diff --git a/docs/reference-defs.md b/docs/reference-defs.md
index 2a1b560c..e673f110 100644
--- a/docs/reference-defs.md
+++ b/docs/reference-defs.md
@@ -4,7 +4,7 @@
 
 ```yml
 {%
-    include-markdown "../swmmanywhere/defs/demo_config.yml"
+    include-markdown "../src/swmmanywhere/defs/demo_config.yml"
     comments=false
 %}
 ```
@@ -13,7 +13,7 @@
 
 ```yml
 {%
-    include-markdown "../swmmanywhere/defs/schema.yml"
+    include-markdown "../src/swmmanywhere/defs/schema.yml"
     comments=false
 %}
 ```
diff --git a/pyproject.toml b/pyproject.toml
index 6b8d7712..7b7acd2c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,6 +9,7 @@ requires = [
 name = "swmmanywhere"
 description = "SWMManywhere software"
 readme = "README.md"
+license-files = { paths = ["LICENSE", "src/netcomp/LICENSE.txt"] }
 authors = [
     { name = "Barnaby Dobson", email = "b.dobson@imperial.ac.uk" },
     { name = "Imperial College London RSE Team", email = "ict-rse-team@imperial.ac.uk" }
@@ -17,7 +18,7 @@ requires-python = ">=3.10"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
+  "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3 :: Only",
@@ -85,10 +86,10 @@ Issues = "https://github.com/ImperialCollegeLondon/SWMManywhere/issues"
 Source = "https://github.com/ImperialCollegeLondon/SWMManywhere"
 
 [tool.hatch.build.targets.sdist]
-only-include = ["swmmanywhere", "netcomp"]
+packages = [ "src" ]
 
 [tool.hatch.build.targets.wheel]
-only-include = ["swmmanywhere", "netcomp"]
+packages = [ "src" ]
 
 [tool.hatch.version]
 source = "vcs"
@@ -101,24 +102,49 @@ select = ["D", "E", "F", "I"] # pydocstyle, pycodestyle, Pyflakes, isort
 
 [tool.ruff.lint.per-file-ignores]
 "tests/*" = ["D100", "D104"]
-"netcomp/*" = ["D", "F"] # Ignore all checks for netcomp
+"src/netcomp/*" = ["D", "F"] # Ignore all checks for netcomp
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
 [tool.ruff.lint.isort]
 required-imports = ["from __future__ import annotations"]
+known-first-party = ["swmmanywhere", "netcomp"]
 
 [tool.codespell]
-skip = "swmmanywhere/defs/iso_converter.yml,*.inp"
+skip = "src/swmmanywhere/defs/iso_converter.yml,*.inp"
 ignore-words-list = "gage,gages"
 
 [tool.pytest.ini_options]
-addopts = "-v --import-mode=importlib --cov=swmmanywhere --cov-report=html --doctest-modules --ignore=swmmanywhere/logging.py"
+addopts = "-v --cov=src/swmmanywhere --cov-report=html --doctest-modules --ignore=src/swmmanywhere/logging.py"
 markers = [
   "downloads: mark a test as requiring downloads",
 ]
 
