CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, with an added List of PRs section and links to the relevant PRs on the individal updates. This project adheres to Semantic Versioning.

Unreleased

Added

• Add epoch 67 #573
• Add epoch 66 #569
• Add epochs 64 and 65 #568
• Support for Python 3.10 #334
• Add access to epoch 63 #563

Changed

• Minor changes to docstring formatting throughout based on updated mkdocs versions #334
• Minor changes for matplotlib 3.7: add angle kwarg to Ellipse and change matplotlib.pyplot.cm.get_cmap to matplotlib.colormaps.get_cmap #334
• Refreshed dependencies - major changes are python 3.10, mkdocs (and related packages), astropy v5 and matplotlib v3.7 #334
• Update emoji names to reflect latest fontawesome naming scheme#334
• Fixed minor typos in docs and docstrings #334
• Updated old contact information #334
• Updated github actions to latest versions #562
• Updated 2023 workshop notebook - fixed Query options and general cleanup #558

Fixed

• Correctly calculate plot_lightcurve y-axis range for multi-frequency upper limits #567
• Fixed formatting of new epoch addition git example #568
• Directly compare stmoc times, avoiding conversion to JD, and replace equality requirement with isclose #334

Removed

• Removed lightgallery functionality from docs #334

List of PRs

• #573: feat: Add epoch 67
• #569: feat: Add epoch 66
• #567: fix: Correctly calculate plot_lightcurve y-axis range for multi-frequency upper limits
• #568: feat, docs: Add epochs 64 and 65, and fix new epoch addition docs page syntax
• #334: fix, docs, feat: Dependency refresh including python 3.10 support and corresponding minor updates
• #563: feat: Add access to epoch 63
• #562: fix: Updated github actions to latest versions
• #558: docs: Updated 2023 workshop notebook - fixed Query options and general cleanup

3.1.1 (2024-07-30)

Added

• Added 2023 workshop notebook to docs #552

Changed

• Updated author email addresses #553
• Explicitly require setuptools in pyproject.toml #553
• Pin mkdocs=1.3.1 #553
• Force jinja2==3.0.3 #551

Fixed

• Temporary fix for pydantic version breaking vaex #553
• Downgraded jinja2 to fix bug in docs deployment #551

Removed

List of PRs

• #553: fix, dep: Pin versions to fix dependency issues, update author email addresses
• #551: fix, dep: Downgrade jinja2 to fix bug in docs deployment
• #552: feat: Add 2023 workshop notebook to docs

3.1.0 (2024-07-26)

Added

• Add epoch 61 #537
• Add epochs 58-60 #535
• Added extra logging in Query to improve clarity of data selection #515
• Added support for post-processed data #515
• Added epoch 40 as a base epoch to allow query of full VAST extragalactic fields #522
• Added support for epochs 42-51 #522

Changed

• Convert all Source names to strings #537
• Updated README #535
• Changed default behaviour to using post-processed TILES data #515

Fixed

• Fix errors when creating a Source with an int name #537
• Fix incorrect warnings when using COMBINED data #538
• Fix forced fitting of compressed fits files #534
• Fix checking length of HDUl that should have been fixed by #526 #528
• Disable auto-scaling for show_png_cutout to allow users to specify the scaling #527
• Fix open_fits handling of unprocessed files #526
• Update open_fits to check HDU list contents rather than the file extension #524

Removed

List of PRs

• #537: fix: Convert all Source names to strings
• #538: fix: Fix incorrect warnings when using COMBINED data
• #537: feat: Add epoch 61
• #535: feat: Add epochs 58-60 and updated README
• #534: fix: Fix forced fitting of compressed fits files
• #515: fix, docs, feat: Support post-procesed data, make it the default and improve clarity of what data has been selected in a query.
• #528: fix: Fix checking length of HDUl that should have been fixed by #526
• #527: fix: Disable auto-scaling for show_png_cutout to allow users to specify the scaling
• #526: fix: Fix open_fits handling of unprocessed files
• #524: fix: Update open_fits to check HDU list contents rather than the file extension
• #522: fix, feat: Add support for extrgalactic queries and epochs 42-51

3.0.1 (2023-09-24)

Changed

• Bumped mkdocstrings to version 0.17.0 to avoid mkdocstrings error #496.
• Pinned jinja2 to version 3.0.3 to avoid mkdocs_autoref error #496.
• Update github workflows to latest versions #496
• Exit nicely when invalid survey is requested for SkyView contour plot #497

Fixed

• Fixed docs build process #496.

