From e339f0a1fbf7463ca9d11d9878c01a5efd9957b8 Mon Sep 17 00:00:00 2001
From: Nick Cao <nickcao@nichi.co>
Date: Tue, 19 Mar 2024 15:05:45 -0400
Subject: [PATCH 01/30] nixos/systemd-sysusers: make uid/gid allocation stable

---
 .../modules/system/boot/systemd/sysusers.nix  | 21 +++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/nixos/modules/system/boot/systemd/sysusers.nix b/nixos/modules/system/boot/systemd/sysusers.nix
index c619c2d91eb0..9eda862f0003 100644
--- a/nixos/modules/system/boot/systemd/sysusers.nix
+++ b/nixos/modules/system/boot/systemd/sysusers.nix
@@ -12,7 +12,7 @@ let
     ${lib.concatLines (lib.mapAttrsToList
       (username: opts:
         let
-          uid = if opts.uid == null then "-" else toString opts.uid;
+          uid = if opts.uid == null then "/var/lib/nixos/uid/${username}" else toString opts.uid;
         in
           ''u ${username} ${uid}:${opts.group} "${opts.description}" ${opts.home} ${utils.toShellPath opts.shell}''
       )
@@ -21,7 +21,7 @@ let
 
     # Groups
     ${lib.concatLines (lib.mapAttrsToList
-      (groupname: opts: ''g ${groupname} ${if opts.gid == null then "-" else toString opts.gid}'') userCfg.groups)
+      (groupname: opts: ''g ${groupname} ${if opts.gid == null then "/var/lib/nixos/gid/${groupname}" else toString opts.gid}'') userCfg.groups)
     }
 
     # Group membership
@@ -106,6 +106,23 @@ in
             };
           })
           (lib.filterAttrs (_username: opts: opts.home != "/var/empty") userCfg.users);
+
+        # Create uid/gid marker files for those without an explicit id
+        tmpfiles.settings.nixos-uid = lib.mapAttrs'
+          (username: opts: lib.nameValuePair "/var/lib/nixos/uid/${username}" {
+            f = {
+              user = username;
+            };
+          })
+          (lib.filterAttrs (_username: opts: opts.uid == null) userCfg.users);
+
+        tmpfiles.settings.nixos-gid = lib.mapAttrs'
+          (groupname: opts: lib.nameValuePair "/var/lib/nixos/gid/${groupname}" {
+            f = {
+              group = groupname;
+            };
+          })
+          (lib.filterAttrs (_groupname: opts: opts.gid == null) userCfg.groups);
       })
 
       (lib.mkIf config.users.mutableUsers {

From 733527fec99c78ab8ef4b504298940dfb886dacf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sun, 21 Apr 2024 19:21:19 -0700
Subject: [PATCH 02/30] python311Packages.quil: 0.7.1 -> 0.9.1

Diff: https://github.com/rigetti/quil-rs/compare/quil-py/v0.7.1...quil-py/v0.9.1

Changelog: https://github.com/rigetti/quil-rs/blob/quil-py/v0.9.1/quil-py/CHANGELOG.md
---
 pkgs/development/python-modules/quil/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/quil/default.nix b/pkgs/development/python-modules/quil/default.nix
index 41f79d79bdf3..08ee222043e6 100644
--- a/pkgs/development/python-modules/quil/default.nix
+++ b/pkgs/development/python-modules/quil/default.nix
@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "quil";
-  version = "0.7.1";
+  version = "0.9.1";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -20,13 +20,13 @@ buildPythonPackage rec {
     owner = "rigetti";
     repo = "quil-rs";
     rev = "quil-py/v${version}";
-    hash = "sha256-GFePbCJnVbzL4cpQ7fy1tk2l7NhAyTVW63lVYTv0/Oo=";
+    hash = "sha256-c9nFF74Mr6S2b7NthRVUnarwxFZ9s5RUaoxYruE6QvI=";
   };
 
   cargoDeps = rustPlatform.fetchCargoTarball {
     name = "${pname}-${version}";
     inherit src;
-    hash = "sha256-catUGCFbkvov1z52f6eyxogflu61VcjIItgEVEWzkpY=";
+    hash = "sha256-FNkXdBLfKnrD9aUe25uJHi+TtApgFSCryYCY1r8ebho=";
   };
 
   buildAndTestSubdir = "quil-py";

From cb6c01fff80ba50cc978cb74e9d5ffe7b7009820 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sun, 21 Apr 2024 19:40:26 -0700
Subject: [PATCH 03/30] python311Packages.qcs-sdk-python: 0.17.4 -> 0.17.7

Diff: https://github.com/rigetti/qcs-sdk-rust/compare/python/v0.17.4...python/v0.17.7

Changelog: https://github.com/rigetti/qcs-sdk-rust/blob/python/v0.17.7/crates/python/CHANGELOG.md
---
 .../python-modules/qcs-sdk-python/Cargo.lock  | 24 +++++++++----------
 .../python-modules/qcs-sdk-python/default.nix |  6 ++---
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/pkgs/development/python-modules/qcs-sdk-python/Cargo.lock b/pkgs/development/python-modules/qcs-sdk-python/Cargo.lock
index 0c1265d5ac40..fc65e87b236e 100644
--- a/pkgs/development/python-modules/qcs-sdk-python/Cargo.lock
+++ b/pkgs/development/python-modules/qcs-sdk-python/Cargo.lock
@@ -912,7 +912,7 @@ dependencies = [
  "futures-sink",
  "futures-util",
  "http",
- "indexmap 2.2.5",
+ "indexmap 2.2.6",
  "slab",
  "tokio",
  "tokio-util",
@@ -1180,9 +1180,9 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.2.5"
+version = "2.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b0b929d511467233429c45a44ac1dcaa21ba0f5ba11e4879e6ed28ddb4f9df4"
+checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
 dependencies = [
  "equivalent",
  "hashbrown 0.14.3",
@@ -1901,7 +1901,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9"
 dependencies = [
  "fixedbitset",
- "indexmap 2.2.5",
+ "indexmap 2.2.6",
 ]
 
 [[package]]
@@ -2124,7 +2124,7 @@ dependencies = [
 
 [[package]]
 name = "qcs"
-version = "0.21.4"
+version = "0.21.7"
 dependencies = [
  "assert2",
  "async-trait",
@@ -2136,7 +2136,7 @@ dependencies = [
  "float-cmp",
  "futures",
  "hex",
- "indexmap 1.9.3",
+ "indexmap 2.2.6",
  "insta",
  "itertools 0.11.0",
  "lazy_static",
@@ -2260,7 +2260,7 @@ dependencies = [
 
 [[package]]
 name = "qcs-sdk-python"
-version = "0.17.4"
+version = "0.17.7"
 dependencies = [
  "async-trait",
  "numpy",
@@ -2290,11 +2290,11 @@ checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
 
