===================
desispec Change Log
===================

0.72.0 (unreleased)
-------------------

Changes made for daily operations (daily branch) while Matterhorn was running.
These changes were not used in Matterhorn.

* Fix flat selection when CTE flats come in between calib flats (PR `#2720`_).
* Add test for CTE flats interleaved between lamp flat sequences (PR `#2721`_).

.. _`#2720`: https://github.com/desihub/desispec/pull/2720
.. _`#2721`: https://github.com/desihub/desispec/pull/2721

0.71.5 (2026-06-02)
-------------------

Updated tag for Matterhorn zcatalogs.

* Add uniqpix support to desi_zcatalog v2; allow COADD_FIBERSTATUS=VARIABLE as GOOD_SPEC. (PR `#2762`_).

For daily ops:

* Prioritize 3s/10s CTE flats before science fallback for CTE QA (PR `#2763`_).
* Fix nightqa cterowbyrow plot range (PR `#2764`_).

.. _`#2762`: https://github.com/desihub/desispec/pull/2762
.. _`#2763`: https://github.com/desihub/desispec/pull/2763
.. _`#2764`: https://github.com/desihub/desispec/pull/2764

0.71.4 (2026-05-28)
-------------------

* Update to `desi_resubmit_zpix` bookkeeping for matterhorn (PR `#2759`_).

.. _`#2759`: https://github.com/desihub/desispec/pull/2759

0.71.3 (2026-05-21)
-------------------

Further updates for Matterhorn, tagged before running cross-tile spectra.

Major data organization change:

* Use adaptively-sized "uniqpix" instead of fixed-size healpix for cross tile coadds (PR `#2755`_, `#2758`_).

Other changes

* Fix program-to-efftime in zcatalog (PR `#2746`_).
* Add CCD history script (PR `#2751`_).
* Calculate ``SIGMA_COADD_NORM`` from final recomputed coadd norm (PR `#2753`_).
* Add more TSNR afterburner information to exposure-qa files (PR `#2756`_).

.. _`#2746`: https://github.com/desihub/desispec/pull/2746
.. _`#2751`: https://github.com/desihub/desispec/pull/2751
.. _`#2753`: https://github.com/desihub/desispec/pull/2753
.. _`#2755`: https://github.com/desihub/desispec/pull/2755
.. _`#2756`: https://github.com/desihub/desispec/pull/2756
.. _`#2758`: https://github.com/desihub/desispec/pull/2758


0.71.2 (2026-05-01)
-------------------

* Don't drop first 2 calib zeros if they are needed to get to full 15 required (PR `#2743`_).

.. _`#2743`: https://github.com/desihub/desispec/pull/2743

0.71.1 (2026-04-27)
-------------------

This is the second tag used by Matterhorn.  One change is not backwards
compatible with 0.71.0, impacting exactly which standard stars are selected.

* Don't median-normalize flat-to-psf corr per petal when selecting standards (PR `#2724`_).

Other changes are backwards compatible or otherwise consistent with how
Matterhorn jobs were launched.

* Correct POORPOSITION description (PR `#2719`_).
* use_reservation add biasnight,biaspdark; handle DependencyNeverSatisfied (PR `#2722`_).
* Fix to crossnight camword bug in submitting biasnight (PR `#2731`_).

.. _`#2719`: https://github.com/desihub/desispec/pull/2719
.. _`#2722`: https://github.com/desihub/desispec/pull/2722
.. _`#2724`: https://github.com/desihub/desispec/pull/2724
.. _`#2731`: https://github.com/desihub/desispec/pull/2731

0.71.0 (2026-04-10)
-------------------

First tag used for Matterhorn production.

Major algorithmic changes:

* Rescale individual exposures before coaddition (PR `#2606`_, `#2713`_).
* Update BAD2DFIT mask for better cosmics rejection (PR `#2612`_).
* Adjust the resolution matrix for flux calibration (PR `#2642`_).
* Adjust the cframe resolution matrix for per-fiber heliocentric corrections (PR `#2648`_).
* Fix emlinefit outliers (PR `#2685`_)

Other:

* Set ``$DESI_SPECTRO_ROBUST=True`` for preproc to proceed anyway
  even without dark or bias models (PR `#2577`_).
* Update _find_zeros to also use exptable PROGRAM (PR `#2578`_).
* Set FIBERSTATUS=UNASSIGNED for targets with OBJTYPE != TGT or SKY (PR `#2579`_).
* ``assemble_fibermap`` set OBJTYPE=BAD for non-SKY non-TGT targets (PR `#2580`_).
* Improve robustness of ``desi_compute_psf`` and ``desi_average_psf`` when
  individual bundles fail (PR `#2584`_).
* For zcatalogs, make ``EFFTIME_SPEC`` program-dependent to match tile usage (PR `#2583`_).
* Add ``flagged_fibers.ecsv`` to flag fibers for specific exposures (PR `#2588`_).
* Add ``copy`` argument to Spectra object (PR `#2590`_).
* Apply gains to preprocessed darks (PR `#2591`_).
* Add ``FLAT_TO_PSF_FLUX`` to fibermap (PR `#2597`_).
* Make ``FLAT_TO_PSF_FLUX`` and ``PSF_TO_FIBER_SPECFLUX`` float32 (PR `#2598`_).
* Add detailed control over ordering in zall files (PR `#2568`_).
* Add tile info in tile QA (PR `#2600`_).
* Only include biases that are in the exposure table for making a master bias to avoid corrupted data (PR `#2602`_).
* Darknight date cutoff (PR `#2603`_).
* Add coadd_spectra that doesn't modify input (PR `#2608`_).
* Add unit test for coadd_spectra non-mutation guarantee (PR `#2609`_).
* Dark restart (PR `#2610`_).
* Fix cte expids during job creation (PR `#2614`_).
* Add --kill-on-invalid-dep=yes to sbatch calls (PR `#2617`_).
* Fix preproc_darks_mpi.py ragged array and cleanup some MPI therein (PR `#2619`_).
* Only process biasnight for night in question and include as dependency (PR `#2625`_).
* Save tilenight timing (PR `#2626`_).
* Add regression test for no_darknight=True suppressing surrounding-night biasnight submissions (PR `#2628`_).
* Logic to ignore a badcol if all values are NaN in raw and not in fa. (PR `#2629`_).
* Fix desi_resubmit_queue_failures corner cases (PR `#2630`_).
* Only preproc darks in night_qa based on findfile. (PR `#2631`_).
* make test_preproc thread-safe using tempfile (PR `#2633`_).
* Changes to decrease the sbtach time for biases (PR `#2635`_).
* Replace binary_closing with closing. (PR `#2636`_).
* trace shift spot fitting bugfix plus tests (PR `#2637`_).
* Revert "Changes to decrease the sbtach time for biases" (PR `#2638`_).
* replace .error() by .warning() in annotate_fibermap() (PR `#2640`_).
* Update bias and pdark resource logic (PR `#2643`_).
* first version of copilot instructions (PR `#2646`_).
* read_image options to skip HDUs; use that to save memory for darks (PR `#2651`_).
* turn off --kill-on-invalid-dep=yes (PR `#2658`_).
* Cast yaml dates as int for dark reset logic (PR `#2659`_).
* Fix duplicate HDUs in psf- files (PR `#2662`_).
* Remove Spectrum1D import in test (PR `#2665`_).
* fix DATE-OBS-END str vs. int; add tests (PR `#2666`_).
* Make test_dateobs_begin_end_type_handling_sm1r hermetic by unsetting DESI_SPECTRO_DARK (PR `#2667`_).
* Fix write_frame duplicating FIBERMAP HDU when fibermap kwarg is supplied (PR `#2671`_).
* Fix misplaced bracket causing TypeError when coadding multiple spectra files (PR `#2673`_).
* Add unit test for resolution matrix update in apply_flux_calibration (PR `#2675`_).
* Fix inspect_dark BADCOLUMN vs. BADFIBER typo (PR `#2679`_).
* Reduce parallelism due to memory constraints for ccdcalib darknight (PR `#2688`_).
* Update desi_tile_vi to automatically validate backup tiles (PR `#2693`_)
* Jobs that depend on unsubmitted jobs shouldn't be submitted (PR `#2668`_).
* Add regression tests for submit_batch_script dependency failure and sbatch failure handling (PR `#2676`_).
* Update flagged_fibers  (PR `#2678`_).
* Update link dependency logic (PR `#2680`_).
* Add regression tests for linkcal cross-night dependency logic (PR `#2681`_).
* Fix stale docstring defaults in `emlines_gaussfit` (PR `#2686`_).
* Add synthetic unit tests for emlinefit flux normalization and CHI2 calculation (PR `#2687`_).
* freeze iers before any heliocentric corrections (PR `#2690`_).
* spec/coadd keys in both HDU 0 and FIBERMAP (PR `#2691`_).
* Fix so that biasnight is now dependent on linkcal (PR `#2695`_).
* Fix desi_submit_prod and desi_proc_night logic bug (PR `#2696`_).
* Improved outlier handling for sky-PCA (PR `#2698`_).
* Submit future biaspdarks even if current one exists (PR `#2699`_).
* Add regression tests for submit_future_biaspdarks path in proc_night (PR `#2700`_).
* avoid divide by zero in ff gradient calc (PR `#2704`_).
* Change default min dark exposures from 6 to 5 (PR `#2705`_).
* fix tileqa crash for non-gzipped fiberassign file (PR `#2710`_).
* Add outlier masking script for the skycorr PCA templates (PR `#2712`_).
* Propagate badfiber bit for unphysical COADD_NORM (PR `#2713`_).
* Allow psfnight to skip over bundles that are purposefully skipped (PR `#2714`_).
* Fix submission bug for linked biasnight jobs (PR `#2716`_).

.. _`#2568`: https://github.com/desihub/desispec/pull/2568
.. _`#2577`: https://github.com/desihub/desispec/pull/2577
.. _`#2578`: https://github.com/desihub/desispec/pull/2578
.. _`#2579`: https://github.com/desihub/desispec/pull/2579
.. _`#2580`: https://github.com/desihub/desispec/pull/2580
.. _`#2583`: https://github.com/desihub/desispec/pull/2583
.. _`#2584`: https://github.com/desihub/desispec/pull/2584
.. _`#2588`: https://github.com/desihub/desispec/pull/2588
.. _`#2590`: https://github.com/desihub/desispec/pull/2590
.. _`#2591`: https://github.com/desihub/desispec/pull/2591
.. _`#2597`: https://github.com/desihub/desispec/pull/2597
.. _`#2598`: https://github.com/desihub/desispec/pull/2598
.. _`#2600`: https://github.com/desihub/desispec/pull/2600
.. _`#2602`: https://github.com/desihub/desispec/pull/2602
.. _`#2603`: https://github.com/desihub/desispec/pull/2603
.. _`#2606`: https://github.com/desihub/desispec/pull/2606
.. _`#2608`: https://github.com/desihub/desispec/pull/2608
.. _`#2609`: https://github.com/desihub/desispec/pull/2609
.. _`#2610`: https://github.com/desihub/desispec/pull/2610
.. _`#2612`: https://github.com/desihub/desispec/pull/2612
.. _`#2614`: https://github.com/desihub/desispec/pull/2614
.. _`#2617`: https://github.com/desihub/desispec/pull/2617
.. _`#2619`: https://github.com/desihub/desispec/pull/2619
.. _`#2625`: https://github.com/desihub/desispec/pull/2625
.. _`#2626`: https://github.com/desihub/desispec/pull/2626
.. _`#2628`: https://github.com/desihub/desispec/pull/2628
.. _`#2629`: https://github.com/desihub/desispec/pull/2629
.. _`#2630`: https://github.com/desihub/desispec/pull/2630
.. _`#2631`: https://github.com/desihub/desispec/pull/2631
.. _`#2633`: https://github.com/desihub/desispec/pull/2633
.. _`#2635`: https://github.com/desihub/desispec/pull/2635
.. _`#2636`: https://github.com/desihub/desispec/pull/2636
.. _`#2637`: https://github.com/desihub/desispec/pull/2637
.. _`#2638`: https://github.com/desihub/desispec/pull/2638
.. _`#2640`: https://github.com/desihub/desispec/pull/2640
.. _`#2642`: https://github.com/desihub/desispec/pull/2642
.. _`#2643`: https://github.com/desihub/desispec/pull/2643
.. _`#2646`: https://github.com/desihub/desispec/pull/2646
.. _`#2648`: https://github.com/desihub/desispec/pull/2648
.. _`#2651`: https://github.com/desihub/desispec/pull/2651
.. _`#2658`: https://github.com/desihub/desispec/pull/2658
.. _`#2659`: https://github.com/desihub/desispec/pull/2659
.. _`#2662`: https://github.com/desihub/desispec/pull/2662
.. _`#2665`: https://github.com/desihub/desispec/pull/2665
.. _`#2666`: https://github.com/desihub/desispec/pull/2666
.. _`#2667`: https://github.com/desihub/desispec/pull/2667
.. _`#2671`: https://github.com/desihub/desispec/pull/2671
.. _`#2673`: https://github.com/desihub/desispec/pull/2673
.. _`#2675`: https://github.com/desihub/desispec/pull/2675
.. _`#2679`: https://github.com/desihub/desispec/pull/2679
.. _`#2685`: https://github.com/desihub/desispec/pull/2685
.. _`#2688`: https://github.com/desihub/desispec/pull/2688
.. _`#2693`: https://github.com/desihub/desispec/pull/2693
.. _`#2668`: https://github.com/desihub/desispec/pull/2668
.. _`#2676`: https://github.com/desihub/desispec/pull/2676
.. _`#2678`: https://github.com/desihub/desispec/pull/2678
.. _`#2680`: https://github.com/desihub/desispec/pull/2680
.. _`#2681`: https://github.com/desihub/desispec/pull/2681
.. _`#2686`: https://github.com/desihub/desispec/pull/2686
.. _`#2687`: https://github.com/desihub/desispec/pull/2687
.. _`#2690`: https://github.com/desihub/desispec/pull/2690
.. _`#2691`: https://github.com/desihub/desispec/pull/2691
.. _`#2695`: https://github.com/desihub/desispec/pull/2695
.. _`#2696`: https://github.com/desihub/desispec/pull/2696
.. _`#2698`: https://github.com/desihub/desispec/pull/2698
.. _`#2699`: https://github.com/desihub/desispec/pull/2699
.. _`#2700`: https://github.com/desihub/desispec/pull/2700
.. _`#2704`: https://github.com/desihub/desispec/pull/2704
.. _`#2705`: https://github.com/desihub/desispec/pull/2705
.. _`#2710`: https://github.com/desihub/desispec/pull/2710
.. _`#2712`: https://github.com/desihub/desispec/pull/2712
.. _`#2713`: https://github.com/desihub/desispec/pull/2713
.. _`#2714`: https://github.com/desihub/desispec/pull/2714
.. _`#2716`: https://github.com/desihub/desispec/pull/2716

0.70.0 (2025-12-04)
-------------------

Algorithms / core features:

* Improve calibration uncertainty (PR `#2496`_).
* Add PSF correction to ``RCALIBFRAC`` (PR `#2484`_).
* Use custom fiber cross talk correction (PR `#2482`_).
* Changes to ``desi_compute_pixmask`` (PR `#2469`_).
* New zcatalog v2 format, splitting sets of columns into separate files (PR `#2396`_).
* Fix coadd_cameras for model coaddition and duplicate TARGETID handling (PR `#2488`_).
* Update master dark script 2025 (PR `#2495`_).
* Fix ``read_spectra`` indexing error (PR `#2508`_).
* Magnitude calculation by photons not flux (PR `#2515`_).
* Adjust cosmics parameters for red ITL CCDs (PR `#2557`_).
* New ``plot_preproc`` script to plot specific tile/fiber/wavelength
  thumbnails (PR `#2570`_).
* Add ``desi_compute_psf --mpi`` option for MPI parallelism from the
  command line (PR `#2576`_).

Pipeline:

* Add nightly dark processing (PR `#2531`_, `#2527`_).
* Allow 1200s dark for bad col selection (PR `#2499`_).
* Nightqa: handle bright1b/dark1b (PR `#2490`_).
* ``desi_tile_vi``: enable main/dark1b tiles (PR `#2487`_).
* Tile qa plot: update reference ``n(z)`` to handle ``DARK1B`` (PR `#2485`_).
* Update ``nightly_bias.py`` to use 50 zeros by default (again) (PR `#2478`_).
* Revert PR `#2475`_ (PR `#2477`_).
* Update ``nightly_bias.py`` to use 50 zeros by default (PR `#2476`_).
* Nightqa v29 (PR `#2475`_).
* Have ``desi_compute_nightly_bias`` gracefully exit if default bias is missing (PR `#2468`_).
* Copy purged redux files to attic (PR `#2464`_).
* make_tile_qa_plot(): adapt n(z) xlim for bright1b (PR `#2503`_).
* ``desi_tile_vi``: enable main/bright1b tiles (PR `#2509`_).
* Goaltype and program in exposures file for dark1b/bright1b tiles (PR `#2511`_).
* ``desi_archive_tilenight`` --survey and --program filters (PR `#2512`_, `#2513`_).
* Support nightlybias and darks without a calib config (PR `#2518`_).
* emline use tempfile for output (PR `#2519`_).
* Fix readonly write when no sky fibers (PR `#2523`_).
* Purge dark_preproc in desi_purge_night (PR `#2553`_).
* Make compute_dark crashes more explicit (PR `#2554`_).
* Require minimum 6 darks instead of 4 for nightly dark (PR `#2575`_).

Cleanup:

* Improve NumPy 2 support (PR `#2502`_).
* Can coadd spectra with no resolution data (PR `#2492`_).
* :func:`scipy.linalg.eigh` deprecated ``turbo`` option (PR `#2474`_).
* NumPy 2 support, first pass (PR `#2471`_).
* :func:`sys.exit` in script for ``nightly_bias`` not function (PR `#2470`_).
* Check whether the CCD is read to the left or to the right (PR `#2467`_).
* Added support to return redrock models in ``read_spectra`` (PR `#2466`_).
* New DESI calibration configuration editor (PR `#2465`_).
* ``DESI_COMPRESSION`` (PR `#2462`_).
* ``IN_COADD_B/R/Z`` cols and new FA keywords when stacking spectra (PR `#2461`_).
* Avoid warning about unit style (PR `#2460`_).
* Fix ``read_frame_as_spectra`` (PR `#2459`_).
* Log error when arc/flat set are rejected due to large time difference (PR `#2457`_).
* Save bias filename in header (PR `#2525`_).
* Fix healpix job frame bookkeeping (PR `#2530`_).
* Technical debt cleanup, addressing warnings (PR `#2538`_).
* Use readonly path in nightqa unless actually generating new file (PR `#2540`_).
* Make readonly call in tsnr skymag calc (PR `#2541`_).
* Dark spanning NIGHT rollover (PR `#2543`_).
* Only Raise Error if CalibFinder Asked for Bias or Dark it can't Find (PR `#2552`_).
* Additional logging of desi_compute_psf commands (PR `#2555`_).
* Write dark via temp file (PR `#2556`_).
* Remove pin on pip version (PR `#2562`_).
* Fix zall blank string bug (PR `#2566`_).
* Add pyproject.toml and update top-level files (PR `#2569`_).
* Fix bug in zall zcatlog PROGRAM and SURVEY header keywords (PR `#2572`_).
* Installation and testing updates in prep for PyPI upload (PR `#2573`_).

.. _`#2531`: https://github.com/desihub/desispec/pull/2531
.. _`#2502`: https://github.com/desihub/desispec/pull/2502
.. _`#2499`: https://github.com/desihub/desispec/pull/2499
.. _`#2496`: https://github.com/desihub/desispec/pull/2496
.. _`#2492`: https://github.com/desihub/desispec/pull/2492
.. _`#2490`: https://github.com/desihub/desispec/pull/2490
.. _`#2487`: https://github.com/desihub/desispec/pull/2487
.. _`#2485`: https://github.com/desihub/desispec/pull/2485
.. _`#2484`: https://github.com/desihub/desispec/pull/2484
.. _`#2482`: https://github.com/desihub/desispec/pull/2482
.. _`#2478`: https://github.com/desihub/desispec/pull/2478
.. _`#2477`: https://github.com/desihub/desispec/pull/2477
.. _`#2476`: https://github.com/desihub/desispec/pull/2476
.. _`#2475`: https://github.com/desihub/desispec/pull/2475
.. _`#2474`: https://github.com/desihub/desispec/pull/2474
.. _`#2471`: https://github.com/desihub/desispec/pull/2471
.. _`#2470`: https://github.com/desihub/desispec/pull/2470
.. _`#2469`: https://github.com/desihub/desispec/pull/2469
.. _`#2468`: https://github.com/desihub/desispec/pull/2468
.. _`#2467`: https://github.com/desihub/desispec/pull/2467
.. _`#2466`: https://github.com/desihub/desispec/pull/2466
.. _`#2465`: https://github.com/desihub/desispec/pull/2465
.. _`#2464`: https://github.com/desihub/desispec/pull/2464
.. _`#2462`: https://github.com/desihub/desispec/pull/2462
.. _`#2461`: https://github.com/desihub/desispec/pull/2461
.. _`#2460`: https://github.com/desihub/desispec/pull/2460
.. _`#2459`: https://github.com/desihub/desispec/pull/2459
.. _`#2457`: https://github.com/desihub/desispec/pull/2457
.. _`#2396`: https://github.com/desihub/desispec/pull/2396
.. _`#2488`: https://github.com/desihub/desispec/pull/2488
.. _`#2495`: https://github.com/desihub/desispec/pull/2495
.. _`#2503`: https://github.com/desihub/desispec/pull/2503
.. _`#2508`: https://github.com/desihub/desispec/pull/2508
.. _`#2509`: https://github.com/desihub/desispec/pull/2509
.. _`#2511`: https://github.com/desihub/desispec/pull/2511
.. _`#2512`: https://github.com/desihub/desispec/pull/2512
.. _`#2513`: https://github.com/desihub/desispec/pull/2513
.. _`#2515`: https://github.com/desihub/desispec/pull/2515
.. _`#2518`: https://github.com/desihub/desispec/pull/2518
.. _`#2519`: https://github.com/desihub/desispec/pull/2519
.. _`#2523`: https://github.com/desihub/desispec/pull/2523
.. _`#2525`: https://github.com/desihub/desispec/pull/2525
.. _`#2527`: https://github.com/desihub/desispec/pull/2527
.. _`#2530`: https://github.com/desihub/desispec/pull/2530
.. _`#2538`: https://github.com/desihub/desispec/pull/2538
.. _`#2540`: https://github.com/desihub/desispec/pull/2540
.. _`#2541`: https://github.com/desihub/desispec/pull/2541
.. _`#2543`: https://github.com/desihub/desispec/pull/2543
.. _`#2552`: https://github.com/desihub/desispec/pull/2552
.. _`#2553`: https://github.com/desihub/desispec/pull/2553
.. _`#2554`: https://github.com/desihub/desispec/pull/2554
.. _`#2555`: https://github.com/desihub/desispec/pull/2555
.. _`#2556`: https://github.com/desihub/desispec/pull/2556
.. _`#2557`: https://github.com/desihub/desispec/pull/2557
.. _`#2562`: https://github.com/desihub/desispec/pull/2562
.. _`#2566`: https://github.com/desihub/desispec/pull/2566
.. _`#2569`: https://github.com/desihub/desispec/pull/2569
.. _`#2570`: https://github.com/desihub/desispec/pull/2570
.. _`#2572`: https://github.com/desihub/desispec/pull/2572
.. _`#2573`: https://github.com/desihub/desispec/pull/2573
.. _`#2575`: https://github.com/desihub/desispec/pull/2575
.. _`#2576`: https://github.com/desihub/desispec/pull/2576


0.69.0 (2025-03-14)
-------------------

Algorithms:

* Fix bug in fiber aperature correction impacting ivar [PR `#2452`_]
* Fix fiber aperture correction: normalization and sky fibers [PR `#2454`_]
* Add option to select good overscan region in preproc [PR `#2438`_]
* Trace shifts accomodate large offsets [PRs `#2440`_. `#2444`_, `#2386`_]
* Fluxcalib variance fix (PR `#2422`_).

