Fix periodogram units and normalization

.github/workflows/lightkurve-tests.yml

@@ -41,7 +41,7 @@ jobs:
             python-version: '3.10'
             pytest-command: poetry run pytest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -63,7 +63,7 @@ jobs:
         name: [3.8]
         python-version: [3.8]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -84,7 +84,7 @@ jobs:
       matrix:
         python-version: [3.8]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -105,7 +105,7 @@ jobs:
       matrix:
         python-version: [3.8]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:

AUTHORS.rst

@@ -15,7 +15,7 @@ developer, please open an issue!
 - `Jessie Dotson <https://github.com/jessie-dotson>`_
 - `Nicholas Saunders <https://github.com/nksaunders>`_
 - `Michael Gully-Santiago <https://github.com/gully>`_
-- `Daniel Hey <https://github.com/danielhey>`_
+- `Daniel Hey <https://github.com/danhey>`_
 - `Oliver Hall <https://github.com/ojhall94>`_
 
 

CHANGES.rst

@@ -1,14 +1,29 @@
-2.4.1dev (unreleased)
+2.5.0 (unreleased)
 =====================
 
+- Fixed memory leak in reading Lightcurve / TargetPixel FITS files in v2.4.2 [#1390]
+- Added support for changes in QLP High Level Science Product
+  in TESS sectors 56 and later. [#1392]
+
+
+2.4.2 (2023-11-03)
+=====================
+
+- Fixed download issue due to MAST API change [#1380]
+
+2.4.1 (2023-09-06)
+=====================
+
+- Updated interact features to work with JupyterHub (e.g. TiKE) [#1349]
+- Exposed niters parameter in the PCA function of design matrix
+- Fixed the aperture parsing functions inside TPFs to be compliant with `numpy` v1.25 [#1360]
 - Made `LombScarglePeriodogram` compatible with Astropy v5.3 [#1342]
 - Updated the TPF plotting function to work correctly with WCS plotting [#1298]
 - Added the ability to open light curves from the TGLC High Level Science Product
 
 2.4.0 (2023-02-14)
 ==================
 
-
 - Added the ability to configure the default cache directory used by
   ``SearchResult.download()`` / ``SearchResult.download_all()``. [#1214]
 

docs/source/tutorials/1-getting-started/searching-for-data-products.ipynb

@@ -163,7 +163,7 @@
     "id": "4tPVyNq4XIVl"
    },
    "source": [
-    "`search_lightcurve` returns a `SearchResult` table, which contains information about the data products available to download. This search result tells us that KIC 3733346 was observed in *Kepler* Quarters 1–16. \n",
+    "`search_lightcurve` returns a `SearchResult` table, which contains information about the data products available to download. This search result tells us that KIC 3733346 was observed in *Kepler* Quarters 1–17. \n",
     "\n",
     "You can select an individual entry in this search result by indexing the search result."
    ]

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "lightkurve"
-version = "2.4.1dev"
+version = "2.5.0dev"
 description = "A friendly package for Kepler & TESS time series analysis in Python."
 license = "MIT"
 authors = ["Geert Barentsen <hello@geert.io>"]
@@ -79,6 +79,3 @@ testpaths = [
     "tests",
     "src",
 ]
-filterwarnings = [
-    "error::ResourceWarning",
-]

src/lightkurve/correctors/designmatrix.py

@@ -249,7 +249,7 @@ def standardize(self, inplace=False):
         dm.df = new_df
         return dm
 
-    def pca(self, nterms=6):
+    def pca(self, nterms=6, n_iter=10):
         """Returns a new `.DesignMatrix` with a smaller number of regressors.
 
         This method will use Principal Components Analysis (PCA) to reduce
@@ -260,6 +260,10 @@ def pca(self, nterms=6):
         nterms : int
             Number of columns in the new matrix.
 
