diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 2cab74ba..65af5d3e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -9,7 +9,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.8", "3.10", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -31,9 +31,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e '.[tests]'
 
       - name: Test with pytest
         run: |
-          pip install PyYAML pytest pytest-cov pytest-benchmark mock
           pytest --cov=jcvi tests
diff --git a/.gitignore b/.gitignore
index 4855cfe6..41823e69 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,15 @@
-# Created by http://www.gitignore.io
+# Mac stuff
+.DS_Store
+
+# Development
+dev/
+
+# Versioning
+src/jcvi/_version.py
+
+# Ignore Cython generated C files
+src/jcvi/assembly/chic.c
+src/jcvi/formats/cblast.c
 
 # Dev testing
 dev
@@ -7,6 +18,7 @@ dev
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
@@ -17,12 +29,15 @@ env/
 build/
 develop-eggs/
 dist/
+downloads/
 eggs/
+.eggs/
 lib/
 lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -35,9 +50,12 @@ pip-delete-this-directory.txt
 htmlcov/
 .tox/
 .coverage
+.coverage.*
 .cache
 nosetests.xml
 coverage.xml
+*.cover
+.hypothesis/
 
 # Translations
 *.mo
@@ -51,3 +69,4 @@ docs/_build/
 
 # gffutils temp DB file
 *.db
+src/jcvi/version.py
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 708975ee..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,4 +0,0 @@
-recursive-exclude .github *
-recursive-exclude docker *
-recursive-exclude tests *
-exclude .*
\ No newline at end of file
diff --git a/README.md b/README.md
index e5e9c9ec..e6767f86 100644
--- a/README.md
+++ b/README.md
@@ -104,49 +104,77 @@ full-fledged applications.
 
 ## Dependencies
 
-Following are a list of third-party python packages that are used by
-some routines in the library. These dependencies are _not_ mandatory
-since they are only used by a few modules.
+JCVI requires Python3 between v3.8 and v3.12.
 
-- [Biopython](http://www.biopython.org)
-- [numpy](http://numpy.scipy.org)
-- [matplotlib](http://matplotlib.org/)
+A few modules may ask for locations of external programs,
+if the executable cannot be found in your `PATH`. 
 
-There are other Python modules here and there in various scripts. The
-best way is to install them via `pip install` when you see
-`ImportError`.
+The external programs that are often used are:
+
+- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)
+- [BEDTOOLS](http://code.google.com/p/bedtools/)
+- [EMBOSS](http://emboss.sourceforge.net/)
 
 ## Installation
 
-The easiest way is to install it via PyPI:
+**Installing JCVI in a Conda environment:**
 
-```console
-pip install jcvi
+You can create a Conda environment with Python 3.12 and basic dependencies for JCVI using the YAML files in this repo.
+
+If you are new to Conda, we recommend the [Miniforge](https://conda-forge.org/download/) distribution.
+
+
+```bash
+conda env create -f environment.yml
+
+conda activate jcvi
 ```
 
-To install the development version:
+Note: If you are using a Mac with an ARM64 (Apple Silicon) processor, some dependencies are not currently available from Bioconda for this architecture. 
 
-```console
+You can instead create a virtual OSX64 (intel) env like this:
+
+```bash
+conda env create -f env_osx64.yml
+
+conda activate jcvi-osx64
+```
+
+After activating the Conda environment install JCVI using one of the following options.
+
+
+**Installation options:**  
+
+1) Use pip to install the latest development version directly from this repo.
+
+```bash
 pip install git+git://github.com/tanghaibao/jcvi.git
 ```
 
-Alternatively, if you want to install manually:
+2) Install latest release from PyPi.
 
-```console
-cd ~/code  # or any directory of your choice
-git clone git://github.com/tanghaibao/jcvi.git
-pip install -e .
+```bash
+pip install jcvi
 ```
 
-In addition, a few module might ask for locations of external programs,
-if the extended cannot be found in your `PATH`. The external programs
-that are often used are:
+3) Alternatively, if you want to install in development mode.
 
-- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)
-- [BEDTOOLS](http://code.google.com/p/bedtools/)
-- [EMBOSS](http://emboss.sourceforge.net/)
+```bash
+git clone git://github.com/tanghaibao/jcvi.git && cd jcvi
+pip install -e '.[tests]'
+```
+
+**Test Installation:**  
+
+If installed successfully, you can check the version with:
+
+```bash
+jcvi --version
+```
+
+Use `python -m` to call any of the modules installed with JCVI.
 
-Most of the scripts in this package contains multiple actions. To use
+Most of the modules in this package contains multiple actions. To use
 the `fasta` example:
 