Pipeline:

* Allow ``desi_proc_tilenight`` to submit new redshift jobs even if
  tilenight exists [PR `#2441`_]
* Resolve unknown statuses in the dashboard [PR `#2442`_]
* Fix tsnr afterburner bug causing crash on nights with no good data [PR `#2447`_]
* Allow user to specify exposures or tiles to resubmit [PR `#2450`_]
* better error message when updating $DESI_SPECTRO_DARK (PR `#2404`_).
* allow fallback to darks/biases in DESI_SPECTRO_CALIB if running ccdcalib (PR `#2405`_).
* Add a new wrapper to create all of the zcatalogs with a single command (PR `#2410`_).
* Resubmit all jobs in daily twice before giving up in desi_proc_night (PR `#2416`_).
* Add desi_find_file (PR `#2417`_).
* Update nightqa multiprocessing and add new options for skipping some steps (PR `#2418`_).
* Updated wrap_rrdesi to fix multiple use cases. (PR `#2429`_).
* Remove future night redshifts when running purge night (PR `#2430`_).
* Add option to not resub failed exposures in proc_night (PR `#2435`_).

Cleanup:

* Fix installation when using desiutil/3.5.0, dropping support of
  `python setup.py test` as a side-effect [PR `#2437`_]
* Prevent error when read_spectra sees unexpected extension [PR `#2339`_]
* Update readthedocs configuration [PR `#2446`_]
* ``$DESI_SPECTRO_REDUX`` default to ``$DESI_ROOT/spectro/redux`` for
  ``desispec.io.findfile`` [PR `#2448`_]
* improve top-level import speed with deferred imports (PR `#2394`_).
* save the trace shift offsets in the psf file (PR `#2411`_).
* Fix zcatalog columns when reading from many epochs of redshift catalog types (PR `#2415`_).
* Improve desi_purge_tilenight removal of ancillary information (PR `#2424`_).
* Remove unused code and expand unit tests (PR `#2425`_).
* Update to new output from fit_trace_shifts. (PR `#2426`_).
* Fix the traceshift undefined variable bug (PR `#2428`_).

.. _`#2437`: https://github.com/desihub/desispec/pull/2437
.. _`#2438`: https://github.com/desihub/desispec/pull/2438
.. _`#2439`: https://github.com/desihub/desispec/pull/2439
.. _`#2440`: https://github.com/desihub/desispec/pull/2440
.. _`#2441`: https://github.com/desihub/desispec/pull/2441
.. _`#2442`: https://github.com/desihub/desispec/pull/2442
.. _`#2444`: https://github.com/desihub/desispec/pull/2444
.. _`#2446`: https://github.com/desihub/desispec/pull/2446
.. _`#2447`: https://github.com/desihub/desispec/pull/2447
.. _`#2448`: https://github.com/desihub/desispec/pull/2448
.. _`#2450`: https://github.com/desihub/desispec/pull/2450
.. _`#2452`: https://github.com/desihub/desispec/pull/2452
.. _`#2454`: https://github.com/desihub/desispec/pull/2454
.. _`#2386`: https://github.com/desihub/desispec/pull/2386
.. _`#2394`: https://github.com/desihub/desispec/pull/2394
.. _`#2404`: https://github.com/desihub/desispec/pull/2404
.. _`#2405`: https://github.com/desihub/desispec/pull/2405
.. _`#2410`: https://github.com/desihub/desispec/pull/2410
.. _`#2411`: https://github.com/desihub/desispec/pull/2411
.. _`#2415`: https://github.com/desihub/desispec/pull/2415
.. _`#2416`: https://github.com/desihub/desispec/pull/2416
.. _`#2417`: https://github.com/desihub/desispec/pull/2417
.. _`#2418`: https://github.com/desihub/desispec/pull/2418
.. _`#2422`: https://github.com/desihub/desispec/pull/2422
.. _`#2424`: https://github.com/desihub/desispec/pull/2424
.. _`#2425`: https://github.com/desihub/desispec/pull/2425
.. _`#2426`: https://github.com/desihub/desispec/pull/2426
.. _`#2428`: https://github.com/desihub/desispec/pull/2428
.. _`#2429`: https://github.com/desihub/desispec/pull/2429
.. _`#2430`: https://github.com/desihub/desispec/pull/2430
.. _`#2435`: https://github.com/desihub/desispec/pull/2435


0.68.1 (2024-11-08)
-------------------

Used for rerunning the QuasarNet afterburner on Loa. Compatible with
0.68.0 tag for files that succeeded with that tag.

* Fix QuasarNet afterburner indexing bug when all input spectra are masked
  (PR `#2409`_).

.. _`#2409`: https://github.com/desihub/desispec/pull/2409

0.68.0 (2024-11-07)
-------------------

Used for rerunning the QuasarNet afterburner on Loa.

* Allow `desi_proc_night` to restart midway in calibrations (PR `#2392`_).
* Remove E(B-V) factor in backup tile EFFTIME calculations (PR `#2395`_, `#2406`_).
* Fix undefined variables reported by static checker (PR `#2400`_).
* QuasarNet afterburner runs LOZ and HIZ templates together;
  Add input provenance to output files including $QN_MODEL_FILE (PR `#2402`_).
* Use slurm job status to color and inform processing dashboards (PR `#2403`_).
* Update QuasarNet afterburner outputs - add columns, don't run SKY fibers
  (PR `#2407`_).
* No E(B-V) for effective exposure times of backup program (PR `#2370`_).

.. _`#2370`: https://github.com/desihub/desispec/pull/2370
.. _`#2392`: https://github.com/desihub/desispec/pull/2392
.. _`#2395`: https://github.com/desihub/desispec/pull/2395
.. _`#2400`: https://github.com/desihub/desispec/pull/2400
.. _`#2402`: https://github.com/desihub/desispec/pull/2402
.. _`#2403`: https://github.com/desihub/desispec/pull/2403
.. _`#2406`: https://github.com/desihub/desispec/pull/2406
.. _`#2407`: https://github.com/desihub/desispec/pull/2407

0.67.0 (2024-10-11)
-------------------

Used for Loa production.

Major algorithmic change to coadds

* Fix coaddition of Resolution matrices and identification of cosmics
  in coadds (PR `#2377`).

Other

* Fix indexing bug with backup EFFTIME (PR `#2365`_).
* Add "UPDATED" timestamp column to tiles file (PR `#2373`_).
* Support reading old zbest files (now redrock) (PR `#2374`_).
* Add script to update processing tabel column layout (PR `#2376`_).
* zproc runs coadd_spectra instead of group_spectra if spectra file already
  exists (PR `#2383`_).
* Fix column incompatibility in :func:`desispec.specstatus.update_specstatus`
  (PR `#2384`_).
* Add desi_update_proctable_status script and standardize dry-run levels
  (PR `#2385`_).
* Enable zproc.main to be called from other scripts (PR `#2391`_).
* Improvements to Workflow Queue Tools (PR `#2351`_).

.. _`#2365`: https://github.com/desihub/desispec/pull/2365
.. _`#2373`: https://github.com/desihub/desispec/pull/2373
.. _`#2374`: https://github.com/desihub/desispec/pull/2374
.. _`#2376`: https://github.com/desihub/desispec/pull/2376
.. _`#2377`: https://github.com/desihub/desispec/pull/2377
.. _`#2383`: https://github.com/desihub/desispec/pull/2383
.. _`#2384`: https://github.com/desihub/desispec/pull/2384
.. _`#2385`: https://github.com/desihub/desispec/pull/2385
.. _`#2391`: https://github.com/desihub/desispec/pull/2391
.. _`#2351`: https://github.com/desihub/desispec/pull/2351

0.66.3 (2024-09-13)
-------------------

Final tag used for Kibo.

* nightqa fixes for old nights with earlier formats (PR `#2361`_).
* fix missing zall TSNR2 columns (PR `#2368`_).

.. _`#2361`: https://github.com/desihub/desispec/pull/2361
.. _`#2368`: https://github.com/desihub/desispec/pull/2368

0.66.2 (2024-08-27)
-------------------

* Add desi_use_reservation script (PR `#2346`_).
* Improve workflow for resubmitted Kibo jobs (PR `#2348`_)

.. _`#2346`: https://github.com/desihub/desispec/pull/2346
.. _`#2348`: https://github.com/desihub/desispec/pull/2348

0.66.1 (2024-08-26)
-------------------

* Fix ztile tile-qa dependency checking (PR `#2344`_).

.. _`#2344`: https://github.com/desihub/desispec/pull/2344

0.66.0 (2024-08-23)
-------------------

First tag used for Kibo/Y3 run.

* Update TPCORR parameter creation code (PR `#2318`_).
* Minor changes to desi_compute_dark_nonlinear (PR `#2326`_).
* Fix parsing of old daily proctables (PR `#2327`_).
* Script for fitting large trace shifts (PR `#2334`_).
* Work around NaNs in GFA pipeline inputs (PR `#2336`_).
* Fix usage of FIBERSTATUS VARIABLETHRU bit (PR `#2337`_).
* Fix pertile bug and remove deprecated desi_run_night script (PR `#2339`_).
* cross-tile spectra stacking header cleanup (PR `#2340`_).
* Fix TSNR2 for masked spectra and targets with large positioning offsets
  (PR `#2341`_).

.. _`#2318`: https://github.com/desihub/desispec/pull/2318
.. _`#2326`: https://github.com/desihub/desispec/pull/2326
.. _`#2327`: https://github.com/desihub/desispec/pull/2327
.. _`#2334`: https://github.com/desihub/desispec/pull/2334
.. _`#2336`: https://github.com/desihub/desispec/pull/2336
.. _`#2337`: https://github.com/desihub/desispec/pull/2337
.. _`#2339`: https://github.com/desihub/desispec/pull/2339
.. _`#2340`: https://github.com/desihub/desispec/pull/2340
.. _`#2341`: https://github.com/desihub/desispec/pull/2341

0.65.0 (2024-08-16)
-------------------

* plot_fiber_traces --fibers allow true fiber numbers, not just 0-499 (PR `#2289`_).
* optionally parallelize group_spectra (PR `#2291`_).
* Rerun Redrock with dynamic priors based on QN redshift (PR `#2298`_).
* healpix grouping memory and I/O efficiency improvements (PR `#2290`_).
* Eliminate hard-coded paths to find fiberassign and surveyops files.
  Obtain the path to fiberassign files with :func:`~desispec.io.meta.findfile`,
  which will use :envvar:`FIBER_ASSIGN_DIR`. Use :envvar:`DESI_SURVEYOPS`
  to find surveyops files (PR `#2294`_).
* add desi_spcalib_history to print history of changes in configurations in
  desi_spectro_calib yaml files (PR `#2296`_).
* desi_group_spectra header propagation cleanup (PR `#2302`_).
* zproc requires exposure-qa files for tileqa step (PR `#2306`_).
* Re-add support for custom tile groups like 1x_depth (PR `#2309`_)
* Don't set envs in desispec.module that are now set in desimodules
  (PR `#2310`_).
* New FIBERSTATUS NEARCHARGETRAP and VARIABLETHRU set in
  desispec.io.fibermap.assemble_fibermap based on content
  of DESI_SPECTRO_CALIB yaml files (PR `#2313`_).
* Use read noise estimated per CCD row for some amplifiers (PR `#2314`_).
* Allow certain old redrock files in daily reductions to be read (PR `#2317`_).
* Fix assemble_fibermap and unit tests for old data without dark models
  (PR `#2319`_).
* merge_psf option to not include input psf for sims (PR `#2320`_).
* Add cross-night dependency tracking for cumulative ztile jobs (PR `#2321`_).
* Modernize submit_prod (PR `#2322`_).
* FIBERSTATUS VARIABLETHRU bad for sky and stdstars (PR `#2323`_).
* faflavor2program for special tiles: fix other to bright or dark (PR `#2325`_).
* cleanup redirected stdout crash before re-redirecting (PR `#2311`_).
* Night_qa: introduce new ctedet row-by-row diagnosis plot (PR `#2312`_).

.. _`#2289`: https://github.com/desihub/desispec/pull/2289
.. _`#2291`: https://github.com/desihub/desispec/pull/2291
.. _`#2298`: https://github.com/desihub/desispec/pull/2298
.. _`#2290`: https://github.com/desihub/desispec/pull/2290
.. _`#2294`: https://github.com/desihub/desispec/pull/2294
.. _`#2296`: https://github.com/desihub/desispec/pull/2296
.. _`#2302`: https://github.com/desihub/desispec/pull/2302
.. _`#2306`: https://github.com/desihub/desispec/pull/2306
.. _`#2309`: https://github.com/desihub/desispec/pull/2309
.. _`#2310`: https://github.com/desihub/desispec/pull/2310
.. _`#2313`: https://github.com/desihub/desispec/pull/2313
.. _`#2314`: https://github.com/desihub/desispec/pull/2314
.. _`#2317`: https://github.com/desihub/desispec/pull/2317
.. _`#2319`: https://github.com/desihub/desispec/pull/2319
.. _`#2320`: https://github.com/desihub/desispec/pull/2320
.. _`#2321`: https://github.com/desihub/desispec/pull/2321
.. _`#2322`: https://github.com/desihub/desispec/pull/2322
.. _`#2323`: https://github.com/desihub/desispec/pull/2323
.. _`#2325`: https://github.com/desihub/desispec/pull/2325
.. _`#2311`: https://github.com/desihub/desispec/pull/2311
.. _`#2312`: https://github.com/desihub/desispec/pull/2312


0.64.0 (2024-07-01)
-------------------

0.64.x and beyond reserved for post-Jura changes.

* Refactor read_gfa_function to support gfa_proc writing main-thruNIGHT
  files instead of sv3-thruNIGHT files (PR `#2252`_).
* night_qa use temporary files for outputs (PR `#2273`_).
* Adapt desi_compute_gain to 2-amp mode (PR `#2274`_).
* Revert QN_MODEL_FILE to old weights (PR `#2280`_).
* Add cross-night information to zdashboard (PR `#2285`_).

.. _`#2252`: https://github.com/desihub/desispec/pull/2252
.. _`#2273`: https://github.com/desihub/desispec/pull/2273
.. _`#2274`: https://github.com/desihub/desispec/pull/2274
.. _`#2280`: https://github.com/desihub/desispec/pull/2280
.. _`#2285`: https://github.com/desihub/desispec/pull/2285

0.63.7 (2024-07-01)
-------------------

0.63.x tags reserved for Jura prods, based off of "jura" branch.

* Parallelize zpix check (PR `#2275`_).
* Fix desi_assemble_tilepix for Jura (PR `#2284`_)

.. _`#2275`: https://github.com/desihub/desispec/pull/2275
.. _`#2284`: https://github.com/desihub/desispec/pull/2284

0.63.6 (2024-05-30)
-------------------

* Fix healpix=0 keyword propagation bug (PR `#2271`_).

.. _`#2271`: https://github.com/desihub/desispec/pull/2271

0.63.5 (2024-04-28)
-------------------

Additional features for Jura healpix redshifts.

* I/O optimizations for creating exposures and tiles files (PR `#2265`_).
* Add ``desi_healpix_redshifts --dry-run-level N`` option (PR `#2266`_).

.. _`#2265`: https://github.com/desihub/desispec/pull/2265
.. _`#2266`: https://github.com/desihub/desispec/pull/2266

0.63.4 (2024-05-20)
-------------------

Bugfixes for Jura.

* Dashboard bugfix (PR `#2259`_, followup to `#2258`_).
* Bugfixes for resubmitting single tiles on partially processed nights
  (PR `#2261`_).

.. _`#2259`: https://github.com/desihub/desispec/pull/2259
.. _`#2261`: https://github.com/desihub/desispec/pull/2261

0.63.3 (2024-05-17)
-------------------

Bugfixes for Jura.

* Support linkcal overrides for subset of cameras (PR `#2257`_).
* Processing dashboard fix for nights with badamps (PR `#2258`_).

.. _`#2257`: https://github.com/desihub/desispec/pull/2257
.. _`#2258`: https://github.com/desihub/desispec/pull/2258

0.63.2 (2024-05-16)
-------------------

Bugfixes for Jura.

* Update desispec.module for post-Jura desi_spectro_dark/v2405 (Jura env
  retains v2209) (PR `#2245`_).
* select_calib_darks picks first dark with most cameras (PR `#2253`_).
* Only select CTE in proc_night if a good 120s flat exists (PR `#2254`_)

.. _`#2245`: https://github.com/desihub/desispec/pull/2245
.. _`#2253`: https://github.com/desihub/desispec/pull/2253
.. _`#2254`: https://github.com/desihub/desispec/pull/2254

0.63.1 (2024-05-10)
-------------------

Used for Jura.

* Change ordering of ``DESINAME`` computation in :func:`~desispec.io.fibermap.assemble_fibermap`
  to after fixing NaN RA/Dec (PR `#2239`_).
* Adjust job timing for Jura run (PR `#2242`_).

.. _`#2239`: https://github.com/desihub/desispec/pull/2239
.. _`#2242`: https://github.com/desihub/desispec/pull/2242

0.63.0 (2024-05-03)
-------------------

Used for Jura. Requires QuasarNP >=2.x and Redrock >=20.x

* PSF with bad amp (PR `#2217`_).
* Allow different CTE functions for different nights / cameras. (PR `#2221`_).
* Remove redundant assemble_fibermap script (PR `#2222`_).
* Enable qproc on obstype="other" for tests (PR `#2223`_).
* Optionally gather Tractor phot from just north or south (PR `#2224`_).
* Add rrdesi --model option to pre-generate model files (PR `#2226`_).
* Reduce submission time with lower sleep and slurm state caching (PR `#2228`_).
* New CCD pixmask generation algorithm (PR `#2229`_).
* Use new QuasarNET model trained on DESI data (PR `#2230`_).
* Update QuasarNET afterburner to use new redrock template structure
  (PR `#2232`_).
* Fix badamp processing (PR `#2233`_).
* Only count bad readnoise on amps not already flagged as bad (PR `#2234`_).
* Add reservation parsing for CPUs vs. GPUs (PR `#2235`_).
* Move nightlyflat to gpu job (PR `#2236`_).

.. _`#2217`: https://github.com/desihub/desispec/pull/2217
.. _`#2221`: https://github.com/desihub/desispec/pull/2221
.. _`#2222`: https://github.com/desihub/desispec/pull/2222
.. _`#2223`: https://github.com/desihub/desispec/pull/2223
.. _`#2224`: https://github.com/desihub/desispec/pull/2224
.. _`#2226`: https://github.com/desihub/desispec/pull/2226
.. _`#2228`: https://github.com/desihub/desispec/pull/2228
.. _`#2229`: https://github.com/desihub/desispec/pull/2229
.. _`#2230`: https://github.com/desihub/desispec/pull/2230
.. _`#2232`: https://github.com/desihub/desispec/pull/2232
.. _`#2233`: https://github.com/desihub/desispec/pull/2233
.. _`#2234`: https://github.com/desihub/desispec/pull/2234
.. _`#2235`: https://github.com/desihub/desispec/pull/2235
.. _`#2236`: https://github.com/desihub/desispec/pull/2236

0.62.0 (2024-04-24)
-------------------

Major API/functional changes:

* Dark missing from ``DESI_SPECTRO_DARK`` is now a fatal error unless
  preproc with ``--fallback-on-dark-not-found`` (PR `#2162`_).
* New CTE modeling on selected CCDs; requires matching DESI_SPECTRO_CALIB
  update post 0.5.1 (PR `#2163`_, `#2192`_, `#2194`_).
* Add fiberflat gradient correction option (PR `#2180`_, `#2190`_, `#2208`_).
* New desi_proc_night unified daily/production processing script with options
  to override default calibrations with config files
  (PR `#2187`_, `#2201`_, `#2213`_, `#2214`_).

Smaller items and new features:

* Better handling of copyprod links (PR `#2160`_).
* Add desi_link_calibnight script (PR `#2165`_).
* Fix redrock API change templates_dir vs. template_path (PR `#2168`_).
* Add read_spectra_parallel (PR `#2169`_).
* Propagate units and comments in ``FIBERMAP`` HDUs (PR `#2176`_).
* Update dashboard for CTE flats (PR `#2177`_).
* Preproc interpolate overscan if active region entirely masked (PR `#2178`_).
* Simplify installation requirements (PR `#2183`_).
* Night QA support CCD 2amp mode (PR `#2184`_).
* Expand zcatalog "minimal" column set (PR `#2185`_).
* Increase dark model temperature difference acceptance window (PR `#2188`_).
* emlinefit do not fit EBV>2 spectra (PR `#2195`_).
* New wrap_rrdesi script to run Redrock on many input files (PR `#2196`_).
* Fix desi_group_spectra metadata with more than 1000 input files (PR `#2199`_).
* Fix qproc fallback on dark file not found (PR `#2205`_).
* Improve nightqa dark selection robustness (PR `#2206`_, `#2207`_).
* Replace NaN ``TARGET_RA/DEC`` values with ``FIBER`` values (PR `#2216`_).
* Add 5 missing columns to the fibermap (PR `#2219`_).