 [[package]]
 name = "quil-rs"
-version = "0.23.0"
-source = "git+https://github.com/rigetti/quil-rs?tag=quil-py/v0.7.0#3bb618124c2165b7329c58c0f217d8ee9d816e67"
+version = "0.25.1"
+source = "git+https://github.com/rigetti/quil-rs?tag=quil-py/v0.9.1#4179fb03feff6b83edfb7a0448b0b3967ed28212"
 dependencies = [
  "approx",
- "indexmap 2.2.5",
+ "indexmap 2.2.6",
  "itertools 0.12.1",
  "lexical",
  "ndarray",
@@ -3381,7 +3381,7 @@ version = "0.19.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1b5bb770da30e5cbfde35a2d7b9b8a2c4b8ef89548a7a6aeab5c9a576e3e7421"
 dependencies = [
- "indexmap 2.2.5",
+ "indexmap 2.2.6",
  "serde",
  "serde_spanned",
  "toml_datetime",
@@ -3394,7 +3394,7 @@ version = "0.22.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c12219811e0c1ba077867254e5ad62ee2c9c190b0d957110750ac0cda1ae96cd"
 dependencies = [
- "indexmap 2.2.5",
+ "indexmap 2.2.6",
  "serde",
  "serde_spanned",
  "toml_datetime",
diff --git a/pkgs/development/python-modules/qcs-sdk-python/default.nix b/pkgs/development/python-modules/qcs-sdk-python/default.nix
index 100a7874fd18..669552abf5b5 100644
--- a/pkgs/development/python-modules/qcs-sdk-python/default.nix
+++ b/pkgs/development/python-modules/qcs-sdk-python/default.nix
@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "qcs-sdk-python";
-  version = "0.17.4";
+  version = "0.17.7";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -21,13 +21,13 @@ buildPythonPackage rec {
     owner = "rigetti";
     repo = "qcs-sdk-rust";
     rev = "python/v${version}";
-    hash = "sha256-Z/NK+xnugFieJqAbvGaVvxUaz9RC1vpWb4ydZTVbZeU=";
+    hash = "sha256-6Rh5gQH+ObpWGR9rYJfkXnGfG1GjKLn+ckiR7RhKzoE=";
   };
 
   cargoDeps = rustPlatform.importCargoLock {
     lockFile = ./Cargo.lock;
     outputHashes = {
-      "quil-rs-0.23.0" = "sha256-l9wj1j7PJ5L497dPlkEpJ4ctAfjUIada5Vbn2h5ioVE=";
+      "quil-rs-0.25.1" = "sha256-zC4DEjCN6y9XeZlzmXHSTbVTpFQ4Srozix89IHDhHXc=";
     };
   };
 

From db195a8bedc44d62266582a8aacbf64c0b294607 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sun, 21 Apr 2024 19:56:32 -0700
Subject: [PATCH 04/30] python311Packages.qcs-api-client: 0.25.0 -> 0.25.1

Diff: https://github.com/rigetti/qcs-api-client-python/compare/refs/tags/v0.25.0...v0.25.1

Changelog: https://github.com/rigetti/qcs-api-client-python/releases/tag/v0.25.1
---
 pkgs/development/python-modules/qcs-api-client/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/qcs-api-client/default.nix b/pkgs/development/python-modules/qcs-api-client/default.nix
index 98e3b05812f1..dca4664778a7 100644
--- a/pkgs/development/python-modules/qcs-api-client/default.nix
+++ b/pkgs/development/python-modules/qcs-api-client/default.nix
@@ -23,16 +23,16 @@
 
 buildPythonPackage rec {
   pname = "qcs-api-client";
-  version = "0.25.0";
+  version = "0.25.1";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   src = fetchFromGitHub {
     owner = "rigetti";
     repo = "qcs-api-client-python";
     rev = "refs/tags/v${version}";
-    hash = "sha256-dKjiicrPLRlaIwHwSqpY5dBMTzrZD4xfw3h54IN3rh0=";
+    hash = "sha256-GtHAV4BvBdexjJxlT1jcNklSogYor2aWoQI2QNs/dOQ=";
   };
 
   patches = [

From cb2a4266c1fbb6d578e2de5d7fe68e28fabe5749 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sun, 21 Apr 2024 20:13:17 -0700
Subject: [PATCH 05/30] python311Packages.pyquil: 4.8.0 -> 4.9.2

Diff: https://github.com/rigetti/pyquil/compare/refs/tags/v4.8.0...v4.9.2

Changelog: https://github.com/rigetti/pyquil/blob/v4.9.2/CHANGELOG.md
---
 pkgs/development/python-modules/pyquil/default.nix | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/pkgs/development/python-modules/pyquil/default.nix b/pkgs/development/python-modules/pyquil/default.nix
index dc718777af70..77f2f3df334e 100644
--- a/pkgs/development/python-modules/pyquil/default.nix
+++ b/pkgs/development/python-modules/pyquil/default.nix
@@ -3,7 +3,6 @@
   buildPythonPackage,
   deprecated,
   fetchFromGitHub,
-  importlib-metadata,
   ipython,
   lark,
   matplotlib-inline,
@@ -12,7 +11,6 @@
   numpy,
   packaging,
   poetry-core,
-  pydantic,
   pytest-asyncio,
   pytest-mock,
   pytestCheckHook,
@@ -27,20 +25,21 @@
   types-deprecated,
   types-python-dateutil,
   types-retry,
+  typing-extensions,
 }:
 
 buildPythonPackage rec {
   pname = "pyquil";
-  version = "4.8.0";
+  version = "4.9.2";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   src = fetchFromGitHub {
     owner = "rigetti";
     repo = "pyquil";
     rev = "refs/tags/v${version}";
-    hash = "sha256-MGI+R3oteqDWsXP+SlAGSRGiQiAj44YG6V7o90A4Krc=";
+    hash = "sha256-TxmQ9QXTTr4Xv37WmgArfK8Q5H1zAu8qx8wRsvK+vVM=";
   };
 
   pythonRelaxDeps = [
@@ -61,7 +60,6 @@ buildPythonPackage rec {
     networkx
     numpy
     packaging
-    pydantic
     qcs-sdk-python
     rpcq
     scipy
@@ -69,7 +67,8 @@ buildPythonPackage rec {
     types-deprecated
     types-python-dateutil
     types-retry
-  ] ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
+    typing-extensions
+  ];
 
   nativeCheckInputs = [
     nest-asyncio

From d69d444fe1d1628782a911820fd8d17c2b7906e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A1szl=C3=B3=20Kupcsik?= <koopac@gmail.com>
Date: Sat, 13 Apr 2024 00:07:36 +0200
Subject: [PATCH 06/30] rPackages.immunotation: cache external URLs

---
 pkgs/development/r-modules/default.nix        | 37 +++++++++++++++
 .../r-modules/patches/immunotation.patch      | 47 +++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 pkgs/development/r-modules/patches/immunotation.patch

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 096bfd6b1bdd..4c5bd91e35e4 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -1318,6 +1318,43 @@ let
       buildInputs = [ cacert ] ++ attrs.buildInputs;
     });
 
