AstroToolkit 1.7.1__tar.gz → 2.0.1__tar.gz

astrotoolkit-2.0.1/.github/workflows/publish.yml

@@ -0,0 +1,93 @@
+name: Publish
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch: {} 
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    if: |
+      startsWith(github.ref, 'refs/tags/v') &&
+      (contains(github.ref_name, 'a') ||
+       contains(github.ref_name, 'b') ||
+       contains(github.ref_name, 'rc'))
+
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    if: |
+      startsWith(github.ref, 'refs/tags/v') &&
+      !contains(github.ref_name, 'a')
+
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    needs: publish-pypi
+    runs-on: ubuntu-latest
+    if: |
+      startsWith(github.ref, 'refs/tags/v') &&
+      !contains(github.ref_name, 'a') &&
+      !contains(github.ref_name, 'b') &&
+      !contains(github.ref_name, 'rc')
+
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v2

astrotoolkit-2.0.1/.gitignore

@@ -0,0 +1,21 @@
+*.pyc
+*.html
+*.fits
+
+dist/
+__pycache__/
+docs/build/
+docs/source/auto_tutorials/
+*.egg-info/
+testing/
+
+!src/ATK/plotting/hrd/backdrop_hrd_allmags.fits
+
+!docs/source/**/*.fits
+!docs/_templates/*
+docs/source/_static/animations/media/*
+!docs/source/_static/animations/media/videos/
+!docs/source/_static/animations/media/videos/*/
+!docs/source/_static/animations/media/videos/*/1080p60/
+!docs/source/_static/animations/media/videos/*/1080p60/*.mp4
+docs/source/_static/animations/media/videos/*/1080p60/partial_movie_files/

astrotoolkit-2.0.1/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method : pip
+      path: .
+    - requirements: docs/requirements.txt

astrotoolkit-2.0.1/MANIFEST.in

@@ -0,0 +1 @@
+include src/ATK/plotting/hrd/*.fits.gz

astrotoolkit-2.0.1/PKG-INFO

@@ -0,0 +1,60 @@
+Metadata-Version: 2.4
+Name: AstroToolkit
+Version: 2.0.1
+Summary: A package for the gathering, plotting and analysis of astronomical data.
+Author-email: Ethan Moorfield <ethan.moorfield@hotmail.co.uk>
+Project-URL: Homepage, https://github.com/WD-planets/AstroToolkit
+Project-URL: Issues, https://github.com/WD-planets/AstroToolkit/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: astropy
+Requires-Dist: astroquery
+Requires-Dist: beautifulsoup4
+Requires-Dist: bokeh
+Requires-Dist: lightkurve
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas>3.0.0
+Requires-Dist: PyYAML
+Requires-Dist: reproject
+Requires-Dist: scipy
+Requires-Dist: skypatrol
+Requires-Dist: sparclclient
+Dynamic: license-file
+
+AstroToolkit
+============
+AstroToolkit (ATK) is a set of tools for fetching, plotting, and analysing astronomical data.
+
+<br>
+
+Installation
+============
+To install the package from PyPI, use:
+
+```
+pip install AstroToolkit
+```
+
+<br>
+
+Documentation
+=============
+Full documentation for the package can be found [here](https://astrotoolkit.readthedocs.io/en/latest/).
+
+<br> 
+
+Acknowledgements
+================
+This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101020057).
+
+<p align="center">
+    <picture>
+        <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_dark.png">
+        <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png">
+        <img src="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png" width="200">
+    </picture>
+</p>

astrotoolkit-2.0.1/README.md

@@ -0,0 +1,33 @@
+AstroToolkit
+============
+AstroToolkit (ATK) is a set of tools for fetching, plotting, and analysing astronomical data.
+
+<br>
+
+Installation
+============
+To install the package from PyPI, use:
+
+```
+pip install AstroToolkit
+```
+
+<br>
+
+Documentation
+=============
+Full documentation for the package can be found [here](https://astrotoolkit.readthedocs.io/en/latest/).
+
+<br> 
+
+Acknowledgements
+================
+This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101020057).
+
+<p align="center">
+    <picture>
+        <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_dark.png">
+        <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png">
+        <img src="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png" width="200">
+    </picture>
+</p>