.. _`#2160`: https://github.com/desihub/desispec/pull/2160
.. _`#2162`: https://github.com/desihub/desispec/pull/2162
.. _`#2163`: https://github.com/desihub/desispec/pull/2163
.. _`#2165`: https://github.com/desihub/desispec/pull/2165
.. _`#2168`: https://github.com/desihub/desispec/pull/2168
.. _`#2169`: https://github.com/desihub/desispec/pull/2169
.. _`#2176`: https://github.com/desihub/desispec/pull/2176
.. _`#2177`: https://github.com/desihub/desispec/pull/2177
.. _`#2178`: https://github.com/desihub/desispec/pull/2178
.. _`#2180`: https://github.com/desihub/desispec/pull/2180
.. _`#2183`: https://github.com/desihub/desispec/pull/2183
.. _`#2184`: https://github.com/desihub/desispec/pull/2184
.. _`#2185`: https://github.com/desihub/desispec/pull/2185
.. _`#2187`: https://github.com/desihub/desispec/pull/2187
.. _`#2188`: https://github.com/desihub/desispec/pull/2188
.. _`#2190`: https://github.com/desihub/desispec/pull/2190
.. _`#2192`: https://github.com/desihub/desispec/pull/2192
.. _`#2194`: https://github.com/desihub/desispec/pull/2194
.. _`#2195`: https://github.com/desihub/desispec/pull/2195
.. _`#2196`: https://github.com/desihub/desispec/pull/2196
.. _`#2199`: https://github.com/desihub/desispec/pull/2199
.. _`#2201`: https://github.com/desihub/desispec/pull/2201
.. _`#2205`: https://github.com/desihub/desispec/pull/2205
.. _`#2206`: https://github.com/desihub/desispec/pull/2206
.. _`#2207`: https://github.com/desihub/desispec/pull/2207
.. _`#2208`: https://github.com/desihub/desispec/pull/2208
.. _`#2213`: https://github.com/desihub/desispec/pull/2213
.. _`#2214`: https://github.com/desihub/desispec/pull/2214
.. _`#2216`: https://github.com/desihub/desispec/pull/2216
.. _`#2219`: https://github.com/desihub/desispec/pull/2219

0.61.0 (2024-01-15)
-------------------

* Set psferr=0.04 for blue cameras (PR `#2129`_).
* Add VCCDSEC info to tile_qa_plot (PR `#2136`_).
* Don't skip exp_fibermap in io.spectra.read_spectra (PR `#2137`_).
* Don't require a resolution matrix when coadding across cameras (PR `#2139`_).
* Add new methods to convert to and from ``spectra.Spectra`` and
  ``specutils.SpectrumList`` objects (PR `#2141`_).
* New row-by-row extraction and CTE correction modules (PR `#2144`_).
* Add ``--zscale`` and ``--mask`` options to ``plot_fiber_traces`` (PR
  `#2145`_).
* Fix traceshifts when half CCD amps are masked (PR `#2150`_).
* In ``create_petalnz_pdf``, look for Redrock instead of zmtl files (PR
  `#2151`_).
* Fix failing ``io.photo`` unit tests at NERSC (PR `#2154`_).
* Remove deprecated test_suite functions from all unit tests that use it (PR
  `#2155`_).
* Various bug fixes and updates to ``io.read_tile_spectra`` (PR `#2156`_).
* Deprecate ``pkg_resources`` in favor of ``importlib`` (PR `#2157`_).
* Check for VCCDSEC and VCCDON when generating bias and dark models (PR
  `#2158`_).
* Check CCDTEMP when generating bias and dark models (PR `#2159`_).

.. _`#2129`: https://github.com/desihub/desispec/pull/2129
.. _`#2136`: https://github.com/desihub/desispec/pull/2136
.. _`#2137`: https://github.com/desihub/desispec/pull/2137
.. _`#2139`: https://github.com/desihub/desispec/pull/2139
.. _`#2141`: https://github.com/desihub/desispec/pull/2141
.. _`#2144`: https://github.com/desihub/desispec/pull/2144
.. _`#2145`: https://github.com/desihub/desispec/pull/2145
.. _`#2150`: https://github.com/desihub/desispec/pull/2150
.. _`#2151`: https://github.com/desihub/desispec/pull/2151
.. _`#2154`: https://github.com/desihub/desispec/pull/2154
.. _`#2155`: https://github.com/desihub/desispec/pull/2155
.. _`#2156`: https://github.com/desihub/desispec/pull/2156
.. _`#2157`: https://github.com/desihub/desispec/pull/2157
.. _`#2158`: https://github.com/desihub/desispec/pull/2158
.. _`#2159`: https://github.com/desihub/desispec/pull/2159

0.60.2 (2023-10-26)
-------------------

* Update validredshifts.validate() to work on SV observations (PR `#2122`_).
* Add desi_exposure_info script (PR `#2124`_).
* Fix exp_fibermap when specifying targetids to read_spectra (PR `#2126`_).
* Add desi_average_flux_calibration --unflat option (PR `#2127`_).
* io.photo use read-only mount (PR `#2132`_).

.. _`#2122`: https://github.com/desihub/desispec/pull/2122
.. _`#2124`: https://github.com/desihub/desispec/pull/2124
.. _`#2126`: https://github.com/desihub/desispec/pull/2126
.. _`#2127`: https://github.com/desihub/desispec/pull/2127
.. _`#2132`: https://github.com/desihub/desispec/pull/2132

0.60.1 (2023-09-25)
-------------------

* zcatalog FIRSTNIGHT/LASTNIGHT when missing petals (PR `#2118`_).
* night_qa: protect against missing OBSTYPE keyword (PR `#2120`_).
* zcatalog usage cleanup (PR `#2121`_).

.. _`#2118`: https://github.com/desihub/desispec/pull/2118
.. _`#2120`: https://github.com/desihub/desispec/pull/2120
.. _`#2121`: https://github.com/desihub/desispec/pull/2121

0.60.0 (2023-09-14)
-------------------

Updates for patching Iron/DR1 redshift catalogs

* coadd_fibermap handle RA wraparound (PR `#2090`_).
* Update COADD_FIBERSTATUS to bitwise OR when all inputs are bad (PR `#2093`_).
* Coadd bitwise OR of input targeting bits, e.g. DESI_TARGET (PR `#2094`_).
* Add IN_COADD/B/R/Z columns to EXP_FIBERMAP (PR `#2100`_).
* Fix dtype of ``*_NSPEC`` columns to int16 (PR `#2103`_).
* desi_zcatalog --recoadd-fibermap option (PR `#2109`_, `#2116`_).
* fix HPXNEST header type (PR `#2110`_).
* desi_zcatalog --add-units option for DR1 patching (PR `#2111`_).
* Refactor desi_zcatalog options, add parallelism (PR `#2117`_).

Algorithmic Updates

* Fix incorrect weights in trace shift polyfit (PR `#2105`_).
* Improve trace shifts for bright/backup data (PR `#2106`_, `#2115`_).

Miscellaneous

* Add read_spectra options to read subsets by targetids or rows (PR `#2052`_).
* Night QA flab calibs later than first science rather than absolute
  timestamp (PR `#2089`_).
* Night QA orient images and display CCD amp names (PR `#2091`_).
* Add desi_compute_fiberflat_vs_humidity --first-night option (PR `#2101`_).
* Add desi_compute_gains exposure time flexibility (PR `#2107`_).
* Update readthedocs configuration (PR `#2112`_).

.. _`#2052`: https://github.com/desihub/desispec/pull/2052
.. _`#2089`: https://github.com/desihub/desispec/pull/2089
.. _`#2090`: https://github.com/desihub/desispec/pull/2090
.. _`#2091`: https://github.com/desihub/desispec/pull/2091
.. _`#2093`: https://github.com/desihub/desispec/pull/2093
.. _`#2094`: https://github.com/desihub/desispec/pull/2094
.. _`#2100`: https://github.com/desihub/desispec/pull/2100
.. _`#2101`: https://github.com/desihub/desispec/pull/2101
.. _`#2103`: https://github.com/desihub/desispec/pull/2103
.. _`#2105`: https://github.com/desihub/desispec/pull/2105
.. _`#2106`: https://github.com/desihub/desispec/pull/2106
.. _`#2107`: https://github.com/desihub/desispec/pull/2107
.. _`#2109`: https://github.com/desihub/desispec/pull/2109
.. _`#2110`: https://github.com/desihub/desispec/pull/2110
.. _`#2111`: https://github.com/desihub/desispec/pull/2111
.. _`#2112`: https://github.com/desihub/desispec/pull/2112
.. _`#2114`: https://github.com/desihub/desispec/pull/2114
.. _`#2115`: https://github.com/desihub/desispec/pull/2115
.. _`#2116`: https://github.com/desihub/desispec/pull/2116
.. _`#2117`: https://github.com/desihub/desispec/pull/2117


0.59.2 (2023-08-04)
-------------------

* Add recovery robustness for partially completed PSF jobs (PR `#2059`_).
* Propagate joint fit error code (PR `#2063`_).
* night_qa optional override of reprocessing darks (PR `#2066`_).
* desi_vi_tile defaults to only new tiles (PR `#2073`_).
* Optionally match to DR10 photometry (PR `#2079`_).
* Move desi_archive_tilenight contents into callable funcs (PR `#2081`_).
* Add (re-)archive options when missing petals (PR `#2082`_).
* Fix circular imports with trace_shifts (PR `#2084`_).

.. _`#2059`: https://github.com/desihub/desispec/pull/2059
.. _`#2063`: https://github.com/desihub/desispec/pull/2063
.. _`#2066`: https://github.com/desihub/desispec/pull/2066
.. _`#2073`: https://github.com/desihub/desispec/pull/2073
.. _`#2079`: https://github.com/desihub/desispec/pull/2079
.. _`#2081`: https://github.com/desihub/desispec/pull/2081
.. _`#2082`: https://github.com/desihub/desispec/pull/2082
.. _`#2084`: https://github.com/desihub/desispec/pull/2084

0.59.1 (2023-06-23)
-------------------

* Add desi_daily_proc_manager --exp-cadence-time option (PR `#2076`_)

.. _`#2076`: https://github.com/desihub/desispec/pull/2076

0.59.0 (2023-06-12)
-------------------

* Focus (PR `#2042`_).
* Night_qa: dark: add possibility of plots with --bkgsub-for-science (PR `#2043`_).
* Perform final processing check in desi_run_night when processing table is empty (PR `#2056`_).
* ``desispec.coaddition.coadd_fiberstatus`` bugfixes and add columns
  FIRSTNIGHT, LASTNIGHT, MIN_MJD, MEAN_MJD, MAX_MJD.  Used for EDR zcat VAC.
  (PRs `#2065`_, `#2067`_, `#2070`_)

.. _`#2065`: https://github.com/desihub/desispec/pull/2065
.. _`#2067`: https://github.com/desihub/desispec/pull/2067
.. _`#2070`: https://github.com/desihub/desispec/pull/2070
.. _`#2042`: https://github.com/desihub/desispec/pull/2042
.. _`#2043`: https://github.com/desihub/desispec/pull/2043
.. _`#2056`: https://github.com/desihub/desispec/pull/2056

0.58.4 (2023-06-02)
-------------------

* desispec.photo handle non-unique bricknames when patching 9010
  tractor photometry (PR `#2062`_, followup to `#2057`_).

.. _`#2062`: https://github.com/desihub/desispec/pull/2062

0.58.3 (2023-06-01)
-------------------

* Workaround for sbatch bug on Perlmutter (PR `#2037`_).
* Warn that purge_night was a dry run (PR `#2040`_).
* Restore desi_daily_proc_manager dry run and add sacct retries (PR `#2044`_).
* Add optional masking of specific CCD regions per exposure (PR `#2050`_).
* Avoid TSNR and EFFTIME NaN when traces are off CCD (PR `#2053`_).
* desispec.photo handle release 9010 vs. 9012 burst buffer bug, needed
  for lsdr9 photometry VAC (PR `#2057`_).

.. _`#2037`: https://github.com/desihub/desispec/pull/2037
.. _`#2040`: https://github.com/desihub/desispec/pull/2040
.. _`#2044`: https://github.com/desihub/desispec/pull/2044
.. _`#2050`: https://github.com/desihub/desispec/pull/2050
.. _`#2053`: https://github.com/desihub/desispec/pull/2053
.. _`#2057`: https://github.com/desihub/desispec/pull/2057

0.58.2 (2023-05-03)
-------------------

* Add option to process cumulative redshifts for all tiles in desi_run_night
  (PR `#2036`_).

.. _`#2036`: https://github.com/desihub/desispec/pull/2036

0.58.1 (2023-05-02)
-------------------

* daily proc non-tilenight skybub exp fix
  [PR `#2034`_, followup to PR `#2028`_]

.. _`#2034`: https://github.com/desihub/desispec/pull/2034

0.58.0 (2023-05-02)
-------------------

Major:

* Add tilenight support to :command:`desi_daily_proc_manager` (PR `#2028`_).
* Change CTE fitting to be offset+ramp instead of just offset (PR `#2033`_).

Smaller / bugfixes:

* Flag calibration files performed on a different day (PR `#2011`_).
* Coadd spectra files with ``COADD_FIBERMAP`` instead of ``FIBERMAP``
  (PR `#2013`_).
* Fix bug in :command:`desi_proc_tilenight` which was causing it to ignore
  ``--cameras`` (PR `#2014`_).
* Propagate the ``--laststeps`` option to :command:`desi_proc_tilenight`
  (PR `#2015`_).
* NightQA preproc dark bugfix when misisng cameras (PR `#2016`_).
* Fix failing ``io.photo`` unit tests (PR `#2017`_).
* Fix documentation test failures due to missing ``pytz`` (PR `#2019`_).
* Fix indexing error in targetid selection for :command:`plot_spectra`
  (PR `#2020`_).
* Fix crash in :command:`desi_run_night` when processing ``LASTSTEP=skysub``
  exposures (PR `#2022`_).
* Fix failing ``bootcalib`` unit tests (PR `#2029`_).
* Don't create exposures outdir for darks with no output (PR `#2031`_).

.. _`#2011`: https://github.com/desihub/desispec/pull/2011
.. _`#2013`: https://github.com/desihub/desispec/pull/2013
.. _`#2014`: https://github.com/desihub/desispec/pull/2014
.. _`#2015`: https://github.com/desihub/desispec/pull/2015
.. _`#2016`: https://github.com/desihub/desispec/pull/2016
.. _`#2017`: https://github.com/desihub/desispec/pull/2017
.. _`#2019`: https://github.com/desihub/desispec/pull/2019
.. _`#2020`: https://github.com/desihub/desispec/pull/2020
.. _`#2022`: https://github.com/desihub/desispec/pull/2022
.. _`#2028`: https://github.com/desihub/desispec/pull/2028
.. _`#2029`: https://github.com/desihub/desispec/pull/2029
.. _`#2031`: https://github.com/desihub/desispec/pull/2031
.. _`#2033`: https://github.com/desihub/desispec/pull/2033

0.57.0 (2023-02-17)
-------------------

* ``desi_compute_sky`` options to override sky TARGETIDs.
  Adds new SKYTARGETIDS HDU to output sky files (PR `#2001`_).
* Update functionality of ``io.photo`` to support Iron release (PR `#2008`_).

.. _`#2001`: https://github.com/desihub/desispec/pull/2001
.. _`#2008`: https://github.com/desihub/desispec/pull/2008

0.56.5 (2023-02-01)
-------------------

Last tag used for Iron run.

* Fix healpix redshift (zpix) bookkeeping of bad data (PR `#1991`_).

.. _`#1991`: https://github.com/desihub/desispec/pull/1991

0.56.4 (2023-01-27)
-------------------

Bugfix update for Iron re-processing.

* Completely sync daily -> tiles-specstatus, not just new data (PR `#1976`_).
* Cleanup API documentation, changing many files (PR `#1981`_).
* Add calibnight jobs to exposure dashboard (PR `#1982`_).
* BUGFIX: define psfnight and nightlyflat cameras based upon all
  input arcs/flats instead of just the first one (PR `#1984`_).
* Add new desi_queue_status script (PR `#1986`_).
* Don't hardcode $DESI_ROOT_READONLY in batch scripts (PR `#1987`_).

.. _`#1976`: https://github.com/desihub/desispec/pull/1976
.. _`#1981`: https://github.com/desihub/desispec/pull/1981
.. _`#1982`: https://github.com/desihub/desispec/pull/1982
.. _`#1984`: https://github.com/desihub/desispec/pull/1984
.. _`#1986`: https://github.com/desihub/desispec/pull/1986
.. _`#1987`: https://github.com/desihub/desispec/pull/1987

0.56.3 (2023-01-24)
-------------------

* Minor fixes to io.photo (followup to PR `#1971`_).
* Remove imports from deprecated scipy.ndimage.filters namespace (PR `#1977`_).

.. _`#1971`: https://github.com/desihub/desispec/pull/1971
.. _`#1977`: https://github.com/desihub/desispec/pull/1977

0.56.2 (2023-01-13)
-------------------

* Minor fixes to io.photo (PR `#1971`_).

.. _`#1971`: https://github.com/desihub/desispec/pull/1971

0.56.1 (2023-01-13)
-------------------

* Increase flat job time limit (PR `#1970`_).

.. _`#1970`: https://github.com/desihub/desispec/pull/1970

0.56.0 (2023-01-12)
-------------------

QA and pipelining updates in support of daily ops and Iron/DR1:

* Assess the redshift quality of DESI galaxies and quasars (PR `#1765`_).
* Add a python script for spectral grouping and redshifting (PR `#1904`_).
* Merge current daily branch into main to pick up changes for perlmutter (PR `#1948`_, `#1958`_, `#1965`_).
* Add update_survey_keywords to standardize early FA headers (PR `#1858`_).
* Standardize GPU options (opt-out with --no-gpu) and fix options for
  desi_run_night auto-deriving GPU vs. CPU per job (PR `#1901`_).
* cosmics parameters in yaml file for 500 micron mosaic z5 CCD (PR `#1905`_).
* cosmics_nsig default cleanup (PR `#1906`_).
* Reduce size of jobgraph diagrams (PR `#1910`_).
* Fluxcalib logging include cameras (PR `#1912`_).
* tilenight options and bug fixes (PR `#1913`_).
* poststd bugfix for expected cameras compared to stdstar fit (PR `#1916`_).
* QA updates (PRs `#1917`_, `#1926`_, `#1938`_, `#1944`_, `#1945`_, `#1947`_,
  `#1954`_, `#1962`_)
* distribute_ranks_to_blocks bugfix (PR `#1919`_).
* desi_run_night robust to exposure tables without BADCAMWORD (PR `#1921`_).
* Improved calibfinder logging (PR `#1922`_).
* tsnr_afterburner MPI+multiprocessing updates; use fitsio (PR `#1924`_).
* NaN fix for negative CCD bkg (PR `#1927`_, `#1939`_).
* Merge ongoing work on spectroscopic production database in preparation for
  EDR (PR `#1928`_).
* healpix redshifts added to zproc (PR `#1931`_, `#1966`_).
* Check for type of dark option in preprocessing (PR `#1936`_).
* Add ``desi_run_night --do-cte-flat`` option (PR `#1937`_).
* Don't set ivar=0 for unassigned fibers by default (PR `#1942`_).
* Fix tsnr_afterburner when no cframes on a night (PR `#1950`_).
* Submit cumulative redshifts only for last night of each tile (PR `#1955`_).
* Use desimodel/0.18.0 for testing for scipy/1.10.0 support (PR `#1957`_).
* Allow cutoff date for tile completion during reprocessing (PR `#1959`_).
* copyprod support for missing exposure tables (PR `#1964`_).
* Change zproc on cori realtime to 2 nodes and 30 minutes
  (PRs `#1968`_, `#1969`_).

.. _`#1765`: https://github.com/desihub/desispec/pull/1765
.. _`#1904`: https://github.com/desihub/desispec/pull/1904
.. _`#1948`: https://github.com/desihub/desispec/pull/1948
.. _`#1958`: https://github.com/desihub/desispec/pull/1958
.. _`#1965`: https://github.com/desihub/desispec/pull/1965
.. _`#1858`: https://github.com/desihub/desispec/pull/1858
.. _`#1901`: https://github.com/desihub/desispec/pull/1901
.. _`#1905`: https://github.com/desihub/desispec/pull/1905
.. _`#1906`: https://github.com/desihub/desispec/pull/1906
.. _`#1910`: https://github.com/desihub/desispec/pull/1910
.. _`#1912`: https://github.com/desihub/desispec/pull/1912
.. _`#1913`: https://github.com/desihub/desispec/pull/1913
.. _`#1916`: https://github.com/desihub/desispec/pull/1916
.. _`#1917`: https://github.com/desihub/desispec/pull/1917
.. _`#1919`: https://github.com/desihub/desispec/pull/1919
.. _`#1921`: https://github.com/desihub/desispec/pull/1921
.. _`#1922`: https://github.com/desihub/desispec/pull/1922
.. _`#1924`: https://github.com/desihub/desispec/pull/1924
.. _`#1926`: https://github.com/desihub/desispec/pull/1926
.. _`#1927`: https://github.com/desihub/desispec/pull/1927
.. _`#1928`: https://github.com/desihub/desispec/pull/1928
.. _`#1931`: https://github.com/desihub/desispec/pull/1931
.. _`#1936`: https://github.com/desihub/desispec/pull/1936
.. _`#1937`: https://github.com/desihub/desispec/pull/1937
.. _`#1938`: https://github.com/desihub/desispec/pull/1938
.. _`#1939`: https://github.com/desihub/desispec/pull/1939
.. _`#1942`: https://github.com/desihub/desispec/pull/1942
.. _`#1944`: https://github.com/desihub/desispec/pull/1944
.. _`#1945`: https://github.com/desihub/desispec/pull/1945
.. _`#1947`: https://github.com/desihub/desispec/pull/1947
.. _`#1950`: https://github.com/desihub/desispec/pull/1950
.. _`#1954`: https://github.com/desihub/desispec/pull/1954
.. _`#1955`: https://github.com/desihub/desispec/pull/1955
.. _`#1957`: https://github.com/desihub/desispec/pull/1957
.. _`#1959`: https://github.com/desihub/desispec/pull/1959
.. _`#1962`: https://github.com/desihub/desispec/pull/1962
.. _`#1964`: https://github.com/desihub/desispec/pull/1964
.. _`#1966`: https://github.com/desihub/desispec/pull/1966
.. _`#1968`: https://github.com/desihub/desispec/pull/1968
.. _`#1969`: https://github.com/desihub/desispec/pull/1969

0.55.0 (2022-11-11)
-------------------

Major:

* Restore sky-modeling sector offsets (PR `#1825`_).
* Add emlinefit afterburner to redshift scripts (PR `#1852`_).
* emlinefit (1+z) normalization bugfix (PR `#1878`_).
* Sky model use TPCORR to adjust sky line amplitudes, but not continuum
  (PRs `#1886`_, `#1895`_).