+
+    immunotation = let
+      MHC41alleleList = fetchurl {
+        url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list";
+        hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg=";
+      };
+
+      MHCII40alleleList = fetchurl {
+        url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list";
+        hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40=";
+      };
+
+      # List of valid countries, regions and ethnic groups
+      # The original page is changing a bit every day, but the relevant
+      # content does not. Use archive.org to get a stable snapshot.
+      # It can be updated from time to time, or when the package becomes
+      # deficient. This may be difficult to know.
+      # Update the snapshot date, and add id_ after it, as described here:
+      # https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/
+      validGeographics = fetchurl {
+        url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp";
+        hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak=";
+      };
+    in old.immunotation.overrideAttrs (attrs: {
+      patches = [ ./patches/immunotation.patch ];
+      postPatch = ''
+        substituteInPlace "R/external_resources_input.R" --replace-fail \
+          "nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
+
+        substituteInPlace "R/external_resources_input.R" --replace-fail \
+          "nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
+
+        substituteInPlace "R/AFND_interface.R" --replace-fail \
+          "nix-valid-geographics" ${validGeographics}
+      '';
+    });
+
     rstan = old.rstan.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
diff --git a/pkgs/development/r-modules/patches/immunotation.patch b/pkgs/development/r-modules/patches/immunotation.patch
new file mode 100644
index 000000000000..2019e8e50a02
--- /dev/null
+++ b/pkgs/development/r-modules/patches/immunotation.patch
@@ -0,0 +1,47 @@
+diff --git a/R/AFND_interface.R b/R/AFND_interface.R
+index b62e8e0..0f22d85 100644
+--- a/R/AFND_interface.R
++++ b/R/AFND_interface.R
+@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
+ #' @return list of valid countries, regions and ethnic origin
+ #' @keywords internal
+ get_valid_geographics <- function() {
+-    url <- "http://www.allelefrequencies.net/hla6006a.asp?"
+-    html_input <- getURL(url, read_method = "html")
+-    
++    # http://www.allelefrequencies.net/hla6006a.asp?
++    html_input <- xml2::read_html("nix-valid-geographics")
++      
+     rvest_tables <- rvest::html_table(html_input, fill = TRUE)
+     
+     # country
+diff --git a/R/external_resources_input.R b/R/external_resources_input.R
+index c4b1dc1..8fc5881 100644
+--- a/R/external_resources_input.R
++++ b/R/external_resources_input.R
+@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
+ # MHC I
+ # netmhcI_input_template is an internal variable containing list of valid 
+ # NetMHCpan input alleles
+-netmhcI_input_template <- getURL(
+-    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
+-    read_method = "delim", delim = "\t",
+-    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
++netmhcI_input_template <- readr::read_delim(
++        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
++	"nix-NetMHCpan-4.1-allele-list",
++	delim = "\t",
++	skip = 0,
++        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
++    )
+ 
+ # MHC II
+-lines <- getURL(
+-    URL = paste0("https://services.healthtech.dtu.dk/services/",
+-    "NetMHCIIpan-4.0/alleles_name.list"),
+-    read_method = "lines")
++# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
++lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
+ lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
+ netmhcII_input_template <- suppressWarnings(
+     suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))

From 361874c944599d40faf1e810a287b3c1d4d29610 Mon Sep 17 00:00:00 2001
From: Gavin John <>
Date: Tue, 14 May 2024 11:38:21 -0500
Subject: [PATCH 07/30] licenses: Add NCBI-PD

---
 lib/licenses.nix | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/lib/licenses.nix b/lib/licenses.nix
index 7d2a22bc25a4..8dbdf27fa845 100644
--- a/lib/licenses.nix
+++ b/lib/licenses.nix
@@ -902,6 +902,17 @@ in mkLicense lset) ({
     free = false;
   };
 
+  ncbiPd = {
+    spdxId = "NCBI-PD";
+    fullname = "NCBI Public Domain Notice";
+    # Due to United States copyright law, anything with this "license" does not have a copyright in the
+    # jurisdiction of the United States. However, other jurisdictions may assign the United States
+    # government copyright to the work, and the license explicitly states that in such a case, no license
+    # is granted. This is nonfree and nonredistributable in most jurisdictions other than the United States.
+    free = false;
+    redistributable = false;
+  };
+
   ncsa = {
     spdxId = "NCSA";
     fullName = "University of Illinois/NCSA Open Source License";

From 438273dac74c61f3c03c81a06dfce4b96454120c Mon Sep 17 00:00:00 2001
From: Gavin John <>
Date: Tue, 14 May 2024 11:38:53 -0500
Subject: [PATCH 08/30] sratoolkit: Assign correct license

---
 pkgs/applications/science/biology/sratoolkit/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix
index a36157ed5d16..fa406716fd0f 100644
--- a/pkgs/applications/science/biology/sratoolkit/default.nix
+++ b/pkgs/applications/science/biology/sratoolkit/default.nix
@@ -49,7 +49,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     homepage = "https://github.com/ncbi/sra-tools";
     description = "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.";
-    license = licenses.publicDomain;
+    license = licenses.ncbiPd;
     maintainers = with maintainers; [ thyol ];
     platforms = [ "x86_64-linux" ];
   };

From 43d607fe97ce2bac78586b68bc20f59dd28da7c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Sat, 11 May 2024 13:26:29 -0700
Subject: [PATCH 09/30] bitwarden-cli: 2024.3.1 -> 2024.4.1

Diff: https://github.com/bitwarden/clients/compare/cli-v2024.3.1...cli-v2024.4.1

Changelog: https://github.com/bitwarden/clients/releases/tag/cli-v2024.4.0
           https://github.com/bitwarden/clients/releases/tag/cli-v2024.4.1
---
 pkgs/by-name/bi/bitwarden-cli/package.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/bi/bitwarden-cli/package.nix b/pkgs/by-name/bi/bitwarden-cli/package.nix
index 656c1e60ec21..690535b3a7b4 100644
--- a/pkgs/by-name/bi/bitwarden-cli/package.nix
+++ b/pkgs/by-name/bi/bitwarden-cli/package.nix
@@ -10,18 +10,18 @@
 
 buildNpmPackage rec {
   pname = "bitwarden-cli";
-  version = "2024.3.1";
+  version = "2024.4.1";
 
   src = fetchFromGitHub {
     owner = "bitwarden";
     repo = "clients";
     rev = "cli-v${version}";
-    hash = "sha256-JBEP4dNGL4rYKl2qNyhB2y/wZunikaGFltGVXLxgMWI=";
+    hash = "sha256-Dz7EActqXd97kNxEaNINj2O6TLZWEgHHg1lOIa2+Lt4=";
   };
 
   nodejs = nodejs_18;
 
