diff --git a/.gitignore b/.gitignore
index d42fcdc7e7..919cdccd05 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,10 +18,10 @@ sourmash.egg-info
 .coverage
 .pytest_cache
 .python-version
-sourmash/version.py
+src/sourmash/version.py
 *.DS_Store
 .tox
-sourmash/_lowlevel*.py
+src/sourmash/_lowlevel*.py
 .env
 Pipfile
 Pipfile.lock
diff --git a/MANIFEST.in b/MANIFEST.in
index a142c5c73e..1d2b9be999 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,10 +1,4 @@
-include LICENSE Makefile Dockerfile LICENSE Makefile README.md requirements.txt
-include index.ipynb
-include sourmash VERSION
-recursive-include sourmash_lib *
-recursive-include sourmash *
-recursive-include src *.rs
-recursive-include benches *.rs
+include LICENSE Makefile README.md requirements.txt
 include Cargo.toml
 include include/sourmash.h
 prune .eggs
diff --git a/pyproject.toml b/pyproject.toml
index fa69b6136e..f941122703 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 requires = [
-    "setuptools >= 42",
-    "setuptools_scm[toml] >= 3.4.0, <4",
+    "setuptools >= 48",
+    "setuptools_scm[toml] >= 4, <5",
     "setuptools_scm_git_archive",
     "milksnake",
     "wheel >= 0.29.0",
@@ -9,8 +9,8 @@ requires = [
 build-backend = 'setuptools.build_meta'
 
 [tool.setuptools_scm]
-write_to = "sourmash/version.py"
-git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"    
+write_to = "src/sourmash/version.py"
+git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"
 
 [tool.isort]
 known_third_party = ["deprecation", "hypothesis", "mmh3", "numpy", "pkg_resources", "pytest", "screed", "setuptools", "sourmash_tst_utils"]
diff --git a/setup.cfg b/setup.cfg
index 5dc5977dda..dbab5d58e5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -29,10 +29,8 @@ project_urls =
 
 [options]
 zip_safe = False
-platforms = any
 packages = find:
-#package_dir =
-#    =src
+platforms = any
 include_package_data = True
 install_requires =
     screed>=1.0
@@ -44,15 +42,12 @@ install_requires =
     cachetools>=4,<5
 python_requires = >=3.7
 
-[options.packages.find]
-#where = src
-exclude =
-    tests
-    benchmarks
-
 [bdist_wheel]
 universal = 1
 
+[options.packages.find]
+where = src
+
 # for explanation of %(extra)s syntax see:
 # https://github.com/pypa/setuptools/issues/1260#issuecomment-438187625
 # this syntax may change in the future
@@ -100,7 +95,7 @@ norecursedirs =
     .asv
     .eggs
 python_files =
-    sourmash/*.py
+    src/sourmash/*.py
     tests/*.py
 testpaths =
     tests
diff --git a/setup.py b/setup.py
index 3ec2f72103..f416ff3336 100644
--- a/setup.py
+++ b/setup.py
@@ -29,4 +29,5 @@ def build_native(spec):
 