Minor:

* Fix desi_proc stdstar args (PR `#1822`_).
* Set default system_name while parsing args (PR `#1824`_).
* Add ``desi_purge_night`` script (PR `#1828`_).
* Fix ``find_overscan_cosmics_trails`` in 2-amp CCD readout mode (PR `#1831`_).
* Fix ``iotime.parse_logfile`` when there aren't any iotime messages (PR `#1833`_).
* Make $SPECPROD optional for running ``desi_preproc`` (PR `#1835`_).
* Catch exceptions in tilenight and update Perlmutter runtimes (PR `#1837`_).
* Add biasnight check to nightqa (PR `#1841`_).
* ``desi_run_night`` only launches obs completed tiles by default (PR `#1843`_).
* Fix 2-amp readout biasnight (PR `#1844`_).
* Add color coding to the nightly and monthly buttons in dashboards (PR `#1845`_).
* Sort on EXPID as well as TILEID in desi_run_night (PR `#1848`_).
* biasnight job shouldn't "fail" if default bias is better anyway (PR `#1850`_).
* improve cframe file globbing to avoid tempfiles (PR `#1853`_).
* tilenight exit early if no good exposures (PR `#1854`_).
* fix psferr option in desi_extract_spectra (PR `#1855`_).
* Add support for NERSC CFS readonly mount (PRs `#1856`_, `#1888`_, `#1891`_).
* Use non-calibration zeros if not enough calib zeros are available (PR `#1857`_).
* Perlmutter use CPU for nightlybias, ccdcalib, arcs; GPUs otherwise (PR `#1859`_).
* Have desi_night_qa announce its completion (PR `#1860`_).
* Handle NaNs and zeros in skytpcorr, skygradpca x/y inputs (PR `#1865`_).
* Don't wait for new data when override_night set in daily_proc_manager (PR `#1866`_).
* Ensure expids are ints in ccdcalib (PR `#1868`_).
* Give more time to stdstar jobs (PR `#1869`_).
* Fix stdstar indexing crash (PR `#1872`_).
* desi_run_night support case of no good zeros (PR `#1875`_).
* avoid stdstars joint fit makedirs race condition (PR `#1879`_).
* fix fallback to DESI_SPECTRO_CALIB if DESI_SPECTRO_DARK is set but doesn't
  have suitable files for date range (PR `#1882`_).
* desi_proc options for sims (PR `#1885`_)
* Add ``copyprod --tiles`` option (PR `#1893`_).
* Fix fibermap indexing bug when mix of LEGACY and GAIA (PR `#1894`_).
* Add ``desi_job_graph`` to make job dependency graph webpages (PR `#1896`_).
* Apply job timefactor to nightlyflat jobs too (PR `#1898`_).
* Add GPU memory and rank allocation tools (PR `#1899`_).
* Add desi spectro dark (PR `#1818`_).
* EDR redshift database (PR `#1819`_).
* add --use-specter to desi_run_night (PR `#1883`_).

.. _`#1818`: https://github.com/desihub/desispec/pull/1818
.. _`#1819`: https://github.com/desihub/desispec/pull/1819
.. _`#1822`: https://github.com/desihub/desispec/pull/1822
.. _`#1824`: https://github.com/desihub/desispec/pull/1824
.. _`#1825`: https://github.com/desihub/desispec/pull/1825
.. _`#1828`: https://github.com/desihub/desispec/pull/1828
.. _`#1831`: https://github.com/desihub/desispec/pull/1831
.. _`#1833`: https://github.com/desihub/desispec/pull/1833
.. _`#1835`: https://github.com/desihub/desispec/pull/1835
.. _`#1837`: https://github.com/desihub/desispec/pull/1837
.. _`#1841`: https://github.com/desihub/desispec/pull/1841
.. _`#1843`: https://github.com/desihub/desispec/pull/1843
.. _`#1844`: https://github.com/desihub/desispec/pull/1844
.. _`#1845`: https://github.com/desihub/desispec/pull/1845
.. _`#1848`: https://github.com/desihub/desispec/pull/1848
.. _`#1850`: https://github.com/desihub/desispec/pull/1850
.. _`#1852`: https://github.com/desihub/desispec/pull/1852
.. _`#1853`: https://github.com/desihub/desispec/pull/1853
.. _`#1854`: https://github.com/desihub/desispec/pull/1854
.. _`#1855`: https://github.com/desihub/desispec/pull/1855
.. _`#1856`: https://github.com/desihub/desispec/pull/1856
.. _`#1857`: https://github.com/desihub/desispec/pull/1857
.. _`#1859`: https://github.com/desihub/desispec/pull/1859
.. _`#1860`: https://github.com/desihub/desispec/pull/1860
.. _`#1865`: https://github.com/desihub/desispec/pull/1865
.. _`#1866`: https://github.com/desihub/desispec/pull/1866
.. _`#1868`: https://github.com/desihub/desispec/pull/1868
.. _`#1869`: https://github.com/desihub/desispec/pull/1869
.. _`#1872`: https://github.com/desihub/desispec/pull/1872
.. _`#1875`: https://github.com/desihub/desispec/pull/1875
.. _`#1878`: https://github.com/desihub/desispec/pull/1878
.. _`#1879`: https://github.com/desihub/desispec/pull/1879
.. _`#1882`: https://github.com/desihub/desispec/pull/1882
.. _`#1883`: https://github.com/desihub/desispec/pull/1883
.. _`#1885`: https://github.com/desihub/desispec/pull/1885
.. _`#1886`: https://github.com/desihub/desispec/pull/1886
.. _`#1888`: https://github.com/desihub/desispec/pull/1888
.. _`#1891`: https://github.com/desihub/desispec/pull/1891
.. _`#1893`: https://github.com/desihub/desispec/pull/1893
.. _`#1894`: https://github.com/desihub/desispec/pull/1894
.. _`#1895`: https://github.com/desihub/desispec/pull/1895
.. _`#1896`: https://github.com/desihub/desispec/pull/1896
.. _`#1898`: https://github.com/desihub/desispec/pull/1898
.. _`#1899`: https://github.com/desihub/desispec/pull/1899


0.54.0 (2022-08-15)
-------------------

* Fix rank race condition bug in specex.py (PR `#1809`_).
* Stdstar use correct sky and flat fiber; scale ivar (PR `#1817`_).
* Stdstar memory optimization (PR `#1820`_).
* Major: Replace TPCORR per-fiber corrections with a model (PR `#1801`_)

.. _`#1801`: https://github.com/desihub/desispec/pull/1801
.. _`#1809`: https://github.com/desihub/desispec/pull/1809
.. _`#1817`: https://github.com/desihub/desispec/pull/1817
.. _`#1820`: https://github.com/desihub/desispec/pull/1820

0.53.2 (2022-07-22)
-------------------

* Validate redshift catalog metadata and generate Tractor photometric catalogs
  for all objects with a redshift in a given data release (PR `#1716`_).
* Add batch script for :command:`desi_proc_tilenight` jobs (PR `#1792`_).
* Add :command:`desi_psf_fit` which wraps specex_ (PR `#1794`_).
* Parallelize :command:`desi_night_qa` (PR `#1795`_).
* Enable redshift status board (PR `#1797`_).
* Correct flux units for emission lines (PR `#1798`_).
* Update QSO afterburners for new templates (PR `#1805`_).
* Fix function used by fastspecfit_ (PR `#1808`_).

.. _`#1716`: https://github.com/desihub/desispec/pull/1716
.. _`#1792`: https://github.com/desihub/desispec/pull/1792
.. _`#1794`: https://github.com/desihub/desispec/pull/1794
.. _`#1795`: https://github.com/desihub/desispec/pull/1795
.. _`#1797`: https://github.com/desihub/desispec/pull/1797
.. _`#1798`: https://github.com/desihub/desispec/pull/1798
.. _`#1805`: https://github.com/desihub/desispec/pull/1805
.. _`#1808`: https://github.com/desihub/desispec/pull/1808
.. _fastspecfit: https://github.com/desihub/fastspecfit
.. _specex: https://github.com/desihub/specex


0.53.1 (2022-05-19)
-------------------

* QSO afterburners use temporary file when writing (PR `#1768`_).
* Fix ``desi_run_night`` crash with non-consecutive obs of same tile
  (PR `#1771`_).
* Set batch-friendly matplotlib backend (PR `#1772`_).
* Increase stdstar job requested time by 2 min (direct push, no PR).

.. _`#1768`: https://github.com/desihub/desispec/pull/1768
.. _`#1771`: https://github.com/desihub/desispec/pull/1771
.. _`#1772`: https://github.com/desihub/desispec/pull/1772

0.53.0 (2022-05-15)
-------------------

Major:

* gzip intermediate files, including spectra files (PR `#1756`_).
* refactor pipeline to call functions instead of spawn scripts for
  MPI compatibility on NERSC Perlmutter.  No user facing impact but major
  under-the-hood change (PR `#1743`_).

Minor / backwards compatible:

* Add ifmain wrapper to setup.py for testing (PR `#1745`_).
* Allow QA of already QAed tiles (PR `#1747`_).
* Update recipe for find_overscan_cosmic_trails (PR `#1748`_, `#1758`_).
* desi_daily_proc_manager retry failed sbatch before giving up (PR `#1749`_).
* Enable trace shifts by default (PR `#1750`_).
* Improve error handling for specex (PR `#1751`_).
* ``desi_group_spectra --coadd`` option (PR `#1753`_).
* QA bugfix: handle nqso_rr if no valid fibers (PR `#1754`_).
* Improve fiberflat vs. humidity (PR `#1757`_).
* Night QA use findfile and fitsio (PR `#1766`_.)

.. _`#1743`: https://github.com/desihub/desispec/pull/1743
.. _`#1745`: https://github.com/desihub/desispec/pull/1745
.. _`#1747`: https://github.com/desihub/desispec/pull/1747
.. _`#1748`: https://github.com/desihub/desispec/pull/1748
.. _`#1749`: https://github.com/desihub/desispec/pull/1749
.. _`#1750`: https://github.com/desihub/desispec/pull/1750
.. _`#1751`: https://github.com/desihub/desispec/pull/1751
.. _`#1753`: https://github.com/desihub/desispec/pull/1753
.. _`#1754`: https://github.com/desihub/desispec/pull/1754
.. _`#1756`: https://github.com/desihub/desispec/pull/1756
.. _`#1757`: https://github.com/desihub/desispec/pull/1757
.. _`#1758`: https://github.com/desihub/desispec/pull/1758
.. _`#1766`: https://github.com/desihub/desispec/pull/1766

0.52.0 (2022-04-19)
-------------------

Used to create combined ``zcatalog/zall-*.fits`` files in fuji and guadalupe.

* qproc/nightwatch: fix deggy=0 for traceshifts (PR `#1719`_).
* Ignore overscan rows with large cosmic charge deposit in nearby columns
  (PR `#1720`_)
* Add tools to create combined/summary catalogs for specprods (PR `#1721`_).
* Use tile-median E(B-V) for LOWEFFTIME QA calculation (PR `#1722`_).
* tile QA: highlight secondary-only fibers in z vs. fiber (PR `#1729`_).
* Enable GPUs on perlmutter in rrdesi_mpi slurm script (PR `#1730`_, `#1734`_).
* Adjust main survey minimum exposure efftime_etc (PR `#1731`_).
* Warning files produced by QSO afterburners will now be called
  ``.misscamera.txt`` (PR `#1732`_).
* Cleanup: make ``find_overscan_cosmic_trails`` separate function for testing
  (PR `#1733`_).
* Pipeline: add CTE flat class to dashboard so it reflects expected files
  (PR `#1736`_).
* Fix traceshift infinite iteration bug (PR `#1742`_).
* Fix doctest config for GitHub actions (PR `#1744`_).

.. _`#1719`: https://github.com/desihub/desispec/pull/1719
.. _`#1720`: https://github.com/desihub/desispec/pull/1720
.. _`#1721`: https://github.com/desihub/desispec/pull/1721
.. _`#1722`: https://github.com/desihub/desispec/pull/1722
.. _`#1729`: https://github.com/desihub/desispec/pull/1729
.. _`#1730`: https://github.com/desihub/desispec/pull/1730
.. _`#1731`: https://github.com/desihub/desispec/pull/1731
.. _`#1732`: https://github.com/desihub/desispec/pull/1732
.. _`#1733`: https://github.com/desihub/desispec/pull/1733
.. _`#1734`: https://github.com/desihub/desispec/pull/1734
.. _`#1736`: https://github.com/desihub/desispec/pull/1736
.. _`#1742`: https://github.com/desihub/desispec/pull/1742
.. _`#1744`: https://github.com/desihub/desispec/pull/1744

0.51.13 (2022-02-28)
--------------------

* ``desi_zcatalog --patch-missing-ivar-w12`` option to patch missing
  FLUX_IVAR_W1/W2 values that weren't propagated by early fiberassign
  (PR `#1717`_).

.. _`#1717`: https://github.com/desihub/desispec/pull/1717

0.51.12 (2022-02-23)
--------------------

* Remove unnecessary ``specter.psf`` import, which also allows ``desispec``
  utilities to be imported without explicitly requiring ``specter`` (PR
  `#1709`_).
* Let plot_spectra show errors even with --rebin (PR `#1714`_, `#1708`_).
* add SPGRPVAL to desi_zcatalog for custom coadds/redshift group tracking
  (PR `#1712`_).
* desi_assemble_tilepix replacement for desi_map_tilepix (PR `#1713`_).
* fix read_tile_spectra for group='cumulative' (PR `#1696`_).

.. _`#1696`: https://github.com/desihub/desispec/pull/1696
.. _`#1708`: https://github.com/desihub/desispec/pull/1708
.. _`#1709`: https://github.com/desihub/desispec/pull/1709
.. _`#1712`: https://github.com/desihub/desispec/pull/1712
.. _`#1713`: https://github.com/desihub/desispec/pull/1713
.. _`#1714`: https://github.com/desihub/desispec/pull/1714

0.51.11 (2022-02-21)
--------------------

* qso_qn afterburner fix for case when all inputs are masked (PR `#1704`_).

.. _`#1704`: https://github.com/desihub/desispec/pull/1704

0.51.10 (2022-02-18)
--------------------

* tile-qa avoid divide-by-zero crash on unknown goaltime (PR `#1698`_).
* propagate HEALPIX into zpix redshift catalogs (PR `#1699`_).
* Fix GOALTIME in exposures FRAMES HDU; avoid EFFTIME_ETC NaN (PR `#1701`_).

.. _`#1698`: https://github.com/desihub/desispec/pull/1698
.. _`#1699`: https://github.com/desihub/desispec/pull/1699
.. _`#1701`: https://github.com/desihub/desispec/pull/1701

0.51.9 (2022-02-17)
-------------------

Fuji cleanup bugfixes.

* tile-qa goaltime special case for tiles 80715,80718 (PR `#1689`_).
* qso afterburner output breadcrumb file if missing input camera (PR `#1691`_).
* fix unwisebrightblue PROGRAM=other not bright (PR `#1694`_).
* fix tsnr afterburner GOALTIME exp vs. tile consistency (PR `#1694`_).
* fix plot_spectra with astropy 5 (PR `#1695`_).

.. _`#1689`: https://github.com/desihub/desispec/pull/1689
.. _`#1691`: https://github.com/desihub/desispec/pull/1691
.. _`#1694`: https://github.com/desihub/desispec/pull/1694
.. _`#1695`: https://github.com/desihub/desispec/pull/1695

0.51.8 (2022-02-13)
-------------------

Bugfixes for Fuji; all impacted tiles/nights/healpix rerun with this tag,
remaining tiles/nights/healpix are backwards compatible.

* Set specmask BADFIBER only for impacted cameras, not all BRZ
  (PRs `#1674`_ (master), `#1678`_ (fuji))
* Fix assemble_fibermap with input NaNs for astropy 5.0 (PR `#1681`_).
* Use only 120s flats for nightlyflat (PR `#1682`_).
* Add desi_purge_tilenight script (PR `#1683`_).
* Fix healpix input expid bookkeeping (PR `#1684`_).

.. _`#1674`: https://github.com/desihub/desispec/pull/1674
.. _`#1678`: https://github.com/desihub/desispec/pull/1678
.. _`#1681`: https://github.com/desihub/desispec/pull/1681
.. _`#1682`: https://github.com/desihub/desispec/pull/1682
.. _`#1683`: https://github.com/desihub/desispec/pull/1683
.. _`#1684`: https://github.com/desihub/desispec/pull/1684

0.51.7 (2022-02-10)
-------------------

* fix tile-qa expid bookkeeping (PR `#1670`_).
* desi_tile_qa exposure/night bookkeeping fix (PR `#1672`_).
* Fix tsnr_afterburner exposure files SURVEY column (PR `#1675`_).

.. _`#1670`: https://github.com/desihub/desispec/pull/1670
.. _`#1672`: https://github.com/desihub/desispec/pull/1672
.. _`#1675`: https://github.com/desihub/desispec/pull/1675

0.51.6 (2022-02-09)
-------------------

Used for Fuji healpix redshifts and cleanup of failed tile-qa.
Backwards compatible with previously run steps.

* Make tile-qa robust to missing cameras (PR `#1665`_)
* Refactor healpix redshifts workflow (PR `#1668`_)

.. _`#1665`: https://github.com/desihub/desispec/pull/1665
.. _`#1668`: https://github.com/desihub/desispec/pull/1668

0.51.5 (2022-02-07)
-------------------

Used for processing nightly biases for Fuji nights 20210331 and 20210422,
and Guadalupe night 20210629.  Backwards compatible with other nights.

* Additional desi_compute_nightlybias options for flexibility on which ZEROs
  to use (PR `#1662`_).

.. _`#1662`: https://github.com/desihub/desispec/pull/1662

0.51.4 (2022-02-04)
-------------------

Pipelining fix for Fuji; previously run impacted nights will be resubmitted.

* Fix stdstar camword logic when input exposures have different cameras
  available (PR `#1658`_).

.. _`#1658`: https://github.com/desihub/desispec/pull/1658

0.51.3 (2022-01-31)
-------------------

NOTE: this tag fixes a crash, but also produces slightly different humidity
correction for a small set Fuji/Guadalupe exposures already run with an
earlier tag.  This note will be updated if those exposures are reprocessed
with this tag.

* Fix fiberflat humidity correction indexing bug when hear (but not at)
  upper limit of model humidity range (PR `#1642`_).

.. _`#1642`: https://github.com/desihub/desispec/pull/1642

0.51.2 (2022-01-27)
-------------------

Fuji bug fixes (impacted nights will be re-run; nights run with earlier
tags not impacted)

* fix pipeline bug on nights with multiple 300s darks (PR `#1635`_).
* fix ``io.findfile(..., groupname='perexp')`` (PR `#1637`_).

.. _`#1635`: https://github.com/desihub/desispec/pull/1635
.. _`#1637`: https://github.com/desihub/desispec/pull/1637

0.51.1 (2022-01-26)
-------------------

Fuji bugfix tag made from the fuji branch mid-processing.  These changes
fix crashes but do not impact any data that were already successfully run.

* Updated desi_find_badpos script to cross-reference flagged petals against
  existing bad-exposure tables.
* Fix fiberflat crash when almost all input data are masked for a fiber
  (PR `#1629`_).
* Fix tile QA for cases when input fiberassign file is not gzipped
  (PR `#1630`_).
* Fix zcat stacking typo (PR `#1633`_).

.. _`#1629`: https://github.com/desihub/desispec/pull/1629
.. _`#1630`: https://github.com/desihub/desispec/pull/1630
.. _`#1633`: https://github.com/desihub/desispec/pull/1633

0.51.0 (2022-01-24)
-------------------

This version will be used for Fuji.

Algorithm update:

* Normalize fiberflat variation of each fiber for humidity correction
  (PR `#1621`_).

Metadata tracking updates:

* Add BADAMP[BRZ] bits to QAFIBERSTATUS (PR `#1610`_).
* specgroup metadata in spectra, coadd, zcat files (PR `#1618`_).

New and fixed scripts / functions:

* Add desispec.zcatalog.find_primary_spectra (PR `#1609`_).
* Add desispec.tile_qa.get_tilecov tile coverage plotting
  (PRs `#1613`_, `#1617`_).
* Fix bookkeeping of nights and tiles in coadds (issue `#1349`_) and enable
  coadding of previously coadded cframe files (issue `#1359`_) (PR `#1616`_).
* Ensure ``tilepix.fits`` only contains healpixels with reduced data (issue
  `#1374`_). Also fix issues `#1373`_ and `#1379`_ (PR `#1614`_).
* Add desi_find_badpos script to find exp-petals with catastrophic positioning
  (PR `#1620`_).

.. _`#1349`: https://github.com/desihub/desispec/issues/1349
.. _`#1359`: https://github.com/desihub/desispec/issues/1359
.. _`#1373`: https://github.com/desihub/desispec/issues/1373
.. _`#1374`: https://github.com/desihub/desispec/issues/1374
.. _`#1379`: https://github.com/desihub/desispec/issues/1379
.. _`#1609`: https://github.com/desihub/desispec/pull/1609
.. _`#1610`: https://github.com/desihub/desispec/pull/1610
.. _`#1613`: https://github.com/desihub/desispec/pull/1613
.. _`#1614`: https://github.com/desihub/desispec/pull/1614
.. _`#1616`: https://github.com/desihub/desispec/pull/1616
.. _`#1617`: https://github.com/desihub/desispec/pull/1617
.. _`#1618`: https://github.com/desihub/desispec/pull/1618
.. _`#1620`: https://github.com/desihub/desispec/pull/1620
.. _`#1621`: https://github.com/desihub/desispec/pull/1621

0.50.1 (2022-01-20)
-------------------

* Modification extname in QN afterburner outputs. Add flag in
  desi_qso_catalog_maker for retro-compatibility (PR `#1597`_).
* Outlier rejection in skycor PCA (PR `#1598`_).
* Include FAILED jobs in resubmissions (PR `#1602`_).
* tile-qa updates for special tiles (PR `#1603`_).
* Better masking behavior for BADCOLUMN (PR `#1605`_).
* Add DEPNAM/DEPVER to fibermap HDUs (PR `#1607`_).
* desi_run_night enhancements and bug fixes (PR `#1608`_).

