==================
redrock Change Log
==================

0.22.1 (unreleased)
-------------------

* No changes yet.

0.22.0 (2026-03-18)
-------------------

* Set ZWARN BAD_TARGET for OBJTYPE != (SKY or TGT).  (PR `#344`_).
* Fix bug for case of single template (PR `#346`_).
* Downgrade rr columns to lower precision (PR `#347`_).
* Support numpy/2 and cupy/14 linalg.solve shape requirements (PR `#348`_).
* Fix np.NaN -> np.nan for numpy 2.x compatibility (PR `#350`_).
* Prevent too many open files error in multiprocessing mode (PR `#351`_).

.. _`#344`: https://github.com/desihub/redrock/pull/344
.. _`#346`: https://github.com/desihub/redrock/pull/346
.. _`#347`: https://github.com/desihub/redrock/pull/347
.. _`#348`: https://github.com/desihub/redrock/pull/348
.. _`#350`: https://github.com/desihub/redrock/pull/350
.. _`#351`: https://github.com/desihub/redrock/pull/351


0.21.0 (2025-12-04)
-------------------

First version with numpy/2.x support and first version on PyPI.

* Use single precision for outputs; update readers (PR `#329`_).
* Fix ``native_endian`` for numpy 2.x (PR `#332`_).
* Bug fix for ``--archetypes-no-legendre`` mode failure and other issues (PR `#334`_).
* Fix crash when using ``--allspec`` (PR `#336`_).
* Update test matrix to catch additional NumPy 2 warnings; add
  ``pyproject.toml`` file; update other top-level metadata files (PR `#341`_).
* Track PCA/NMF coeffcients in archetype mode (PR `#342`_).
* Make DESI packages options for installation (PR `#343`_).

.. _`#329`: https://github.com/desihub/redrock/pull/329
.. _`#332`: https://github.com/desihub/redrock/pull/332
.. _`#334`: https://github.com/desihub/redrock/pull/334
.. _`#336`: https://github.com/desihub/redrock/pull/336
.. _`#341`: https://github.com/desihub/redrock/pull/341
.. _`#342`: https://github.com/desihub/redrock/pull/342
.. _`#343`: https://github.com/desihub/redrock/pull/343


0.20.4 (2025-03-14)
-------------------

* Remove DesiTest usage; drops ``setup.py test`` support (PR `#323`_)
* Update readthedocs configuration (PR `#324`_)
* Remove deprecated test_suite code (PR `#326`_)
* Add ``install_redrock_templates`` script (PR `#327`_)

.. _`#323`: https://github.com/desihub/redrock/pull/323
.. _`#324`: https://github.com/desihub/redrock/pull/324
.. _`#326`: https://github.com/desihub/redrock/pull/326
.. _`#327`: https://github.com/desihub/redrock/pull/327

0.20.3 (2024-11-05)
-------------------

* Support `--templates` accepting multiple files, not just single file or
  text file with list of files (PR `#320`_).

.. _`#320`: https://github.com/desihub/redrock/pull/320

0.20.2 (2024-08-15)
-------------------

* Module file cleanup env vars moved to desimodules (PR `#313`_).
* Propagate header keywords to the ``REDSHIFTS`` HDU (PR `#314`_).
* Changes to address issues with ``max_velo_diff`` variable (PR `#317`_).
* Add ``asdict`` header keyword to :func:`~redrock.templates.load_templates_from_header` (direct commit to main `66a93c77`_).

.. _`#313`: https://github.com/desihub/redrock/pull/313
.. _`#314`: https://github.com/desihub/redrock/pull/314
.. _`#317`: https://github.com/desihub/redrock/pull/317
.. _`66a93c77`: https://github.com/desihub/redrock/commit/66a93c7773cdeec391cf9c17d0964edbf4a13d3e


0.20.1 (2024-06-04)
-------------------

Update for Jura run to finish extra large healpix.

* Better MPI memory management for very large inputs (PRs `#310`_, `#311`_).

.. _`#310`: https://github.com/desihub/redrock/pull/310
.. _`#311`: https://github.com/desihub/redrock/pull/311

0.20.0 (2024-05-03)
-------------------

Used for DESI Jura run.