+        n_iter : int
+            Number of iterations that will be run by the power iteration
+            algorithm to compute the principal components.
+
         Returns
         -------
         `.DesignMatrix`
@@ -274,7 +278,7 @@ def pca(self, nterms=6):
         # produces more stable results.
         from fbpca import pca  # local import because not used elsewhere
 
-        new_values, _, _ = pca(self.values, nterms, n_iter=10)
+        new_values, _, _ = pca(self.values, nterms, n_iter=n_iter)
         return DesignMatrix(new_values, name=self.name)
 
     def append_constant(self, prior_mu=0, prior_sigma=np.inf, inplace=False):

src/lightkurve/correctors/regressioncorrector.py

@@ -177,7 +177,6 @@ def _fit_coefficients(
 
         if prior_sigma is not None:
             sigma_w_inv = sigma_w_inv + np.diag(1.0 / prior_sigma ** 2)
-        if prior_sigma is not None:
             B = B + (prior_mu / prior_sigma ** 2)
 
         # Solve for weights w

src/lightkurve/correctors/sffcorrector.py

@@ -502,7 +502,12 @@ def _estimate_arclength(centroid_col, centroid_row):
     """
     col = centroid_col - np.nanmin(centroid_col)
     row = centroid_row - np.nanmin(centroid_row)
+    if np.all((col == 0) & (row == 0)):
+        raise RuntimeError("Arclength cannot be computed because there is no "
+                           "centroid motion. Make sure that the aperture of "
+                           "the TPF at least two pixels.")
     # Force c to be correlated not anticorrelated
     if np.polyfit(col.data, row.data, 1)[0] < 0:
         col = np.nanmax(col) - col
-    return (col ** 2 + row ** 2) ** 0.5
+    arclength = (col ** 2 + row ** 2) ** 0.5
+    return arclength 

src/lightkurve/interact.py

@@ -28,7 +28,8 @@
 import pandas as pd
 from pandas import Series
 
-from .utils import KeplerQualityFlags, LightkurveWarning, LightkurveError
+
+from .utils import KeplerQualityFlags, LightkurveWarning, LightkurveError, finalize_notebook_url
 
 log = logging.getLogger(__name__)
 
@@ -138,8 +139,8 @@ def _get_corrected_coordinate(tpf_or_lc):
     ra_corrected, dec_corrected, pm_corrected = _correct_with_proper_motion(
             ra * u.deg, dec *u.deg,
             pm_ra * pm_unit, pm_dec * pm_unit,
-            # e.g., equinox 2000 is treated as J2000 is set to be noon of 2000-01-01 TT
-            Time(equinox, format="decimalyear", scale="tt") + 0.5,
+            # we assume the data is in J2000 epoch
+            Time('2000', format='byear'),
             new_time)
     return ra_corrected.to(u.deg).value,  dec_corrected.to(u.deg).value, pm_corrected
 
@@ -460,7 +461,6 @@ def _add_nearby_tics_if_tess(tpf, magnitude_limit, result):
 
     # nearby TICs from ExoFOP
     tab = _search_nearby_of_tess_target(tic_id)
-
     gaia_ids = result['Source'].array
 
     # merge the TICs with matching Gaia entries
@@ -536,7 +536,7 @@ def add_gaia_figure_elements(tpf, fig, magnitude_limit=18):
     """Make the Gaia Figure Elements"""
 
     result = _get_nearby_gaia_objects(tpf, magnitude_limit)
-
+    
     source_colnames_extras = []
     tooltips_extras = []
     try:
@@ -555,7 +555,6 @@ def add_gaia_figure_elements(tpf, fig, magnitude_limit=18):
             tpf.time[0])
     result.RA_ICRS = ra_corrected.to(u.deg).value
     result.DE_ICRS = dec_corrected.to(u.deg).value
-
     # Convert to pixel coordinates
     radecs = np.vstack([result["RA_ICRS"], result["DE_ICRS"]]).T
     coords = tpf.wcs.all_world2pix(radecs, 0)
@@ -978,7 +977,7 @@ def make_default_export_name(tpf, suffix="custom-lc"):
 
 def show_interact_widget(
     tpf,
-    notebook_url="localhost:8888",
+    notebook_url=None,
     lc=None,
     max_cadences=200000,
     aperture_mask="default",
@@ -1013,6 +1012,9 @@ def show_interact_widget(
         will need to supply this value for the application to display
         properly. If no protocol is supplied in the URL, e.g. if it is
         of the form "localhost:8888", then "http" will be used.
+        For use with JupyterHub, set the environment variable LK_JUPYTERHUB_EXTERNAL_URL
+        to the public hostname of your JupyterHub and notebook_url will
+        be defined appropriately automatically.
     max_cadences: int
         Raise a RuntimeError if the number of cadences shown is larger than
         this value. This limit helps keep browsers from becoming unresponsive.
@@ -1065,6 +1067,8 @@ def show_interact_widget(
         )
         return None
 
