Merge staging-next into staging

30 files changed, 94 insertions, 143 deletions

diff --git a/pkgs/development/guile-modules/guile-reader/default.nix b/pkgs/development/guile-modules/guile-reader/default.nix
index edc6d73fffc..fcb6e8c7a8a 100644
--- a/pkgs/development/guile-modules/guile-reader/default.nix
+++ b/pkgs/development/guile-modules/guile-reader/default.nix
@@ -27,7 +27,11 @@ stdenv.mkDerivation rec {
     libffi
   ];
 
-  env.GUILE_SITE = "${guile-lib}/${guile.siteDir}";
+  env = {
+    GUILE_SITE = "${guile-lib}/${guile.siteDir}";
+  } // lib.optionalAttrs stdenv.cc.isClang {
+    NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration";
+  };
 
   configureFlags = [ "--with-guilemoduledir=$(out)/${guile.siteDir}" ];
 
diff --git a/pkgs/development/libraries/gtk4-layer-shell/default.nix b/pkgs/development/libraries/gtk4-layer-shell/default.nix
index ec1f00cdc36..d6997019308 100644
--- a/pkgs/development/libraries/gtk4-layer-shell/default.nix
+++ b/pkgs/development/libraries/gtk4-layer-shell/default.nix
@@ -16,7 +16,7 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "gtk4-layer-shell";
-  version = "1.0.1";
+  version = "1.0.2";
 
   outputs = [ "out" "dev" "devdoc" ];
   outputBin = "devdoc";
@@ -25,7 +25,7 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "wmww";
     repo = "gtk4-layer-shell";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-MG/YW4AhC2joUX93Y/pzV4s8TrCo5Z/I3hAT70jW8dw=";
+    hash = "sha256-decjPkFkYy7kIjyozsB7BEmw33wzq1EQyIBrxO36984=";
   };
 
   strictDeps = true;
diff --git a/pkgs/development/libraries/libsolv/default.nix b/pkgs/development/libraries/libsolv/default.nix
index 76931b12fc0..4b40eacaa03 100644
--- a/pkgs/development/libraries/libsolv/default.nix
+++ b/pkgs/development/libraries/libsolv/default.nix
@@ -16,14 +16,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.25";
+  version = "0.7.26";
   pname = "libsolv";
 
   src = fetchFromGitHub {
     owner = "openSUSE";
     repo = "libsolv";
     rev = version;
-    sha256 = "sha256-OSYfv8dTyoa2f1T/zCEruKczickP5jS05xjYLQQiFaY=";
+    sha256 = "sha256-NGybpl/Fd46pmSYMNGocStQQCXr5pX34PCmN/hFKeyk=";
   };
 
   cmakeFlags = [
diff --git a/pkgs/development/libraries/neatvnc/default.nix b/pkgs/development/libraries/neatvnc/default.nix
index 4eba7cbbd8e..f5efbdcc082 100644
--- a/pkgs/development/libraries/neatvnc/default.nix
+++ b/pkgs/development/libraries/neatvnc/default.nix
@@ -15,13 +15,13 @@
 
 stdenv.mkDerivation rec {
   pname = "neatvnc";
-  version = "0.7.0";
+  version = "0.7.1";
 
   src = fetchFromGitHub {
     owner = "any1";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-R+PvD7E/z+Gc7h2y0pUYaCkzfgpxzwToOr4pKSrOnxU=";
+    sha256 = "sha256-bRlz5RW+NUSTgzjRM9alZjSrzmF8/7p4IIXqK/HEcJo=";
   };
 
   strictDeps = true;
diff --git a/pkgs/development/python-modules/ailment/default.nix b/pkgs/development/python-modules/ailment/default.nix
index 4b301548b43..e433aa42599 100644
--- a/pkgs/development/python-modules/ailment/default.nix
+++ b/pkgs/development/python-modules/ailment/default.nix
@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "ailment";
-  version = "9.2.75";
+  version = "9.2.76";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-k3CX0ntqbKBL9xLTPifwjTqwYEDLlNdEHlIPiokkkPA=";
+    hash = "sha256-RIYGWPvQ2n+NgZHw2pGEvgWAtbpb/rdyb6/K4JClRxM=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/angr/default.nix b/pkgs/development/python-modules/angr/default.nix
index 5b142f2be1e..e3d0f027114 100644
--- a/pkgs/development/python-modules/angr/default.nix
+++ b/pkgs/development/python-modules/angr/default.nix
@@ -32,7 +32,7 @@
 