* Add rrdesi --model option to pre-generate model files (PR `#283`_).
* Add load_templates_from_header (PR `#290`_).
* Add units to fibermap output (PR `#292`_).
* Set ZWARN/NODATA to z=0 GALAXY, no SUBTYPE, zero coefficients (PR `#294`_).
* Add TEMFILnn keywords to header to support non-standard template names
  (PR `#295`_).
* Fix read_zscan; add make_fulltype, parse_fulltype to standardize
  fulltype,spectype,subtype parsing (PR `#297`_).
* Fix warning from zero-sized array (PR `#298`_).
* Standardize wavelength -> [-1,1] mapping for Legendre poly (PR `#299`_).
* Set max_velo_diff to 100 km/s for stars (PR `#300`_).
* Ensure `FITMETHOD` holds 4-string `NONE` (addresses `#301`) (PR `#303`_).
* Fix FITMETHOD bytes vs. str for details file output (PR `#304`_).
* Remove unnecessary desispec dependency (PR `#306`_).
* refactor template/archetype model eval (PR `#293`_).
* include negative [OII] flux penalty in final minimization (PR `#296`_).
* fix max_velo_diff for archetypes (PR `#302`_).

.. _`#283`: https://github.com/desihub/redrock/pull/283
.. _`#290`: https://github.com/desihub/redrock/pull/290
.. _`#292`: https://github.com/desihub/redrock/pull/292
.. _`#293`: https://github.com/desihub/redrock/pull/293
.. _`#294`: https://github.com/desihub/redrock/pull/294
.. _`#295`: https://github.com/desihub/redrock/pull/295
.. _`#296`: https://github.com/desihub/redrock/pull/296
.. _`#297`: https://github.com/desihub/redrock/pull/297
.. _`#298`: https://github.com/desihub/redrock/pull/298
.. _`#299`: https://github.com/desihub/redrock/pull/299
.. _`#300`: https://github.com/desihub/redrock/pull/300
.. _`#301`: https://github.com/desihub/redrock/issues/301
.. _`#302`: https://github.com/desihub/redrock/pull/302
.. _`#303`: https://github.com/desihub/redrock/pull/303
.. _`#304`: https://github.com/desihub/redrock/pull/304
.. _`#306`: https://github.com/desihub/redrock/pull/306


0.19.0 (2024-04-19)
-------------------

* Write test files to temporary directory (PR `#263`_).
* Check template dimension so code works on a single template (PR `#264`_).
* Versioned templates, NMF support, and updated IGM models (PR `#271`_).
* Mask significantly negative flux (PR `#282`_).
* Add ``results.read_zscan(..., select=targetids=...)`` option (PR `#289`_).
* Support for Fastspec PCA templates (PR `#260`_).
* Archetype updates:

  * Added default --nminima for archetypes (PR `#265`_).
  * Adjust coeff size for Legendre for archetypes (PR `#266`_).
  * Docstring cleanup (PR `#267`_).
  * Fix --archetype_nnearest option (PR `#272`_).
  * fix --archetype-legendre-degree=0 crash corner case (PR `#278`_).
  * per camera prior gpu (PR `#255`_, `#259`_).

.. _`#255`: https://github.com/desihub/redrock/pull/255
.. _`#259`: https://github.com/desihub/redrock/pull/259
.. _`#260`: https://github.com/desihub/redrock/pull/260
.. _`#263`: https://github.com/desihub/redrock/pull/263
.. _`#264`: https://github.com/desihub/redrock/pull/264
.. _`#265`: https://github.com/desihub/redrock/pull/265
.. _`#266`: https://github.com/desihub/redrock/pull/266
.. _`#267`: https://github.com/desihub/redrock/pull/267
.. _`#271`: https://github.com/desihub/redrock/pull/271
.. _`#272`: https://github.com/desihub/redrock/pull/272
.. _`#278`: https://github.com/desihub/redrock/pull/278
.. _`#282`: https://github.com/desihub/redrock/pull/282
.. _`#289`: https://github.com/desihub/redrock/pull/289


0.18.0 (2023-09-14)
-------------------

Significant speedups through GPU support, and bug fixes for archetype mode.

