Merge master into staging-next

nixos/modules/services/hardware/kanata.nix

@@ -5,6 +5,8 @@ with lib;
 let
   cfg = config.services.kanata;
 
+  upstreamDoc = "See [the upstream documentation](https://github.com/jtroo/kanata/blob/main/docs/config.adoc) and [example config files](https://github.com/jtroo/kanata/tree/main/cfg_samples) for more information.";
+
   keyboard = {
     options = {
       devices = mkOption {
@@ -22,28 +24,16 @@ let
         type = types.lines;
         example = ''
           (defsrc
-            grv  1    2    3    4    5    6    7    8    9    0    -    =    bspc
-            tab  q    w    e    r    t    y    u    i    o    p    [    ]    \
-            caps a    s    d    f    g    h    j    k    l    ;    '    ret
-            lsft z    x    c    v    b    n    m    ,    .    /    rsft
-            lctl lmet lalt           spc            ralt rmet rctl)
+            caps)
 
-          (deflayer qwerty
-            grv  1    2    3    4    5    6    7    8    9    0    -    =    bspc
-            tab  q    w    e    r    t    y    u    i    o    p    [    ]    \
-            @cap a    s    d    f    g    h    j    k    l    ;    '    ret
-            lsft z    x    c    v    b    n    m    ,    .    /    rsft
-            lctl lmet lalt           spc            ralt rmet rctl)
-
-          (defalias
-            ;; tap within 100ms for capslk, hold more than 100ms for lctl
-            cap (tap-hold 100 100 caps lctl))
+          (deflayermap (default-layer)
+            ;; tap caps lock as caps lock, hold caps lock as left control
+            caps (tap-hold 100 100 caps lctl))
         '';
         description = ''
           Configuration other than `defcfg`.
 
-          See [example config files](https://github.com/jtroo/kanata)
-          for more information.
+          ${upstreamDoc}
         '';
       };
       extraDefCfg = mkOption {
@@ -55,8 +45,7 @@ let
           from the devices option) and
           `linux-continue-if-no-devs-found` (hardcoded to be yes).
 
-          See [example config files](https://github.com/jtroo/kanata)
-          for more information.
+          ${upstreamDoc}
         '';
       };
       extraArgs = mkOption {
@@ -153,7 +142,7 @@ in
   options.services.kanata = {
     enable = mkEnableOption "kanata, a tool to improve keyboard comfort and usability with advanced customization";
     package = mkPackageOption pkgs "kanata" {
-      example = "kanata-with-cmd";
+      example = [ "kanata-with-cmd" ];
       extraDescription = ''
         ::: {.note}
         If {option}`danger-enable-cmd` is enabled in any of the keyboards, the