 buildPythonPackage rec {
   pname = "angr";
-  version = "9.2.75";
+  version = "9.2.76";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -41,7 +41,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "angr";
     rev = "refs/tags/v${version}";
-    hash = "sha256-tDOO0wn5gYxK1CuMWhu/i4Xk3CfcuhPvxsG0LI7BlA4=";
+    hash = "sha256-B3oYh0okbIeEvBjBHvY29QTqPyR2TTzLmz6fMsIRcs0=";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/archinfo/default.nix b/pkgs/development/python-modules/archinfo/default.nix
index 14fea5e4835..2e5ebe9e8e0 100644
--- a/pkgs/development/python-modules/archinfo/default.nix
+++ b/pkgs/development/python-modules/archinfo/default.nix
@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "archinfo";
-  version = "9.2.75";
+  version = "9.2.76";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-t8kxGwLEVVp1WMFA+yFLMAPJBT46m0ZFG2lhWMxoolw=";
+    hash = "sha256-g1qlcaSByXhF+6ffxwbV/0tXFdmLySH3TcDuok4y6xw=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/claripy/default.nix b/pkgs/development/python-modules/claripy/default.nix
index 8907b8b8ac2..c185d1148bd 100644
--- a/pkgs/development/python-modules/claripy/default.nix
+++ b/pkgs/development/python-modules/claripy/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "claripy";
-  version = "9.2.75";
+  version = "9.2.76";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "claripy";
     rev = "refs/tags/v${version}";
-    hash = "sha256-ErPk93hDKV1QyGOjxYNaLzNuq6Od374G8qOxWiJwpuo=";
+    hash = "sha256-BwhM5J+20ZvP0d+9TAqy0AgRuPU6XoLKgM88WJdf3Qg=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/cle/default.nix b/pkgs/development/python-modules/cle/default.nix
index 3f4e7addb77..efc5c616819 100644
--- a/pkgs/development/python-modules/cle/default.nix
+++ b/pkgs/development/python-modules/cle/default.nix
@@ -16,14 +16,14 @@
 
 let
   # The binaries are following the argr projects release cycle
-  version = "9.2.75";
+  version = "9.2.76";
 
   # Binary files from https://github.com/angr/binaries (only used for testing and only here)
   binaries = fetchFromGitHub {
     owner = "angr";
     repo = "binaries";
     rev = "refs/tags/v${version}";
-    hash = "sha256-xiYkXC3/JPgXJ23ISl0LVrdm368hDPCG5NqQM6lDXf4=";
+    hash = "sha256-01Y4UKTkaO6bYtVTvv4KFzkEdj4qKiWKaC80/iKa/Eg=";
   };
 
 in
@@ -38,7 +38,7 @@ buildPythonPackage rec {
     owner = "angr";
     repo = "cle";
     rev = "refs/tags/v${version}";
-    hash = "sha256-F2kgEffFWK7i1BgU5ulsNJitGcGcEziYRU+y86wKgXU=";
+    hash = "sha256-uMT9LvDkXl3SueR80pgGJRkWbymDRmGEn8HV93K/VNc=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/flax/default.nix b/pkgs/development/python-modules/flax/default.nix
index b68f56a11f4..fa0f053f86d 100644
--- a/pkgs/development/python-modules/flax/default.nix
+++ b/pkgs/development/python-modules/flax/default.nix
@@ -4,14 +4,17 @@
 , jaxlib
 , pythonRelaxDepsHook
 , setuptools-scm
-, cloudpickle
 , jax
-, matplotlib
 , msgpack
 , numpy
 , optax
+, pyyaml
 , rich
 , tensorstore
+, typing-extensions
+, matplotlib
+, cloudpickle
+, einops
 , keras
 , pytest-xdist
 , pytestCheckHook
@@ -37,24 +40,27 @@ buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
-    cloudpickle
     jax
-    matplotlib
     msgpack
     numpy
     optax
+    pyyaml
     rich
     tensorstore
+    typing-extensions
   ];
 