 ```console
diff --git a/build.py b/build.py
new file mode 100644
index 00000000..ea014d38
--- /dev/null
+++ b/build.py
@@ -0,0 +1,9 @@
+import subprocess
+from hatchling.builders.hooks.plugin.interface import BuildHookInterface
+
+
+class CustomBuildHook(BuildHookInterface):
+    def initialize(self, version, build_data):
+        # Run setup.py build_ext before main build
+        subprocess.check_call(["python", "setup.py", "build_ext", "--inplace"])
+        return super().initialize(version, build_data)
diff --git a/env_osx64.yml b/env_osx64.yml
new file mode 100644
index 00000000..74bf21e8
--- /dev/null
+++ b/env_osx64.yml
@@ -0,0 +1,14 @@
+name: jcvi-osx64
+channels:
+  - conda-forge/osx-64
+  - bioconda/osx-64
+dependencies:
+  - python 3.12
+  - bedtools
+  - imagemagick
+  - libmagic  # System-level magic library
+  - wand  # Python bindings for ImageMagick
+  - pip
+  - pip:
+      - hatch
+      - pytest
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 00000000..f47d16c7
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,14 @@
+name: jcvi
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python 3.12
+  - bedtools
+  - imagemagick
+  - libmagic  # System-level magic library
+  - wand  # Python bindings for ImageMagick
+  - pip
+  - pip:
+      - pytest
+      - hatch
diff --git a/jcvi/__init__.py b/jcvi/__init__.py
deleted file mode 100644
index 89bf10ae..00000000
--- a/jcvi/__init__.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from datetime import datetime
-from importlib.metadata import version, PackageNotFoundError
-
-
-__author__ = (
-    "Haibao Tang",
-    "Vivek Krishnakumar",
-    "Xingtan Zhang",
-    "Won Cheol Yim",
-)
-__copyright__ = f"Copyright (c) 2010-{datetime.now().year}, Haibao Tang"
-__email__ = "tanghaibao@gmail.com"
-__license__ = "BSD"
-__status__ = "Development"
-
-
-try:
-    VERSION = version(__name__)
-except PackageNotFoundError:  # pragma: no cover
-    try:
-        from .version import version as VERSION  # noqa
-    except ImportError as exc:  # pragma: no cover
-        raise ImportError(
-            "Failed to find (autogenerated) version.py. "
-            "This might be because you are installing from GitHub's tarballs, "
-            "use the PyPI ones."
-        ) from exc
-__version__ = VERSION
diff --git a/pyproject.toml b/pyproject.toml
index 3adcf6e8..a87b262b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,15 +1,110 @@
+# Specifies the build system requirements and backend
 [build-system]
 requires = [
-    "Cython",
-    "numpy",
-    "setuptools",
-    "setuptools_scm[toml]",
-    "setuptools_scm_git_archive",
-    "wheel",
-]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools_scm]
-write_to = "jcvi/version.py"
-git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"
-version_scheme = "no-guess-dev"
\ No newline at end of file
+    "hatchling",  # Build backend
+    "hatch-vcs",  # Version control system plugin for dynamic versioning
+    "setuptools",  # Setuptools for compiling C extensions
+    "cython",  # Cython for compiling C extensions
+    "numpy",      # NumPy for numerical operations and C extension includes
+]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.hooks.custom]
+path = "build.py"
+
+# Project metadata and configuration
+[project]
+name = "jcvi"
+description = "Python utility libraries on genome assembly, annotation and comparative genomics"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "BSD"}
+authors = [
+    {name = "Haibao Tang", email = "tanghaibao@gmail.com"},
+    {name = "Vivek Krishnakumar"},
+    {name = "Jingping Li"}
+]
+
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+
+dependencies = [
+    "biopython",
+    "boto3",
+    "brewer2mpl",
+    "CrossMap",
+    "cython",
+    "deap",
+    "ete3",
+    "ftpretty",
+    "genomepy",
+    "gffutils",
+    "goatools",
+    "graphviz",
+    "jinja2",
+    "matplotlib",
+    "more-itertools",
+    "natsort",
+    "networkx",
+    "numpy<2",
+    "ortools",
+    "pybedtools",
+    "pyefd",
+    "pypdf",
+    "pytesseract",
+    "rich",
+    "scikit-image",
+    "scipy",
+    "seaborn",
+    "Wand",
+    "webcolors"
+]
+
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = [
+    "mock",
+    "pytest-benchmark",
+    "pytest-cov",
+    "pytest",
+    "PyYAML",
+]
+
+[project.urls]
+homepage = "http://github.com/tanghaibao/jcvi"
+
+# Command-line script entry point
+[project.scripts]
+jcvi = "jcvi.cli:main"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build]
+packages = ["src/jcvi"]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/jcvi/_version.py"
+
+[tool.hatch.version.vcs]
+tag-pattern = "v*"
+fallback-version = "0.0.0"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/**/*.py",
+    "src/**/*.pyx",
+    "README.md",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/jcvi"]
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 547730ae..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,64 +0,0 @@
-[metadata]
-name = jcvi
-author = Haibao Tang, Vivek Krishnakumar, Jingping Li
-author_email = tanghaibao@gmail.com
-license = BSD
-description = Python utility libraries on genome assembly, annotation and comparative genomics
-url = http://github.com/tanghaibao/jcvi
-long_description = file: README.md
-long_description_content_type = text/markdown
-classifiers =
-    Development Status :: 4 - Beta
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: BSD License
-    Programming Language :: Python
-    Programming Language :: Python :: 3
-    Topic :: Scientific/Engineering :: Bio-Informatics
-
-[options]
-packages =
-    jcvi
-    jcvi.formats
-    jcvi.variation
-    jcvi.compara
-    jcvi.assembly
-    jcvi.projects
-    jcvi.algorithms
-    jcvi.annotation
-    jcvi.utils
-    jcvi.graphics
-    jcvi.apps
-    jcvi.utils.data
-zip_safe = False
-setup_requires = setuptools>=18.0; cython
-install_requires =
-    CrossMap
-    Wand
-    biopython
-    boto3
-    brewer2mpl
-    deap
-    ete3
-    ftpretty
-    gffutils
-    goatools
-    genomepy
-    graphviz
-    jinja2
-    matplotlib
-    more-itertools
-    natsort
-    networkx
-    numpy<2
-    ortools
-    pybedtools
-    pyefd
-    pypdf
-    pytesseract
-    rich
-    scikit-image
-    scipy
-    seaborn
-    webcolors
-include_package_data = True
-tests_require = PyYAML; pytest; pytest-cov; pytest-benchmark; mock
diff --git a/setup.py b/setup.py
index 09fe097b..5fe88135 100644
--- a/setup.py
+++ b/setup.py
@@ -1,26 +1,26 @@
 #!/usr/bin/env python
 
-"""Package setup"""
+"""Package setup for Cython extensions only"""
 
 from Cython.Build import build_ext
 from setuptools import setup, Extension
-
 import numpy as np
 
 ext_modules = [
     Extension(
         "jcvi.assembly.chic",
-        ["jcvi/assembly/chic.pyx"],
+        ["src/jcvi/assembly/chic.pyx"],
         include_dirs=[np.get_include()],
         extra_compile_args=["-O3"],
     ),
     Extension(
-        "jcvi.formats.cblast", ["jcvi/formats/cblast.pyx"], extra_compile_args=["-O3"]
+        "jcvi.formats.cblast",
+        ["src/jcvi/formats/cblast.pyx"],
+        extra_compile_args=["-O3"],
     ),
 ]
 