astrotoolkit-2.0.1/changelog.md

@@ -0,0 +1,148 @@
+=======
+Changes
+=======
+- Rewrote entire package from the ground up, should be a lot easier to develop in the future
+
+- All coordinate/source handling now done via a central Target class
+    - A Target is automatically generated if a source_id or SkyCoord is entered, or one can be manually created via Target.from_coord() or Target.from_id()
+    - Reduces explicit dependency on Gaia, so future astrometric surveys like LSST will be a lot easier to implement, just need to provide an equivalent to get_gaia_target (i.e. converts LSST id -> ATK Target with LSST astrometry)
+    - Added an "astrometric_backend" config key, which will (in future) select the default astrometry survey (currently only Gaia is supported)
+    - Coordinates can be provided in any frame, automatically transformed to ICRS
+- Configuration setup now far more robust
+    - Improved cross-platform file opening
+    - Config files now stored in hidden HOME/.AstroToolkit directory
+- Improved .show() (previously .showdata()), now recursively handles the printing of arbitrarily complex structures in an improved format + can optionally show types via show_all_types = True
+    - .show() is now supported on all ATK objects (e.g. DataSets, Containers, and Targets)
+- Improved file saving to adaptively store structures as fits files
+- Improved file reading to adaptively generate ATK structures from fits files
+- Opened figures now save to HOME/.AstroToolkit/cached_figures/ temporarily, with a duration given by the config
+- Image bands now correctly supported, and added 2 new colour maps - viridis (default) and false colour. Latter converts filter wavelength to an approximate real colour. Can choose colour map by passing cmap = 'viridis' | 'false_colour' | 'grey' to plot()
+- Image plotting can now utilise relatives axes (i.e. +- arcsec from the centre, now default)
+- Unified all structures into a single class DataSet
+- Unified .data attribute - all query types now stored data as a list of ATK data containers
+- SkyMapper image queries updated to SkyMapper DR4, and now sorted by exposure time (desc) and air mass (asc) to return best image
+- Image queries to DSS1/DSS2 now properly implemented
+- Added support for WISE, 2MASS and SDSS image queries 
+- Improved image plotting
+    - images should now always be near-perfect squares, regardless of plotting options
+- Added an optional parameter "disable_corrections" to query(), which disable all astrometric corrections if True (defaults to False)
+- SEDs now retain all detections in specified radius
+- Added support for DESI DR1 spectral queries
+- Improved filtering of ATLAS photometry
+- Light curve queries now accept a kwarg "split", which will assign each returned light curve a per-survey object ID (where possible)
+    - This defaults to True. Disabling it essentially makes every light curve survey a forced photometry (e.g. ATLAS) query
+    - Light curve plotting now automatically splits light curves into per-survey and per-id figures
+- Added kwarg 'cmap' to light curve plotting, which may be "mean" or "flat". The former uses a gradient colour map with a band of darker colour at the mean magnitude, while the latter uses a single flat colour per band. Defaults to "mean"
+- User is now warned if ATK version does not match at time of fits file reading/writing
+- Added integration with astropy units. Where relevant, parameters are treated and stored as astropy Quantities.
+    - Input parameters may also use astropy quantities, e.g. a radius of 2 * u.arcmin may be requested for a 2 arcmin search
+    - Added global config option 'unit_format' = 'text'/'symbol' to print units as text or symbol representations (defaults to 'symbol')
+- Added query settings config option 'default_scale' = 'arcsec'/'arcmin'/'deg' to choose the default unit for query radius/image sizes (defaults to 'arcsec')
+- Significantly reduced the number of dependencies
+- added ability to query multiple targets at once
+    - DataSets now store targets and a mapping between the query target and the returned data containers, added .fetch_by_id(), .fetch_by_coord() and .fetch_by_target() methods to extract data per-source
+- added kwarg "background" to HRD plotting, which limits the background sample to a given fraction of the full sample (e.g. 0.5 would half the number of background points to reduced file size and lag)
