main_window.py               | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_widget.py b/src/napari_micromanager/_gui_objects/_startup_widget.py
index 98d00bd5..1125fa97 100644
--- a/src/napari_micromanager/_gui_objects/_startup_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_widget.py
@@ -25,7 +25,7 @@
 NEW = "New Configuration"
 
 
-class ConfigurationsDialog(QDialog):
+class ConfigurationsHandler(QDialog):
     """A dialog to select the MicroManager configuration files."""
 
     def __init__(self, parent: QWidget | None = None) -> None:
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 16512c96..67c7af8d 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -13,7 +13,7 @@
 from pymmcore_widgets import ConfigWizard
 
 from ._core_link import CoreViewerLink
-from ._gui_objects._startup_widget import NEW, ConfigurationsDialog
+from ._gui_objects._startup_widget import NEW, ConfigurationsHandler
 from ._gui_objects._toolbar import MicroManagerToolbar
 
 if TYPE_CHECKING:
@@ -58,7 +58,7 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        self.config_dialog = ConfigurationsDialog(self.viewer.window._qt_window)
+        self.configs_handler = ConfigurationsHandler(self.viewer.window._qt_window)
 
         # if a config is passed, load it
         self._handle_system_configuration(config)
@@ -68,13 +68,13 @@ def _handle_system_configuration(self, config: str | Path | None) -> None:
         if config is not None:
             self._load_system_configuration(config)
             # add the path to the json file
-            self.config_dialog.add_path_to_json(config)
+            self.configs_handler.add_path_to_json(config)
             return
 
         # if no config is passed, show the startup dialog
-        self._center_dialog_in_viewer(self.config_dialog)
-        if self.config_dialog.exec_():
-            config = self.config_dialog.value()
+        self._center_dialog_in_viewer(self.configs_handler)
+        if self.configs_handler.exec_():
+            config = self.configs_handler.value()
             # if the user selected NEW, show the config wizard
             if config == NEW:
                 # TODO: subclass to load the new cfg if created and to add it to the

From 81c1552772ca7d9cd2d9112f48baf57b8012f4f8 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 21:16:39 -0500
Subject: [PATCH 09/36] fix: move logic into ConfigurationsHandler

---
 ...t.py => _startup_configurations_widget.py} | 105 ++++++++++++------
 .../_gui_objects/_toolbar.py                  |  17 +--
 src/napari_micromanager/main_window.py        |  51 +--------
 3 files changed, 82 insertions(+), 91 deletions(-)
 rename src/napari_micromanager/_gui_objects/{_startup_widget.py => _startup_configurations_widget.py} (67%)

diff --git a/src/napari_micromanager/_gui_objects/_startup_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
similarity index 67%
rename from src/napari_micromanager/_gui_objects/_startup_widget.py
rename to src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 1125fa97..1b3156ea 100644
--- a/src/napari_micromanager/_gui_objects/_startup_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -1,12 +1,13 @@
 from __future__ import annotations
 
 import json
-import warnings
 from pathlib import Path
 from typing import cast
+from warnings import warn
 
 from platformdirs import user_config_dir
-from pymmcore_plus import find_micromanager
+from pymmcore_plus import CMMCorePlus, find_micromanager
+from pymmcore_widgets import ConfigWizard
 from qtpy.QtWidgets import (
     QComboBox,
     QDialog,
@@ -28,9 +29,18 @@
 class ConfigurationsHandler(QDialog):
     """A dialog to select the MicroManager configuration files."""
 
-    def __init__(self, parent: QWidget | None = None) -> None:
+    def __init__(
+        self,
+        parent: QWidget | None = None,
+        *,
+        config: Path | str | None = None,
+        mmcore: CMMCorePlus | None = None,
+    ) -> None:
         super().__init__(parent)
-        self.setWindowTitle("System Configurations")
+        self.setWindowTitle("Micro-Manager System Configurations")
+
+        self._mmc = mmcore or CMMCorePlus.instance()
+        self._config = config
 
         # label
         cfg_lbl = QLabel("Configuration file:")
@@ -65,33 +75,33 @@ def __init__(self, parent: QWidget | None = None) -> None:
 
         self._initialize()
 
-    def value(self) -> str:
-        """Return the selected value."""
-        return str(self.cfg_combo.currentText())
-
-    def add_path_to_json(self, path: Path | str) -> None:
-        """Uopdate the json file with the new path."""
-        if isinstance(path, Path):
-            path = str(path)
-
-        # Read the existing data
-        try:
-            with open(USER_CONFIGS_PATHS) as f:
-                data = json.load(f)
-        except json.JSONDecodeError:
-            data = {"paths": []}
-
-        # Append the new path. using insert so we leave the empty string at the end
-        paths = cast(list, data.get("paths", []))
-        if path not in paths:
-            paths.insert(0, path)
-
-        # Write the data back to the file
-        with open(USER_CONFIGS_PATHS, "w") as f:
-            json.dump({"paths": paths}, f)
+        self.resize(500, self.minimumSizeHint().height())
+
+        # if a config was not passed, show the dialog
+        if config is None:
+            if self.exec_():
+                config = self.cfg_combo.currentText()
+                # if the user selected NEW, show the config wizard
+                if config == NEW:
+                    # TODO: subclass to load the new cfg if created and to add it to the
+                    # json file. use if exec_() instead of show() and check the return
+                    self._cfg_wizard = ConfigWizard(parent=self)
+                    self._cfg_wizard.show()
+                # otherwise load the selected config
+                else:
+                    self._load_system_configuration(config)
+        # if a config was passed, load it
+        else:
+            self._load_system_configuration(config)
 
     def _initialize(self) -> None:
-        """Initialize the dialog with the configuration files."""
+        """Initialize the dialog with the configuration files.
+
+        This method reads the stored paths in the USER_CONFIGS_PATHS jason file (or
+        create one if it doesn't exist) and adds them to the combo box. It also adds the
+        Micro-Manager configuration files form the Micro-Manager folder if they are not
+        already in the list.
+        """
         # create USER_CONFIGS_PATHS if it doesn't exist
         if not USER_CONFIGS_PATHS.exists():
             USER_DIR.mkdir(parents=True, exist_ok=True)
@@ -137,9 +147,13 @@ def _get_config_paths(self) -> list[str]:
                     # using insert so we leave the empty string at the end
                     paths.insert(0, str(cfg))
 
+            # if a config was passed, add it to the list if it's not already there
+            if self._config is not None and str(self._config) not in paths:
+                paths.insert(0, str(self._config))
+
         except json.JSONDecodeError:
             paths = []
-            warnings.warn("Error reading the json file.", stacklevel=2)
+            warn("Error reading the json file.", stacklevel=2)
 
         return paths
 
@@ -155,6 +169,14 @@ def _get_micromanager_cfg_files(self) -> list[Path]:
 
         return cfg_files
 
+    def _load_system_configuration(self, config: str | Path) -> None:
+        """Load a Micro-Manager system configuration file."""
+        try:
+            self._mmc.loadSystemConfiguration(config)
+        except FileNotFoundError:
+            # don't crash if the user passed an invalid config
+            warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
+
     def _on_browse_clicked(self) -> None:
         """Open a file dialog to select a file."""
         path, _ = QFileDialog.getOpenFileName(
@@ -164,4 +186,25 @@ def _on_browse_clicked(self) -> None:
             # using insert so we leave the empty string at the end
             self.cfg_combo.insertItem(0, path)
             self.cfg_combo.setCurrentText(path)
-            self.add_path_to_json(path)
+            self._add_path_to_json(path)
+
+    def _add_path_to_json(self, path: Path | str) -> None:
+        """Uopdate the json file with the new path."""
+        if isinstance(path, Path):
+            path = str(path)
+
+        # Read the existing data
+        try:
+            with open(USER_CONFIGS_PATHS) as f:
+                data = json.load(f)
+        except json.JSONDecodeError:
+            data = {"paths": []}
+
+        # Append the new path. using insert so we leave the empty string at the end
+        paths = cast(list, data.get("paths", []))
+        if path not in paths:
+            paths.insert(0, path)
+
+        # Write the data back to the file
+        with open(USER_CONFIGS_PATHS, "w") as f:
+            json.dump({"paths": paths}, f)
diff --git a/src/napari_micromanager/_gui_objects/_toolbar.py b/src/napari_micromanager/_gui_objects/_toolbar.py
index dd551a43..dec1a08f 100644
--- a/src/napari_micromanager/_gui_objects/_toolbar.py
+++ b/src/napari_micromanager/_gui_objects/_toolbar.py
@@ -9,7 +9,6 @@
     CameraRoiWidget,
     ChannelGroupWidget,
     ChannelWidget,
-    ConfigurationWidget,
     DefaultCameraExposureWidget,
     GroupPresetTableWidget,
     LiveButton,
@@ -103,14 +102,13 @@ def __init__(self, viewer: napari.viewer.Viewer) -> None:
         self._dock_widgets: dict[str, QDockWidget] = {}
         # add toolbar items
         toolbar_items = [
-            ConfigToolBar(self),
-            ChannelsToolBar(self),
             ObjectivesToolBar(self),
-            None,
-            ShuttersToolBar(self),
-            SnapLiveToolBar(self),
+            ChannelsToolBar(self),
             ExposureToolBar(self),
+            SnapLiveToolBar(self),
             ToolsToolBar(self),
+            None,
+            ShuttersToolBar(self),
         ]
         for item in toolbar_items:
             if item:
@@ -241,13 +239,6 @@ def addSubWidget(self, wdg: QWidget) -> None:
         cast("QHBoxLayout", self.frame.layout()).addWidget(wdg)
 
 
-class ConfigToolBar(MMToolBar):
-    def __init__(self, parent: QWidget) -> None:
-        super().__init__("Configuration", parent)
-        self.addSubWidget(ConfigurationWidget())
-        self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
-
-
 class ObjectivesToolBar(MMToolBar):
     def __init__(self, parent: QWidget) -> None:
         super().__init__("Objectives", parent=parent)
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 67c7af8d..f748a61c 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -4,23 +4,20 @@
 import contextlib
 import logging
 from typing import TYPE_CHECKING, Any, Callable
-from warnings import warn
 
 import napari
 import napari.layers
 import napari.viewer
 from pymmcore_plus import CMMCorePlus
-from pymmcore_widgets import ConfigWizard
 
 from ._core_link import CoreViewerLink
-from ._gui_objects._startup_widget import NEW, ConfigurationsHandler
+from ._gui_objects._startup_configurations_widget import ConfigurationsHandler
 from ._gui_objects._toolbar import MicroManagerToolbar
 
 if TYPE_CHECKING:
     from pathlib import Path
 
     from pymmcore_plus.core.events._protocol import PSignalInstance
-    from qtpy.QtWidgets import QDialog
 
