Pypeit

Latest version: v1.16.0

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1.3.2

-------------------

- (Hotfix) Bug in content type of README file that prevented upload to
PyPI

1.3.1

-------------------

- pypeit_chk_wavecalib script
- Option to limit channels shown for pypeit_show_2dspec
- sigdetect on in full_template
- Added new ArI, ArII lines
- Improved 1Dfit QA
- Final wavelength template for DEIMOS 900ZD
- Fix a bug in `pypeit/core/arc.py` and `pypeit/core/wavecal/autoid.py` due
to the padding to the arc frames
- Added a new XeI line
- Turn off sigma clipping for DEIMOS arc frames.
- Refactor setup.py to use setup.cfg to define package configuration
- Refactor version handling to use setuptools_scm to grab version info from git tags
- Add support for testing within isolated environments via tox
- Refactor CI to use tox to run tests
- Add cron-scheduled tests to CI
- Add tests to CI to cover macos, windows, and conda installations
- Refactor wrapper scripts in bin/ to be entry_points defined in setup.cfg
- Deprecate check_requirements now that dependencies are handled by the installation

1.3.0

-------------------

- DATE-OBS, UTC, AMPMODE, and MOSMODE added to metadata for DEIMOS, and
the first three are now included in the auto-generated pypeit files.
- DEIMOS AMPMODE is now included in the list of metadata used to
determine the DEIMOS configuration (setup).
- Frames ignored by
`pypeit.metadata.PypeItMetaData.unique_configurations` used to
establish the unique configurations are now set by
`pypeit.spectrographs.spectrograph.Spectrograph.config_independent_frames`.
These default to 'bias' and 'dark' frames.
- `pypeit.spectrographs.spectrograph.Spectrograph.config_independent_frames`
can also return a *single* keyword selecting the metadata column used
to match these frames to a given configuration. For DEIMOS, this is
used to match bias and dark frames to a configuration observed on the
same date. Currently these frames can only be set to a single
configuration.
- Added `pypeit.metadata.PypeItMetaData.clean_configurations` that
ignores frames that cannot be reduced by pypeit, as set by
`pypeit.spectrographs.spectrograph.Spectrograph.valid_configuration_values`.
For DEIMOS, this is used to ignore frames that are taken in
direct-imaging mode or using anything except the B amplifier to read
the data. The ignored frames are removed from the metadata table
(`fitstbl`).
- `update_docs` script now builds the html as well as the api rst files.
It also prints a pass/fail comment.
- Added tests to `pypeit/tests/test_setups.py` to test that PypeIt
correctly and automatically identifies frames from multiple DEIMOS
configurations and that `pypeit.pypeitsetup.PypeItSetup` correctly
produces separate pypeit files for each configuration.
- Added a development document reporting that PypeIt now satisfies the
`PD-3` requirement Keck outlined for the DEIMOS PypeIt pipeline.
- Building the docs now dynamically generates an example pypeit and
sorted file for inclusion in the PypeIt documentation.
- The setup block is now a simple listing of the keywords and values
used to identify the instrument configuration.
- Refactor identify GUI and improve its docs
- Modest refactoring of templates.py
- Construction of wavelength arxiv files for DEIMOS 1200B and blue 1200G
- Pypeit now adds DEIMOS slits that are expected from the slitmask design
but not found in the tracing process.
- PypeIt now flags as “BOXSLT” DEIMOS slits that are expected to be
alignment boxes from slitmask design.
- Added a table with DEIMOS slitmask design and objects info to the
SlitTraceSet datamodel
- Add support for MMTO Blue Channel Spectrograph
- Add GitHub Actions CI workflow
- Incorporates a procedure to enable GMOS Nod and Shuffle observations
- New GMOS wavelength solutions
- Remove Travis CI config
- General housecleaning of spectrographs
- Documentation improvements
- Dynamically builds table of available spectrographs; see
`pypeit.spectrographs.available_spectrographs`
- `pypeit.defs` is now deprecated
- Removed usage from `pypeit.pypmsgs` and moved it to `run_pypeit.py`
- Many Spectrograph instance attributes are now class attributes; in
particular, previous instance attribute `spectrograph` is now `name`.
- Added class attributes that set if the spectrograph is supported and any
comments for the summary table.
- `default_pypeit_par` is now a class method, which allows the name of the
spectrograph to be defined in a single place
- Valid spectrographs are no longer checked by
`pypeit.par.pypeitpar.ReduxPar`. This caused a circular import in the
new strucuture. The parameter `par['rdx']['spectrograph']` is virtually
always checked by `load_spectrograph`, so I don't think this is a
problem.
- Kastr 300 grating solutions
- Hotfix to include the solutions!
- Improved DEIMOS slitmask design matching
- Assign RA/DEC to DEIMOS extractions
- DEIMOS object RA, Dec, and name returned when running `pypeit_show_1d --list` and saved in
the .txt file with the list of 1d spectra.
- DEIMOS object name and `maskdef_id` visible in ginga when running `pypeit_show_2d`
- Fix sigma clipping bug!