-if __name__ == "__main__":
-    setup(
-        cmdclass={"build_ext": build_ext},
-        ext_modules=ext_modules,
-    )
+setup(
+    ext_modules=ext_modules,
+    cmdclass={"build_ext": build_ext},
+)
diff --git a/src/jcvi/__init__.py b/src/jcvi/__init__.py
new file mode 100644
index 00000000..e03ec50e
--- /dev/null
+++ b/src/jcvi/__init__.py
@@ -0,0 +1,21 @@
+from datetime import datetime
+
+__author__ = (
+    "Haibao Tang",
+    "Vivek Krishnakumar",
+    "Xingtan Zhang",
+    "Won Cheol Yim",
+)
+__copyright__ = f"Copyright (c) 2010-{datetime.now().year}, Haibao Tang"
+__email__ = "tanghaibao@gmail.com"
+__license__ = "BSD"
+__status__ = "Development"
+
+try:
+    from ._version import __version__  # noqa
+except ImportError as exc:  # pragma: no cover
+    raise ImportError(
+        "Failed to find (autogenerated) _version.py. "
+        "This might be because you are installing from GitHub's tarballs, "
+        "use the PyPI ones."
+    ) from exc
diff --git a/jcvi/algorithms/__init__.py b/src/jcvi/algorithms/__init__.py
similarity index 100%
rename from jcvi/algorithms/__init__.py
rename to src/jcvi/algorithms/__init__.py
diff --git a/jcvi/algorithms/__main__.py b/src/jcvi/algorithms/__main__.py
similarity index 100%
rename from jcvi/algorithms/__main__.py
rename to src/jcvi/algorithms/__main__.py
diff --git a/jcvi/algorithms/ec.py b/src/jcvi/algorithms/ec.py
similarity index 100%
rename from jcvi/algorithms/ec.py
rename to src/jcvi/algorithms/ec.py
diff --git a/jcvi/algorithms/formula.py b/src/jcvi/algorithms/formula.py
similarity index 100%
rename from jcvi/algorithms/formula.py
rename to src/jcvi/algorithms/formula.py
diff --git a/jcvi/algorithms/graph.py b/src/jcvi/algorithms/graph.py
similarity index 100%
rename from jcvi/algorithms/graph.py
rename to src/jcvi/algorithms/graph.py
diff --git a/jcvi/algorithms/lis.py b/src/jcvi/algorithms/lis.py
similarity index 100%
rename from jcvi/algorithms/lis.py
rename to src/jcvi/algorithms/lis.py
diff --git a/jcvi/algorithms/lpsolve.py b/src/jcvi/algorithms/lpsolve.py
similarity index 100%
rename from jcvi/algorithms/lpsolve.py
rename to src/jcvi/algorithms/lpsolve.py
diff --git a/jcvi/algorithms/matrix.py b/src/jcvi/algorithms/matrix.py
similarity index 100%
rename from jcvi/algorithms/matrix.py
rename to src/jcvi/algorithms/matrix.py
diff --git a/jcvi/algorithms/maxsum.py b/src/jcvi/algorithms/maxsum.py
similarity index 100%
rename from jcvi/algorithms/maxsum.py
rename to src/jcvi/algorithms/maxsum.py
diff --git a/jcvi/algorithms/supermap.py b/src/jcvi/algorithms/supermap.py
similarity index 100%
rename from jcvi/algorithms/supermap.py
rename to src/jcvi/algorithms/supermap.py
diff --git a/jcvi/algorithms/tsp.py b/src/jcvi/algorithms/tsp.py
similarity index 100%
rename from jcvi/algorithms/tsp.py
rename to src/jcvi/algorithms/tsp.py
diff --git a/jcvi/annotation/__init__.py b/src/jcvi/annotation/__init__.py
similarity index 100%
rename from jcvi/annotation/__init__.py
rename to src/jcvi/annotation/__init__.py
diff --git a/jcvi/annotation/__main__.py b/src/jcvi/annotation/__main__.py
similarity index 100%
rename from jcvi/annotation/__main__.py
rename to src/jcvi/annotation/__main__.py
diff --git a/jcvi/annotation/ahrd.py b/src/jcvi/annotation/ahrd.py
similarity index 100%
rename from jcvi/annotation/ahrd.py
rename to src/jcvi/annotation/ahrd.py
diff --git a/jcvi/annotation/automaton.py b/src/jcvi/annotation/automaton.py
similarity index 100%
rename from jcvi/annotation/automaton.py
rename to src/jcvi/annotation/automaton.py
diff --git a/jcvi/annotation/depth.py b/src/jcvi/annotation/depth.py
similarity index 100%
rename from jcvi/annotation/depth.py
rename to src/jcvi/annotation/depth.py
diff --git a/jcvi/annotation/evm.py b/src/jcvi/annotation/evm.py
similarity index 100%
rename from jcvi/annotation/evm.py
rename to src/jcvi/annotation/evm.py
diff --git a/jcvi/annotation/maker.py b/src/jcvi/annotation/maker.py
similarity index 100%
rename from jcvi/annotation/maker.py
rename to src/jcvi/annotation/maker.py
diff --git a/jcvi/annotation/pasa.py b/src/jcvi/annotation/pasa.py
similarity index 100%
rename from jcvi/annotation/pasa.py
rename to src/jcvi/annotation/pasa.py
diff --git a/jcvi/annotation/qc.py b/src/jcvi/annotation/qc.py
similarity index 100%
rename from jcvi/annotation/qc.py
rename to src/jcvi/annotation/qc.py
diff --git a/jcvi/annotation/reformat.py b/src/jcvi/annotation/reformat.py
similarity index 100%
rename from jcvi/annotation/reformat.py
rename to src/jcvi/annotation/reformat.py
diff --git a/jcvi/annotation/stats.py b/src/jcvi/annotation/stats.py
similarity index 100%
rename from jcvi/annotation/stats.py
rename to src/jcvi/annotation/stats.py
diff --git a/jcvi/annotation/train.py b/src/jcvi/annotation/train.py
similarity index 100%
rename from jcvi/annotation/train.py
rename to src/jcvi/annotation/train.py
diff --git a/jcvi/annotation/trinity.py b/src/jcvi/annotation/trinity.py
similarity index 100%
rename from jcvi/annotation/trinity.py
rename to src/jcvi/annotation/trinity.py
diff --git a/jcvi/apps/__init__.py b/src/jcvi/apps/__init__.py
similarity index 100%
rename from jcvi/apps/__init__.py
rename to src/jcvi/apps/__init__.py
diff --git a/jcvi/apps/__main__.py b/src/jcvi/apps/__main__.py
similarity index 100%
rename from jcvi/apps/__main__.py
rename to src/jcvi/apps/__main__.py
diff --git a/jcvi/apps/align.py b/src/jcvi/apps/align.py
similarity index 100%
rename from jcvi/apps/align.py
rename to src/jcvi/apps/align.py
diff --git a/jcvi/apps/base.py b/src/jcvi/apps/base.py
similarity index 99%
rename from jcvi/apps/base.py
rename to src/jcvi/apps/base.py
index cdee0853..2dcbe53b 100644
--- a/jcvi/apps/base.py
+++ b/src/jcvi/apps/base.py
@@ -29,6 +29,9 @@
 from typing import Any, Collection, List, Optional, Tuple, Union
 from urllib.parse import urlencode
 
+# from optparse import OptionParser as OptionP, OptionGroup, SUPPRESS_HELP
+
+
 from natsort import natsorted
 from rich.console import Console
 from rich.logging import RichHandler
@@ -1232,7 +1235,7 @@ def setup_magick_home():
             if op.isdir(magick_home):
                 os.environ["MAGICK_HOME"] = magick_home
         else:
-            logger.error("MAGICK_HOME not set")
+            logger.warning("MAGICK_HOME not set")
 
 
 def popen(cmd, debug=True, shell="/bin/bash"):
diff --git a/jcvi/apps/biomart.py b/src/jcvi/apps/biomart.py
similarity index 99%
rename from jcvi/apps/biomart.py
rename to src/jcvi/apps/biomart.py
index d5f9dcac..39ff2cb0 100644
--- a/jcvi/apps/biomart.py
+++ b/src/jcvi/apps/biomart.py
@@ -133,7 +133,7 @@ def __init__(
         port="80",
         name="ensembl",
         virtual_schema="default",
-        **attrib
+        **attrib,
     ):
 
         self.__dict__ = attrib.copy()
diff --git a/jcvi/apps/blastplus.py b/src/jcvi/apps/blastplus.py
similarity index 100%
rename from jcvi/apps/blastplus.py
rename to src/jcvi/apps/blastplus.py
diff --git a/jcvi/apps/bowtie.py b/src/jcvi/apps/bowtie.py
similarity index 100%
rename from jcvi/apps/bowtie.py
rename to src/jcvi/apps/bowtie.py
diff --git a/jcvi/apps/bwa.py b/src/jcvi/apps/bwa.py
similarity index 100%
rename from jcvi/apps/bwa.py
rename to src/jcvi/apps/bwa.py
diff --git a/jcvi/apps/cdhit.py b/src/jcvi/apps/cdhit.py
similarity index 100%
rename from jcvi/apps/cdhit.py
rename to src/jcvi/apps/cdhit.py
diff --git a/jcvi/apps/emboss.py b/src/jcvi/apps/emboss.py
similarity index 100%
rename from jcvi/apps/emboss.py
rename to src/jcvi/apps/emboss.py
diff --git a/jcvi/apps/fetch.py b/src/jcvi/apps/fetch.py
similarity index 100%
rename from jcvi/apps/fetch.py
rename to src/jcvi/apps/fetch.py
diff --git a/jcvi/apps/gbsubmit.py b/src/jcvi/apps/gbsubmit.py
similarity index 100%
rename from jcvi/apps/gbsubmit.py
rename to src/jcvi/apps/gbsubmit.py
diff --git a/jcvi/apps/gmap.py b/src/jcvi/apps/gmap.py
similarity index 100%
rename from jcvi/apps/gmap.py
rename to src/jcvi/apps/gmap.py
diff --git a/jcvi/apps/grid.py b/src/jcvi/apps/grid.py
similarity index 100%
rename from jcvi/apps/grid.py
rename to src/jcvi/apps/grid.py
diff --git a/jcvi/apps/lastz.py b/src/jcvi/apps/lastz.py
similarity index 100%
rename from jcvi/apps/lastz.py
rename to src/jcvi/apps/lastz.py
diff --git a/jcvi/apps/mask.py b/src/jcvi/apps/mask.py
similarity index 100%
rename from jcvi/apps/mask.py
rename to src/jcvi/apps/mask.py
diff --git a/jcvi/apps/phylo.py b/src/jcvi/apps/phylo.py
similarity index 99%
rename from jcvi/apps/phylo.py
rename to src/jcvi/apps/phylo.py
index e93485e7..15fd2564 100644
--- a/jcvi/apps/phylo.py
+++ b/src/jcvi/apps/phylo.py
@@ -106,7 +106,7 @@ def __init__(
         outtreefile,
         command=FPHYLIP_BIN("ffitch"),
         intreefile=None,
-        **kwargs
+        **kwargs,
     ):
 