.. _`#1597`: https://github.com/desihub/desispec/pull/1597
.. _`#1598`: https://github.com/desihub/desispec/pull/1598
.. _`#1602`: https://github.com/desihub/desispec/pull/1602
.. _`#1603`: https://github.com/desihub/desispec/pull/1603
.. _`#1605`: https://github.com/desihub/desispec/pull/1605
.. _`#1607`: https://github.com/desihub/desispec/pull/1607
.. _`#1608`: https://github.com/desihub/desispec/pull/1608

0.50.0 (2022-01-16)
-------------------

Used for the f5 test run part II.

* Algorithmic changes:

  * Use sky fibers to correct for serial readout CTE problems (PR `#1571`_).
  * Bug fixes for fiberflat_vs_humidity when near edge of model range
    (PRs `#1589`_, `#1594`_).

* Miscellaneous:

  * Approximate for missing turbulence corrections in FIBER_RA/DEC
    during Dec 2021 (PR `#1539`_).
  * nightqa improved selection of which 5min dark was used (PR `#1584`_).
  * findfile(tileqapng) bugfix for tile/night QA (PR `#1585`_).
  * night QA 5min DARK expid selection bug fix (PR `#1586`_).
  * fix qprod non-empty fibermaps (PR `#1587`_).
  * desi_update_specstatus --lastnight and --all options (PR `#1588`_).
  * better desi_proc error tracking (PR `#1590`_).
  * assemble_fibermap fail faster on invalid inputs (PR `#1592`_).

.. _`#1539`: https://github.com/desihub/desispec/pull/1539
.. _`#1571`: https://github.com/desihub/desispec/pull/1571
.. _`#1584`: https://github.com/desihub/desispec/pull/1584
.. _`#1585`: https://github.com/desihub/desispec/pull/1585
.. _`#1586`: https://github.com/desihub/desispec/pull/1586
.. _`#1587`: https://github.com/desihub/desispec/pull/1587
.. _`#1588`: https://github.com/desihub/desispec/pull/1588
.. _`#1589`: https://github.com/desihub/desispec/pull/1589
.. _`#1590`: https://github.com/desihub/desispec/pull/1590
.. _`#1592`: https://github.com/desihub/desispec/pull/1592
.. _`#1594`: https://github.com/desihub/desispec/pull/1594

0.49.1 (2022-01-10)
-------------------

Used for the f5 test run part I.

* Fix propagation of per-camera keywords into per-camera fibermap
  (commit #0c7aa720)

0.49.0 (2022-01-10)
-------------------

* Major algorithmic updates:

  * Fit CCD residual background between blocks of fiber traces
    (PR `#1551`_, `#1581`_).
  * Correction for fiberflat variations with humidity (PR `#1565`_).

* Other algorithmic updates:

  * Updated readnoise estimation when doing overscan per row (PR `#1564`_).
  * Remove average of overscan cols to overscan rows (PR `#1575`_).
  * Avoid false positive bad column mask on noisy input data (PR `#1579`_).
  * Improvements to desi_interpolate_fiber_psf (PR `#1557`_).

* Miscellaneous:

  * run nightlybias on nights without a dark (PR `#1553`_).
  * nightqa petal n(z) support programs with no tiles (PR `#1549`_, `#1554`_).
  * Fix GitHub tests fitsio/numpy incompatibility issues (PR `#1566`_).
  * Bad readnoise PSF failure robustness (PR `#1568`_).
  * Bad exposure bookkeeping for darks and biases (PR `#1570`_).
  * don't flag a tile as archived if archiving failed (PR `#1572`_).
  * Tile QA plotting updates (PR `#1577`_, )
  * Fix fitsverify errors when creating preproc files (PR `#1582`_).
  * Added ``assemble_fibermap --tilepix`` option (PR `#1583`_)

.. _`#1549`: https://github.com/desihub/desispec/pull/1549
.. _`#1551`: https://github.com/desihub/desispec/pull/1551
.. _`#1553`: https://github.com/desihub/desispec/pull/1553
.. _`#1554`: https://github.com/desihub/desispec/pull/1554
.. _`#1557`: https://github.com/desihub/desispec/pull/1557
.. _`#1564`: https://github.com/desihub/desispec/pull/1564
.. _`#1565`: https://github.com/desihub/desispec/pull/1565
.. _`#1566`: https://github.com/desihub/desispec/pull/1566
.. _`#1568`: https://github.com/desihub/desispec/pull/1568
.. _`#1570`: https://github.com/desihub/desispec/pull/1570
.. _`#1572`: https://github.com/desihub/desispec/pull/1572
.. _`#1575`: https://github.com/desihub/desispec/pull/1575
.. _`#1577`: https://github.com/desihub/desispec/pull/1577
.. _`#1579`: https://github.com/desihub/desispec/pull/1579
.. _`#1581`: https://github.com/desihub/desispec/pull/1581
.. _`#1582`: https://github.com/desihub/desispec/pull/1582
.. _`#1583`: https://github.com/desihub/desispec/pull/1583

0.48.1 (2021-12-21)
-------------------

Used for the f4 test run (albeit pre-tag).

* Fix deprecation warnings for latest numpy (PR `#1525`_).
* Support astropy 5.x masked columns (PR `#1526`_).
* More robust when fiberassign file is in earlier expid (PR `#1529`_, `#1536`_).
* Approximate FP coords if missing from coordinates file (PR `#1532`_).
* desi_run_night --surveys option (PR `#1533`_).
* night_qa v3 (PR `#1535`_).
* Update and standardize exposure tables (PR `#1537`_).
* Fix desi_proc spexec wrapper for single camera (PR `#1540`_).
* Fix desi_proc MPI logic bug if missing PSF input (PR `#1542`_).
* Change nightlybias OSTEP to be local instead of global diff (PR `#1543`_).
* Run nightlybias for all cameras (PR `#1546`_).
* Tune nightlybias running logic (PR `#1547`_).
* Add emlinefit afterburner (PR `#1386`_).

.. _`#1386`: https://github.com/desihub/desispec/pull/1386
.. _`#1525`: https://github.com/desihub/desispec/pull/1525
.. _`#1526`: https://github.com/desihub/desispec/pull/1526
.. _`#1529`: https://github.com/desihub/desispec/pull/1529
.. _`#1532`: https://github.com/desihub/desispec/pull/1532
.. _`#1533`: https://github.com/desihub/desispec/pull/1533
.. _`#1535`: https://github.com/desihub/desispec/pull/1535
.. _`#1536`: https://github.com/desihub/desispec/pull/1536
.. _`#1537`: https://github.com/desihub/desispec/pull/1537
.. _`#1540`: https://github.com/desihub/desispec/pull/1540
.. _`#1542`: https://github.com/desihub/desispec/pull/1542
.. _`#1543`: https://github.com/desihub/desispec/pull/1543
.. _`#1546`: https://github.com/desihub/desispec/pull/1546
.. _`#1547`: https://github.com/desihub/desispec/pull/1547

0.48.0 (2021-12-10)
-------------------

* Fix TSNR afterburner "unknown" entries (PR `#1495`_).
* Tile QA skip n(x) comparison for backup program (PR `#1497`_).
* assemble_fibermap robust to missing guider EXPTIME (PR `#1498`_).
* update job dependencies to be afterok instead of afterany (PR `#1502`_).
* Add desi_night_qa (PR `#1503`_, `#1522`_).
* desi_tile_vi only show main dark/bright tiles by default (PR `#1505`_).
* Add support for short QA flats in pipeline (PR `#1507`_, `#1517`_).
* Revise size of KNL batch jobs for arc fits (PR `#1508`_, `#1521`_).
* fix proctable entries with 0-length arrays (PR `#1509`_).
* flag FIBER_X/Y==0 as FIBERSTATUS MISSING (PR `#1514`_).
* Separate tile QA from tile archiving (PR `#1519`_).
* Improve pipeline operations on KNL (PR `#1523`_).

.. _`#1495`: https://github.com/desihub/desispec/pull/1495
.. _`#1497`: https://github.com/desihub/desispec/pull/1497
.. _`#1498`: https://github.com/desihub/desispec/pull/1498
.. _`#1502`: https://github.com/desihub/desispec/pull/1502
.. _`#1503`: https://github.com/desihub/desispec/pull/1503
.. _`#1505`: https://github.com/desihub/desispec/pull/1505
.. _`#1507`: https://github.com/desihub/desispec/pull/1507
.. _`#1508`: https://github.com/desihub/desispec/pull/1508
.. _`#1509`: https://github.com/desihub/desispec/pull/1509
.. _`#1514`: https://github.com/desihub/desispec/pull/1514
.. _`#1517`: https://github.com/desihub/desispec/pull/1517
.. _`#1519`: https://github.com/desihub/desispec/pull/1519
.. _`#1521`: https://github.com/desihub/desispec/pull/1521
.. _`#1522`: https://github.com/desihub/desispec/pull/1522
.. _`#1523`: https://github.com/desihub/desispec/pull/1523


0.47.1 (2021-11-24)
-------------------

* New desi_resubmit_queue_failures script (PR `#1482`_).
* fix CAMERA column name in stdstars INPUT_FRAMES HDU (PR `#1484`_).
* raise exception when no valid sky fibers (PR `#1486`_, `#1488`_).
* Update qso_catalog_maker to include all targets (PR `#1487`_).
* Fix TSNR2 calculation and exposure QA for 2-amp readout (PR `#1489`_).
* Exclude masked pixels in stdstar RMS QA (PR `#1490`_).
* Support for very early fiberassign files in
  :func:`~desispec.io.fibermap.assemble_fibermap` (PR `#1492`_).
* desi_tile_vi --qastatus option (PR `#1493`_).

.. _`#1482`: https://github.com/desihub/desispec/pull/1482
.. _`#1484`: https://github.com/desihub/desispec/pull/1484
.. _`#1486`: https://github.com/desihub/desispec/pull/1486
.. _`#1487`: https://github.com/desihub/desispec/pull/1487
.. _`#1488`: https://github.com/desihub/desispec/pull/1488
.. _`#1489`: https://github.com/desihub/desispec/pull/1489
.. _`#1490`: https://github.com/desihub/desispec/pull/1490
.. _`#1492`: https://github.com/desihub/desispec/pull/1492
.. _`#1493`: https://github.com/desihub/desispec/pull/1493

0.47.0 (2021-11-11)
-------------------

* tsnr_afterburner support for old HDU names (PR `#1403`_).
* Tiles tables and QA cleanup (PRs `#1406`_, `#1407`_, `#1409`_, `#1410`_,
  `#1430`_, `#1442`_, `#1445`_, `#1449`_, `#1458`_, `#1475`_).
* Support averaging PSFs with different wavelength ranges (PR `#1411`_).
* QSO afterburner add blank file when no targets to write (PR `#1412`_).
* Update airmass dependence for exposure quality cuts (PR `#1413`_).
* Only use good sky fibers for sky model (PR `#1414`_).
* Switch EFFTIME_SPEC to be based upon LRG instead of ELG (PR `#1417`_).
* specex job scheduler for improved performance (PR `#1418`_).
* Add desi_update_tiles_specstatus script (PR `#1421`_).
* Parallelize fiberflatnight and cleanup tempfiles (PR `#1427`_).
* Cleanup bad fiber tracking BROKENFIBERS, BADCOLUMNFIBERS,
  LOWTRANSMISSIONFIBERS (PR `#1429`_).
* Select calibration stars per exposure across petals (PR `#1434`_).
* QSO afterburner run on all targets, not just QSO (PR `#1435`_).
* Set OMP_NUM_THREADS in batch script (`#1437`_).
* Allow fiberassign svn to have different negative TARGETID (PR `#1444`_).
* Arc jobs restricted to <= 10 nodes even on KNL (PR `#1450`_).
* Sky model bug fix to avoid fake z~4.3 QSO (PR `#1452`_).
* desi_edit_exposure_table useability improvements (PR `#1453`_).
* switch io.read_fibermap to use fitsio to avoid astropy masked columns
  (PR `#1454`_, `#1479`_)
* daily pipeline runner cache exposures after every new exp (PR `#1455`_).
* Hartmann doors analysis script (PR `#1457`_).
* Ensure consistent output from :func:`~desispec.io.fibermap.assemble_fibermap` (PR `#1458`_).
* New desi_compute_nightly_bias script (PR `#1460`_).
* Incorporate nightly bias and bad column identification into daily pipeline
  (PR `#1463`_).
* Add OSTEP metric for variation of overscan per row (PR `#1464`_).
* Add nightly bias and bad column flagging to pipeline
  (PR `#1465`_, `#1467`_)
* Fix check_for_outputs bug and teach findfile about fit-psf (PR `#1469`_).
* Set fibermap.FIBERSTATUS BADREADNOISE and BADAMP[BRZ] (PR `#1472`_).
* Don't use PSFs with bad amps (PR `#1473`_).
* Support 2-amp readout (PR `#1476`_).
* Use only offset traceshifts when amplifier is masked (PR `#1477`_).
* desi_archive_tilenight to archive nights after tile QA approval (PR `#1478`_).
* processing dashboard useability updates (PR `#1480`_).
* use desitarget.skybricks to check stuck sky locations (PR `#1481`_).

.. _`#1403`: https://github.com/desihub/desispec/pull/1403
.. _`#1406`: https://github.com/desihub/desispec/pull/1406
.. _`#1407`: https://github.com/desihub/desispec/pull/1407
.. _`#1409`: https://github.com/desihub/desispec/pull/1409
.. _`#1410`: https://github.com/desihub/desispec/pull/1410
.. _`#1411`: https://github.com/desihub/desispec/pull/1411
.. _`#1412`: https://github.com/desihub/desispec/pull/1412
.. _`#1413`: https://github.com/desihub/desispec/pull/1413
.. _`#1414`: https://github.com/desihub/desispec/pull/1414
.. _`#1417`: https://github.com/desihub/desispec/pull/1417
.. _`#1418`: https://github.com/desihub/desispec/pull/1418
.. _`#1421`: https://github.com/desihub/desispec/pull/1421
.. _`#1427`: https://github.com/desihub/desispec/pull/1427
.. _`#1429`: https://github.com/desihub/desispec/pull/1429
.. _`#1430`: https://github.com/desihub/desispec/pull/1430
.. _`#1434`: https://github.com/desihub/desispec/pull/1434
.. _`#1435`: https://github.com/desihub/desispec/pull/1435
.. _`#1437`: https://github.com/desihub/desispec/pull/1437
.. _`#1442`: https://github.com/desihub/desispec/pull/1442
.. _`#1444`: https://github.com/desihub/desispec/pull/1444
.. _`#1445`: https://github.com/desihub/desispec/pull/1445
.. _`#1449`: https://github.com/desihub/desispec/pull/1449
.. _`#1450`: https://github.com/desihub/desispec/pull/1450
.. _`#1452`: https://github.com/desihub/desispec/pull/1452
.. _`#1453`: https://github.com/desihub/desispec/pull/1453
.. _`#1454`: https://github.com/desihub/desispec/pull/1454
.. _`#1455`: https://github.com/desihub/desispec/pull/1455
.. _`#1457`: https://github.com/desihub/desispec/pull/1457
.. _`#1458`: https://github.com/desihub/desispec/pull/1458
.. _`#1459`: https://github.com/desihub/desispec/pull/1459
.. _`#1460`: https://github.com/desihub/desispec/pull/1460
.. _`#1463`: https://github.com/desihub/desispec/pull/1463
.. _`#1464`: https://github.com/desihub/desispec/pull/1464
.. _`#1465`: https://github.com/desihub/desispec/pull/1465
.. _`#1467`: https://github.com/desihub/desispec/pull/1467
.. _`#1469`: https://github.com/desihub/desispec/pull/1469
.. _`#1472`: https://github.com/desihub/desispec/pull/1472
.. _`#1473`: https://github.com/desihub/desispec/pull/1473
.. _`#1475`: https://github.com/desihub/desispec/pull/1475
.. _`#1476`: https://github.com/desihub/desispec/pull/1476
.. _`#1477`: https://github.com/desihub/desispec/pull/1477
.. _`#1478`: https://github.com/desihub/desispec/pull/1478
.. _`#1479`: https://github.com/desihub/desispec/pull/1479
.. _`#1480`: https://github.com/desihub/desispec/pull/1480
.. _`#1481`: https://github.com/desihub/desispec/pull/1481

0.46.1 (2021-09-03)
-------------------

* Restore ``desi_zcatalog`` backwards compatibility for inputs without a
  separate EXP_FIBERMAP (PR `#1392`_).
* ``tsnr_afterburner`` robustness to missing/different columns, e.g. from
  reprocessed daily exposures (PR `#1396`_).
* Save STDSTAR_FIBERMAP in fluxcalib file recording which stars were used
  (PR `#1400`_).
* stdstars robust to missing individual frames (PR `#1402`_).

.. _`#1392`: https://github.com/desihub/desispec/pull/1392
.. _`#1396`: https://github.com/desihub/desispec/pull/1396
.. _`#1400`: https://github.com/desihub/desispec/pull/1400
.. _`#1402`: https://github.com/desihub/desispec/pull/1402

0.46.0 (2021-09-01)
-------------------

* Detect and flag sky fibers affected by a bright source (PR `#1367`_)
* Adjust spectral traces when computing CCD variance in preprocessing (PR `#1368`_, `#1378`_).
* Detect bad CCD columns in nightly dark; use to mask impacted wavelengths
  of individual spectra (PR `#1371`_).
* Model CCD readnoise with Poisson noise from the zero exposure dark current
  (PR `#1372`_).
* Speed up coadd_cameras (PR `#1377`_).
* Improve sky subtraction with PCA model of wavelength and LSF sigma
  adjustments (PR `#1381`_).
* Swap fibers 3402 and 3429 if input fiber:location map is wrong (PR `#1382`_).
* Tile QA minor fixes (PR `#1385`_).
* Allow fiberassign SVN to override raw data fiberassign (PR `#1387`_).
* Add ``desi_run_night --tiles`` option (PR `#1391`_).

.. _`#1367`: https://github.com/desihub/desispec/pull/1367
.. _`#1368`: https://github.com/desihub/desispec/pull/1368
.. _`#1371`: https://github.com/desihub/desispec/pull/1371
.. _`#1372`: https://github.com/desihub/desispec/pull/1372
.. _`#1377`: https://github.com/desihub/desispec/pull/1377
.. _`#1378`: https://github.com/desihub/desispec/pull/1378
.. _`#1381`: https://github.com/desihub/desispec/pull/1381
.. _`#1382`: https://github.com/desihub/desispec/pull/1382
.. _`#1385`: https://github.com/desihub/desispec/pull/1385
.. _`#1387`: https://github.com/desihub/desispec/pull/1387
.. _`#1391`: https://github.com/desihub/desispec/pull/1391

0.45.3 (2021-07-29)
-------------------

Everest cleanup PRs; in 21.7e software release.

* Fix "unknown" entries in tsnr/exposures file (PR `#1321`_).
* desi_healpix_redshift options for extra memory (PR `#1343`_).
* desi_zcatalog for new fibermap format (PR `#1347`_).
* Include TILERA, TILEDEC, MJD in tiles/exposures output tables (PR `#1348`_).
* desi_group_spectra --healpix option (PR `#1350`_).
* desi_tile_redshifts --group cumulative bug fixes (PR `#1353`_).
* desi_map_tilepix script (PR `#1358`_).
* merge of above PRs into main/master (PR `#1360`_).

.. _`#1321`: https://github.com/desihub/desispec/pull/1321
.. _`#1343`: https://github.com/desihub/desispec/pull/1343
.. _`#1347`: https://github.com/desihub/desispec/pull/1347
.. _`#1348`: https://github.com/desihub/desispec/pull/1348
.. _`#1350`: https://github.com/desihub/desispec/pull/1350
.. _`#1353`: https://github.com/desihub/desispec/pull/1353
.. _`#1358`: https://github.com/desihub/desispec/pull/1358
.. _`#1360`: https://github.com/desihub/desispec/pull/1360

0.45.2 (2021-07-20)
-------------------

Everest bookkeeping update for sv1 spectra regrouping and sv3 redshift cleanup.

* desi_group_spectra options to filter and group by survey and faprogram,
  including ``desispec.io.meta.faflavor2program`` to handle special cases
  for sv1 (PR `#1341`_).
* desi_healpix_redshifts options for memory usage (PR `#1341`_).

.. _`#1342`: https://github.com/desihub/desispec/pull/1341

0.45.1 (2021-07-15)
-------------------

For Everest tile spectra+coadds+redshifts; in 21.7d

* Recompute proccamword from exptable for proecessing dashboard (PR `#1340`_).
* Add support for healpix coadd+redshift jobs (PR `#1341`_).

.. _`#1340`: https://github.com/desihub/desispec/pull/1340
.. _`#1341`: https://github.com/desihub/desispec/pull/1341

0.45.0 (2021-07-14)
-------------------

For Everest tile spectra+coadds+redshifts; in 21.7c

Note: this is a major format change to coadd and redrock (formerly zbest) files:

* FIBERMAP split into FIBERMAP (coadded) + EXP_FIBERMAP (per-exposure)
* zbest files renamed redrock

Requires redrock >= 0.15.0

Details / PRs:

* tune tile QA parameters
* Add desi_qso_catalog_maker (PRs `#1322`_, `#1339`_).
* QSO afterburner cross checks and bug fixes (PRs `#1334`_, `#1335`_)
* Fix exposure table loading typo (PR `#1337`_).
* Rename zbest -> redrock (PR `#1338`_).
* Split coadd FIBERMAP into FIBERMAP + EXP_FIBERMAP (PR `#1330`_).
* QSO afterburners run in desi_tile_redshifts by default (PR `#1330`_).

.. _`#1322`: https://github.com/desihub/desispec/pull/1322
.. _`#1330`: https://github.com/desihub/desispec/pull/1330
.. _`#1334`: https://github.com/desihub/desispec/pull/1334
.. _`#1335`: https://github.com/desihub/desispec/pull/1335
.. _`#1337`: https://github.com/desihub/desispec/pull/1337
.. _`#1338`: https://github.com/desihub/desispec/pull/1338
.. _`#1339`: https://github.com/desihub/desispec/pull/1339

0.44.2 (2021-07-07)
-------------------

Intended for Everest science exposures through cframes; in 21.7b.

* Fixed data/qa/ installation.

0.44.1 (2021-07-07)
-------------------

* Add fibermap PLATE_RA,PLATE_DEC if missing from fiberassign file for
  sv3 and main survey data model consistency (PR `#1331`_).
* Set FIBERSTATUS POORPOSITION bit when positioner is offset by
  30-100 microns.  Don't use these for stdstar fitting but otherwise
  process as normal. (PR `#1333`_).

.. _`#1331`: https://github.com/desihub/desispec/pull/1331
.. _`#1333`: https://github.com/desihub/desispec/pull/1333

0.44.0 (2021-07-06)
-------------------

First tag used for Everest arc/flat calibs; in 21.7a.

