AstroToolkit 2.0.2__tar.gz → 2.0.4__tar.gz

astrotoolkit-2.0.4/LICENSE.rst

@@ -0,0 +1,11 @@
+Copyright 2025-2026 Ethan Moorfield
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{astrotoolkit-2.0.2/src/AstroToolkit.egg-info → astrotoolkit-2.0.4}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: AstroToolkit
-Version: 2.0.2
+Version: 2.0.4
 Summary: A package for the gathering, plotting and analysis of astronomical data.
-Author-email: Ethan Moorfield <ethan.moorfield@hotmail.co.uk>
+Author-email: Ethan Moorfield <ethan.moorfield@outlook.com>
+License-Expression: BSD-3-Clause
 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
+License-File: LICENSE.rst
 Requires-Dist: astropy
 Requires-Dist: astroquery
 Requires-Dist: beautifulsoup4
@@ -58,3 +59,8 @@ This project has received funding from the European Research Council (ERC) under
         <img src="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png" width="200">
     </picture>
 </p>
+
+License
+=======
+
+This project is licensed under the BSD 3-Clause License. See the LICENSE.rst file for details.

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/README.md

@@ -31,3 +31,8 @@ This project has received funding from the European Research Council (ERC) under
         <img src="https://raw.githubusercontent.com/WD-planets/AstroToolkit/latest/docs/source/_static/erc_logo_light.png" width="200">
     </picture>
 </p>
+
+License
+=======
+
+This project is licensed under the BSD 3-Clause License. See the LICENSE.rst file for details.

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/changelog.md

@@ -96,6 +96,23 @@ Changes
 + other stuff that I forgot to write down
 
 
+2.0.4 Changes
+=============
+- Fixed datapages save_by_id not receiving fname
+- DataSets now more reliably retain container/plot order
+- Improved DataTable aesthetics, and stored text now dynamically downsizes to fit table
+- Added vizier_mirror and simbad_mirror config keys to allow the use of Vizier and SIMBAD mirrors while CDS is experiencing issues
+- Added vizier_caching option to enable/disable caching of astroquery Vizier data. Enabled by default
+
+===============
+To-Do Pre-Paper
+===============
+- units currently get converted to a set of pre-defined units - users should be able to use whatever valid units they want
+- pandas series vs numpy arrays
+- improve spectral fitting/radial velocity fitting
+    - max_width gets triggered too easily if spectrum is cropped since it is based on a fraction of the width, not the resolution
+    - Scoring: The score only measures how tightly the matched lines fit. It doesn’t reward the number of matches, so a chance two-line coincidence can beat a real four-line match. Ranking by match count, with scatter as the tiebreak, would be more robust.
+    - Could also weight matches based on line strength
 
 =========
 To-Do Now
@@ -104,6 +121,8 @@ To-Do Now
     - replace 'star' with e.g. system, source, etc.
     - check docstrings / comments
     - check type hints
+- add spectral fitting to technical docs
+- test sub groups of frequency peaks in power spectra (currently if signal is dominated by a weird signal like 0.001 etc., this and its harmonics are tested, which leaves the other possible real signals untested)
 
 
 ===========
@@ -111,6 +130,7 @@ To-Do Later
 ===========
 improved testing
 
+- add option to switch between grid/row/column layout for multiple figs
 - 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)?
@@ -144,5 +164,3 @@ improved testing
 - add annotations to ATK keywords in fits headers
 - let spectral peak fitting work in velocity-space (?)
 - image overlay DataFrame -> Table
-
-- AI thing (?)