 
 # this is very verbose
@@ -58,49 +55,9 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        self.configs_handler = ConfigurationsHandler(self.viewer.window._qt_window)
-
-        # if a config is passed, load it
-        self._handle_system_configuration(config)
-
-    def _handle_system_configuration(self, config: str | Path | None) -> None:
-        """Handle the system configuration file. If None, show the startup dialog."""
-        if config is not None:
-            self._load_system_configuration(config)
-            # add the path to the json file
-            self.configs_handler.add_path_to_json(config)
-            return
-
-        # if no config is passed, show the startup dialog
-        self._center_dialog_in_viewer(self.configs_handler)
-        if self.configs_handler.exec_():
-            config = self.configs_handler.value()
-            # if the user selected NEW, show the config wizard
-            if config == NEW:
-                # TODO: subclass to load the new cfg if created and to add it to the
-                # json file. instead of show() should use exec_() and check the return
-                self._cfg_wizard = ConfigWizard(parent=self.viewer.window._qt_window)
-                self._cfg_wizard.show()
-            else:
-                self._load_system_configuration(config)
-
-    def _load_system_configuration(self, config: str | Path) -> None:
-        """Load a Micro-Manager system configuration file."""
-        try:
-            self._mmc.loadSystemConfiguration(config)
-        except FileNotFoundError:
-            # don't crash if the user passed an invalid config
-            warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
-
-    def _center_dialog_in_viewer(self, startup: QDialog) -> None:
-        """Center the dialog in the viewer window."""
-        startup.move(
-            self.viewer.window.qt_viewer.geometry().center()
-            - startup.geometry().center()
-        )
-        startup.resize(
-            int(self.viewer.window.qt_viewer.geometry().width() / 2),
-            startup.sizeHint().height(),
+        # handle the system configurations at startup
+        self._configs_handler = ConfigurationsHandler(
+            self.viewer.window._qt_window, config=config, mmcore=self._mmc
         )
 
     def _cleanup(self) -> None:

From 5bd034005b6f7d0e99e1585acdca4e41f9d7bd3c Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 21:18:13 -0500
Subject: [PATCH 10/36] fix: rename

---
 .../_gui_objects/_startup_configurations_widget.py          | 2 +-
 src/napari_micromanager/main_window.py                      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 1b3156ea..51f7476d 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -26,7 +26,7 @@
 NEW = "New Configuration"
 
 
-class ConfigurationsHandler(QDialog):
+class StartupConfigurations(QDialog):
     """A dialog to select the MicroManager configuration files."""
 
     def __init__(
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index f748a61c..5bb6cde0 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -11,7 +11,7 @@
 from pymmcore_plus import CMMCorePlus
 
 from ._core_link import CoreViewerLink
-from ._gui_objects._startup_configurations_widget import ConfigurationsHandler
+from ._gui_objects._startup_configurations_widget import StartupConfigurations
 from ._gui_objects._toolbar import MicroManagerToolbar
 
 if TYPE_CHECKING:
@@ -56,8 +56,8 @@ def __init__(
         atexit.register(self._cleanup)
 
         # handle the system configurations at startup
-        self._configs_handler = ConfigurationsHandler(
-            self.viewer.window._qt_window, config=config, mmcore=self._mmc
+        self._startup_configs = StartupConfigurations(
+            parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
         )
 
     def _cleanup(self) -> None:

From 4743ef97bcfd3534f5c03f29fcb60e7e2fa0ffa1 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 21:51:18 -0500
Subject: [PATCH 11/36] feat: subclass ConfigWizard

---
 .../_startup_configurations_widget.py         | 107 ++++++++++++------
 1 file changed, 72 insertions(+), 35 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 51f7476d..2f0d6042 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -8,6 +8,7 @@
 from platformdirs import user_config_dir
 from pymmcore_plus import CMMCorePlus, find_micromanager
 from pymmcore_widgets import ConfigWizard
+from pymmcore_widgets.hcwizard.finish_page import DEST_CONFIG
 from qtpy.QtWidgets import (
     QComboBox,
     QDialog,
@@ -23,11 +24,48 @@
 USER_DIR = Path(user_config_dir("napari_micromanager"))
 USER_CONFIGS_PATHS = USER_DIR / "system_configurations.json"
 FIXED = QSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
-NEW = "New Configuration"
+NEW = "New Hardware Configuration"
+
+
+def _add_path_to_json(path: Path | str) -> None:
+    """Uopdate the json file with the new path."""
+    if isinstance(path, Path):
+        path = str(path)
+
+    # create USER_CONFIGS_PATHS if it doesn't exist
+    if not USER_CONFIGS_PATHS.exists():
+        USER_DIR.mkdir(parents=True, exist_ok=True)
+        with open(USER_CONFIGS_PATHS, "w") as f:
+            json.dump({"paths": []}, f)
+
+    # Read the existing data
+    try:
+        with open(USER_CONFIGS_PATHS) as f:
+            data = json.load(f)
+    except json.JSONDecodeError:
+        data = {"paths": []}
+
+    # Append the new path. using insert so we leave the empty string at the end
+    paths = cast(list, data.get("paths", []))
+    if path not in paths:
+        paths.insert(0, path)
+
+    # Write the data back to the file
+    with open(USER_CONFIGS_PATHS, "w") as f:
+        json.dump({"paths": paths}, f)
+
+
+def _load_system_configuration(mmcore: CMMCorePlus, config: str | Path) -> None:
+    """Load a Micro-Manager system configuration file."""
+    try:
+        mmcore.loadSystemConfiguration(config)
+    except FileNotFoundError:
+        # don't crash if the user passed an invalid config
+        warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
 
 
 class StartupConfigurations(QDialog):
-    """A dialog to select the MicroManager configuration files."""
+    """A dialog to select the Micro-Manager Hardware configuration files at startup."""
 
     def __init__(
         self,
@@ -37,7 +75,7 @@ def __init__(
         mmcore: CMMCorePlus | None = None,
     ) -> None:
         super().__init__(parent)
-        self.setWindowTitle("Micro-Manager System Configurations")
+        self.setWindowTitle("Micro-Manager Hardware System Configurations")
 
         self._mmc = mmcore or CMMCorePlus.instance()
         self._config = config
@@ -75,7 +113,7 @@ def __init__(
 
         self._initialize()
 
-        self.resize(500, self.minimumSizeHint().height())
+        self.resize(600, self.minimumSizeHint().height())
 
         # if a config was not passed, show the dialog
         if config is None:
@@ -83,16 +121,14 @@ def __init__(
                 config = self.cfg_combo.currentText()
                 # if the user selected NEW, show the config wizard
                 if config == NEW:
-                    # TODO: subclass to load the new cfg if created and to add it to the
-                    # json file. use if exec_() instead of show() and check the return
-                    self._cfg_wizard = ConfigWizard(parent=self)
+                    self._cfg_wizard = HardwareConfigWizard(parent=self)
                     self._cfg_wizard.show()
                 # otherwise load the selected config
                 else:
-                    self._load_system_configuration(config)
+                    _load_system_configuration(self._mmc, config)
         # if a config was passed, load it
         else:
-            self._load_system_configuration(config)
+            _load_system_configuration(self._mmc, config)
 
     def _initialize(self) -> None:
         """Initialize the dialog with the configuration files.
@@ -169,14 +205,6 @@ def _get_micromanager_cfg_files(self) -> list[Path]:
 
         return cfg_files
 
-    def _load_system_configuration(self, config: str | Path) -> None:
-        """Load a Micro-Manager system configuration file."""
-        try:
-            self._mmc.loadSystemConfiguration(config)
-        except FileNotFoundError:
-            # don't crash if the user passed an invalid config
-            warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
-
     def _on_browse_clicked(self) -> None:
         """Open a file dialog to select a file."""
         path, _ = QFileDialog.getOpenFileName(
@@ -186,25 +214,34 @@ def _on_browse_clicked(self) -> None:
             # using insert so we leave the empty string at the end
             self.cfg_combo.insertItem(0, path)
             self.cfg_combo.setCurrentText(path)
-            self._add_path_to_json(path)
+            _add_path_to_json(path)
 
-    def _add_path_to_json(self, path: Path | str) -> None:
-        """Uopdate the json file with the new path."""
-        if isinstance(path, Path):
-            path = str(path)
 
-        # Read the existing data
-        try:
-            with open(USER_CONFIGS_PATHS) as f:
-                data = json.load(f)
-        except json.JSONDecodeError:
-            data = {"paths": []}
+class HardwareConfigWizard(ConfigWizard):
+    """A wizard to create a new Micro-Manager hardware configuration file.
 
-        # Append the new path. using insert so we leave the empty string at the end
-        paths = cast(list, data.get("paths", []))
-        if path not in paths:
-            paths.insert(0, path)
+    Subclassing to load the newly created configuration file and to add it to the
+    USER_CONFIGS_PATHS json file.
+    """
 
-        # Write the data back to the file
-        with open(USER_CONFIGS_PATHS, "w") as f:
-            json.dump({"paths": paths}, f)
+    def __init__(
+        self,
+        config_file: str = "",
+        core: CMMCorePlus | None = None,
+        parent: QWidget | None = None,
+    ):
+        super().__init__(config_file, core, parent)
+
+        self.setWindowTitle("Micro-Manager Hardware Configuration Wizard")
+
+    def accept(self) -> None:
+        """Accept the wizard and save the configuration to a file.
+
+        Overriding to add the new configuration file to the USER_CONFIGS_PATHS json file
+        and to load it.
+        """
+        dest = self.field(DEST_CONFIG)
+        dest_path = Path(dest)
+        _add_path_to_json(dest_path)
+        super().accept()
+        _load_system_configuration(self._core, dest_path)

From 9ba4e61eb393b16b77dec4045b01e6510ba07900 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 21:55:30 -0500
Subject: [PATCH 12/36] fix: accept

---
 .../_gui_objects/_startup_configurations_widget.py           | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 2f0d6042..35f9b2e8 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -241,7 +241,6 @@ def accept(self) -> None:
         and to load it.
         """
         dest = self.field(DEST_CONFIG)
-        dest_path = Path(dest)
-        _add_path_to_json(dest_path)
+        _add_path_to_json(dest)
         super().accept()
-        _load_system_configuration(self._core, dest_path)
+        _load_system_configuration(self._core, dest)

