diff --git a/.coveragerc b/.coveragerc
deleted file mode 100644
index 09b80d8275..0000000000
--- a/.coveragerc
+++ /dev/null
@@ -1,10 +0,0 @@
-[run]
-include=
-    sourmash/*.py
-    sourmash_lib/*.py
-omit =
-    doc/conf.py
-    setup.py
-    tests/*
-    .tox/*
-    benchmarks/*
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/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000000..c4c2868f0e
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,62 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.2.0
+  hooks:
+  - id: check-ast
+#  - id: check-builtin-literals
+  - id: check-docstring-first
+  - id: check-merge-conflict
+  - id: check-yaml
+  - id: check-toml
+  - id: debug-statements
+#  - id: end-of-file-fixer
+#    exclude: 'tests/test-data'
+#  - id: trailing-whitespace
+#    exclude: 'tests/test-data'
+#- repo: https://github.com/asottile/pyupgrade
+#  rev: v2.7.2
+#  hooks:
+#  - id: pyupgrade
+#- repo: https://github.com/pre-commit/mirrors-isort
+#  rev: v5.4.2
+#  hooks:
+#  - id: isort
+#    additional_dependencies: [toml]
+#- repo: https://github.com/psf/black
+#  rev: 20.8b1
+#  hooks:
+#  - id: black
+#    args:
+#    - --safe
+#    language_version: python3.8
+#- repo: https://github.com/asottile/blacken-docs
+#  rev: v1.8.0
+#  hooks:
+#  - id: blacken-docs
+#    additional_dependencies:
+#    - black==19.10b0
+#    language_version: python3.8
+#- repo: https://github.com/asottile/add-trailing-comma
+#  rev: v2.0.1
+#  hooks:
+#  - id: add-trailing-comma
+#- repo: https://github.com/pre-commit/pygrep-hooks
+#  rev: v1.6.0
+#  hooks:
+#  - id: rst-backticks
+#- repo: https://github.com/asottile/setup-cfg-fmt
+#  rev: v1.11.0
+#  hooks:
+#  - id: setup-cfg-fmt
+#    args:
+#    - --min-py3-version
+#    - '3.7'
+#- repo: https://gitlab.com/pycqa/flake8
+#  rev: 3.8.3
+#  hooks:
+#  - id: flake8
+#    additional_dependencies:
+#    - flake8-bugbear == 20.1.2
+#    language_version: python3.8
diff --git a/MANIFEST.in b/MANIFEST.in
index 1d206dc896..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
@@ -12,5 +6,5 @@ global-exclude *.rlib
 global-exclude *.orig
 global-exclude *.pyc
 global-exclude *.so
-prune tests/test-data/
-global-exclude *.git/
+prune tests/test-data
+global-exclude *.git
diff --git a/Makefile b/Makefile
index 95dbe62eae..65b55db68b 100644
--- a/Makefile
+++ b/Makefile
@@ -18,13 +18,12 @@ install: all
 dist: FORCE
 	$(PYTHON) setup.py sdist
 
-test: all
-	$(PYTHON) -m pip install -e '.[test]'
-	$(PYTHON) -m pytest
+test:
+	tox -e py38
 	cargo test
 
-doc: build .PHONY
-	cd doc && make html
+doc: .PHONY
+	tox -e docs
 
 include/sourmash.h: src/core/src/lib.rs \
                     src/core/src/ffi/hyperloglog.rs \
@@ -36,8 +35,7 @@ include/sourmash.h: src/core/src/lib.rs \
 	RUSTUP_TOOLCHAIN=nightly cbindgen -c cbindgen.toml . -o ../../$@
 
 coverage: all
-	$(PYTHON) setup.py build_ext -i
-	$(PYTHON) -m pytest --cov=. --cov-report term-missing --cov-report=xml
+	tox -e coverage
 