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/build.sh

@@ -1,3 +1,5 @@
+pip install --editable ..
+
 make clean
 
 rm -rf source/auto_tutorials/
@@ -13,6 +15,8 @@ fi
 
 make html
 
+python source/_intro_image.py
+
 # run again to ensure no argument change warnings, and to ensure includes are built
 make clean
 make html

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/source/conf.py

@@ -9,10 +9,17 @@ from bokeh.layouts import Column, GridBox, Row
 from bokeh.plotting import figure
 from bokeh.resources import CDN
 
+from ATK.Config import CONFIG
 from ATK.utilities.docstrings import ATTR_DOCSTRINGS
 
 release = pkg_version("AstroToolkit").split(".dev")[0]
 
+CONFIG["plot_settings"]["titles"] = False
+CONFIG["datapage_settings"]["grid_size"] = 150
+CONFIG["datapage_settings"]["font_size"] = 6
+CONFIG["global_settings"]["vizier_mirror"] = "vizier.cfa.harvard.edu"
+CONFIG["global_settings"]["simbad_mirror"] = "simbad.harvard.edu"
+
 print(f"\nBUILDING UNDER CURRENT ATK VERSION: {release}\n")
 
 

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/source/tutorials/datapages/datapage_plotting.py

@@ -10,7 +10,7 @@ ATK supports the creation of **datapages** as a means of neatly combining plots
 # isort: skip_file
 from bokeh.document import Document
 from ATK.Config import CONFIG
-CONFIG.reset()
+# CONFIG.reset()
 CONFIG["datapage_settings"]["grid_size"] = 150
 CONFIG["datapage_settings"]["font_size"] = 6
 # sphinx_gallery_end_ignore

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/source/tutorials/getting_started/data_query.py

@@ -116,7 +116,7 @@ pass
 # 
 # The majority of the returned :class:`~ATK.Models.DataSet`'s attributes are immediately clear, but there are a couple details to note:
 # 
-# - :attr:`~ATK.Models.DataSet.targets` lists every :class:`ATK.Models.Target` of the search **as they were entered** (coordinates, frame and epoch).
+# - :attr:`~ATK.Models.DataSet.targets` lists every :class:`~ATK.Models.Target` of the search **as they were entered** (coordinates, frame and epoch).
 #
 # - :attr:`~ATK.Models.DataSet.exception` states whether any exceptions were encountered. If :attr:`~ATK.Models.DataSet.exception` is ``True``, then the query encountered something unexpected. The most common cause of this is that service being utilised (in this case `Vizier <https://vizier.cds.unistra.fr/>`_) is experiencing downtime.
 #
@@ -145,7 +145,7 @@ pass
 #
 # Using the Returned Data
 # =======================
-# A :class:`ATK.Models.DataSet` **store any returned data as a list of containers matching the** ``kind`` **of data that was requested**. Since this tutorial performed a `Vizier <https://vizier.cds.unistra.fr/>`_ query for one target, the returned :class:`~ATK.Models.DataSet` contains a single :class:`~ATK.Models.Record`:
+# A :class:`~ATK.Models.DataSet` **store any returned data as a list of containers matching the** ``kind`` **of data that was requested**. Since this tutorial performed a `Vizier <https://vizier.cds.unistra.fr/>`_ query for one target, the returned :class:`~ATK.Models.DataSet` contains a single :class:`~ATK.Models.Record`:
 
 galex_entry = galex_query.data[0]
 # sphinx_gallery_start_ignore

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/source/tutorials/getting_started/data_saving.py

@@ -2,7 +2,7 @@
 ##################
 Local Data Storage
 ##################
-A :class:`ATK.Models.DataSet` of any kind can be stored as a local FITS file. These files can then be read to recreate the original :class:`~ATK.Models.DataSet`.
+A :class:`~ATK.Models.DataSet` of any kind can be stored as a local FITS file. These files can then be read to recreate the original :class:`~ATK.Models.DataSet`.
 
 |
 

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/docs/source/tutorials/images/image_plotting.py

@@ -84,7 +84,7 @@ figure
 #
 # Configuring Axes Coordinates
 # ============================
-# So far, all images have had coordinate axes that are defined relative to the image centre, i.e. ``relative_axes = True`` (default). To instead use absolute coordinates on the sky, `pass ``relative_axes = False``:
+# So far, all images have had coordinate axes that are defined relative to the image centre, i.e. ``relative_axes = True`` (default). To instead use absolute coordinates on the sky, pass ``relative_axes = False``:
 
