Update requirements, spectra logic

requirements.txt

@@ -1,87 +1,79 @@
-antiorm==1.2.1
-asdf==4.1.0
-asdf-astropy==0.7.0
-asdf_coordinates_schemas==0.3.0
-asdf_standard==1.1.1
-asdf_transform_schemas==0.5.0
-asdf_wcs_schemas==0.4.0
-astrodbkit==2.2
-astropy==5.3.4
-astroquery==0.4.9.post1
-attrs==25.1.0
+asdf==5.0.0
+asdf-astropy==0.8.0
+asdf_coordinates_schemas==0.4.0
+asdf_standard==1.4.0
+asdf_transform_schemas==0.6.0
+asdf_wcs_schemas==0.5.0
+astrodbkit==2.4
+astropy==7.1.0
+astropy-iers-data==0.2025.9.22.0.37.25
+astroquery==0.4.11
+attrs==25.3.0
 backports.tarfile==1.2.0
-beautifulsoup4==4.13.3
+beautifulsoup4==4.13.5
 blinker==1.9.0
-bokeh==3.7.3
-certifi==2025.1.31
-cffi==1.17.1
-charset-normalizer==3.4.1
-click==8.1.8
-contourpy==1.3.1
-cryptography==44.0.0
-db==0.1.1
-db-sqlite3==0.0.1
-dill==0.3.9
-distlib==0.3.9
-distro==1.9.0
-filelock==3.16.1
-Flask==3.1.0
-Flask-Cors==4.0.2
+bokeh==3.8.0
+certifi==2025.8.3
+cffi==2.0.0
+charset-normalizer==3.4.3
+click==8.3.0
+contourpy==1.3.3
+cryptography==46.0.1
+dill==0.4.0
+Flask==3.1.2
+flask-cors==6.0.1
 Flask-WTF==1.2.2
-greenlet==3.1.1
-gwcs==0.21.0
+gitdb==4.0.12
+GitPython==3.1.41
+greenlet==3.2.4
+gwcs==0.26.0
 html5lib==1.1
 idna==3.10
-importlib_metadata==8.6.1
-iniconfig==2.0.0
-iniparse==0.5
+importlib_metadata==8.7.0
+iniconfig==2.1.0
 itsdangerous==2.2.0
 jaraco.classes==3.4.0
 jaraco.context==6.0.1
-jaraco.functools==4.1.0
-jeepney==0.8.0
-Jinja2==3.1.5
+jaraco.functools==4.3.0
+jeepney==0.9.0
+Jinja2==3.1.6
 jmespath==1.0.1
 keyring==25.6.0
-markdown2==2.5.3
+markdown2==2.5.4
 MarkupSafe==3.0.2
-more-itertools==10.6.0
-multiprocess==0.70.17
-narwhals==1.41.0
-ndcube==2.3.0
-numpy==1.26.4
-packaging==24.2
-pandas==2.0.3
-pathlib2==2.3.7.post1
-pillow==11.1.0
-platformdirs==4.3.6
-pluggy==1.5.0
-pycparser==2.22
+more-itertools==10.8.0
+multiprocess==0.70.18
+narwhals==2.5.0
+ndcube==2.3.2
+numpy==2.3.3
+packaging==25.0
+pandas==2.3.2
+pillow==11.3.0
+pluggy==1.6.0
+pycparser==2.23
 pyerfa==2.0.1.5
-PyMySQL==1.1.1
-pyOpenSSL==24.3.0
-pysqlite3==0.5.4
-pytest==8.3.4
+Pygments==2.19.2
+pytest==8.4.2
 python-dateutil==2.9.0.post0
-pytz==2024.2
-pyvo==1.6
+pytz==2025.2
+pyvo==1.7
 PyYAML==6.0.2
-requests==2.32.3
-scipy==1.15.1
-SecretStorage==3.3.3
+requests==2.32.5
+scipy==1.16.2
+SecretStorage==3.4.0
 semantic-version==2.10.0
 six==1.17.0
-soupsieve==2.6
+smmap==5.0.2
+soupsieve==2.8
 specutils==2.1.0
-SQLAlchemy==2.0.38
-tornado==6.4.2
+SQLAlchemy==2.0.43
+tornado==6.5.2
 tqdm==4.67.1
-typing_extensions==4.12.2
-tzdata==2025.1
-urllib3==2.3.0
-virtualenv==20.28.0
+typing_extensions==4.15.0
+tzdata==2025.2
+urllib3==2.5.0
 webencodings==0.5.1
 Werkzeug==3.1.3
 WTForms==3.2.1
-xyzservices==2025.1.0
-zipp==3.21.0
+xyzservices==2025.4.0
+zipp==3.23.0

simple_app/plots.py

@@ -149,6 +149,7 @@ def normalise() -> np.ndarray:
         return flux  # unable to normalise by first 0.01um
 
     # query the database for the spectra
+    # Using spectra= in table() reads with the astrodbkit loaders
     db = SimpleDB(db_file)  # open database
     t_spectra: Table = db.query(db.Spectra).\
         filter(db.Spectra.c.source == query).\
@@ -173,7 +174,14 @@ def normalise() -> np.ndarray:
 
     # checking each spectra in table
     for spec in t_spectra:
-        spectrum = Spectrum.read(spec['access_url'])
+        # When reading the table, astrodbkit should have already created Spectrum objects
+        spectrum = spec["access_url"]
+        if isinstance(spectrum, str):
+            print("Re-attempting spectra conversion")
+            try:
+                spectrum = Spectrum.read(spec["access_url"])
+            except Exception as e:
+                print(f"Unable to read {spectrum}. Error: {e}")
 
         # checking spectrum has good units and not only NaNs or 0s
         try:

simple_app/simports.py

@@ -24,6 +24,7 @@
 import numpy as np  # numerical python
 import pandas as pd  # running dataframes
 import pytest  # testing
+from specutils import Spectrum
 from sqlalchemy.exc import ResourceClosedError, OperationalError, ProgrammingError  # errors from sqlalchemy
 from sqlite3 import Warning as SqliteWarning  # errors from sqlite
 from tqdm import tqdm  # progress bars