+- added kwarg 'combine' to HRD plotting, if False one HRD will be plotted for each source (primarily for datapage creation where each datapage will want its own hrd)
+- added tab titles to plots when opened in browser
+- added targeting information to figure titles (i.e. identifier or coordinates)
+- improved SED/spectra overlay functionality
+    - uses target matching to automatically match SEDs and spectra
+    - plots with overlays now keep all interactive elements from both plot types
+    - can now overlay both ways, i.e. can overlay spectra on an SED as before, but can also overlay an SED over spectra
+    - overlaying multiple spectra for a single source (i.e. if a survey returned multiple spectra for the same source) now produces duplicated SEDs with a separate spectrum overlay for each one
+- 'check_exists' kwarg in queries replaced by 'path' kwarg with same functionality
+    - DataSets now use a checksum system -> changes in any query parameters will now automatically re-run the query and overwrite the local file
+    - local file will also be overwritten if working ATK version doesn't match that at time of local file creation
+- light curve binning now much faster
+- usability of all data methods (e.g. lightcurve .bin(),.crop() etc.) significantly improved:
+    - added method .apply() to DataSet, applies a given method to all stored containers
+    - argument 'inplace' can be used to modify the structure/container in-place or perform modifications on a copy which is then returned
+- powspec ('pspec') and phasefolding ('fold') now done via the .apply() method, allowing this data to be stored rather than being performed at plot-time
+    - added 'multiband' kwarg to both of the above. If True, analyses all bands simultaneously to increase SNR and produce a single freq/period. If False, each band is treated entirely separately
+    - added 'subtract' kwarg to phase folding. If 'median', all bands are median-subtracted. If 'mean', all bands are mean-subtracted. If None, no subtraction is performed.
+- crop data method now supported by SEDs, spectra and power spectra
+- bin data method now supported by spectra
+- improved structure of user-accessible imports
+    - main functions now available via: from ATK import ...
+    - all ATK models available via: from ATK.Models import ...
+- added spectral feature fitting functionality via plot method 'fit'
+- added spectral radial velocity functionality via plot method 'rv_fit'
+    - can detect multi-component radial velocities
+- simplified datapage creation, layout now given as a list (columns) of lists (rows) of datasets
+- optimized datapage plotting to minimise whitespace, align axes and force square images as best as possible
+- greatly simplified DataTable creation
+    - now just takes a dict in form survey: <list of cols> to include, automatically provides survey/catalogue/correction/separation columns and fetches parameter/value columns using Vizier queries
+- DataTables now shrink in height to match table, and will grow in height up to requested size
+- DataTables store data as an astropy Table under the .table attribute
+    - when plotted, DataTables now have a unit column
+- Datapages now returned as a DataPages object, with show(), show_by_target(), show_by_id(), and show_by_coords() methods to show all datapages or single out those of individual targets
+- data is now saved via the .store() method, while plots are saved with the .save() method (the latter is also used for DataPages)
+- Made spectral lines hidden by default
+- Rewrote + significantly improved all documentation
+    - Full tutorials added
+    - Tutorials written with sphinx-gallery, now automatically run code and embed bokeh plots/terminal output, etc.
+    - Tutorials now downloadable
+- figure legends now dynamically shrink font size to remain inside bounds
+- local files can now be compressed by providing a compressed file extension (e.g. .fits.gz)
+- phase folding now uses phase dispersion minimisation to discern between the real frequency and its harmonics
+- folded light curves can now be automatically aligned by passing align = "mean", "median", "max", "min" to align to the mean/median magnitude or a maxima/minima
+- Vizier data containers (Records) now store their data as an astropy Table under the .table attribute
+    - Returned Vizier data now maintains units