* Update API documentation for completeness (PR `#229`_).
* Fix to force mpprocs=1 when using GPU mode with multiprocessing (PR `#230`_).
* Remove multiprocessing from rebin (PR `#232`_).
* Bugfixes for crashes when MPI ranks > ntargets (PR `#233`_).
* Refactored np.linalg.solve into solve_matrices (PR `#234`_).
* Fix used of max_gpuprocs (PR `#236`_).
* Bug fixes for archetype mode (PR `#238`_).
* Added min/maxwave to templates.py that store wave[0] (PR `#239`_).
* Fix archetype mode numba conflict (PR `#240`_, `#241`_).
* Fix archetype mode with wrong input dir (PR `#244`_).
* Refactor GPU to CPU copying for big speedup (PR `#245`_).
* Fix unit test_gpu_zscan (PR `#247`_).
* Update readthedocs config (PR `#252`_).
* xmax typo leading to segfaults (PR `#258`_).
* Modified unit tests to ensure that both cupy install and CUDA device (PR `#228`_).

.. _`#228`: https://github.com/desihub/redrock/pull/228
.. _`#229`: https://github.com/desihub/redrock/pull/229
.. _`#230`: https://github.com/desihub/redrock/pull/230
.. _`#232`: https://github.com/desihub/redrock/pull/232
.. _`#233`: https://github.com/desihub/redrock/pull/233
.. _`#234`: https://github.com/desihub/redrock/pull/234
.. _`#236`: https://github.com/desihub/redrock/pull/236
.. _`#238`: https://github.com/desihub/redrock/pull/238
.. _`#239`: https://github.com/desihub/redrock/pull/239
.. _`#240`: https://github.com/desihub/redrock/pull/240
.. _`#241`: https://github.com/desihub/redrock/pull/241
.. _`#244`: https://github.com/desihub/redrock/pull/244
.. _`#245`: https://github.com/desihub/redrock/pull/245
.. _`#247`: https://github.com/desihub/redrock/pull/247
.. _`#252`: https://github.com/desihub/redrock/pull/252
.. _`#258`: https://github.com/desihub/redrock/pull/258


0.17.9 (2023-12-01)
-------------------

This is a tag of the "opticaldepth" branch used by Allyson Brodzeller
to re-process Iron production z>1.6 QSOs with a new HIZ template
(redrock-templates tag 0.8.1) and updated optical depth coefficients
to match Kamble et al. 2020 (Arxiv: 1904.01110).
Although this tag was made after 0.18.0, it was branched prior to that
tag and includes all of the 0.18.0 PRs except:

* Refactor GPU to CPU copying for big speedup (PR `#245`_).
* Update readthedocs config (PR `#252`_).

This branch will not be merged into main as-is, but the updated coefficients
will be included in a future tag to handle multiple optical depth models
to support templates trained with different models.

0.17.0 (2023-01-12)
-------------------

* Major refactor to expand GPU support; 2x faster on GPUs, 25% faster on CPUs.
  Also fixes support for files with more than 1k input targets
  (PR `#211`_, `#225`_, `#226`_).

.. _`#211`: https://github.com/desihub/redrock/pull/211
.. _`#225`: https://github.com/desihub/redrock/pull/225
.. _`#226`: https://github.com/desihub/redrock/pull/226

0.16.0 (2022-08-08)
-------------------

* Add rrdesi ``if __name__ == "__main__"`` wrapper for multiprocessing
  robustness (PR `#209`_).
* Update GitHub test automation (PR `#210`_).
* Avoid bad fits when ranking zchi2 vs. z minima; fixes redshift pileup
  for new QSO templates at edges of zscan range (PR `#218`_).
* gpu-ify zscan (PR `#204`_).
* Simplify distribution of work to processes  (PR `#207`_).

.. _`#204`: https://github.com/desihub/redrock/pull/204
.. _`#207`: https://github.com/desihub/redrock/pull/207
.. _`#209`: https://github.com/desihub/redrock/pull/209
.. _`#210`: https://github.com/desihub/redrock/pull/210
.. _`#218`: https://github.com/desihub/redrock/pull/218

0.15.4 (2022-02-28)
-------------------

* Add redrock.templates.eval_model convenience routine (PR `#206`_).