 # sphinx_gallery_start_ignore
 ps_query.plot(relative_axes=False)

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/pyproject.toml

@@ -19,8 +19,10 @@ line-length = 240
 name = "AstroToolkit"
 dynamic = ["version"]
 authors = [
-  { name="Ethan Moorfield", email="ethan.moorfield@hotmail.co.uk"},
+  { name="Ethan Moorfield", email="ethan.moorfield@outlook.com"},
 ]
+license = "BSD-3-Clause"
+license-files = ["LICENSE.rst"]
 description = "A package for the gathering, plotting and analysis of astronomical data."
 readme = "README.md"
 requires-python = ">=3.11"

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/Tools/query.py

@@ -196,9 +196,7 @@ def query(kind: str, targets: int | SkyCoord | Target | list[int | SkyCoord | Ta
     if any(target is RETURNS.EXCEPTION for target in targets):
         warnings.warn("Failed to generate requested targets, this is likely due to a Vizier fault.")
 
-        structure = DataSet[kind](
-            kind=None, survey=arguments.get("survey", None), targets=None, radius=arguments.get("radius", None), exception=True
-        )
+        structure = DataSet[kind](kind=None, survey=arguments.get("survey", None), targets=None, radius=arguments.get("radius", None), exception=True)
 
         return structure
 
@@ -206,9 +204,7 @@ def query(kind: str, targets: int | SkyCoord | Target | list[int | SkyCoord | Ta
     if not arguments.get("corrections", True):
         for target in targets:
             initial_coords = target.initial_coords
-            target.initial_coords = SkyCoord(
-                ra=initial_coords.ra, dec=initial_coords.dec, frame=initial_coords.frame, obstime=initial_coords.obstime
-            )
+            target.initial_coords = SkyCoord(ra=initial_coords.ra, dec=initial_coords.dec, frame=initial_coords.frame, obstime=initial_coords.obstime)
             target.coords = initial_coords
             target.identifier = None
             target.survey = None

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/configuration/defaults/base_defaults.py

@@ -3,7 +3,7 @@ from pathlib import Path
 PATH = Path.home() / ".AstroToolkit" / "ATK_config.ini"
 
 DEFAULTS = {
-    "global_settings": {"unit_format": "symbol"},
+    "global_settings": {"unit_format": "symbol", "vizier_mirror": "vizier.cds.unistra.fr", "simbad_mirror": "simbad.cds.unistra.fr", "vizier_caching": True},
     "plot_settings": {
         "cache_time": 3600,
         "size": 500,
@@ -22,7 +22,10 @@ DEFAULTS = {
 
 CONFIG_KEY_DEFS = {
     "global_settings": {
-        "unit_format": "Sets the default format when printing an astropy :class:`~astropy.units.Quantity`, from (symbol, text)."
+        "unit_format": "Sets the default format when printing an astropy :class:`~astropy.units.Quantity`, from (symbol, text).",
+        "vizier_mirror": "Sets the default mirror to use in Vizier queries throughout the package. Can be helpful if Vizier is experiencing downtime.",
+        "simbad_mirror": "Sets the default mirror to use in SIMBAD queries throughout the package. Can be helpful is SIMBAD is experiencing downtime.",
+        "vizier_caching": "If true, vizier results are read from the local cache where available.",
     },
     "plot_settings": {
         "cache_time": "Sets the duration for which figures (i.e. HTML pages) are cached to the ``~/.AstroToolkit/cached_figures`` directory in seconds.",

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/io/plot_io.py

@@ -68,7 +68,8 @@ def dispatch_plotting(
         all_figures = do_plotting(all_figures, plotting_func, plot_method, containers, target, **kwargs)
 
     else:
-        surveys = list(set(ctnr.survey for ctnr in containers))
+        # preserve order
+        surveys = list(dict.fromkeys(ctnr.survey for ctnr in containers))
 
         for survey in surveys:
             survey_containers = [ctnr for ctnr in containers if ctnr.survey == survey]