pkgs/applications/editors/apostrophe/default.nix

@@ -1,59 +0,0 @@
-{ lib, stdenv, fetchFromGitLab, meson, ninja
-, wrapGAppsHook3, pkg-config, desktop-file-utils
-, appstream-glib, pythonPackages, glib, gobject-introspection
-, gtk3, webkitgtk, glib-networking, gnome, gspell, texliveMedium
-, shared-mime-info, libhandy, fira, sassc
-}:
-
-let
-  pythonEnv = pythonPackages.python.withPackages(p: with p; [
-    regex setuptools levenshtein pyenchant
-    pygobject3 pycairo pypandoc chardet
-  ]);
-
-in stdenv.mkDerivation rec {
-  pname = "apostrophe";
-  version = "2.6.3";
-
-  src = fetchFromGitLab {
-    owner  = "World";
-    repo   = pname;
-    domain = "gitlab.gnome.org";
-    rev    = "v${version}";
-    sha256 = "sha256-RBrrG1TO810LidIelYGNaK7PjDq84D0cA8VcMojAW3M=";
-  };
-
-  nativeBuildInputs = [ meson ninja pkg-config desktop-file-utils
-    appstream-glib wrapGAppsHook3 sassc gobject-introspection ];
-
-  buildInputs = [ glib pythonEnv gtk3
-    gnome.adwaita-icon-theme webkitgtk gspell texliveMedium
-    glib-networking libhandy ];
-
-  postPatch = ''
-    substituteInPlace data/media/css/web/base.css                                        \
-      --replace 'url("/app/share/fonts/FiraSans-Regular.ttf") format("ttf")'             \
-                'url("${fira}/share/fonts/opentype/FiraSans-Regular.otf") format("otf")' \
-      --replace 'url("/app/share/fonts/FiraMono-Regular.ttf") format("ttf")'             \
-                'url("${fira}/share/fonts/opentype/FiraMono-Regular.otf") format("otf")'
-
-    patchShebangs --build build-aux/meson_post_install.py
-  '';
-
-  preFixup = ''
-    gappsWrapperArgs+=(
-      --prefix PYTHONPATH : "$out/lib/python${pythonEnv.pythonVersion}/site-packages/"
-      --prefix PATH : "${texliveMedium}/bin"
-      --prefix XDG_DATA_DIRS : "${shared-mime-info}/share"
-    )
-  '';
-
-  meta = with lib; {
-    homepage = "https://gitlab.gnome.org/World/apostrophe";
-    description = "A distraction free Markdown editor for GNU/Linux";
-    license = licenses.gpl3;
-    platforms = platforms.linux;
-    maintainers = [ maintainers.sternenseemann ];
-    mainProgram = "apostrophe";
-  };
-}

pkgs/applications/science/math/lrcalc/default.nix

@@ -1,6 +1,9 @@
 { lib, stdenv
 , fetchFromBitbucket
 , autoreconfHook
+
+# Reverse dependency
+, sage
 }:
 
 stdenv.mkDerivation rec {
@@ -20,6 +23,8 @@ stdenv.mkDerivation rec {
     autoreconfHook
   ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Littlewood-Richardson calculator";
     homepage = "http://math.rutgers.edu/~asbuch/lrcalc/";

pkgs/applications/science/math/qalculate-gtk/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "qalculate-gtk";
-  version = "5.0.0";
+  version = "5.1.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-hlGNL7aMzxBxtATWJBqJTFEQqMv10oC3sRCdtRLHOww=";
+    hash = "sha256-yI+8TrNZJt4eJnDX5mk6RozBe2ZeP7sTyAjsgiYQPck=";
   };
 
   hardeningDisable = [ "format" ];

pkgs/applications/science/math/qalculate-qt/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "qalculate-qt";
-  version = "5.0.0";
+  version = "5.1.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-qt";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-X7IY2yXpZiyE+T2dl0G4tWpJ5O6MVCy/sOY3v9inma0=";
+    hash = "sha256-gJfIC5HdA10gb/Dh/yhJbkCZfhUnN0zihqyfDjPv6ow=";
   };
 
   nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ];