 benchmark:
 	asv continuous latest `git rev-parse HEAD`
diff --git a/nix.shell b/nix.shell
new file mode 100644
index 0000000000..57ba5d1039
--- /dev/null
+++ b/nix.shell
@@ -0,0 +1,51 @@
+let
+  moz_overlay = import (builtins.fetchTarball https://github.com/mozilla/nixpkgs-mozilla/archive/master.tar.gz);
+  nixpkgs = import <nixpkgs> { overlays = [ moz_overlay ]; };
+  ruststable = (nixpkgs.latest.rustChannels.stable.rust);
+
+  mach-nix = import (
+    builtins.fetchGit {
+      url = "https://github.com/DavHau/mach-nix/";
+      ref = "2.0.0";
+    }
+  );
+
+  customPython = mach-nix.mkPython {
+    python = nixpkgs.python38;
+    requirements = ''
+       screed>=0.9
+       cffi>=1.14.0
+       numpy
+       matplotlib
+       scipy
+       deprecation>=2.0.6
+       cachetools >=4,<5
+       setuptools>=38.6.0
+       milksnake
+       setuptools_scm>=3.2.0
+       setuptools_scm_git_archive
+       pytest
+       pytest-cov
+       hypothesis
+       tox
+    '';
+  };
+
+in
+  with nixpkgs;
+
+  nixpkgs.mkShell {
+    buildInputs = [
+      customPython
+      git
+      stdenv
+      ruststable
+      stdenv.cc.cc.lib
+   ];
+
+  shellHook = ''
+     # workaround for https://github.com/NixOS/nixpkgs/blob/48dfc9fa97d762bce28cc8372a2dd3805d14c633/doc/languages-frameworks/python.section.md#python-setuppy-bdist_wheel-cannot-create-whl
+     export SOURCE_DATE_EPOCH=315532800 # 1980
+     export LD_LIBRARY_PATH="${stdenv.cc.cc.lib}/lib64:$LD_LIBRARY_PATH";
+  '';
+}
diff --git a/pyproject.toml b/pyproject.toml
index f30ae840cc..f941122703 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,3 +7,15 @@ requires = [
     "wheel >= 0.29.0",
 ]
 build-backend = 'setuptools.build_meta'
+
+[tool.setuptools_scm]
+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"]
+multi_line_output = 3 
+include_trailing_comma = true
+force_grid_wrap = 0
+line_length = 88
+known_first_party = ["sourmash"]
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index 3b174ff089..0000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-[pytest]
-addopts = --doctest-glob='doc/*.md' --ignore=setup.py
-python_files = sourmash/*.py tests/*.py
-norecursedirs = utils build buildenv .tox .asv .eggs
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000000..f4e2d072df
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,102 @@
+[metadata]
+name = sourmash
+description = tools for comparing DNA sequences with MinHash sketches
+long_description = file: README.md
+long_description_content_type = text/markdown; charset=UTF-8
+url = https://github.com/dib-lab/sourmash
+author = C. Titus Brown
+author_email = titus@idyll.org
+license = BSD 3-clause
+license_file = LICENSE
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Environment :: Console
+    Environment :: MacOS X
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: BSD License
+    Natural Language :: English
+    Operating System :: POSIX :: Linux
+    Operating System :: MacOS :: MacOS X
+    Programming Language :: Rust
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Topic :: Scientific/Engineering :: Bio-Informatics
+project_urls = 
+    Documentation = https://sourmash.readthedocs.io
+    CI = https://travis-ci.com/dib-lab/sourmash
+    Source = https://github.com/dib-lab/sourmash
+    Tracker = https://github.com/dib-lab/sourmash/issues
+
+[options]
+zip_safe = False
+packages = find:
+platforms = any
+include_package_data = True
+install_requires =
+    screed>=1.0
+    cffi>=1.14.0
+    numpy
+    matplotlib
+    scipy
+    deprecation>=2.0.6
+    cachetools>=4,<5
+python_requires = >=3.7
+
+[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
+[options.extras_require]
+test =
+    pytest>=6
+    pytest-cov<2.6
+    recommonmark
+    hypothesis
+demo =
+    jupyter
+    jupyter_client
+    ipython
+doc =
+    sphinx
+    myst-parser[sphinx]>=0.12.2
+    alabaster
+    sphinxcontrib-napoleon
+    nbsphinx
+    ipython
+10x =
+    bam2fasta==1.0.4
+storage =
+    ipfshttpclient>=0.4.13
+    redis
+all = 
+    %(test)s
+    %(demo)s
+    %(doc)s
+    %(10x)s
+    %(storage)s
+
+[options.entry_points]
+console_scripts =
+    sourmash = sourmash.__main__:main
+
+[tool:pytest]
+addopts =
+    --doctest-glob='doc/*.md'
+norecursedirs =
+    utils
+    build
+    buildenv
+    .tox
+    .asv
+    .eggs
+python_files =
+    src/sourmash/*.py
+    tests/*.py
+testpaths =
+    tests
+    doc
diff --git a/setup.py b/setup.py
index 310abf82ae..f416ff3336 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,8 @@
 import os
-from setuptools import setup, find_packages
 import sys
 