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/plotting/datapage/plot_datapage.py

@@ -2,7 +2,7 @@ from bokeh.models import GridBox, InlineStyleSheet, Label, Range1d, TabPanel, Ta
 from bokeh.plotting import figure
 
 from ...configuration.base_config import BASE_CONFIG
-from ...plotting.datatable.plot_datatable import autosize_table
+from ...plotting.datatable.plot_datatable import fit_table_font, autosize_table
 from ...structures.DataPages import DataPages
 from ...structures.DataSet import DataSet
 from ...structures.methods.apply import unpack_layout
@@ -15,19 +15,19 @@ TEXT_FONT = str(BASE_CONFIG._get("datapage_settings", "font"))
 
 def format_datatable(table, height, width):
     grid_size = BASE_CONFIG._get("datapage_settings", "grid_size")
+    target_width = grid_size * width
+    target_height = grid_size * height
 
     table.min_width = 0
-    table = autosize_table(table, table.source, TEXT_SIZE, grid_size * height)
-    table.width = grid_size * width
-    table.height = grid_size * height
 
-    table.sizing_mode = "fixed"
-
-    style_sheet = InlineStyleSheet(
-        css=f".slick-header-columns {{background-color: #e0e0e0 !important;font-family: {TEXT_FONT.lower()};font-size: {int(TEXT_SIZE[:-2])}pt; font-weight: normal}}.slick-row {{font-size: {int(TEXT_SIZE[:-2])}pt; font-weight: normal}}"
-    )
+    base_font_pt = float(str(TEXT_SIZE).replace("pt", ""))
+    text_font = str(BASE_CONFIG._get("plot_settings", "font"))
+    font_pt = fit_table_font(table, target_width, base_font_pt, text_font)
 
-    table.stylesheets = [style_sheet]
+    table = autosize_table(table, table.source, f"{font_pt}pt", target_height)
+    table.width = target_width
+    table.height = target_height
+    table.sizing_mode = "fixed"
 
     return table
 
@@ -219,6 +219,7 @@ def prepare_datasets(key: str, datasets: list[DataSet]):
     plot_dict, ctnr_dict, plot_ctnr_map = {}, {}, {}
     for dataset in datasets:
         ctnrs = [ctnr for ctnr in dataset.data if ctnr._target_key == key]
+
         if not dataset.figure:
             dataset.plot()
         plot_ids = [ctnr._plot_id for ctnr in ctnrs]
@@ -282,6 +283,10 @@ def get_datapage(layout: list[list]):
     for index, key in enumerate(target_keys):
         plots, ctnrs, plot_ctnr_map = prepare_datasets(key, datasets)
 
+        # print(plots)
+        # print(ctnrs)
+        # print(plot_ctnr_map)
+
         grid_children = []
 
         for region in regions:

