Miscellaneous improvements

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
   # Lint and format with ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.2
+    rev: v0.7.4
     hooks:
       # Run the linter.
       - id: ruff
@@ -43,7 +43,7 @@ repos:
 
   # Commitizen
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v3.30.0
+    rev: v3.31.0
     hooks:
       - id: commitizen
         additional_dependencies: [ cz-changeup ]

docs/source/conf.py

@@ -200,6 +200,7 @@ def setup(app):
     "NXgroup": "`NXgroup <nexusformat.nexus.tree.NXgroup>`",
     "NXlink": "`NXlink <nexusformat.nexus.tree.NXlink>`",
     "NXdata": "`NXdata <nexusformat.nexus.tree.NXdata>`",
+    "NXentry": "`NXentry <nexusformat.nexus.tree.NXentry>`",
     "lmfit.Parameters": "`lmfit.Parameters <lmfit.parameter.Parameters>`",
     "lmfit.Model": "`lmfit.Model <lmfit.model.Model>`",
 }

docs/source/user-guide/imagetool.rst

@@ -99,11 +99,15 @@ execution is a blocking call. This means that you cannot run any other code whil
 tool is running. As a workaround, we provide :class:`ImageToolManager
 <erlab.interactive.imagetool.ImageToolManager>`.
 
-In the environment where ERLabPy installed, run ``itool-manager`` in a shell to start
-the manager application. Subsequent invocations of ImageTool from :func:`itool
-<erlab.interactive.imagetool.itool>` and :class:`qshow
-<erlab.accessors.general.InteractiveDataArrayAccessor>` will open the tool in the
-manager application, leaving the notebook free to run other code.
+In the environment where ERLabPy installed, run ``itool-manager`` in a terminal to start
+the manager application. Subsequent calls to :func:`itool
+<erlab.interactive.imagetool.itool>` and :meth:`DataArray.qshow
+<erlab.accessors.general.InteractiveDataArrayAccessor.__call__>` will open the ImageTool
+in the manager.
+
+Alternatively, you can run the following code in a python environment where ERLabPy is installed: ::
+
+    python -m erlab.interactive.imagetool.manager
 
 .. note::
 
@@ -116,3 +120,25 @@ manager application, leaving the notebook free to run other code.
     directly while the manager is running by passing `use_manager=False` to :func:`itool
     <erlab.interactive.imagetool.itool>` or :class:`qshow
     <erlab.accessors.general.InteractiveDataArrayAccessor>`.
+
+The manager application consists of a small window that shows the list of opened
+ImageTools, along with some buttons to manage them. Hovering over the buttons will show
+tooltips that explain what each button does.
+
+There are three ways to open an ImageTool with the manager:
+
+- Invocations of ImageTool from :func:`itool <erlab.interactive.imagetool.itool>` and :class:`qshow
+  <erlab.accessors.general.InteractiveDataArrayAccessor>` from any python script or
+  Jupyter notebook will automatically be added to the manager.
+
+- Open files through the ``File`` menu in the menu bar of the manager application.
+
+- Drag and drop supported files to the manager window.
+
+One of the main features of the manager is that it can save and load the state of
+ImageTool windows to a HDF5 file. You can save all ImageTool windows in the manager to a
+single file through the ``Save Workspace As...`` menu item in the ``File`` menu. The
+saved windows can later be restored through the ``Open Workspace...`` item in the same
+menu.
+
+Try exploring the menubar of the manager application to see what you can do!

docs/source/user-guide/io.ipynb

@@ -695,7 +695,7 @@
     "\n",
     "- The experimental geometry should be stored in the ``'configuration'`` attribute as an\n",
     "  integer. See :ref:`Nomenclature <nomenclature>` and :class:`AxesConfiguration\n",
-    "  <erlab.analysis.kspace.AxesConfiguration>` for more information.\n",
+    "  <erlab.constants.AxesConfiguration>` for more information.\n",
     "\n",
     "- All standard angle coordinates must follow the naming conventions in\n",
     "  :ref:`Nomenclature <nomenclature>`.\n",

pyproject.toml

@@ -85,7 +85,7 @@ Changelog = "https://github.com/kmnhan/erlabpy/blob/main/CHANGELOG.md"
 erlab-igor = "erlab.io.igor:IgorBackendEntrypoint"
 
