Include missing files in sdist

[thatch]

Include missing files in sdist for #46

Tested with

++ mktemp -d
+ D=/tmp/tmp.SuiScHd1E5
+ trap 'rm -rf /tmp/tmp.SuiScHd1E5' EXIT
+ python -m venv /tmp/tmp.SuiScHd1E5
+ python setup.py sdist -d /tmp/tmp.SuiScHd1E5
running sdist
running egg_info
writing metabolisHMM.egg-info/PKG-INFO
writing dependency_links to metabolisHMM.egg-info/dependency_links.txt
writing requirements to metabolisHMM.egg-info/requires.txt
writing top-level names to metabolisHMM.egg-info/top_level.txt
reading manifest file 'metabolisHMM.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'metabolisHMM.egg-info/SOURCES.txt'
running check
creating metabolisHMM-2.22
creating metabolisHMM-2.22/bin
creating metabolisHMM-2.22/metabolisHMM.egg-info
copying files to metabolisHMM-2.22...
copying MANIFEST.in -> metabolisHMM-2.22
copying README.md -> metabolisHMM-2.22
copying requirements.txt -> metabolisHMM-2.22
copying setup.py -> metabolisHMM-2.22
copying bin/__init__.py -> metabolisHMM-2.22/bin
copying bin/create-genome-phylogeny -> metabolisHMM-2.22/bin
copying bin/search-custom-markers -> metabolisHMM-2.22/bin
copying bin/single-marker-phylogeny -> metabolisHMM-2.22/bin
copying bin/summarize-metabolism -> metabolisHMM-2.22/bin
copying metabolisHMM.egg-info/PKG-INFO -> metabolisHMM-2.22/metabolisHMM.egg-info
copying metabolisHMM.egg-info/SOURCES.txt -> metabolisHMM-2.22/metabolisHMM.egg-info
copying metabolisHMM.egg-info/dependency_links.txt -> metabolisHMM-2.22/metabolisHMM.egg-info
copying metabolisHMM.egg-info/not-zip-safe -> metabolisHMM-2.22/metabolisHMM.egg-info
copying metabolisHMM.egg-info/requires.txt -> metabolisHMM-2.22/metabolisHMM.egg-info
copying metabolisHMM.egg-info/top_level.txt -> metabolisHMM-2.22/metabolisHMM.egg-info
Writing metabolisHMM-2.22/setup.cfg
Creating tar archive
removing 'metabolisHMM-2.22' (and everything under it)
+ cd /
+ /tmp/tmp.SuiScHd1E5/bin/pip install /tmp/tmp.SuiScHd1E5/metabolisHMM-2.22.tar.gz
Processing /tmp/tmp.SuiScHd1E5/metabolisHMM-2.22.tar.gz
Collecting pandas (from metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/f5/10/40688389f5e234bde06aa84e6f3ccf5beea6269f57e2bef67866d3b43268/pandas-1.0.3-cp38-cp38-manylinux1_x86_64.whl
Collecting biopython (from metabolisHMM==2.22)
  Downloading https://files.pythonhosted.org/packages/40/5e/3a963cb5b4b4e33db0595ccbddff1df05e11a6664436ad8c9b1584d39e16/biopython-1.76-cp38-cp38-manylinux1_x86_64.whl (2.3MB)
Collecting numpy (from metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/cf/5d/e8198f11dd73a91f7bde15ca88a2b78913fa2b416ae2dc2a6aeafcf4c63d/numpy-1.18.4-cp38-cp38-manylinux1_x86_64.whl
Collecting matplotlib (from metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/01/9d/416ca5d453c776fa8db35d1bbfed65809e06ae021154f86c45d34f44ce39/matplotlib-3.2.1-cp38-cp38-manylinux1_x86_64.whl
Collecting seaborn (from metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/c7/e6/54aaaafd0b87f51dfba92ba73da94151aa3bc179e5fe88fc5dfb3038e860/seaborn-0.10.1-py3-none-any.whl
Collecting python-dateutil>=2.6.1 (from pandas->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting pytz>=2017.2 (from pandas->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/36/ac/c8627c214954b18b197f137ee96bc99e1cc31913d80d7ad59fbab3b05945/kiwisolver-1.2.0-cp38-cp38-manylinux1_x86_64.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting scipy>=1.0.1 (from seaborn->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/f3/08/8bdcdcd149ea41b655956feb7c19ebf7e1f561738bd5570b6ae015daf411/scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl
Collecting six>=1.5 (from python-dateutil>=2.6.1->pandas->metabolisHMM==2.22)
  Using cached https://files.pythonhosted.org/packages/ee/ff/48bde5c0f013094d729fe4b0316ba2a24774b3ff1c52d924a8a4cb04078a/six-1.15.0-py2.py3-none-any.whl
Installing collected packages: six, python-dateutil, numpy, pytz, pandas, biopython, kiwisolver, pyparsing, cycler, matplotlib, scipy, seaborn, metabolisHMM
  Running setup.py install for metabolisHMM: started
    Running setup.py install for metabolisHMM: finished with status 'done'
Successfully installed biopython-1.76 cycler-0.10.0 kiwisolver-1.2.0 matplotlib-3.2.1 metabolisHMM-2.22 numpy-1.18.4 pandas-1.0.3 pyparsing-2.4.7 python-dateutil-2.8.1 pytz-2020.1 scipy-1.4.1 seaborn-0.10.1 six-1.15.0
WARNING: You are using pip version 19.2.3, however version 20.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
+ echo Success
Success
++ rm -rf /tmp/tmp.SuiScHd1E5