-  # See https://github.com/google/flax/pull/2882.
-  pythonRemoveDeps = [ "orbax" ];
+  passthru.optional-dependencies = {
+    all = [ matplotlib ];
+  };
 
   pythonImportsCheck = [
     "flax"
   ];
 
   nativeCheckInputs = [
+    cloudpickle
+    einops
     keras
     pytest-xdist
     pytestCheckHook
@@ -85,22 +91,6 @@ buildPythonPackage rec {
     "tests/checkpoints_test.py"
   ];
 
-  disabledTests = [
-    # See https://github.com/google/flax/issues/2554.
-    "test_async_save_checkpoints"
-    "test_jax_array0"
-    "test_jax_array1"
-    "test_keep0"
-    "test_keep1"
-    "test_optimized_lstm_cell_matches_regular"
-    "test_overwrite_checkpoints"
-    "test_save_restore_checkpoints_target_empty"
-    "test_save_restore_checkpoints_target_none"
-    "test_save_restore_checkpoints_target_singular"
-    "test_save_restore_checkpoints_w_float_steps"
-    "test_save_restore_checkpoints"
-  ];
-
   meta = with lib; {
     description = "Neural network library for JAX";
     homepage = "https://github.com/google/flax";
diff --git a/pkgs/development/python-modules/folium/default.nix b/pkgs/development/python-modules/folium/default.nix
index 09c2137872d..8b29b61fe69 100644
--- a/pkgs/development/python-modules/folium/default.nix
+++ b/pkgs/development/python-modules/folium/default.nix
@@ -18,7 +18,7 @@
 
 buildPythonPackage rec {
   pname = "folium";
-  version = "0.14.0";
+  version = "0.15.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     owner = "python-visualization";
     repo = "folium";
     rev = "refs/tags/v${version}";
-    hash = "sha256-zxLFj5AeTVAxE0En7ZlbBdJEm3WrcPv23MgOhyfNi14=";
+    hash = "sha256-xaz9oelkyS8lWECCmKs8P3mHB3Usv0KMUoh/K7rBnAs=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;
diff --git a/pkgs/development/python-modules/formencode/default.nix b/pkgs/development/python-modules/formencode/default.nix
index 1323f2902cf..1b7dd1fc2ef 100644
--- a/pkgs/development/python-modules/formencode/default.nix
+++ b/pkgs/development/python-modules/formencode/default.nix
@@ -11,14 +11,14 @@
 
 buildPythonPackage rec {
   pname = "formencode";
-  version = "2.0.1";
+  version = "2.1.0";
 
   disabled = isPy27;
 
   src = fetchPypi {
     pname = "FormEncode";
     inherit version;
-    sha256 = "8f2974112c2557839d5bae8b76490104c03830785d923abbdef148bf3f710035";
+    sha256 = "sha256-63TSIweKKM8BX6iJZsbjTy0Y11EnMY1lwUS+2a/EJj8=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/nilearn/default.nix b/pkgs/development/python-modules/nilearn/default.nix
index f8273e30ae7..3c21b0b62e5 100644
--- a/pkgs/development/python-modules/nilearn/default.nix
+++ b/pkgs/development/python-modules/nilearn/default.nix
@@ -17,14 +17,14 @@
 
 buildPythonPackage rec {
   pname = "nilearn";
-  version = "0.10.1";
+  version = "0.10.2";
   pyproject = true;
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-koo2Tn7XfRXQK38icZfqfHj0Ty/ngP61VdbXz5Iy+EY=";
+    hash = "sha256-A+9Npy0a6HsuPyi3cdx+BUZKoXliblfDAFlWJahlQnM=";
   };
 
