From b8e7504c2b8f38c37af2bc0063a6683a7570ff1d Mon Sep 17 00:00:00 2001
From: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
Date: Tue, 22 Jun 2021 17:15:38 -0400
Subject: [PATCH 1/3] pythonPackages.connection-pool: init at 0.0.3

---
 .../connection-pool/default.nix               | 27 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 29 insertions(+)
 create mode 100644 pkgs/development/python-modules/connection-pool/default.nix

diff --git a/pkgs/development/python-modules/connection-pool/default.nix b/pkgs/development/python-modules/connection-pool/default.nix
new file mode 100644
index 000000000000..26e958f095ef
--- /dev/null
+++ b/pkgs/development/python-modules/connection-pool/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "connection-pool";
+  version = "0.0.3";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    pname = "connection_pool";
+    inherit version;
+    sha256 = "bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc";
+  };
+
+  doCheck = false; # no tests
+  pythonImportsCheck = [ "connection_pool" ];
+
+  meta = with lib; {
+    description = "Thread-safe connection pool";
+    homepage = "https://github.com/zhouyl/ConnectionPool";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 29913ff47bc0..47f5f8154195 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1337,6 +1337,8 @@ in {
 
   connect-box = callPackage ../development/python-modules/connect_box { };
 
+  connection-pool = callPackage ../development/python-modules/connection-pool { };
+
   coqpit = callPackage ../development/python-modules/coqpit { };
 
   cerberus = callPackage ../development/python-modules/cerberus { };

From 97d56c16c69af24fe4e39aedf0aa4d63546b7116 Mon Sep 17 00:00:00 2001
From: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
Date: Tue, 22 Jun 2021 17:17:43 -0400
Subject: [PATCH 2/3] pythonPackages.stopit: init at 1.1.2

---
 .../python-modules/stopit/default.nix         | 26 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/development/python-modules/stopit/default.nix

diff --git a/pkgs/development/python-modules/stopit/default.nix b/pkgs/development/python-modules/stopit/default.nix
new file mode 100644
index 000000000000..4d504da674c5
--- /dev/null
+++ b/pkgs/development/python-modules/stopit/default.nix
@@ -0,0 +1,26 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+}:
+
+buildPythonPackage rec {
+  pname = "stopit";
+  version = "1.1.2";
+
+  # tests are missing from the PyPi tarball
+  src = fetchFromGitHub {
+    owner = "glenfant";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-uXJUA70JOGWT2NmS6S7fPrTWAJZ0mZ/hICahIUzjfbw=";
+  };
+
+  pythonImportsCheck = [ "stopit" ];
+
+  meta = with lib; {
+    description = "Raise asynchronous exceptions in other thread, control the timeout of blocks or callables with a context manager or a decorator";
+    homepage = "https://github.com/glenfant/stopit";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 47f5f8154195..adb3b9e89082 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -8239,6 +8239,8 @@ in {
 
   stone = callPackage ../development/python-modules/stone { };
 
+  stopit = callPackage ../development/python-modules/stopit { };
+
   strategies = callPackage ../development/python-modules/strategies { };
 
   stravalib = callPackage ../development/python-modules/stravalib { };

From e3678ae8a6c08e1c2b39cfccfa521ffb0e23087d Mon Sep 17 00:00:00 2001
From: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
Date: Tue, 22 Jun 2021 17:18:35 -0400
Subject: [PATCH 3/3] snakemake: 6.0.5 -> 6.5.0

---
 pkgs/applications/science/misc/snakemake/default.nix | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 0818ca79622f..8919f85e44d9 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -2,11 +2,12 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "6.0.5";
+  version = "6.5.0";
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
     ConfigArgParse
+    connection-pool
     datrie
     docutils
     filelock
@@ -19,13 +20,15 @@ python3Packages.buildPythonApplication rec {
     ratelimiter
     requests
     smart-open
+    stopit
+    tabulate
     toposort
     wrapt
   ];
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "9441169034cce46086a8b45486d75175db645b932e766d28fed312ec837792d3";
+    sha256 = "b166ec74537e02553fcaf0ddcffc32dfdb9dcaa1260af297a56eded6a179b2ee";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json