snakemake: add new version and update plugins (#43437)

8 files changed, 78 insertions, 16 deletions

diff --git a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-generic/package.py b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-generic/package.py
index 54e8d64dee..cd7944bb93 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-generic/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-generic/package.py
@@ -13,15 +13,19 @@ class PySnakemakeExecutorPluginClusterGeneric(PythonPackage):
     homepage = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic"
     pypi = (
         "snakemake_executor_plugin_cluster_generic/"
-        "snakemake_executor_plugin_cluster_generic-1.0.7.tar.gz"
+        "snakemake_executor_plugin_cluster_generic-1.0.9.tar.gz"
     )
 
     license("MIT")
 
+    version("1.0.9", sha256="ad0dc2d8bde7d4f336364bebe11a3b2209653c481ce8fbb0ae8bec81016a9a14")
     version("1.0.7", sha256="093808e63cc48294a9d1eb0b620cdff8cc970806294a2f6ba127a49f8a81d473")
 
     depends_on("py-snakemake-interface-common@1.13:1", type=("build", "run"))
-    depends_on("py-snakemake-interface-executor-plugins@8.1:8", type=("build", "run"))
+    depends_on("py-snakemake-interface-executor-plugins@9", type=("build", "run"), when="@1.0.9:")
+    depends_on(
+        "py-snakemake-interface-executor-plugins@8.1:8", type=("build", "run"), when="@:1.0.8"
+    )
 
     depends_on("python@3.11:3", type=("build", "run"))
     depends_on("py-poetry-core", type="build")
diff --git a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-sync/package.py b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-sync/package.py
index afbf359c68..820568fa6a 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-sync/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-cluster-sync/package.py
@@ -13,15 +13,19 @@ class PySnakemakeExecutorPluginClusterSync(PythonPackage):
     homepage = "https://github.com/snakemake/snakemake-executor-plugin-cluster-sync"
     pypi = (
         "snakemake_executor_plugin_cluster_sync/"
-        "snakemake_executor_plugin_cluster_sync-0.1.3.tar.gz"
+        "snakemake_executor_plugin_cluster_sync-0.1.4.tar.gz"
     )
 
     license("MIT")
 
+    version("0.1.4", sha256="6a6dcb2110d4c2ee74f9a48ea68e0fd7ddd2800672ebef00a01faa4affa835ad")
     version("0.1.3", sha256="c30fca6ccb98a3f7ca52ca8a95414c71360a3d4a835bd4a097a13445d6fce2ac")
 
     depends_on("py-snakemake-interface-common@1.14:1", type=("build", "run"))
-    depends_on("py-snakemake-interface-executor-plugins@8.1:8", type=("build", "run"))
+    depends_on("py-snakemake-interface-executor-plugins@9", type=("build", "run"), when="@0.1.4:")
+    depends_on(
+        "py-snakemake-interface-executor-plugins@8.1:8", type=("build", "run"), when="@:0.1.3"
+    )
 
     depends_on("python@3.11:3", type=("build", "run"))
     depends_on("py-poetry-core", type="build")
diff --git a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm-jobstep/package.py b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm-jobstep/package.py
index 15593ccf5b..83d1ce32da 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm-jobstep/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm-jobstep/package.py
@@ -14,15 +14,21 @@ class PySnakemakeExecutorPluginSlurmJobstep(PythonPackage):
     homepage = "https://github.com/snakemake/snakemake-executor-plugin-slurm-jobstep"
     pypi = (
         "snakemake_executor_plugin_slurm_jobstep/"
-        "snakemake_executor_plugin_slurm_jobstep-0.1.9.tar.gz"
+        "snakemake_executor_plugin_slurm_jobstep-0.2.1.tar.gz"
     )
+    maintainers("w8jcik")
 
     license("MIT")
 
+    version("0.2.1", sha256="58894d52b5998a34fa6f60ec511ff0bfde4a9ec96714bcaa3cd2f46cf8a33859")
+    version("0.1.11", sha256="cafdac937796ab0dfc0354c42380167a44a1db00c4edc98ab736a6ace2201a94")
     version("0.1.10", sha256="321b6bdf7883a8fb40ff4aeeb88633502e4db8394e40b6628db41a430c2eae2b")
 
     depends_on("py-snakemake-interface-common@1.13:1", type=("build", "run"))
-    depends_on("py-snakemake-interface-executor-plugins@8.2:8", type=("build", "run"))
+    depends_on("py-snakemake-interface-executor-plugins@9", type=("build", "run"), when="@0.1.11:")
+    depends_on(
+        "py-snakemake-interface-executor-plugins@8.2:8", type=("build", "run"), when="@:0.1.10"
+    )
 
     depends_on("python@3.11:3", type=("build", "run"))
     depends_on("py-poetry-core", type="build")
diff --git a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm/package.py b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm/package.py
index 1b15b631b7..ecfeaec56d 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-executor-plugin-slurm/package.py
@@ -11,17 +11,36 @@ class PySnakemakeExecutorPluginSlurm(PythonPackage):
     """A Snakemake executor plugin for submitting jobs to a SLURM cluster."""
 