From b47fd5e9cc3e81379e1132d8395ce37b05124ab3 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 22:01:55 -0500
Subject: [PATCH 13/36] fix: update _get_micromanager_cfg_files

---
 .../_gui_objects/_startup_configurations_widget.py    | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 35f9b2e8..23a29c70 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -194,14 +194,11 @@ def _get_config_paths(self) -> list[str]:
         return paths
 
     def _get_micromanager_cfg_files(self) -> list[Path]:
-        """Return all the .cfg files in the MicroManager folders."""
-        mm_dir = find_micromanager()
-
-        if mm_dir is None:
-            return []
-
+        """Return all the .cfg files from all the MicroManager folders."""
+        mm: list = find_micromanager(False)
         cfg_files: list[Path] = []
-        cfg_files.extend(Path(mm_dir).glob("*.cfg"))
+        for mm_dir in mm:
+            cfg_files.extend(Path(mm_dir).glob("*.cfg"))
 
         return cfg_files
 

From 891bc0c8ce407efdf86f30a313905f6bdf8894d0 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 22:03:31 -0500
Subject: [PATCH 14/36] fix: move resize into _initialize

---
 .../_gui_objects/_startup_configurations_widget.py            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 23a29c70..1bb45ae2 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -113,8 +113,6 @@ def __init__(
 
         self._initialize()
 
-        self.resize(600, self.minimumSizeHint().height())
-
         # if a config was not passed, show the dialog
         if config is None:
             if self.exec_():
@@ -154,6 +152,8 @@ def _initialize(self) -> None:
         with open(USER_CONFIGS_PATHS, "w") as f:
             json.dump({"paths": configs_paths}, f)
 
+        self.resize(600, self.minimumSizeHint().height())
+
     def _get_config_paths(self) -> list[str]:
         """Return the paths from the json file.
 

From 04de0fa8b1b46f2027f8c3fcc842c5e99f7add73 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 22:48:27 -0500
Subject: [PATCH 15/36] fix: subclass GroupPresetTableWidget

---
 .../_startup_configurations_widget.py         | 57 ++++---------------
 .../_gui_objects/_toolbar.py                  | 39 ++++++++++++-
 src/napari_micromanager/_util.py              | 52 ++++++++++++++++-
 3 files changed, 99 insertions(+), 49 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 1bb45ae2..e30c25dd 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -5,7 +5,6 @@
 from typing import cast
 from warnings import warn
 
-from platformdirs import user_config_dir
 from pymmcore_plus import CMMCorePlus, find_micromanager
 from pymmcore_widgets import ConfigWizard
 from pymmcore_widgets.hcwizard.finish_page import DEST_CONFIG
@@ -21,49 +20,17 @@
     QWidget,
 )
 
-USER_DIR = Path(user_config_dir("napari_micromanager"))
-USER_CONFIGS_PATHS = USER_DIR / "system_configurations.json"
+from napari_micromanager._util import (
+    USER_CONFIGS_PATHS,
+    USER_DIR,
+    add_path_to_config_json,
+    load_system_configuration,
+)
+
 FIXED = QSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
 NEW = "New Hardware Configuration"
 
 
-def _add_path_to_json(path: Path | str) -> None:
-    """Uopdate the json file with the new path."""
-    if isinstance(path, Path):
-        path = str(path)
-
-    # create USER_CONFIGS_PATHS if it doesn't exist
-    if not USER_CONFIGS_PATHS.exists():
-        USER_DIR.mkdir(parents=True, exist_ok=True)
-        with open(USER_CONFIGS_PATHS, "w") as f:
-            json.dump({"paths": []}, f)
-
-    # Read the existing data
-    try:
-        with open(USER_CONFIGS_PATHS) as f:
-            data = json.load(f)
-    except json.JSONDecodeError:
-        data = {"paths": []}
-
-    # Append the new path. using insert so we leave the empty string at the end
-    paths = cast(list, data.get("paths", []))
-    if path not in paths:
-        paths.insert(0, path)
-
-    # Write the data back to the file
-    with open(USER_CONFIGS_PATHS, "w") as f:
-        json.dump({"paths": paths}, f)
-
-
-def _load_system_configuration(mmcore: CMMCorePlus, config: str | Path) -> None:
-    """Load a Micro-Manager system configuration file."""
-    try:
-        mmcore.loadSystemConfiguration(config)
-    except FileNotFoundError:
-        # don't crash if the user passed an invalid config
-        warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
-
-
 class StartupConfigurations(QDialog):
     """A dialog to select the Micro-Manager Hardware configuration files at startup."""
 
@@ -123,10 +90,10 @@ def __init__(
                     self._cfg_wizard.show()
                 # otherwise load the selected config
                 else:
-                    _load_system_configuration(self._mmc, config)
+                    load_system_configuration(self._mmc, config)
         # if a config was passed, load it
         else:
-            _load_system_configuration(self._mmc, config)
+            load_system_configuration(self._mmc, config)
 
     def _initialize(self) -> None:
         """Initialize the dialog with the configuration files.
@@ -211,7 +178,7 @@ def _on_browse_clicked(self) -> None:
             # using insert so we leave the empty string at the end
             self.cfg_combo.insertItem(0, path)
             self.cfg_combo.setCurrentText(path)
-            _add_path_to_json(path)
+            add_path_to_config_json(path)
 
 
 class HardwareConfigWizard(ConfigWizard):
@@ -238,6 +205,6 @@ def accept(self) -> None:
         and to load it.
         """
         dest = self.field(DEST_CONFIG)
-        _add_path_to_json(dest)
+        add_path_to_config_json(dest)
         super().accept()
-        _load_system_configuration(self._core, dest)
+        load_system_configuration(self._core, dest)
diff --git a/src/napari_micromanager/_gui_objects/_toolbar.py b/src/napari_micromanager/_gui_objects/_toolbar.py
index dec1a08f..ea056ef3 100644
--- a/src/napari_micromanager/_gui_objects/_toolbar.py
+++ b/src/napari_micromanager/_gui_objects/_toolbar.py
@@ -17,6 +17,11 @@
     SnapButton,
 )
 
+from napari_micromanager._util import (
+    add_path_to_config_json,
+    load_system_configuration,
+)
+
 try:
     # this was renamed
     from pymmcore_widgets import ObjectivesPixelConfigurationWidget
@@ -26,6 +31,7 @@
 from qtpy.QtCore import QEvent, QObject, QSize, Qt
 from qtpy.QtWidgets import (
     QDockWidget,
+    QFileDialog,
     QFrame,
     QHBoxLayout,
     QLabel,
@@ -50,10 +56,41 @@
 TOOL_SIZE = 35
 
 
+class GroupsAndPresets(GroupPresetTableWidget):
+    """Subclass of GroupPresetTableWidget.
+
+    Overwrite the save and load methods to store the saced or loaded configuration in
+    the USER_CONFIGS_PATHS json config file.
+    """
+
+    def __init__(
+        self, *, parent: QWidget | None = None, mmcore: CMMCorePlus | None = None
+    ) -> None:
+        super().__init__(parent=parent, mmcore=mmcore)
+
+    def _save_cfg(self) -> None:
+        (filename, _) = QFileDialog.getSaveFileName(
+            self, "Save Micro-Manager Configuration."
+        )
+        if filename:
+            filename = filename if str(filename).endswith(".cfg") else f"{filename}.cfg"
+            self._mmc.saveSystemConfiguration(filename)
+            add_path_to_config_json(filename)
+
+    def _load_cfg(self) -> None:
+        """Open file dialog to select a config file."""
+        (filename, _) = QFileDialog.getOpenFileName(
+            self, "Select a Micro-Manager configuration file", "", "cfg(*.cfg)"
+        )
+        if filename:
+            add_path_to_config_json(filename)
+            load_system_configuration(mmcore=self._mmc, config=filename)
+
+
 # Dict for QObject and its QPushButton icon
 DOCK_WIDGETS: Dict[str, Tuple[type[QWidget], str | None]] = {  # noqa: U006
     "Device Property Browser": (PropertyBrowser, MDI6.table_large),
-    "Groups and Presets Table": (GroupPresetTableWidget, MDI6.table_large_plus),
+    "Groups and Presets Table": (GroupsAndPresets, MDI6.table_large_plus),
     "Illumination Control": (IlluminationWidget, MDI6.lightbulb_on),
     "Stages Control": (MMStagesWidget, MDI6.arrow_all),
     "Camera ROI": (CameraRoiWidget, MDI6.crop),
diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index 686459f2..5da8d92a 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -1,11 +1,17 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+from pathlib import Path
+from typing import TYPE_CHECKING, cast
+from warnings import warn
 
-if TYPE_CHECKING:
-    from pathlib import Path
+from platformdirs import user_config_dir
 
+if TYPE_CHECKING:
     import useq
+    from pymmcore_plus import CMMCorePlus
+
+USER_DIR = Path(user_config_dir("napari_micromanager"))
+USER_CONFIGS_PATHS = USER_DIR / "system_configurations.json"
 
 # key in MDASequence.metadata to store napari-micromanager metadata
 # note that this is also used in napari layer metadata
@@ -68,3 +74,43 @@ def ensure_unique(path: Path, extension: str = ".tif", ndigits: int = 3) -> Path
     # build new path name
     number = f"_{current_max+1:0{ndigits}d}"
     return path.parent / f"{stem}{number}{extension}"
+
+
+def add_path_to_config_json(path: Path | str) -> None:
+    """Uopdate the st=ystem configurations json file with the new path."""
+    import json
+
+    if isinstance(path, Path):
+        path = str(path)
+
+    # create USER_CONFIGS_PATHS if it doesn't exist
+    if not USER_CONFIGS_PATHS.exists():
+        USER_DIR.mkdir(parents=True, exist_ok=True)
+        with open(USER_CONFIGS_PATHS, "w") as f:
+            json.dump({"paths": []}, f)
+
+    # Read the existing data
+    try:
+        with open(USER_CONFIGS_PATHS) as f:
+            data = json.load(f)
+    except json.JSONDecodeError:
+        data = {"paths": []}
+
+    # Append the new path. using insert so we leave the empty string at the end
+    paths = cast(list, data.get("paths", []))
+    if path not in paths:
+        paths.insert(0, path)
+
+    # Write the data back to the file
+    with open(USER_CONFIGS_PATHS, "w") as f:
+        json.dump({"paths": paths}, f)
+
+
+def load_system_configuration(mmcore: CMMCorePlus, config: str | Path) -> None:
+    """Load a Micro-Manager system configuration file."""
+    try:
+        mmcore.unloadAllDevices()
+        mmcore.loadSystemConfiguration(config)
+    except FileNotFoundError:
+        # don't crash if the user passed an invalid config
+        warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)

From 59a378460b92ce95fdcedd4a76ec559946e815cd Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 22:54:21 -0500
Subject: [PATCH 16/36] fix: docstring

---
 .../_gui_objects/_startup_configurations_widget.py        | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index e30c25dd..35a70ff4 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -98,10 +98,10 @@ def __init__(
     def _initialize(self) -> None:
         """Initialize the dialog with the configuration files.
 