         self.datafile = datafile
@@ -144,7 +144,7 @@ def __init__(
         a_ext,
         command=TREEFIX_BIN("treefix"),
         r=False,
-        **kwargs
+        **kwargs,
     ):
 
         self.input = input
@@ -175,7 +175,7 @@ def run_treefix(
     a_ext=".fasta",
     o_ext=".dnd",
     n_ext=".treefix.dnd",
-    **kwargs
+    **kwargs,
 ):
     """
     get the ML tree closest to the species tree
@@ -187,7 +187,7 @@ def run_treefix(
         a_ext=a_ext,
         o=o_ext,
         n=n_ext,
-        **kwargs
+        **kwargs,
     )
     outtreefile = input.rsplit(o_ext, 1)[0] + n_ext
     print("TreeFix:", cl, file=sys.stderr)
@@ -435,7 +435,7 @@ def build_ml_raxml(alignment, outfile, work_dir=".", **kwargs):
         num_replicates=100,
         name="aln",
         working_dir=raxml_work,
-        **kwargs
+        **kwargs,
     )
 
     logger.debug("Building ML tree using RAxML: %s" % raxml_cl)
@@ -1048,7 +1048,7 @@ def _draw_trees(
                 reroot=False,
                 supportcolor="r",
                 SH=SH,
-                **kwargs
+                **kwargs,
             )
 
         root.set_xlim(0, 1)
diff --git a/jcvi/apps/r.py b/src/jcvi/apps/r.py
similarity index 100%
rename from jcvi/apps/r.py
rename to src/jcvi/apps/r.py
diff --git a/jcvi/apps/restriction.py b/src/jcvi/apps/restriction.py
similarity index 100%
rename from jcvi/apps/restriction.py
rename to src/jcvi/apps/restriction.py
diff --git a/jcvi/apps/softlink.py b/src/jcvi/apps/softlink.py
similarity index 100%
rename from jcvi/apps/softlink.py
rename to src/jcvi/apps/softlink.py
diff --git a/jcvi/apps/uclust.py b/src/jcvi/apps/uclust.py
similarity index 100%
rename from jcvi/apps/uclust.py
rename to src/jcvi/apps/uclust.py
diff --git a/jcvi/apps/uniprot.py b/src/jcvi/apps/uniprot.py
similarity index 100%
rename from jcvi/apps/uniprot.py
rename to src/jcvi/apps/uniprot.py
diff --git a/jcvi/apps/vecscreen.py b/src/jcvi/apps/vecscreen.py
similarity index 100%
rename from jcvi/apps/vecscreen.py
rename to src/jcvi/apps/vecscreen.py
diff --git a/jcvi/apps/wga2ribbon.py b/src/jcvi/apps/wga2ribbon.py
similarity index 100%
rename from jcvi/apps/wga2ribbon.py
rename to src/jcvi/apps/wga2ribbon.py
diff --git a/jcvi/assembly/__init__.py b/src/jcvi/assembly/__init__.py
similarity index 100%
rename from jcvi/assembly/__init__.py
rename to src/jcvi/assembly/__init__.py
diff --git a/jcvi/assembly/__main__.py b/src/jcvi/assembly/__main__.py
similarity index 100%
rename from jcvi/assembly/__main__.py
rename to src/jcvi/assembly/__main__.py
diff --git a/jcvi/assembly/allmaps.py b/src/jcvi/assembly/allmaps.py
similarity index 100%
rename from jcvi/assembly/allmaps.py
rename to src/jcvi/assembly/allmaps.py
diff --git a/jcvi/assembly/allpaths.py b/src/jcvi/assembly/allpaths.py
similarity index 100%
rename from jcvi/assembly/allpaths.py
rename to src/jcvi/assembly/allpaths.py
diff --git a/jcvi/assembly/automaton.py b/src/jcvi/assembly/automaton.py
similarity index 100%
rename from jcvi/assembly/automaton.py
rename to src/jcvi/assembly/automaton.py
diff --git a/jcvi/assembly/base.py b/src/jcvi/assembly/base.py
similarity index 100%
rename from jcvi/assembly/base.py
rename to src/jcvi/assembly/base.py
diff --git a/jcvi/assembly/chic.pyx b/src/jcvi/assembly/chic.pyx
similarity index 100%
rename from jcvi/assembly/chic.pyx
rename to src/jcvi/assembly/chic.pyx
diff --git a/jcvi/assembly/coverage.py b/src/jcvi/assembly/coverage.py
similarity index 100%
rename from jcvi/assembly/coverage.py
rename to src/jcvi/assembly/coverage.py
diff --git a/jcvi/assembly/gaps.py b/src/jcvi/assembly/gaps.py
similarity index 100%
rename from jcvi/assembly/gaps.py
rename to src/jcvi/assembly/gaps.py
diff --git a/jcvi/assembly/geneticmap.py b/src/jcvi/assembly/geneticmap.py
similarity index 100%
rename from jcvi/assembly/geneticmap.py
rename to src/jcvi/assembly/geneticmap.py
diff --git a/jcvi/assembly/goldenpath.py b/src/jcvi/assembly/goldenpath.py
similarity index 100%
rename from jcvi/assembly/goldenpath.py
rename to src/jcvi/assembly/goldenpath.py
diff --git a/jcvi/assembly/hic.py b/src/jcvi/assembly/hic.py
similarity index 100%
rename from jcvi/assembly/hic.py
rename to src/jcvi/assembly/hic.py
diff --git a/jcvi/assembly/kmer.py b/src/jcvi/assembly/kmer.py
similarity index 100%
rename from jcvi/assembly/kmer.py
rename to src/jcvi/assembly/kmer.py
diff --git a/jcvi/assembly/opticalmap.py b/src/jcvi/assembly/opticalmap.py
similarity index 100%
rename from jcvi/assembly/opticalmap.py
rename to src/jcvi/assembly/opticalmap.py
diff --git a/jcvi/assembly/patch.py b/src/jcvi/assembly/patch.py
similarity index 100%
rename from jcvi/assembly/patch.py
rename to src/jcvi/assembly/patch.py
diff --git a/jcvi/assembly/postprocess.py b/src/jcvi/assembly/postprocess.py
similarity index 100%
rename from jcvi/assembly/postprocess.py