pkgs/by-name/ap/apostrophe/package.nix

@@ -0,0 +1,118 @@
+{
+  lib,
+  fetchFromGitLab,
+  gtksourceview5,
+  libspelling,
+  fetchFromGitHub,
+  python3Packages,
+  meson,
+  ninja,
+  pkg-config,
+  wrapGAppsHook4,
+  desktop-file-utils,
+  gobject-introspection,
+  libadwaita,
+  webkitgtk_6_0,
+  texliveMedium,
+  shared-mime-info,
+}:
+
+let
+  version = "3.0";
+
+  src = fetchFromGitLab {
+    owner = "World";
+    repo = "apostrophe";
+    domain = "gitlab.gnome.org";
+    rev = "v${version}";
+    sha256 = "sha256-wKxRCU00nSk7F8IZNWoLRtGs3m6ol3UBnArtppUOz/g=";
+  };
+
+  # Patches are required by upstream. Without the patches
+  # typing `- aaa`, newline, `- bbb` the program crashes
+  gtksourceview5-patched = gtksourceview5.overrideAttrs (prev: {
+    patches = (prev.patches or [ ]) ++ [ "${src}/build-aux/flatpak/sourceview_text_commits.patch" ];
+  });
+
+  libspelling-patched =
+    (libspelling.override { gtksourceview5 = gtksourceview5-patched; }).overrideAttrs
+      (prev: {
+        patches = (prev.patches or [ ]) ++ [ "${src}/build-aux/flatpak/libspelling_text_commits.patch" ];
+      });
+
+  reveal-js = fetchFromGitHub {
+    owner = "hakimel";
+    repo = "reveal.js";
+
+    # keep in sync with upstream shipped version
+    # in build-aux/flatpak/org.gnome.gitlab.somas.Apostrophe.json
+    rev = "4.6.0";
+    hash = "sha256-a+J+GasFmRvu5cJ1GLXscoJ+owzFXsLhCbeDbYChkyQ=";
+  };
+in
+python3Packages.buildPythonApplication rec {
+  inherit version src;
+  pname = "apostrophe";
+  pyproject = false;
+
+  postPatch =
+    ''
+      substituteInPlace build-aux/meson_post_install.py \
+        --replace-fail 'gtk-update-icon-cache' 'gtk4-update-icon-cache'
+
+      patchShebangs --build build-aux/meson_post_install.py
+    ''
+    # Should be done in postInstall, but meson checks this eagerly before build
+    + ''
+      install -d $out/share/apostrophe/libs
+      cp -r ${reveal-js} $out/share/apostrophe/libs/reveal.js
+    '';
+
+  nativeBuildInputs = [
+    meson
+    ninja
+    pkg-config
+    wrapGAppsHook4
+    desktop-file-utils
+    gobject-introspection
+  ];
+
+  buildInputs = [
+    libadwaita
+    gtksourceview5-patched
+    libspelling-patched
+    webkitgtk_6_0
+  ];
+
+  propagatedBuildInputs = with python3Packages; [
+    pygobject3
+    pypandoc
+    chardet
+  ];
+
+  dontWrapGApps = true;
+
+  preFixup = ''
+    makeWrapperArgs+=(
+      ''${gappsWrapperArgs[@]}
+      --prefix PATH : "${texliveMedium}/bin"
+      --prefix XDG_DATA_DIRS : "${shared-mime-info}/share"
+    )
+  '';
+
+  passthru = {
+    inherit gtksourceview5-patched libspelling-patched reveal-js;
+  };
+
+  meta = {
+    homepage = "https://gitlab.gnome.org/World/apostrophe";
+    description = "A distraction free Markdown editor for GNU/Linux";
+    license = lib.licenses.gpl3Plus;
+    platforms = lib.platforms.linux;
+    maintainers = with lib.maintainers; [
+      sternenseemann
+      aleksana
+    ];
+    mainProgram = "apostrophe";
+  };
+}

pkgs/by-name/ca/cargo-expand/package.nix

@@ -5,16 +5,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-expand";
-  version = "1.0.85";
+  version = "1.0.86";
 
   src = fetchFromGitHub {
     owner = "dtolnay";
     repo = pname;
     rev = version;
-    hash = "sha256-2i9FAWF9b1tNdDbTwCzQY8Mh/h85uigR5IT9kzPft00=";
+    hash = "sha256-wp4JYuAHtZrHer4db0vBCchf8mQIt6jXWqjqpGKws4o=";
   };
 