-        This method reads the stored paths in the USER_CONFIGS_PATHS jason file (or
-        create one if it doesn't exist) and adds them to the combo box. It also adds the
-        Micro-Manager configuration files form the Micro-Manager folder if they are not
-        already in the list.
+        This method reads the paths in the USER_CONFIGS_PATHS json file (it creates
+        one if it doesn't exist) and adds them to the combo box. It also adds the
+        Micro-Manager configuration files form all the Micro-Manager folder if they are
+        not already in the list.
         """
         # create USER_CONFIGS_PATHS if it doesn't exist
         if not USER_CONFIGS_PATHS.exists():

From 986fc2892244dfbab966007ab5f068aae122c3a1 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 6 Mar 2024 22:56:22 -0500
Subject: [PATCH 17/36] fix: todo

---
 .../_gui_objects/_startup_configurations_widget.py              | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index 35a70ff4..e2c38618 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -103,6 +103,8 @@ def _initialize(self) -> None:
         Micro-Manager configuration files form all the Micro-Manager folder if they are
         not already in the list.
         """
+        # TODO: move this method to main_window.py and leave here only the combo update
+
         # create USER_CONFIGS_PATHS if it doesn't exist
         if not USER_CONFIGS_PATHS.exists():
             USER_DIR.mkdir(parents=True, exist_ok=True)

From 302e77a92ec266a18ac1ff64a8f9331143e4c103 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 10:04:10 -0500
Subject: [PATCH 18/36] fix: docstrings and comments

---
 .../_startup_configurations_widget.py         | 27 +++++++++++--------
 src/napari_micromanager/main_window.py        |  4 ++-
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
index e2c38618..7ce5c088 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
@@ -96,15 +96,13 @@ def __init__(
             load_system_configuration(self._mmc, config)
 
     def _initialize(self) -> None:
-        """Initialize the dialog with the configuration files.
+        """Initialize the dialog with the Micro-Manager configuration files.
 
-        This method reads the paths in the USER_CONFIGS_PATHS json file (it creates
-        one if it doesn't exist) and adds them to the combo box. It also adds the
-        Micro-Manager configuration files form all the Micro-Manager folder if they are
-        not already in the list.
+        This method is called everytime the widget is created (and so when
+        napari-micromanage is loaded) and it updates (or create if does not yet exists)
+        the list of  Micro-Manager configurations paths saved in the USER_CONFIGS_PATHS
+        json file.
         """
-        # TODO: move this method to main_window.py and leave here only the combo update
-
         # create USER_CONFIGS_PATHS if it doesn't exist
         if not USER_CONFIGS_PATHS.exists():
             USER_DIR.mkdir(parents=True, exist_ok=True)
@@ -114,13 +112,14 @@ def _initialize(self) -> None:
         # get the paths from the json file
         configs_paths = self._get_config_paths()
 
-        # add the paths to the combo box
-        self.cfg_combo.addItems([*configs_paths, NEW])
-
         # write the data back to the file
         with open(USER_CONFIGS_PATHS, "w") as f:
             json.dump({"paths": configs_paths}, f)
 
+        # add the paths to the combo box
+        self.cfg_combo.addItems([*configs_paths, NEW])
+
+        # resize the widget so its width is not too small
         self.resize(600, self.minimumSizeHint().height())
 
     def _get_config_paths(self) -> list[str]:
@@ -172,7 +171,11 @@ def _get_micromanager_cfg_files(self) -> list[Path]:
         return cfg_files
 
     def _on_browse_clicked(self) -> None:
-        """Open a file dialog to select a file."""
+        """Open a file dialog to select a file.
+
+        If a file path is provided, it is added to the USER_CONFIGS_PATHS json file and
+        to the combo box.
+        """
         path, _ = QFileDialog.getOpenFileName(
             self, "Open file", "", "MicroManager files (*.cfg)"
         )
@@ -180,6 +183,7 @@ def _on_browse_clicked(self) -> None:
             # using insert so we leave the empty string at the end
             self.cfg_combo.insertItem(0, path)
             self.cfg_combo.setCurrentText(path)
+            # add the path to the USER_CONFIGS_PATHS list
             add_path_to_config_json(path)
 
 
@@ -207,6 +211,7 @@ def accept(self) -> None:
         and to load it.
         """
         dest = self.field(DEST_CONFIG)
+        # add the path to the USER_CONFIGS_PATHS list
         add_path_to_config_json(dest)
         super().accept()
         load_system_configuration(self._core, dest)
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 5bb6cde0..f448a121 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -55,7 +55,9 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        # handle the system configurations at startup
+        # handle the system configurations at startup. with this we also create/update
+        # the list of the Micro-Manager system configurations files path stored a s a
+        # json file in the user's configuration file directory (USER_CONFIGS_PATHS)
         self._startup_configs = StartupConfigurations(
             parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
         )

From b2b6b94e6989188bf4b8a9068a703c21abe718e8 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 10:46:38 -0500
Subject: [PATCH 19/36] feat: nove login into InitializeSystemConfigurations
 object

---
 ...ions_widget.py => _init_system_configs.py} | 160 ++++++++++--------
 src/napari_micromanager/_util.py              |   6 +-
 src/napari_micromanager/main_window.py        |  12 +-
 3 files changed, 104 insertions(+), 74 deletions(-)
 rename src/napari_micromanager/{_gui_objects/_startup_configurations_widget.py => _init_system_configs.py} (78%)

diff --git a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py b/src/napari_micromanager/_init_system_configs.py
similarity index 78%
rename from src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
rename to src/napari_micromanager/_init_system_configs.py
index 7ce5c088..74d364d0 100644
--- a/src/napari_micromanager/_gui_objects/_startup_configurations_widget.py
+++ b/src/napari_micromanager/_init_system_configs.py
@@ -8,6 +8,7 @@
 from pymmcore_plus import CMMCorePlus, find_micromanager
 from pymmcore_widgets import ConfigWizard
 from pymmcore_widgets.hcwizard.finish_page import DEST_CONFIG
+from qtpy.QtCore import QObject
 from qtpy.QtWidgets import (
     QComboBox,
     QDialog,
@@ -31,77 +32,34 @@
 NEW = "New Hardware Configuration"
 
 
-class StartupConfigurations(QDialog):
-    """A dialog to select the Micro-Manager Hardware configuration files at startup."""
-
+class InitializeSystemConfigurations(QObject):
     def __init__(
         self,
-        parent: QWidget | None = None,
-        *,
+        parent: QObject | None = None,
         config: Path | str | None = None,
         mmcore: CMMCorePlus | None = None,
     ) -> None:
         super().__init__(parent)
-        self.setWindowTitle("Micro-Manager Hardware System Configurations")
 
         self._mmc = mmcore or CMMCorePlus.instance()
-        self._config = config
-
-        # label
-        cfg_lbl = QLabel("Configuration file:")
-        cfg_lbl.setSizePolicy(FIXED)
-
-        # combo box
-        self.cfg_combo = QComboBox()
-        # `AdjustToMinimumContents` is not available in all qtpy backends so using
-        # `AdjustToMinimumContentsLengthWithIcon` instead
-        self.cfg_combo.setSizeAdjustPolicy(
-            QComboBox.SizeAdjustPolicy.AdjustToMinimumContentsLengthWithIcon
-        )
-
-        # browse button
-        self.browse_btn = QPushButton("...")
-        self.browse_btn.setSizePolicy(FIXED)
-        self.browse_btn.clicked.connect(self._on_browse_clicked)
-
-        # Create OK and Cancel buttons
-        button_box = QDialogButtonBox(
-            QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-        )
-        button_box.accepted.connect(self.accept)
-        button_box.rejected.connect(self.reject)
-
-        # add widgets to layout
-        wdg_layout = QGridLayout(self)
-        wdg_layout.addWidget(cfg_lbl, 0, 0)
-        wdg_layout.addWidget(self.cfg_combo, 0, 1)
-        wdg_layout.addWidget(self.browse_btn, 0, 2)
-        wdg_layout.addWidget(button_box, 2, 0, 1, 3)
 
         self._initialize()
 
-        # if a config was not passed, show the dialog
-        if config is None:
-            if self.exec_():
-                config = self.cfg_combo.currentText()
-                # if the user selected NEW, show the config wizard
-                if config == NEW:
-                    self._cfg_wizard = HardwareConfigWizard(parent=self)
-                    self._cfg_wizard.show()
-                # otherwise load the selected config
-                else:
-                    load_system_configuration(self._mmc, config)
-        # if a config was passed, load it
-        else:
+        if config is not None:
+            add_path_to_config_json(config)
             load_system_configuration(self._mmc, config)
+        else:
+            self._startup_dialog = StartupConfigurationsDialog(
+                parent=self.parent(), config=config, mmcore=self._mmc
+            )
+            self._startup_dialog.show()
 
     def _initialize(self) -> None:
-        """Initialize the dialog with the Micro-Manager configuration files.
+        """Create or update the list of Micro-Manager hardware configurations paths.
 
-        This method is called everytime the widget is created (and so when
-        napari-micromanage is loaded) and it updates (or create if does not yet exists)
-        the list of  Micro-Manager configurations paths saved in the USER_CONFIGS_PATHS
-        json file.
+        This method is called everytime napari-micromanager is loaded and it updates (or
+        create if does not yet exists) the list of  Micro-Manager configurations paths
+        saved in the USER_CONFIGS_PATHS as a json file.
         """
         # create USER_CONFIGS_PATHS if it doesn't exist
         if not USER_CONFIGS_PATHS.exists():
@@ -116,12 +74,6 @@ def _initialize(self) -> None:
         with open(USER_CONFIGS_PATHS, "w") as f:
             json.dump({"paths": configs_paths}, f)
 
-        # add the paths to the combo box
-        self.cfg_combo.addItems([*configs_paths, NEW])
-
-        # resize the widget so its width is not too small
-        self.resize(600, self.minimumSizeHint().height())
-
     def _get_config_paths(self) -> list[str]:
         """Return the paths from the json file.
 