-  npmDepsHash = "sha256-vNudSHIMmF7oXGz+ZymQahyHebs/CBDc6Oy1g0A5nqA=";
+  npmDepsHash = "sha256-fjYez3nSDsG5kYtrun3CkDCz1GNAjNlwPzEL+/9qQRU=";
 
   nativeBuildInputs = [
     python3

From 0b43348b0679f6bf92054e4b56e23e6feef5e45a Mon Sep 17 00:00:00 2001
From: Tomo <68489118+tomodachi94@users.noreply.github.com>
Date: Mon, 20 May 2024 15:50:29 -0700
Subject: [PATCH 10/30] mpack: move to pkgs/by-name/mp

---
 pkgs/{tools/networking => by-name/mp}/mpack/CVE-2011-4919.patch | 0
 pkgs/{tools/networking => by-name/mp}/mpack/build-fix.patch     | 0
 .../mpack/default.nix => by-name/mp/mpack/package.nix}          | 0
 .../networking => by-name/mp}/mpack/sendmail-via-execvp.diff    | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 5 files changed, 2 deletions(-)
 rename pkgs/{tools/networking => by-name/mp}/mpack/CVE-2011-4919.patch (100%)
 rename pkgs/{tools/networking => by-name/mp}/mpack/build-fix.patch (100%)
 rename pkgs/{tools/networking/mpack/default.nix => by-name/mp/mpack/package.nix} (100%)
 rename pkgs/{tools/networking => by-name/mp}/mpack/sendmail-via-execvp.diff (100%)

diff --git a/pkgs/tools/networking/mpack/CVE-2011-4919.patch b/pkgs/by-name/mp/mpack/CVE-2011-4919.patch
similarity index 100%
rename from pkgs/tools/networking/mpack/CVE-2011-4919.patch
rename to pkgs/by-name/mp/mpack/CVE-2011-4919.patch
diff --git a/pkgs/tools/networking/mpack/build-fix.patch b/pkgs/by-name/mp/mpack/build-fix.patch
similarity index 100%
rename from pkgs/tools/networking/mpack/build-fix.patch
rename to pkgs/by-name/mp/mpack/build-fix.patch
diff --git a/pkgs/tools/networking/mpack/default.nix b/pkgs/by-name/mp/mpack/package.nix
similarity index 100%
rename from pkgs/tools/networking/mpack/default.nix
rename to pkgs/by-name/mp/mpack/package.nix
diff --git a/pkgs/tools/networking/mpack/sendmail-via-execvp.diff b/pkgs/by-name/mp/mpack/sendmail-via-execvp.diff
similarity index 100%
rename from pkgs/tools/networking/mpack/sendmail-via-execvp.diff
rename to pkgs/by-name/mp/mpack/sendmail-via-execvp.diff
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index ce162c99e57e..6a5a2b12f8fa 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11011,8 +11011,6 @@ with pkgs;
 
   mkgmap-splitter = callPackage ../applications/misc/mkgmap/splitter { };
 
-  mpack = callPackage ../tools/networking/mpack { };
-
   mtm = callPackage ../tools/misc/mtm { };
 
   op-geth = callPackage ../applications/blockchains/optimism/geth.nix {

From 86a7622c74a862e124adc0f1f510a1f1b89311b5 Mon Sep 17 00:00:00 2001
From: Tomo <68489118+tomodachi94@users.noreply.github.com>
Date: Mon, 20 May 2024 15:51:54 -0700
Subject: [PATCH 11/30] mpack: format with nixfmt-rfc-style

---
 pkgs/by-name/mp/mpack/package.nix | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/pkgs/by-name/mp/mpack/package.nix b/pkgs/by-name/mp/mpack/package.nix
index 669ef500c455..3722d5c610e2 100644
--- a/pkgs/by-name/mp/mpack/package.nix
+++ b/pkgs/by-name/mp/mpack/package.nix
@@ -1,4 +1,8 @@
-{ lib, stdenv, fetchurl }:
+{
+  lib,
+  stdenv,
+  fetchurl,
+}:
 
 stdenv.mkDerivation rec {
   pname = "mpack";
@@ -9,7 +13,11 @@ stdenv.mkDerivation rec {
     sha256 = "0k590z96509k96zxmhv72gkwhrlf55jkmyqlzi72m61r7axhhh97";
   };
 
-  patches = [ ./build-fix.patch ./sendmail-via-execvp.diff ./CVE-2011-4919.patch ];
+  patches = [
+    ./build-fix.patch
+    ./sendmail-via-execvp.diff
+    ./CVE-2011-4919.patch
+  ];
 
   postPatch = ''
     for f in *.{c,man,pl,unix} ; do

From 84b113b900e65f0434a9847222f3f0ad440df552 Mon Sep 17 00:00:00 2001
From: Tomo <68489118+tomodachi94@users.noreply.github.com>
Date: Mon, 20 May 2024 15:52:12 -0700
Subject: [PATCH 12/30] mpack: adopt

---
 pkgs/by-name/mp/mpack/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/mp/mpack/package.nix b/pkgs/by-name/mp/mpack/package.nix
index 3722d5c610e2..1f1de3817ff7 100644
--- a/pkgs/by-name/mp/mpack/package.nix
+++ b/pkgs/by-name/mp/mpack/package.nix
@@ -40,5 +40,6 @@ stdenv.mkDerivation rec {
     description = "Utilities for encoding and decoding binary files in MIME";
     license = licenses.free;
     platforms = platforms.linux;
+    maintainers = with maintainers; [ tomodachi94 ];
   };
 }

From c2e1c242f469f2d11c6a077ee2de4b1e26701905 Mon Sep 17 00:00:00 2001
From: Tomo <68489118+Tomodachi94@users.noreply.github.com>
Date: Mon, 20 May 2024 16:03:31 -0700
Subject: [PATCH 13/30] mpack: add passthru.tests.version

---
 pkgs/by-name/mp/mpack/package.nix | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/pkgs/by-name/mp/mpack/package.nix b/pkgs/by-name/mp/mpack/package.nix
index 1f1de3817ff7..d428fbe664c9 100644
--- a/pkgs/by-name/mp/mpack/package.nix
+++ b/pkgs/by-name/mp/mpack/package.nix
@@ -2,6 +2,8 @@
   lib,
   stdenv,
   fetchurl,
+  testers,
+  mpack,
 }:
 
 stdenv.mkDerivation rec {
@@ -36,6 +38,16 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  passthru.tests = {
+    version = testers.testVersion {
+      command = ''
+        mpack 2>&1 || echo "mpack exited with error code $?"
+      '';
+      package = mpack;
+      version = "mpack version ${version}";
+    };
+  };
+
   meta = with lib; {
     description = "Utilities for encoding and decoding binary files in MIME";
     license = licenses.free;

From ead03f474aa2d9e9af2b3479b279fe9d140b3429 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <nix@dotlambda.de>
Date: Thu, 23 May 2024 15:34:02 -0700
Subject: [PATCH 14/30] chatty: 0.8.2 -> 0.8.3