astrotoolkit-2.0.4/src/ATK/plotting/datatable/plot_datatable.py

@@ -0,0 +1,115 @@
+from bokeh.models import ColumnDataSource
+from bokeh.models import DataTable as bokeh_DataTable
+from bokeh.models import TableColumn
+from ...configuration.base_config import BASE_CONFIG
+from ...structures.DataTable import DataTable
+from ...utilities.defaults import PLOT_DIMENSIONS
+
+from bokeh.models import InlineStyleSheet
+
+# never shrink text past this, no matter how narrow the table gets
+MIN_FONT_PT = 6.0
+
+
+def autosize_table(table, source, font_size_pt, max_height=None):
+    # convert pt -> pixels
+    font_px = int(float(font_size_pt.replace("pt", "")) * 1.333)
+    # scale row + header height
+    row_height = max(int(font_px * 1.6), 25)
+    header_height = max(int(font_px * 1.8), 30)
+    table.row_height = row_height
+    # number of rows
+    n_rows = len(source.data.get(next(iter(source.data)), []))
+    height = header_height + n_rows * row_height
+    if max_height:
+        height = min(height, max_height)
+    table.height = height
+
+    return table
+
+
+def _get_max_len(col, values):
+    if values is None:
+        return len(col)
+    return max([len(str(v)) for v in values] + [len(col)])
+
+
+def _get_col_width(max_len, char_px):
+    return int(max_len * char_px) + 16
+
+
+def _char_px_for_font(font_pt):
+    """
+    (Rough) Pixels-per-character for a given point size.
+    """
+
+    return (font_pt * 1.333) * 0.55
+
+
+def fit_table_font(table, target_width, base_font_pt, text_font):
+    fields = [col.field for col in table.columns]
+    max_lens = [_get_max_len(f, table.source.data.get(f)) for f in fields]
+    total_chars = sum(max_lens) or 1
+    overhead = 16 * len(fields)
+    natural_char_px = _char_px_for_font(base_font_pt)
+    max_char_px = (target_width - overhead) / total_chars
+    char_px = min(natural_char_px, max(max_char_px, 0))
+    font_pt = max(char_px / (1.333 * 0.55), MIN_FONT_PT)
+
+    for col, max_len in zip(table.columns, max_lens):
+        col.width = _get_col_width(max_len, char_px)
+
+    header_pt = round(font_pt, 1)
+    row_pt = round(max(font_pt - round(0.2 * font_pt, 1), MIN_FONT_PT), 0)
+    # stop letters like (g,y,p) from clipping through bottom of header
+    header_px = max(int(font_pt * 1.333 * 1.8), 30)
+
+    css = (
+        f".slick-header-columns {{background-color: #e0e0e0 !important;"
+        f"font-family: {text_font.lower()};font-size: {header_pt}pt; font-weight: normal;"
+        f"height: {header_px}px !important;}}"
+        f".slick-header-column {{height: {header_px}px !important;"
+        f"box-sizing: border-box !important;"
+        f"padding-top: 0px !important;"
+        f"line-height: {header_px}px !important;}}"
+        f".slick-row {{font-size: {row_pt}pt; font-weight: normal}}"
+    )
+
+    table.stylesheets = [InlineStyleSheet(css=css)]
+
+    return font_pt
+
+
+def plot(dt: DataTable, **kwargs):
+    source = ColumnDataSource(dt.table.to_pandas())
+
+    text_size = str(BASE_CONFIG._get("plot_settings", "font_size"))
+    if not text_size.endswith("pt"):
+        text_size += "pt"
+    text_font = str(BASE_CONFIG._get("plot_settings", "font"))
+    base_font_pt = float(text_size[:-2])
+
+    dimensions = PLOT_DIMENSIONS["datatable"]
+    target_width = int(BASE_CONFIG._get("plot_settings", "size")) * dimensions[0]
+
+    cols = [TableColumn(field=c, title=c) for c in dt.table.colnames]
+
+    table = bokeh_DataTable(
+        source=source,
+        columns=cols,
+        height=400,
+        autosize_mode="force_fit",
+        sizing_mode="stretch_width",
+        min_width=target_width,
+    )
+
+    # Sets column widths + stylesheet font-size in place, returns the font
+    # size actually applied (<= base_font_pt) so it fits target_width.
+    font_pt = fit_table_font(table, target_width, base_font_pt, text_font)
+
+    height = int(BASE_CONFIG._get("plot_settings", "size")) * dimensions[1]
+    table = autosize_table(table, source, f"{font_pt}pt", height)
+
+    dt._plot_id = table.id
+    return table
+

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/plotting/formatting.py

@@ -63,6 +63,9 @@ def format_plot(kind: str, plot: figure, force_square: bool = False):
     Formats the aesthetics of plots using the ATK config
     """
 