+[tool.coverage.report]
+exclude_lines = [
+  "if TYPE_CHECKING:",
+]
+omit = [
+  "**/__init__.py",
+]
+ignore_errors = true
+
+[tool.coverage.paths]
+source = [ "src", "*/site-packages" ]
+omit = [
+  "**/__init__.py",
+]
+
+[tool.coverage.run]
+branch = true
+source = [
+  "swmmanywhere",
+]
+omit = [
+  "**/__init__.py",
+]
+
 [tool.mypy]
 disallow_any_explicit = false
 disallow_any_generics = false
diff --git a/netcomp/LICENSE.txt b/src/netcomp/LICENSE.txt
similarity index 100%
rename from netcomp/LICENSE.txt
rename to src/netcomp/LICENSE.txt
diff --git a/netcomp/README.md b/src/netcomp/README.md
similarity index 100%
rename from netcomp/README.md
rename to src/netcomp/README.md
diff --git a/netcomp/__init__.py b/src/netcomp/__init__.py
similarity index 100%
rename from netcomp/__init__.py
rename to src/netcomp/__init__.py
diff --git a/netcomp/distance/__init__.py b/src/netcomp/distance/__init__.py
similarity index 100%
rename from netcomp/distance/__init__.py
rename to src/netcomp/distance/__init__.py
diff --git a/netcomp/distance/exact.py b/src/netcomp/distance/exact.py
similarity index 100%
rename from netcomp/distance/exact.py
rename to src/netcomp/distance/exact.py
diff --git a/netcomp/distance/features.py b/src/netcomp/distance/features.py
similarity index 100%
rename from netcomp/distance/features.py
rename to src/netcomp/distance/features.py
diff --git a/netcomp/exception.py b/src/netcomp/exception.py
similarity index 100%
rename from netcomp/exception.py
rename to src/netcomp/exception.py
diff --git a/netcomp/linalg/__init__.py b/src/netcomp/linalg/__init__.py
similarity index 100%
rename from netcomp/linalg/__init__.py
rename to src/netcomp/linalg/__init__.py
diff --git a/netcomp/linalg/eigenstuff.py b/src/netcomp/linalg/eigenstuff.py
similarity index 100%
rename from netcomp/linalg/eigenstuff.py
rename to src/netcomp/linalg/eigenstuff.py
diff --git a/netcomp/linalg/fast_bp.py b/src/netcomp/linalg/fast_bp.py
similarity index 100%
rename from netcomp/linalg/fast_bp.py
rename to src/netcomp/linalg/fast_bp.py
diff --git a/netcomp/linalg/matrices.py b/src/netcomp/linalg/matrices.py
similarity index 100%
rename from netcomp/linalg/matrices.py
rename to src/netcomp/linalg/matrices.py
diff --git a/netcomp/linalg/resistance.py b/src/netcomp/linalg/resistance.py
similarity index 100%
rename from netcomp/linalg/resistance.py
rename to src/netcomp/linalg/resistance.py
diff --git a/swmmanywhere/__init__.py b/src/swmmanywhere/__init__.py
similarity index 100%
rename from swmmanywhere/__init__.py
rename to src/swmmanywhere/__init__.py
diff --git a/swmmanywhere/__main__.py b/src/swmmanywhere/__main__.py
similarity index 100%
rename from swmmanywhere/__main__.py
rename to src/swmmanywhere/__main__.py
diff --git a/swmmanywhere/defs/basic_drainage_all_bits.inp b/src/swmmanywhere/defs/basic_drainage_all_bits.inp
similarity index 100%
rename from swmmanywhere/defs/basic_drainage_all_bits.inp
rename to src/swmmanywhere/defs/basic_drainage_all_bits.inp
diff --git a/swmmanywhere/defs/demo_config.yml b/src/swmmanywhere/defs/demo_config.yml
similarity index 100%
rename from swmmanywhere/defs/demo_config.yml
rename to src/swmmanywhere/defs/demo_config.yml
diff --git a/swmmanywhere/defs/iso_converter.yml b/src/swmmanywhere/defs/iso_converter.yml
similarity index 100%
rename from swmmanywhere/defs/iso_converter.yml
rename to src/swmmanywhere/defs/iso_converter.yml
diff --git a/swmmanywhere/defs/schema.yml b/src/swmmanywhere/defs/schema.yml
similarity index 100%
rename from swmmanywhere/defs/schema.yml
rename to src/swmmanywhere/defs/schema.yml
diff --git a/swmmanywhere/defs/storm.dat b/src/swmmanywhere/defs/storm.dat
similarity index 100%
rename from swmmanywhere/defs/storm.dat
rename to src/swmmanywhere/defs/storm.dat
diff --git a/swmmanywhere/defs/swmm_conversion.yml b/src/swmmanywhere/defs/swmm_conversion.yml
similarity index 100%
rename from swmmanywhere/defs/swmm_conversion.yml
rename to src/swmmanywhere/defs/swmm_conversion.yml
diff --git a/swmmanywhere/examples/data.py b/src/swmmanywhere/examples/data.py
similarity index 100%
rename from swmmanywhere/examples/data.py
rename to src/swmmanywhere/examples/data.py
diff --git a/swmmanywhere/examples/demo_graph.json b/src/swmmanywhere/examples/demo_graph.json
similarity index 100%
rename from swmmanywhere/examples/demo_graph.json
rename to src/swmmanywhere/examples/demo_graph.json
diff --git a/swmmanywhere/filepaths.py b/src/swmmanywhere/filepaths.py
