Merge branch 'main' into dev

CHANGELOG.md

@@ -2,6 +2,122 @@
 
 
 
+## v2.3.0 (2024-04-22)
+
+### Chore
+
+* cleanup directory ([`40e1f8d`](https://github.com/kmnhan/erlabpy/commit/40e1f8dcce66d53f9de6fd5905cef3c690633c98))
+
+* customize issue template chooser ([`0aa7617`](https://github.com/kmnhan/erlabpy/commit/0aa7617e7794449756df0abfc3260c6e545f97a3))
+
+* update issue templates ([`5dfb250`](https://github.com/kmnhan/erlabpy/commit/5dfb25098a6843f378303486499a89489e00ee76))
+
+### Ci
+
+* (**github**) update test requirements ([`21080cc`](https://github.com/kmnhan/erlabpy/commit/21080ccb5553e3c753db29d8fa372f6000ea59a7))
+
+* (**readthedocs**) rollback to 3.11 due to bug in python 3.12.0 and 3.12.1 ([`5eb6152`](https://github.com/kmnhan/erlabpy/commit/5eb615266ed78473583ca53a2e38f11ee58fc13f))
+
+### Documentation
+
+* update documentation ([`ab32920`](https://github.com/kmnhan/erlabpy/commit/ab3292032bcfa6e6e39e3b367090909a09ea813b))
+
+  Updated requirements, contrib page, fitting guide. Source button now links to github.
+
+* fix typo in getting-started.rst ([`3304a18`](https://github.com/kmnhan/erlabpy/commit/3304a182a7e46b7799977af93966bae9c5d3a95c))
+
+* fix typos and add compat notes to getting-started ([`3bb2ac5`](https://github.com/kmnhan/erlabpy/commit/3bb2ac576ad029cacaf2d2043a3bf57a184ace24))
+
+* add masking section, WIP ([`0844f6a`](https://github.com/kmnhan/erlabpy/commit/0844f6a58b971684a5cc02867dd36f61263e8c6c))
+
+* add imagetool to user guide ([`84d3586`](https://github.com/kmnhan/erlabpy/commit/84d35866f9c221f82af7a4dfdcfbd871a88e4eaf))
+
+* update io and plotting documentation and cleanup contributing ([`b4c4f7c`](https://github.com/kmnhan/erlabpy/commit/b4c4f7ce028cc03e87d4a54fefc72c8a610ce0ac))
+
+* update badges ([`5e373f4`](https://github.com/kmnhan/erlabpy/commit/5e373f4f6a4f45ba90600f18a76dfd4830bb075e))
+
+* enable latexpdf generation ([`7469271`](https://github.com/kmnhan/erlabpy/commit/746927115faba6c76a791c94aee3ef026fd11bf5))
+
+### Feature
+
+* (**kspace**) rewrite conversion with `xarray.apply_ufunc` ([`156cef8`](https://github.com/kmnhan/erlabpy/commit/156cef830582e01dc378a7437a0c85f4c7efc077))
+
+  Momentum conversion now relies on xarray broadcasting for all computations, and objects with extra dimensions such as temperature can be automatically broadcasted. Dask arrays can also be converted.
+
+* (**exampledata**) enable specifying seed for noise rng ([`aa542e8`](https://github.com/kmnhan/erlabpy/commit/aa542e8c288ff1ca64820960f469b2c244ca5c95))
+
+* (**interpolate**) enable fast interpolation for 1D arrays ([`ff333a0`](https://github.com/kmnhan/erlabpy/commit/ff333a05803d7079034e36f2e1dc3d22d0b686f7))
+
+* make both arguments optional for loader_context ([`6780197`](https://github.com/kmnhan/erlabpy/commit/6780197f68abfe7a9edbda951d804a9bc5ba56e9))
+
+* (**kspace**) automatically detect kinetic energy axis and convert to binding ([`bbde447`](https://github.com/kmnhan/erlabpy/commit/bbde44717155d1dd9ffefbc286da32b0bfac2180))
+
+* add more output and parallelization to fit accessor ([`59b35f5`](https://github.com/kmnhan/erlabpy/commit/59b35f53f3ef7f518aec92e05854dba42ddba56f))
+
+  Allows dictionary of `DataArray`s as parameter to fit accessor. Now, the return `Dataset` contains the data and the best fit array. Relevant tests have been added.
+
+* add callable fit accessor using apply_ufunc ([`11e3546`](https://github.com/kmnhan/erlabpy/commit/11e35466fec158e40d0e8e738dd81ed10225d83c))
+
+  Add a `Dataset.modelfit` and `DataArray.modelfit` accessor with similar syntax and output as `Dataset.curvefit`. Closes #22
+
+* add option to plot_array_2d so that users can pass non-normalized color array ([`74cf961`](https://github.com/kmnhan/erlabpy/commit/74cf961532a50d9c324189318460a9f840291a85))
+
+* (**analysis.gold**) add option to normalize energy axis in fitting ([`3dffad6`](https://github.com/kmnhan/erlabpy/commit/3dffad65993520c4b9a9a3afd6be85671bac9d3a))
+
+  This improves performance and results when eV is large like ~100eV.
+
+### Fix
+
+* (**exampledata**) change noise generation parameters ([`b213f11`](https://github.com/kmnhan/erlabpy/commit/b213f1151ed2555fc80374e9ebe3fc0856a13948))
+
+* (**fit**) make FermiEdge2dModel compatible with flattened meshgrid-like input arrays ([`c0dba26`](https://github.com/kmnhan/erlabpy/commit/c0dba261670774862f2dfae62c770bbab81aac2f))
+
+* fix progress bar for parallel objects that return generators ([`23d41b3`](https://github.com/kmnhan/erlabpy/commit/23d41b31a3f3ee6c7343d471f7cec34dc374bafa))
+
+  Tqdm imports are also simplified. We no longer handle `is_notebook` ourselves, but just import from `tqdm.auto`
+
+* (**plotting**) fix 2d colormaps ([`8299576`](https://github.com/kmnhan/erlabpy/commit/8299576ce3cbcbaec106bef952c6df148bb7ca18))
+
+  Allow images including nan to be plotted with gen_2d_colormap, also handle plot_array_2d colorbar aspect
+
+### Refactor
+
+* fix some type hints ([`2dfa5e1`](https://github.com/kmnhan/erlabpy/commit/2dfa5e1b4582e00d0631376ee32aa7d0b1b945b6))
+
+* (**example**) move exampledata from interactive to io ([`1fc7e6c`](https://github.com/kmnhan/erlabpy/commit/1fc7e6c22ce477fe7ebbd8b0c6844d1a85df3fcf))
+
+  Also add sample data generation for fermi edge
+
+* refactor accessors as submodule ([`9fc37bd`](https://github.com/kmnhan/erlabpy/commit/9fc37bd4825de519e4c4b6e30e9e32bf9392ed2d))
+
+* rewrite either_dict_or_kwargs with public api ([`34953d1`](https://github.com/kmnhan/erlabpy/commit/34953d10b6fd67720b1c29dbed1ab7a24e4d3060))
+
+* move correct_with_edge from era.utilities to era.gold ([`08a906f`](https://github.com/kmnhan/erlabpy/commit/08a906ff61a74febc0f47ed08ac24e7a4cd0977f))
+
+  Calling from utilities will now raise a DeprecationWarning. The erlab.analysis namespace is unchanged, so the affect will be minimal.
+
+* qsel now raises a warning upon scalar indexing outside coordinate bounds ([`d6ed628`](https://github.com/kmnhan/erlabpy/commit/d6ed628111be8ac594d3a1b83cc2785a31e3f06e))
+
+### Unknown
+
+* Merge pull request #23 from kmnhan/dev ([`4514a23`](https://github.com/kmnhan/erlabpy/commit/4514a234716e86c77329b48ff8615df193731514))
+
+  Added new interface for fitting, see #22 for discussions.
+  Made loader argument optional for `erlab.io.loader_context` so it can be used to just change the data directory.
+  Momentum conversion has been rewritten using `xarray.apply_ufunc`, and is now dask-compatible. It also automatically determines the current energy axis (kinetic or binding).
+
+* Merge remote-tracking branch 'origin/main' into dev ([`fd8e1ad`](https://github.com/kmnhan/erlabpy/commit/fd8e1ad14b345664289810c4c8a605df6b299c3a))
+
+* Merge pull request #20 from kmnhan/pre-commit-ci-update-config ([`f1b965e`](https://github.com/kmnhan/erlabpy/commit/f1b965e84f79d6976ee1cabf692847fe25f58306))
+
+  [pre-commit.ci] pre-commit autoupdate
+
+* [pre-commit.ci] pre-commit autoupdate ([`7e3a89e`](https://github.com/kmnhan/erlabpy/commit/7e3a89e22bb5491f7d4a2bcb21f5a7baeead8773))
+
+  updates:
+  - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
+
+
 ## v2.2.2 (2024-04-15)
 