rename to src/jcvi/assembly/postprocess.py
diff --git a/jcvi/assembly/preprocess.py b/src/jcvi/assembly/preprocess.py
similarity index 100%
rename from jcvi/assembly/preprocess.py
rename to src/jcvi/assembly/preprocess.py
diff --git a/jcvi/assembly/sim.py b/src/jcvi/assembly/sim.py
similarity index 100%
rename from jcvi/assembly/sim.py
rename to src/jcvi/assembly/sim.py
diff --git a/jcvi/assembly/soap.py b/src/jcvi/assembly/soap.py
similarity index 100%
rename from jcvi/assembly/soap.py
rename to src/jcvi/assembly/soap.py
diff --git a/jcvi/assembly/syntenypath.py b/src/jcvi/assembly/syntenypath.py
similarity index 100%
rename from jcvi/assembly/syntenypath.py
rename to src/jcvi/assembly/syntenypath.py
diff --git a/src/jcvi/cli.py b/src/jcvi/cli.py
new file mode 100644
index 00000000..b55e091a
--- /dev/null
+++ b/src/jcvi/cli.py
@@ -0,0 +1,12 @@
+# cli.py
+import argparse
+from . import __version__
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--version', action='version', 
+                       version=f'%(prog)s {__version__}')
+    args = parser.parse_args()
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/jcvi/compara/__init__.py b/src/jcvi/compara/__init__.py
similarity index 100%
rename from jcvi/compara/__init__.py
rename to src/jcvi/compara/__init__.py
diff --git a/jcvi/compara/__main__.py b/src/jcvi/compara/__main__.py
similarity index 100%
rename from jcvi/compara/__main__.py
rename to src/jcvi/compara/__main__.py
diff --git a/jcvi/compara/base.py b/src/jcvi/compara/base.py
similarity index 100%
rename from jcvi/compara/base.py
rename to src/jcvi/compara/base.py
diff --git a/jcvi/compara/blastfilter.py b/src/jcvi/compara/blastfilter.py
similarity index 100%
rename from jcvi/compara/blastfilter.py
rename to src/jcvi/compara/blastfilter.py
diff --git a/jcvi/compara/catalog.py b/src/jcvi/compara/catalog.py
similarity index 100%
rename from jcvi/compara/catalog.py
rename to src/jcvi/compara/catalog.py
diff --git a/jcvi/compara/fractionation.py b/src/jcvi/compara/fractionation.py
similarity index 100%
rename from jcvi/compara/fractionation.py
rename to src/jcvi/compara/fractionation.py
diff --git a/jcvi/compara/ks.py b/src/jcvi/compara/ks.py
similarity index 100%
rename from jcvi/compara/ks.py
rename to src/jcvi/compara/ks.py
diff --git a/jcvi/compara/pad.py b/src/jcvi/compara/pad.py
similarity index 100%
rename from jcvi/compara/pad.py
rename to src/jcvi/compara/pad.py
diff --git a/jcvi/compara/pedigree.py b/src/jcvi/compara/pedigree.py
similarity index 100%
rename from jcvi/compara/pedigree.py
rename to src/jcvi/compara/pedigree.py
diff --git a/jcvi/compara/phylogeny.py b/src/jcvi/compara/phylogeny.py
similarity index 100%
rename from jcvi/compara/phylogeny.py
rename to src/jcvi/compara/phylogeny.py
diff --git a/jcvi/compara/quota.py b/src/jcvi/compara/quota.py
similarity index 100%
rename from jcvi/compara/quota.py
rename to src/jcvi/compara/quota.py
diff --git a/jcvi/compara/reconstruct.py b/src/jcvi/compara/reconstruct.py
similarity index 100%
rename from jcvi/compara/reconstruct.py
rename to src/jcvi/compara/reconstruct.py
diff --git a/jcvi/compara/synfind.py b/src/jcvi/compara/synfind.py
similarity index 100%
rename from jcvi/compara/synfind.py
rename to src/jcvi/compara/synfind.py
diff --git a/jcvi/compara/synteny.py b/src/jcvi/compara/synteny.py
similarity index 99%
rename from jcvi/compara/synteny.py
rename to src/jcvi/compara/synteny.py
index 190b5b36..2e51711c 100755
--- a/jcvi/compara/synteny.py
+++ b/src/jcvi/compara/synteny.py
@@ -41,7 +41,7 @@ def __init__(self, filename, defaultcolor="#fb8072", header=False):
         data = []
         highlight = []
         for row in fp:
-            if row[0] == '#':
+            if row[0] == "#":
                 continue
             hl = "*" in row
             # r* highlights the block in red color
diff --git a/jcvi/formats/__init__.py b/src/jcvi/formats/__init__.py
similarity index 100%
rename from jcvi/formats/__init__.py
rename to src/jcvi/formats/__init__.py
diff --git a/jcvi/formats/__main__.py b/src/jcvi/formats/__main__.py
similarity index 100%
rename from jcvi/formats/__main__.py
rename to src/jcvi/formats/__main__.py
diff --git a/jcvi/formats/agp.py b/src/jcvi/formats/agp.py
similarity index 100%
rename from jcvi/formats/agp.py
rename to src/jcvi/formats/agp.py
diff --git a/jcvi/formats/base.py b/src/jcvi/formats/base.py
similarity index 100%
rename from jcvi/formats/base.py
rename to src/jcvi/formats/base.py
diff --git a/jcvi/formats/bed.py b/src/jcvi/formats/bed.py
similarity index 100%
rename from jcvi/formats/bed.py
rename to src/jcvi/formats/bed.py
diff --git a/jcvi/formats/blast.py b/src/jcvi/formats/blast.py
similarity index 99%
rename from jcvi/formats/blast.py
rename to src/jcvi/formats/blast.py
index 75de55f6..ab632eec 100644
--- a/jcvi/formats/blast.py
+++ b/src/jcvi/formats/blast.py
@@ -23,10 +23,11 @@
 