@@ -151,10 +103,6 @@ def _get_config_paths(self) -> list[str]:
                     # using insert so we leave the empty string at the end
                     paths.insert(0, str(cfg))
 
-            # if a config was passed, add it to the list if it's not already there
-            if self._config is not None and str(self._config) not in paths:
-                paths.insert(0, str(self._config))
-
         except json.JSONDecodeError:
             paths = []
             warn("Error reading the json file.", stacklevel=2)
@@ -170,6 +118,86 @@ def _get_micromanager_cfg_files(self) -> list[Path]:
 
         return cfg_files
 
+
+class StartupConfigurationsDialog(QDialog):
+    """A dialog to select the Micro-Manager Hardware configuration files at startup."""
+
+    def __init__(
+        self,
+        parent: QWidget | None = None,
+        *,
+        config: Path | str | None = None,
+        mmcore: CMMCorePlus | None = None,
+    ) -> None:
+        super().__init__(parent)
+        self.setWindowTitle("Micro-Manager Hardware System Configurations")
+
+        self._mmc = mmcore or CMMCorePlus.instance()
+        self._config = config
+
+        # label
+        cfg_lbl = QLabel("Configuration file:")
+        cfg_lbl.setSizePolicy(FIXED)
+
+        # combo box
+        self.cfg_combo = QComboBox()
+        # `AdjustToMinimumContents` is not available in all qtpy backends so using
+        # `AdjustToMinimumContentsLengthWithIcon` instead
+        self.cfg_combo.setSizeAdjustPolicy(
+            QComboBox.SizeAdjustPolicy.AdjustToMinimumContentsLengthWithIcon
+        )
+
+        # browse button
+        self.browse_btn = QPushButton("...")
+        self.browse_btn.setSizePolicy(FIXED)
+        self.browse_btn.clicked.connect(self._on_browse_clicked)
+
+        # Create OK and Cancel buttons
+        button_box = QDialogButtonBox(
+            QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        )
+        button_box.accepted.connect(self.accept)
+        button_box.rejected.connect(self.reject)
+
+        # add widgets to layout
+        wdg_layout = QGridLayout(self)
+        wdg_layout.addWidget(cfg_lbl, 0, 0)
+        wdg_layout.addWidget(self.cfg_combo, 0, 1)
+        wdg_layout.addWidget(self.browse_btn, 0, 2)
+        wdg_layout.addWidget(button_box, 2, 0, 1, 3)
+
+        self._initialize()
+
+    def accept(self) -> None:
+        super().accept()
+        config = self.cfg_combo.currentText()
+        # if the user selected NEW, show the config wizard
+        if config == NEW:
+            self._cfg_wizard = HardwareConfigWizard(parent=self)
+            self._cfg_wizard.show()
+        else:
+            load_system_configuration(self._mmc, config)
+
+    def _initialize(self) -> None:
+        """Initialize the dialog with the Micro-Manager configuration files."""
+        # return if the json file doesn't exist
+        if not USER_CONFIGS_PATHS.exists():
+            return
+
+        # Read the existing data
+        try:
+            with open(USER_CONFIGS_PATHS) as f:
+                configs_paths = json.load(f)
+        except json.JSONDecodeError:
+            configs_paths = {"paths": []}
+
+        configs_paths = cast(list, configs_paths.get("paths", []))
+        # add the paths to the combo box
+        self.cfg_combo.addItems([*configs_paths, NEW])
+
+        # resize the widget so its width is not too small
+        self.resize(600, self.minimumSizeHint().height())
+
     def _on_browse_clicked(self) -> None:
         """Open a file dialog to select a file.
 
diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index 5da8d92a..d7ed9e05 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -92,12 +92,12 @@ def add_path_to_config_json(path: Path | str) -> None:
     # Read the existing data
     try:
         with open(USER_CONFIGS_PATHS) as f:
-            data = json.load(f)
+            configs_paths = json.load(f)
     except json.JSONDecodeError:
-        data = {"paths": []}
+        configs_paths = {"paths": []}
 
     # Append the new path. using insert so we leave the empty string at the end
-    paths = cast(list, data.get("paths", []))
+    paths = cast(list, configs_paths.get("paths", []))
     if path not in paths:
         paths.insert(0, path)
 
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index f448a121..e5c2babe 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -11,8 +11,8 @@
 from pymmcore_plus import CMMCorePlus
 
 from ._core_link import CoreViewerLink
-from ._gui_objects._startup_configurations_widget import StartupConfigurations
 from ._gui_objects._toolbar import MicroManagerToolbar
+from ._init_system_configs import InitializeSystemConfigurations
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -55,10 +55,12 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        # handle the system configurations at startup. with this we also create/update
-        # the list of the Micro-Manager system configurations files path stored a s a
-        # json file in the user's configuration file directory (USER_CONFIGS_PATHS)
-        self._startup_configs = StartupConfigurations(
+        # handle the system configurations at startup. with this we create/update the
+        # list of the Micro-Manager hardware system configurations files path stored as
+        # a json file in the user's configuration file directory (USER_CONFIGS_PATHS).
+        # a dialog will be also displayed if no system configuration file is provided
+        # to select one from the list of available ones or to create a new one
+        self._init_cfg = InitializeSystemConfigurations(
             parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
         )
 

From 0772d140da9b18851002f61042018dbdf15e1f26 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 10:48:06 -0500
Subject: [PATCH 20/36] fix: comment

---
 src/napari_micromanager/main_window.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index e5c2babe..37968d1e 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -59,7 +59,7 @@ def __init__(
         # list of the Micro-Manager hardware system configurations files path stored as
         # a json file in the user's configuration file directory (USER_CONFIGS_PATHS).
         # a dialog will be also displayed if no system configuration file is provided
-        # to select one from the list of available ones or to create a new one
+        # to either select one from the list of available ones or to create a new one.
         self._init_cfg = InitializeSystemConfigurations(
             parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
         )

From 4cefd8d8eca87cc8583d23a2e52b0291b4c85b5f Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 13:51:24 -0500
Subject: [PATCH 21/36] feat: add menue + update save and load methods

---
 .../_gui_objects/_toolbar.py                  | 21 ++------
 .../_init_system_configs.py                   | 16 +++---
 src/napari_micromanager/_util.py              | 44 ++++++++++-----
 src/napari_micromanager/main_window.py        | 54 ++++++++++++++++++-
 4 files changed, 96 insertions(+), 39 deletions(-)

diff --git a/src/napari_micromanager/_gui_objects/_toolbar.py b/src/napari_micromanager/_gui_objects/_toolbar.py
index ea056ef3..bc62face 100644
--- a/src/napari_micromanager/_gui_objects/_toolbar.py
+++ b/src/napari_micromanager/_gui_objects/_toolbar.py
@@ -18,8 +18,8 @@
 )
 
 from napari_micromanager._util import (
-    add_path_to_config_json,
-    load_system_configuration,
+    load_sys_config_dialog,
+    save_sys_config_dialog,
 )
 
 try:
@@ -31,7 +31,6 @@
 from qtpy.QtCore import QEvent, QObject, QSize, Qt
 from qtpy.QtWidgets import (
     QDockWidget,
-    QFileDialog,
     QFrame,
     QHBoxLayout,
     QLabel,
@@ -69,22 +68,12 @@ def __init__(
         super().__init__(parent=parent, mmcore=mmcore)
 
     def _save_cfg(self) -> None:
-        (filename, _) = QFileDialog.getSaveFileName(
-            self, "Save Micro-Manager Configuration."
-        )
-        if filename:
-            filename = filename if str(filename).endswith(".cfg") else f"{filename}.cfg"
-            self._mmc.saveSystemConfiguration(filename)
-            add_path_to_config_json(filename)
+        """Open file dialog to save the current configuration."""
+        save_sys_config_dialog(parent=self, mmcore=self._mmc)
 
     def _load_cfg(self) -> None:
         """Open file dialog to select a config file."""
-        (filename, _) = QFileDialog.getOpenFileName(
-            self, "Select a Micro-Manager configuration file", "", "cfg(*.cfg)"
-        )
-        if filename:
-            add_path_to_config_json(filename)
-            load_system_configuration(mmcore=self._mmc, config=filename)
+        load_sys_config_dialog(parent=self, mmcore=self._mmc)
 
 
 # Dict for QObject and its QPushButton icon
diff --git a/src/napari_micromanager/_init_system_configs.py b/src/napari_micromanager/_init_system_configs.py
index 74d364d0..d13a96e0 100644
--- a/src/napari_micromanager/_init_system_configs.py
+++ b/src/napari_micromanager/_init_system_configs.py
@@ -25,7 +25,6 @@
     USER_CONFIGS_PATHS,
     USER_DIR,
     add_path_to_config_json,
-    load_system_configuration,
 )
 
 FIXED = QSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
@@ -46,8 +45,10 @@ def __init__(
         self._initialize()
 
         if config is not None:
+            # add the config to the system configurations json and set it as the
+            # current configuration path.
             add_path_to_config_json(config)
-            load_system_configuration(self._mmc, config)
+            self._mmc.loadSystemConfiguration(config)
         else:
             self._startup_dialog = StartupConfigurationsDialog(
                 parent=self.parent(), config=config, mmcore=self._mmc
@@ -58,7 +59,7 @@ def _initialize(self) -> None:
         """Create or update the list of Micro-Manager hardware configurations paths.
 