   nativeBuildInputs = [ hatch-vcs ];
diff --git a/pkgs/development/python-modules/orange-canvas-core/default.nix b/pkgs/development/python-modules/orange-canvas-core/default.nix
index 814c90a698d..e40a9a03e76 100644
--- a/pkgs/development/python-modules/orange-canvas-core/default.nix
+++ b/pkgs/development/python-modules/orange-canvas-core/default.nix
@@ -18,11 +18,11 @@
 
 buildPythonPackage rec {
   pname = "orange-canvas-core";
-  version = "0.1.33";
+  version = "0.1.35";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-w3krij7+CtJl1XoJz3RRAAp2aKqMCQg/PBh5erf/Phs=";
+    hash = "sha256-xLCwjeNDx9RqxlNkIWMo0Pcrg7akGuu4Rv9oRDgOK18=";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/orange3/default.nix b/pkgs/development/python-modules/orange3/default.nix
index c8939f01e93..1100ae7f6dc 100644
--- a/pkgs/development/python-modules/orange3/default.nix
+++ b/pkgs/development/python-modules/orange3/default.nix
@@ -44,7 +44,7 @@
 let
   self = buildPythonPackage rec {
     pname = "orange3";
-    version = "3.36.1";
+    version = "3.36.2";
 
     disabled = pythonOlder "3.7";
 
@@ -52,7 +52,7 @@ let
       owner = "biolab";
       repo = "orange3";
       rev = "refs/tags/${version}";
-      hash = "sha256-O5ZN5O1vMkqiv83Q5UoaDefGnqVnDLPmYLLG20cdajk=";
+      hash = "sha256-v9lk5vGhBaR2PHZ+Jq0hy1WaCsbeLe+vZlTaHBkfacU=";
     };
 
     postPatch = ''
diff --git a/pkgs/development/python-modules/pydrawise/default.nix b/pkgs/development/python-modules/pydrawise/default.nix
index 22c281dce3e..dc36f149a9b 100644
--- a/pkgs/development/python-modules/pydrawise/default.nix
+++ b/pkgs/development/python-modules/pydrawise/default.nix
@@ -17,7 +17,7 @@
 
 buildPythonPackage rec {
   pname = "pydrawise";
-  version = "2023.10.0";
+  version = "2023.11.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.10";
@@ -26,7 +26,7 @@ buildPythonPackage rec {
     owner = "dknowles2";
     repo = "pydrawise";
     rev = "refs/tags/${version}";
-    hash = "sha256-CSjYLiOvnm1kFp4DL3w/YmAsDcbaCfLfGT0xUZy+GZ0=";
+    hash = "sha256-gKOyTvdETGzKlpU67UKaHYTIvnAX9znHIynP3BiVbt4=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;
diff --git a/pkgs/development/python-modules/pyparted/default.nix b/pkgs/development/python-modules/pyparted/default.nix
index 4d473ae094d..84d8439a536 100644
--- a/pkgs/development/python-modules/pyparted/default.nix
+++ b/pkgs/development/python-modules/pyparted/default.nix
@@ -1,11 +1,11 @@
 { lib, stdenv
 , fetchFromGitHub
-, fetchpatch
 , buildPythonPackage
 , isPyPy
 , pkgs
 , python
 , six
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
@@ -31,31 +31,14 @@ buildPythonPackage rec {
       tests/test__ped_ped.py
   '';
 
-  patches = [
-    ./fix-test-pythonpath.patch
-    (fetchpatch {
-      url = "https://github.com/dcantrell/pyparted/commit/07ba882d04fa2099b53d41370416b97957d2abcb.patch";
-      hash = "sha256-yYfLdy+TOKfN3gtTMgOWPebPTRYyaOYh/yFTowCbdjg=";
-    })
-    (fetchpatch {
-      url = "https://github.com/dcantrell/pyparted/commit/a01b4eeecf63b0580c192c7c2db7a5c406a7ad6d.patch";
-      hash = "sha256-M/8hYiKUBzaTOxPYDFK5BAvCm6WJGx+693qwj3HzdRA=";
-    })
-  ];
-
   preConfigure = ''
     PATH="${pkgs.parted}/sbin:$PATH"
   '';
 
   nativeBuildInputs = [ pkgs.pkg-config ];
-  nativeCheckInputs = [ six ];
+  nativeCheckInputs = [ six pytestCheckHook ];
   propagatedBuildInputs = [ pkgs.parted ];
 