List of PRs

• #496: fix: Update github workflows to latest versions
• #497: feat: Exit nicely when invalid survey is requested for SkyView contour plot

3.0.0 (2023-09-02)

Added

• Raise exception when simbad name query returns more names than there are objects queried #490
• Added open_fits function to correctly handle compressed image HDUs #480
• Added epoch 41 #470
• Added warning when querying corrected data #465
• Added epochs 38, 39 and 40 #466
• Added epoch 37 #458
• Added epoch 36 #455
• Added epochs 34 and 35 #454
• Added automatic generation of resource (csvs/pickles) paths #431
• Added SkyCoord pickle functionality (creation, loading and implementation) #431
• Added access to epoch 33 #434
• Added "search_all_fields" option to Query and find_sources, which returns all data available at the source location rather than just that associated with the closest/best field #418
• Added option to specify which dask scheduler to use to Query, PipeRun, PipeAnalysis objects, and argument to find_sources.py #430
• Added access to epoch 32 #429
• Added access to epoch 31 #427
• Added access to epoch 30 #419
• Added access to epoch 27 #414
• Added access to epochs 22, 23, 24, 25, 26, 28 (RACS-high), 29 (RACS-low-2) #406
• Added _validate files to query.Query class to ensure that only accessible data is queried #370
• Added logging to pipeline.PipeRun #383
• Added tools.wise_color_color_plot to create WISE color-color plots #379
• Added access to epoch 21 #351
• Added check for existence of requested data in Query init #346
• Added pylint github action for pull requests and flake8 dev dependency #338.
• Added observing frequency to all fields csv files #311
• Added OBSERVED_EPOCHS variable for epochs that have been observed but not yet released #311
• Added access to epochs up 17, 18, 19 #311
• Added BASE_EPOCHS variable #311
• Added tools.offset_postagestamp_axes which allows users to display postagestamps with offset (rather than absolute) coordinates #315
• Added Dask RuntimeError warning to query.md docs #317
• Added tools for new epoch addition: add datetimes to fits images create fields csv files, create and update MOCs #298

Changed

• Changed opening of all fits files to use open_fits function #480
• Changed default behaviour of Image.measure_coord_pixel_values to have img=False #476
• Changed Fields.direction to be loaded from pickle rather than generated at each call #431
• Updated RACS dec limit to +50 #438
• Updated Query._get_epochs to allow lists and ints #421
• Bumped pytest and lint github workflow from ubuntu-18.04 -> ubuntu-20.04 #425
• Changed path generation to allow for image/rms/background files to contain ".conv" #410
• Changed handling of data product generation from epoch-based to index-based #403
• Updated GitHub actions Gr1N/setup-poetry to v7 #385
• Updated numpy to ~1.22.1 #380
• Removed epoch 12 warning #361
• Updated RELEASED_EPOCHS to include epochs 14 and 20 #351
• Enabled access to full TILES data #325
• Allow query epochs to be specified as list #327.
• Changed plot legend to show frequency rather than selavy/forced #311
• General changes throughout to allow observing frequency to propagate through a query #311
• Updated access to field centres csvs to distinguish between low/mid bands #311
• Updated find_sources.py to automatically query all epochs #311
• Updated handling of RACS epochs #311
• Updated default values of query epochs and imsize #311
• Allow users to specify whether to write generated MOCs, and to use arbitrary STMOC #323
• Changed source.Source.make_png to create postagestamps using coordinate offsets #315
• Minor documentation edits #298

Fixed

• Exit nicely when users try to use measurement pairs but they do not exist #478
• Ensure that full image data does not persist when creating FITS cutouts from compressed HDUs #483
• Fixed missing RMS measurements for non-detections #476
• Removed duplicates in field matching #472
• Fix read_selavy to force all flux & flux_err values to be positive #463
• Fix planet matching to correctly handle field names with/without 'A' suffix #453
• Correctly handle empty df in Query.init_sources() #453
• Updated VASTMOCS to correctly handle fields with/without 'A' suffix #452
• Updated github pytest workflow to use Gr1N/setup-poetry@v8 #449
• Updated default value of Query.max_sep to 1.5 degrees #440
• Correctly handle show_all_png_cutouts(save=True) file naming #437
• Ensure selected_fields is defined for all field matching cases #435
• Updated Query._get_epochs to exit nicely when no epochs are available #421
• Update match_planet_to_field to handle empty groups #416
• Added corrected_data to Source class to ensure correct image paths are used #412
• Fixed handling of Stokes Q/U/V selavy files #410
• Fixed naming of fits cutout functions #407
• Changed field name handling to correctly convert RACS -> VAST #405
• Fixed variable names in query documentation example #398
• Updated logging in query.py to correctly reference the file type it was dealing with #398
• Fixed handling of empty list of planets in query #390
• Fix bug where cutouts could not be created #389
• Correctly plot integrated flux histograms in eta-V bokeh plots #383
• Fixed handling of negative values in eta-V bokeh plots #383
• Fixed incorrect selavy filenames for EPOCH00 tiles #373
• Fixed search_around_coordinates option in query #365
• Fixed handling of RACS-mid fields #368
• Fixed handling of RACS filenames and epochs #358
• Fixed issue with ncpu exceeding number of unique sources in Query._init_sources #363
• Fixed plot_lightcurve legend creation #345
• Fixed pipeline eta-v matplotlib plot #340
• Fixed pandas dataframe and series append deprecation by using pd.concat #337.
• Fixed metadata for islands queries #328
• Updated missing values in RACS beam info csv file #311