     homepage = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
-    pypi = "snakemake_executor_plugin_slurm/snakemake_executor_plugin_slurm-0.3.1.tar.gz"
+    pypi = "snakemake_executor_plugin_slurm/snakemake_executor_plugin_slurm-0.10.0.tar.gz"
+    maintainers("w8jcik")
 
     license("MIT")
 
+    version("0.10.0", sha256="d970bd08e00f1664adbd3c421c956b2ce926359ff10a4d7650c444c1179bec3f")
     version("0.3.2", sha256="3912f2895eab1270d7a42959a2e221ce53428dfffb847e03ec6bc4eead88e30b")
 
     depends_on("py-throttler@1.2.2:1", type=("build", "run"))
 
     depends_on("py-snakemake-interface-common@1.13:1", type=("build", "run"))
-    depends_on("py-snakemake-interface-executor-plugins@8.2:8", type=("build", "run"))
-    depends_on("py-snakemake-executor-plugin-slurm-jobstep@0.1.10:0.1", type=("build", "run"))
+
+    depends_on(
+        "py-snakemake-interface-executor-plugins@9.1.1:9", type=("build", "run"), when="@0.4.4:"
+    )
+    depends_on(
+        "py-snakemake-interface-executor-plugins@9", type=("build", "run"), when="@0.4.2:0.4.3"
+    )
+    depends_on(
+        "py-snakemake-interface-executor-plugins@8.2:8", type=("build", "run"), when="@:0.4.1"
+    )
+
+    depends_on(
+        "py-snakemake-executor-plugin-slurm-jobstep@0.2", type=("build", "run"), when="@0.4.4:"
+    )
+    depends_on(
+        "py-snakemake-executor-plugin-slurm-jobstep@0.1.10:0.1",
+        type=("build", "run"),
+        when="@:0.4.3",
+    )
 
     depends_on("python@3.11:3", type=("build", "run"))
     depends_on("py-poetry-core", type="build")
diff --git a/var/spack/repos/builtin/packages/py-snakemake-interface-common/package.py b/var/spack/repos/builtin/packages/py-snakemake-interface-common/package.py
index 017b928098..51ec9cf546 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-interface-common/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-interface-common/package.py
@@ -11,10 +11,12 @@ class PySnakemakeInterfaceCommon(PythonPackage):
     """Common functions and classes for Snakemake and its plugins."""
 
     homepage = "https://github.com/snakemake/snakemake-interface-common"
-    pypi = "snakemake_interface_common/snakemake_interface_common-1.17.1.tar.gz"
+    pypi = "snakemake_interface_common/snakemake_interface_common-1.17.3.tar.gz"
+    maintainers("w8jcik")
 
     license("MIT")
 
+    version("1.17.3", sha256="cca6e2c728072a285a8e750f00fdd98d9c50063912184c41f8b89e4cab66c7b0")
     version("1.17.1", sha256="555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae")
 
     depends_on("py-argparse-dataclass@2", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-snakemake-interface-executor-plugins/package.py b/var/spack/repos/builtin/packages/py-snakemake-interface-executor-plugins/package.py
index e0932eb1a9..7c95062efe 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-interface-executor-plugins/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-interface-executor-plugins/package.py
@@ -12,10 +12,12 @@ class PySnakemakeInterfaceExecutorPlugins(PythonPackage):
     executor plugins."""
 
     homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins"
-    pypi = "snakemake_interface_executor_plugins/snakemake_interface_executor_plugins-8.2.0.tar.gz"
+    pypi = "snakemake_interface_executor_plugins/snakemake_interface_executor_plugins-9.2.0.tar.gz"
+    maintainers("w8jcik")
 
     license("MIT")
 
+    version("9.2.0", sha256="67feaf438a0b8b041ec5f1a1dd859f729036c70c07c9fdad895135f5b949e40a")
     version("8.2.0", sha256="4c74e3e1751bab6b266baf8688e854b8b4c5c5e10f5e34c581f42d69af4ff13b")
 
     depends_on("py-argparse-dataclass@2", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-snakemake-interface-storage-plugins/package.py b/var/spack/repos/builtin/packages/py-snakemake-interface-storage-plugins/package.py
index e9ba417de4..1ff4436dae 100644
--- a/var/spack/repos/builtin/packages/py-snakemake-interface-storage-plugins/package.py
+++ b/var/spack/repos/builtin/packages/py-snakemake-interface-storage-plugins/package.py
@@ -12,10 +12,12 @@ class PySnakemakeInterfaceStoragePlugins(PythonPackage):
     plugins."""
 