+from setuptools import setup
+
 
 DEBUG_BUILD = os.environ.get("SOURMASH_DEBUG") == "1"
 
@@ -26,67 +27,7 @@ def build_native(spec):
         rtld_flags=rtld_flags,
     )
 
-
-CLASSIFIERS = [
-    "Environment :: Console",
-    "Environment :: MacOS X",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
-    "Natural Language :: English",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: MacOS :: MacOS X",
-    "Programming Language :: Rust",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-]
-
-CLASSIFIERS.append("Development Status :: 5 - Production/Stable")
-
-with open("README.md", "r") as readme:
-    LONG_DESCRIPTION = readme.read()
-
-SETUP_METADATA = {
-    "name": "sourmash",
-    "description": "tools for comparing DNA sequences with MinHash sketches",
-    "long_description": LONG_DESCRIPTION,
-    "long_description_content_type": "text/markdown",
-    "url": "https://github.com/dib-lab/sourmash",
-    "author": "C. Titus Brown",
-    "author_email": "titus@idyll.org",
-    "license": "BSD 3-clause",
-    "packages": find_packages(exclude=["tests", "benchmarks"]),
-    "entry_points": {'console_scripts': [
-        'sourmash = sourmash.__main__:main'
-        ]
-    },
-    "install_requires": ['screed>=0.9', 'cffi>=1.14.0', 'numpy',
-                         'matplotlib', 'scipy', 'deprecation>=2.0.6',
-                         'cachetools >=4,<5'],
-    "setup_requires": [
-        "setuptools>=48",
-        "milksnake",
-        "setuptools_scm[toml] >= 4, <5",
-        "setuptools_scm_git_archive",
-        "wheel >= 0.29.0",
-    ],
-    "use_scm_version": {
-        "write_to": "sourmash/version.py",
-        "git_describe_command": "git describe --dirty --tags --long --match v* --first-parent"
-    },
-    "zip_safe": False,
-    "platforms": "any",
-    "extras_require": {
-        'test' : ['pytest', 'pytest-cov', 'recommonmark', 'hypothesis'],
-        'demo' : ['jupyter', 'jupyter_client', 'ipython'],
-        'doc' : ['sphinx', 'myst-parser[sphinx]>=0.12.2', 'alabaster',
-                 "sphinxcontrib-napoleon", "nbsphinx",
-                 "ipython"],
-        'storage': ["ipfshttpclient>=0.4.13", "redis"]
-    },
-    "include_package_data": True,
-    "classifiers": CLASSIFIERS,
-    "milksnake_tasks": [build_native],
-}
-
-setup(**SETUP_METADATA)
+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/__init__.py b/tests/__init__.py
deleted file mode 100644
index 1019c178fc..0000000000
--- a/tests/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-import matplotlib.pyplot as plt
-plt.rcParams.update({'figure.max_open_warning': 0})
diff --git a/tests/conftest.py b/tests/conftest.py
index 26ea6846fe..91a12dd0a9 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,8 @@
 import os
 