-  checkPhase = ''
-    patchShebangs Makefile
-    make test PYTHON=${python.executable}
-  '';
-
   meta = with lib; {
     homepage = "https://github.com/dcantrell/pyparted/";
     description = "Python interface for libparted";
diff --git a/pkgs/development/python-modules/pyparted/fix-test-pythonpath.patch b/pkgs/development/python-modules/pyparted/fix-test-pythonpath.patch
deleted file mode 100644
index 740bffbef6d..00000000000
--- a/pkgs/development/python-modules/pyparted/fix-test-pythonpath.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff -ur a/Makefile b/Makefile
---- a/Makefile	1980-01-02 00:00:00.000000000 +0100
-+++ b/Makefile	2020-02-18 20:04:14.068243263 +0100
-@@ -39,19 +39,19 @@
- 	@$(PYTHON) setup.py build
- 
- test: all
--	@env PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src \
-+	@env PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src:$$PYTHONPATH \
- 	$(PYTHON) -m unittest discover -v
- 
- coverage: all
- 	@echo "*** Running unittests with $(COVERAGE) for $(PYTHON) ***"
--	@env PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src \
-+	@env PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src:$$PYTHONPATH \
- 	$(COVERAGE) run --branch -m unittest discover -v
- 	$(COVERAGE) report --include="build/lib.*/parted/*" --show-missing
- 	$(COVERAGE) report --include="build/lib.*/parted/*" > coverage-report.log
- 
- check: clean
- 	env PYTHON=python3 $(MAKE) ; \
--	env PYTHON=python3 PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src \
-+	env PYTHON=python3 PYTHONPATH=$$(find $$(pwd) -name "*.so" | head -n 1 | xargs dirname):src/parted:src:$$PYTHONPATH \
- 	tests/pylint/runpylint.py
- 
- dist:
diff --git a/pkgs/development/python-modules/pyvex/default.nix b/pkgs/development/python-modules/pyvex/default.nix
index c19e16cae96..c2af4be8df8 100644
--- a/pkgs/development/python-modules/pyvex/default.nix
+++ b/pkgs/development/python-modules/pyvex/default.nix
@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "pyvex";
-  version = "9.2.75";
+  version = "9.2.76";
   pyproject = true;
 
   disabled = pythonOlder "3.11";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-8P8xOb4P1JsbPZya8s1Bl16VsYtHQdAD05sc8EAcEpM=";
+    hash = "sha256-JlwqxKJaJ3sk2mROUOaF0N5d4V7LM43VqEXnuSO45BY=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/tensorflow-probability/default.nix b/pkgs/development/python-modules/tensorflow-probability/default.nix
index 8e017cc55b0..e81e9736c26 100644
--- a/pkgs/development/python-modules/tensorflow-probability/default.nix
+++ b/pkgs/development/python-modules/tensorflow-probability/default.nix
@@ -27,17 +27,17 @@
 }:
 
 let
-  version = "0.19.0";
-  pname = "tensorflow_probability";
+  version = "0.21.0";
+  pname = "tensorflow-probability";
 
   # first build all binaries and generate setup.py using bazel
   bazel-wheel = buildBazelPackage {
-    name = "${pname}-${version}-py2.py3-none-any.whl";
+    name = "tensorflow_probability-${version}-py2.py3-none-any.whl";
     src = fetchFromGitHub {
       owner = "tensorflow";
       repo = "probability";
-      rev = "v" + version;
-      hash = "sha256-ZkQ20Qt/RF/leVP6Kc38tGgPz+C6lEuHvoL+s97oksE=";
+      rev = "refs/tags/v${version}";
+      hash = "sha256-DsJd1E5n86xNS7Ci0DXxoUxQ9jH8OwTZq2UuLlQtMUU=";
     };
     nativeBuildInputs = [
       # needed to create the output wheel in installPhase
@@ -54,8 +54,7 @@ let
     LIBTOOL = lib.optionalString stdenv.isDarwin "${cctools}/bin/libtool";
 