similarity index 100%
rename from swmmanywhere/filepaths.py
rename to src/swmmanywhere/filepaths.py
diff --git a/swmmanywhere/geospatial_utilities.py b/src/swmmanywhere/geospatial_utilities.py
similarity index 100%
rename from swmmanywhere/geospatial_utilities.py
rename to src/swmmanywhere/geospatial_utilities.py
diff --git a/swmmanywhere/graph_utilities.py b/src/swmmanywhere/graph_utilities.py
similarity index 100%
rename from swmmanywhere/graph_utilities.py
rename to src/swmmanywhere/graph_utilities.py
diff --git a/swmmanywhere/graphfcns/__init__.py b/src/swmmanywhere/graphfcns/__init__.py
similarity index 100%
rename from swmmanywhere/graphfcns/__init__.py
rename to src/swmmanywhere/graphfcns/__init__.py
diff --git a/swmmanywhere/graphfcns/design_graphfcns.py b/src/swmmanywhere/graphfcns/design_graphfcns.py
similarity index 100%
rename from swmmanywhere/graphfcns/design_graphfcns.py
rename to src/swmmanywhere/graphfcns/design_graphfcns.py
diff --git a/swmmanywhere/graphfcns/network_cleaning_graphfcns.py b/src/swmmanywhere/graphfcns/network_cleaning_graphfcns.py
similarity index 100%
rename from swmmanywhere/graphfcns/network_cleaning_graphfcns.py
rename to src/swmmanywhere/graphfcns/network_cleaning_graphfcns.py
diff --git a/swmmanywhere/graphfcns/outfall_graphfcns.py b/src/swmmanywhere/graphfcns/outfall_graphfcns.py
similarity index 100%
rename from swmmanywhere/graphfcns/outfall_graphfcns.py
rename to src/swmmanywhere/graphfcns/outfall_graphfcns.py
diff --git a/swmmanywhere/graphfcns/subcatchment_graphfcns.py b/src/swmmanywhere/graphfcns/subcatchment_graphfcns.py
similarity index 100%
rename from swmmanywhere/graphfcns/subcatchment_graphfcns.py
rename to src/swmmanywhere/graphfcns/subcatchment_graphfcns.py
diff --git a/swmmanywhere/graphfcns/topology_graphfcns.py b/src/swmmanywhere/graphfcns/topology_graphfcns.py
similarity index 100%
rename from swmmanywhere/graphfcns/topology_graphfcns.py
rename to src/swmmanywhere/graphfcns/topology_graphfcns.py
diff --git a/swmmanywhere/logging.py b/src/swmmanywhere/logging.py
similarity index 100%
rename from swmmanywhere/logging.py
rename to src/swmmanywhere/logging.py
diff --git a/swmmanywhere/metric_utilities.py b/src/swmmanywhere/metric_utilities.py
similarity index 100%
rename from swmmanywhere/metric_utilities.py
rename to src/swmmanywhere/metric_utilities.py
diff --git a/swmmanywhere/misc/debug_derive_rc.py b/src/swmmanywhere/misc/debug_derive_rc.py
similarity index 100%
rename from swmmanywhere/misc/debug_derive_rc.py
rename to src/swmmanywhere/misc/debug_derive_rc.py
diff --git a/swmmanywhere/misc/debug_metrics.py b/src/swmmanywhere/misc/debug_metrics.py
similarity index 100%
rename from swmmanywhere/misc/debug_metrics.py
rename to src/swmmanywhere/misc/debug_metrics.py
diff --git a/swmmanywhere/misc/debug_topology.py b/src/swmmanywhere/misc/debug_topology.py
similarity index 100%
rename from swmmanywhere/misc/debug_topology.py
rename to src/swmmanywhere/misc/debug_topology.py
diff --git a/swmmanywhere/parameters.py b/src/swmmanywhere/parameters.py
similarity index 100%
rename from swmmanywhere/parameters.py
rename to src/swmmanywhere/parameters.py
diff --git a/swmmanywhere/post_processing.py b/src/swmmanywhere/post_processing.py
similarity index 100%
rename from swmmanywhere/post_processing.py
rename to src/swmmanywhere/post_processing.py
diff --git a/swmmanywhere/prepare_data.py b/src/swmmanywhere/prepare_data.py
similarity index 100%
rename from swmmanywhere/prepare_data.py
rename to src/swmmanywhere/prepare_data.py
diff --git a/swmmanywhere/preprocessing.py b/src/swmmanywhere/preprocessing.py
similarity index 100%
rename from swmmanywhere/preprocessing.py
rename to src/swmmanywhere/preprocessing.py
diff --git a/swmmanywhere/shortest_path_utils.py b/src/swmmanywhere/shortest_path_utils.py
similarity index 100%
rename from swmmanywhere/shortest_path_utils.py
rename to src/swmmanywhere/shortest_path_utils.py
diff --git a/swmmanywhere/swmmanywhere.py b/src/swmmanywhere/swmmanywhere.py
similarity index 100%
rename from swmmanywhere/swmmanywhere.py
rename to src/swmmanywhere/swmmanywhere.py
diff --git a/swmmanywhere/utilities.py b/src/swmmanywhere/utilities.py
similarity index 100%
rename from swmmanywhere/utilities.py
rename to src/swmmanywhere/utilities.py
diff --git a/tests/test_post_processing.py b/tests/test_post_processing.py
index 864dce19..a49bd0b9 100644
--- a/tests/test_post_processing.py
+++ b/tests/test_post_processing.py
@@ -16,6 +16,7 @@
 