.. _`#206`: https://github.com/desihub/redrock/pull/206

0.15.3 (2022-02-11)
-------------------

* Propagate SURVEY and PROGRAM keywords from input files (PR `#203`_).

.. _`#203`: https://github.com/desihub/redrock/pull/203

0.15.2 (2022-01-23)
-------------------

* Propagate spec group keywords from input files (PR `#202`_).

.. _`#202`: https://github.com/desihub/redrock/pull/202

0.15.1 (2022-01-20)
-------------------

* update top hat prior (PR `#199`_).
* add dependency keywords to redrock output (PR `#200`_).
* set zwarn LITTLE_COVERAGE for badamp/badcol (PR `#201`_).

.. _`#199`: https://github.com/desihub/redrock/pull/199
.. _`#200`: https://github.com/desihub/redrock/pull/200
.. _`#201`: https://github.com/desihub/redrock/pull/201

0.15.0 (2021-07-14)
-------------------

Note: Major changes to output formats; requires desispec >= 0.45.0

* Split FIBERMAP into FIBERMAP (coadded) and EXP_FIBERMAP (per-exposure)
  (PR `#196`_).
* Add additional ZWARN bit masking for known bad input data (PR `#196`_).
* Rename zbest -> redrock output, update rrdesi option names (PR `#198`_).

.. _`#196`: https://github.com/desihub/redrock/pull/196
.. _`#198`: https://github.com/desihub/redrock/pull/198

0.14.6 (2021-07-06)
-------------------

* reserve ZWARN bits 16-23 for end-user; redrock will not set these.
* Add tophap prior option (PR `#194`_).
* Switch to github actions for testing (PR `#195`_).

.. _`#194`: https://github.com/desihub/redrock/pull/194
.. _`#195`: https://github.com/desihub/redrock/pull/195

0.14.5 (2021-02-15)
-------------------

* Use temporary files + rename to avoid partially written files with the
  final name in case of timeout (PR `#186`_).

.. _`#186`: https://github.com/desihub/redrock/pull/186

0.14.4 (2020-08-03)
-------------------

* Re-enable ability for templates to specify their redshift range
  (one line update to master).

0.14.3 (2020-04-07)
-------------------

* Allow :func:`redrock.external.boss.read_spectra` to receive a
  string as well as a list of files (PR `#173`_).
* Support coadds that don't have EXPID in fibermap (master update).

.. _`#173`: https://github.com/desihub/redrock/pull/173


0.14.2 (2019-10-17)
-------------------

* Bug fix for specfiles of different sizes (PR `#167`_).
* Fix plotting subset of input spectra (PR `#168`_).
* Add `--no-mpi-abort` option (PR `#170`_)

.. _`#167`: https://github.com/desihub/redrock/pull/167
.. _`#168`: https://github.com/desihub/redrock/pull/168
.. _`#170`: https://github.com/desihub/redrock/pull/170

0.14.1 (2019-08-09)
-------------------

* Minor code cleanup (PRs `#162`_, `#164`_).
* Add `and_mask` option for BOSS (PR `#165`_).

.. _`#162`: https://github.com/desihub/redrock/pull/162
.. _`#164`: https://github.com/desihub/redrock/pull/164
.. _`#165`: https://github.com/desihub/redrock/pull/165

0.14.0 (2018-12-16)
-------------------

* Adds optional cosmic ray rejection during coadds (PR `#156`_).
* No longer requires BRICKNAME (PR `#157`_).
* Fix interactive plotspec window disappearing (PR `#161`_).

.. _`#156`: https://github.com/desihub/redrock/pull/156
.. _`#157`: https://github.com/desihub/redrock/pull/157
.. _`#161`: https://github.com/desihub/redrock/pull/161

0.13.2 (2018-11-07)
-------------------

Version used for 18.11 software release.

* Codacy style recommendations (PR `#155`_).
* Optional redshift prior (PR `#152`_).