     fetchAttrs = {
-      # FIXME: tensorflow is currently marked as broken, update the hash once it's fixed
-      sha256 = "sha256-0ChXujA2XpnkybrraN3FIJA/QkxLCfX97id2jMFzFJk=";
+      sha256 = "sha256-1iO/eXz1wvSIRTmGuGZDF9VeDVTiWYnjw0Cby4n/6HM=";
     };
 
     buildAttrs = {
@@ -117,6 +116,6 @@ in buildPythonPackage {
     description = "Library for probabilistic reasoning and statistical analysis";
     homepage = "https://www.tensorflow.org/probability/";
     license = licenses.asl20;
-    maintainers = with maintainers; [];  # This package is maintainerless.
+    maintainers = with maintainers; [ GaetanLepage ];
   };
 }
diff --git a/pkgs/development/python-modules/tlds/default.nix b/pkgs/development/python-modules/tlds/default.nix
index 207b605070a..3967781bb0f 100644
--- a/pkgs/development/python-modules/tlds/default.nix
+++ b/pkgs/development/python-modules/tlds/default.nix
@@ -6,14 +6,14 @@
 
 buildPythonPackage rec {
   pname = "tlds";
-  version = "2023102600";
+  version = "2023110300";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "kichik";
     repo = "tlds";
     rev = "refs/tags/${version}";
-    hash = "sha256-ncbgR/syMChIL0/FGLOHxHJMUzH0G+rZX9aCXun7yc4=";
+    hash = "sha256-rmKqY7Z4bBR4r+w4gH04g0Xm9N7QeMVcuFR3pB/pOQY=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/wikitextparser/default.nix b/pkgs/development/python-modules/wikitextparser/default.nix
index b65f18b6c6e..b7af5aeeb65 100644
--- a/pkgs/development/python-modules/wikitextparser/default.nix
+++ b/pkgs/development/python-modules/wikitextparser/default.nix
@@ -8,14 +8,14 @@
 
 buildPythonPackage rec {
   pname = "wikitextparser";
-  version = "0.54.0";
+  version = "0.55.5";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "5j9";
     repo = "wikitextparser";
     rev = "v${version}";
-    hash = "sha256-AGQfjUNxeleuTS200QMdZS8CSD2t4ah5NMm9TIYjVHk=";
+    hash = "sha256-cmzyRbq4tCbuyrNnT0UYxoxuwXrFkIcWdrogSTfxSys=";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/tools/godot/4/default.nix b/pkgs/development/tools/godot/4/default.nix
index 986d2d7745f..b7dc3b04ac5 100644
--- a/pkgs/development/tools/godot/4/default.nix
+++ b/pkgs/development/tools/godot/4/default.nix
@@ -43,14 +43,14 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "godot";
-  version = "4.1.1";
-  commitHash = "bd6af8e0ea69167dd0627f3bd54f9105bda0f8b5";
+  version = "4.1.3-stable";
+  commitHash = "fc79201851a16215f9554884aa242ed957801b10";
 
   src = fetchFromGitHub {
     owner = "godotengine";
     repo = "godot";
     rev = commitHash;
-    hash = "sha256-0CErsMTrBC/zYcabAtjYn8BWAZ1HxgozKdgiqdsn3q8=";
+    hash = "sha256-z5JRPhdEO20AodS12MApgur0BMHGToUjo2r2eI77nNc=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/tools/language-servers/csharp-ls/default.nix b/pkgs/development/tools/language-servers/csharp-ls/default.nix
index efc6307f1a6..cefb7a969a4 100644
--- a/pkgs/development/tools/language-servers/csharp-ls/default.nix
+++ b/pkgs/development/tools/language-servers/csharp-ls/default.nix
@@ -8,9 +8,9 @@ in
 
 buildDotnetGlobalTool rec {
   pname = "csharp-ls";
-  version = "0.8.0";
+  version = "0.10.0";
 
