Merge pull request #299256 from NixOS/pr/snakemake-storage-plugin-s3_init

python311Packages.snakemake-storage-plugin-{s3,xrootd}: init

pkgs/development/python-modules/snakemake-storage-plugin-s3/default.nix

@@ -0,0 +1,54 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, boto3
+, botocore
+, poetry-core
+, snakemake
+, snakemake-interface-storage-plugins
+, snakemake-interface-common
+, urllib3
+}:
+
+buildPythonPackage rec {
+  pname = "snakemake-storage-plugin-s3";
+  version = "0.2.10";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-k21DRQdSUFkdwNb7MZJmClhIg+pdSc7H6FkDrbf4DT8=";
+  };
+
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace ">=2.0,<2.2" "*"
+  '';
+
+  nativeBuildInputs = [
+    poetry-core
+  ];
+
+  propagatedBuildInputs = [
+    boto3
+    botocore
+    snakemake-interface-storage-plugins
+    snakemake-interface-common
+    urllib3
+  ];
+
+  nativeCheckInputs = [
+    snakemake
+  ];
+
+  pythonImportsCheck = [ "snakemake_storage_plugin_s3" ];
+
+  meta = with lib; {
+    description = "A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)";
+    homepage = "https://github.com/snakemake/snakemake-storage-plugin-s3";
+    license = licenses.mit;
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

pkgs/development/python-modules/snakemake-storage-plugin-xrootd/default.nix

@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, poetry-core
+, snakemake
+, snakemake-interface-storage-plugins
+, snakemake-interface-common
+, xrootd
+}:
+
+buildPythonPackage rec {
+  pname = "snakemake-storage-plugin-xrootd";
+  version = "unstable-2023-12-16";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = pname;
+    rev = "408f1e956b5427c34b49eeca340492a438e8eccb";
+    hash = "sha256-CcSG//D9kz0Q4LtaSngJpCtY0dbNFFuKMVmBxR1fcMo=";
+  };
+
+  # xrootd<6.0.0,>=5.6.4 not satisfied by version 5.7rc20240303
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace 'xrootd = "^5.6.4"' ""
+  '';
+
+  nativeBuildInputs = [
+    poetry-core
+  ];
+
+  propagatedBuildInputs = [
+    snakemake-interface-storage-plugins
+    snakemake-interface-common
+    xrootd
+  ];
+
+  nativeCheckInputs = [
+    snakemake
+  ];
+
+  pythonImportsCheck = [ "snakemake_storage_plugin_xrootd" ];
+
+  meta = with lib; {
+    description = "A Snakemake storage plugin for handling input and output via XRootD";
+    homepage = "https://github.com/snakemake/snakemake-storage-plugin-xrootd";
+    license = licenses.mit;
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -13914,6 +13914,10 @@ self: super: with self; {
     inherit (self) python;
   });
 
+  snakemake = toPythonModule (pkgs.snakemake.override {
+    python3 = python;
+  });
+
   snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };
 
   snakemake-interface-common = callPackage ../development/python-modules/snakemake-interface-common { };
@@ -13924,6 +13928,10 @@ self: super: with self; {
 
   snakemake-interface-storage-plugins = callPackage ../development/python-modules/snakemake-interface-storage-plugins { };
 
+  snakemake-storage-plugin-s3 = callPackage ../development/python-modules/snakemake-storage-plugin-s3 { };
+
+  snakemake-storage-plugin-xrootd = callPackage ../development/python-modules/snakemake-storage-plugin-xrootd { };
+
   snakebite = callPackage ../development/python-modules/snakebite { };
 
   snakeviz = callPackage ../development/python-modules/snakeviz { };