 [tool.commitizen]
-change_type_map = { "BREAKING CHANGE" = "Breaking Changes", "feat" = "Features", "fix" = "Bug Fixes", "refactor" = "Code Refactor", "perf" = "Performance" }
+change_type_map = { "BREAKING CHANGE" = "🚨 Breaking Changes", "feat" = "✨ Features", "fix" = "🐞 Bug Fixes", "perf" = "⚡️ Performance",  "refactor" = "🛠 Code Refactor" }
 
 version_provider = "pep621"
 update_changelog_on_bump = true
@@ -94,11 +94,11 @@ changelog_start_rev = "v1.2.1"
 changelog_merge_prerelease = true
 name = 'cz_changeup'
 change_type_order = [
-    "Breaking Changes",
-    "Features",
-    "Bug Fixes",
-    "Code Refactor",
-    "Performance",
+    "🚨 Breaking Changes",
+    "✨ Features",
+    "🐞 Bug Fixes",
+    "⚡️ Performance",
+    "🛠 Code Refactor",
 ]
 # cz-changeup configuration
 changeup_repo_base_url = "https://github.com/kmnhan/erlabpy"

src/erlab/accessors/fit.py

@@ -12,10 +12,8 @@
 import copy
 import itertools
 from collections.abc import Collection, Hashable, Iterable, Mapping, Sequence
-from typing import Any, Literal, cast
+from typing import TYPE_CHECKING, Any, Literal, cast
 
-import joblib
-import lmfit
 import numpy as np
 import tqdm.auto
 import xarray as xr
@@ -25,6 +23,10 @@
 from erlab.utils.misc import emit_user_level_warning
 from erlab.utils.parallel import joblib_progress
 
+if TYPE_CHECKING:
+    # Avoid importing until runtime for initial import performance
+    import lmfit
+
 
 def _nested_dict_vals(d):
     for v in d.values():
@@ -55,6 +57,8 @@ def _concat_along_keys(d: dict[str, xr.DataArray], dim_name: str) -> xr.DataArra
 def _parse_params(
     d: dict[str, Any] | lmfit.Parameters, dask: bool
 ) -> xr.DataArray | _ParametersWrapper:
+    import lmfit
+
     if isinstance(d, lmfit.Parameters):
         # Input to apply_ufunc cannot be a Mapping, so wrap in a class
         return _ParametersWrapper(d)
@@ -70,6 +74,8 @@ def _parse_params(
 
 
 def _parse_multiple_params(d: dict[str, Any], as_str: bool) -> xr.DataArray:
+    import lmfit
+
     for k in d:
         if isinstance(d[k], int | float | complex | xr.DataArray):
             d[k] = {"value": d[k]}
@@ -252,6 +258,8 @@ def __call__(
         scipy.optimize.curve_fit
 
         """
+        import lmfit
+
         # Implementation analogous to xarray.Dataset.curve_fit
 
         if params is None:
@@ -539,6 +547,9 @@ def _output_wrapper(name, da, out=None) -> dict:
         }
 
         if parallel:
+            # Avoid importing until runtime for initial import performance
+            import joblib
+
             if is_dask:
                 emit_user_level_warning(
                     "The input Dataset is chunked. Parallel fitting will not offer any "

src/erlab/accessors/general.py

@@ -13,7 +13,6 @@
 from collections.abc import Hashable, Mapping
 from typing import Any
 
-import matplotlib.pyplot as plt
 import numpy as np
 import xarray as xr
 
@@ -54,14 +53,16 @@ def __call__(self, *args, **kwargs):
             Keyword arguments to be passed to the plotting function.
 
         """
+        import matplotlib.pyplot
+
         from erlab.plotting.erplot import fancy_labels, plot_array
 
         if len(self._obj.dims) == 2:
             return plot_array(self._obj, *args, **kwargs)
 
         ax = kwargs.pop("ax", None)
         if ax is None:
-            ax = plt.gca()
+            ax = matplotlib.pyplot.gca()
         kwargs["ax"] = ax
 
         out = self._obj.plot(*args, **kwargs)