+import matplotlib.pyplot as plt
+plt.rcParams.update({'figure.max_open_warning': 0})
+
 from hypothesis import settings, Verbosity
 import pytest
 
diff --git a/tests/test__minhash.py b/tests/test__minhash.py
index dbad4bba6b..96b26e8e90 100644
--- a/tests/test__minhash.py
+++ b/tests/test__minhash.py
@@ -49,7 +49,7 @@
 )
 from sourmash import signature
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 # add:
 # * get default params from Python
diff --git a/tests/test_api.py b/tests/test_api.py
index fd8a66cabd..8be3396085 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -1,7 +1,7 @@
 import pytest
 import sourmash
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 
 def test_sourmash_signature_api():
diff --git a/tests/test_bugs.py b/tests/test_bugs.py
index 20608f0a0d..4870f0faf3 100644
--- a/tests/test_bugs.py
+++ b/tests/test_bugs.py
@@ -1,4 +1,4 @@
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 def test_bug_781():
     with utils.TempDirectory() as location:
diff --git a/tests/test_cmd_signature.py b/tests/test_cmd_signature.py
index a1925a9d76..a65270ab0c 100644
--- a/tests/test_cmd_signature.py
+++ b/tests/test_cmd_signature.py
@@ -7,7 +7,7 @@
 
 import pytest
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 import sourmash
 
 ## command line tests
diff --git a/tests/test_compare.py b/tests/test_compare.py
index 9555993c6b..005c96c575 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -6,7 +6,7 @@
 
 import sourmash
 from sourmash.compare import compare_all_pairs, compare_parallel, compare_serial
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 
 @pytest.fixture()
diff --git a/tests/test_deprecated.py b/tests/test_deprecated.py
index 9e69f50694..fdd9acc53c 100644
--- a/tests/test_deprecated.py
+++ b/tests/test_deprecated.py
@@ -1,5 +1,5 @@
 from sourmash import signature
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 def test_load_textmode(track_abundance):
     # ijson required a file in binary mode or bytes,
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_index.py b/tests/test_index.py
index 5933004c12..7174db282d 100644
--- a/tests/test_index.py
+++ b/tests/test_index.py
@@ -6,7 +6,8 @@
 from sourmash import load_one_signature, SourmashSignature
 from sourmash.index import LinearIndex
 from sourmash.sbt import SBT, GraphFactory, Leaf
-from . import sourmash_tst_utils as utils
+
+import sourmash_tst_utils as utils
 
 
 def test_simple_index(n_children):
diff --git a/tests/test_jaccard.py b/tests/test_jaccard.py
index 475f73a482..709f71b3aa 100644
--- a/tests/test_jaccard.py
+++ b/tests/test_jaccard.py
@@ -5,7 +5,8 @@
 
 import pytest
 from sourmash import MinHash
-from . import sourmash_tst_utils as utils
+
+import sourmash_tst_utils as utils
 
 # below, 'track_abundance' is toggled to both True and False by py.test --
 # see conftest.py.
diff --git a/tests/test_lca.py b/tests/test_lca.py
index e530588197..2226c473ae 100644
--- a/tests/test_lca.py
+++ b/tests/test_lca.py
@@ -7,7 +7,7 @@
 import pytest
 import glob
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 import sourmash
 from sourmash import load_one_signature, SourmashSignature
 
diff --git a/tests/test_nodegraph.py b/tests/test_nodegraph.py
index 94750c301e..68283dd620 100644
--- a/tests/test_nodegraph.py
+++ b/tests/test_nodegraph.py
@@ -4,7 +4,7 @@
 
