PennChopMicrobiomeProgram · Ulthran · Sep 12, 2025 · Sep 12, 2025 · Copilot · Sep 12, 2025
diff --git a/.gitignore b/.gitignore
@@ -4,4 +4,4 @@ website/core.db
 build/
 __pycache__/
 *.sqlite3
-env/
+env
diff --git a/app/__init__.py b/app/__init__.py
diff --git a/app/sample_registry/pyproject.toml → pyproject.toml b/app/sample_registry/pyproject.toml → pyproject.toml
@@ -27,10 +27,12 @@ classifiers = [
   "Programming Language :: Python :: 3 :: Only",
 ]
 
-dependencies = [
-    "sqlalchemy",
-    "seqbackup @ git+https://github.com/PennChopMicrobiomeProgram/seqBackup.git@master",
-]
+dependencies = [
+    "flask",
+    "flask-sqlalchemy",
+    "sqlalchemy",
+    "seqbackup @ git+https://github.com/PennChopMicrobiomeProgram/seqBackup.git@master",
+]
 
 [project.optional-dependencies] # Optional
 dev = ["black"]
@@ -56,11 +58,16 @@ export_samples = "sample_registry.export:export_samples"
 create_test_db = "sample_registry.db:create_test_db"
 sample_registry_version = "sample_registry:sample_registry_version"
 
-[tool.setuptools]
-
-[build-system]
-requires = ["setuptools>=61.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
+[tool.setuptools.package-data]
+"sample_registry" = [
+    "templates/*.html",
+    "static/*",
+    "static/img/*",
+]
+
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools.dynamic]
-version = {attr = "sample_registry.__version__"}
+version = {attr = "sample_registry.__version__"}
diff --git a/..._registry/src/sample_registry/__init__.py → sample_registry/__init__.py b/..._registry/src/sample_registry/__init__.py → sample_registry/__init__.py
@@ -21,7 +21,7 @@ def sample_registry_version():
     sys.stdout.write(
         "Missing database connection information in environment, using test SQLite database\n"
     )
-    SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.parent.parent.parent.resolve()}/sample_registry.sqlite3"
+    SQLALCHEMY_DATABASE_URI = f"sqlite:///{Path(__file__).parent.parent.resolve()}/sample_registry.sqlite3"
 
 
 if "PYTEST_VERSION" in os.environ:

