Rename astrodb_scripts to astrodb_utils (#485)

* astrodb_scripts -> astrodb_utils name change and updates

.devcontainer/devcontainer.json

@@ -13,7 +13,7 @@
 	"forwardPorts": [5432],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip install astrodbkit2 pytest psycopg2 ads git+https://github.com/astrodbtoolkit/astrodb_scripts.git@main",
+	"postCreateCommand": "pip install astrodbkit2 pytest psycopg2 ads git+https://github.com/astrodbtoolkit/astrodb_utils.git@main",
 	// python scripts/tutorials/generate_database.py sqlite
 	// python scripts/tutorials/generate_database.py postgres postgres://postgres@localhost:5432
 

.github/workflows/gen-db.yml

@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install astrodbkit2
-        pip install git+https://github.com/astrodbtoolkit/astrodb_scripts.git@main
+        pip install git+https://github.com/astrodbtoolkit/astrodb_utils.git@main
 
     - name: Generate sqlite (file) database
       run: |

.github/workflows/python-app.yml

@@ -26,7 +26,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install pytest ads matplotlib
         pip install astrodbkit2
-        pip install git+https://github.com/astrodbtoolkit/astrodb_scripts.git@main
+        pip install git+https://github.com/astrodbtoolkit/astrodb_utils.git@main
 
     - name: Test with pytest
       run: |

.github/workflows/scheduled-tests.yml

@@ -26,7 +26,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install pytest ads
         pip install astrodbkit2
-        pip install git+https://github.com/astrodbtoolkit/astrodb_scripts.git@main
+        pip install git+https://github.com/astrodbtoolkit/astrodb_utils.git@main
 
     - name: Test with pytest
       run: |

environment.yml

@@ -75,4 +75,4 @@ dependencies:
       - webencodings==0.5.1
       - werkzeug==2.2.2
       - zipp==3.13.0
-      - git+https://github.com/astrodbtoolkit/astrodb_scripts.git@main
+      - git+https://github.com/astrodbtoolkit/astrodb_utils.git@main

simple/utils/astrometry.py

@@ -2,7 +2,7 @@
 import logging
 from sqlalchemy import and_
 import sqlalchemy.exc
-from astrodb_scripts import (
+from astrodb_utils import (
     AstroDBError,
     find_source_in_db,
 )

simple/utils/companions.py

@@ -1,6 +1,6 @@
 import logging
 import sqlalchemy.exc
-from astrodb_scripts import (
+from astrodb_utils import (
     AstroDBError,
 )
 

simple/utils/spectra.py

@@ -14,10 +14,10 @@
 from specutils import Spectrum1D
 
 from astrodbkit2.astrodb import Database
-from astrodb_scripts import (
+from astrodb_utils import (
     AstroDBError,
     find_source_in_db,
-    check_internet_connection,
+    internet_connection,
     find_publication,
 )
 
@@ -190,7 +190,7 @@ def ingest_spectrum(
         else:
             return flags
     else:
-        good_reference = find_publication(db, reference)
+        good_reference = find_publication(db, reference=reference)
         if good_reference[0] is False:
             msg = (
                 f"Spectrum for {source} could not be added to the database because the "
@@ -219,7 +219,7 @@ def ingest_spectrum(
 
     # Check if spectrum file is accessible
     # First check for internet
-    internet = check_internet_connection()
+    internet = internet_connection()
     if internet:
         request_response = requests.head(spectrum)
         status_code = (
@@ -466,7 +466,8 @@ def spectrum_plottable(spectrum_path, raise_error=True, show_plot=False):
             return False
     except u.UnitConversionError as e:
         msg = (
-            e + f"Skipping {spectrum_path}: unable to convert spectral axis to microns"
+            f"{str(e)} \n"
+            f"Skipping {spectrum_path}: unable to convert spectral axis to microns"
         )
         if raise_error:
             logger.error(msg)
@@ -475,7 +476,7 @@ def spectrum_plottable(spectrum_path, raise_error=True, show_plot=False):
             logger.warning(msg)
             return False
     except ValueError as e:
-        msg = e + f"Skipping {spectrum_path}: Value error"
+        msg = f"{str(e)} \nSkipping {spectrum_path}: Value error"
         if raise_error:
             logger.error(msg)
             raise AstroDBError(msg)

simple/utils/spectral_types.py

@@ -3,7 +3,7 @@
 import logging
 from sqlalchemy import and_
 import sqlalchemy.exc
-from astrodb_scripts import (
+from astrodb_utils import (
     AstroDBError,
     find_source_in_db,
 )

tests/conftest.py

@@ -3,9 +3,9 @@
 import sys
 import logging
 from astrodbkit2.astrodb import create_database, Database
-sys.path.append("./simple")
-# from schema import REFERENCE_TABLES
-from schema import *
+sys.path.append("./")
+from simple.schema import REFERENCE_TABLES
+from simple.schema import *
 
 
 logger = logging.getLogger("AstroDB")

tests/scheduled_checks.py

@@ -4,11 +4,11 @@
 import requests
 from tqdm import tqdm
 from astrodbkit2.astrodb import create_database, Database
-from astrodb_scripts import check_internet_connection
+from astrodb_utils.utils import check_internet_connection
 
 sys.path.append(".")
-from schema.schema import *
-from . import REFERENCE_TABLES
+from simple.schema import *
+from simple.schema import REFERENCE_TABLES
 
 
 DB_NAME = "temp.sqlite"

tests/test_spectra_utils.py

@@ -1,11 +1,8 @@
 # temp_db and logger is defined in conftest.py
 import pytest
-import sys
-from astrodb_scripts.utils import (
+from astrodb_utils.utils import (
     AstroDBError,
 )
-
-sys.path.append("./")
 from simple.utils.spectra import (
     ingest_spectrum,
     # ingest_spectrum_from_fits,
@@ -194,7 +191,8 @@ def test_ingest_spectrum_errors(temp_db):
 )  # : astropy.io.fits uses zero-based indexing.
 @pytest.mark.filterwarnings("ignore:'datfix' made the change 'Set MJD-OBS to")
 @pytest.mark.filterwarnings(
-    "ignore:'erg/cm2/s/A' contains multiple slashes, which is discouraged by the FITS standard"
+    "ignore:'erg/cm2/s/A' contains multiple slashes,"
+    " which is discouraged by the FITS standard"
 )
 @pytest.mark.filterwarnings("ignore")
 def test_ingest_spectrum_works(temp_db):
@@ -221,7 +219,8 @@ def test_ingest_spectrum_works(temp_db):
 @pytest.mark.filterwarnings(
     "ignore",
     message=(
-        "'erg/cm2/s/A' contains multiple slashes, which is discouraged by the FITS standard.*",
+        "'erg/cm2/s/A' contains multiple slashes, "
+        "which is discouraged by the FITS standard.*",
     ),
 )
 @pytest.mark.filterwarnings("ignore")

tests/test_utils.py

@@ -1,9 +1,10 @@
 import pytest
 import sys
 from astropy.table import Table
-from astrodb_scripts.utils import (
+from astrodb_utils.utils import (
     AstroDBError,
 )
+
 sys.path.append("./")
 from simple.utils.spectral_types import (
     convert_spt_string_to_code,