 from sourmash.nodegraph import Nodegraph, extract_nodegraph_info, calc_expected_collisions
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 
 def test_nodegraph_to_khmer_basic():
diff --git a/tests/test_sbt.py b/tests/test_sbt.py
index 4d7bb51db6..2ae5f6c5e6 100644
--- a/tests/test_sbt.py
+++ b/tests/test_sbt.py
@@ -13,7 +13,7 @@
 from sourmash.sbt_storage import (FSStorage, RedisStorage,
                                   IPFSStorage, ZipStorage)
 
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 
 def test_simple(n_children):
diff --git a/tests/test_signature.py b/tests/test_signature.py
index e3054d76e5..18654ce8a0 100644
--- a/tests/test_signature.py
+++ b/tests/test_signature.py
@@ -5,7 +5,7 @@
 import sourmash
 from sourmash.signature import SourmashSignature, save_signatures, \
     load_signatures, load_one_signature
-from . import sourmash_tst_utils as utils
+import sourmash_tst_utils as utils
 
 
 def test_compare(track_abundance):
diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
index 6cde335e23..331a53da5d 100644
--- a/tests/test_sourmash.py
+++ b/tests/test_sourmash.py
@@ -12,7 +12,8 @@
 import sys
 import zipfile
 
-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/tests/test_sourmash_compute.py b/tests/test_sourmash_compute.py
index 659d83b020..44210fcf5e 100644
--- a/tests/test_sourmash_compute.py
+++ b/tests/test_sourmash_compute.py
@@ -10,7 +10,8 @@
 import csv
 import pytest
 
-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/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 b859ff129f..dfa82b59f1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,28 +1,167 @@
 [tox]
-envlist=py39,py38,py37,docs
+envlist =
+  py39,
+  coverage,
+  docs,
+  package_description
+  py38,
+  py37,
+#  fix_lint,
+minversion = 3.12
+isolated_build = true
+skip_missing_interpreters = true
 
 [testenv]
-passenv = CI TRAVIS TRAVIS_* PYTHONDEVMODE
-whitelist_externals=
-  make
-extras = 
-  test
-  storage
-deps=
-  pip>=19.3.1
-  codecov
-commands=
-  make coverage
+description = run the tests with pytest under {basepython}
+setenv =
+    PIP_DISABLE_VERSION_CHECK = 1
+    COVERAGE_FILE = {toxworkdir}/.coverage.{envname}
+    VIRTUALENV_NO_DOWNLOAD = 1
+    PIP_EXTRA_INDEX_URL = https://antocuni.github.io/pypy-wheels/manylinux2010
+passenv =
+    CURL_CA_BUNDLE
+    http_proxy
+    https_proxy
+    no_proxy
+    REQUESTS_CA_BUNDLE
+    SSL_CERT_FILE
+    PYTEST_*
+    PIP_CACHE_DIR
+    CI
+    TRAVIS
+    TRAVIS_*
+    PYTHONDEVMODE
+deps =
+    pip>=19.3.1
+extras =
+    test
+    storage
+changedir = tests
+commands = pytest \
+           --cov "{envsitepackagesdir}/sourmash" \
+           --cov-config "{toxinidir}/tox.ini" \
+           --junitxml {toxworkdir}/junit.{envname}.xml \
+           {posargs:.}
+
+[testenv:pypy]
+deps =
+  pip >= 19.3.1
+  psutil <= 5.6.7
 
 [testenv:docs]
-basepython = python3.7
+description = invoke sphinx-build to build the HTML docs
+basepython = python3.8
 extras = doc
+whitelist_externals = pandoc
 passenv = HOME
+changedir = {toxinidir}
+#commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -W -bhtml {posargs}
 commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -bhtml {posargs}
            python -c 'import pathlib; print("documentation available under file://\{0\}".format(pathlib.Path(r"{toxworkdir}") / "docs_out" / "index.html"))'
 
