Snakemake: New Version 6.12.3 (#28252)

* snakemake: New version
The newer versions of snakemake have a lot of new dependencies. The
optional dependencies still have to be added.

* removed comment

* some changes

* added reports variant

* deprecate older version and add me as maintainer

* Added dependency py-ratelimiter

2 files changed, 52 insertions, 3 deletions

diff --git a/var/spack/repos/builtin/packages/py-ratelimiter/package.py b/var/spack/repos/builtin/packages/py-ratelimiter/package.py
new file mode 100644
index 0000000000..d501855f8b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ratelimiter/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2021 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 PyRatelimiter(PythonPackage):
+    """Simple Python module providing rate limiting."""
+
+    homepage = 'https://github.com/RazerM/ratelimiter'
+    pypi = 'ratelimiter/ratelimiter-1.2.0.post0.tar.gz'
+
+    maintainers = ['marcusboden']
+
+    version('1.2.0.post0', '5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py
index 3cc12feacd..73302ac437 100644
--- a/var/spack/repos/builtin/packages/snakemake/package.py
+++ b/var/spack/repos/builtin/packages/snakemake/package.py
@@ -10,11 +10,41 @@ class Snakemake(PythonPackage):
     """Snakemake is an MIT-licensed workflow management system."""
 
     homepage = "https://snakemake.readthedocs.io/en/stable/"
-    pypi = "snakemake/snakemake-3.11.2.tar.gz"
+    pypi = "snakemake/snakemake-6.12.3.tar.gz"
+    maintainers = ['marcusboden']
 
-    version('3.11.2', sha256='f7a3b586bc2195f2dce4a4817b7ec828b6d2a0cff74a04e0f7566dcd923f9761')
+    version('6.12.3', sha256='af86af9a540da3dceb05dad1040f1d3d733e6a695f8b3f8c30f8cf3bc6570a88')
+    version('3.11.2', sha256='f7a3b586bc2195f2dce4a4817b7ec828b6d2a0cff74a04e0f7566dcd923f9761', deprecated=True)
 
-    depends_on('python@3.3:3.6')
     depends_on('py-requests', type=('build', 'run'))
     depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-wrapt', type=('build', 'run'))
+
+    depends_on('python@3.3:3.6', when='@:5')
+
+    with when('@6:'):
+        depends_on('python@3.5:')
+        depends_on('py-pyyaml', type=('build', 'run'))
+        depends_on('py-configargparse', type=('build', 'run'))
+        depends_on('py-appdirs', type=('build', 'run'))
+        depends_on('py-datrie', type=('build', 'run'))
+        depends_on('py-jsonschema', type=('build', 'run'))
+        depends_on('py-docutils', type=('build', 'run'))
+        depends_on('py-gitpython', type=('build', 'run'))
+        depends_on('py-psutil', type=('build', 'run'))
+        depends_on('py-nbformat', type=('build', 'run'))
+        depends_on('py-toposort', type=('build', 'run'))
+        depends_on('py-connectionpool@0.0.3:', type=('build', 'run'))
+        depends_on('py-pulp@2.0:', type=('build', 'run'))
+        depends_on('py-smart-open@3.0:', type=('build', 'run'))
+        depends_on('py-filelock', type=('build', 'run'))
+        depends_on('py-stopit', type=('build', 'run'))
+        depends_on('py-tabulate', type=('build', 'run'))
+        depends_on('py-ratelimiter', type=('build', 'run'))
+
+        variant('reports', default=False, description='Generate self-contained HTML reports')
+        with when('+reports'):
+            depends_on('py-jinja2', type=('build', 'run'))
+            depends_on('py-networkx', type=('build', 'run'))
+            depends_on('py-pygments', type=('build', 'run'))
+            depends_on('py-pygraphviz', type=('build', 'run'))