* Add QSO afterburners for MgII and QuasarNet (PR `#1312`_).
* Spectra I/O for extra catalog (PR `#1313`_).
* Expand Spectra.select and .update functionality (PR `#1319`_).
* Add optional support for gpu_specter for extractions (PR `#993`_).
* Fix extra_catalog support for grouping by healpix (PR `#1325`_).
* Pipeline progress bug fixes and features (PRs `#1326`_, `#1329`_).

.. _`#993`: https://github.com/desihub/desispec/pull/993
.. _`#1312`: https://github.com/desihub/desispec/pull/1312
.. _`#1313`: https://github.com/desihub/desispec/pull/1313
.. _`#1319`: https://github.com/desihub/desispec/pull/1319
.. _`#1325`: https://github.com/desihub/desispec/pull/1325
.. _`#1326`: https://github.com/desihub/desispec/pull/1326
.. _`#1329`: https://github.com/desihub/desispec/pull/1329

0.43.0 (2021-06-21)
-------------------

This version was used for QA assessment of the first 315 main survey tiles
released for unlocking overlapping tiles.  That was done pre-tag under the
development version "0.42.0.dev5412".

* Improved stitching of sky spectra from different cameras (PR `#1273`_).
* TSNR updates (PR `#1274`_ and branch PRs `#1275`_, `#1277`_, `#1279`_,
  `#1282`_, `#1283`_, `#1285`_).
* qproc robust to blank SEEING keyword (PR `#1289`_).
* update SV1-SV3 average throughtput (PR `#1291`_).
* fix x traceshift indexing bug (PR `#1292`_).
* desi_tile_redshifts --run_zqso option (PR `#1293`_).
* pre-write speclog when generating dark model scripts (PR `#1300`_).
* Add spectroscopic QA (PR `#1302`_, `#1316`_).
* Improve pipeline metadata handling and implement QA cuts (PR `#1304`_).
* Check for completely masked fibers in qfiberflat (PR `#1306`_).
* Pipeline robustness when reading ETC values from raw data (PR `#1309`_).
* Adjust exposure QA cuts, cleanup outputs (PRs `#1316`_, `#1318`_).
* Simplified tile QA (PR `#1317`_).
* zmtl using tile QA to set ZWARN bits (PR `#1310`_).
* Look for manifest files in nightly processing (PR `#1320`_).

.. _`#1273`: https://github.com/desihub/desispec/issues/1273
.. _`#1274`: https://github.com/desihub/desispec/issues/1274
.. _`#1275`: https://github.com/desihub/desispec/issues/1275
.. _`#1277`: https://github.com/desihub/desispec/issues/1277
.. _`#1279`: https://github.com/desihub/desispec/issues/1279
.. _`#1282`: https://github.com/desihub/desispec/issues/1282
.. _`#1283`: https://github.com/desihub/desispec/issues/1283
.. _`#1285`: https://github.com/desihub/desispec/issues/1285
.. _`#1289`: https://github.com/desihub/desispec/issues/1289
.. _`#1291`: https://github.com/desihub/desispec/issues/1291
.. _`#1292`: https://github.com/desihub/desispec/issues/1292
.. _`#1293`: https://github.com/desihub/desispec/issues/1293
.. _`#1300`: https://github.com/desihub/desispec/issues/1300
.. _`#1302`: https://github.com/desihub/desispec/issues/1302
.. _`#1304`: https://github.com/desihub/desispec/issues/1304
.. _`#1306`: https://github.com/desihub/desispec/issues/1306
.. _`#1309`: https://github.com/desihub/desispec/issues/1309
.. _`#1310`: https://github.com/desihub/desispec/issues/1310
.. _`#1316`: https://github.com/desihub/desispec/issues/1316
.. _`#1317`: https://github.com/desihub/desispec/issues/1317
.. _`#1318`: https://github.com/desihub/desispec/issues/1318
.. _`#1320`: https://github.com/desihub/desispec/issues/1320

0.42.0 (2021-05-14)
-------------------

Requires desiutil >= 3.2.1 for new dust extinction calculations.

* Wrap ``bin/desi_proc`` and ``bin/desi_proc_joint_fit`` in functions to
  facilitate pipeline wrappers (PRs `#1242`_ and `#1244`_).
* Use less restrictive gfaproc extension 2 instead of 3 for EFFTIME_GFA
  (PR `#1245`_).
* Add MPI to stdstar ``match_templates`` (PR `#1248`_).
* Updates to ``desi_average_flux_calibration`` (PR `#1252`_).
* ``desi_fit_stdstars --std-targetids`` option to override stdstars for testing
  and custom fields (PR `#1257`_, `#1259`_).
* Launch redshifts automatically as part of pipeline (PR `#1260`_).
* Support stuck positioners assigned to sky locations (PR `#1266`_).
* Use desiutil.dust for extinction including Gaia (PR `#1269`_).
* Fix running instance checking in daily pipeline (PR `#1270`_).

.. _`#1242`: https://github.com/desihub/desispec/issues/1242
.. _`#1244`: https://github.com/desihub/desispec/issues/1244
.. _`#1245`: https://github.com/desihub/desispec/issues/1245
.. _`#1248`: https://github.com/desihub/desispec/issues/1248
.. _`#1252`: https://github.com/desihub/desispec/issues/1252
.. _`#1257`: https://github.com/desihub/desispec/issues/1257
.. _`#1259`: https://github.com/desihub/desispec/issues/1259
.. _`#1260`: https://github.com/desihub/desispec/issues/1260
.. _`#1266`: https://github.com/desihub/desispec/issues/1266
.. _`#1269`: https://github.com/desihub/desispec/issues/1269
.. _`#1270`: https://github.com/desihub/desispec/issues/1270

0.41.0 (2021-04-16)
-------------------

Although most of the Denali production was run with tag 0.40.1, the following
updates where made for final steps to recover some missing coadds and make
the final tsnr and tiles files:

* Exposure and tiles files updates, including merging GFA data.
  (PR `#1226`_, `#1232`_, `#1236`_, plus commits directly to master on Apr 12).
* Fix coadds with missing TSNR columns due to missing cameras (PR `#1239`_).

Changes that also occured in the meantime but were not used for Denali
processing (they impact earlier steps):

* Flag fibers that are mis-positioned by >100 um as bad. (PR `#1233`_).
* Correct bit flagging and support split exposures with
  ``bin/assemble_fibermap`` (PR `#1235`_).
* Also write fibercorr to the fluxcalibration when using low S/N simplified
  calibration (direct fix to master).

.. _`#1226`: https://github.com/desihub/desispec/issues/1226
.. _`#1232`: https://github.com/desihub/desispec/issues/1232
.. _`#1233`: https://github.com/desihub/desispec/issues/1233
.. _`#1235`: https://github.com/desihub/desispec/issues/1235
.. _`#1236`: https://github.com/desihub/desispec/issues/1236
.. _`#1239`: https://github.com/desihub/desispec/issues/1239

0.40.1 (2020-04-01)
-------------------

Installation and job submission fixes for Denali; no algorithmic changes.

* fix data installation (PR `#1221`_).
* ``desi_tile_redshifts --batch-reservation`` fix for Denali run (PR `#1222`_).

.. _`#1221`: https://github.com/desihub/desispec/issues/1221
.. _`#1222`: https://github.com/desihub/desispec/issues/1222

0.40.0 (2021-03-31)
-------------------

First tag for 21.3/Denali run

* Add fiber crosstalk correction (PR `#1138`_).
* Handle missing NIGHT in coadded fibermap (PR `#1195`_).
* Add ``desi_tiles_completeness`` script with TSNR2-based tile
  completeness calculations for survey ops (PR `#1196`_, `#1200`_, `#1204`_,
  `#1206`_, `#1212`_).
* TSNR2 camera coadd fix (PR `#1197`_).
* refactor `desi_tile_redshifts` for more flexibility (PR `#1198`_, `#1208`_,
  `#1211`_).
* processing dashboard: cache night info (PR `#1199`_).
* speed up sky calculation with different sparse matrices (PR `#1209`_).
* Check file outputs before submitting jobs (PR `#1217`_).
* improve noise of master dark model fit (PR `#1219`_).
* Add workflow hooks for KNL (PR `#1220`_).

.. _`#1138`: https://github.com/desihub/desispec/issues/1138
.. _`#1195`: https://github.com/desihub/desispec/issues/1195
.. _`#1196`: https://github.com/desihub/desispec/issues/1196
.. _`#1197`: https://github.com/desihub/desispec/issues/1197
.. _`#1198`: https://github.com/desihub/desispec/issues/1198
.. _`#1199`: https://github.com/desihub/desispec/issues/1199
.. _`#1200`: https://github.com/desihub/desispec/issues/1200
.. _`#1204`: https://github.com/desihub/desispec/issues/1204
.. _`#1206`: https://github.com/desihub/desispec/issues/1206
.. _`#1208`: https://github.com/desihub/desispec/issues/1208
.. _`#1209`: https://github.com/desihub/desispec/issues/1209
.. _`#1211`: https://github.com/desihub/desispec/issues/1211
.. _`#1212`: https://github.com/desihub/desispec/issues/1212
.. _`#1219`: https://github.com/desihub/desispec/issues/1219
.. _`#1217`: https://github.com/desihub/desispec/issues/1217
.. _`#1220`: https://github.com/desihub/desispec/issues/1220

0.39.3 (2020-03-04)
-------------------

Cascades update tag for final catalog creation.

Note: datamodel changes to coadd SCORES and FIBERMAP

* Propagate TSNR2 into coadd SCORES; update coadd FIBERMAP columns (PR `#1166`_)
* ``bin/desi_tsnr_afterburner`` use pre-calculated TSNR2 from frame files
  unless requested to recalculate (PR `#1167`_).

.. _`#1166`: https://github.com/desihub/desispec/issues/1166
.. _`#1167`: https://github.com/desihub/desispec/issues/1167

0.39.2 (2021-03-02)
-------------------

Cascades update tag to fix coadd and tSNR crashes, and postfacto tag
``desi_spectro_calib`` version in desispec module file.

* Processing dashboard useability updates (PR `#1152`_).
* Undo heliocentric correction in throughput analysis not used for
  production processing (PR `#1154`_).
* Fix coadd crash (PR `#1163`_).
* Fix tSNR alpha<0.8 crash (PR `#1164`_).
* Updated desi_spectro_calib version to 0.2.4.

.. _`#1152`: https://github.com/desihub/desispec/issues/1152
.. _`#1154`: https://github.com/desihub/desispec/issues/1154
.. _`#1163`: https://github.com/desihub/desispec/issues/1163
.. _`#1164`: https://github.com/desihub/desispec/issues/1164

0.39.1 (2021-02-23)
-------------------

Cascades update tag to add functionality for using a queue reservation and for
debugging, without algorithmically impacting what has already been run
with the 0.39.0 tag.

* Add ``desi_run_night --reservation`` option (PR `#1145`_).
* Fix ``desi_process_exposure --no-zero-ivar`` option (PR `#1146`_).

.. _`#1145`: https://github.com/desihub/desispec/issues/1145
.. _`#1146`: https://github.com/desihub/desispec/issues/1146

0.39.0 (2021-02-16)
-------------------

Initial tag for Cascades run.

Major updates:

* Update exposure table formats and pipeline workflow (PR `#1135`_, `#1139`_).
* Add template S/N (TSNR) depth calculations (PR `#1136`_).

Smaller updates:

* Propagate fiberassign HDU 0 keywords into fibermap header in addition to
  ``FIBERASSIGN`` (HDU 1) keywords (PR `#1137`_).
* ``desi_proc_joint_fit`` exit with error code if all cameras fail
  (PR `#1140`_).
*  Frame units "electron/Angstrom" instead of "count/Angstrom" (PR `#1142`_).

.. _`#1135`: https://github.com/desihub/desispec/issues/1135
.. _`#1136`: https://github.com/desihub/desispec/issues/1136
.. _`#1137`: https://github.com/desihub/desispec/issues/1137
.. _`#1139`: https://github.com/desihub/desispec/issues/1139
.. _`#1140`: https://github.com/desihub/desispec/issues/1140
.. _`#1142`: https://github.com/desihub/desispec/issues/1142

0.38.0 (2021-02-10)
-------------------

* Change how specex PSF fitting is called; requires specex>=0.7.0 (PR `#1082`_)

.. _`#1082`: https://github.com/desihub/desispec/issues/1082

0.37.0 (2021-02-10)
-------------------

Major updates:

* Support Gaia stdstars (PR `#1105`_, `#1109`_, `#1114`_, `#1133`_).
* Fix cosmics masking in coaddition (PR `#1113`_).
* Improved sky modeling (PR `#1125`_).

Smaller (but important) updates:

* Standardize getting NIGHT from raw data headers (PR `#1083`_, `#1120`_).
* Use acquisition guide file if full guide file isn't available (PR `#1084`_).
* Updates to flux calibration averages used by nightwatch (PR `#1085`_).
* New read_tile_spectra and Spectra class slicing (PR `#1107`_).
* Add token to fix coverage tests (PR `#1112`_).
* Flux calibration robustness for low transmission exposures (PR `#1116`_).
* Apply heliocentric correction to fiberflat (PR `#1118`_).
* Robustness and feature updates to dark model generation
  (PR `#1119`_, `#1123`_)
* More flexible CCD calibration configuration (PR `#1121`_).
* Processing dashboard useability updates (PR `#1127`_).
* NIGHT int vs. str bugfix in QA (PR `#1129`_).
* Support coaddition of fibermaps with different columns (PR `#1130`_).

.. _`#1083`: https://github.com/desihub/desispec/issues/1083
.. _`#1084`: https://github.com/desihub/desispec/issues/1084
.. _`#1085`: https://github.com/desihub/desispec/issues/1085
.. _`#1105`: https://github.com/desihub/desispec/issues/1105
.. _`#1107`: https://github.com/desihub/desispec/issues/1107
.. _`#1109`: https://github.com/desihub/desispec/issues/1109
.. _`#1112`: https://github.com/desihub/desispec/issues/1112
.. _`#1113`: https://github.com/desihub/desispec/issues/1113
.. _`#1114`: https://github.com/desihub/desispec/issues/1114
.. _`#1116`: https://github.com/desihub/desispec/issues/1116
.. _`#1118`: https://github.com/desihub/desispec/issues/1118
.. _`#1119`: https://github.com/desihub/desispec/issues/1119
.. _`#1120`: https://github.com/desihub/desispec/issues/1120
.. _`#1121`: https://github.com/desihub/desispec/issues/1121
.. _`#1123`: https://github.com/desihub/desispec/issues/1123
.. _`#1125`: https://github.com/desihub/desispec/issues/1125
.. _`#1127`: https://github.com/desihub/desispec/issues/1127
.. _`#1129`: https://github.com/desihub/desispec/issues/1129
.. _`#1130`: https://github.com/desihub/desispec/issues/1130
.. _`#1133`: https://github.com/desihub/desispec/issues/1133

0.36.1 (2021-01-04)
-------------------

* Fix PSF traceshifts when a fiber is completely masked (PR `#1080`_).
* Robust to NaN in desi_average_flux_calibration (commit f1de1ac).
* Increase arc and flat runtimes (commit 7cb294c).

.. _`#1080`: https://github.com/desihub/desispec/issues/1080

0.36.0 (2020-12-23)
-------------------

This is the primary tag for the Mt. Blanc spectro pipeline run.

* Major updates:

  * Coadd fluxes in multi-exp standard stars before fitting (PR `#1059`_).
  * New model of CCD pixel-level variance (PR `#1062`_).
  * Adjust sky-line variance based on model chi2 (PR `#1062`_).

* Smaller (but important) updates:

  * Fixes assemble_fibermap for older data
    (PR `#1047`_, bug introduced in PR `#1045`_).
  * Use EBV instead of MW_TRANSMISSION_G/R/Z from fiberassign (PR `#1048`_).
  * Fallback to using FA_TYPE if no stdstars in (SVn\_)DESI_TARGET
    (PR `#1050`_).
  * Use GitHub Actions for testing instead of Travis (PR `#1053`_).
  * Fix stdstar absolute symlinks (PR `#1056`_).
  * Adjust nodes per job (PR `#1056`_ and `#1068`_).
  * Workflow options for bad exposures and new end-of-cals manifests
    (PR `#1057`_).
  * stdstar robustness if petal is disabled (PR `#1060`_).
  * improved camera argument parsing (PR `#1061`_).
  * Fix unphysical spike at edge of calibration vectors (PR `#1065`_).
  * Add header keywords for input calib provenance (PR `#1069`_).
  * More logging about stdstar selection cuts (PR `#1070`_).
  * Only uses fiberassign .fits and .fits.gz (but not .fits.orig) (PR `#1072`_).
  * Support "unpositioned" exposures; propagate FIBER_RA/DEC if present
    (PR `#1073`_).
  * Use desi_spectro_calib tag 0.2.1

.. _`#1047`: https://github.com/desihub/desispec/issues/1047
.. _`#1048`: https://github.com/desihub/desispec/issues/1048
.. _`#1050`: https://github.com/desihub/desispec/issues/1050
.. _`#1053`: https://github.com/desihub/desispec/issues/1053
.. _`#1056`: https://github.com/desihub/desispec/issues/1056
.. _`#1057`: https://github.com/desihub/desispec/issues/1057
.. _`#1059`: https://github.com/desihub/desispec/issues/1059
.. _`#1060`: https://github.com/desihub/desispec/issues/1060
.. _`#1061`: https://github.com/desihub/desispec/issues/1061
.. _`#1062`: https://github.com/desihub/desispec/issues/1062
.. _`#1065`: https://github.com/desihub/desispec/issues/1065
.. _`#1068`: https://github.com/desihub/desispec/issues/1068
.. _`#1069`: https://github.com/desihub/desispec/issues/1069
.. _`#1070`: https://github.com/desihub/desispec/issues/1070
.. _`#1072`: https://github.com/desihub/desispec/issues/1072
.. _`#1073`: https://github.com/desihub/desispec/issues/1073


0.35.0 (2020-12-11)
-------------------

* Major updates:

  * New opts to model image variance and improve sky subtraction (PR `#1008`_).
  * Refactor desi_proc and daily processing workflow
    (PRs `#1012`_, `#1014`_, `#1030`_)
  * New bias+dark model ("non-linear dark y1D") in desi_spectro_calib 0.2.0
    (PR `#1029`_)

* Smaller (but important) updates:

  * etc/desispec.modules uses desi_spectro_calib 0.2.0
  * Default saturation 2**16-1; updated keywords (PR `#1046`_).
  * Fix preproc header keyword propagation (PR `#1045`_).
  * Add support for gzipped fiberassign files (PR `#1042`_).
  * Fix tests on single-core machines (PR `#1035`_).
  * `desi_paste_preproc` for future use combining short+long arcs (PR `#1034`_).
  * `desi_proc` more robust to `specex` failures (PR `#1033`_).
  * Add parallelism to `desi_preproc` (PRs `#1032`_, `#1036`_, `#1038`_).
  * Fix specex empty path bug (PR `#1031`_).
  * Better qproc warnings for test slit exposures (PR `#1028`_).
  * `desi_focus` focus scan analysis (PR `#1027`_).
  * Fix/add BUNIT header keyword (PR `#1023`_).
  * Adds `desi_compute_broadband_pixel_flatfield` (PR `#1022`_).
  * Update desi_proc timing logging (PR `#1003`_, `#1026`_).
  * desispec.module sets MPICH_GNI_FORK_MODE=FULLCOPY for MPI+multiprocessing
    (PR `#1007`_).
  * Fix dark CCD calibration corrections (PR `#1002`_).

.. _`#1002`: https://github.com/desihub/desispec/issues/1002
.. _`#1003`: https://github.com/desihub/desispec/issues/1003
.. _`#1007`: https://github.com/desihub/desispec/issues/1007
.. _`#1008`: https://github.com/desihub/desispec/issues/1008
.. _`#1012`: https://github.com/desihub/desispec/issues/1012
.. _`#1014`: https://github.com/desihub/desispec/issues/1014
.. _`#1022`: https://github.com/desihub/desispec/issues/1022
.. _`#1023`: https://github.com/desihub/desispec/issues/1023
.. _`#1026`: https://github.com/desihub/desispec/issues/1026
.. _`#1027`: https://github.com/desihub/desispec/issues/1027
.. _`#1028`: https://github.com/desihub/desispec/issues/1028
.. _`#1029`: https://github.com/desihub/desispec/issues/1029
.. _`#1030`: https://github.com/desihub/desispec/issues/1030
.. _`#1031`: https://github.com/desihub/desispec/issues/1031
.. _`#1032`: https://github.com/desihub/desispec/issues/1032
.. _`#1033`: https://github.com/desihub/desispec/issues/1033
.. _`#1034`: https://github.com/desihub/desispec/issues/1034
.. _`#1035`: https://github.com/desihub/desispec/issues/1035
.. _`#1036`: https://github.com/desihub/desispec/issues/1036
.. _`#1038`: https://github.com/desihub/desispec/issues/1038
.. _`#1042`: https://github.com/desihub/desispec/issues/1042
.. _`#1045`: https://github.com/desihub/desispec/issues/1045
.. _`#1046`: https://github.com/desihub/desispec/issues/1046

0.34.7 (2020-09-01)
-------------------

* Switch desi_proc to use fitsio instead of astropy.io.fits to work around
  incompatibility between mpi4py and astropy 4 (PR `#996`_).

.. _`#996`: https://github.com/desihub/desispec/issues/996

0.34.6 (2020-08-04)
-------------------

* Extend runtime limit for spectra regrouping task (hotfix to master).

0.34.5 (2020-08-04)
-------------------

* Faster desi_zcatalog merging with target table (PR `#994`_).
* Python 3.8 support (PR `#990`_).
* Astropy 4.x support (PR `#989`_).
* Update CCD mask generation code (PR `#987`_).
* Update desispec.io.download to use data.desi.lbl.gov (PR `#972`_).
* Use middle of exposure for barycentric correction time (PR `#971`_).

.. _`#994`: https://github.com/desihub/desispec/issues/994
.. _`#990`: https://github.com/desihub/desispec/issues/990
.. _`#989`: https://github.com/desihub/desispec/issues/989
.. _`#987`: https://github.com/desihub/desispec/issues/987
.. _`#972`: https://github.com/desihub/desispec/issues/972
.. _`#971`: https://github.com/desihub/desispec/issues/971

0.34.4 (2020-04-21)
-------------------

* Add `desi_proc --batch-opts ...` option for specifying extras like
  queue reservation (direct push to master).

0.34.3 (2020-04-17)
-------------------

* Run desi_proc arc and flat jobs on max 10 nodes instead of 5 (PR `#958`_).