Changelog: https://gitlab.gnome.org/World/Chatty/-/blob/v0.8.3/NEWS
---
 .../instant-messengers/chatty/default.nix          | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/networking/instant-messengers/chatty/default.nix b/pkgs/applications/networking/instant-messengers/chatty/default.nix
index ea43f470e8bb..c939412e152f 100644
--- a/pkgs/applications/networking/instant-messengers/chatty/default.nix
+++ b/pkgs/applications/networking/instant-messengers/chatty/default.nix
@@ -15,6 +15,7 @@
 , gnome-desktop
 , gspell
 , gtk4
+, gtksourceview5
 , gst_all_1
 , json-glib
 , libgcrypt
@@ -28,17 +29,17 @@
 , plugins ? [ ]
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "chatty";
-  version = "0.8.2";
+  version = "0.8.3";
 
   src = fetchFromGitLab {
     domain = "gitlab.gnome.org";
     owner = "World";
     repo = "Chatty";
-    rev = "v${version}";
+    rev = "v${finalAttrs.version}";
     fetchSubmodules = true;
-    hash = "sha256-7SdoN9JjGwELOdISJwS1Afcydp/rE2uq/tHO/UrFKNU=";
+    hash = "sha256-Ywed/8PhOgmzcka+5dyxjmWTcDBPF90LW+C2eeQmyLo=";
   };
 
   nativeBuildInputs = [
@@ -59,6 +60,7 @@ stdenv.mkDerivation rec {
     gnome-desktop
     gspell
     gtk4
+    gtksourceview5
     gst_all_1.gstreamer
     json-glib
     libgcrypt
@@ -82,9 +84,9 @@ stdenv.mkDerivation rec {
     description = "XMPP and SMS messaging via libpurple and ModemManager";
     mainProgram = "chatty";
     homepage = "https://gitlab.gnome.org/World/Chatty";
-    changelog = "https://gitlab.gnome.org/World/Chatty/-/blob/${src.rev}/NEWS";
+    changelog = "https://gitlab.gnome.org/World/Chatty/-/blob/${finalAttrs.src.rev}/NEWS";
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ dotlambda ];
     platforms = platforms.linux;
   };
-}
+})

From 72b6de3b3338aa4018a8d89d3fca6b95c8509c51 Mon Sep 17 00:00:00 2001
From: Tristan Ross <tristan.ross@midstall.com>
Date: Fri, 24 May 2024 18:16:15 -0700
Subject: [PATCH 15/30] tbb: fix cross compiling for i686

---
 pkgs/development/libraries/tbb/2020_3.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/development/libraries/tbb/2020_3.nix b/pkgs/development/libraries/tbb/2020_3.nix
index 55bb9849d919..aa526591eb9e 100644
--- a/pkgs/development/libraries/tbb/2020_3.nix
+++ b/pkgs/development/libraries/tbb/2020_3.nix
@@ -57,6 +57,7 @@ stdenv.mkDerivation rec {
   ] ++ (lib.optional (stdenv.buildPlatform != stdenv.hostPlatform)
     (if stdenv.hostPlatform.isAarch64 then "arch=arm64"
     else if stdenv.hostPlatform.isx86_64 then "arch=intel64"
+    else if stdenv.hostPlatform.isi686 then "arch=ia32"
     else throw "Unsupported cross architecture"));
 
   enableParallelBuilding = true;

From ab7735598b27f92c04d828d1edb38fc0f3df0f9c Mon Sep 17 00:00:00 2001
From: Borja Clemente <borja.clemente@gmail.com>
Date: Sat, 25 May 2024 15:22:31 +0200
Subject: [PATCH 16/30] maintainers: add clebs

Signed-off-by: Borja Clemente <borja.clemente@gmail.com>
---
 maintainers/maintainer-list.nix | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index 1785b1acdb26..7baf35c5781a 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -3808,6 +3808,15 @@
     githubId = 199180;
     name = "Claes Wallin";
   };
+  clebs = {
+    email = "borja.clemente@gmail.com";
+    github = "clebs";
+    githubId = 1059661;
+    name = "Borja Clemente";
+    keys = [{
+      fingerprint = "C4E1 58BD FD33 3C77 B6C7  178E 2539 757E F64C 60DD";
+    }];
+  };
   cleeyv = {
     email = "cleeyv@riseup.net";
     github = "cleeyv";

From 64973309bba193864683109d56bb7d64987b57e1 Mon Sep 17 00:00:00 2001
From: superherointj <5861043+superherointj@users.noreply.github.com>
Date: Wed, 22 May 2024 21:39:31 -0300
Subject: [PATCH 17/30] nginx: make image filter optional

Reduces nginx package size from 109.88 MiB to 41.99 MiB. Reduction of -67.88 MiB.

GD (libgd.github.io) is a library for the dynamic creation of images.

Co-authored-by: @ulrikstrid
---
 pkgs/servers/http/nginx/generic.nix | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/pkgs/servers/http/nginx/generic.nix b/pkgs/servers/http/nginx/generic.nix
index 67e84f08448e..11171a331ba9 100644
--- a/pkgs/servers/http/nginx/generic.nix
+++ b/pkgs/servers/http/nginx/generic.nix
@@ -4,6 +4,7 @@ outer@{ lib, stdenv, fetchurl, fetchpatch, openssl, zlib, pcre, libxml2, libxslt
 , nixosTests
 , installShellFiles, substituteAll, removeReferencesTo, gd, geoip, perl
 , withDebug ? false
+, withImageFilter ? false
 , withKTLS ? true
 , withStream ? true
 , withMail ? false
@@ -64,9 +65,10 @@ stdenv.mkDerivation {
     removeReferencesTo
   ] ++ nativeBuildInputs;
 
-  buildInputs = [ openssl zlib pcre libxml2 libxslt gd geoip perl ]
+  buildInputs = [ openssl zlib pcre libxml2 libxslt geoip perl ]
     ++ buildInputs
-    ++ mapModules "inputs";
+    ++ mapModules "inputs"
+    ++ lib.optional withImageFilter gd;
 
   configureFlags = [
     "--sbin-path=bin/nginx"
@@ -112,8 +114,8 @@ stdenv.mkDerivation {
     "--with-http_perl_module"
     "--with-perl=${perl}/bin/perl"
     "--with-perl_modules_path=lib/perl5"
-  ] ++ lib.optional withSlice "--with-http_slice_module"
-    ++ lib.optional (gd != null) "--with-http_image_filter_module"
+  ] ++ lib.optional withImageFilter "--with-http_image_filter_module"
+    ++ lib.optional withSlice "--with-http_slice_module"
     ++ lib.optional (geoip != null) "--with-http_geoip_module"
     ++ lib.optional (withStream && geoip != null) "--with-stream_geoip_module"
     ++ lib.optional (with stdenv.hostPlatform; isLinux || isFreeBSD) "--with-file-aio"

From e3e087e9ead7aa8892f38a5fa7443cbc9a0f5cbd Mon Sep 17 00:00:00 2001
From: superherointj <5861043+superherointj@users.noreply.github.com>
Date: Thu, 23 May 2024 07:35:40 -0300
Subject: [PATCH 18/30] nginx: make geoip optional