-  cargoHash = "sha256-Vl0zC9TPhiFv2SiZtzIUV7GftB1y9K1gLy1ajisP8Y0=";
+  cargoHash = "sha256-QNH3G34yTEecZyVgw2a1RJnd1CMfV4aw1OJqes/cK2s=";
 
   meta = with lib; {
     description = "Cargo subcommand to show result of macro expansion";

pkgs/by-name/fa/fastfetch/package.nix

@@ -47,13 +47,13 @@ let
 in
 stdenv'.mkDerivation (finalAttrs: {
   pname = "fastfetch";
-  version = "2.11.3";
+  version = "2.11.5";
 
   src = fetchFromGitHub {
     owner = "fastfetch-cli";
     repo = "fastfetch";
     rev = finalAttrs.version;
-    hash = "sha256-kKtJvGnPncosmwjfTKa14G5jQiSkzkURBATvBmavdys=";
+    hash = "sha256-5Chyw4+U2n935YP/Msw8PJ+5iLMES71O+uABn6nVtiI=";
   };
 
   outputs = [ "out" "man" ];

pkgs/by-name/go/go-cover-treemap/package.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildGoModule
+, fetchFromGitHub
+}:
+
+buildGoModule rec {
+  pname = "go-cover-treemap";
+  version = "1.4.2";
+
+  src = fetchFromGitHub {
+    owner = "nikolaydubina";
+    repo = "go-cover-treemap";
+    rev = "v${version}";
+    hash = "sha256-MSkPot8uYcr8pxsIkJh2FThVK9xpzkN9Y69KeiQnQlA=";
+  };
+
+  vendorHash = "sha256-k/k+EGkuBnZFHrcWxnzLG8efWgb2i35Agf/sWbgTc4g=";
+
+  ldflags = [ "-s" "-w" ];
+
+  meta = with lib; {
+    description = "Go code coverage to SVG treemap";
+    homepage = "https://github.com/nikolaydubina/go-cover-treemap";
+    license = licenses.mit;
+    maintainers = with maintainers; [ doronbehar ];
+    mainProgram = "go-cover-treemap";
+  };
+}

pkgs/development/libraries/libqalculate/default.nix

@@ -18,13 +18,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "libqalculate";
-  version = "5.0.0";
+  version = "5.1.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "libqalculate";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-VhaGgtSU6+7eMY7ksQMpybmt2JBI80Nwgu7PCKrTorA=";
+    hash = "sha256-74P8jIeg0Pge+/U0cQsrEfE+P8upBAr8xSyLhB4zOVU=";
   };
 
   outputs = [ "out" "dev" "doc" ];

pkgs/development/libraries/qmenumodel/default.nix

@@ -12,6 +12,7 @@
 , python3
 , qtbase
 , qtdeclarative
+, gobject-introspection
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -55,6 +56,7 @@ stdenv.mkDerivation (finalAttrs: {
   nativeCheckInputs = [
     dbus
     dbus-test-runner
+    gobject-introspection
     (python3.withPackages (ps: with ps; [
       dbus-python
       pygobject3

pkgs/development/python-modules/biom-format/default.nix

@@ -0,0 +1,71 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  fetchpatch,
+  setuptools,
+  cython,
+  click,
+  numpy,
+  scipy,
+  pandas,
+  h5py,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "biom-format";
+  version = "2.1.15";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "biocore";
+    repo = "biom-format";
+    rev = "refs/tags/${version}";
+    hash = "sha256-WRBc+C/UWme7wYogy4gH4KTIdIqU3KmBm2jWzGNxGQg=";
+  };
+
+  patches = [
+    # fixes a test, can be removed in next version after 2.1.15
+    (fetchpatch {
+      name = "fix-dataframe-comparison.patch";
+      url = "https://github.com/biocore/biom-format/commit/5d1c921ca2cde5d7332508503ce990a7209d1fdc.patch";
+      hash = "sha256-nyHi469ivjJSQ01yIk/6ZMXFdoo9wVuazJHnFdy2nBg=";
+    })
+  ];
+
+  build-system = [
+    setuptools
+    cython
+    numpy
+  ];
+
+  dependencies = [
+    click
+    numpy
+    scipy
+    pandas
+    h5py
+  ];
+
+  # make pytest resolve the package from $out
+  # some tests don't work if we change the level of directory nesting
+  preCheck = ''
+    mkdir biom_tests
+    mv biom/tests biom_tests/tests
+    rm -r biom
+  '';
+
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  pytestFlagsArray = [ "biom_tests/tests" ];
+
+  pythonImportsCheck = [ "biom" ];
+
+  meta = {
+    homepage = "http://biom-format.org/";
+    description = "Biological Observation Matrix (BIOM) format";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ tomasajt ];
+  };
+}