 setup(
   milksnake_tasks=[build_native],
+  package_dir={"": "src"},
 )
diff --git a/sourmash/__init__.py b/src/sourmash/__init__.py
similarity index 100%
rename from sourmash/__init__.py
rename to src/sourmash/__init__.py
diff --git a/sourmash/__main__.py b/src/sourmash/__main__.py
similarity index 100%
rename from sourmash/__main__.py
rename to src/sourmash/__main__.py
diff --git a/sourmash/cli/.gitignore b/src/sourmash/cli/.gitignore
similarity index 100%
rename from sourmash/cli/.gitignore
rename to src/sourmash/cli/.gitignore
diff --git a/sourmash/cli/__init__.py b/src/sourmash/cli/__init__.py
similarity index 100%
rename from sourmash/cli/__init__.py
rename to src/sourmash/cli/__init__.py
diff --git a/sourmash/cli/categorize.py b/src/sourmash/cli/categorize.py
similarity index 100%
rename from sourmash/cli/categorize.py
rename to src/sourmash/cli/categorize.py
diff --git a/sourmash/cli/compare.py b/src/sourmash/cli/compare.py
similarity index 100%
rename from sourmash/cli/compare.py
rename to src/sourmash/cli/compare.py
diff --git a/sourmash/cli/compute.py b/src/sourmash/cli/compute.py
similarity index 100%
rename from sourmash/cli/compute.py
rename to src/sourmash/cli/compute.py
diff --git a/sourmash/cli/gather.py b/src/sourmash/cli/gather.py
similarity index 100%
rename from sourmash/cli/gather.py
rename to src/sourmash/cli/gather.py
diff --git a/sourmash/cli/import_csv.py b/src/sourmash/cli/import_csv.py
similarity index 100%
rename from sourmash/cli/import_csv.py
rename to src/sourmash/cli/import_csv.py
diff --git a/sourmash/cli/index.py b/src/sourmash/cli/index.py
similarity index 100%
rename from sourmash/cli/index.py
rename to src/sourmash/cli/index.py
diff --git a/sourmash/cli/info.py b/src/sourmash/cli/info.py
similarity index 100%
rename from sourmash/cli/info.py
rename to src/sourmash/cli/info.py
diff --git a/sourmash/cli/lca/__init__.py b/src/sourmash/cli/lca/__init__.py
similarity index 100%
rename from sourmash/cli/lca/__init__.py
rename to src/sourmash/cli/lca/__init__.py
diff --git a/sourmash/cli/lca/classify.py b/src/sourmash/cli/lca/classify.py
similarity index 100%
rename from sourmash/cli/lca/classify.py
rename to src/sourmash/cli/lca/classify.py
diff --git a/sourmash/cli/lca/compare_csv.py b/src/sourmash/cli/lca/compare_csv.py
similarity index 100%
rename from sourmash/cli/lca/compare_csv.py
rename to src/sourmash/cli/lca/compare_csv.py
diff --git a/sourmash/cli/lca/gather.py b/src/sourmash/cli/lca/gather.py
similarity index 100%
rename from sourmash/cli/lca/gather.py
rename to src/sourmash/cli/lca/gather.py
diff --git a/sourmash/cli/lca/index.py b/src/sourmash/cli/lca/index.py
similarity index 100%
rename from sourmash/cli/lca/index.py
rename to src/sourmash/cli/lca/index.py
diff --git a/sourmash/cli/lca/rankinfo.py b/src/sourmash/cli/lca/rankinfo.py
similarity index 100%
rename from sourmash/cli/lca/rankinfo.py
rename to src/sourmash/cli/lca/rankinfo.py
diff --git a/sourmash/cli/lca/summarize.py b/src/sourmash/cli/lca/summarize.py
similarity index 100%
rename from sourmash/cli/lca/summarize.py
rename to src/sourmash/cli/lca/summarize.py
diff --git a/sourmash/cli/migrate.py b/src/sourmash/cli/migrate.py
similarity index 100%
rename from sourmash/cli/migrate.py
rename to src/sourmash/cli/migrate.py
diff --git a/sourmash/cli/multigather.py b/src/sourmash/cli/multigather.py
similarity index 100%
rename from sourmash/cli/multigather.py
rename to src/sourmash/cli/multigather.py
diff --git a/sourmash/cli/plot.py b/src/sourmash/cli/plot.py
similarity index 100%
rename from sourmash/cli/plot.py
rename to src/sourmash/cli/plot.py
diff --git a/sourmash/cli/sbt_combine.py b/src/sourmash/cli/sbt_combine.py
similarity index 100%
rename from sourmash/cli/sbt_combine.py
rename to src/sourmash/cli/sbt_combine.py
diff --git a/sourmash/cli/search.py b/src/sourmash/cli/search.py
similarity index 100%
rename from sourmash/cli/search.py
rename to src/sourmash/cli/search.py
diff --git a/sourmash/cli/sig/__init__.py b/src/sourmash/cli/sig/__init__.py
similarity index 100%
rename from sourmash/cli/sig/__init__.py
rename to src/sourmash/cli/sig/__init__.py
diff --git a/sourmash/cli/sig/cat.py b/src/sourmash/cli/sig/cat.py
similarity index 100%
rename from sourmash/cli/sig/cat.py
rename to src/sourmash/cli/sig/cat.py
diff --git a/sourmash/cli/sig/describe.py b/src/sourmash/cli/sig/describe.py
similarity index 100%
rename from sourmash/cli/sig/describe.py