+    if plot is None:
+        return None
+
     # resize
     dimensions = PLOT_DIMENSIONS[kind]
     width = int(BASE_CONFIG._get("plot_settings", "size")) * dimensions[0]

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/plotting/spectrum/spectrum_overlay.py

@@ -10,18 +10,26 @@ from ..colours import get_palette
 
 # wavelengths in Angstroms
 OVERLAY_LINES = [
-    {"label": "Hydrogen", "wavelength": 8503},
-    {"label": "Hydrogen", "wavelength": 8454},
-    {"label": "Hydrogen", "wavelength": 8598},
-    {"label": "Hydrogen", "wavelength": 8665},
-    {"label": "Hydrogen", "wavelength": 6562, "line_label": r"\[\text{H}\alpha\]"},
-    {"label": "Hydrogen", "wavelength": 4862, "line_label": r"\[\text{H}\beta\]"},
-    {"label": "Hydrogen", "wavelength": 4340, "line_label": r"\[\text{H}\gamma\]"},
+    # Paschen series (n=18 -> 10 -> 3)
+    *[{"label": "Hydrogen", "wavelength": w} for w in [8437.959, 8467.257, 8502.486, 8545.386, 8598.395, 8665.022, 8750.476, 8862.786, 9014.913]],
+    # Balmer series
+    {"label": "Hydrogen", "wavelength": 6562.797, "line_label": r"\[\text{H}\alpha\]"},
+    {"label": "Hydrogen", "wavelength": 4861.329, "line_label": r"\[\text{H}\beta\]"},
+    {"label": "Hydrogen", "wavelength": 4340.462, "line_label": r"\[\text{H}\gamma\]"},
     {"label": "Hydrogen", "wavelength": 4101.734, "line_label": r"\[\text{H}\delta\]"},
-    *[{"label": "Helium", "wavelength": w} for w in [4472, 4686, 4713, 4921, 5016, 5876, 6678]],
-    *[{"label": "Sodium", "wavelength": w} for w in [8183, 8195]],
-    *[{"label": "Calcium", "wavelength": w} for w in [3934, 3967, 8498, 8542, 8662]],
-    *[{"label": "Calcium II", "wavelength": w} for w in [3608, 3854, 4109, 4383, 4737, 5165, 5636, 6191]],
+    {"label": "Hydrogen", "wavelength": 3970.071, "line_label": r"\[\text{H}\epsilon\]"},
+    {"label": "Hydrogen", "wavelength": 3889.048, "line_label": r"\[\text{H}8\]"},
+    {"label": "Hydrogen", "wavelength": 3835.384, "line_label": r"\[\text{H}9\]"},
+    {"label": "Hydrogen", "wavelength": 3797.897, "line_label": r"\[\text{H}10\]"},
+    # He I, plus He II 4685.684 and 5411.52
+    *[{"label": "Helium", "wavelength": w} for w in [3888.643, 4026.206, 4387.929, 4471.501, 4685.684, 4713.174, 4921.931, 5015.678, 5411.52, 5875.671, 6678.152, 7065.249, 7281.351]],
+    *[{"label": "Sodium", "wavelength": w} for w in [5889.950, 5895.924, 8183.256, 8194.821]],
+    # Ca II H & K, Ca I 4226.727, Ca II infrared triplet
+    *[{"label": "Calcium", "wavelength": w} for w in [3933.661, 3968.467, 4226.727, 8498.018, 8542.089, 8662.140]],
+    # Mg II 4481 blend, Mg I b triplet
+    *[{"label": "Magnesium", "wavelength": w} for w in [4481.222, 5167.322, 5172.684, 5183.604]],
+    # unchanged from the previous list - not atomic Ca II
+    # *[{"label": "Calcium II", "wavelength": w} for w in [3608, 3854, 4109, 4383, 4737, 5165, 5636, 6191]],
 ]
 
 