---
 pkgs/servers/http/nginx/generic.nix | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pkgs/servers/http/nginx/generic.nix b/pkgs/servers/http/nginx/generic.nix
index 11171a331ba9..bc97c4972be7 100644
--- a/pkgs/servers/http/nginx/generic.nix
+++ b/pkgs/servers/http/nginx/generic.nix
@@ -4,6 +4,7 @@ outer@{ lib, stdenv, fetchurl, fetchpatch, openssl, zlib, pcre, libxml2, libxslt
 , nixosTests
 , installShellFiles, substituteAll, removeReferencesTo, gd, geoip, perl
 , withDebug ? false
+, withGeoIP ? false
 , withImageFilter ? false
 , withKTLS ? true
 , withStream ? true
@@ -65,9 +66,10 @@ stdenv.mkDerivation {
     removeReferencesTo
   ] ++ nativeBuildInputs;
 
-  buildInputs = [ openssl zlib pcre libxml2 libxslt geoip perl ]
+  buildInputs = [ openssl zlib pcre libxml2 libxslt perl ]
     ++ buildInputs
     ++ mapModules "inputs"
+    ++ lib.optional withGeoIP geoip
     ++ lib.optional withImageFilter gd;
 
   configureFlags = [
@@ -116,8 +118,7 @@ stdenv.mkDerivation {
     "--with-perl_modules_path=lib/perl5"
   ] ++ lib.optional withImageFilter "--with-http_image_filter_module"
     ++ lib.optional withSlice "--with-http_slice_module"
-    ++ lib.optional (geoip != null) "--with-http_geoip_module"
-    ++ lib.optional (withStream && geoip != null) "--with-stream_geoip_module"
+    ++ lib.optionals withGeoIP ([ "--with-http_geoip_module" ] ++ lib.optional withStream "--with-stream_geoip_module")
     ++ lib.optional (with stdenv.hostPlatform; isLinux || isFreeBSD) "--with-file-aio"
     ++ configureFlags
     ++ map (mod: "--add-module=${mod.src}") modules;

From f2a202ff38bdca293e8b96de05e983f1f603365a Mon Sep 17 00:00:00 2001
From: superherointj <5861043+superherointj@users.noreply.github.com>
Date: Sat, 25 May 2024 12:12:50 -0300
Subject: [PATCH 19/30] nixos/doc/rl-2411: nginx now has gd, geoip as an
 optional

---
 nixos/doc/manual/release-notes/rl-2411.section.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nixos/doc/manual/release-notes/rl-2411.section.md b/nixos/doc/manual/release-notes/rl-2411.section.md
index 343c1fc5933d..2338cf6e6fee 100644
--- a/nixos/doc/manual/release-notes/rl-2411.section.md
+++ b/nixos/doc/manual/release-notes/rl-2411.section.md
@@ -12,6 +12,8 @@
 
 ## Backward Incompatibilities {#sec-release-24.11-incompatibilities}
 
+- `nginx` package no longer includes `gd` and `geoip` dependencies. For enabling it, override `nginx` package with the optionals `withImageFilter` and `withGeoIP`.
+
 - `nvimpager` was updated to version 0.13.0, which changes the order of user and
   nvimpager settings: user commands in `-c` and `--cmd` now override the
   respective default settings because they are executed later.

From fce0a3529351b896acc8bf763fb23a8ecf69f820 Mon Sep 17 00:00:00 2001
From: Borja Clemente <borja.clemente@gmail.com>
Date: Sat, 25 May 2024 15:23:03 +0200
Subject: [PATCH 20/30] libideviceactivation: init at 1.1.1

Signed-off-by: Borja Clemente <borja.clemente@gmail.com>
---
 .../li/libideviceactivation/package.nix       | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 pkgs/by-name/li/libideviceactivation/package.nix

diff --git a/pkgs/by-name/li/libideviceactivation/package.nix b/pkgs/by-name/li/libideviceactivation/package.nix
new file mode 100644
index 000000000000..74ee9ddc2cc9
--- /dev/null
+++ b/pkgs/by-name/li/libideviceactivation/package.nix
@@ -0,0 +1,55 @@
+{
+  stdenv,
+  fetchFromGitHub,
+  lib,
+  pkg-config,
+  automake,
+  autoreconfHook,
+  libtool,
+  libplist,
+  libimobiledevice,
+  libxml2,
+  curl,
+  usbmuxd,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "libideviceactivation";
+  version = "1.1.1";
+
+  src = fetchFromGitHub {
+    owner = "libimobiledevice";
+    repo = "libideviceactivation";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-owcQpCN4+A785oy9pCboJIyfpgZ6X+8PRzqGtWpYl2w=";
+  };
+
+  nativeBuildInputs = [
+    pkg-config
+    automake
+    autoreconfHook
+  ];
+
+  buildInputs = [
+    libtool
+    libplist
+    libimobiledevice
+    libxml2
+    curl
+    usbmuxd
+  ];
+
+  installFlags = [ "PREFIX=$(out)" ];
+
+  meta = {
+    description = "A library to manage the activation process of Apple iOS devices.";
+    homepage = "https://libimobiledevice.org";
+    license = with lib.licenses; [
+      lgpl21
+      gpl3
+    ];
+    mainProgram = "ideviceactivation";
+    platforms = lib.platforms.linux;
+    maintainers = with lib.maintainers; [ clebs ];
+  };
+})

From b28f7c5303a1ccb8a0d73b91df415b6d86c8eb9d Mon Sep 17 00:00:00 2001
From: Connor Baker <connor.baker@tweag.io>
Date: Sat, 25 May 2024 01:40:05 +0000
Subject: [PATCH 21/30] python3Packages.apricot-select: move scikit-learn and
 torchvision to dependencies

These are needed when building the package, not just during the checkPhase. This can be observed by setting
doCheck to false.
---
 pkgs/development/python-modules/apricot-select/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/apricot-select/default.nix b/pkgs/development/python-modules/apricot-select/default.nix
index b50707e96e6f..20d47913d19b 100644
--- a/pkgs/development/python-modules/apricot-select/default.nix
+++ b/pkgs/development/python-modules/apricot-select/default.nix
@@ -37,15 +37,15 @@ buildPythonPackage rec {
   dependencies = [
     numba
     numpy
+    scikit-learn
     scipy
+    torchvision
     tqdm
   ];
 
   nativeCheckInputs = [
     pynose
     pytestCheckHook
-    scikit-learn
-    torchvision
   ];
 
   pythonImportsCheck = [ "apricot" ];

From ea95a42ccdabbf5f262491f85a4eacb2fa3a03e0 Mon Sep 17 00:00:00 2001
From: StarrFox <StarrFox6312@gmail.com>
Date: Sat, 25 May 2024 21:29:40 -0500
Subject: [PATCH 22/30] python3Packages.import-expression: 1.1.4 -> 1.1.5