1.2.0

-------------------

- Frame-typing tweaks for DEIMOS
- Exposure-time ranges removed
- All frame types now key off OBSTYPE
- Added more detail on citation policy to main page on readthedocs
- Added docs for BitMasks
- Altered scripts interface to allow for dynamically making the help doc
files
- full spatial/spectral flexure and heliocentric corrections implemented
for IFU reductions
- optimal weights in datacube generation
- Docs for skysub, extraction, flat fielding
- New skysub options for masking and suppressing local
- Added `pypeit/core/convert_DEIMOSsavfiles.py` to convert .sav files
into fits files
- Added "amap" and "bmap" fits files in
`pypeit/data/static_calibs/keck_deimos/` for DEIMOS optical model
- Added `pypeit/core/slitdesign_matching.py` and `maskdesign_matching`
to `EdgeTraceSet`
- Added ParSet for switching ON the slit-mask design matching. Default
is ON for `keck_deimos`
- Pypeit registers `maskdef_id` in SlitTraceSet if instrument is
`keck_deimos`
- Fix assignment bug in fitting bspline

1.1.1

-------------------

- (Hotfix) Fluxing doc edits
- (Hotfix) Fix sdist pip installation

1.1.0

------------------

- Fixed a bug for IR reductions for cases where only negative object
traces are identified. These were accidentally being written to the
spec1d file.
- Fixed a bug fixes a bug in full_template wavelength reidentification
for situations where extreme wavelength coverage slits results in
reidentification with a purely zero-padded array.
- Fixed a bug fixes a bug in full_template wavelength reidentification
for situations where extreme wavelength coverage slits results in
reidentification with a purely zero-padded array.
- Fixed another such bug arising from these zero-padded arrays.
- (Hotfix) Deal with chk_calibs test
- Script to generate combined datacubes for IFU data.
- Changed numpy (> 1.18.0) and scipy (> 1.4.0) version requirements
- Allow show2d_spec, chk_edges, chk_flats to load older Spec2DObj
datamodel versions
- Implemented a plugin kindly provided by the ginga developers to
display images with a secondary wavelength image WCS.
- Removes dependency on profxj's ginga fork, and avoids a bug when
using WCS image registration in that fork.
- `pypeit/ginga.py` moved to `pypeit/display/display.py` and ginga
plugin added to `pypeit/diplay` directory.
- ginga plugin registered as an entry point in `setup.py`
- Added a script to check that the plugins are all available.
- Installation docs updated. Both `ginga` and `linetools` are now
installed via pip.
- Deprecated `pypeit/debugger.py` and `pypeit/data/settings`
- Removed h5py as a dependency
- `linetools` is now listed in `pypeit/requirements.txt` until I can
check if it still causes readthedocs to fail...
- Modify Spec2DObj 2D model for float32 images
- `pypeit.tracepca.TracePCA` and `pypeit.edgetrace.EdgeTraceSet` now
subclass from `pypeit.datamodel.DataContainer`
- Refactor WaveCalib into a DataContainer
- Refactor fitting + PypeItFit DataContainer
- Coadd2D bug fixes
- Coadd2D without spec1d files
- Coadd2D offsets
- Some Coadd2D docs
- Manual extraction
- Improve LBT/LUCI
- Add MMT/MMIRS
- QL script for Keck/MOSFIRE (beta version)
- Correct det bug in keck_lris
- Modifications to allow for flailing LRISr detector
- Modifications for parse LRIS LAMPS prior to 2010 upgrade
- Added support for P200/DBSP and P200/TripleSpec

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