Removed

• Removed '#' from get_components dataframe except when it is used in search_around_coordinates queries #365

List of PRs

• #490: feat: Raise exception when simbad name query returns more names than there are objects queried
• #478: fix: Account for pipeline runs with no measurement pairs file
• #483: fix: Ensure that full image data does not persist when creating FITS cutouts from compressed HDUs
• #480: feat: Added open_fits function to handle compressed image HDUs
• #476: fix: Fixed missing RMS measurements for non-detections
• #472: fix: Remove duplicates in field matching
• #470: feat: Added epoch 41
• #465: feat: Added warning when querying corrected data
• #466: feat: Added epochs 38, 39 and 40
• #463: fix: Fix read_selavy to force all flux & flux_err values to be positive
• #458: feat: Added epoch 37
• #453: fix: Fix planet matching to correctly handle field names with/without 'A' suffix, and correctly handle empty df in init_sources
• #455: feat: Added epoch 36
• #454: feat: Added epochs 34 and 35
• #452: fix: Updated VASTMOCS to correctly handle fields with/without 'A' suffix
• #431: feat, docs, tests: Store beam centre SkyCoords as serialised objects rather than generating them on the fly
• #449: fix: Updated github pytest workflow to use Gr1N/setup-poetry@v8
• #440: fix: Updated default value of Query.max_sep to 1.5 degrees
• #438: feat: Updated RACS dec limit to +50
• #437: fix: Correctly handle show_all_png_cutouts(save=True) file naming
• #435: fix: Ensure selected_fields is defined for all field matching cases
• #434: feat: Added access to epoch 33
• #418: feat: Added option to return all data at the available position rather than one field per epoch.
• #430: feat: Allow users to specify which dask scheduler to use for multi-processing
• #421: feat, fix, docs: Updated Query._get_epochs to exit nicely when no epochs available & to allow lists and ints to be passed.
• #429: feat: Added access to epoch 32
• #427: feat: Added access to epoch 31
• #425: fix: Bumped pytest and lint github workflow from ubuntu-18.04 -> ubuntu-20.04
• #419: feat: Added access to epoch 30
• #416: fix: Update match_planet_to_field to handle empty groups
• #414: feat: Added access to epoch 27
• #412: fix: Added corrected_data to Source class to ensure correct image paths are used
• #410: fix: Fix handling of Stokes V products and image naming scheme
• #406: feat: Add epochs 22, 23, 24, 25, 26, 28 (RACS-high), 29 (RACS-low-2)
• #407: fix: Fixed naming of fits cutout functions
• #403: feat, docs: Changed data product generation from epoch-based to index-based
• #405: fix: Fix incorrect handling of RACS-named fields
• #370: feat, docs: Add file validation to check what data is available and remove anything that is not available from the query.
• #398: fix, docs: Fix incorrect logging in query.py and incorrect variable names in query documentation
• #390: fix: Update handling of planets to be consistent with regular sources.
• #389: fix: Fix cutout creation bug.
• #385: dep: Update Gr1N/setup-poetry to v7.
• #380: dep: Update numpy to ~1.22.1.
• #379: feat: Add function to create WISE color-color plots.
• #373: fix: Fixed incorrect selavy filenames for RACS tiles
• #365: fix, tests: Fix query search_around_coordinates option.
• #368: fix, docs: Ensure find_fields returns RACS fields.
• #361: feat, docs: remove epoch 12 warning.
• #358: fix: Fix RACS file paths and epoch handling.
• #363: fix: Update dask npartition specification in Query._init_sources call.
• #351: fix, feat: Add epoch 21.
• #346: feat, fix, tests: Check if requested data exists in Query init.
• #345: fix: Fixed plot_lightcurve.
• #338: feat, dep: Added pylint workflow for pull requests.
• #340: fix: Fixed eta-v plot.
• #337: fix: Fixed pandas append deprecation.
• #325: tests, feat: Enabled access to full TILES data.
• #328: fix, docs: Fixed metadata for islands queries.
• #327: feat, docs: Allow query epochs to be specified as list.
• #311: tests, docs, feat: Added multi-frequency handling and small updates.
• #323: feat, tests: New options for MOC generation.
• #315: tests, docs, feat: Use offset, rather than absolute, coordinates for postagestamps.
• #317: docs: Added warning to docs.
• #298: tests, docs, feat: Added tools for new epoch addition.

