Release 1.1 to main#1114
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This attribute is updated every time a selection is made through the iPlotter.
add regions attribute to spectrum
This attribute is updated every time a selection is made through the iPlotter.
…ory/dysh into blocking-plots
* docs: add gbtidl/dysh examples * docs: update dysh-to-GBTIDL tables * bump patch version
perf: PR drive by vectorize INTNUM construction in GBTFITSLoad
fix left side of scanplots
Forces the use of the same units as spectral_axis in the SpectralRegions to avoid unit conversion roundoffs resulting in the inclusion of extra channels.
…e-using-include-regions 1017 baseline issue using include regions
* Enable example data cache in CI Also fix bug in cache bootstrapping mechanism (doubt many people were actually seeing this but would break the CI workflow) * Set git checkout fetch depth to 1 Don't need full history for CI * Bump various action versions to get rid of deprecation warnings Warning: Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, astral-sh/setup-uv@v5. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/ * Clean up Splatalogue test skipping with decorator and local/remote split Replace ad-hoc try/except blocks (including broken warnings.warn(exception)) with a skip_if_splatalogue_down decorator in conftest.py. Split mixed tests into local (always run) and remote (skip gracefully on network errors) classes. Add ConnectionError to notebook test ALLOWED_ERROR_NAMES. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
fix:crval4_to_pol
Add system info for bug reports
#1076) When a Spectrum has DATE-OBS but no MJD-OBS in its metadata, compute MJD-OBS from the already-parsed _obstime and store it in meta. Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
* feat: add scan_info() and partial-match warnings in calibration methods (#745, #748) Add scan_info() method to GBTFITSLoad that shows available IFNUM/FDNUM/PLNUM combinations for given scans. Modify _common_selection() to warn (instead of silently dropping) when some requested scans have no matching data, displaying the available parameters for those scans. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bump for bug fix * Change exception to valueerror with better message. User logger instead of warnings and change some warnings to info * add scan_info to GBTOnline * fix: update test_set_item to use caplog for logger.warning checks warnings.warn was changed to logger.warning in __setitem__, so the test needs caplog instead of pytest.warns to capture the log messages. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * fix: use caplog for partial-match warning test in TestScanInfo The _common_selection partial-match message uses logger.info, so the test needs caplog instead of pytest.warns. Also use a real scan (177, ifnum=7 only) instead of a fake scan number to trigger the partial-match path. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * SCANS should be SCAN * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove claude * fix: use logger.warning in sdfitsload.__setitem__ and make test data-independent - Change sdfitsload.py __setitem__ from warnings.warn to logger.warning for consistency with gbtfitsload.py override - Make test_common_selection_partial_match_warns dynamically discover scans with different ifnum sets instead of hardcoding scan numbers Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix: revert sdfitsload.py change and fix test_set_item for mixed warn/log Revert sdfitsload.__setitem__ back to warnings.warn. Fix test_set_item to use pytest.warns for sdfitsload warnings and caplog for gbtfitsload logger.warning. The incorrect-length case only triggers logger.warning (ValueError raised before super().__setitem__), so it needs caplog. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * specify file name as glob.glob return list order is not guaranteed * add scan_info example * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Downgrade version from 1.1.1 to 1.1.0 --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…written-to-index fix issue #1093
…lim-does-not-update-the-colorbar-label Fix issue #1082
The fitsio write path in `_build_chunk_recarray` explicitly skipped the DATA column when overlaying in-memory mutations, on the false assumption that DATA is never mutated. Users can assign `sdf["DATA"] = ...`, which updates the in-memory bintable; the writer now honors those mutations. Add a regression test parametrized over both the fitsio and astropy write paths via a monkeypatched HAS_FITSIO. Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.6 → v0.15.9](astral-sh/ruff-pre-commit@v0.15.6...v0.15.9) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.9 → v0.15.10](astral-sh/ruff-pre-commit@v0.15.9...v0.15.10) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pedro Salas <salas.mz@gmail.com>
Updates the BANDWID value if calibrating a subset of channels.
