Erlab

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 remote-tracking branch &39;origin/main&39; into dev ([`fd8e1ad`](https://github.com/kmnhan/erlabpy/commit/fd8e1ad14b345664289810c4c8a605df6b299c3a))

* [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)

Chore

* cleanup pyproject.toml ([`0331132`](https://github.com/kmnhan/erlabpy/commit/033113247ea5d8fa8bc4afb9513b349b95080bed))

* (**deps**) add ipywidgets to optional dependency group viz ([`0062966`](https://github.com/kmnhan/erlabpy/commit/00629663742ada02ade556cb19ca0b14bd864fec))

Ci

* (**readthdocs**) update build python version and add zip format ([`b2cc6fc`](https://github.com/kmnhan/erlabpy/commit/b2cc6fc1f732bab8904f90e10e194d4dffee5d57))

Documentation

* (**io**) add tutorial for writing advanced plugins ([`11f289e`](https://github.com/kmnhan/erlabpy/commit/11f289edd451e10773d99ae1c9fc47cde22b06dc))

* add ipywidgets to intersphinx mapping ([`0ee46f8`](https://github.com/kmnhan/erlabpy/commit/0ee46f8c6d783f2ee63cad807abf5e8582cfaa31))

Fix

* (**io**) unify call signature for summarize ([`e2782c8`](https://github.com/kmnhan/erlabpy/commit/e2782c898d5aaaa1443b2bc82bb61fb40a28d232))

* resolve failing tests due to changes in sample data generation ([`80f0045`](https://github.com/kmnhan/erlabpy/commit/80f004574950834e42dbfa7677031d0f9f113bda))

* (**interactive.exampledata**) properly generate 2D data ([`825260c`](https://github.com/kmnhan/erlabpy/commit/825260c8ceb0a79b8c071750003529b91cda3573))

Performance

* (**io**) speedup merlin summary generation by excluding duplicates ([`d6b4253`](https://github.com/kmnhan/erlabpy/commit/d6b42537ce48232b5112daef8f31e5cf86ea921a))

Refactor

* (**io**) allow for more complex setups ([`f67b2e4`](https://github.com/kmnhan/erlabpy/commit/f67b2e4c7b092b7ca2db00ce02a23647879c514b))

LoaderBase.infer_index now returns a second argument, which is a dictionary containing optional keyword arguments to load.

* (**io**) provide rich interactive summary ([`b075a9e`](https://github.com/kmnhan/erlabpy/commit/b075a9ee59b61892462fc475e78b036a54408099))

* (**io**) include &34;Path&34; column in ssrl loader summary ([`ae1d8ae`](https://github.com/kmnhan/erlabpy/commit/ae1d8aee051aa71563f6a6009ce9672e56edfae7))

* (**io**) improve array formatting in summary ([`1718529`](https://github.com/kmnhan/erlabpy/commit/171852957db7fe53ff6a5c5c5f843530078d4b46))

Test

* add test for dataloader ([`64cde09`](https://github.com/kmnhan/erlabpy/commit/64cde099dbb13d8b148e67d1fe23a8849041dae4))

Chore

* (**deps**) pin lmfit<1.3.0 ([`915fc60`](https://github.com/kmnhan/erlabpy/commit/915fc60e8e7e8a2dfc9a56bbc1afd1c737bcc3d5))

Documentation

* rephrase some docstrings ([`e67597c`](https://github.com/kmnhan/erlabpy/commit/e67597c90e009748d1bd39c43c03a8cc1b439840))

* add link to changelog ([`fbb6d32`](https://github.com/kmnhan/erlabpy/commit/fbb6d3254ae254278dec74b2ce9965e20a4dc88d))

* add ipywidgets as requirement ([`41024eb`](https://github.com/kmnhan/erlabpy/commit/41024ebbef02609d9a2fc70c4630fec06aa96012))

* temporarily pin lmfit<1.3.0 to build docs ([`6b86ac2`](https://github.com/kmnhan/erlabpy/commit/6b86ac2f89c2a822753f3fbe106eb5dfaa2cb22c))