+- old 'raw' argument in light curve queries is now 'filter', disables all non-required filtering if False (default=True)
+- DataSets can be merged with DataSet_1.merge(DataSet_2), and split with DataSet.split(<targeting info>)
+- Datapages now automatically generate tabs so that if multiple plots are present in an included DataSet (e.g. if multiple data products are returned from a query or if DataSet.merge() was used to combine multiple surveys), user can now freely switch between them
+- migrated docs from ReadTheDocs theme to PyData
+
++ other stuff that I forgot to write down
+
+
+
+=========
+To-Do Now
+=========
+- read through docs
+    - replace 'star' with e.g. system, source, etc.
+    - check docstrings / comments
+    - check type hints
+
+
+===========
+To-Do Later
+===========
+improved testing
+
+- get full set of spectral lines from NIST for rv fitting?
+- rename tutorial .py files
+- function/docs links in code examples (like for external libraries)?
+- talk to boris about my rv_fit process
+- clean up pm correction
+    - main issue is e.g. overlays.py cannot be vectorised -> astropy doesn't let you define non-scalar SkyCoords with varying validity of distance/pm information, so you cannot reliably correct a grouped SkyCoord. Luckily, not used much as usually things are handled as single coordinates anyway
+    - distance and pm ONLY matter for corrections, in searches its fine to lose this information and hence stay vectorised
+- add a way to tell if any significant periodicity was detected in powspec
+- pdm implementation
+    - improve true frequency detection across range of orbital morphologies
+- providing a SkyCoord with proper motion measurements
+- clean up and improve generalisation of data methods (pass struct instead of arrays)
+- rich text output option (https://realpython.com/python-rich-package/)
+- calibrating + combining multiple light curves to make one massive light curve
+- decouple from Gaia with a properly implemented astrometric backend system
+- add best-epoch separation to light curves?
+- add matplotlib as an optional plotting backend to avoid issues with many data points (e.g. hrd/tess/power spectra)?
+- don't change coordinates to icrs/celestial straight away, keep these and just change in query() without affecting Target.initial_coords?
+- possibly store metadata, e.g. object IDs from light curve surveys in a .meta attribute
+- add search_pos to SEDs?
+- allow any magnitudes to be used in hrd query - i.e. user searches with Gaia ID to make sure there is a valid distance (if not return no data) -> supplied two bands are fetched from a Vizier query to get the colour?
+- Let Vizier catalogue names be used in overlays (as a fallback if alias not in alias file)
+- move most globals (or things that need to be edited on occasion) to one place (?) + include global prefix to make sure that these aren't edited (?)
+- sort defaults for kwargs (should be in function definitions/config - or somewhere else, not as default arg in kwargs.get()) (?)
+- used ValueError too much, should only be used for argument errors
+- struct vs ctnr vs etc.
+- option to only return closest photometry from each survey in SED queries
+- light curve overlays in images as way to show how to recombine data
+    - more generally, be able to pass any structure to image plotting -> extracts positional data + overlay
+- improve warnings/logging (no print statements?)
+- add annotations to ATK keywords in fits headers
+- let spectral peak fitting work in velocity-space (?)
+- image overlay DataFrame -> Table
+
+- AI thing (?)

astrotoolkit-2.0.1/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

astrotoolkit-2.0.1/docs/build.sh

@@ -0,0 +1,18 @@
+make clean
+
+rm -rf source/auto_tutorials/
+
+if [ "$1" = "wipe" ]; then
+    echo "Wiping all .fits and .fits.gz files under ./source/tutorials/..."
+
+    find source/tutorials/ \
+        -path "source/tutorials/extension" -prune -o \
+        -type f \( -name "*.fits" -o -name "*.fits.gz" \) \
+        -exec rm -f {} +
+fi
+
+make html
+
+# run again to ensure no argument change warnings, and to ensure includes are built
+make clean
+make html

astrotoolkit-2.0.1/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

astrotoolkit-2.0.1/docs/requirements.txt

@@ -0,0 +1,7 @@
+sphinx
+pydata-sphinx-theme
+numpydoc
+sphinx-gallery
+sphinxcontrib-video
+bokeh
+astropy

astrotoolkit-2.0.1/docs/sim_rtd.sh

@@ -0,0 +1 @@
+sphinx-build -b html source build/html -W