pkgs/development/python-modules/cypari2/default.nix

@@ -7,6 +7,9 @@
 , gmp
 , cython
 , cysignals
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -53,6 +56,8 @@ buildPythonPackage rec {
     make check
   '';
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Cython bindings for PARI";
     license = licenses.gpl2Plus;

pkgs/development/python-modules/cysignals/default.nix

@@ -4,6 +4,9 @@
 , buildPythonPackage
 , cython
 , pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
+
+# Reverse dependency
+, sage
 }:
 
 assert pariSupport -> pari != null;
@@ -46,6 +49,8 @@ buildPythonPackage rec {
 
   enableParallelBuilding = true;
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Interrupt and signal handling for Cython";
     mainProgram = "cysignals-CSI";

pkgs/development/python-modules/cython/default.nix

@@ -8,6 +8,9 @@
 , gdb
 , numpy
 , ncurses
+
+# Reverse dependency
+, sage
 }:
 
 let
@@ -57,6 +60,8 @@ in buildPythonPackage rec {
   doCheck = false;
   # doCheck = !stdenv.isDarwin;
 
+  passthru.tests = { inherit sage; };
+
   # force regeneration of generated code in source distributions
   # https://github.com/cython/cython/issues/5089
   setupHook = ./setup-hook.sh;

pkgs/development/python-modules/fpylll/default.nix

@@ -15,6 +15,9 @@
 , fplll
 , numpy
 
+# Reverse dependency
+, sage
+
 # tests
 , pytestCheckHook
 }:
@@ -72,6 +75,8 @@ buildPythonPackage rec {
     export PY_IGNORE_IMPORTMISMATCH=1
   '';
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "A Python interface for fplll";
     changelog = "https://github.com/fplll/fpylll/releases/tag/${version}";

pkgs/development/python-modules/gmpy2/default.nix

@@ -5,6 +5,9 @@
 , gmp
 , mpfr
 , libmpc
+
+# Reverse dependency
+, sage
 }:
 
 let
@@ -29,6 +32,8 @@ buildPythonPackage {
 
   pythonImportsCheck = [ "gmpy2" ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x";
     homepage = "https://github.com/aleaxit/gmpy/";

pkgs/development/python-modules/importlib-metadata/default.nix

@@ -7,6 +7,9 @@
 , typing-extensions
 , toml
 , zipp
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -41,6 +44,8 @@ buildPythonPackage rec {
     "importlib_metadata"
   ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Read metadata from Python packages";
     homepage = "https://importlib-metadata.readthedocs.io/";

pkgs/development/python-modules/importlib-resources/default.nix

@@ -10,6 +10,9 @@
 # dependencies
 , importlib-metadata
 
+# Reverse dependency
+, sage
+
 # tests
 , jaraco-collections
 , pytestCheckHook
@@ -46,6 +49,8 @@ buildPythonPackage rec {
     "importlib_resources"
   ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Read resources from Python packages";
     homepage = "https://importlib-resources.readthedocs.io/";

pkgs/development/python-modules/ipykernel/default.nix

@@ -18,6 +18,9 @@
 , pyzmq
 , tornado
 , traitlets
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -63,6 +66,7 @@ buildPythonPackage rec {
 
   passthru.tests = {
     pytest = callPackage ./tests.nix { };
+    inherit sage;
   };
 
