Update repo urls

Signed-off-by: James Noss <[email protected]>

CITATION.cff

@@ -18,4 +18,4 @@ authors:
   orcid: "https://orcid.org/0000-0001-9239-012X"
 title: "BioSpecDB"
 doi: "10048242"
-url: "https://github.com/ssec-jhu/biospecdb"
+url: "https://github.com/rispadd/biospecdb"

CODEOWNERS

@@ -1 +1 @@
-*    @ssec-jhu/team
+

README.md

@@ -1,9 +1,9 @@
 # SSEC-JHU BioSpecDB
 
-[![CI](https://github.com/ssec-jhu/biospecdb/actions/workflows/ci.yml/badge.svg)](https://github.com/ssec-jhu/biospecdb/actions/workflows/ci.yml)
+[![CI](https://github.com/rispadd/biospecdb/actions/workflows/ci.yml/badge.svg)](https://github.com/rispadd/biospecdb/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/biospecdb/badge/?version=latest)](https://biospecdb.readthedocs.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/ssec-jhu/biospecdb/graph/badge.svg?token=P9I3UXlmOc)](https://codecov.io/gh/ssec-jhu/biospecdb)
-[![Security](https://github.com/ssec-jhu/biospecdb/actions/workflows/security.yml/badge.svg)](https://github.com/ssec-jhu/biospecdb/actions/workflows/security.yml)
+[![codecov](https://codecov.io/gh/rispadd/biospecdb/graph/badge.svg?token=P9I3UXlmOc)](https://codecov.io/gh/rispadd/biospecdb)
+[![Security](https://github.com/rispadd/biospecdb/actions/workflows/security.yml/badge.svg)](https://github.com/rispadd/biospecdb/actions/workflows/security.yml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10048241.svg)](https://doi.org/10.5281/zenodo.10048241)
 
 ![SSEC-JHU Logo](docs/_static/SSEC_logo_horiz_blue_1152x263.png)

biospecdb/apps/uploader/base_models.py

@@ -133,4 +133,4 @@ def save(self, *args, update_view=True, **kwargs):
                 sql_view.update_view()
 
     def asave(self, *args, **kwargs):
-        raise NotImplementedError("See https://github.com/ssec-jhu/biospecdb/issues/66")
+        raise NotImplementedError("See https://github.com/rispadd/biospecdb/issues/66")

biospecdb/apps/uploader/io.py

@@ -100,7 +100,7 @@ def _read_raw_data(file, ext=None):
     # ‘NULL’, ‘NaN’, ‘None’, ‘n/a’, ‘nan’, ‘null’.
 
     # NOTE: When the file size is > 2.5M Django will chunk and this will need to be handled. See
-    # https://github.com/ssec-jhu/biospecdb/issues/38
+    # https://github.com/rispadd/biospecdb/issues/38
     if ext == FileFormats.CSV:
         data = pd.read_csv(file, **kwargs)
     elif ext == FileFormats.XLSX:

biospecdb/apps/uploader/loaddata.py

@@ -112,7 +112,7 @@ def save_data_to_db(meta_data, spectral_data, center=None, joined_data=None, dry
                         continue
 
                     # TODO: Should the following logic belong to Observation.__init__()?
-                    #  See https://github.com/ssec-jhu/biospecdb/issues/42
+                    #  See https://github.com/rispadd/biospecdb/issues/42
                     observation_value = Observable.Types(observable.value_class).cast(observation_value)
                     observation = Observation(observable=observable,
                                               visit=visit,

biospecdb/apps/uploader/models.py

@@ -744,10 +744,10 @@ def clean(self):
             self.data = cleaned_file
 
     #@transaction.atomic(using="bsr")  # Really? Not sure if this even can be if run in background...
-    # See https://github.com/ssec-jhu/biospecdb/issues/77
+    # See https://github.com/rispadd/biospecdb/issues/77
     def annotate(self, annotator=None, force=False) -> list:
         # TODO: This needs to return early and run in the background.
-        # See https://github.com/ssec-jhu/biospecdb/issues/77
+        # See https://github.com/rispadd/biospecdb/issues/77
 
         existing_annotators = self.get_annotators()
 