rename to src/sourmash/cli/sig/describe.py
diff --git a/sourmash/cli/sig/downsample.py b/src/sourmash/cli/sig/downsample.py
similarity index 100%
rename from sourmash/cli/sig/downsample.py
rename to src/sourmash/cli/sig/downsample.py
diff --git a/sourmash/cli/sig/export.py b/src/sourmash/cli/sig/export.py
similarity index 100%
rename from sourmash/cli/sig/export.py
rename to src/sourmash/cli/sig/export.py
diff --git a/sourmash/cli/sig/extract.py b/src/sourmash/cli/sig/extract.py
similarity index 100%
rename from sourmash/cli/sig/extract.py
rename to src/sourmash/cli/sig/extract.py
diff --git a/sourmash/cli/sig/filter.py b/src/sourmash/cli/sig/filter.py
similarity index 100%
rename from sourmash/cli/sig/filter.py
rename to src/sourmash/cli/sig/filter.py
diff --git a/sourmash/cli/sig/flatten.py b/src/sourmash/cli/sig/flatten.py
similarity index 100%
rename from sourmash/cli/sig/flatten.py
rename to src/sourmash/cli/sig/flatten.py
diff --git a/sourmash/cli/sig/ingest.py b/src/sourmash/cli/sig/ingest.py
similarity index 100%
rename from sourmash/cli/sig/ingest.py
rename to src/sourmash/cli/sig/ingest.py
diff --git a/sourmash/cli/sig/intersect.py b/src/sourmash/cli/sig/intersect.py
similarity index 100%
rename from sourmash/cli/sig/intersect.py
rename to src/sourmash/cli/sig/intersect.py
diff --git a/sourmash/cli/sig/merge.py b/src/sourmash/cli/sig/merge.py
similarity index 100%
rename from sourmash/cli/sig/merge.py
rename to src/sourmash/cli/sig/merge.py
diff --git a/sourmash/cli/sig/overlap.py b/src/sourmash/cli/sig/overlap.py
similarity index 100%
rename from sourmash/cli/sig/overlap.py
rename to src/sourmash/cli/sig/overlap.py
diff --git a/sourmash/cli/sig/rename.py b/src/sourmash/cli/sig/rename.py
similarity index 100%
rename from sourmash/cli/sig/rename.py
rename to src/sourmash/cli/sig/rename.py
diff --git a/sourmash/cli/sig/split.py b/src/sourmash/cli/sig/split.py
similarity index 100%
rename from sourmash/cli/sig/split.py
rename to src/sourmash/cli/sig/split.py
diff --git a/sourmash/cli/sig/subtract.py b/src/sourmash/cli/sig/subtract.py
similarity index 100%
rename from sourmash/cli/sig/subtract.py
rename to src/sourmash/cli/sig/subtract.py
diff --git a/sourmash/cli/sketch/__init__.py b/src/sourmash/cli/sketch/__init__.py
similarity index 100%
rename from sourmash/cli/sketch/__init__.py
rename to src/sourmash/cli/sketch/__init__.py
diff --git a/sourmash/cli/sketch/dna.py b/src/sourmash/cli/sketch/dna.py
similarity index 100%
rename from sourmash/cli/sketch/dna.py
rename to src/sourmash/cli/sketch/dna.py
diff --git a/sourmash/cli/sketch/protein.py b/src/sourmash/cli/sketch/protein.py
similarity index 100%
rename from sourmash/cli/sketch/protein.py
rename to src/sourmash/cli/sketch/protein.py
diff --git a/sourmash/cli/sketch/translate.py b/src/sourmash/cli/sketch/translate.py
similarity index 100%
rename from sourmash/cli/sketch/translate.py
rename to src/sourmash/cli/sketch/translate.py
diff --git a/sourmash/cli/storage/__init__.py b/src/sourmash/cli/storage/__init__.py
similarity index 100%
rename from sourmash/cli/storage/__init__.py
rename to src/sourmash/cli/storage/__init__.py
diff --git a/sourmash/cli/storage/convert.py b/src/sourmash/cli/storage/convert.py
similarity index 100%
rename from sourmash/cli/storage/convert.py
rename to src/sourmash/cli/storage/convert.py
diff --git a/sourmash/cli/utils.py b/src/sourmash/cli/utils.py
similarity index 100%
rename from sourmash/cli/utils.py
rename to src/sourmash/cli/utils.py
diff --git a/sourmash/cli/watch.py b/src/sourmash/cli/watch.py
similarity index 100%
rename from sourmash/cli/watch.py
rename to src/sourmash/cli/watch.py
diff --git a/sourmash/command_compute.py b/src/sourmash/command_compute.py
similarity index 100%
rename from sourmash/command_compute.py
rename to src/sourmash/command_compute.py
diff --git a/sourmash/command_sketch.py b/src/sourmash/command_sketch.py
similarity index 100%
rename from sourmash/command_sketch.py
rename to src/sourmash/command_sketch.py
diff --git a/sourmash/commands.py b/src/sourmash/commands.py
similarity index 100%
rename from sourmash/commands.py
rename to src/sourmash/commands.py
diff --git a/sourmash/compare.py b/src/sourmash/compare.py
similarity index 100%
rename from sourmash/compare.py
rename to src/sourmash/compare.py
diff --git a/sourmash/exceptions.py b/src/sourmash/exceptions.py
similarity index 100%
rename from sourmash/exceptions.py