-  nugetSha256 = "sha256-F3N6ESE/VmQA5sOMm3eqSkhSNVCCsnAXTCC+McsAnQw=";
+  nugetSha256 = "sha256-1t8U2Q4lIlj2QwbnevAMMGcqtpPh5zk0Bd7EHa7qvCI=";
 
   dotnet-sdk = sdk_7_0;
   dotnet-runtime = sdk_7_0;
diff --git a/pkgs/development/tools/misc/opengrok/default.nix b/pkgs/development/tools/misc/opengrok/default.nix
index 5c9589920a6..37593e0090c 100644
--- a/pkgs/development/tools/misc/opengrok/default.nix
+++ b/pkgs/development/tools/misc/opengrok/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "opengrok";
-  version = "1.12.15";
+  version = "1.12.21";
 
   # binary distribution
   src = fetchurl {
     url = "https://github.com/oracle/opengrok/releases/download/${version}/${pname}-${version}.tar.gz";
-    hash = "sha256-AEKzhNSNJOOyK/fiAepqios7xoexAi4M4zbMTPdyyeA=";
+    hash = "sha256-SjA5J9fILU/FBNXRS/cvGZVWAK2qqOyMsd6wC/CJYaE=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/development/tools/nest-cli/default.nix b/pkgs/development/tools/nest-cli/default.nix
index 9fdb579b542..7fa9595e182 100644
--- a/pkgs/development/tools/nest-cli/default.nix
+++ b/pkgs/development/tools/nest-cli/default.nix
@@ -8,16 +8,16 @@
 
 buildNpmPackage rec {
   pname = "nest-cli";
-  version = "10.1.17";
+  version = "10.2.1";
 
   src = fetchFromGitHub {
     owner = "nestjs";
     repo = pname;
     rev = version;
-    hash = "sha256-03GDrKjlvl3O3kJlbbyDYxtlfwLkZbvxC9gvP534zSY=";
+    hash = "sha256-vnF+ES6RK4iiIJsWUV57DqoLischh+1MlmlK46Z6USY=";
   };
 
-  npmDepsHash = "sha256-nZ9ant2c+15bRBikFcKZW8aiFqI3WC6hktSiBfnma/I=";
+  npmDepsHash = "sha256-9yd+k+HpARM63/esW+av0zfcuAVsp9Lkfp6hmUQO5Yg=";
 
   env = {
     npm_config_build_from_source = true;
@@ -37,6 +37,5 @@ buildNpmPackage rec {
     license = licenses.mit;
     mainProgram = "nest";
     maintainers = [ maintainers.ehllie ];
-    broken = stdenv.isDarwin; # https://github.com/nestjs/nest-cli/pull/2281
   };
 }
diff --git a/pkgs/development/tools/oh-my-posh/default.nix b/pkgs/development/tools/oh-my-posh/default.nix
index 1ef8ff9d35f..aeff229f832 100644
--- a/pkgs/development/tools/oh-my-posh/default.nix
+++ b/pkgs/development/tools/oh-my-posh/default.nix
@@ -6,16 +6,16 @@
 
 buildGoModule rec {
   pname = "oh-my-posh";
-  version = "18.11.0";
+  version = "18.22.0";
 
   src = fetchFromGitHub {
     owner = "jandedobbeleer";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-sUP2xBrh7JpAaHhiMm6AilgEUNIfK1U2hbloUJYHn6c=";
+    hash = "sha256-lQqDXiT+DRLmU+4DBvj2Gnd1RjaRgMorhXo1BmJLQqU=";
   };
 