         This method is called everytime napari-micromanager is loaded and it updates (or
-        create if does not yet exists) the list of  Micro-Manager configurations paths
+        create if does not yet exists) the list of Micro-Manager configurations paths
         saved in the USER_CONFIGS_PATHS as a json file.
         """
         # create USER_CONFIGS_PATHS if it doesn't exist
@@ -176,7 +177,7 @@ def accept(self) -> None:
             self._cfg_wizard = HardwareConfigWizard(parent=self)
             self._cfg_wizard.show()
         else:
-            load_system_configuration(self._mmc, config)
+            self._mmc.loadSystemConfiguration(config)
 
     def _initialize(self) -> None:
         """Initialize the dialog with the Micro-Manager configuration files."""
@@ -211,7 +212,8 @@ def _on_browse_clicked(self) -> None:
             # using insert so we leave the empty string at the end
             self.cfg_combo.insertItem(0, path)
             self.cfg_combo.setCurrentText(path)
-            # add the path to the USER_CONFIGS_PATHS list
+            # add the config to the system configurations json and set it as the
+            # current configuration path.
             add_path_to_config_json(path)
 
 
@@ -238,8 +240,8 @@ def accept(self) -> None:
         Overriding to add the new configuration file to the USER_CONFIGS_PATHS json file
         and to load it.
         """
+        super().accept()
         dest = self.field(DEST_CONFIG)
         # add the path to the USER_CONFIGS_PATHS list
         add_path_to_config_json(dest)
-        super().accept()
-        load_system_configuration(self._core, dest)
+        self._core.loadSystemConfiguration(dest)
diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index d7ed9e05..7bcd0663 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -2,13 +2,13 @@
 
 from pathlib import Path
 from typing import TYPE_CHECKING, cast
-from warnings import warn
 
 from platformdirs import user_config_dir
+from pymmcore_plus import CMMCorePlus
+from qtpy.QtWidgets import QFileDialog, QWidget
 
 if TYPE_CHECKING:
     import useq
-    from pymmcore_plus import CMMCorePlus
 
 USER_DIR = Path(user_config_dir("napari_micromanager"))
 USER_CONFIGS_PATHS = USER_DIR / "system_configurations.json"
@@ -77,7 +77,7 @@ def ensure_unique(path: Path, extension: str = ".tif", ndigits: int = 3) -> Path
 
 
 def add_path_to_config_json(path: Path | str) -> None:
-    """Uopdate the st=ystem configurations json file with the new path."""
+    """Update the stystem configurations json file with the new path."""
     import json
 
     if isinstance(path, Path):
@@ -92,12 +92,12 @@ def add_path_to_config_json(path: Path | str) -> None:
     # Read the existing data
     try:
         with open(USER_CONFIGS_PATHS) as f:
-            configs_paths = json.load(f)
+            data = json.load(f)
     except json.JSONDecodeError:
-        configs_paths = {"paths": []}
+        data = {"paths": []}
 
     # Append the new path. using insert so we leave the empty string at the end
-    paths = cast(list, configs_paths.get("paths", []))
+    paths = cast(list, data.get("paths", []))
     if path not in paths:
         paths.insert(0, path)
 
@@ -106,11 +106,27 @@ def add_path_to_config_json(path: Path | str) -> None:
         json.dump({"paths": paths}, f)
 
 
-def load_system_configuration(mmcore: CMMCorePlus, config: str | Path) -> None:
-    """Load a Micro-Manager system configuration file."""
-    try:
-        mmcore.unloadAllDevices()
-        mmcore.loadSystemConfiguration(config)
-    except FileNotFoundError:
-        # don't crash if the user passed an invalid config
-        warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
+def save_sys_config_dialog(
+    parent: QWidget | None = None, mmcore: CMMCorePlus | None = None
+) -> None:
+    (filename, _) = QFileDialog.getSaveFileName(
+        parent, "Save Micro-Manager Configuration."
+    )
+    if filename:
+        filename = filename if str(filename).endswith(".cfg") else f"{filename}.cfg"
+        mmcore = mmcore or CMMCorePlus.instance()
+        mmcore.saveSystemConfiguration(filename)
+        add_path_to_config_json(filename)
+
+
+def load_sys_config_dialog(
+    parent: QWidget | None = None, mmcore: CMMCorePlus | None = None
+) -> None:
+    """Open file dialog to select a config file."""
+    (filename, _) = QFileDialog.getOpenFileName(
+        parent, "Select a Micro-Manager configuration file", "", "cfg(*.cfg)"
+    )
+    if filename:
+        add_path_to_config_json(filename)
+        mmcore = mmcore or CMMCorePlus.instance()
+        mmcore.loadSystemConfiguration(filename)
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 37968d1e..aa44d907 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -3,16 +3,23 @@
 import atexit
 import contextlib
 import logging
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any, Callable, cast
 
 import napari
 import napari.layers
 import napari.viewer
 from pymmcore_plus import CMMCorePlus
+from pymmcore_widgets.hcwizard.intro_page import SRC_CONFIG
+from qtpy.QtWidgets import QAction, QMenuBar
+
+from napari_micromanager._util import (
+    load_sys_config_dialog,
+    save_sys_config_dialog,
+)
 
 from ._core_link import CoreViewerLink
 from ._gui_objects._toolbar import MicroManagerToolbar
-from ._init_system_configs import InitializeSystemConfigurations
+from ._init_system_configs import HardwareConfigWizard, InitializeSystemConfigurations
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -33,6 +40,8 @@ def __init__(
     ) -> None:
         super().__init__(viewer)
 
+        self._add_menu()
+
         # get global CMMCorePlus instance
         self._mmc = CMMCorePlus.instance()
         # this object mediates the connection between the viewer and core events
@@ -55,6 +64,9 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
+        # Micro-Manager HArdware Configuration Wizard
+        self._wiz = HardwareConfigWizard(parent=self.viewer.window._qt_window)
+
         # handle the system configurations at startup. with this we create/update the
         # list of the Micro-Manager hardware system configurations files path stored as
         # a json file in the user's configuration file directory (USER_CONFIGS_PATHS).
@@ -77,3 +89,41 @@ def _update_max_min(self, *_: Any) -> None:
         self.minmax.update_from_layers(
             lr for lr in visible if isinstance(lr, napari.layers.Image)
         )
+
+    def _add_menu(self) -> None:
+        if (win := getattr(self.viewer.window, "_qt_window", None)) is None:
+            return
+
+        menubar = cast(QMenuBar, win.menuBar())
+
+        # main Micro-Manager menu
+        mm_menu = menubar.addMenu("Micro-Manager")
+
+        # Configurations Sub-Menu
+        configurations_menu = mm_menu.addMenu("System Configurations")
+        self.act_save_configuration = QAction("Save Configuration", self)
+        self.act_save_configuration.triggered.connect(self._save_cfg)
+        configurations_menu.addAction(self.act_save_configuration)
+        self.act_load_configuration = QAction("Load Configuration", self)
+        self.act_load_configuration.triggered.connect(self._load_cfg)
+        configurations_menu.addAction(self.act_load_configuration)
+        self.act_cfg_wizard = QAction("Hardware Configuration Wizard", self)
+        self.act_cfg_wizard.triggered.connect(self._show_config_wizard)
+        configurations_menu.addAction(self.act_cfg_wizard)
+
+    def _save_cfg(self) -> None:
+        """Save the current Micro-Manager system configuration."""
+        save_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
+
+    def _load_cfg(self) -> None:
+        """Load a Micro-Manager system configuration."""
+        load_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
+
+    def _show_config_wizard(self) -> None:
+        """Show the Micro-Manager Hardware Configuration Wizard."""
+        if self._wiz.isVisible():
+            self._wiz.raise_()
+        else:
+            current_cfg = self._mmc.systemConfigurationFile() or ""
+            self._wiz.setField(SRC_CONFIG, current_cfg)
+            self._wiz.show()

From 34afce82e0ff9b46bc9e327ddf9d328f70ebf778 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 13:55:27 -0500
Subject: [PATCH 22/36] fix: docstings and comments

---
 src/napari_micromanager/_util.py       | 11 ++++++++++-
 src/napari_micromanager/main_window.py |  3 +++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index 7bcd0663..2b19c110 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -109,6 +109,11 @@ def add_path_to_config_json(path: Path | str) -> None:
 def save_sys_config_dialog(
     parent: QWidget | None = None, mmcore: CMMCorePlus | None = None
 ) -> None:
+    """Open file dialog to save a config file.
+
+    The file will be also saved in the USER_CONFIGS_PATHS jason file if it doesn't
+    yet exist.
+    """
     (filename, _) = QFileDialog.getSaveFileName(
         parent, "Save Micro-Manager Configuration."
     )
@@ -122,7 +127,11 @@ def save_sys_config_dialog(
 def load_sys_config_dialog(
     parent: QWidget | None = None, mmcore: CMMCorePlus | None = None
 ) -> None:
-    """Open file dialog to select a config file."""
+    """Open file dialog to select a config file.
+
+    The loaded file will be also saved in the USER_CONFIGS_PATHS jason file if it
+    doesn't yet exist.
+    """
     (filename, _) = QFileDialog.getOpenFileName(
         parent, "Select a Micro-Manager configuration file", "", "cfg(*.cfg)"
     )
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index aa44d907..683864f4 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -101,12 +101,15 @@ def _add_menu(self) -> None:
 
         # Configurations Sub-Menu
         configurations_menu = mm_menu.addMenu("System Configurations")
+        # save cfg
         self.act_save_configuration = QAction("Save Configuration", self)
         self.act_save_configuration.triggered.connect(self._save_cfg)
         configurations_menu.addAction(self.act_save_configuration)
+        # load cfg
         self.act_load_configuration = QAction("Load Configuration", self)
         self.act_load_configuration.triggered.connect(self._load_cfg)
         configurations_menu.addAction(self.act_load_configuration)
+        # cfg wizard
         self.act_cfg_wizard = QAction("Hardware Configuration Wizard", self)
         self.act_cfg_wizard.triggered.connect(self._show_config_wizard)
         configurations_menu.addAction(self.act_cfg_wizard)

From e390b1a1a73a5321aa4ba0f4f861d3ed127d68e7 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 20:21:49 -0500
Subject: [PATCH 23/36] test: add init test

---
 .../_init_system_configs.py                   |  2 +
 tests/test_configurations.py                  | 48 +++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 tests/test_configurations.py

diff --git a/src/napari_micromanager/_init_system_configs.py b/src/napari_micromanager/_init_system_configs.py
index d13a96e0..79703b64 100644
--- a/src/napari_micromanager/_init_system_configs.py
+++ b/src/napari_micromanager/_init_system_configs.py
@@ -44,11 +44,13 @@ def __init__(
 
         self._initialize()
 