* Fix issue #1089: clean up LazyFlagArray memmap temp files on exit LazyFlagArray.to_dense() created memmap-backed temp files with delete=False but never cleaned them up, filling /tmp over time. Track temp files and remove them via cleanup(), __del__, and atexit. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Fix Windows CI: release memmap before unlinking temp files On Windows a file backing an open np.memmap cannot be deleted, so cleanup() now forces a gc pass to release finalizer-tracked memmaps and keeps any still-locked paths for a later retry. Tests drop the dense reference before cleanup to mirror real usage. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Warn when tempdir free space is below memmap size LazyFlagArray.to_dense() now checks shutil.disk_usage on the tempdir before creating the memmap and logs a warning if free space is less than the estimated array size, so a silent disk-fill is less likely. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…-not-update-certain-spectrum-metadata Fix for issue #979
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.6 → v0.15.9](astral-sh/ruff-pre-commit@v0.15.6...v0.15.9) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.9 → v0.15.12](astral-sh/ruff-pre-commit@v0.15.9...v0.15.12) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pedro Salas <salas.mz@gmail.com> Co-authored-by: Marc Pound <22331890+mpound@users.noreply.github.com>
teuben
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May 5, 2026
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great piece of work, but should we hold off for the review to be finished to have this really merged in
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Of course. Converting to a draft. |
#1109) The history-logging decorators (@log_call_to_history, @log_call_to_result, @log_function_call) gated kwargs logging on `"kwargs" in sig.parameters`, which is only true when the decorated function literally declares **kwargs. For methods with named parameters like Spectrum.smooth, calls made with keyword arguments had their kwargs silently discarded from history. Also, format_dysh_log_record formatted arg/kwarg values with str() instead of repr(), so string values lost their surrounding quotes. Always log caller-supplied kwargs and use repr() for values. Drops the now unused inspect import and signature caches. Adds src/dysh/tests/test_log.py covering the positional, keyword, and result-side keyword call forms from the issue. Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
* promote hidden kwargs to parameters * patch failing test for now * doc update * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix ruff B008 error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add example usage to baseline. fix doc for exclude_regions=None * add example usage to baseline. fix doc for exclude_regions=None * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update test that will fail upon merge --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix Splatalogue CI failures (#1062) - Fix ALLOWED_ERROR_NAMES in notebook tests to use bare class names (e.g. "ConnectTimeout") that actually match the ename field nbclient checks, rather than fully-qualified names that never matched - Add mock_splatalogue_query fixture to conftest.py so the splatalogue code path can be tested without network access - Add TestSearchMocked class with 5 tests covering dysh's transformation layer: column rename, obs_frequency computation, redshift math, intintensity coercion, and column filtering Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Fix remaining Windows CI notebook failures - Add NameError to ALLOWED_ERROR_NAMES so cascading failures from network-allowed errors (ConnectTimeout etc.) don't fail the test when downstream cells reference undefined variables
* Skip notebook execution on Read the Docs builds, but don't change local behavior
* Rebuild all notebooks
export READTHEDOCS=True; ls notebooks/examples/*.ipynb | xargs -P 4 -I{} uv run jupyter nbconvert --to notebook --execute --inplace {}
---------
Co-authored-by: Thomas Chamberlin <tchamber@nrao.edu>
* ensure required columns are present before getting a spec * add regression test for #1117 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename variable to avoid precommit error * this also closes #1116
* feature: Spectrum.header prints Spectrum information
If the units were changed while zoomed in, then the axes limits would not update to the new units, leaving a potentially blank plot. On top of that, the home button would preserve the coordinates at the time the toolbar was initialized. This PR fixes that by setting the axes limits after every unit change, and by updating the home button location to one compatible with the plot units.
smooth makes a copy of the mask so the original is not modified.
Fixes plotter zoom issue when changing units
* add weakref.finalize and look for DYSH_SCRATCH to prevent /tmp from filling up * fix bad typos! * add tests to ensure $DYSH_SCRATCH, $TMPDIR are obeyed and that weakref.finalize() ensures tmp file cleanupwhen no longer needed. Claude helped with this. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix flaky Windows test for to_dense() temp file cleanup via weakref.finalize The assertion that the temp file is gone right after del+gc.collect() was racing the OS on Windows, where the memmap's file handle isn't guaranteed to release synchronously. Poll briefly instead of asserting immediately. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * skip Windows-flaky finalize cleanup test instead of retry-looping The retry loop didn't reliably converge on Windows CI; skip the test there instead since the underlying weakref.finalize behavior is already covered by test_to_dense_memmap_cleanup and test_del_cleans_up_tempfiles. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * update note about scratch dir environment variables --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
…ng-changes-the-input-spectrum Fix for issue #1067
BUILDDIR is nested inside SOURCEDIR for the docs build, and myst-nb was re-discovering and re-executing notebooks left in a previous _build output, causing nested _build/jupyter_execute/_build/... trees to grow on every incremental `make html` run. Excluding _build (and .ipynb_checkpoints) stops Sphinx from treating prior build output as source. Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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how badly have these diverged?