diff --git a/app/app.py → sample_registry/app.py b/app/app.py → sample_registry/app.py
diff --git a/...sample_registry/src/sample_registry/db.py → sample_registry/db.py b/...sample_registry/src/sample_registry/db.py → sample_registry/db.py
diff --git a/...e_registry/src/sample_registry/mapping.py → sample_registry/mapping.py b/...e_registry/src/sample_registry/mapping.py → sample_registry/mapping.py
diff --git a/...le_registry/src/sample_registry/models.py → sample_registry/models.py b/...le_registry/src/sample_registry/models.py → sample_registry/models.py
diff --git a/..._registry/src/sample_registry/register.py → sample_registry/register.py b/..._registry/src/sample_registry/register.py → sample_registry/register.py
diff --git a/...registry/src/sample_registry/registrar.py → sample_registry/registrar.py b/...registry/src/sample_registry/registrar.py → sample_registry/registrar.py
diff --git a/app/static/favicon.ico → sample_registry/static/favicon.ico b/app/static/favicon.ico → sample_registry/static/favicon.ico
diff --git a/app/static/img/back_disabled.jpg → sample_registry/static/img/back_disabled.jpg b/app/static/img/back_disabled.jpg → sample_registry/static/img/back_disabled.jpg
diff --git a/app/static/img/back_enabled.jpg → sample_registry/static/img/back_enabled.jpg b/app/static/img/back_enabled.jpg → sample_registry/static/img/back_enabled.jpg
diff --git a/app/static/img/forward_disabled.jpg → ..._registry/static/img/forward_disabled.jpg b/app/static/img/forward_disabled.jpg → ..._registry/static/img/forward_disabled.jpg
diff --git a/app/static/img/forward_enabled.jpg → ...e_registry/static/img/forward_enabled.jpg b/app/static/img/forward_enabled.jpg → ...e_registry/static/img/forward_enabled.jpg
diff --git a/app/static/img/mainlogo.jpg → sample_registry/static/img/mainlogo.jpg b/app/static/img/mainlogo.jpg → sample_registry/static/img/mainlogo.jpg
diff --git a/app/static/img/ricks_dna.png → sample_registry/static/img/ricks_dna.png b/app/static/img/ricks_dna.png → sample_registry/static/img/ricks_dna.png
diff --git a/app/static/img/sort_asc.png → sample_registry/static/img/sort_asc.png b/app/static/img/sort_asc.png → sample_registry/static/img/sort_asc.png
diff --git a/app/static/img/sort_asc_disabled.png → ...registry/static/img/sort_asc_disabled.png b/app/static/img/sort_asc_disabled.png → ...registry/static/img/sort_asc_disabled.png
diff --git a/app/static/img/sort_both.png → sample_registry/static/img/sort_both.png b/app/static/img/sort_both.png → sample_registry/static/img/sort_both.png
diff --git a/app/static/img/sort_desc.png → sample_registry/static/img/sort_desc.png b/app/static/img/sort_desc.png → sample_registry/static/img/sort_desc.png
diff --git a/app/static/img/sort_desc_disabled.png → ...egistry/static/img/sort_desc_disabled.png b/app/static/img/sort_desc_disabled.png → ...egistry/static/img/sort_desc_disabled.png
diff --git a/app/templates/base.html → sample_registry/templates/base.html b/app/templates/base.html → sample_registry/templates/base.html
diff --git a/app/templates/browse_runs.html → sample_registry/templates/browse_runs.html b/app/templates/browse_runs.html → sample_registry/templates/browse_runs.html
diff --git a/app/templates/browse_tags.html → sample_registry/templates/browse_tags.html b/app/templates/browse_tags.html → sample_registry/templates/browse_tags.html
diff --git a/app/templates/description.html → sample_registry/templates/description.html b/app/templates/description.html → sample_registry/templates/description.html
diff --git a/app/templates/failed_export.html → sample_registry/templates/failed_export.html b/app/templates/failed_export.html → sample_registry/templates/failed_export.html
diff --git a/app/templates/show_run.html → sample_registry/templates/show_run.html b/app/templates/show_run.html → sample_registry/templates/show_run.html
diff --git a/app/templates/show_stats.html → sample_registry/templates/show_stats.html b/app/templates/show_stats.html → sample_registry/templates/show_stats.html
diff --git a/app/templates/show_tag.html → sample_registry/templates/show_tag.html b/app/templates/show_tag.html → sample_registry/templates/show_tag.html
diff --git a/app/templates/show_tag_value.html → ...le_registry/templates/show_tag_value.html b/app/templates/show_tag_value.html → ...le_registry/templates/show_tag_value.html
diff --git a/...mple_registry/src/sample_registry/util.py → sample_registry/util.py b/...mple_registry/src/sample_registry/util.py → sample_registry/util.py
diff --git a/app/sample_registry/test/__init__.py → tests/__init__.py b/app/sample_registry/test/__init__.py → tests/__init__.py
diff --git a/app/sample_registry/test/test_mapping.py → tests/test_mapping.py b/app/sample_registry/test/test_mapping.py → tests/test_mapping.py
@@ -1,5 +1,5 @@
 import io
-from src.sample_registry.mapping import SampleTable
+from sample_registry.mapping import SampleTable
 
 
 NORMAL_TSV = """\

diff --git a/app/sample_registry/test/test_register.py → tests/test_register.py b/app/sample_registry/test/test_register.py → tests/test_register.py
@@ -6,17 +6,17 @@
 from sqlalchemy import and_, create_engine, select
 from sqlalchemy.orm import Session, sessionmaker
 from typing import Generator
-from src.sample_registry.db import create_test_db
-from src.sample_registry.mapping import SampleTable
-from src.sample_registry.models import (
+from sample_registry.db import create_test_db
+from sample_registry.mapping import SampleTable
+from sample_registry.models import (
     Annotation,
     Base,
     Run,
     Sample,
     StandardHostSpecies,
     StandardSampleType,
 )
-from src.sample_registry.register import (
+from sample_registry.register import (
     register_run,
     register_sample_annotations,
     unregister_samples,

diff --git a/app/sample_registry/test/test_registrar.py → tests/test_registrar.py b/app/sample_registry/test/test_registrar.py → tests/test_registrar.py
@@ -2,17 +2,17 @@
 import pytest
 from sqlalchemy import create_engine, func, select
 from sqlalchemy.orm import Session, sessionmaker
-from src.sample_registry.db import create_test_db
-from src.sample_registry.mapping import SampleTable
-from src.sample_registry.models import (
+from sample_registry.db import create_test_db
+from sample_registry.mapping import SampleTable
+from sample_registry.models import (
     Annotation,
     Base,
     Run,
     Sample,
     StandardHostSpecies,
     StandardSampleType,
-)
-from src.sample_registry.registrar import SampleRegistry
+)
+from sample_registry.registrar import SampleRegistry
 
 recs = [
     {

diff --git a/app/sample_registry/test/test_util.py → tests/test_util.py b/app/sample_registry/test/test_util.py → tests/test_util.py
@@ -1,6 +1,6 @@
 import collections
 import io
-from src.sample_registry.util import (
+from sample_registry.util import (
     key_by_attr,
     dict_from_eav,
     local_filepath,
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,4 +4,4 @@ website/core.db @@
     build/
     __pycache__/
     *.sqlite3
-    env/
+    env