+        # if a config is provided, load it
         if config is not None:
             # add the config to the system configurations json and set it as the
             # current configuration path.
             add_path_to_config_json(config)
             self._mmc.loadSystemConfiguration(config)
+        # if no config is provided, show a dialog to select one or to create a new one
         else:
             self._startup_dialog = StartupConfigurationsDialog(
                 parent=self.parent(), config=config, mmcore=self._mmc
diff --git a/tests/test_configurations.py b/tests/test_configurations.py
new file mode 100644
index 00000000..bff5f00b
--- /dev/null
+++ b/tests/test_configurations.py
@@ -0,0 +1,48 @@
+import json
+from pathlib import Path
+
+import pytest
+from napari_micromanager._init_system_configs import (
+    InitializeSystemConfigurations,
+)
+from napari_micromanager._util import USER_CONFIGS_PATHS
+from pymmcore_plus import CMMCorePlus
+from pytestqt.qtbot import QtBot
+
+DEMO = "MMConfig_demo.cfg"
+
+
+configs = [None, Path(__file__).parent / "test_config.cfg"]
+
+
+@pytest.mark.parametrize("config", configs)
+def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None):
+    init = InitializeSystemConfigurations(mmcore=core, config=config)
+
+    with open(USER_CONFIGS_PATHS) as f:
+        data = json.load(f)
+        # the default config should be in the json file
+        assert DEMO in [Path(path).name for path in data["paths"]]
+
+        if config is None:
+            assert len(data["paths"]) == 1
+            assert init._startup_dialog.isVisible()
+            combo = init._startup_dialog.cfg_combo
+            current_cfg = combo.currentText()
+            assert Path(current_cfg).name == DEMO
+            assert [Path(combo.itemText(i)).name for i in range(combo.count())] == [
+                DEMO,
+                "New Hardware Configuration",
+            ]
+            # simulate click on ok
+            init._startup_dialog.accept()
+
+        else:
+            assert len(data["paths"]) == 2
+            assert not hasattr(init, "_startup_dialog")
+            current_cfg = config
+            assert str(current_cfg) in data["paths"]
+
+        assert core.systemConfigurationFile() == str(current_cfg)
+
+    USER_CONFIGS_PATHS.unlink()

From 21e07282b526e7c355fad9663eec5e4fd25315f7 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 20:23:45 -0500
Subject: [PATCH 24/36] test: fix

---
 tests/test_configurations.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index bff5f00b..addc3455 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -10,7 +10,7 @@
 from pytestqt.qtbot import QtBot
 
 DEMO = "MMConfig_demo.cfg"
-
+NEW = "New Hardware Configuration"
 
 configs = [None, Path(__file__).parent / "test_config.cfg"]
 
@@ -30,9 +30,8 @@ def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None):
             combo = init._startup_dialog.cfg_combo
             current_cfg = combo.currentText()
             assert Path(current_cfg).name == DEMO
-            assert [Path(combo.itemText(i)).name for i in range(combo.count())] == [
-                DEMO,
-                "New Hardware Configuration",
+            assert [DEMO, NEW] == [
+                Path(combo.itemText(i)).name for i in range(combo.count())
             ]
             # simulate click on ok
             init._startup_dialog.accept()

From 8d5fffa30baa0018424224c0aeeebcd1ae5a68e5 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 20:26:03 -0500
Subject: [PATCH 25/36] test: update

---
 tests/test_configurations.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index addc3455..019f89c5 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -17,6 +17,8 @@
 
 @pytest.mark.parametrize("config", configs)
 def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None):
+    assert not USER_CONFIGS_PATHS.exists()
+
     init = InitializeSystemConfigurations(mmcore=core, config=config)
 
     with open(USER_CONFIGS_PATHS) as f:

From 4aba582de98c972f30d020ed87bc7284e18ad565 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 21:36:48 -0500
Subject: [PATCH 26/36] fix: add option to init the confics

---
 src/napari_micromanager/_util.py       |  9 +++-----
 src/napari_micromanager/main_window.py | 31 ++++++++++++++++----------
 tests/conftest.py                      |  2 +-
 3 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index 2b19c110..dea7a7a5 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -80,15 +80,12 @@ def add_path_to_config_json(path: Path | str) -> None:
     """Update the stystem configurations json file with the new path."""
     import json
 
+    if not USER_CONFIGS_PATHS.exists():
+        return
+
     if isinstance(path, Path):
         path = str(path)
 
-    # create USER_CONFIGS_PATHS if it doesn't exist
-    if not USER_CONFIGS_PATHS.exists():
-        USER_DIR.mkdir(parents=True, exist_ok=True)
-        with open(USER_CONFIGS_PATHS, "w") as f:
-            json.dump({"paths": []}, f)
-
     # Read the existing data
     try:
         with open(USER_CONFIGS_PATHS) as f:
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 683864f4..131d226b 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -36,7 +36,11 @@ class MainWindow(MicroManagerToolbar):
     """The main napari-micromanager widget that gets added to napari."""
 
     def __init__(
-        self, viewer: napari.viewer.Viewer, config: str | Path | None = None
+        self,
+        viewer: napari.viewer.Viewer,
+        config: str | Path | None = None,
+        *,
+        init_configs: bool = True,
     ) -> None:
         super().__init__(viewer)
 
@@ -64,17 +68,20 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        # Micro-Manager HArdware Configuration Wizard
-        self._wiz = HardwareConfigWizard(parent=self.viewer.window._qt_window)
-
-        # handle the system configurations at startup. with this we create/update the
-        # list of the Micro-Manager hardware system configurations files path stored as
-        # a json file in the user's configuration file directory (USER_CONFIGS_PATHS).
-        # a dialog will be also displayed if no system configuration file is provided
-        # to either select one from the list of available ones or to create a new one.
-        self._init_cfg = InitializeSystemConfigurations(
-            parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
-        )
+        if init_configs:
+            # Micro-Manager HArdware Configuration Wizard
+            self._wiz = HardwareConfigWizard(parent=self.viewer.window._qt_window)
+
+            # handle the system configurations at startup. with this we create/update
+            # the list of the Micro-Manager hardware system configurations files path
+            # stored as a json file in the user's configuration file directory
+            # (USER_CONFIGS_PATHS).
+            # a dialog will be also displayed if no system configuration file is
+            # provided to either select one from the list of available ones or to create
+            # a new one.
+            self._init_cfg = InitializeSystemConfigurations(
+                parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
+            )
 
     def _cleanup(self) -> None:
         for signal, slot in self._connections:
diff --git a/tests/conftest.py b/tests/conftest.py
index cde3cad5..6010a2e2 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -21,7 +21,7 @@ def core(monkeypatch):
 @pytest.fixture
 def main_window(core: CMMCorePlus, make_napari_viewer):
     viewer = make_napari_viewer()
-    win = MainWindow(viewer=viewer)
+    win = MainWindow(viewer=viewer, init_configs=False)
     assert core == win._mmc
     return win
 

From 0e75583b411c42933f84255a719375f50c894df6 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 21:38:27 -0500
Subject: [PATCH 27/36] test: fix

---
 tests/test_main_window.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_main_window.py b/tests/test_main_window.py
index ef4d3a1f..3ed01b0c 100644
--- a/tests/test_main_window.py
+++ b/tests/test_main_window.py
@@ -17,7 +17,7 @@ def test_main_window(qtbot: QtBot, core: CMMCorePlus) -> None:
     This test should remain fast.
     """
     viewer = MagicMock()
-    wdg = MainWindow(viewer)
+    wdg = MainWindow(viewer, init_configs=False)
     qtbot.addWidget(wdg)
 
     viewer.layers.events.connect.assert_called_once_with(wdg._update_max_min)

From dafc357759d0d66ece36cd24fa28996e2c9f88c3 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 22:05:03 -0500
Subject: [PATCH 28/36] fix: avoid error when loading a cfg + update test

---
 src/napari_micromanager/_init_system_configs.py |  7 ++++---
 src/napari_micromanager/_util.py                | 11 +++++++++++
 src/napari_micromanager/main_window.py          | 14 +++++++++++---
 tests/test_main.py                              |  4 ++++
 4 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/napari_micromanager/_init_system_configs.py b/src/napari_micromanager/_init_system_configs.py
index 79703b64..7dedb3a9 100644
--- a/src/napari_micromanager/_init_system_configs.py
+++ b/src/napari_micromanager/_init_system_configs.py
@@ -25,6 +25,7 @@
     USER_CONFIGS_PATHS,
     USER_DIR,
     add_path_to_config_json,
+    load_sys_config,
 )
 
 FIXED = QSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
@@ -49,7 +50,7 @@ def __init__(
             # add the config to the system configurations json and set it as the
             # current configuration path.
             add_path_to_config_json(config)
-            self._mmc.loadSystemConfiguration(config)
+            load_sys_config(config)
         # if no config is provided, show a dialog to select one or to create a new one
         else:
             self._startup_dialog = StartupConfigurationsDialog(
@@ -179,7 +180,7 @@ def accept(self) -> None:
             self._cfg_wizard = HardwareConfigWizard(parent=self)
             self._cfg_wizard.show()
         else:
-            self._mmc.loadSystemConfiguration(config)
+            load_sys_config(config)
 
     def _initialize(self) -> None:
         """Initialize the dialog with the Micro-Manager configuration files."""
@@ -246,4 +247,4 @@ def accept(self) -> None:
         dest = self.field(DEST_CONFIG)
         # add the path to the USER_CONFIGS_PATHS list
         add_path_to_config_json(dest)
-        self._core.loadSystemConfiguration(dest)
+        load_sys_config(dest)
diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index dea7a7a5..5c1d49fa 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -2,6 +2,7 @@
 
 from pathlib import Path
 from typing import TYPE_CHECKING, cast
+from warnings import warn
 
 from platformdirs import user_config_dir
 from pymmcore_plus import CMMCorePlus
@@ -136,3 +137,13 @@ def load_sys_config_dialog(
         add_path_to_config_json(filename)
         mmcore = mmcore or CMMCorePlus.instance()
         mmcore.loadSystemConfiguration(filename)
+
+
+def load_sys_config(config: Path | str, mmcore: CMMCorePlus | None = None) -> None:
+    """Load a system configuration with a warning if the file is not found."""
+    mmcore = mmcore or CMMCorePlus.instance()
+    try:
+        mmcore.loadSystemConfiguration(config)
+    except FileNotFoundError:
+        # don't crash if the user passed an invalid config
+        warn(f"Config file {config} not found. Nothing loaded.", stacklevel=2)
diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 131d226b..d77fc8cd 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -13,6 +13,7 @@
 from qtpy.QtWidgets import QAction, QMenuBar
 
 from napari_micromanager._util import (
+    load_sys_config,
     load_sys_config_dialog,
     save_sys_config_dialog,
 )
@@ -68,10 +69,10 @@ def __init__(
         self.destroyed.connect(self._cleanup)
         atexit.register(self._cleanup)
 
-        if init_configs:
-            # Micro-Manager HArdware Configuration Wizard
-            self._wiz = HardwareConfigWizard(parent=self.viewer.window._qt_window)
+        # Micro-Manager Hardware Configuration Wizard
+        self._wiz: HardwareConfigWizard | None = None
 