---
 .../import-expression/default.nix             | 20 ++++++-------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/pkgs/development/python-modules/import-expression/default.nix b/pkgs/development/python-modules/import-expression/default.nix
index 4dc6d053154d..5415d3db5989 100644
--- a/pkgs/development/python-modules/import-expression/default.nix
+++ b/pkgs/development/python-modules/import-expression/default.nix
@@ -1,7 +1,7 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
+  fetchPypi,
   fetchpatch,
   pytestCheckHook,
   astunparse,
@@ -9,23 +9,15 @@
 }:
 buildPythonPackage rec {
   pname = "import-expression";
-  version = "1.1.4";
+  version = "1.1.5";
   pyproject = true;
 
-  src = fetchFromGitHub {
-    owner = "ioistired";
-    repo = "import-expression-parser";
-    rev = "refs/tags/v${version}";
-    hash = "sha256-mll2NePB7fthzltLOk6D9BgaDpH6GaW4psqcGun/0qM=";
+  src = fetchPypi {
+    inherit version;
+    pname = "import_expression";
+    hash = "sha256-mVlYj8/I3LFEoHJRds/vbCjH2x/C1oNiUCXmh1FtQME=";
   };
 
-  patches = [
-    (fetchpatch {
-      url = "https://github.com/ioistired/import-expression-parser/commit/3daf968c3163b64685aa529740e132f0df5ab262.patch";
-      hash = "sha256-2Ubv3onor2D26udZbDDMb3iNLopEIRnIcO/X6WUVmJU=";
-    })
-  ];
-
   nativeBuildInputs = [ setuptools ];
   propagatedBuildInputs = [ astunparse ];
   nativeCheckInputs = [ pytestCheckHook ];

From b1c46e1d2e20ba001be75dd197ad3adbe19b89d2 Mon Sep 17 00:00:00 2001
From: Connor Baker <connor.baker@tweag.io>
Date: Sat, 25 May 2024 01:40:55 +0000
Subject: [PATCH 23/30] python3Packages.apricot-select: disable flaky tests

---
 .../python-modules/apricot-select/default.nix          | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/pkgs/development/python-modules/apricot-select/default.nix b/pkgs/development/python-modules/apricot-select/default.nix
index 20d47913d19b..4b735ec1c98e 100644
--- a/pkgs/development/python-modules/apricot-select/default.nix
+++ b/pkgs/development/python-modules/apricot-select/default.nix
@@ -56,6 +56,16 @@ buildPythonPackage rec {
     "tests/test_optimizers/test_knapsack_feature_based.py"
   ];
 
+  # NOTE: These tests seem to be flaky.
+  disabledTests = [
+    "test_digits_modular"
+    "test_digits_modular_object"
+    "test_digits_modular_sparse"
+    "test_digits_sqrt_modular"
+    "test_digits_sqrt_modular_object"
+    "test_digits_sqrt_modular_sparse"
+  ];
+
   meta = with lib; {
     description = "Module for submodular optimization for the purpose of selecting subsets of massive data sets";
     homepage = "https://github.com/jmschrei/apricot";

From 2005aa65a1fd01d6dca149655d4e7f7b6c90428b Mon Sep 17 00:00:00 2001
From: luftmensch-luftmensch <valentinobocchetti59@gmail.com>
Date: Wed, 22 May 2024 18:38:39 +0200
Subject: [PATCH 24/30] errands: 46.2 -> 46.2.2

---
 pkgs/by-name/er/errands/package.nix | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/pkgs/by-name/er/errands/package.nix b/pkgs/by-name/er/errands/package.nix
index b5114b5e49e5..3c695781d28e 100644
--- a/pkgs/by-name/er/errands/package.nix
+++ b/pkgs/by-name/er/errands/package.nix
@@ -17,7 +17,7 @@
 }:
 python3Packages.buildPythonApplication rec {
   pname = "errands";
-  version = "46.2";
+  version = "46.2.2";
 
   pyproject = false;
 
@@ -25,7 +25,7 @@ python3Packages.buildPythonApplication rec {
     owner = "mrvladus";
     repo = "Errands";
     rev = "refs/tags/${version}";
-    hash = "sha256-p/2dHLWSdDAe0+xTvOgmGscTUPLG+0ddIVHMcHY86xg=";
+    hash = "sha256-lX0exxZMbq/iC41bByMfT478vhOQadPJAN72PHiznKc=";
   };
 
   nativeBuildInputs = [
@@ -59,12 +59,13 @@ python3Packages.buildPythonApplication rec {
     makeWrapperArgs+=("''${gappsWrapperArgs[@]}")
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Manage your tasks";
+    changelog = "https://github.com/mrvladus/Errands/releases/tag/${version}";
     homepage = "https://github.com/mrvladus/Errands";
-    license = licenses.mit;
+    license = lib.licenses.mit;
     mainProgram = "errands";
-    maintainers = with maintainers; [
+    maintainers = with lib.maintainers; [
       luftmensch-luftmensch
       sund3RRR
     ];

From c792626170654fb953cfe5c55f9ee47a1b6da946 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sun, 26 May 2024 18:05:59 +0000
Subject: [PATCH 25/30] neocmakelsp: 0.6.25 -> 0.6.26

---
 .../tools/language-servers/neocmakelsp/default.nix          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/tools/language-servers/neocmakelsp/default.nix b/pkgs/development/tools/language-servers/neocmakelsp/default.nix
index fe2678be6d2c..d3c8d86a14e1 100644
--- a/pkgs/development/tools/language-servers/neocmakelsp/default.nix
+++ b/pkgs/development/tools/language-servers/neocmakelsp/default.nix
@@ -5,16 +5,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "neocmakelsp";
-  version = "0.6.25";
+  version = "0.6.26";
 
   src = fetchFromGitHub {
     owner = "Decodetalkers";
     repo = "neocmakelsp";
     rev = "v${version}";
-    hash = "sha256-2eZ1f0oxCNf0hJEQ8hkvsTwCaAWJrIYCyIY5PNfaxI4=";
+    hash = "sha256-9pCi7bevgE2tO0n1LvhLIcFV8sVpAagkVB8l5WWdIbM=";
   };
 
-  cargoHash = "sha256-mo/d99Y41/pxMzVvI6LkjnhotGV5j0ee4GItly0aqpY=";
+  cargoHash = "sha256-xm+8IDLvPDOFJ6FyeQdpbWgQ9XE6bW5i29W0S9JSQzc=";
 
   meta = with lib; {
     description = "A cmake lsp based on tower-lsp and treesitter";

From 610ee378fcf718b9cc655efa81dc34cf907c72ad Mon Sep 17 00:00:00 2001
From: sternenseemann <sternenseemann@systemli.org>
Date: Mon, 27 May 2024 02:07:07 +0200
Subject: [PATCH 26/30] Revert "srcOnly: reflink if possible and preserve
 attributes"

This reverts commit 7173eb87b8720da79989bbf1ed1fa72465323778.