   meta = {

pkgs/development/python-modules/ipython/default.nix

@@ -29,6 +29,9 @@
 , notebook
 , qtconsole
 
+# Reverse dependency
+, sage
+
 # Test dependencies
 , pickleshare
 , pytest-asyncio
@@ -106,6 +109,8 @@ buildPythonPackage rec {
     "test_clipboard_get"
   ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "IPython: Productive Interactive Computing";
     downloadPage = "https://github.com/ipython/ipython/";

pkgs/development/python-modules/jinja2/default.nix

@@ -12,6 +12,9 @@
 , pallets-sphinx-themes
 , sphinxcontrib-log-cabinet
 , sphinx-issues
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -75,6 +78,8 @@ buildPythonPackage rec {
     inherit meta;
   };
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     changelog = "https://github.com/pallets/jinja/blob/${version}/CHANGES.rst";
     description = "Very fast and expressive template engine";

pkgs/development/python-modules/jupyter-core/default.nix

@@ -7,6 +7,9 @@
 , traitlets
 , pip
 , pytestCheckHook
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -61,6 +64,8 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "jupyter_core" ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Base package on which Jupyter projects rely";
     homepage = "https://jupyter.org/";

pkgs/development/python-modules/matplotlib/default.nix

@@ -69,6 +69,9 @@
 # required for headless detection
 , libX11
 , wayland
+
+# Reverse dependency
+, sage
 }:
 
 let
@@ -183,6 +186,8 @@ buildPythonPackage rec {
     };
   };
 
+  passthru.tests = { inherit sage; };
+
   env.MPLSETUPCFG = writeText "mplsetup.cfg" (lib.generators.toINI {} passthru.config);
 
   # Encountering a ModuleNotFoundError, as describved and investigated at:

pkgs/development/python-modules/memory-allocator/default.nix

@@ -2,6 +2,9 @@
 , fetchPypi
 , buildPythonPackage
 , cython
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -19,6 +22,8 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "memory_allocator" ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "An extension class to allocate memory easily with cython";
     homepage = "https://github.com/sagemath/memory_allocator/";

pkgs/development/python-modules/mpmath/default.nix

@@ -5,6 +5,9 @@
 , isPyPy
 , setuptools
 , pytestCheckHook
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -29,6 +32,8 @@ buildPythonPackage rec {
     ];
   };
 
+  passthru.tests = { inherit sage; };
+
   nativeCheckInputs = [
     pytestCheckHook
   ];

pkgs/development/python-modules/networkx/default.nix

@@ -19,6 +19,9 @@
 # tests
 , pytest-xdist
 , pytestCheckHook
+
+# reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -53,6 +56,8 @@ buildPythonPackage rec {
     ];
   };
 
+  passthru.tests = { inherit sage; };
+
   nativeCheckInputs = [
     pytest-xdist
     pytestCheckHook

pkgs/development/python-modules/numpy/default.nix

@@ -19,6 +19,9 @@
 , blas
 , lapack
 
+# Reverse dependency
+, sage
+
 # tests
 , hypothesis
 , pytest-xdist
@@ -177,6 +180,7 @@ in buildPythonPackage rec {
     blas = blas.provider;
     blasImplementation = blas.implementation;
     inherit cfg;
+    tests = { inherit sage; };
   };
 
   # Disable test

pkgs/development/python-modules/pexpect/default.nix

@@ -3,6 +3,9 @@
 , fetchPypi
 , setuptools
 , ptyprocess
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage (rec {
@@ -24,6 +27,8 @@ buildPythonPackage (rec {
 
   propagatedBuildInputs = [ ptyprocess ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     homepage = "http://www.noah.org/wiki/Pexpect";
     description = "Automate interactive console applications such as ssh, ftp, etc";

