From 312ce6e2e5c6eab36021f7f1df59df8172e49294 Mon Sep 17 00:00:00 2001 From: kyehn Date: Fri, 26 Sep 2025 13:19:00 +0800 Subject: [PATCH 1/5] snakemake: 9.5.1 -> 9.11.6 Changelog: https://github.com/snakemake/snakemake/blob/v9.11.6/CHANGELOG.md --- pkgs/by-name/sn/snakemake/package.nix | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/pkgs/by-name/sn/snakemake/package.nix b/pkgs/by-name/sn/snakemake/package.nix index f1ae8a21a218..6549271c5ed5 100644 --- a/pkgs/by-name/sn/snakemake/package.nix +++ b/pkgs/by-name/sn/snakemake/package.nix @@ -10,14 +10,14 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "9.5.1"; + version = "9.11.6"; pyproject = true; src = fetchFromGitHub { owner = "snakemake"; repo = "snakemake"; tag = "v${version}"; - hash = "sha256-cSFqPSLeM7hw1bxQZ2FhlHUP+O3iyrwBz4+Jz90Zck8="; + hash = "sha256-bbwpLSWCYKezFJj7EVn6wOLSzO/vShP98MMicKzdGSQ="; }; postPatch = '' @@ -58,6 +58,7 @@ python3Packages.buildPythonApplication rec { snakemake-interface-logger-plugins snakemake-interface-storage-plugins snakemake-interface-report-plugins + snakemake-interface-scheduler-plugins stopit tabulate throttler @@ -140,6 +141,11 @@ python3Packages.buildPythonApplication rec { # Requires snakemake-storage-plugin-http "test_keep_local" "test_retrieve" + + # Requires conda + "test_jupyter_notebook" + "test_jupyter_notebook_nbconvert" + "test_jupyter_notebook_draft" ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ # Unclear failure: From ea7b9bfc3d01c065b0994a8a65206abe31bf03da Mon Sep 17 00:00:00 2001 From: kyehn Date: Fri, 26 Sep 2025 13:20:49 +0800 Subject: [PATCH 2/5] python313Packages.snakemake-interface-common: 1.17.4 -> 1.21.0 Changelog: https://github.com/snakemake/snakemake-interface-common/releases/tag/v1.21.0 --- .../snakemake-interface-common/default.nix | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/pkgs/development/python-modules/snakemake-interface-common/default.nix b/pkgs/development/python-modules/snakemake-interface-common/default.nix index 3ec3baca2d5a..06c5f2bfe703 100644 --- a/pkgs/development/python-modules/snakemake-interface-common/default.nix +++ b/pkgs/development/python-modules/snakemake-interface-common/default.nix @@ -4,43 +4,40 @@ buildPythonPackage, configargparse, fetchFromGitHub, - poetry-core, - pythonOlder, - pytestCheckHook, + setuptools, }: buildPythonPackage rec { pname = "snakemake-interface-common"; - version = "1.17.4"; + version = "1.21.0"; pyproject = true; - disabled = pythonOlder "3.8"; - src = fetchFromGitHub { owner = "snakemake"; repo = "snakemake-interface-common"; tag = "v${version}"; - hash = "sha256-PMEs7yeVfSnZKbabLrbXfIKCIPteNV1wzbt9RIDG3qU="; + hash = "sha256-8QISVZZ/kwWBNFtndzysnxFuuemkDXcWqEtCdVVsANo="; }; - build-system = [ poetry-core ]; + build-system = [ setuptools ]; dependencies = [ argparse-dataclass configargparse ]; - nativeCheckInputs = [ pytestCheckHook ]; - pythonImportsCheck = [ "snakemake_interface_common" ]; - enabledTestPaths = [ "tests/tests.py" ]; + # test_snakemake_version: No module named 'snakemake' + # nativeCheckInputs = [ pytestCheckHook ]; - meta = with lib; { + # enabledTestPaths = [ "tests/tests.py" ]; + + meta = { description = "Common functions and classes for Snakemake and its plugins"; homepage = "https://github.com/snakemake/snakemake-interface-common"; changelog = "https://github.com/snakemake/snakemake-interface-common/releases/tag/v${version}"; - license = licenses.mit; - maintainers = with maintainers; [ veprbl ]; + license = lib.licenses.mit; + maintainers = with lib.maintainers; [ veprbl ]; }; } From bb9ff85a590a1160040c680ec920417aa8db584f Mon Sep 17 00:00:00 2001 From: kyehn Date: Fri, 26 Sep 2025 13:48:22 +0800 Subject: [PATCH 3/5] python313Packages.snakemake-interface-scheduler-plugins: init at 2.0.1 --- .../default.nix | 42 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 4 ++ 2 files changed, 46 insertions(+) create mode 100644 pkgs/development/python-modules/snakemake-interface-scheduler-plugins/default.nix diff --git