.. _`#152`: https://github.com/desihub/redrock/pull/152
.. _`#155`: https://github.com/desihub/redrock/pull/155

0.13.1 (2018-09-26)
-------------------

* Fixed problem with new format of ``make_templates`` (PR `#153`_).
* Update code based on codacy recommendations (PR `#154`_).

.. _`#153`: https://github.com/desihub/redrock/pull/153
.. _`#154`: https://github.com/desihub/redrock/pull/154

0.13.0 (2018-08-31)
-------------------

* Lower galaxy z_min from +0.005 to -0.005 (PR `#136`_).
* Support for simutaneous fits of multiple e/BOSS spPlates (PR `#137`_,
  `#141`_, `#147`_).
* Bug fix when using subset of targetids (PR `#139`_).
* Small interface useability updates (PR `#142`_, `#143`_).
* Fix R normalization cut bug impacting tags 0.12.0 and 0.12.1 (PR `#144`_).
* Fix bug dictionnary results (PR `#145`_).
* Mask sky lines 5577 and 9793.5 (PR `#146`_).
* Standarize ZBEST output format for easier concatenating tables (PR `#149`_).

.. _`#136`: https://github.com/desihub/redrock/pull/136
.. _`#137`: https://github.com/desihub/redrock/pull/137
.. _`#139`: https://github.com/desihub/redrock/pull/139
.. _`#141`: https://github.com/desihub/redrock/pull/141
.. _`#142`: https://github.com/desihub/redrock/pull/142
.. _`#143`: https://github.com/desihub/redrock/pull/143
.. _`#144`: https://github.com/desihub/redrock/pull/144
.. _`#145`: https://github.com/desihub/redrock/pull/145
.. _`#146`: https://github.com/desihub/redrock/pull/146
.. _`#147`: https://github.com/desihub/redrock/pull/147
.. _`#149`: https://github.com/desihub/redrock/pull/149

0.12.1 (2018-07-26)
-------------------

* Update DELTACHI2 column definition to match how it is used in ZWARN flag,
  i.e. excluding other candidates with nearby redshifts (PR `#134`_).

.. _`#134`: https://github.com/desihub/redrock/pull/134

0.12.0 (2018-07-18)
-------------------

* Adds optional archetypes (PR `#119`_).
* Include blank fibers in output with ZWARN NODATA flag (PR `#123`_).
* Include template name in output (PR `#124`_).
* Include template and archetype version numbers in zbest output
  (PR `#126`_, `#128`_, and `#131`_).
* Update travis testing to astropy=2 python=3 (PR `#127`_).
* Increase QSO redshift range to z=6 (PR `#130`_).
* rrplot option for a subset of targetids (PR `#132`_).

.. _`#119`: https://github.com/desihub/redrock/pull/119
.. _`#123`: https://github.com/desihub/redrock/pull/123
.. _`#124`: https://github.com/desihub/redrock/pull/124
.. _`#126`: https://github.com/desihub/redrock/pull/126
.. _`#127`: https://github.com/desihub/redrock/pull/127
.. _`#128`: https://github.com/desihub/redrock/pull/128
.. _`#130`: https://github.com/desihub/redrock/pull/130
.. _`#131`: https://github.com/desihub/redrock/pull/131
.. _`#132`: https://github.com/desihub/redrock/pull/132

0.11.0 (2018-05-10)
-------------------

* Catch LinAlgErrors from bad input data (PR `#109`_).
* Add --nminima option (PR `#113`_).
* Improve spectra reading speed (PR `#114`_).
* hdf5 file locking workaround (PR `#116`_).
* Fix MPI version of LyA transmission correction (PR `#117`_).
* WD DA and DB templates (PR `#118`_).

.. _`#109`: https://github.com/desihub/redrock/pull/109
.. _`#113`: https://github.com/desihub/redrock/pull/113
.. _`#114`: https://github.com/desihub/redrock/pull/114
.. _`#116`: https://github.com/desihub/redrock/pull/116
.. _`#117`: https://github.com/desihub/redrock/pull/117
.. _`#118`: https://github.com/desihub/redrock/pull/118

0.10.1 (2018-03-30)
-------------------

* Default QSO redshift range 0.05-4.0 instead of 0.5-4.0 (PR `#107`_).