Reason for revert: This causes too big a rebuild for master (since GHC
uses srcOnly). This went unnoticed due to a stale ofborg rebuild count.
---
 pkgs/build-support/src-only/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/build-support/src-only/default.nix b/pkgs/build-support/src-only/default.nix
index cd8572629cad..2b0db0e267aa 100644
--- a/pkgs/build-support/src-only/default.nix
+++ b/pkgs/build-support/src-only/default.nix
@@ -13,7 +13,7 @@ let
 in
 stdenv.mkDerivation (args // {
   name = "${name}-source";
-  installPhase = "cp -pr --reflink=auto -- . $out";
+  installPhase = "cp -r . $out";
   outputs = [ "out" ];
   separateDebugInfo = false;
   dontUnpack = false;

From 7568ee06c9f8db787588c2168895301a5db4cded Mon Sep 17 00:00:00 2001
From: Connor Baker <connorbaker01@gmail.com>
Date: Sun, 26 May 2024 14:50:31 -0400
Subject: [PATCH 27/30] python3Packages.apricot-select: disable tests by
 default

They can run for hours on Hydra: https://hydra.nixos.org/build/261011861
---
 pkgs/development/python-modules/apricot-select/default.nix | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/pkgs/development/python-modules/apricot-select/default.nix b/pkgs/development/python-modules/apricot-select/default.nix
index 4b735ec1c98e..f05e9b8e5e95 100644
--- a/pkgs/development/python-modules/apricot-select/default.nix
+++ b/pkgs/development/python-modules/apricot-select/default.nix
@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  apricot-select,
   numba,
   numpy,
   pynose,
@@ -66,6 +67,11 @@ buildPythonPackage rec {
     "test_digits_sqrt_modular_sparse"
   ];
 
+  # NOTE: Tests are disabled by default because they can run for hours and timeout on Hydra.
+  doCheck = false;
+
+  passthru.tests.check = apricot-select.overridePythonAttrs { doCheck = true; };
+
   meta = with lib; {
     description = "Module for submodular optimization for the purpose of selecting subsets of massive data sets";
     homepage = "https://github.com/jmschrei/apricot";

From ad43b9c0cf4bd6584c80f50b5388b366ae489621 Mon Sep 17 00:00:00 2001
From: StarrFox <StarrFox6312@gmail.com>
Date: Sun, 26 May 2024 20:02:42 -0500
Subject: [PATCH 28/30] python3Packages.import-expression: update legacy
 attributes

---
 pkgs/development/python-modules/import-expression/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/import-expression/default.nix b/pkgs/development/python-modules/import-expression/default.nix
index 5415d3db5989..3407aa277152 100644
--- a/pkgs/development/python-modules/import-expression/default.nix
+++ b/pkgs/development/python-modules/import-expression/default.nix
@@ -18,8 +18,8 @@ buildPythonPackage rec {
     hash = "sha256-mVlYj8/I3LFEoHJRds/vbCjH2x/C1oNiUCXmh1FtQME=";
   };
 
-  nativeBuildInputs = [ setuptools ];
-  propagatedBuildInputs = [ astunparse ];
+  build-system = [ setuptools ];
+  dependencies = [ astunparse ];
   nativeCheckInputs = [ pytestCheckHook ];
   pytestFlagsArray = [ "tests.py" ];
 

From 150a859d345353d6a42876360dbe70a038a5c786 Mon Sep 17 00:00:00 2001
From: Vincent Laporte <Vincent.Laporte@gmail.com>
Date: Thu, 23 May 2024 09:26:42 +0200
Subject: [PATCH 29/30] =?UTF-8?q?coqPackages.mathcomp-infotheo:=200.6.1=20?=
 =?UTF-8?q?=E2=86=92=200.7.1?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pkgs/development/coq-modules/mathcomp-infotheo/default.nix | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgs/development/coq-modules/mathcomp-infotheo/default.nix b/pkgs/development/coq-modules/mathcomp-infotheo/default.nix
index 6a14e67844c8..cc7d6973c468 100644
--- a/pkgs/development/coq-modules/mathcomp-infotheo/default.nix
+++ b/pkgs/development/coq-modules/mathcomp-infotheo/default.nix
@@ -7,10 +7,12 @@
   inherit version;
 
   defaultVersion = with lib.versions; lib.switch [ coq.version mathcomp-analysis.version] [
+    { cases = [ (isGe "8.17") (isGe "1.0") ];                    out = "0.7.1"; }
     { cases = [ (isGe "8.17") (range "0.6.6" "0.7.0") ];         out = "0.6.1"; }
     { cases = [ (range "8.17" "8.18") (range "0.6.0" "0.6.7") ]; out = "0.5.2"; }
     { cases = [ (range "8.15" "8.16") (range "0.5.4" "0.6.5") ]; out = "0.5.1"; }
   ] null;
+  release."0.7.1".sha256 = "sha256-/4Elb35SmscG6EjEcHYDo+AmWrpBUlygZL0WhaD+fcY=";
   release."0.6.1".sha256 = "sha256-tFB5lrwRPIlHkP+ebgcJwu03Cc9yVaOINOAo8Bf2LT4=";
   release."0.5.1".sha256 = "sha256-yBBl5l+V+dggsg5KM59Yo9CULKog/xxE8vrW+ZRnX7Y=";
   release."0.5.2".sha256 = "sha256-8WAnAV53c0pMTdwj8XcUDUkLZbpUgIQbEOgOb63uHQA=";

From 69992537d5e8720abb153d8cfadef9ee6a0f8116 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Mon, 27 May 2024 04:05:12 +0000
Subject: [PATCH 30/30] home-assistant-custom-lovelace-modules.android-tv-card:
 3.7.3 -> 3.7.4

---
 .../custom-lovelace-modules/android-tv-card/default.nix     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/servers/home-assistant/custom-lovelace-modules/android-tv-card/default.nix b/pkgs/servers/home-assistant/custom-lovelace-modules/android-tv-card/default.nix
index 54186a99ab2d..bf98c9a9438a 100644
--- a/pkgs/servers/home-assistant/custom-lovelace-modules/android-tv-card/default.nix
+++ b/pkgs/servers/home-assistant/custom-lovelace-modules/android-tv-card/default.nix
@@ -5,18 +5,18 @@
 
 buildNpmPackage rec {
   pname = "android-tv-card";
-  version = "3.7.3";
+  version = "3.7.4";
 
   src = fetchFromGitHub {
     owner = "Nerwyn";
     repo = "android-tv-card";
     rev = version;
-    hash = "sha256-uhdo4K5JqKogQGKr0dkFl579YeAQNbhOwHAFTLpqY6Y=";
+    hash = "sha256-5GdN6zCE24kGLM4ka8vHdpIEWTQAzve/1l3+5OV95i0=";
   };
 
   patches = [ ./dont-call-git.patch ];
 
-  npmDepsHash = "sha256-wrmj4lewxBnWVlpkb/AP3lfuGNcvYGf+HWBQw7bcr1Q=";
+  npmDepsHash = "sha256-fVnqGe/ao0Ilk/mWbHGscYQlIIk3K0mpm1wS4F8Lio4=";
 
   installPhase = ''
     runHook preInstall