a/pkgs/development/python-modules/snakemake-interface-scheduler-plugins/default.nix b/pkgs/development/python-modules/snakemake-interface-scheduler-plugins/default.nix new file mode 100644 index 000000000000..ccad1ca6f6a2 --- /dev/null +++ b/pkgs/development/python-modules/snakemake-interface-scheduler-plugins/default.nix @@ -0,0 +1,42 @@ +{ + lib, + buildPythonPackage, + fetchFromGitHub, + hatchling, + snakemake-interface-common, +}: + +let + version = "2.0.1"; + + src = fetchFromGitHub { + owner = "snakemake"; + repo = "snakemake-interface-scheduler-plugins"; + tag = "v${version}"; + hash = "sha256-Z/rJGkby9AcYB+Gil00xhbrySChqEIEOtzLyzQPhObk="; + }; +in +buildPythonPackage { + pname = "snakemake-interface-scheduler-plugins"; + inherit version src; + pyproject = true; + + build-system = [ hatchling ]; + + dependencies = [ snakemake-interface-common ]; + + pythonImportsCheck = [ "snakemake_interface_scheduler_plugins" ]; + + # test_scheduler: No module named 'snakemake' + # nativeCheckInputs = [ pytestCheckHook ]; + + # enabledTestPaths = [ "tests/tests.py" ]; + + meta = { + description = "Provides a stable interface for interactions between Snakemake and its scheduler plugins"; + homepage = "https://github.com/snakemake/snakemake-interface-scheduler-plugins"; + changelog = "https://github.com/snakemake/snakemake-interface-scheduler-plugins/blob/${src.rev}/CHANGELOG.md"; + license = lib.licenses.mit; + maintainers = with lib.maintainers; [ kyehn ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 17d4e0e52f13..88e15d4effa3 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -17013,6 +17013,10 @@ self: super: with self; { callPackage ../development/python-modules/snakemake-interface-report-plugins { }; + snakemake-interface-scheduler-plugins = + callPackage ../development/python-modules/snakemake-interface-scheduler-plugins + { }; + snakemake-interface-storage-plugins = callPackage ../development/python-modules/snakemake-interface-storage-plugins { }; From 6fafb5e4ce390c441d68172cea1102f7cf7facc8 Mon Sep 17 00:00:00 2001 From: kyehn <228304369+kyehn@users.noreply.github.com> Date: Fri, 3 Oct 2025 00:36:02 +0000 Subject: [PATCH 4/5] snakemake: 9.11.6 -> 9.11.8 Changelog: https://github.com/snakemake/snakemake/blob/v9.11.8/CHANGELOG.md --- pkgs/by-name/sn/snakemake/package.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/by-name/sn/snakemake/package.nix b/pkgs/by-name/sn/snakemake/package.nix index 6549271c5ed5..00340e211bf3 100644 --- a/pkgs/by-name/sn/snakemake/package.nix +++ b/pkgs/by-name/sn/snakemake/package.nix @@ -10,14 +10,14 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "9.11.6"; + version = "9.11.8"; pyproject = true; src = fetchFromGitHub { owner = "snakemake"; repo = "snakemake"; tag = "v${version}"; - hash = "sha256-bbwpLSWCYKezFJj7EVn6wOLSzO/vShP98MMicKzdGSQ="; + hash = "sha256-fQCpQ3LB0Q1USZ9YTEniR5iKq68Zri9+14zqa/jzO2o="; }; postPatch = '' From 0c1fde6fad566e295920f8cbb7082b39ab3bc289 Mon Sep 17 00:00:00 2001 From: kyehn <228304369+kyehn@users.noreply.github.com> Date: Fri, 3 Oct 2025 00:38:08 +0000 Subject: [PATCH 5/5] python313Packages.snakemake-interface-common: 1.21.0 -> 1.22.0 Changelog: https://github.com/snakemake/snakemake-interface-common/releases/tag/v1.22.0 --- .../python-modules/snakemake-interface-common/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/snakemake-interface-common/default.nix b/pkgs/development/python-modules/snakemake-interface-common/default.nix index 06c5f2bfe703..b1deaa0b84dd 100644 --- a/pkgs/development/python-modules/snakemake-interface-common/default.nix +++ b/pkgs/development/python-modules/snakemake-interface-common/default.nix @@ -9,14 +9,14 @@ buildPythonPackage rec { pname = "snakemake-interface-common"; - version = "1.21.0"; + version = "1.22.0"; pyproject = true; src = fetchFromGitHub { owner = "snakemake"; repo = "snakemake-interface-common"; tag = "v${version}"; - hash = "sha256-8QISVZZ/kwWBNFtndzysnxFuuemkDXcWqEtCdVVsANo="; + hash = "sha256-DxbB/UaBkLbG18CGHyDMo7dmRlVY2tD3BhO0MShbnq4="; }; build-system = [ setuptools ];