 try:
     from .cblast import BlastLine
-except:
+except ImportError as e:
+    logger.error(f"Failed to import cblast: {e}")
     from .pyblast import BlastLine
 
-    logger.error("Fall back to Python implementation of BlastLine")
+    logger.warning("Fall back to Python implementation of BlastLine")
 
 
 class BlastSlow(LineFile):
diff --git a/jcvi/formats/cblast.pyx b/src/jcvi/formats/cblast.pyx
similarity index 100%
rename from jcvi/formats/cblast.pyx
rename to src/jcvi/formats/cblast.pyx
diff --git a/jcvi/formats/cdt.py b/src/jcvi/formats/cdt.py
similarity index 100%
rename from jcvi/formats/cdt.py
rename to src/jcvi/formats/cdt.py
diff --git a/jcvi/formats/chain.py b/src/jcvi/formats/chain.py
similarity index 100%
rename from jcvi/formats/chain.py
rename to src/jcvi/formats/chain.py
diff --git a/jcvi/formats/contig.py b/src/jcvi/formats/contig.py
similarity index 100%
rename from jcvi/formats/contig.py
rename to src/jcvi/formats/contig.py
diff --git a/jcvi/formats/coords.py b/src/jcvi/formats/coords.py
similarity index 100%
rename from jcvi/formats/coords.py
rename to src/jcvi/formats/coords.py
diff --git a/jcvi/formats/excel.py b/src/jcvi/formats/excel.py
similarity index 100%
rename from jcvi/formats/excel.py
rename to src/jcvi/formats/excel.py
diff --git a/jcvi/formats/fasta.py b/src/jcvi/formats/fasta.py
similarity index 100%
rename from jcvi/formats/fasta.py
rename to src/jcvi/formats/fasta.py
diff --git a/jcvi/formats/fastq.py b/src/jcvi/formats/fastq.py
similarity index 100%
rename from jcvi/formats/fastq.py
rename to src/jcvi/formats/fastq.py
diff --git a/jcvi/formats/genbank.py b/src/jcvi/formats/genbank.py
similarity index 100%
rename from jcvi/formats/genbank.py
rename to src/jcvi/formats/genbank.py
diff --git a/jcvi/formats/gff.py b/src/jcvi/formats/gff.py
similarity index 100%
rename from jcvi/formats/gff.py
rename to src/jcvi/formats/gff.py
diff --git a/jcvi/formats/html.py b/src/jcvi/formats/html.py
similarity index 100%
rename from jcvi/formats/html.py
rename to src/jcvi/formats/html.py
diff --git a/jcvi/formats/maf.py b/src/jcvi/formats/maf.py
similarity index 100%
rename from jcvi/formats/maf.py
rename to src/jcvi/formats/maf.py
diff --git a/jcvi/formats/obo.py b/src/jcvi/formats/obo.py
similarity index 100%
rename from jcvi/formats/obo.py
rename to src/jcvi/formats/obo.py
diff --git a/jcvi/formats/paf.py b/src/jcvi/formats/paf.py
similarity index 100%
rename from jcvi/formats/paf.py
rename to src/jcvi/formats/paf.py
diff --git a/jcvi/formats/pdf.py b/src/jcvi/formats/pdf.py
similarity index 100%
rename from jcvi/formats/pdf.py
rename to src/jcvi/formats/pdf.py
diff --git a/jcvi/formats/psl.py b/src/jcvi/formats/psl.py
similarity index 100%
rename from jcvi/formats/psl.py
rename to src/jcvi/formats/psl.py
diff --git a/jcvi/formats/pyblast.py b/src/jcvi/formats/pyblast.py
similarity index 100%
rename from jcvi/formats/pyblast.py
rename to src/jcvi/formats/pyblast.py
diff --git a/jcvi/formats/sam.py b/src/jcvi/formats/sam.py
similarity index 100%
rename from jcvi/formats/sam.py
rename to src/jcvi/formats/sam.py
diff --git a/jcvi/formats/sizes.py b/src/jcvi/formats/sizes.py
similarity index 100%
rename from jcvi/formats/sizes.py
rename to src/jcvi/formats/sizes.py
diff --git a/jcvi/formats/vcf.py b/src/jcvi/formats/vcf.py
similarity index 100%
rename from jcvi/formats/vcf.py
rename to src/jcvi/formats/vcf.py
diff --git a/jcvi/graphics/__init__.py b/src/jcvi/graphics/__init__.py
similarity index 100%
rename from jcvi/graphics/__init__.py
rename to src/jcvi/graphics/__init__.py
diff --git a/jcvi/graphics/__main__.py b/src/jcvi/graphics/__main__.py
similarity index 100%
rename from jcvi/graphics/__main__.py
rename to src/jcvi/graphics/__main__.py
diff --git a/jcvi/graphics/align.py b/src/jcvi/graphics/align.py
similarity index 100%
rename from jcvi/graphics/align.py
rename to src/jcvi/graphics/align.py
diff --git a/jcvi/graphics/assembly.py b/src/jcvi/graphics/assembly.py
similarity index 100%
rename from jcvi/graphics/assembly.py
rename to src/jcvi/graphics/assembly.py
diff --git a/jcvi/graphics/base.py b/src/jcvi/graphics/base.py
similarity index 98%
rename from jcvi/graphics/base.py
rename to src/jcvi/graphics/base.py
index c52a6d70..62113be5 100644
--- a/jcvi/graphics/base.py
+++ b/src/jcvi/graphics/base.py
@@ -1,9 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 -*-
 
-from os import remove
 import copy
-import logging
 import os.path as op
 import re
 import sys
@@ -348,11 +346,15 @@ def savefig(figname, dpi=150, iopts=None, cleanup=True, transparent=False):
     except:
         format = "pdf"
     try:
-        logging.debug(f"Matplotlib backend is: {mpl.get_backend()}")
-        logging.debug(f"Attempting save as: {figname}")
+        logger.debug(f"Matplotlib backend is: {mpl.get_backend()}")
+        logger.debug(f"Attempting save as: {figname}")
         plt.savefig(figname, dpi=dpi, format=format, transparent=transparent)
     except Exception as e:
-        logger.error("savefig failed with message:\n%s", e)
+        message = "savefig failed with message:"
+        message += "\n{0}".format(str(e))
+        logger.error(message)
+        logger.debug(f"Matplotlib backend is: {mpl.get_backend()}")
+        logger.debug(f"Attempted save as: {format}")
         logger.info("Try running again with --notex option to disable latex.")
         if op.exists(figname):
             if op.getsize(figname) < 1000:
diff --git a/jcvi/graphics/blastplot.py b/src/jcvi/graphics/blastplot.py
similarity index 100%
rename from jcvi/graphics/blastplot.py
rename to src/jcvi/graphics/blastplot.py
diff --git a/jcvi/graphics/chromosome.py b/src/jcvi/graphics/chromosome.py
similarity index 100%
rename from jcvi/graphics/chromosome.py
rename to src/jcvi/graphics/chromosome.py
diff --git a/jcvi/graphics/coverage.py b/src/jcvi/graphics/coverage.py
similarity index 100%
rename from jcvi/graphics/coverage.py
rename to src/jcvi/graphics/coverage.py
diff --git a/jcvi/graphics/dotplot.py b/src/jcvi/graphics/dotplot.py
similarity index 100%
rename from jcvi/graphics/dotplot.py
rename to src/jcvi/graphics/dotplot.py
diff --git a/jcvi/graphics/glyph.py b/src/jcvi/graphics/glyph.py
similarity index 99%
rename from jcvi/graphics/glyph.py
rename to src/jcvi/graphics/glyph.py
index d6de01a1..43a21b95 100644
--- a/jcvi/graphics/glyph.py
+++ b/src/jcvi/graphics/glyph.py
@@ -76,7 +76,7 @@ def __init__(self, ax, x1, x2, t, lw=0, fill=False, fc="lavender", **kwargs):
             t,
             ha="center",
             bbox=dict(boxstyle="round", fill=fill, fc=fc, lw=lw),
-            **kwargs
+            **kwargs,
         )
 
 
@@ -167,7 +167,7 @@ def __init__(
         size=12,
         zorder=4,
         fontweight="bold",
-        **kwargs
+        **kwargs,
     ):
         width, height = get_asymmetry(ax, radius)
         circle = Ellipse((x, y), width, height, fc=fc, ec=fc, zorder=zorder, **kwargs)
@@ -182,7 +182,7 @@ def __init__(
             size=size,
             zorder=zorder + 1,
             fontweight=fontweight,
-            **kwargs
+            **kwargs,
         )
 
 
@@ -273,7 +273,7 @@ def __init__(
         ec="gainsboro",
         lw=0,
         style="box",
-        **kwargs
+        **kwargs,
     ):
         """Draw a region that represent an interval feature, e.g. gene or repeat
 
@@ -302,7 +302,7 @@ def __init__(
                 fc=fc,
                 ec=ec,
                 lw=lw,
-                **kwargs
+                **kwargs,
             )
         else:
             patch = Rectangle(p1, width, height, fc=fc, ec=ec, lw=lw, **kwargs)
@@ -320,7 +320,7 @@ def __init__(
                         fc="w",
                         lw=0,
                         alpha=0.1,
-                        **kwargs
+                        **kwargs,
                     )
                 )
 
@@ -357,7 +357,7 @@ def __init__(
         tip=0.0025,
         color="k",
         shadow=False,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(ax)
         # Figure out the polygon vertices first
diff --git a/jcvi/graphics/grabseeds.py b/src/jcvi/graphics/grabseeds.py
similarity index 99%
rename from jcvi/graphics/grabseeds.py
rename to src/jcvi/graphics/grabseeds.py
index 14bcbe09..756a2d78 100644
--- a/jcvi/graphics/grabseeds.py
+++ b/src/jcvi/graphics/grabseeds.py
@@ -18,6 +18,7 @@
 
 from ..apps.base import setup_magick_home
 
+# Attempt to set MACICK_HOME ENV variable if imagemagick installed with homebrew on Mac
 setup_magick_home()
 