 ### Chore

docs/environment.yml

@@ -2,27 +2,29 @@ name: erlabrtd
 channels:
   - conda-forge
 dependencies:
-  - python>=3.11
-  - pip>=19.3
-  - ipykernel
+  - h5netcdf>=1.2.0
   - igor2>=0.5.6
-  - numpy>=1.22.0
+  - iminuit>=2.25.2
+  - ipykernel
+  - joblib>=1.3.2
+  - lmfit>=1.2.0,!=1.3.0
   - matplotlib>=3.8.0
-  - hvplot
-  - xarray
-  - h5netcdf
-  - varname
-  - numba>=0.56.2
-  - numbagg
-  - numba-progress
-  - joblib
-  - lmfit>=1.2.0
+  - numba>=0.59.0
+  - numbagg>=0.8.1
+  - numpy>=1.26.0
+  - pip>=19.3
+  - pyperclip>=1.8.2
   - pyqtgraph>=0.13.1
-  - tqdm
+  - python>=3.11
+  - qtawesome>=1.3.1
+  - qtpy>=2.4.1
+  - scipy>=1.12.0
+  - superqt>=0.6.2
+  - tqdm>=4.66.2
   - uncertainties>=3.0.1
-  - qtawesome
-  - superqt
-  - qtpy
+  - varname>=0.13.0
+  - xarray>=2024.02.0
+  - hvplot
   - sphinx
   - sphinx-autodoc-typehints
   - sphinx-copybutton
@@ -33,9 +35,8 @@ dependencies:
   - sphinx-design
   - pyperclip
   - ipywidgets
-  - ipython
   - pip:
     - pyqt6>=6.2.2
     - csaps
-    - -e git+https://github.com/kmnhan/erlabpy.git#egg=erlab
     - sphinx-qt-documentation
+    - -e .