.. _`#958`: https://github.com/desihub/desispec/issues/958

0.34.2 (2020-04-16)
-------------------

* Include `data/spec-arc-lamps.dat` with installed data.
* Mask high readnoise CCD amps (PR `#957`_).

.. _`#957`: https://github.com/desihub/desispec/issues/957

0.34.1 (2020-04-15)
-------------------

* Expanded scan range for y traceshifts from +-3 to +-10 A
  (commit 26279d8 direct to master)
* Improved traceshift robusteness for very large shifts of arcs (PR `#954`).
* Added scripts for creating bad pixels masks from darks (PR `#946`_).
* etc/desispec.module use desi_spectro_calib tag 0.1.1 (PR `#955`_).
* import specter only if needed to run, not requiring it just to
  import desispec.io (PR `#955`_).

Note: `python setup.py install` of this version incorrectly doesn't copy
`data/spec-arc-lamps.dat` into the final installed data directory;
that is fixed in next version, and was fixed by hand in NERSC 0.34.1 install.

.. _`#946`: https://github.com/desihub/desispec/issues/946
.. _`#954`: https://github.com/desihub/desispec/issues/954
.. _`#955`: https://github.com/desihub/desispec/issues/955

0.34.0 (2020-04-13)
-------------------

Compatibility notes:

  * Requires desiutil >= 2.0.3 (PR `#951`_).
  * Backwards incompatible change to sky model format (PR `#939`_.

Changes:

* Refactor S/N fit for QA (PR `#917`_)
* Speed up QA (PR `#917`_)
* Don't mask extreme mask fiberflat >2 or <0.1 in routine autocalib_fiberflat
  because the fiberflat includes the throughput difference between
  spectrographs (push to master to address issue `#897`_).
* Modify overscan methods.  Default is to no longer analyze the ORSEC region
  (PR `#838`_).
* Fix sky subtraction with ivar=0 (PR `#920`_).
* Tweaks for logging nightly redshifts and srun (PR `#921`_).
* Added calib config management utilities (PR `#926`_).
* Coadd robustness when missing a camera (PR `#927`_).
* Shorter desi_proc job names (PR `#928`_).
* Set fiberstatus to mask fibers in bad regions of CCDs (PR `#930`_).
* Fix code generating fits reserved keyword warnings (PR `#933`_, `#935`_).
* Try fibermap header if primary header doesn't have RA,DEC (PR `#934`_).
* Force assemble_fibermap for nights before or during 20200310 (PR `#936`_).
* Don't fit traceshifts in y for dome and twilight flats (PR `#937`_).
* Calculate sky model throughput corrections when making sky model instead
  of while applying model.  Note: changes data model.  (PR `#939`_).
* Improve averaging of fiberflats (PR `#940`_).
* Fix incorrect multiple calls to bary_corr depending upon MPI parallelism,
  and merge extract main and main_mpi (PR `#943`_).
* Propagate MJD to spectra fibermap (PR `#944`_).
* Generate spectra files by default and don't coadd across cameras (PR `#945`_).
* Allow coadding across cameras of coadds (PR `#948`_).
* Implement fibermaps per camera (PR `#949`_).
* Use desiutil.iers.freeze_iers instead of desisurvey; requires desiutil>=2.0.3
  (PR `#951`_).
* Module file users desi_spectro_calib tag 0.1

.. _`#838`: https://github.com/desihub/desispec/issues/838
.. _`#897`: https://github.com/desihub/desispec/issues/897
.. _`#917`: https://github.com/desihub/desispec/issues/917
.. _`#920`: https://github.com/desihub/desispec/issues/920
.. _`#921`: https://github.com/desihub/desispec/issues/921
.. _`#926`: https://github.com/desihub/desispec/issues/926
.. _`#927`: https://github.com/desihub/desispec/issues/927
.. _`#928`: https://github.com/desihub/desispec/issues/928
.. _`#930`: https://github.com/desihub/desispec/issues/930
.. _`#933`: https://github.com/desihub/desispec/issues/933
.. _`#934`: https://github.com/desihub/desispec/issues/934
.. _`#935`: https://github.com/desihub/desispec/issues/935
.. _`#936`: https://github.com/desihub/desispec/issues/936
.. _`#937`: https://github.com/desihub/desispec/issues/937
.. _`#939`: https://github.com/desihub/desispec/issues/939
.. _`#940`: https://github.com/desihub/desispec/issues/940
.. _`#943`: https://github.com/desihub/desispec/issues/943
.. _`#944`: https://github.com/desihub/desispec/issues/944
.. _`#945`: https://github.com/desihub/desispec/issues/945
.. _`#948`: https://github.com/desihub/desispec/issues/948
.. _`#949`: https://github.com/desihub/desispec/issues/949
.. _`#951`: https://github.com/desihub/desispec/issues/951

0.33.0 (2020-03-05)
-------------------

* Metadata bookkeeping for early CMX data (PR `#857`_)
* Improved PSF handling in desi_proc (PR `#858`_)
* Modeling scattered light (PR `#859`_, `#861`_, `#862`_)
* desi_proc --calibnight option (PR `#860`_)
* expanding flux calib stdstar bits (PR `#862`_)
* new assemble_fibermap script (PR `#864`_, `#902`_)
* improved sky subtraction and flux calibration robustness (PR `#865`_)
* new desi_group_tileframes script; coadd frames directly (PR `#866`_)
* flux calibration improvements (PR `#868`_, `#871`_, `#880`_, `#898`_)
* more efficient desi_proc --batch parallelism packing (PR `#869`_)
* new desi_proc_dashboard script (PR `#870`_, `#901`_)
* new desi_dailyproc script (PR `#872`_, `#881`_, `#895`_)
* more robustness to missing inputs (PR `#875`_, `#876`_, `#883`_)
* groundwork for improving cosmics masking (PR `#878`_)
* enable barycentric correction in desi_proc (PR `#879`_)
* new plot_spectra script (PR `#890`_)
* new desi_nightly_redshifts script (PR `#892`_)
* Generate QA for a given night + QA bug fixes (PR `#894`_)
* coadd metadata propagation (PR `#900`_)
* don't use FIBERSTATUS!=0 spectra in coadds (PR `#903`_)
* desi_proc more control options for minisv2 run (PR `#904`_)
* Two hotfixes to master to re-enable daily processing:

  * make assemble_fibermap more robust to missing input columns
    in the platmaker coordinates files.
  * better packing of extraction MPI ranks

.. _`#857`: https://github.com/desihub/desispec/pull/857
.. _`#858`: https://github.com/desihub/desispec/pull/858
.. _`#859`: https://github.com/desihub/desispec/pull/859
.. _`#860`: https://github.com/desihub/desispec/pull/860
.. _`#861`: https://github.com/desihub/desispec/pull/861
.. _`#862`: https://github.com/desihub/desispec/pull/862
.. _`#864`: https://github.com/desihub/desispec/pull/864
.. _`#865`: https://github.com/desihub/desispec/pull/865
.. _`#866`: https://github.com/desihub/desispec/pull/869
.. _`#868`: https://github.com/desihub/desispec/pull/868
.. _`#869`: https://github.com/desihub/desispec/pull/869
.. _`#870`: https://github.com/desihub/desispec/pull/870
.. _`#871`: https://github.com/desihub/desispec/pull/871
.. _`#872`: https://github.com/desihub/desispec/pull/872
.. _`#875`: https://github.com/desihub/desispec/pull/875
.. _`#876`: https://github.com/desihub/desispec/pull/876
.. _`#878`: https://github.com/desihub/desispec/pull/878
.. _`#879`: https://github.com/desihub/desispec/pull/879
.. _`#880`: https://github.com/desihub/desispec/pull/880
.. _`#881`: https://github.com/desihub/desispec/pull/881
.. _`#883`: https://github.com/desihub/desispec/pull/883
.. _`#890`: https://github.com/desihub/desispec/pull/890
.. _`#892`: https://github.com/desihub/desispec/pull/892
.. _`#894`: https://github.com/desihub/desispec/pull/894
.. _`#895`: https://github.com/desihub/desispec/pull/895
.. _`#898`: https://github.com/desihub/desispec/pull/898
.. _`#900`: https://github.com/desihub/desispec/pull/900
.. _`#901`: https://github.com/desihub/desispec/pull/901
.. _`#902`: https://github.com/desihub/desispec/pull/902
.. _`#903`: https://github.com/desihub/desispec/pull/903
.. _`#904`: https://github.com/desihub/desispec/pull/904

0.32.1 (2019-12-27)
-------------------

* Integration test simulate past not current date to workaound
  pixsim header mismatch with :envvar:`DESI_SPECTRO_CALIB` calibrations.
  (direct push to master).

0.32.0 (2019-12-22)
-------------------

* Adding more desi_proc options (PR `#848`_, `#850`_).
* Support PSF bootstrapping with broken fibers (PR `#849`_).
* Hot fixes to desi_proc crashes (pushed directly to master).
* Increase cframe task from 1 min to 2 min (direct to master).
* Adapt to new spectrograph SMn naming (PR `#853`_).
* Workaround fitsio bug by setting blank keywords to ``None``;
  adapt to new fiberassign file names (PR `#855`_).

.. _`#848`: https://github.com/desihub/desispec/pull/848
.. _`#849`: https://github.com/desihub/desispec/pull/849
.. _`#850`: https://github.com/desihub/desispec/pull/850
.. _`#853`: https://github.com/desihub/desispec/pull/853
.. _`#855`: https://github.com/desihub/desispec/pull/855


0.31.0 (2019-10-31)
-------------------

First CMX release with bug fixes for on-sky data.

* Use rrdesi --no-mpi-abort feature (PR `#823`_).
* Added code to generate pixflats (PR `#824`_).
* Support extractions of data without fibermaps (PR `#825`_).
* Propagate FIBERMAP into preproc files (not just frames)
  (PR `#825`_ and `#829`_).
* Allow extraction wavelenghts slightly off CCD (PR `#836`_).
* PSF I/O pause before merging (PR `#836`_).
* Add `bin/desi_proc` single-exposure processing script (PR `#837`_).
* Use OBSTYPE instead of FLAVOR for desi_qproc (PR `#839`_).
* Bug fix for desi_proc double application of fiberflat (PR `#841`_).
* desi_proc options for non-default PSF and fiberflat (PR `#842`_).
* Correct fibermap to match what petal we are in (PR `#843`_).
* Update database loading to match current data model (PR `#844`_).
* Added desi_proc --batch option (PR `#845`_).

.. _`#823`: https://github.com/desihub/desispec/pull/823
.. _`#824`: https://github.com/desihub/desispec/pull/824
.. _`#825`: https://github.com/desihub/desispec/pull/825
.. _`#829`: https://github.com/desihub/desispec/pull/829
.. _`#836`: https://github.com/desihub/desispec/pull/836
.. _`#837`: https://github.com/desihub/desispec/pull/837
.. _`#839`: https://github.com/desihub/desispec/pull/839
.. _`#841`: https://github.com/desihub/desispec/pull/841
.. _`#842`: https://github.com/desihub/desispec/pull/842
.. _`#843`: https://github.com/desihub/desispec/pull/843
.. _`#844`: https://github.com/desihub/desispec/pull/844
.. _`#845`: https://github.com/desihub/desispec/pull/845

0.30.0 (2019-10-17)
-------------------

* qproc updates (PR `#787`_).
* QL bias (PR `#789`_).
* Heliocentric corrections (PR `#790`_).
* Update photometric filter usages (PR `#791`_).
* Add gain output option to desi_compute_gain
* Modify overscan subtraction algorithm in desi.preproc.preproc (PR `#793`_).
* Cleanup timing parameters (PR `#794`_).
* Pipeline docs (PR `#797`_).
* Correct for dark trail in raw images (PR `#798`_).
* `yaml.load()` to `yaml.save_load()` (PR `#801`_).
* help numba know the types (PR `#802`_).
* desi_pipe getready fix (PR `#803`_).
* Move raw data transfer scripts to desitransfer_ (PR `#804`_).
* spectra coaddition (PR `#805`_).
* memory constraints and load balancing (PR `#806`_ and `#809`_).
* preproc header keywords CCDSEC1-4 vs. A-D (PR `#807`_).
* Add `desi_pipe status` command (PR `#810`_).
* Convert any expid input into an int in QA (PR `#814`_).
* Support new FIBERASSIGN_X/Y instead of DESIGN_X/Y (PR `#821`_).
* Added hostname and jobid to task logging (PR `#822`_).

.. _desitransfer: https://github.com/desihub/desitransfer
.. _`#787`: https://github.com/desihub/desispec/pull/787
.. _`#789`: https://github.com/desihub/desispec/pull/789
.. _`#790`: https://github.com/desihub/desispec/pull/790
.. _`#791`: https://github.com/desihub/desispec/pull/791
.. _`#793`: https://github.com/desihub/desispec/pull/793
.. _`#794`: https://github.com/desihub/desispec/pull/794
.. _`#797`: https://github.com/desihub/desispec/pull/797
.. _`#798`: https://github.com/desihub/desispec/pull/798
.. _`#801`: https://github.com/desihub/desispec/pull/801
.. _`#802`: https://github.com/desihub/desispec/pull/802
.. _`#803`: https://github.com/desihub/desispec/pull/803
.. _`#804`: https://github.com/desihub/desispec/pull/804
.. _`#805`: https://github.com/desihub/desispec/pull/805
.. _`#806`: https://github.com/desihub/desispec/pull/806
.. _`#807`: https://github.com/desihub/desispec/pull/807
.. _`#809`: https://github.com/desihub/desispec/pull/809
.. _`#810`: https://github.com/desihub/desispec/pull/810
.. _`#814`: https://github.com/desihub/desispec/pull/814
.. _`#821`: https://github.com/desihub/desispec/pull/821
.. _`#822`: https://github.com/desihub/desispec/pull/822

0.29.0 (2019-05-30)
-------------------

* Add HPSS backup to the raw data transfer script (PR `#765`_).
* Update :mod:`desispec.database.redshift` for latest
  changes in fiberassign tile file data model (PR `#770`_).
* Constants, docs, and test cleanup (PR `#771`_, `#773`_, `#776`_).
* Tune cosmics masking parameters (PR `#775`_).
* Add desi_compute_pixmask (PR `#777`_).
* qproc updates for more flexibility and exposure flavors (PR `#778`_).
* Better io.findfile camera checks (PR `#780`_).
* Support SV1_DESI_TARGET (PR `#786`_).

.. _`#786`: https://github.com/desihub/desispec/pull/786
.. _`#780`: https://github.com/desihub/desispec/pull/780
.. _`#778`: https://github.com/desihub/desispec/pull/778
.. _`#777`: https://github.com/desihub/desispec/pull/777
.. _`#776`: https://github.com/desihub/desispec/pull/776
.. _`#775`: https://github.com/desihub/desispec/pull/775
.. _`#773`: https://github.com/desihub/desispec/pull/773
.. _`#771`: https://github.com/desihub/desispec/pull/771
.. _`#770`: https://github.com/desihub/desispec/pull/770
.. _`#765`: https://github.com/desihub/desispec/pull/765

0.28.0 (2019-02-28)
-------------------

* Update (non-essential) transfer script for spectrograph functional
  verification tests (PR `#758`_).
* New calibration data access (inc var. DESI_SPECTRO_CALIB
  replacing DESI_CCD_CALIBRATION_DATA) (PR `#753`_).
* Fix offline QA S/N vs. mag fits (PR `#763`_).

.. _`#753`: https://github.com/desihub/desispec/pull/753
.. _`#758`: https://github.com/desihub/desispec/pull/758
.. _`#763`: https://github.com/desihub/desispec/pull/763

0.27.1 (2019-01-28)
-------------------

* QL updates for January 2019 readiness review (PRs `#750`_, `#751`_, `#752`_,
  `#754`_, `#755`_, `#756`_, `#757`_).

.. _`#750`: https://github.com/desihub/desispec/pull/750
.. _`#751`: https://github.com/desihub/desispec/pull/751
.. _`#752`: https://github.com/desihub/desispec/pull/752
.. _`#754`: https://github.com/desihub/desispec/pull/754
.. _`#755`: https://github.com/desihub/desispec/pull/755
.. _`#756`: https://github.com/desihub/desispec/pull/756
.. _`#757`: https://github.com/desihub/desispec/pull/757

0.27.0 (2018-12-16)
-------------------

* DB loading targets columns `PRIORITY_INIT` and `NUMOBS_INIT`;
  requires desitarget/0.27.0 or later for DB loading (PR `#747`_).
* Fix S/N QA when inputs have NaNs (PR `#746`_).
* DB exposures table loading allows NaN entries for RA,DEC,SEEING,etc.
  for arc and flat calib exposures (PR `#743`_).
* Use new `desiutil.dust.ext_odonnell` function during flux-calibration
  (PR `#736`_).
* Add support for average flux calibration model in ccd_calibration_data
  repo (PR `#735`_).
* Support mockobs fibermap format with fewer columns (PR `#733`_).
* Upgrade data transfer script and add additional scripts (PR `#732`_).
* Fix desi_zcatalog RA_TARGET vs. TARGET_RA (PR `#723`_).
* Update redshift database data model and workaround a minor bad data problem (PR `#722`_).
* Refactor offline QA (S/N) to work with updated object typing
* Drop `contam_target` DB truth column; no longer in truth files
  (one-line commit to master, no PR).
* Bug fix in QA (S/N) + refactor exposure slurping (PR `#746`_)
* Refactor QA_Exposures, QA_Night, and QA_Prod; Generate new Prod QA (offline)

.. _`#722`: https://github.com/desihub/desispec/pull/722
.. _`#723`: https://github.com/desihub/desispec/pull/723
.. _`#732`: https://github.com/desihub/desispec/pull/732
.. _`#733`: https://github.com/desihub/desispec/pull/733
.. _`#735`: https://github.com/desihub/desispec/pull/735
.. _`#736`: https://github.com/desihub/desispec/pull/736
.. _`#737`: https://github.com/desihub/desispec/pull/737
.. _`#743`: https://github.com/desihub/desispec/pull/743
.. _`#746`: https://github.com/desihub/desispec/pull/746
.. _`#747`: https://github.com/desihub/desispec/pull/747

0.26.0 (2018-11-08)
-------------------

Major non-backwards compatible changes:

* Update to new fibermap format for consistency with targeting and
  fiber assignment (PR `#717`_).
* Include GAIN in preproc headers (PR `#715`_).
* Prototype data transfer status report webpage (PR `#714`_).
* Integrate qproc/qframe into quicklook (PR `#713`_).
* Quicklook flux calib and config edits (PR `#707`_).

.. _`#707`: https://github.com/desihub/desispec/pull/707
.. _`#713`: https://github.com/desihub/desispec/pull/713
.. _`#714`: https://github.com/desihub/desispec/pull/714
.. _`#715`: https://github.com/desihub/desispec/pull/715
.. _`#717`: https://github.com/desihub/desispec/pull/717

0.25.0 (2018-10-24)
-------------------

* QL algorithm, config, and format updates (PRs `#699`_, `#701`_, `#702`_).
  (Includes non-backwards compatible changes).

.. _`#699`: https://github.com/desihub/desispec/pull/699
.. _`#701`: https://github.com/desihub/desispec/pull/701
.. _`#702`: https://github.com/desihub/desispec/pull/702


0.24.0 (2018-01-05)
-------------------

* Quicklook updates (including non-backwards compatible changes)

  * New QL calibration QA metrics (PR `#677`_).
  * Update QL to use xytraceset instead of custom PSF (PR `#682`_).
  * Cleanup for robustness and maintainability (PR `#693`_).

* Offline QA updates

  * Integrates QL S/N QA into offline QA Frame object (PR `#675`_).
  * Additional offline QA plots on S/N (PR `#691`_).

* Spectroscopic pipeline updates

  * Option to generate bash scripts instead of slurm scripts (PR `#686`_).
  * new `desi_pipe go --resume` option (PR `#687`_).
  * `desi_pipe sync --force-spec-done` option (PR `#692`_)

* Miscellaneous

  * Work-around bug that forbids opening memory-mapped files in update mode
    on some NERSC filesystems (PR `#689`_).
  * Do not compress image masks (PR `#696`_).
  * Ensure that FITS files specify FITS-standard-compliant units (PR `#673`_).
  * Integration test fixes (PR `#695`_).

.. _`#673`: https://github.com/desihub/desispec/pull/673
.. _`#675`: https://github.com/desihub/desispec/pull/675
.. _`#677`: https://github.com/desihub/desispec/pull/677
.. _`#682`: https://github.com/desihub/desispec/pull/682
.. _`#686`: https://github.com/desihub/desispec/pull/686
.. _`#687`: https://github.com/desihub/desispec/pull/687
.. _`#689`: https://github.com/desihub/desispec/pull/689
.. _`#691`: https://github.com/desihub/desispec/pull/691
.. _`#692`: https://github.com/desihub/desispec/pull/692
.. _`#693`: https://github.com/desihub/desispec/pull/693
.. _`#695`: https://github.com/desihub/desispec/pull/695
.. _`#696`: https://github.com/desihub/desispec/pull/696

0.23.1 (2018-08-09)
-------------------

* Support STD/STD_FSTAR/STD_FAINT bit names (PR `#674`_).

.. _`#674`: https://github.com/desihub/desispec/pull/674

0.23.0 (2018-07-26)
-------------------

* Adds qproc algorithms and QFrame class (PR `#664`_).
* Adds `desi_pipe go` for production running (PR `#666`_).
* Increase job maxtime for edison realtime queue (PR `#667`_).
* Updates for running desispec on BOSS data (PR `#669`_).
* Fix QL for list vs. array change in specter/master (PR `#670`_).

.. _`#664`: https://github.com/desihub/desispec/pull/664
.. _`#666`: https://github.com/desihub/desispec/pull/666
.. _`#667`: https://github.com/desihub/desispec/pull/667
.. _`#669`: https://github.com/desihub/desispec/pull/669
.. _`#670`: https://github.com/desihub/desispec/pull/670

0.22.1 (2018-07-18)
-------------------

* Update processing of QL metrics (PR `#659`_).
* Refactor pipeline and integration test (PR `#660`_).
* Update redshift database to handle changes to fiberassign data model
  (PR `#662`_).
* Allow rows to be filtered when loading the redshift database (PR `#663`_).

.. _`#659`: https://github.com/desihub/desispec/pull/659
.. _`#660`: https://github.com/desihub/desispec/pull/660
.. _`#662`: https://github.com/desihub/desispec/pull/662
.. _`#663`: https://github.com/desihub/desispec/pull/663

0.22.0 (2018-06-30)
-------------------

This is the version used for mock observing in June 2018.  It includes an
update to the directory substructure where raw data are found, grouping each
exposure into a separate directory `$DESI_SPECTRO_DATA/{YEARMMDD}/{EXPID}/`.