+        if init_configs:
             # handle the system configurations at startup. with this we create/update
             # the list of the Micro-Manager hardware system configurations files path
             # stored as a json file in the user's configuration file directory
@@ -82,6 +83,10 @@ def __init__(
             self._init_cfg = InitializeSystemConfigurations(
                 parent=self.viewer.window._qt_window, config=config, mmcore=self._mmc
             )
+            return
+
+        if config:
+            load_sys_config(config)
 
     def _cleanup(self) -> None:
         for signal, slot in self._connections:
@@ -131,6 +136,9 @@ def _load_cfg(self) -> None:
 
     def _show_config_wizard(self) -> None:
         """Show the Micro-Manager Hardware Configuration Wizard."""
+        if self._wiz is None:
+            self._wiz = HardwareConfigWizard(parent=self.viewer.window._qt_window)
+
         if self._wiz.isVisible():
             self._wiz.raise_()
         else:
diff --git a/tests/test_main.py b/tests/test_main.py
index 5cae6d6b..ba614d10 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -3,6 +3,7 @@
 
 import pytest
 from napari_micromanager.__main__ import main
+from napari_micromanager._util import USER_CONFIGS_PATHS
 from pymmcore_plus import CMMCorePlus
 
 
@@ -35,3 +36,6 @@ def test_cli_main(argv: list) -> None:
     # this is to prevent a leaked widget error in the NEXT test
     napari.current_viewer().close()
     QtViewer._instances.clear()
+
+    if USER_CONFIGS_PATHS.exists():
+        USER_CONFIGS_PATHS.unlink()

From d6686f78505690b82fc02fdee683de2f71bacfa7 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 22:22:05 -0500
Subject: [PATCH 29/36] fix: import annotations

---
 tests/test_configurations.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index 019f89c5..e32d3f3a 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -1,13 +1,18 @@
+from __future__ import annotations
+
 import json
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import pytest
 from napari_micromanager._init_system_configs import (
     InitializeSystemConfigurations,
 )
 from napari_micromanager._util import USER_CONFIGS_PATHS
-from pymmcore_plus import CMMCorePlus
-from pytestqt.qtbot import QtBot
+
+if TYPE_CHECKING:
+    from pymmcore_plus import CMMCorePlus
+    from pytestqt.qtbot import QtBot
 
 DEMO = "MMConfig_demo.cfg"
 NEW = "New Hardware Configuration"

From 097b135e05af9e16dc24c9d779b50725aaed526b Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 22:39:16 -0500
Subject: [PATCH 30/36] test: update test_config_init

---
 tests/test_configurations.py | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index e32d3f3a..20e709cd 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -21,7 +21,8 @@
 
 
 @pytest.mark.parametrize("config", configs)
-def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None):
+@pytest.mark.parametrize("wiz", [True, False])
+def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None, wiz: bool):
     assert not USER_CONFIGS_PATHS.exists()
 
     init = InitializeSystemConfigurations(mmcore=core, config=config)
@@ -32,23 +33,32 @@ def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None):
         assert DEMO in [Path(path).name for path in data["paths"]]
 
         if config is None:
-            assert len(data["paths"]) == 1
             assert init._startup_dialog.isVisible()
             combo = init._startup_dialog.cfg_combo
             current_cfg = combo.currentText()
             assert Path(current_cfg).name == DEMO
-            assert [DEMO, NEW] == [
+            assert DEMO and NEW in [
                 Path(combo.itemText(i)).name for i in range(combo.count())
             ]
+
+            # set the combo to new so that after accepting the config wizard should
+            # be visible
+            combo.setCurrentText(NEW if wiz else DEMO)
+
             # simulate click on ok
             init._startup_dialog.accept()
 
+            # only if DEMO cfg was selected, the config wizard should be visible
+            if wiz:
+                assert init._startup_dialog._cfg_wizard.isVisible()
+
         else:
-            assert len(data["paths"]) == 2
             assert not hasattr(init, "_startup_dialog")
             current_cfg = config
             assert str(current_cfg) in data["paths"]
 
-        assert core.systemConfigurationFile() == str(current_cfg)
+        # a config should have been loaded only if DEMO cfg was selected
+        if not wiz:
+            assert core.systemConfigurationFile() == str(current_cfg)
 
     USER_CONFIGS_PATHS.unlink()

From 4d6980cef44d38fc84fe0f7f6d6d9f065a6c0c10 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 22:43:41 -0500
Subject: [PATCH 31/36] test: todo

---
 tests/test_configurations.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index 20e709cd..e682741f 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -62,3 +62,6 @@ def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None, wiz:
             assert core.systemConfigurationFile() == str(current_cfg)
 
     USER_CONFIGS_PATHS.unlink()
+
+
+# TODO: test the config wizard and the menu actions

From f6ffbfcb8fc8fc5299e81b9d90e6febf7a52f9d3 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Thu, 7 Mar 2024 22:45:11 -0500
Subject: [PATCH 32/36] test: fix test_config_init

---
 tests/test_configurations.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_configurations.py b/tests/test_configurations.py
index e682741f..8eb2e347 100644
--- a/tests/test_configurations.py
+++ b/tests/test_configurations.py
@@ -35,8 +35,6 @@ def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None, wiz:
         if config is None:
             assert init._startup_dialog.isVisible()
             combo = init._startup_dialog.cfg_combo
-            current_cfg = combo.currentText()
-            assert Path(current_cfg).name == DEMO
             assert DEMO and NEW in [
                 Path(combo.itemText(i)).name for i in range(combo.count())
             ]
@@ -44,6 +42,7 @@ def test_config_init(qtbot: QtBot, core: CMMCorePlus, config: Path | None, wiz:
             # set the combo to new so that after accepting the config wizard should
             # be visible
             combo.setCurrentText(NEW if wiz else DEMO)
+            current_cfg = combo.currentText()
 
             # simulate click on ok
             init._startup_dialog.accept()

From 544bf1cc4adfe59cd965a0c604e7ae8f0c99f565 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 13 Mar 2024 13:00:48 -0400
Subject: [PATCH 33/36] fix: _load_cfg

---
 src/napari_micromanager/main_window.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index d77fc8cd..2c5781aa 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -14,7 +14,6 @@
 
 from napari_micromanager._util import (
     load_sys_config,
-    load_sys_config_dialog,
     save_sys_config_dialog,
 )
 
@@ -132,7 +131,10 @@ def _save_cfg(self) -> None:
 
     def _load_cfg(self) -> None:
         """Load a Micro-Manager system configuration."""
-        load_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
+        # load_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
+        InitializeSystemConfigurations(
+            parent=self.viewer.window._qt_window, mmcore=self._mmc
+        )
 
     def _show_config_wizard(self) -> None:
         """Show the Micro-Manager Hardware Configuration Wizard."""

From bbaa2097bd2435c92f109efeea4a00ab383f64f8 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 13 Mar 2024 21:46:28 -0400
Subject: [PATCH 34/36] fix: revert

---
 src/napari_micromanager/main_window.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/napari_micromanager/main_window.py b/src/napari_micromanager/main_window.py
index 2c5781aa..d77fc8cd 100644
--- a/src/napari_micromanager/main_window.py
+++ b/src/napari_micromanager/main_window.py
@@ -14,6 +14,7 @@
 
 from napari_micromanager._util import (
     load_sys_config,
+    load_sys_config_dialog,
     save_sys_config_dialog,
 )
 
@@ -131,10 +132,7 @@ def _save_cfg(self) -> None:
 
     def _load_cfg(self) -> None:
         """Load a Micro-Manager system configuration."""
-        # load_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
-        InitializeSystemConfigurations(
-            parent=self.viewer.window._qt_window, mmcore=self._mmc
-        )
+        load_sys_config_dialog(parent=self.viewer.window._qt_window, mmcore=self._mmc)
 
     def _show_config_wizard(self) -> None:
         """Show the Micro-Manager Hardware Configuration Wizard."""

From f4f048288501e5a5be000b2e6b38b57db0f54de0 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Wed, 13 Mar 2024 21:52:03 -0400
Subject: [PATCH 35/36] fix: move selected cfg to top

---
 src/napari_micromanager/_init_system_configs.py | 6 ++++++
 src/napari_micromanager/_util.py                | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/napari_micromanager/_init_system_configs.py b/src/napari_micromanager/_init_system_configs.py
index 7dedb3a9..5d793ffd 100644
--- a/src/napari_micromanager/_init_system_configs.py
+++ b/src/napari_micromanager/_init_system_configs.py
@@ -175,6 +175,12 @@ def __init__(
     def accept(self) -> None:
         super().accept()
         config = self.cfg_combo.currentText()
+        # if current text is not at index 0, update the json file and insert it at the
+        # first position so it will be shown as the fort option in the combo box next
+        # time the dialog is shown.
+        if config != self.cfg_combo.itemText(0):
+            add_path_to_config_json(config)
+
         # if the user selected NEW, show the config wizard
         if config == NEW:
             self._cfg_wizard = HardwareConfigWizard(parent=self)
diff --git a/src/napari_micromanager/_util.py b/src/napari_micromanager/_util.py
index 5c1d49fa..60c426c8 100644
--- a/src/napari_micromanager/_util.py
+++ b/src/napari_micromanager/_util.py
@@ -96,8 +96,9 @@ def add_path_to_config_json(path: Path | str) -> None:
 
     # Append the new path. using insert so we leave the empty string at the end
     paths = cast(list, data.get("paths", []))
-    if path not in paths:
-        paths.insert(0, path)
+    if path in paths:
+        paths.remove(path)
+    paths.insert(0, path)
 
     # Write the data back to the file
     with open(USER_CONFIGS_PATHS, "w") as f:

From 1a6523a63a8978abec810b4fe474a4b0b3188907 Mon Sep 17 00:00:00 2001
From: fdrgsp <federico.gasparoli@gmail.com>
Date: Sat, 16 Mar 2024 08:50:13 -0400
Subject: [PATCH 36/36] fix: spelling

---
 src/napari_micromanager/_gui_objects/_toolbar.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/napari_micromanager/_gui_objects/_toolbar.py b/src/napari_micromanager/_gui_objects/_toolbar.py
index bc62face..7f638e8e 100644
--- a/src/napari_micromanager/_gui_objects/_toolbar.py
+++ b/src/napari_micromanager/_gui_objects/_toolbar.py
@@ -58,7 +58,7 @@
 class GroupsAndPresets(GroupPresetTableWidget):
     """Subclass of GroupPresetTableWidget.
 
-    Overwrite the save and load methods to store the saced or loaded configuration in
+    Overwrite the save and load methods to store the saved or loaded configuration in
     the USER_CONFIGS_PATHS json config file.
     """