2.0.0 (2021-10-09)

Note Changelog started from PR#273 hence full notes are not available from before this point.

Added

• Added tools sub-module consisting of skymap/MOC interface tools #277.
• Added get_supported_epochs function to survey component #294.
• Added support for epoch 13 (formerly epoch 12) #293.
• Added new data files for epoch 12 #293.
• Added epoch 12 warnings for query and moc components in code and docs #293.
• Added pep8speaks config file to project #290.
• Added a method to recalculate the measurement pairs dataframe (two epoch metrics) #290.
• Docs badge on readme #288.
• Added unit testing for the codebase #285.
• Added documentation on tests #285.
• Added github workflow to run pytest on new PRs #285.
• Added documentation using the mkdocs framework #273.

Changed

• Minor documentation edits #289.
• Updated survey docs page to reflect previous refactoring #294.
• Changed all former epoch 12 data files to epoch 13 #293.
• Updated vaex-core version to 4.5.0 #290.
• Updated docs dependencies versions to fix notebook pages #288.
• Refactored data loading to use importlib.resources #285.
• Refactored some data loading to be method base #285.
• Moved RELEASED_EPOCHS and ALLOWED_PLANETS to top level import #285.
• Changed docstrings to google format for docs compatibility #273.

Fixed

• Fixed docs announcement bar link #289.
• Fixed test_query.py::TestQuery::test_init_failure_base_folder test #291.
• Fixed jsmin dependancy install (2.2.2 -> 3.0.0) #285.
• Remerged docs branch #287.
• Docs branch reverted to avoid squashing to make merge of tests straightforward #286.

Removed

• Removed MANIFEST.in file #289.
• Removed deprecated information from the survey docs page #294.
• Removed EpochInfo class from query as no longer used #285.

List of PRs

• #289: docs: Minor documentation edits.
• #277: tests, docs, feat, dep: Add skymap utils
• #294: docs, feat: Survey code tidy and docs correction.
• #293: feat: Added EPOCH13 support.
• #290: docs, dep, feat: Added a recalc two epoch metrics method.
• #291: tests: Fixed TestQuery::test_init_failure_base_folder test.
• #288: docs, dep: Updated docs dependencies.
• #285: test, feat, dep: Added codebase unit testing.
• #287: docs, dep: Documentation using mkdocs
• #286: docs, dep: Revert "Documentation using mkdocs (#273)"
• #273: docs, dep: Documentation using mkdocs
• #274: fix: fixing typo in exception
• #270: dep: Changed over dependency management to poetry
• #264: feat: Add negative selavy catalogues
• #258: feat: v2.0.0-rc.6
• #257: fix: Fix lightcurve axist limits for forced fits
• #255: fix: Added if statement to catch os.getenv returning None
• #253: feat: Added filter pipeline run by MOC function
• #251: fix: Check self.pipeline inside write_measurements
• #247: feat, dep: Updated forced photometry to be a dependency
• #246: fix: Fixed vaex two epoch metric analysis
• #244: fix, dep: Fix mocpy dependancy
• #243: fix: Fixed dropping level on empty dataframe and selavy-simple
• #242: dep: Frozen dependancies versions
• #238: feat: Update the example notebooks with pipeline catalogue crossmatching and new features
• #236: feat: Added pipeline sources SkyCoord convenience function
• #235: feat: Added recalc_sources functionality to pipeline
• #232: feat: Give project_dir precedence over environment variable
• #230: feat: Improve plotting capabilities
• #228: fix: Fix fits loc issue
• #224: fix: Changed lightcurve y axis start at 0 by default
• #223: fix: Fixes query checks with scaler SkyCoord entry

v2.0.0-rc.5 (2020-10-20)

The release candidate 5 of v2.0.0. This was the release before the changelog was implemented.

List of PRs

• #221 feat: Pipeline add 2 epoch Mooley style plotting
• #220 fix: Issue 219 fix source names
• #218 fix: Removed bad fields from epoch 12 csv