 fid = (
     Path(__file__).parent.parent
+    / "src"
     / "swmmanywhere"
     / "defs"
     / "basic_drainage_all_bits.inp"
@@ -185,6 +186,7 @@ def test_synthetic_write():
         comparison_file = addresses.model_paths.model / "model_base.inp"
         template_fid = (
             Path(__file__).parent.parent
+            / "src"
             / "swmmanywhere"
             / "defs"
             / "basic_drainage_all_bits.inp"
@@ -234,7 +236,9 @@ def test_format_to_swmm_dict():
     data_dict = generate_data_dict()
     data_dict = stt.format_to_swmm_dict(**data_dict)
 
-    rain_fid = Path(__file__).parent.parent / "swmmanywhere" / "defs" / "storm.dat"
+    rain_fid = (
+        Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs" / "storm.dat"
+    )
     with tempfile.TemporaryDirectory() as temp_dir:
         temp_dir = Path(temp_dir)
         shutil.copy(rain_fid, temp_dir / "storm.dat")
diff --git a/tests/test_swmmanywhere.py b/tests/test_swmmanywhere.py
index 84afc800..34617aaa 100644
--- a/tests/test_swmmanywhere.py
+++ b/tests/test_swmmanywhere.py
@@ -1,4 +1,5 @@
 """Tests for the main module."""
+
 from __future__ import annotations
 
 import os
@@ -16,7 +17,7 @@
 
 def test_run():
     """Test the run function."""
-    demo_dir = Path(__file__).parent.parent / "swmmanywhere" / "defs"
+    demo_dir = Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs"
     model = demo_dir / "basic_drainage_all_bits.inp"
     storevars = ["flooding", "flow", "runoff", "depth"]
     results = swmmanywhere.run(model, reporting_iters=50, storevars=storevars)
@@ -39,7 +40,7 @@ def test_swmmanywhere():
     with tempfile.TemporaryDirectory() as temp_dir:
         # Load the config
         test_data_dir = Path(__file__).parent / "test_data"
-        defs_dir = Path(__file__).parent.parent / "swmmanywhere" / "defs"
+        defs_dir = Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs"
         with (defs_dir / "demo_config.yml").open("r") as f:
             config = yaml.safe_load(f)
 
@@ -97,7 +98,7 @@ def test_swmmanywhere():
 def test_load_config_file_validation():
     """Test the file validation of the config."""
     with tempfile.TemporaryDirectory() as temp_dir:
-        defs_dir = Path(__file__).parent.parent / "swmmanywhere" / "defs"
+        defs_dir = Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs"
         base_dir = Path(temp_dir)
 
         # Test file not found
@@ -124,7 +125,7 @@ def test_load_config_file_validation():
 def test_load_config_schema_validation():
     """Test the schema validation of the config."""
     with tempfile.TemporaryDirectory() as temp_dir:
-        defs_dir = Path(__file__).parent.parent / "swmmanywhere" / "defs"
+        defs_dir = Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs"
         base_dir = Path(temp_dir)
 
         # Load the config
@@ -147,7 +148,7 @@ def test_save_config():
     """Test the save_config function."""
     with tempfile.TemporaryDirectory() as temp_dir:
         temp_dir = Path(temp_dir)
-        defs_dir = Path(__file__).parent.parent / "swmmanywhere" / "defs"
+        defs_dir = Path(__file__).parent.parent / "src" / "swmmanywhere" / "defs"
 
         with (defs_dir / "demo_config.yml").open("r") as f:
             config = yaml.safe_load(f)