@@ -784,7 +784,7 @@ def save(self, *args, **kwargs):
         # such that new data is complete such that it has associated QC metrics.
         if settings.AUTO_ANNOTATE:
             # TODO: This should return early and runs async in the background.
-            # See https://github.com/ssec-jhu/biospecdb/issues/77
+            # See https://github.com/rispadd/biospecdb/issues/77
             self.annotate()
 
     def asave(self, *args, **kwargs):
@@ -1011,7 +1011,7 @@ def get_value(self):
             return self.annotator.cast(self.value)
 
     def run(self, save=True):
-        # NOTE: This waits. See https://github.com/ssec-jhu/biospecdb/issues/77
+        # NOTE: This waits. See https://github.com/rispadd/biospecdb/issues/77
         value = self.annotator.run(self.spectral_data)
         self.value = value
 

biospecdb/apps/uploader/tests/test_models.py

@@ -340,7 +340,7 @@ def test_files_added(self, mock_data_from_files):
 
     def test_no_file_validation(self, db):
         """ Test that a validation error is raised rather than any other python exception which would indicate a bug.
-            See https://github.com/ssec-jhu/biospecdb/pull/181
+            See https://github.com/rispadd/biospecdb/pull/181
         """
         data = SpectralData()
         with pytest.raises(ValidationError):
@@ -364,7 +364,7 @@ def test_no_duplicate_data_files(self, mock_data_from_files):
 
     @pytest.mark.skip("Unimplemented See #141")
     def test_all_files_deleted_upon_transaction_failure(self):
-        # I'm not sure how to mock this... See https://github.com/ssec-jhu/biospecdb/issues/141
+        # I'm not sure how to mock this... See https://github.com/rispadd/biospecdb/issues/141
         ...
 
     @pytest.mark.parametrize("ext", uploader.io.FileFormats.list())

biospecdb/apps/uploader/tests/test_qc_models.py

@@ -205,15 +205,15 @@ def test_management_command_no_reruns(self, monkeypatch, qcannotators, mock_data
 
     def test_no_file_validation(self, qcannotators):
         """ Test that a validation error is raised rather than any other python exception which would indicate a bug.
-            See https://github.com/ssec-jhu/biospecdb/pull/182
+            See https://github.com/rispadd/biospecdb/pull/182
         """
         annotation = QCAnnotation(annotator=QCAnnotator.objects.get(name="sum"))
         with pytest.raises(ValidationError):
             annotation.full_clean()
 
     def test_no_file_related_error(self, qcannotators):
         """ Test that a validation error is raised rather than any other python exception which would indicate a bug.
-            See https://github.com/ssec-jhu/biospecdb/pull/182
+            See https://github.com/rispadd/biospecdb/pull/182
         """
         annotation = QCAnnotation(annotator=QCAnnotator.objects.get(name="sum"))
         with pytest.raises(QCAnnotation.spectral_data.RelatedObjectDoesNotExist):

biospecdb/qc/qcmanager.py

@@ -13,7 +13,7 @@ class QcManager:
     def __init__(self):
         if settings.DISABLE_QC_MANAGER:
             # Disable this class for now as #69 made it obsolete, however, there's a very good chance it will be needed
-            # when implementing background tasks for https://github.com/ssec-jhu/biospecdb/pull/77.
+            # when implementing background tasks for https://github.com/rispadd/biospecdb/pull/77.
             raise NotImplementedError()
 
         self._validators = {}

biospecdb/settings/base.py

@@ -304,7 +304,7 @@
 RUN_DEFAULT_ANNOTATORS_WHEN_SAVED = False
 
 # Disable this class for now as #69 made it obsolete, however, there's a very good chance it will be needed
-# when implementing background tasks for https://github.com/ssec-jhu/biospecdb/pull/77.
+# when implementing background tasks for https://github.com/rispadd/biospecdb/pull/77.
 DISABLE_QC_MANAGER = True
 
 # Auto-populate the model field ``Visit.previous_visit`` by searching for existing older visits and choosing the last.

docs/source/conf.py

@@ -53,7 +53,7 @@
             'image_dark': '../_static/SSEC_logo_vert_white_lg_1184x661.png',
             'text': f'{html_title}',
         },
-        'repository_url': 'https://github.com/ssec-jhu/biospecdb',
+        'repository_url': 'https://github.com/rispadd/biospecdb',
         'use_repository_button': True,
     })
 

pyproject.toml

@@ -48,9 +48,9 @@ docs = [
 ]
 
 [project.urls]
-homepage = "https://github.com/ssec-jhu/base-template"
-documentation = "https://github.com/ssec-jhu/base-template"
-repository = "https://github.com/ssec-jhu/base-template"
+homepage = "https://github.com/rispadd/biospecdb"
+documentation = "https://github.com/rispadd/biospecdb"
+repository = "https://github.com/rispadd/biospecdb"
 
 [build-system]
 requires = ["setuptools>=61.2", "setuptools_scm[toml]>=8.0"]