Fix

* (**fit**) add sigma and amplitude expressions to MultiPeakModel parameters ([`3f6ba5e`](https://github.com/kmnhan/erlabpy/commit/3f6ba5e84922129296183e02255506df73da0276))

* (**fit.minuit**) properly handle parameters constrained with expressions ([`d03f012`](https://github.com/kmnhan/erlabpy/commit/d03f012b4fde92f445a24657dca1fb5b3600fa45))

Refactor

* set informative model name for MultiPeakModel ([`d14ee9d`](https://github.com/kmnhan/erlabpy/commit/d14ee9d6ac7962207700de50039a5b7a858fea6a))

* add gaussian and lorentzian for consistency ([`07c0dfb`](https://github.com/kmnhan/erlabpy/commit/07c0dfb9ecfb882e4f5f0ccfe942c1a835b613b2))

Test

* add tests for fit models ([`3f9125c`](https://github.com/kmnhan/erlabpy/commit/3f9125ce19a4a30dd31b9d039d6614a8cae19966))

Documentation

* improve fitting documentation ([`9e0a106`](https://github.com/kmnhan/erlabpy/commit/9e0a10611a32ac75798e68f864cff55b5661330f))

* add curve fitting guide ([`ff9743c`](https://github.com/kmnhan/erlabpy/commit/ff9743c2203eb773af6bdb8d88426907f4300924))

* add docstrings to plotting.colors ([`1a15a70`](https://github.com/kmnhan/erlabpy/commit/1a15a706aa2fd591a18401ea53f950005391c88f))

Feature

* enable component evaluation for MultiPeakModel ([`8875b74`](https://github.com/kmnhan/erlabpy/commit/8875b7443d26313156fcdcc43586d40af4ff4f00))

* (**analysis.fit**) add BCS gap equation and Dynes formula ([`f862aa4`](https://github.com/kmnhan/erlabpy/commit/f862aa4af4d2ba470f1ea074fc90442d9b18b336))

Fix

* curvefittingtool errors ([`9abb99c`](https://github.com/kmnhan/erlabpy/commit/9abb99c35633bc722469276d4837a2372c132042))

Refactor

* cleanup fit namespace ([`906aa99`](https://github.com/kmnhan/erlabpy/commit/906aa99193f78577e705218b2d6c22378611f84b))

* rename ExtendedAffineBroadenedFD to FermiEdgeModel ([`a98aa82`](https://github.com/kmnhan/erlabpy/commit/a98aa82bcbdf22ff8a156d800e336653f9afba07))

* (**interactive**) exclude bad colormaps ([`877c915`](https://github.com/kmnhan/erlabpy/commit/877c915def6eb3dddb3862d6ac64c8c70f456ad3))

Fix

* (**interactive**) update data load functions used in imagetool ([`c3abe35`](https://github.com/kmnhan/erlabpy/commit/c3abe3517046ed603a9221de38b22257322d3a51))

Documentation

* update syntax ([`2b72991`](https://github.com/kmnhan/erlabpy/commit/2b7299150a50af38e6e05d5f9690558cbeb7a9ad))

* improve intro pages ([`ec2a4f8`](https://github.com/kmnhan/erlabpy/commit/ec2a4f816e1ad0ed1ad154d6544e91bea1b5d9c5))

* (**io**) add complete data loading examples ([`63e88c4`](https://github.com/kmnhan/erlabpy/commit/63e88c40b14584214cd45bd0258f8ef7a32d716c))

* (**io**) simplify flowchart ([`355d023`](https://github.com/kmnhan/erlabpy/commit/355d02374e11f7a78b87f8d3159f288a1d15d22d))

Fix

* (**io**) prevent specifying invalid data_dir ([`701b011`](https://github.com/kmnhan/erlabpy/commit/701b011339ecba657a0f4a14e2fef19adeb4bf2b))

* (**io**) fixes merlin summary data type resolving ([`a91ad3d`](https://github.com/kmnhan/erlabpy/commit/a91ad3d4387a23d25ac1b208cba8217e67efbec0))

* (**io**) fix summary loading ([`a5dd84a`](https://github.com/kmnhan/erlabpy/commit/a5dd84af9eec0f835b3116bc7c470e57ef3f3e02))