.. _`#107`: https://github.com/desihub/redrock/pull/107

0.10.0 (2018-03-29)
-------------------

* Correct QSO template for LyA during zscan (PR `#104`_).

.. _`#104`: https://github.com/desihub/redrock/pull/104

0.9.0 (2018-02-23)
------------------

* ivar=0 for edge pix with integral(resolution)<0.99 (PR `#94`_)
* Restore --ncpu option (PR `#95`_)
* Adds wrap-redrock MPI wrapper script (PR `#97`_)
* Robust to input NaN and Inf (PR `#99`_)
* Adds WD templates (PR `#101`_)

.. _`#94`: https://github.com/desihub/redrock/pull/94
.. _`#95`: https://github.com/desihub/redrock/pull/95
.. _`#97`: https://github.com/desihub/redrock/pull/97
.. _`#99`: https://github.com/desihub/redrock/pull/99
.. _`#101`: https://github.com/desihub/redrock/pull/101

0.8.0 (2018-01-30)
------------------

* Major restructure of MPI and multiprocessing dataflow
  (PR `#67`_, `#73`_, `#76`_).
* Fully support desiInstall and DESI infrastructure generally (PR `#65`_).
* Fix import errors that were preventing RTD builds (PR `#91`_).
* Add seed to template generation; increase number of stars used (PR `#93`_).
* Add rrplot script to be called from ipython (PR `#90`_).

.. _`#65`: https://github.com/desihub/redrock/pull/65
.. _`#67`: https://github.com/desihub/redrock/pull/67
.. _`#73`: https://github.com/desihub/redrock/pull/73
.. _`#76`: https://github.com/desihub/redrock/pull/76
.. _`#90`: https://github.com/desihub/redrock/pull/90
.. _`#91`: https://github.com/desihub/redrock/pull/91
.. _`#93`: https://github.com/desihub/redrock/pull/93


0.7.0 (2017-12-20)
------------------

* no ZWARN SMALL_DELTA_CHI2 between same spectype (PR `#47`_)
* rrdesi --templates can now be folder not just file (PR `#44`_)
* Allow templates to optionally include redshift range (PR `#41`_)
* API CHANGE: redrock.io.read_templates() returns dict not list (PR `#41`_)
* set ivar = 0 where mask != 0 (PR `#42`_)
* Add NUMEXP and NUMTILE to zbest output (PR `#59`_)
* Propagate input fibermap into output zbest (PR `#59`_)

.. _`#47`: https://github.com/desihub/desispec/pull/47
.. _`#44`: https://github.com/desihub/desispec/pull/44
.. _`#41`: https://github.com/desihub/desispec/pull/41
.. _`#42`: https://github.com/desihub/desispec/pull/42
.. _`#59`: https://github.com/desihub/desispec/pull/59

0.6.0 (2017-11-10)
------------------

* adds rrboss to process boss spectra (PR `#37`_)
* refactors multiprocessing parallelism to use less memory (PR `#37`_)

.. _`#37`: https://github.com/desihub/desispec/pull/37

0.5.0 (2017-09-29)
------------------

* adds optional MPI parallelism (PR `#34`_)

.. _`#34`: https://github.com/desihub/desispec/pull/34

0.4.2 (2017-08-14)
------------------

* refactored multiprocessing parallelism to use explicit shared memory (PR `#31`_)

.. _`#31`: https://github.com/desihub/desispec/pull/31

0.4.1 (2017-06-16)
------------------

* add support for new DESI spectra format

0.4 (2017-02-03)
----------------

* add optional truth input to plotspec
* Fix bug when first target is missing a channel of data
* external.desi.read_bricks allow glob for list of brick files
* external.desi.read_bricks read subset of targetids from bricks
* add support for stars and template subtypes
* limit galaxy redshift scan to z<1.7

0.3 (2017-01-23)
----------------

* added this file
* python3 updates
* refactor internal data object wrappers
* fit and store multiple minima in chi2 vs. z
* refactor parallelism
* add option to fit coadd instead of individual spectra
* add plotspec
* experimental: penalize GALAXY template fits with negative [OII] flux

0.2 (2016-03-05)
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* tag for DESI zdc1