A list of all relevant changes to build 12.1 of the JWST Operations Pipeline is provided in this article.

Build 12.1 was released as a build candidate in October 2025, and installed as an operations build in November 2025. The information provided here focuses mainly on updates to the JWST Science Calibration Pipeline and associated reference files, but includes information relevant to changes in other subsystems that might affect what users see in their data.

Major updates

Data affected by this build

Provided below is a list of science data products in MAST generated by the JWST Science Calibration Pipeline that may be most significantly affected by the updates in build 12.1. The changes listed in the release notes below may affect other modes as well, but many of these will be transparent to the MAST user.

The data and pipeline stages most affected include:

• Stage 1 processing: Minor updates for nearly all modes.
• Stage 2 processing: significant changes for MIRI imaging, MIRI MRS, imaging TSO, NIRCam coronagraphy, NIRSpec MOS, and NIRSpec IFU.
• Stage 3 processing: significant changes for MIRI imaging, MIRI MRS, imaging TSO, NIRCam coronagraphy, NIRSpec MOS, and NIRSpec IFU.

Release notes

Build 12.1 of the JWST Operations Pipeline was released as a candidate build on October 20, 2025 and installed as an operations build (12.1) for the Barbara A. Mikulski Archive for Space Telescopes (MAST) on November 20, 2025. The build includes changes to the JWST Science Calibration Pipeline released in version 1.20.2 (of the jwst calibration pipeline package via the PyPI repository. This release also includes changes to the JWST Science Data Processing subsystem (SDP) version 2025.4.1 which is the DMS subsystem that creates raw (uncal) products used as input to the calibration pipeline.

General changes

• Ensure that all steps do not modify input datamodels.
• Require Python <3.14 to exclude the recently released 3.14. Once all dependencies that support 3.14 and the code and results are tested with 3.14. this pin will be updated to allow 3.14.

Pipeline modules

• Use read_metadata where possible in calwebb_image3; result is a few percent runtime improvement if in_memory=False.
• Populate S_REGION keyword in level 3 WFSS "x1d" products using cumulative footprint of grism images supplied to Spec3Pipeline.
• Deprecate the save_bsub parameter in calwebb_image2 and calwebb_spec2. Use the background step save_results parameter instead.
• Fix a crash for NIRISS SOSS FULL frame TSO data by skipping the white_light step if 1D extraction does not complete successfully.

Step change list

Changes to specific steps in the pipelines are listed below. 

stpipe

• Deprecate logging configuration files in logcfg arguments. Users should transition to using log configuration command line arguments or directly configuring logging in their Python code.
• New JwstStep.get_stpipe_loggers() method to specify loggers to configure.
• Update cal log scrubber to avoid removing reference file names.

Associations

• Fix an edge case in duplicate association checks affecting NIRCam coronagraphy associations, where a duplicate "rateints" association should be removed, but an equivalent "rate" association is present, and was accidentally removed instead.
• Restore asn_edit.writer to write associations to disk, removed in 1.19.0.

set_telescope_pointing

• Deprecate lib.compute_va_effects and lib.compute_va_effects_vector in favor of stcal versions.

ami_analyze / ami_normalize / ami_average

• Populate AmiOiModels with quad observables in new q4 attribute (OI_Q4 FITS extension). Values and associated errors are now written out to "ami-oi.fits" and "amimulti-oi.fits" files by AmiAnalyze, and they are calibrated in AmiNormalize and written to the final "aminorm-oi.fits" products.

assign_wcs

• Add velocity correction to the inverse WCS transforms for NIRSpec spectroscopic modes to fix a round trip error. (#9783)

background

• Change the background reference file type for WFSS processing from "wfssbkg" to "bkg".
• Included background mask used for WFSS data as extension in output datamodel.
• For WFSS, when the step exits early, the status will be set to FAILED instead of SKIPPED. In this case, the scaling factor is set to 0.0 and the background mask is saved to the output.

clean_flicker_noise

• Catch bad values in the computed weight matrix for the FFT method to avoid setting entire images to NaN.
• Add an autoparam parameter to determine appropriate cleaning parameters from the input data. Initial exposure types supported are NIS_IMAGE and NRC_IMAGE only.

combine_1d

• Allow all-NaN spectra to be skipped instead of causing crashes.

cube_build

• Fix slice width calculation for NIRSpec IFU with a new-style slice map WCS.
• Allow NIRSpec prism IFU cubes to have non-linear wavelength range if output_type=multi.

extract_1d

• Simplify API for get_soss_traces and get_soss_wavemaps; refmodel is no longer required and will be retrieved from CRDS if not set.
• Enable order 3 extractions for NIRISS SOSS data.
• Fixed an intermittent crash in a matrix solver in SOSS extractions.
• Extract single-integration cubes as TSO spectra, to fix a crash in the calwebb_tso3 pipeline when one spectrum has only one integration.

firstframe

• Set bright_use_group1 to True by default. Flag any affected pixels with the FLUX_ESTIMATED flag in the "pixeldq" image.

group_scale

• Remove cast (which consumed 3x the data array size) to improve memory usage.

linearity

• Remove cast (which consumed 3x the data array size) to reduce memory usage.

mrs_imatch

• Removed the deprecated mrs_imatch module and its corresponding MRSIMatchStep step.

outlier_detection

• For cases where the input is not a ModelLibrary, copy the input data before processing to ensure input datamodels are not modified. This will increase peak memory usage for the calwebb_spec3, calwebb_tso3, and calwebb_coron3 pipelines, but performance for large imaging mosaics is not impacted. Fix a crash in intermediate file saving for IFU mode.

photom

• Add support for time dependent photometry corrections for all instruments and modes. Corrections may have linear, exponential, or power law form, or any combination of these.

pixel_replace

• Fixed a crash for an edge case in pixel replacement: a bad pixel with no valid adjacent data.

resample

• Use gwcs.FITSImagingWCSTransform for resampled imaging WCS to provide a consistent serialization of the WCS of resampled products to enable parsing in other languages other than Python.

source_catalog

• Add DAO and IRAF starfinder options, and expose parameters to tune star finding.

superbias

• Remove cast (which used 3x the data array size) to reduce memory usage.

tso_photometry

• Move TSO photometry radii to step parameters instead of reference file.
• Add auto-centroiding options.

wfss_contam

• Vectorize computations to make step run faster. Runtime decreased from several hours to a few minutes for representative NIRCam and NIRISS datasets. Support multiprocessing; maximum_cores parameter existed but did not work before. Add new diagnostic simul_slits model, saved when save_simulated_image is True.
• Replace brightest n objects source selection with source selection based on magnitude limit; brightest_n parameter removed, magnitude_limit parameter added. Add parameter orders to select specific spectral orders to disperse.
• Fix a bug where incorrect pixel locations were fed into the detector-to-grism transform, leading to incorrectly-shaped model traces.
• Fix flux scaling issue for NIRCam data.

white_light

• Use order- and filter-specific default wavelength ranges for SOSS exposures.

JWST Science Data Processing subsystem changes

• Fixed a bug that caused new files created from old observations (or those with minor changes in the filename) to reset the proprietary period and be assigned a public release date later than it should be.