     homepage = "https://github.com/snakemake/snakemake-interface-storage-plugins"
-    pypi = "snakemake_interface_storage_plugins/snakemake_interface_storage_plugins-3.1.0.tar.gz"
+    pypi = "snakemake_interface_storage_plugins/snakemake_interface_storage_plugins-3.3.0.tar.gz"
+    maintainers("w8jcik")
 
     license("MIT")
 
+    version("3.3.0", sha256="203d8f794dfb37d568ad01a6c375fa8beac36df8e488c0f9b9f75984769c362a")
     version("3.1.0", sha256="26e95be235ef2a9716b890ea96c3a9a2e62061c5d72fbb89c2fad2afada87304")
 
     depends_on("py-wrapt@1.15:1", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py
index 754affb32d..501c0076b6 100644
--- a/var/spack/repos/builtin/packages/snakemake/package.py
+++ b/var/spack/repos/builtin/packages/snakemake/package.py
@@ -10,11 +10,12 @@ class Snakemake(PythonPackage):
     """Workflow management system to create reproducible and scalable data analyses."""
 
     homepage = "https://snakemake.readthedocs.io/en"
-    pypi = "snakemake/snakemake-8.4.12.tar.gz"
-    maintainers("marcusboden")
+    pypi = "snakemake/snakemake-8.18.2.tar.gz"
+    maintainers("marcusboden", "w8jcik")
 
     license("MIT")
 
+    version("8.18.2", sha256="7dc8cdc3c836444c2bc3d67a4a7f4d703557c1bf96a90da18f312f4df9daefc4")
     version("8.5.2", sha256="cc94876263182277e4a429e5d371c867400eeddc791c114dfd090d1bb3158975")
     version("7.32.4", sha256="fdc3f15dd7b06fabb7da30d460e0a3b1fba08e4ea91f9c32c47a83705cdc7b6e")
     version("7.31.1", sha256="6fadcc9a051737aa187dccf437879b3b83ddc917fff9bd7d400e056cf17a1788")
@@ -59,20 +60,42 @@ class Snakemake(PythonPackage):
     depends_on("py-pulp@2.3.1:2.8", type=("build", "run"), when="@8.1.2:")
     depends_on("py-pulp@2:", type=("build", "run"), when="@:8.1.1")
     depends_on("py-pyyaml", type=("build", "run"))
+
     depends_on("py-requests@2.8.1:2", type=("build", "run"), when="@8.4.12")
     depends_on("py-requests", type=("build", "run"))
+
     depends_on("py-reretry", type=("build", "run"), when="@7:")
-    depends_on("py-smart-open@3:6", type=("build", "run"), when="@8.4.12:")
+
+    depends_on("py-smart-open@4:7", type=("build", "run"), when="@8.11:")
+    depends_on("py-smart-open@3:7", type=("build", "run"), when="@8.8:8.10")
+    depends_on("py-smart-open@3:6", type=("build", "run"), when="@8.4.12:8.7")
     depends_on("py-smart-open@3:", type=("build", "run"))
+
+    depends_on(
+        "py-snakemake-interface-executor-plugins@9.2:9", type=("build", "run"), when="@8.15.0:"
+    )
+    depends_on(
+        "py-snakemake-interface-executor-plugins@9.1:9", type=("build", "run"), when="@8.10.1:"
+    )
     depends_on(
-        "py-snakemake-interface-executor-plugins@8.1.3:8", type=("build", "run"), when="@8:"
+        "py-snakemake-interface-executor-plugins@9.0.2:9", type=("build", "run"), when="@8.10:"
     )
+    depends_on("py-snakemake-interface-executor-plugins@9", type=("build", "run"), when="@8.6:")
+    depends_on(
+        "py-snakemake-interface-executor-plugins@8.1.3:8", type=("build", "run"), when="@8:8.5"
+    )
+
     depends_on("py-snakemake-interface-common@1.17:1", type=("build", "run"), when="@8.4.10:")
     depends_on("py-snakemake-interface-common@1.15:1", type=("build", "run"), when="@8:")
+
+    depends_on(
+        "py-snakemake-interface-storage-plugins@3.2.3:3", type=("build", "run"), when="@8.15.1:"
+    )
     depends_on(
         "py-snakemake-interface-storage-plugins@3.1:3", type=("build", "run"), when="@8.4.10:"
     )
     depends_on("py-snakemake-interface-storage-plugins@3", type=("build", "run"), when="@8:")
+
     depends_on("py-snakemake-interface-report-plugins@1", type=("build", "run"), when="@8.5:")
     depends_on("py-stopit", type=("build", "run"))
     depends_on("py-tabulate", type=("build", "run"))