New package: py-wub, with supporting fixes (#13773)

* Add py-wub, with supporting fixes

- add py-wub
- add py-pycmd because py-wub needs it
- update py-statsmodels, which needs at least v0.9.0 to work with
  python3.7 because cython.

* Update based on Adam's comments

* Fix dependency types for py-six in py-wub

* statsmodels tests fail, update comment w/ Issue #

The statsmodels tests weren't run in the previous version of the
package.  If I enable them, the fail.

Update the package comment with the statsmodels issue I opened to
track the problem:
https://github.com/statsmodels/statsmodels/issues/6263

* Update dependency types in py-wub/package.py

* flake8 cleanups

* Make statsmodels tests work

- need to use patsy@0.5.1:
- need to run the tests from within the build/lib* dir

4 files changed, 79 insertions, 9 deletions

diff --git a/var/spack/repos/builtin/packages/py-patsy/package.py b/var/spack/repos/builtin/packages/py-patsy/package.py
index d5e744d1d0..0e037ae40e 100644
--- a/var/spack/repos/builtin/packages/py-patsy/package.py
+++ b/var/spack/repos/builtin/packages/py-patsy/package.py
@@ -11,6 +11,8 @@ class PyPatsy(PythonPackage):
     homepage = "https://github.com/pydata/patsy"
     url      = "https://pypi.io/packages/source/p/patsy/patsy-0.4.1.zip"
 
+    version('0.5.1', sha256='f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991',
+            url="https://pypi.io/packages/source/p/patsy/patsy-0.5.1.tar.gz")
     version('0.4.1', sha256='dc1cc280045b0e6e50c04706fd1e26d2a00ea400aa112f88e8142f88b0b7d3d4')
 
     variant('splines', default=False, description="Offers spline related functions")
diff --git a/var/spack/repos/builtin/packages/py-pycmd/package.py b/var/spack/repos/builtin/packages/py-pycmd/package.py
new file mode 100644
index 0000000000..a496a6e47c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pycmd/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPycmd(PythonPackage):
+    """pycmd is a collection of command line tools for helping with Python
+    development."""
+
+    homepage = "https://pypi.org/project/pycmd/"
+    url      = "https://pypi.io/packages/source/p/pycmd/pycmd-1.2.tar.gz"
+
+    version('1.2', sha256='adc1976c0106919e9338db20102b91009256dcfec924a66928d7297026f72477')
+
+    depends_on('py-py@1.4.9:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py
index 79f3ae49be..514aa63a7f 100644
--- a/var/spack/repos/builtin/packages/py-statsmodels/package.py
+++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py
@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import glob
 
 
 class PyStatsmodels(PythonPackage):
@@ -12,19 +13,36 @@ class PyStatsmodels(PythonPackage):
     homepage = "http://www.statsmodels.org"
     url      = "https://pypi.io/packages/source/s/statsmodels/statsmodels-0.8.0.tar.gz"
 
+    version('0.10.1', sha256='320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10')
     version('0.8.0', sha256='26431ab706fbae896db7870a0892743bfbb9f5c83231644692166a31d2d86048')
 
     variant('plotting', default=False, description='With matplotlib')
 
+    depends_on('python@:3.6', when='@:0.8.0', type=('build', 'run'))
+
     # according to http://www.statsmodels.org/dev/install.html earlier versions
     # might work.
     depends_on('py-setuptools@0.6c5:', type='build')
-    depends_on('py-numpy@1.7.0:',      type=('build', 'run'))
-    depends_on('py-scipy@0.11:',       type=('build', 'run'))
-    depends_on('py-pandas@0.12:',      type=('build', 'run'))
-    depends_on('py-patsy@0.2.1:',      type=('build', 'run'))
-    depends_on('py-cython@0.24:',      type=('build', 'run'))
-    depends_on('py-matplotlib@1.3:',   type='run', when='+plotting')
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
+
+    depends_on('py-numpy@1.7.0:',      type=('build', 'run'), when='@0.8.0')
+    depends_on('py-pandas@0.12:',      type=('build', 'run'), when='@0.8.0')
+    depends_on('py-patsy@0.2.1:',      type=('build', 'run'), when='@0.8.0')
+    depends_on('py-scipy@0.11:',       type=('build', 'run'), when='@0.8.0')
+    depends_on('py-matplotlib@1.3:',   type=('build', 'run'), when='@0.8.0 +plotting')
+
+    # patsy@0.5.1 works around a Python change
+    #    https://github.com/statsmodels/statsmodels/issues/5343 and
+    #    https://github.com/pydata/patsy/pull/131
+    depends_on('py-numpy',     type=('build', 'run'), when='@0.10.1')
+    depends_on('py-pandas',    type=('build', 'run'), when='@0.10.1')
+    depends_on('py-patsy',      type=('build', 'run'), when='@0.10.1')
+    depends_on('py-scipy@0.5.1:', type=('build', 'run'), when='@0.10.1')
+    depends_on('py-matplotlib',   type=('build', 'run'), when='@0.10.1 +plotting')
+
+    depends_on('py-pytest', type='test')
+
+    def test(self):
+        dirs = glob.glob("build/lib*")  # There can be only one...
+        with working_dir(dirs[0]):
+            pytest = which('pytest')
+            pytest('statsmodels')
diff --git a/var/spack/repos/builtin/packages/py-wub/package.py b/var/spack/repos/builtin/packages/py-wub/package.py
new file mode 100644
index 0000000000..d86a739b4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-wub/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyWub(PythonPackage):
+    """Bioinformatics tools and a software library developed by the Oxford
+    Nanopore Technologies Applications group.
+    """
+
+    homepage = "https://github.com/nanoporetech/wub"
+    url      = "https://github.com/nanoporetech/wub/archive/v0.4.0.tar.gz"
+
+    version('0.4.0', sha256='1526aa392bccac71b872211c45f5b403ad3d55f5762e0ed34ff9086bc1dab6fd')
+
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-pytest', type=('build', 'run', 'test'))
+    depends_on('py-pycmd', type=('build', 'run', 'test'))
+    depends_on('py-biopython', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run', 'test'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-seaborn', type=('build', 'run'))
+    depends_on('py-editdistance', type=('build', 'run', 'test'))
+    depends_on('py-pandas@0.20.2:', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-tqdm', type=('build', 'run'))
+    depends_on('py-statsmodels', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')