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/queries/image/overlays.py

@@ -33,6 +33,7 @@ def get_overlay_data(image: Image, target: int | SkyCoord, survey: str, survey_i
 
     if not non_gaia_data:
         return pd.DataFrame()
+
     non_gaia_data = non_gaia_data[0].table
 
     gaia_data = query(kind="vizier", targets=image.search_pos, radius=radius, survey="gaia").data
@@ -103,9 +104,7 @@ def get_overlay_data(image: Image, target: int | SkyCoord, survey: str, survey_i
             # if rng < 0.5:
             #     dist_val = None
 
-            gaia_coords.append(
-                SkyCoord(ra=ra, dec=dec, frame="icrs", pm_ra_cosdec=pmra, pm_dec=pmdec, distance=dist_val, obstime=gaia_epoch)
-            )
+            gaia_coords.append(SkyCoord(ra=ra, dec=dec, frame="icrs", pm_ra_cosdec=pmra, pm_dec=pmdec, distance=dist_val, obstime=gaia_epoch))
 
         non_gaia_coords = [c.transform_to("icrs") for c in non_gaia_coords]
         gaia_coords = correct_coords(gaia_coords, non_gaia_epoch)
@@ -132,10 +131,7 @@ def get_overlay_data(image: Image, target: int | SkyCoord, survey: str, survey_i
         if len(matched_index):
             pm_ra[matched_index] = [gaia_coords[i].pm_ra_cosdec.to_value(u.mas / u.yr) for i in index[matched_index]]
             pm_dec[matched_index] = [gaia_coords[i].pm_dec.to_value(u.mas / u.yr) for i in index[matched_index]]
-            dist[matched_index] = [
-                gaia_coords[i].distance.to_value(u.pc) if gaia_coords[i].distance.unit is not u.one else np.nan
-                for i in index[matched_index]
-            ]
+            dist[matched_index] = [gaia_coords[i].distance.to_value(u.pc) if gaia_coords[i].distance.unit is not u.one else np.nan for i in index[matched_index]]
 
         new_coords = []
 
@@ -150,9 +146,7 @@ def get_overlay_data(image: Image, target: int | SkyCoord, survey: str, survey_i
             elif np.isnan(dist_val):
                 raise ValueError("Bad distance.")
 
-            new_coords.append(
-                SkyCoord(ra=c.ra, dec=c.dec, frame="icrs", obstime=c.obstime, pm_ra_cosdec=pmra_val, pm_dec=pmdec_val, distance=dist_val)
-            )
+            new_coords.append(SkyCoord(ra=c.ra, dec=c.dec, frame="icrs", obstime=c.obstime, pm_ra_cosdec=pmra_val, pm_dec=pmdec_val, distance=dist_val))
 
         non_gaia_coords = new_coords
         non_gaia_coords, correction = correct_coords(non_gaia_coords, image.epoch, get_correction=True)
@@ -239,9 +233,7 @@ def get_overlay_data(image: Image, target: int | SkyCoord, survey: str, survey_i
 
     ids = get_ids(final_coords, BASE_CONFIG._get("overlay_settings", "simbad_radius") * u.arcsec)
 
-    if ids is RETURNS.EXCEPTION:
-        return ids
-    elif ids is RETURNS.NULL:
+    if ids is RETURNS.EXCEPTION or ids is RETURNS.NULL:
         final_df["simbad_id"] = "None"
     else:
         final_df["simbad_id"] = ids

{astrotoolkit-2.0.2 → astrotoolkit-2.0.4}/src/ATK/queries/query_core.py

@@ -206,7 +206,7 @@ def recreate_struct(kind: str, targeting: list[Target], **arguments) -> DataSet:
 
         if primary_header["ATK_EXCEPTION"]:
             warnings.warn(
-                f"Exception was encountered during data retrieval for file '{arguments['path']}'.Query will be re-run and local file will be overwritten."
+                f"Exception was encountered during data retrieval for file '{arguments['path']}'. Query will be re-run and local file will be overwritten."
             )
             return None