* Faster traceshift code; requires numba (PR `#634`_).
* Fixed integration tests (PR `#635`_).
* Give empty HDUs am ``EXTNAME`` (PR `#636`_).
* Update redshift database loading in integration test (PR `#638`_).
* Integration test DB loading (PR `#640`_).
* Move ccd_calibration.yaml to SVN repo (PR `#641`_).
* Logging QA metric status for QLF (PR `#642`_).
* Supporting both new and old fibermap via io.read_fibermap (PP `#643`_).
* Faster lower memory preproc using numba (PR `#644`_)
* ivar bugfix in resample_flux interpolation (PR `#646`_).
* Many QL updates from mock observing (PR `#648`_).
* Raw data in NIGHT/EXPID/*.* instead of NIGHT/*.* (PR `#648`_).
* Fix cosmics masking near masked saturated pixels (PR `#649`_).
* Update edison realtime queue config to 25 nodes (PR `#650`_).
* trace_shift code supports PSF formats without "PSF" HDU (PR `#654`_).
* Change keyword ``clobber`` to ``overwrite`` in functions from ``astropy.io.fits`` (PR `#658`_).

.. _`#634`: https://github.com/desihub/desispec/pull/634
.. _`#635`: https://github.com/desihub/desispec/pull/635
.. _`#636`: https://github.com/desihub/desispec/pull/636
.. _`#638`: https://github.com/desihub/desispec/pull/638
.. _`#640`: https://github.com/desihub/desispec/pull/640
.. _`#641`: https://github.com/desihub/desispec/pull/641
.. _`#642`: https://github.com/desihub/desispec/pull/642
.. _`#643`: https://github.com/desihub/desispec/pull/643
.. _`#644`: https://github.com/desihub/desispec/pull/644
.. _`#646`: https://github.com/desihub/desispec/pull/646
.. _`#648`: https://github.com/desihub/desispec/pull/648
.. _`#649`: https://github.com/desihub/desispec/pull/649
.. _`#650`: https://github.com/desihub/desispec/pull/650
.. _`#654`: https://github.com/desihub/desispec/pull/654
.. _`#658`: https://github.com/desihub/desispec/pull/658

0.21.0 (2018-05-25)
-------------------

Major updates including non-backwards compatible changes to QL output format
and pipeline updates for semi-realtime nightly processing.

* Pipeline fix to allow redrock to use a full node per healpix (PR `#585`_).
* Update pipeline maxtime/maxnodes job calculation (PR `#588`_).
* Better sync of pixel tasks and DB sync bugfixes (PR `#590`_).
* Improved handling of errors in case of full job failure (PR `#592`_).
* QA speedups and improvements (PR `#593`_)

  * Add ability to load Frame without reading Resolution matrix
  * Refactor offline QA to use qaprod_dir more sensibly
  * Include hooks in QA to previous fiberflat file location (calib2d)
  * Inhibit scatter plot in skyredidual QA

* Pass MAG into output zbest file (PR `#595`_)
* Allow running multiple task types in a single job (PR `#601`_).
* Pipeline hooks for processing a single exposure (PR `#604`_).
* Override PSF file psferr to avoid masking bright lines.
  Requires specter > 0.8.1 (PR `#606`_).
* QL QA reorganization (PR `#577`_, `#600`_, `#607`_, `#613`_).
* Integration test and QA fixes (PR `#602`_ and `#605`_).
* New desi_night scripts for semi-realtime processing (PR `#609`_).
* Spectro teststand calibration/utility code updates (PR `#610`_)
* QL S/N vs. mag updates (PR `#611`_)
* QL resampling fixes (PR `#615`_)
* Merge database modules (PR `#616`_).
* Add flexure tests to QL (PR `#617`_).
* Added cori and edison realtime queue support (PR `#618`_, `#619`_, `#624`_).
* QL output format updates (PR `#623`_).

.. _`#577`: https://github.com/desihub/desispec/pull/577
.. _`#585`: https://github.com/desihub/desispec/pull/585
.. _`#588`: https://github.com/desihub/desispec/pull/588
.. _`#590`: https://github.com/desihub/desispec/pull/590
.. _`#592`: https://github.com/desihub/desispec/pull/592
.. _`#593`: https://github.com/desihub/desispec/pull/593
.. _`#595`: https://github.com/desihub/desispec/pull/595
.. _`#600`: https://github.com/desihub/desispec/pull/600
.. _`#601`: https://github.com/desihub/desispec/pull/601
.. _`#602`: https://github.com/desihub/desispec/pull/602
.. _`#604`: https://github.com/desihub/desispec/pull/604
.. _`#605`: https://github.com/desihub/desispec/pull/605
.. _`#606`: https://github.com/desihub/desispec/pull/606
.. _`#607`: https://github.com/desihub/desispec/pull/607
.. _`#609`: https://github.com/desihub/desispec/pull/609
.. _`#610`: https://github.com/desihub/desispec/pull/610
.. _`#611`: https://github.com/desihub/desispec/pull/611
.. _`#613`: https://github.com/desihub/desispec/pull/613
.. _`#615`: https://github.com/desihub/desispec/pull/615
.. _`#616`: https://github.com/desihub/desispec/pull/616
.. _`#617`: https://github.com/desihub/desispec/pull/617
.. _`#618`: https://github.com/desihub/desispec/pull/618
.. _`#619`: https://github.com/desihub/desispec/pull/619
.. _`#623`: https://github.com/desihub/desispec/pull/623
.. _`#624`: https://github.com/desihub/desispec/pull/624

0.20.0 (2018-03-29)
-------------------

Multiple non-backwards compatible changes:

* Astropy 2 compatibility (PR `#519`_).
* Update Travis tests to recent versions.
* Integration test fixes (PR `#552`_).
* Adds pipeline db count_task_states (PR `#552`_).
* Standardize spectro filenames/locations (PR `#545`_ and `#559`_).
* Complete rewrite of task pipelining (PR `#520`_, `#523`_, `#536`_, `#537`_,
  `#538`_, `#540`_, `#543`_, `#544`_, `#547`_, )
* QL format updates (`#517`_, `#554`_)
* module file set DESI_CCD_CALIBRATION_DATA (`#564`_).
* Optionally include RA,DEC in merged zcatalog (`#562`_).
* QL updates to S/N calculations (`#556`_).
* fix BUNIT, HPXNSIDE, HPXPIXEL keywords (PR `#566`_)

.. _`#517`: https://github.com/desihub/desispec/pull/517
.. _`#519`: https://github.com/desihub/desispec/pull/519
.. _`#520`: https://github.com/desihub/desispec/pull/520
.. _`#523`: https://github.com/desihub/desispec/pull/523
.. _`#536`: https://github.com/desihub/desispec/pull/536
.. _`#537`: https://github.com/desihub/desispec/pull/537
.. _`#538`: https://github.com/desihub/desispec/pull/538
.. _`#540`: https://github.com/desihub/desispec/pull/540
.. _`#543`: https://github.com/desihub/desispec/pull/543
.. _`#544`: https://github.com/desihub/desispec/pull/544
.. _`#545`: https://github.com/desihub/desispec/pull/545
.. _`#547`: https://github.com/desihub/desispec/pull/547
.. _`#552`: https://github.com/desihub/desispec/pull/552
.. _`#554`: https://github.com/desihub/desispec/pull/554
.. _`#556`: https://github.com/desihub/desispec/pull/556
.. _`#559`: https://github.com/desihub/desispec/pull/559
.. _`#562`: https://github.com/desihub/desispec/pull/562
.. _`#564`: https://github.com/desihub/desispec/pull/564
.. _`#566`: https://github.com/desihub/desispec/pull/566

0.19.0 (2018-03-01)
-------------------

* Update DB loading for desitarget 0.19.0 targets; make DB loading
  API less specific to datachallenge directory structure (PR `#516`_).

.. _`#516`: https://github.com/desihub/desispec/pull/516

0.18.0 (2018-02-23)
-------------------

* Replace deprecated scipy.stats.chisqprob with
  scipy.stats.distributions.chi2.sf for compatibility with
  scipy 1.0. (PR `#503`_)
* Faster desi_group_spectra that also propagates SCORES table
  (PR `#505`_ and `#507`_ )
* Add options for fitting spatially non-uniform sky (PR `#506`_)
* Fix logger redirection (PR `#508`_)
* Add hooks for MPI extraction timing benchmarks (PR `#509`_)
* QuickLook metric renaming (PR `#512`_)

.. _`#503`: https://github.com/desihub/desispec/pull/503
.. _`#505`: https://github.com/desihub/desispec/pull/505
.. _`#506`: https://github.com/desihub/desispec/pull/506
.. _`#507`: https://github.com/desihub/desispec/pull/507
.. _`#508`: https://github.com/desihub/desispec/pull/508
.. _`#509`: https://github.com/desihub/desispec/pull/509
.. _`#512`: https://github.com/desihub/desispec/pull/512

0.17.2 (2018-01-30)
-------------------

* Trace shift optimizations from analyzing teststand data (PR `#482`_).
* Minor QA edits to accommodate minitest (PR `#489`_)
* Additional QA edits including qaprod_root() method (PR `#490`_)
* Introduce QA_Night, QA_MultiExp and refactor QA_Prod accordingly (PR `#491`_)
* Add SCORES HDU to frame files (PR `#492`_)

.. _`#482`: https://github.com/desihub/desispec/pull/482
.. _`#489`: https://github.com/desihub/desispec/pull/489
.. _`#490`: https://github.com/desihub/desispec/pull/490
.. _`#491`: https://github.com/desihub/desispec/pull/491
.. _`#492`: https://github.com/desihub/desispec/pull/492

0.17.1 (2017-12-20)
-------------------

* Refactors spectral regouping to be faster and derive fibermap format
  from inputs (PR `#473`_).
* Removed deprecated Brick class, and unused coadds and redmonder zfind
  that were using Bricks (PR `#473`_).
* Adds skyline QA; fixes QA version usage (PR `#458`_).
* Fixes write_bintable bug if extname=None; fixes missing header comments
* spectro DB database loading updates (PR `#477`_).
* trace shift updates for fiber flats (PR `#479`_).
* Pipeline scaling updates (PR `#459`_ and `#466`_).

.. _`#458`: https://github.com/desihub/desispec/pull/458
.. _`#473`: https://github.com/desihub/desispec/pull/473
.. _`#477`: https://github.com/desihub/desispec/pull/477
.. _`#479`: https://github.com/desihub/desispec/pull/479
.. _`#459`: https://github.com/desihub/desispec/pull/459
.. _`#466`: https://github.com/desihub/desispec/pull/466

0.17.0 (2017-11-10)
-------------------

* Enabled specter.extract.ex2d nsubbundles option for faster extractions.
  Requires specter 0.8.1 (PR `#451`_).
* Fixed bug in :func:`desispec.parallel.dist_discrete` (PR `#446`_)
* Tuned pipeline for scaling tests (PR `#457`_)
* Improved wavelength fitting (via specex update) and sky model error
  propagation (PR `#459`_)
* Added QL fiberflat, py3 fixes, updated algorithms and config
* Many other QL updates (PR `#462`_)
* Enables MPI parallelism for desi_extract_spectra script (PR `#448`_)

.. _`#446`: https://github.com/desihub/desispec/pull/446
.. _`#448`: https://github.com/desihub/desispec/pull/448
.. _`#451`: https://github.com/desihub/desispec/pull/451
.. _`#457`: https://github.com/desihub/desispec/pull/457
.. _`#459`: https://github.com/desihub/desispec/pull/459
.. _`#462`: https://github.com/desihub/desispec/pull/462

0.16.0 (2017-09-29)
-------------------

* Small fixes to desi_qa_prod and qa_prod
* Removes a number of QL metrics from offline qa
* Fixes integration tests for desisim newexp refactor
* Removes spectra grouping by brick; nside=64 healpix grouping default
* Add get_nights method to io.meta (PR `#422`_)
* Add search_for_framefile method to io.frame (PR `#422`_)
* Add desi_qa_frame script to generate frame QA (PR `#424`_)
* Add frame_meta to parameters (for slurping the Frame headers) (PR `#425`_)
* Add get_reduced_frames() method to io.meta (PR `#425`_)
* Modifies QA_Prod meta file output to be JSON (PR `#425`_)
* Add load_meta() method to QA_Exposure (PR `#425`_)
* Add time_series ploting to desi_qa_prod (PR `#425`_)
* Add several new plots for skysub residuals (PR `#425`_)
* Adds method to generate QA Table for Prod (PR `#425`_)
* Refactor of skysubresid script (PR `#425`_)
* Refactor QA files to sit in their own folder tree (PR `#429`_)
* Generate HTML files with links to QA figures (PR `#429`_)
* Enable generation of Exposure level QA (PR `#429`_)
* Normalize fiberflat QA by fiber area (PR `#429`_)
* Fixed exptime in fluxcalib ZP calculation (PR `#429`_)
* Added find_exposure_night() method (PR `#429`_)
* Add MED_SKY metric to QA and bright/dark flag in desi_qa_prod
* Update pipeline code for specex and redrock (PR `#439`_ and `#440`_)
* Adds code for adjusting trace locations to match sky lines (PR `#433`_)
* Updates to DB loading (PR `#431`_)
* Adds pixelflat code (PR `#426`_)

.. _`#422`: https://github.com/desihub/desispec/pull/422
.. _`#424`: https://github.com/desihub/desispec/pull/424
.. _`#425`: https://github.com/desihub/desispec/pull/425
.. _`#426`: https://github.com/desihub/desispec/pull/426
.. _`#429`: https://github.com/desihub/desispec/pull/429
.. _`#431`: https://github.com/desihub/desispec/pull/431
.. _`#433`: https://github.com/desihub/desispec/pull/433
.. _`#439`: https://github.com/desihub/desispec/pull/439
.. _`#440`: https://github.com/desihub/desispec/pull/440

0.15.2 (2017-07-12)
-------------------

* Make the loading of libspecex through ctypes more robust and portable.
* QL configuration cleanup (PR `#389`_).
* Add extrapolate option to resample_flux (PR `#415`_).
* Sphinx and travis tests fixes.

.. _`#389`: https://github.com/desihub/desispec/pull/389
.. _`#415`: https://github.com/desihub/desispec/pull/415

0.15.1 (2017-06-19)
-------------------

* Fixed :func:`desispec.io.findfile` path for zbest and coadd (PR `#411`_).
* Add Notebook tutorial: introduction to reading and manipulating DESI spectra (PR `#408`_, `#410`_).
* Update quicklook configuration (PR `#395`_).
* Rename ``Spectra.fmap`` attribute to ``Spectra.fibermap`` (PR `#407`_).
* Enable ``desi_group_spectra`` to run without pipeline infrastructure (PR `#405`_).
* Update desispec.io.findfile spectra path to match dc17a (PR `#404`_).
* Load redshift catalog data from healpix-based zbest files (PR `#402`_).

.. _`#411`: https://github.com/desihub/desispec/pull/411
.. _`#410`: https://github.com/desihub/desispec/pull/410
.. _`#408`: https://github.com/desihub/desispec/pull/408
.. _`#395`: https://github.com/desihub/desispec/pull/395
.. _`#407`: https://github.com/desihub/desispec/pull/407
.. _`#405`: https://github.com/desihub/desispec/pull/405
.. _`#404`: https://github.com/desihub/desispec/pull/404
.. _`#402`: https://github.com/desihub/desispec/pull/402

0.15.0 (2017-06-15)
-------------------

* Refactor database subpackage and enable loading of both quicksurvey and
  pipeline outputs (PR `#400`_).
* Clean up pipeline script naming to be grouped by night.
* Modify pipeline to use Spectra objects grouped by HEALPix pixels instead
  of bricks.  Add entry point to regroup cframe data by pixel (PR `#394`_).
* Add a new class, Spectra, which encapsulates a grouping of 1D spectra
  in one or more bands.  Includes selection, updating, and I/O.
* Removed ``desispec.brick`` as it's now in :mod:`desiutil.brick` (PR `#392`_).
* Added function to calculate brick vertices at a given location (PR `#388`_).
* Added function to calculate brick areas at a given location (PR `#384`_).
* Add scripts for submitting nightly job chains.
* Production creation now correctly handles slicing by spectrograph.
* Pipeline job concurrency now computed based on task run time and
  efficient packing.
* Set default brick size to 0.25 sq. deg. in desispec.brick (PR `#378`_).
* Added function to calculate BRICKID at a given location (PR `#378`_).
* Additional LOCATION, DEVICE_LOC, and PETAL_LOC columns for fibermap (PR `#379`_).
* Create util.py in tests/ which is intended to contain methods to facilitate test runs
* Add vette() method for Frame class (PR `#386`_)
* Began a desispec parameter file:  data/params/desispec_param.yml
* Flux calibration improvements (PR `#390`_).

.. _`#386`: https://github.com/desihub/desispec/pull/386
.. _`#388`: https://github.com/desihub/desispec/pull/388
.. _`#384`: https://github.com/desihub/desispec/pull/384
.. _`#378`: https://github.com/desihub/desispec/pull/378
.. _`#379`: https://github.com/desihub/desispec/pull/379
.. _`#390`: https://github.com/desihub/desispec/pull/390
.. _`#392`: https://github.com/desihub/desispec/pull/392
.. _`#394`: https://github.com/desihub/desispec/pull/394
.. _`#400`: https://github.com/desihub/desispec/pull/400

0.14.0 (2017-04-13)
-------------------

* Replace all instances of :mod:`desispec.log` with ``desiutil.log``;
  :func:`~desispec.log.get_logger` now prints a warning that users need
  to switch.
* Working DTS delivery script and DTS simulator (PR `#367`_).
* Preproc updates for crosstalk and teststand data (PR `#370`_).
* Flux calibration algorithm updates (PR `#371`_).
* Adds quicklook integration test (PR `#361`_).
* Fixes brickname calculation (PR `#373`_).

.. _`#367`: https://github.com/desihub/desispec/pull/367
.. _`#370`: https://github.com/desihub/desispec/pull/370
.. _`#371`: https://github.com/desihub/desispec/pull/371
.. _`#361`: https://github.com/desihub/desispec/pull/361
.. _`#373`: https://github.com/desihub/desispec/pull/361

0.13.2 (2017-03-27)
-------------------

* Add framework for DTS delivery and nightly processing scripts (PR `#365`_).
* Force documentation errors to cause Travis errors (PR `#364`_).

.. _`#364`: https://github.com/desihub/desispec/pull/364
.. _`#365`: https://github.com/desihub/desispec/pull/365

0.13.1 (2017-03-03)
-------------------

* Fix installation of ``data/ccd/ccd_calibration.yaml``.

0.13.0 (2017-03-03)
-------------------

* Fix brick update corruption (PR `#314`_).
* Close PSF file after initializing PSF object.
* Refactor :mod:`desispec.io.database` to use SQLAlchemy_.
* Fix :func:`~desispec.pipeline.graph.graph_path` usage in workers.
* Update :func:`desispec.io.raw.write_raw` to enable writing simulated raw
  data with new headers.
* Allow ``test_bootcalib`` to run even if NERSC portal is returning 403 errors.
* Add ``bricksize`` property to desispec.brick.Bricks; allow
  `desispec.brick.Bricks.brickname` to specify bricksize.
* Do SVD inverses when cholesky decompositions fail in fiberflat, sky
  subtraction, and flux calibration.
* Algorithm updates for teststand and BOSS data
* pipeline updates for docker/shifter
* quicklook updates

.. _`#314`: https://github.com/desihub/desispec/pull/314
.. _SQLAlchemy: http://www.sqlalchemy.org

0.12.0 (2016-11-09)
-------------------

* Update integration test to use stdstar_templates_v1.1.fits.
* Support asymmetric resolution matrices (PR `#288`_).
* Quicklook updates (PR `#294`_, `#293`_, `#285`_).
* Fix BUNIT and wavelength f4 *versus* f8.
* Significant pipeline code refactor (PR `#300`_ and `#290`_).
* fix docstrings for sphinx build (PR `#308`_).

.. _`#285`: https://github.com/desihub/desispec/pull/285
.. _`#288`: https://github.com/desihub/desispec/pull/288
.. _`#290`: https://github.com/desihub/desispec/pull/290
.. _`#293`: https://github.com/desihub/desispec/pull/293
.. _`#294`: https://github.com/desihub/desispec/pull/294
.. _`#300`: https://github.com/desihub/desispec/pull/300
.. _`#308`: https://github.com/desihub/desispec/pull/308


0.11.0 (2016-10-14)
-------------------

* Update template Module file to reflect DESI+Anaconda infrastructure.
* Update redmonster wrapper for reproducibility.
* `desispec.io.brick.BrickBase.get_target_ids` returns target IDs in the order they appear in input file.
* Set BUNIT header keywords (PR `#284`_).
* Improved pipeline logging robustness.
* MPI updates for robustness and non-NERSC operation.
* More py3 fixes.

.. _`#284`: https://github.com/desihub/desispec/pull/284

0.10.0 (2016-09-10)
-------------------

PR `#266`_ update for Python 3.5:

* Many little updates to work for both python 2.7 and 3.5.
* Internally fibermap is now a :class:`~astropy.table.Table` instead of :class:`~astropy.io.fits.FITS_rec` table.
* Bug fix for flux calibration QA.
* Requires desiutil_ >= 1.8.0.

.. _`#266`: https://github.com/desihub/desispec/pull/266
.. _desiutil: https://github.com/desihub/desiutil

0.9.0 (2016-08-18)
------------------

PR `#258`_ (requires specter_ >= 0.6.0)

* Propagate pixel model goodness of fit to flag outliers from unmasked cosmics.
* desi_extract_spectra --model option to output 2D pixel model
* fix pipeline bug in call to desi_bootcalib (no --qafig option)
* adds extraction tests

Misc:

* desi_qa_skysub -- plots residuals (PR #259)
* More quicklook QA (PR #260 and #262)
* Added support for template groups in redmonster (PR #255)
* Lots more pipeline docs (PR #261)

.. _specter: https://github.com/desihub/specter
.. _`#258`: https://github.com/desihub/desispec/pull/258

0.8.1 (2016-07-18)
------------------

* added QA_Prod
* refactor of fluxcalib QA
* fixed pipeline QA figure output (pdf vs. yaml)

0.8.0 (2016-07-14)
------------------

* bootcalib robustness improvements
* improved fibermap propagation
* PRODNAME -> SPECPROD, TYPE -> SPECTYPE
* meaningful batch job names for each step
* better test coverage; more robust to test data download failures
* more quicklook metrics
* used for "oak1" production

0.7.0 and prior
----------------

* No changes.rst yet