-  vendorHash = "sha256-i5K7f70MevNJcRsP2P9rsMZRpKPVWsTx9M4t2AoEJew=";
+  vendorHash = "sha256-/SVS0Vd6GvKEAzRobxaTwJ+uy8dwCINBOYzQN65ppAs=";
 
   sourceRoot = "${src.name}/src";
 
diff --git a/pkgs/development/tools/pandoc/default.nix b/pkgs/development/tools/pandoc/default.nix
index 1e9eec3f804..528a1b3f535 100644
--- a/pkgs/development/tools/pandoc/default.nix
+++ b/pkgs/development/tools/pandoc/default.nix
@@ -6,6 +6,15 @@ let
 
 in
   (haskell.lib.compose.overrideCabal (drv: {
+    # pandoc-cli's pandoc executable report the libraries version via --version, match that,
+    inherit (static.scope.pandoc) version;
+    # but prevent haskellPackages.mkDerivation from recomputing the src tarball based on that.
+    inherit (static) src;
+    # Make it possible to recover the cli version if necessary.
+    passthru = drv.passthru or {} // {
+      cliVersion = static.version;
+    };
+
     configureFlags = drv.configureFlags or [] ++ ["-fembed_data_files"];
     buildDepends = drv.buildDepends or [] ++ [haskellPackages.file-embed];
     buildTools = (drv.buildTools or []) ++ [ removeReferencesTo ];
diff --git a/pkgs/development/tools/rust/cargo-readme/default.nix b/pkgs/development/tools/rust/cargo-readme/default.nix
index 35d3fb133e8..15c5ad51452 100644
--- a/pkgs/development/tools/rust/cargo-readme/default.nix
+++ b/pkgs/development/tools/rust/cargo-readme/default.nix
@@ -2,27 +2,20 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-readme";
-  version = "3.2.0";
+  version = "3.3.1";
 
   src = fetchFromGitHub {
-    owner = "livioribeiro";
+    owner = "webern";
     repo = pname;
-    # Git tag is missing, see upstream issue:
-    # https://github.com/livioribeiro/cargo-readme/issues/61
-    rev = "cf66017c0120ae198210ebaf58a0be6a78372974";
-    sha256 = "sha256-/ufHHM13L83M3UYi6mjdhIjgXx7bZgzvR/X02Zsx7Fw=";
+    rev = "v${version}";
+    sha256 = "sha256-FFWHADATEfvZvxGwdkj+eTVoq7pnPuoUAhMGTokUkMs=";
   };
 
-  cargoSha256 = "sha256-Isd05qOuVBNfXOI5qsaDOhjF7QIKAG5xrZsBFK2PpQQ=";
+  cargoSha256 = "sha256-OEArMqOiT+PZ+zMRt9h0EzeP7ikFuOYR8mFGtm+xCkQ=";
 
-  patches = [
-    (fetchpatch {
-      # Fixup warning thrown at build when running test-suite
-      # unused return, see upstream PR:
-      # https://github.com/livioribeiro/cargo-readme/pull/62
-      url = "https://github.com/livioribeiro/cargo-readme/commit/060f2daaa2b2cf981bf490dc36bcc6527545ea03.patch";
-      sha256 = "sha256-wlAIgTI9OqtA/Jnswoqp7iOj+1zjrUZA7JpHUiF/n+s=";
-    })
+  # disable doc tests
+  cargoTestFlags = [
+    "--bins" "--lib"
   ];
 
   meta = with lib; {
diff --git a/pkgs/development/tools/squawk/default.nix b/pkgs/development/tools/squawk/default.nix
index 8e7dc13393f..417c66ea3a6 100644
--- a/pkgs/development/tools/squawk/default.nix
+++ b/pkgs/development/tools/squawk/default.nix
@@ -11,16 +11,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "squawk";
-  version = "0.24.1";
+  version = "0.24.2";
 
   src = fetchFromGitHub {
     owner = "sbdchd";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-XQU/1uAas1bT7FSgBzJSPRe4ET9ysjpFGhV+qi23AAY=";
+    hash = "sha256-gFJaW7Mb3HKN6D/qnpfNQVxBOKbxIBZOVWJ63wiGoeU=";
   };
 
-  cargoHash = "sha256-Qg2VcsAqXpYamO35t/lvlXUPTdjAqZ4z3Nm0hYdhjEM=";
+  cargoHash = "sha256-a1kAVIyGnVF3IWkDQbmV3L9cfY+1564RW6eWfBHbTZ8=";
 
   nativeBuildInputs = [
     pkg-config