From 447db2fe8d94c74b10c2dd6a1c952e735b091f04 Mon Sep 17 00:00:00 2001
From: Miles Perry <37849532+Miles-Perry@users.noreply.github.com>
Date: Tue, 4 Sep 2018 14:34:18 -0500
Subject: Feature/py pycogent New-Version (#9095)

* added py-pycogent

* flake8 edits

* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py

* changed python min version to 2.6

* fixed cython to py-cython dep

* fixed mpi4py to py-mpi4py

* fixed py-sqlalchemy

* added 1.5.3 version

* fixed version 1.5.3 install

* changed deps names to reflect convention

* added variants

* changed download URL and added SHA256 hash

* fixed deps

* added github url for 1.5.3

* removed unneeded deps

* doesn't require py-setuptools

* fixed url and added py-setuptools specific to version 1.9

* fixed variant names and changed cython to normal dependency instead of variant

* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi

* fixed dependencies and added py-pymysql dep

* added setup-environment step

* changed download url for 1.5.3 to pypi

* fixed flake8 issue

* updated

* added changes
---
 .../repos/builtin/packages/py-cogent/package.py    | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/py-cogent/package.py b/var/spack/repos/builtin/packages/py-cogent/package.py
index 2fb64fee08..cf910ae6d1 100644
--- a/var/spack/repos/builtin/packages/py-cogent/package.py
+++ b/var/spack/repos/builtin/packages/py-cogent/package.py
@@ -31,7 +31,23 @@ class PyCogent(PythonPackage):
     homepage = "http://pycogent.org"
     url      = "https://pypi.io/packages/source/c/cogent/cogent-1.9.tar.gz"
 
-    version('1.9', '7d9f28cd17664c1cd18c568fc53060d6')
+    version('1.9', sha256='57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14')
+    version('1.5.3', url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz", 
+        sha256='1215ac219070b7b2207b0b47b4388510f3e30ccd88160aa9f02f25d24bcbcd95')
 
-    depends_on('py-setuptools',   type='build')
-    depends_on('py-numpy',        type=('build', 'run'))
+    variant('matplotlib', default=False, description="graphs related to codon usage")
+    variant('mpi', default=False, description='MPI required for parallel computation.')
+    variant('mysql', default=False, description='Required for the Ensembl querying code.')
+
+    depends_on('py-setuptools', type=('build'), when='@1.9')
+    depends_on('python@2.6:2.999', type=('build', 'run'))
+    depends_on('py-numpy@1.3:', type=('build', 'run'))
+    depends_on('zlib')
+    depends_on('py-matplotlib', when='+matplotlib', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+    depends_on('py-sqlalchemy', when='+mysql', type=('build', 'run'))
+    depends_on('py-pymysql', when='+mysql', type=('build', 'run'))
+    depends_on('py-cython@0.17.1:', type='build')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DONT_USE_PYREX', '1')
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