docs/requirements.txt

@@ -1,4 +1,24 @@
-ipykernel
+dask>=2024.4.1
+h5netcdf>=1.2.0
+igor2>=0.5.6
+iminuit>=2.25.2
+joblib>=1.3.2
+lmfit>=1.2.0,!=1.3.0
+matplotlib>=3.8.0
+numba>=0.59.0
+numbagg>=0.8.1
+numpy>=1.26.0
+pyperclip>=1.8.2
+pyqt6>=6.2.2
+pyqtgraph>=0.13.1
+qtawesome>=1.3.1
+qtpy>=2.4.1
+scipy>=1.12.0
+superqt>=0.6.2
+tqdm>=4.66.2
+uncertainties>=3.0.1
+varname>=0.13.0
+xarray>=2024.02.0
 sphinx
 sphinx-autodoc-typehints
 setuptools
@@ -9,28 +29,8 @@ sphinx-qt-documentation
 sphinx-copybutton
 sphinxcontrib-bibtex
 pybtex
-numpy>=1.22.0
-matplotlib>=3.8.0
 hvplot
-xarray
-h5netcdf
-varname
-numba>=0.56.2
-numbagg
-numba-progress
-joblib
-lmfit<1.3.0
-iminuit>=2.25.2
-pyqtgraph>=0.13.1
-tqdm
-uncertainties>=3.0.1
-pyperclip
-pyqt6>=6.2.2
-qtawesome
-superqt
 csaps
-qtpy
-igor2>=0.5.6
+ipykernel
 ipywidgets
-ipython
 -e .

docs/source/contributing.rst

@@ -255,11 +255,11 @@ Commit and push your changes
 Open a pull request
 -------------------
 
-When you're ready or need feedback on your code, open a Pull Request (PR) so that the
-xarray developers can give feedback and eventually include your suggested code into the
-``main`` branch. `Pull requests (PRs) on GitHub
+When you're ready or need feedback on your code, open a Pull Request (PR) so that we can
+give feedback and eventually include your suggested code into the ``main`` branch. `Pull
+requests (PRs) on GitHub
 <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests>`_
-are the mechanism for contributing to xarray's code and documentation.
+are the mechanism for contributing to the code and documentation.
 
 Enter a title for the set of changes with some explanation of what you've done. Mention
 anything you'd like particular attention for - such as a complicated change or some code
@@ -287,7 +287,7 @@ Code standards
       from qtpy import QtWidgets, QtCore, QtGui
 
   * Use fully qualified enum names from Qt6 instead of the short-form enums from Qt5, i.
-    e., ``QtCore.Qt.CheckState.Checked`` instead of ``QtCore.Qt.Checked``.
+    e., `QtCore.Qt.CheckState.Checked` instead of `QtCore.Qt.Checked`.
 
   * Use the signal and slot syntax from PySide6 (``QtCore.Signal`` and ``QtCore.Slot``
     instead of ``QtCore.pyqtSignal`` and ``QtCore.pyqtSlot``)

environment.yml

@@ -7,9 +7,8 @@ dependencies:
   - iminuit>=2.25.2
   - ipykernel
   - joblib>=1.3.2
-  - lmfit>=1.2.0
+  - lmfit>=1.2.0,!=1.3.0
   - matplotlib>=3.8.0
-  - numba-progress>=1.0.0
   - numba>=0.59.0
   - numbagg>=0.8.1
   - numpy>=1.26.0

pyproject.toml

@@ -26,9 +26,8 @@ dependencies = [
     "igor2>=0.5.6",
     "iminuit>=2.25.2",
     "joblib>=1.3.2",
-    "lmfit>=1.2.0, <1.3.0",
+    "lmfit>=1.2.0,!=1.3.0",
     "matplotlib>=3.8.0",
-    "numba-progress>=1.0.0",
     "numba>=0.59.0",
     "numbagg>=0.8.1",
     "numpy>=1.26.0",

requirements.txt

@@ -3,9 +3,8 @@ h5netcdf>=1.2.0
 igor2>=0.5.6
 iminuit>=2.25.2
 joblib>=1.3.2
-lmfit>=1.2.0
+lmfit>=1.2.0,!=1.3.0
 matplotlib>=3.8.0
-numba-progress>=1.0.0
 numba>=0.59.0
 numbagg>=0.8.1
 numpy>=1.26.0

src/erlab/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "2.2.2"
+__version__ = "2.3.0"
 
 import erlab.accessors  # noqa: F401