+    notebook_url = finalize_notebook_url(notebook_url)
+
     aperture_mask = tpf._parse_aperture_mask(aperture_mask)
     if ~aperture_mask.any():
         log.error(
@@ -1297,7 +1301,8 @@ def jump_to_lightcurve_position(attr, old, new):
     return show(create_interact_ui, notebook_url=notebook_url)
 
 
-def show_skyview_widget(tpf, notebook_url="localhost:8888", aperture_mask="empty",  magnitude_limit=18):
+
+def show_skyview_widget(tpf, notebook_url=None, aperture_mask="empty",  magnitude_limit=18):
     """skyview
 
     Parameters
@@ -1313,6 +1318,9 @@ def show_skyview_widget(tpf, notebook_url="localhost:8888", aperture_mask="empty
         will need to supply this value for the application to display
         properly. If no protocol is supplied in the URL, e.g. if it is
         of the form "localhost:8888", then "http" will be used.
+        For use with JupyterHub, set the environment variable LK_JUPYTERHUB_EXTERNAL_URL
+        to the public hostname of your JupyterHub and notebook_url will
+        be defined appropriately automatically.
     aperture_mask : array-like, 'pipeline', 'threshold', 'default', 'background', or 'empty'
         Highlight pixels selected by aperture_mask.
         Default is 'empty': no pixel is highlighted.
@@ -1333,6 +1341,8 @@ def show_skyview_widget(tpf, notebook_url="localhost:8888", aperture_mask="empty
         )
         return None
 
+    notebook_url = finalize_notebook_url(notebook_url)
+
     # Try to identify the "fiducial frame", for which the TPF WCS is exact
     zp = (tpf.pos_corr1 == 0) & (tpf.pos_corr2 == 0)
     (zp_loc,) = np.where(zp)
@@ -1343,7 +1353,6 @@ def show_skyview_widget(tpf, notebook_url="localhost:8888", aperture_mask="empty
         fiducial_frame = 0
 
     aperture_mask = tpf._parse_aperture_mask(aperture_mask)
-
     def create_interact_ui(doc):
         tpf_source = prepare_tpf_datasource(tpf, aperture_mask)
 

src/lightkurve/interact_bls.py

@@ -8,7 +8,7 @@
 from astropy.timeseries import BoxLeastSquares
 import astropy.units as u
 
-from .utils import LightkurveWarning
+from .utils import LightkurveWarning, finalize_notebook_url
 
 log = logging.getLogger(__name__)
 
@@ -598,7 +598,7 @@ def _preprocess_lc_for_bls(lc):
 
 def show_interact_widget(
     lc,
-    notebook_url="localhost:8888",
+    notebook_url=None,
     minimum_period=None,
     maximum_period=None,
     resolution=2000,
@@ -616,6 +616,9 @@ def show_interact_widget(
         will need to supply this value for the application to display
         properly. If no protocol is supplied in the URL, e.g. if it is
         of the form "localhost:8888", then "http" will be used.
+        For use with JupyterHub, set the environment variable LK_JUPYTERHUB_EXTERNAL_URL
+        to the public hostname of your JupyterHub and notebook_url will
+        be defined appropriately automatically.
     minimum_period : float or None
         Minimum period to assess the BLS to. If None, default value of 0.3 days
         will be used.
@@ -1001,4 +1004,5 @@ def _update_bls_plot_help(attr, old, new):
     lc = _preprocess_lc_for_bls(lc)
 
     output_notebook(verbose=False, hide_banner=True)
+    notebook_url = finalize_notebook_url(notebook_url)
     return show(_create_interact_ui, notebook_url=notebook_url)

src/lightkurve/io/detect.py

@@ -84,8 +84,10 @@ def detect_filetype(hdulist: HDUList) -> str:
 
     # Is it a K2VARCAT file?
     # There are no self-identifying keywords in the header, so go by filename.
-    if "hlsp_k2varcat" in (hdulist.filename() or ""):
-        return "K2VARCAT"
+    fname = hdulist.filename() if callable(hdulist.filename) else hdulist.filename
+    if fname is not None:
+        if "hlsp_k2varcat" in fname:
+            return "K2VARCAT"
 
     # Is it a K2SC file?
     if "k2sc" in hdulist[0].header.get("creator", "").lower():