+[testenv:package_description]
+description = check that the long description is valid
+basepython = python3.8
+deps = twine >= 1.12.1
+       # TODO installing readme-renderer[md] should not be necessary
+       readme-renderer[md] >= 24.0
+       pip >= 19.1
+skip_install = true
+changedir = {toxinidir}
+extras =
+commands = pip wheel -w {envtmpdir}/build --no-deps .
+           twine check {envtmpdir}/build/*
+
+[testenv:fix_lint]
+description = format the code base to adhere to our styles, and complain about what we cannot do automatically
+basepython = python3.8
+passenv = {[testenv]passenv}
+          # without PROGRAMDATA cloning using git for Windows will fail with an `error setting certificate verify locations` error
+          PROGRAMDATA
+          PRE_COMMIT_HOME
+extras = lint
+deps = pre-commit>=2
+skip_install = True
+commands = pre-commit run --all-files --show-diff-on-failure {posargs}
+           python -c 'import pathlib; print("hint: run \{\} install to add checks as pre-commit hook".format(pathlib.Path(r"{envdir}") / "bin" / "pre-commit"))'
+
+[testenv:coverage]
+description = [run locally after tests]: combine coverage data and create report;
+              generates a diff coverage against origin/latest (can be changed by setting DIFF_AGAINST env var)
+deps = {[testenv]deps}
+       coverage >= 5.0.1
+       diff_cover
+skip_install = True
+passenv = {[testenv]passenv}
+          DIFF_AGAINST
+setenv = COVERAGE_FILE={toxworkdir}/.coverage
+commands = coverage combine
+           coverage report -i -m
+           coverage xml -i -o {toxworkdir}/coverage.xml
+           coverage html -i -d {toxworkdir}/htmlcov
+           diff-cover --compare-branch {env:DIFF_AGAINST:origin/latest} {toxworkdir}/coverage.xml
+depends = py39, py38, py37, pypy3
+parallel_show_output = True
+
+[testenv:codecov]
+description = [only run on CI]: upload coverage data to codecov (depends on coverage running first)
+passenv = {[testenv]passenv}
+          CODECOV_TOKEN
+deps = codecov
+skip_install = True
+changedir = {toxinidir}
+depends = coverage
+commands = codecov --file "{toxworkdir}/coverage.xml" {posargs}
+
+[testenv:X]
+description = print the positional arguments passed in with echo
+commands = echo {posargs}
+
+[coverage:run]
+branch = true
+parallel = true
+
+[coverage:report]
+skip_covered = True
+show_missing = True
+exclude_lines =
+    \#\s*pragma: no cover
+    ^\s*raise AssertionError\b
+    ^\s*raise NotImplementedError\b
+    ^\s*return NotImplemented\b
+    ^\s*raise$
+    ^if __name__ == ['"]__main__['"]:$
+
+[coverage:paths]
+source = src/sourmash/
+         */.tox/*/lib/python*/site-packages/sourmash
+         */.tox/pypy*/site-packages/sourmash
+         */.tox\*\Lib\site-packages\sourmash
+         */src/sourmash
+         *\src\sourmash
+
 [gh-actions]
 python =
-  3.7: py37,docs
-  3.8: py38
-  3.9: py39
+  3.7: py37, docs, package_description, coverage, codecov
+  3.8: py38, coverage, codecov
+  3.9: py39, coverage, codecov
+
+[flake8]
+max-complexity = 22
+max-line-length = 99
+ignore = E203, W503, C901, E402, B011
+
+[pep8]
+max-line-length = 99
+
+[testenv:dev]
+description = dev environment with all deps at {envdir}
+extras =
+  test
+  10x
+  storage
+  doc
+deps = {[testenv]deps}
+usedevelop = True
+commands = python -m pip list --format=columns
+           python -c "print(r'{envpython}')"