rename to src/sourmash/exceptions.py
diff --git a/sourmash/fig.py b/src/sourmash/fig.py
similarity index 100%
rename from sourmash/fig.py
rename to src/sourmash/fig.py
diff --git a/sourmash/hll.py b/src/sourmash/hll.py
similarity index 100%
rename from sourmash/hll.py
rename to src/sourmash/hll.py
diff --git a/sourmash/index.py b/src/sourmash/index.py
similarity index 100%
rename from sourmash/index.py
rename to src/sourmash/index.py
diff --git a/sourmash/lca/__init__.py b/src/sourmash/lca/__init__.py
similarity index 100%
rename from sourmash/lca/__init__.py
rename to src/sourmash/lca/__init__.py
diff --git a/sourmash/lca/__main__.py b/src/sourmash/lca/__main__.py
similarity index 100%
rename from sourmash/lca/__main__.py
rename to src/sourmash/lca/__main__.py
diff --git a/sourmash/lca/command_classify.py b/src/sourmash/lca/command_classify.py
similarity index 100%
rename from sourmash/lca/command_classify.py
rename to src/sourmash/lca/command_classify.py
diff --git a/sourmash/lca/command_compare_csv.py b/src/sourmash/lca/command_compare_csv.py
similarity index 100%
rename from sourmash/lca/command_compare_csv.py
rename to src/sourmash/lca/command_compare_csv.py
diff --git a/sourmash/lca/command_gather.py b/src/sourmash/lca/command_gather.py
similarity index 100%
rename from sourmash/lca/command_gather.py
rename to src/sourmash/lca/command_gather.py
diff --git a/sourmash/lca/command_index.py b/src/sourmash/lca/command_index.py
similarity index 100%
rename from sourmash/lca/command_index.py
rename to src/sourmash/lca/command_index.py
diff --git a/sourmash/lca/command_rankinfo.py b/src/sourmash/lca/command_rankinfo.py
similarity index 100%
rename from sourmash/lca/command_rankinfo.py
rename to src/sourmash/lca/command_rankinfo.py
diff --git a/sourmash/lca/command_summarize.py b/src/sourmash/lca/command_summarize.py
similarity index 100%
rename from sourmash/lca/command_summarize.py
rename to src/sourmash/lca/command_summarize.py
diff --git a/sourmash/lca/lca_db.py b/src/sourmash/lca/lca_db.py
similarity index 100%
rename from sourmash/lca/lca_db.py
rename to src/sourmash/lca/lca_db.py
diff --git a/sourmash/lca/lca_utils.py b/src/sourmash/lca/lca_utils.py
similarity index 100%
rename from sourmash/lca/lca_utils.py
rename to src/sourmash/lca/lca_utils.py
diff --git a/sourmash/logging.py b/src/sourmash/logging.py
similarity index 100%
rename from sourmash/logging.py
rename to src/sourmash/logging.py
diff --git a/sourmash/minhash.py b/src/sourmash/minhash.py
similarity index 100%
rename from sourmash/minhash.py
rename to src/sourmash/minhash.py
diff --git a/sourmash/nodegraph.py b/src/sourmash/nodegraph.py
similarity index 100%
rename from sourmash/nodegraph.py
rename to src/sourmash/nodegraph.py
diff --git a/sourmash/np_utils.py b/src/sourmash/np_utils.py
similarity index 100%
rename from sourmash/np_utils.py
rename to src/sourmash/np_utils.py
diff --git a/sourmash/sbt.py b/src/sourmash/sbt.py
similarity index 100%
rename from sourmash/sbt.py
rename to src/sourmash/sbt.py
diff --git a/sourmash/sbt_storage.py b/src/sourmash/sbt_storage.py
similarity index 100%
rename from sourmash/sbt_storage.py
rename to src/sourmash/sbt_storage.py
diff --git a/sourmash/sbtmh.py b/src/sourmash/sbtmh.py
similarity index 100%
rename from sourmash/sbtmh.py
rename to src/sourmash/sbtmh.py
diff --git a/sourmash/search.py b/src/sourmash/search.py
similarity index 100%
rename from sourmash/search.py
rename to src/sourmash/search.py
diff --git a/sourmash/sig/__init__.py b/src/sourmash/sig/__init__.py
similarity index 100%
rename from sourmash/sig/__init__.py
rename to src/sourmash/sig/__init__.py
diff --git a/sourmash/sig/__main__.py b/src/sourmash/sig/__main__.py
similarity index 100%
rename from sourmash/sig/__main__.py
rename to src/sourmash/sig/__main__.py
diff --git a/sourmash/signature.py b/src/sourmash/signature.py
similarity index 100%
rename from sourmash/signature.py
rename to src/sourmash/signature.py
diff --git a/sourmash/sourmash_args.py b/src/sourmash/sourmash_args.py
similarity index 100%
rename from sourmash/sourmash_args.py
rename to src/sourmash/sourmash_args.py
diff --git a/sourmash/utils.py b/src/sourmash/utils.py
similarity index 100%
rename from sourmash/utils.py
rename to src/sourmash/utils.py
diff --git a/tests/test_hll.py b/tests/test_hll.py
index 19491ceec2..4e4ce365dd 100644
--- a/tests/test_hll.py
+++ b/tests/test_hll.py
@@ -6,7 +6,7 @@
 