 from PIL.Image import open as iopen
diff --git a/jcvi/graphics/heatmap.py b/src/jcvi/graphics/heatmap.py
similarity index 100%
rename from jcvi/graphics/heatmap.py
rename to src/jcvi/graphics/heatmap.py
diff --git a/jcvi/graphics/histogram.py b/src/jcvi/graphics/histogram.py
similarity index 100%
rename from jcvi/graphics/histogram.py
rename to src/jcvi/graphics/histogram.py
diff --git a/jcvi/graphics/karyotype.py b/src/jcvi/graphics/karyotype.py
similarity index 100%
rename from jcvi/graphics/karyotype.py
rename to src/jcvi/graphics/karyotype.py
diff --git a/jcvi/graphics/landscape.py b/src/jcvi/graphics/landscape.py
similarity index 100%
rename from jcvi/graphics/landscape.py
rename to src/jcvi/graphics/landscape.py
diff --git a/jcvi/graphics/mummerplot.py b/src/jcvi/graphics/mummerplot.py
similarity index 100%
rename from jcvi/graphics/mummerplot.py
rename to src/jcvi/graphics/mummerplot.py
diff --git a/jcvi/graphics/ribbon.py b/src/jcvi/graphics/ribbon.py
similarity index 99%
rename from jcvi/graphics/ribbon.py
rename to src/jcvi/graphics/ribbon.py
index b21a78e8..42330cb2 100644
--- a/jcvi/graphics/ribbon.py
+++ b/src/jcvi/graphics/ribbon.py
@@ -21,11 +21,12 @@
 import numpy as np
 import sys
 
-#from jcvi.formats.base import DictFile
+# from jcvi.formats.base import DictFile
 from jcvi.apps.base import OptionParser, logger
 from jcvi.compara.synteny import BlockFile
 from jcvi.formats.bed import Bed
-from jcvi.graphics.base import (AbstractLayout,
+from jcvi.graphics.base import (
+    AbstractLayout,
     markup,
     mpl,
     Path,
@@ -33,7 +34,7 @@
     plt,
     savefig,
 )
-from jcvi.graphics.glyph import Glyph, RoundLabel #, GeneGlyph
+from jcvi.graphics.glyph import Glyph, RoundLabel  # , GeneGlyph
 from jcvi.utils.cbook import human_size
 
 
@@ -223,6 +224,7 @@ def __init__(
 
         def cv(t):
             return xstart + abs(t - startbp) / scale
+
         hidden = layout.hidden
 
         # Plot Chromosome Bar
@@ -368,7 +370,7 @@ def cv(t):
                         loc_label,
                         color="lightslategrey",
                         size=10,
-                        **kwargs
+                        **kwargs,
                     )
                 else:
                     ax.text(lx, ly, chr_label, color=layout.color, **kwargs)
@@ -817,7 +819,7 @@ def main():
 
     # Check for data files
     if len(args) != 3:
-        logger.error('Requires 3 data file args.')
+        logger.error("Requires 3 data file args.")
         sys.exit(not p.print_help())
 
     # Unpack data file paths
diff --git a/jcvi/graphics/synteny.py b/src/jcvi/graphics/synteny.py
similarity index 100%
rename from jcvi/graphics/synteny.py
rename to src/jcvi/graphics/synteny.py
diff --git a/jcvi/graphics/table.py b/src/jcvi/graphics/table.py
similarity index 100%
rename from jcvi/graphics/table.py
rename to src/jcvi/graphics/table.py
diff --git a/jcvi/graphics/tree.py b/src/jcvi/graphics/tree.py
similarity index 100%
rename from jcvi/graphics/tree.py
rename to src/jcvi/graphics/tree.py
diff --git a/jcvi/graphics/wheel.py b/src/jcvi/graphics/wheel.py
similarity index 100%
rename from jcvi/graphics/wheel.py
rename to src/jcvi/graphics/wheel.py
diff --git a/jcvi/projects/__init__.py b/src/jcvi/projects/__init__.py
similarity index 100%
rename from jcvi/projects/__init__.py
rename to src/jcvi/projects/__init__.py
diff --git a/jcvi/projects/__main__.py b/src/jcvi/projects/__main__.py
similarity index 100%
rename from jcvi/projects/__main__.py
rename to src/jcvi/projects/__main__.py
diff --git a/jcvi/projects/age.py b/src/jcvi/projects/age.py
similarity index 100%
rename from jcvi/projects/age.py
rename to src/jcvi/projects/age.py
diff --git a/jcvi/projects/allmaps.py b/src/jcvi/projects/allmaps.py
similarity index 99%
rename from jcvi/projects/allmaps.py
rename to src/jcvi/projects/allmaps.py
index edf714c3..a67d8067 100644
--- a/jcvi/projects/allmaps.py
+++ b/src/jcvi/projects/allmaps.py
@@ -256,7 +256,7 @@ def estimategaps(args):
         sum(markers) / 2,
         ypos + pad,
         "Distance: 1.29cM $\Leftrightarrow$ 211,824bp (6.1 cM/Mb)",
-        **fontprop
+        **fontprop,
     )
 