 from sourmash.hll import HLL
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 K = 21  # size of kmer
 ERR_RATE = 0.01
diff --git a/tests/test_sourmash_sketch.py b/tests/test_sourmash_sketch.py
index e13ac5db8e..4eca0894ea 100644
--- a/tests/test_sourmash_sketch.py
+++ b/tests/test_sourmash_sketch.py
@@ -11,7 +11,7 @@
 import pytest
 import screed
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 import sourmash
 from sourmash import MinHash
 from sourmash.sbt import SBT, Node
diff --git a/tox.ini b/tox.ini
index 1dcb86030f..9d977a04a0 100644
--- a/tox.ini
+++ b/tox.ini
@@ -39,11 +39,10 @@ extras =
     storage
 changedir = tests
 commands = pytest \
-           --basetemp="{envtmpdir}" \
            --cov "{envsitepackagesdir}/sourmash" \
            --cov-config "{toxinidir}/tox.ini" \
            --junitxml {toxworkdir}/junit.{envname}.xml \
-           {posargs}
+           {posargs:.}
 
 [testenv:pypy]
 deps =
@@ -140,12 +139,12 @@ exclude_lines =
     ^if __name__ == ['"]__main__['"]:$
 
 [coverage:paths]
-source = sourmash/
+source = src/sourmash/
          */.tox/*/lib/python*/site-packages/sourmash
          */.tox/pypy*/site-packages/sourmash
          */.tox\*\Lib\site-packages\sourmash
-         */sourmash
-         *\sourmash
+         */src/sourmash
+         *\src\sourmash
 
 [travis]
 python =