     ypos = y - pad
diff --git a/jcvi/projects/bites.py b/src/jcvi/projects/bites.py
similarity index 100%
rename from jcvi/projects/bites.py
rename to src/jcvi/projects/bites.py
diff --git a/jcvi/projects/ies.py b/src/jcvi/projects/ies.py
similarity index 100%
rename from jcvi/projects/ies.py
rename to src/jcvi/projects/ies.py
diff --git a/jcvi/projects/jcvi.py b/src/jcvi/projects/jcvi.py
similarity index 100%
rename from jcvi/projects/jcvi.py
rename to src/jcvi/projects/jcvi.py
diff --git a/jcvi/projects/misc.py b/src/jcvi/projects/misc.py
similarity index 100%
rename from jcvi/projects/misc.py
rename to src/jcvi/projects/misc.py
diff --git a/jcvi/projects/napus.py b/src/jcvi/projects/napus.py
similarity index 100%
rename from jcvi/projects/napus.py
rename to src/jcvi/projects/napus.py
diff --git a/jcvi/projects/pineapple.py b/src/jcvi/projects/pineapple.py
similarity index 100%
rename from jcvi/projects/pineapple.py
rename to src/jcvi/projects/pineapple.py
diff --git a/jcvi/projects/str.py b/src/jcvi/projects/str.py
similarity index 100%
rename from jcvi/projects/str.py
rename to src/jcvi/projects/str.py
diff --git a/jcvi/projects/sugarcane.py b/src/jcvi/projects/sugarcane.py
similarity index 100%
rename from jcvi/projects/sugarcane.py
rename to src/jcvi/projects/sugarcane.py
diff --git a/jcvi/projects/synfind.py b/src/jcvi/projects/synfind.py
similarity index 100%
rename from jcvi/projects/synfind.py
rename to src/jcvi/projects/synfind.py
diff --git a/jcvi/projects/tgbs.py b/src/jcvi/projects/tgbs.py
similarity index 100%
rename from jcvi/projects/tgbs.py
rename to src/jcvi/projects/tgbs.py
diff --git a/jcvi/projects/vanilla.py b/src/jcvi/projects/vanilla.py
similarity index 100%
rename from jcvi/projects/vanilla.py
rename to src/jcvi/projects/vanilla.py
diff --git a/jcvi/utils/__init__.py b/src/jcvi/utils/__init__.py
similarity index 100%
rename from jcvi/utils/__init__.py
rename to src/jcvi/utils/__init__.py
diff --git a/jcvi/utils/__main__.py b/src/jcvi/utils/__main__.py
similarity index 100%
rename from jcvi/utils/__main__.py
rename to src/jcvi/utils/__main__.py
diff --git a/jcvi/utils/aws.py b/src/jcvi/utils/aws.py
similarity index 100%
rename from jcvi/utils/aws.py
rename to src/jcvi/utils/aws.py
diff --git a/jcvi/utils/cbook.py b/src/jcvi/utils/cbook.py
similarity index 100%
rename from jcvi/utils/cbook.py
rename to src/jcvi/utils/cbook.py
diff --git a/jcvi/utils/console.py b/src/jcvi/utils/console.py
similarity index 100%
rename from jcvi/utils/console.py
rename to src/jcvi/utils/console.py
diff --git a/jcvi/utils/data/Airswing.ttf b/src/jcvi/utils/data/Airswing.ttf
similarity index 100%
rename from jcvi/utils/data/Airswing.ttf
rename to src/jcvi/utils/data/Airswing.ttf
diff --git a/jcvi/utils/data/Collegia.ttf b/src/jcvi/utils/data/Collegia.ttf
similarity index 100%
rename from jcvi/utils/data/Collegia.ttf
rename to src/jcvi/utils/data/Collegia.ttf
diff --git a/jcvi/utils/data/HookedUp.ttf b/src/jcvi/utils/data/HookedUp.ttf
similarity index 100%
rename from jcvi/utils/data/HookedUp.ttf
rename to src/jcvi/utils/data/HookedUp.ttf
diff --git a/jcvi/utils/data/Humor-Sans.ttf b/src/jcvi/utils/data/Humor-Sans.ttf
similarity index 100%
rename from jcvi/utils/data/Humor-Sans.ttf
rename to src/jcvi/utils/data/Humor-Sans.ttf
diff --git a/jcvi/utils/data/TREDs.meta.csv b/src/jcvi/utils/data/TREDs.meta.csv
similarity index 100%
rename from jcvi/utils/data/TREDs.meta.csv
rename to src/jcvi/utils/data/TREDs.meta.csv
diff --git a/jcvi/utils/data/__init__.py b/src/jcvi/utils/data/__init__.py
similarity index 100%
rename from jcvi/utils/data/__init__.py
rename to src/jcvi/utils/data/__init__.py
diff --git a/jcvi/utils/data/adapters.fasta b/src/jcvi/utils/data/adapters.fasta
similarity index 100%
rename from jcvi/utils/data/adapters.fasta
rename to src/jcvi/utils/data/adapters.fasta
diff --git a/jcvi/utils/data/blosum80.mat b/src/jcvi/utils/data/blosum80.mat
similarity index 100%
rename from jcvi/utils/data/blosum80.mat
rename to src/jcvi/utils/data/blosum80.mat
diff --git a/jcvi/utils/data/chrY.hg38.unique_ccn.gc b/src/jcvi/utils/data/chrY.hg38.unique_ccn.gc
similarity index 100%
rename from jcvi/utils/data/chrY.hg38.unique_ccn.gc
rename to src/jcvi/utils/data/chrY.hg38.unique_ccn.gc
diff --git a/jcvi/utils/data/colorchecker.txt b/src/jcvi/utils/data/colorchecker.txt
similarity index 100%
rename from jcvi/utils/data/colorchecker.txt
rename to src/jcvi/utils/data/colorchecker.txt
diff --git a/jcvi/utils/data/hg38.band.txt b/src/jcvi/utils/data/hg38.band.txt
similarity index 100%
rename from jcvi/utils/data/hg38.band.txt
rename to src/jcvi/utils/data/hg38.band.txt
diff --git a/jcvi/utils/data/hg38.chrom.sizes b/src/jcvi/utils/data/hg38.chrom.sizes
similarity index 100%
rename from jcvi/utils/data/hg38.chrom.sizes
rename to src/jcvi/utils/data/hg38.chrom.sizes
diff --git a/jcvi/utils/data/instance.json b/src/jcvi/utils/data/instance.json
similarity index 100%
rename from jcvi/utils/data/instance.json
rename to src/jcvi/utils/data/instance.json
diff --git a/jcvi/utils/db.py b/src/jcvi/utils/db.py
similarity index 100%
rename from jcvi/utils/db.py
rename to src/jcvi/utils/db.py
diff --git a/jcvi/utils/ez_setup.py b/src/jcvi/utils/ez_setup.py
similarity index 97%
rename from jcvi/utils/ez_setup.py
rename to src/jcvi/utils/ez_setup.py
index 65d53c8a..3dfd4d51 100644
--- a/jcvi/utils/ez_setup.py
+++ b/src/jcvi/utils/ez_setup.py
@@ -101,7 +101,9 @@ def has_wget():
     try:
         try:
             subprocess.check_call(cmd, stdout=devnull, stderr=devnull)
-        except FileNotFoundError:
+        except (FileNotFoundError, NotADirectoryError):
+            return False
+        except subprocess.CalledProcessError:
             return False
     finally:
         devnull.close()
diff --git a/jcvi/utils/grouper.py b/src/jcvi/utils/grouper.py
similarity index 100%
rename from jcvi/utils/grouper.py
rename to src/jcvi/utils/grouper.py
diff --git a/jcvi/utils/orderedcollections.py b/src/jcvi/utils/orderedcollections.py
similarity index 100%
rename from jcvi/utils/orderedcollections.py
rename to src/jcvi/utils/orderedcollections.py
diff --git a/jcvi/utils/range.py b/src/jcvi/utils/range.py
similarity index 100%
rename from jcvi/utils/range.py
rename to src/jcvi/utils/range.py
diff --git a/jcvi/utils/table.py b/src/jcvi/utils/table.py
similarity index 100%
rename from jcvi/utils/table.py
rename to src/jcvi/utils/table.py
diff --git a/jcvi/utils/taxonomy.py b/src/jcvi/utils/taxonomy.py
similarity index 100%
rename from jcvi/utils/taxonomy.py
rename to src/jcvi/utils/taxonomy.py
diff --git a/jcvi/utils/validator.py b/src/jcvi/utils/validator.py
similarity index 100%
rename from jcvi/utils/validator.py
rename to src/jcvi/utils/validator.py
diff --git a/jcvi/utils/webcolors.py b/src/jcvi/utils/webcolors.py
similarity index 100%
rename from jcvi/utils/webcolors.py
rename to src/jcvi/utils/webcolors.py
diff --git a/jcvi/variation/__init__.py b/src/jcvi/variation/__init__.py
similarity index 100%
rename from jcvi/variation/__init__.py
rename to src/jcvi/variation/__init__.py
diff --git a/jcvi/variation/__main__.py b/src/jcvi/variation/__main__.py
similarity index 100%
rename from jcvi/variation/__main__.py
rename to src/jcvi/variation/__main__.py
diff --git a/jcvi/variation/cnv.py b/src/jcvi/variation/cnv.py
similarity index 100%
rename from jcvi/variation/cnv.py
rename to src/jcvi/variation/cnv.py
diff --git a/jcvi/variation/deconvolute.py b/src/jcvi/variation/deconvolute.py
similarity index 100%
rename from jcvi/variation/deconvolute.py
rename to src/jcvi/variation/deconvolute.py
diff --git a/jcvi/variation/delly.py b/src/jcvi/variation/delly.py
similarity index 100%
rename from jcvi/variation/delly.py
rename to src/jcvi/variation/delly.py
diff --git a/jcvi/variation/impute.py b/src/jcvi/variation/impute.py
similarity index 100%
rename from jcvi/variation/impute.py
rename to src/jcvi/variation/impute.py
diff --git a/jcvi/variation/phase.py b/src/jcvi/variation/phase.py
similarity index 100%
rename from jcvi/variation/phase.py
rename to src/jcvi/variation/phase.py
diff --git a/jcvi/variation/snp.py b/src/jcvi/variation/snp.py
similarity index 100%
rename from jcvi/variation/snp.py
rename to src/jcvi/variation/snp.py
diff --git a/jcvi/variation/str.py b/src/jcvi/variation/str.py
similarity index 100%
rename from jcvi/variation/str.py
rename to src/jcvi/variation/str.py