pkgs/development/python-modules/pillow/default.nix

@@ -7,7 +7,7 @@
 , defusedxml, olefile, freetype, libjpeg, zlib, libtiff, libwebp, libxcrypt, tcl, lcms2, tk, libX11
 , libxcb, openjpeg, libimagequant, numpy, pytestCheckHook, setuptools
 # for passthru.tests
-, imageio, matplotlib, pilkit, pydicom, reportlab
+, imageio, matplotlib, pilkit, pydicom, reportlab, sage
 }@args:
 
 import ./generic.nix (rec {
@@ -24,7 +24,7 @@ import ./generic.nix (rec {
   };
 
   passthru.tests = {
-    inherit imageio matplotlib pilkit pydicom reportlab;
+    inherit imageio matplotlib pilkit pydicom reportlab sage;
   };
 
   meta = with lib; {

pkgs/development/python-modules/pplpy/default.nix

@@ -9,6 +9,9 @@
 , cysignals
 , gmpy2
 , sphinx
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -54,6 +57,8 @@ buildPythonPackage rec {
     mv docs/build/html "$doc/share/doc/pplpy"
   '';
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "A Python wrapper for ppl";
     homepage = "https://gitlab.com/videlec/pplpy";

pkgs/development/python-modules/primecountpy/default.nix

@@ -4,6 +4,9 @@
 , primecount
 , cython
 , cysignals
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -25,6 +28,8 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "primecountpy" ];
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "Cython interface for C++ primecount library";
     homepage = "https://github.com/dimpase/primecountpy/";

pkgs/development/python-modules/pycparser/default.nix

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, unittestCheckHook }:
+{ lib, buildPythonPackage, fetchPypi, unittestCheckHook, pythonOlder }:
 
 buildPythonPackage rec {
   pname = "pycparser";
@@ -11,6 +11,7 @@ buildPythonPackage rec {
   };
 
   nativeCheckInputs = [ unittestCheckHook ];
+  disabled = pythonOlder "3.8";
 
   unittestFlagsArray = [ "-s" "tests" ];
 

pkgs/development/python-modules/scikit-bio/default.nix

@@ -1,53 +1,64 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, cython
-, lockfile
-, cachecontrol
-, decorator
-, h5py
-, ipython
-, matplotlib
-, natsort
-, numpy
-, pandas
-, scipy
-, hdmedians
-, scikit-learn
-, coverage
-, python
-, isPy3k
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  cython,
+  oldest-supported-numpy,
+  requests,
+  decorator,
+  natsort,
+  numpy,
+  pandas,
+  scipy,
+  h5py,
+  hdmedians,
+  biom-format,
+  python,
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
-  version = "0.6.0";
-  format = "setuptools";
   pname = "scikit-bio";
-  disabled = !isPy3k;
+  version = "0.6.0";
+  pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-EBBafDwVrlkQJEkn8punqjUjSxnr5lE7hIRUc0OywQ8=";
+  src = fetchFromGitHub {
+    owner = "scikit-bio";
+    repo = "scikit-bio";
+    rev = "refs/tags/${version}";
+    hash = "sha256-v8/r52pJpMi34SekPQBf7CqRbs+ZEyPR3WO5RBB7uKg=";
   };
 
-  nativeBuildInputs = [ cython ];
-  nativeCheckInputs = [ coverage ];
-  propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy h5py hdmedians scikit-learn ];
+  build-system = [
+    setuptools
+    cython
+    oldest-supported-numpy
+  ];
 
-  # cython package not included for tests
-  doCheck = false;
+  dependencies = [
+    requests
+    decorator
+    natsort
+    numpy
+    pandas
+    scipy
+    h5py
+    hdmedians
+    biom-format
+  ];
 
-  checkPhase = ''
-    ${python.interpreter} -m skbio.test
-  '';
+  nativeCheckInputs = [ pytestCheckHook ];
+
+  # only the $out dir contains the built cython extensions, so we run the tests inside there
+  pytestFlagsArray = [ "${placeholder "out"}/${python.sitePackages}/skbio" ];
 
   pythonImportsCheck = [ "skbio" ];
 
-  meta = with lib; {
+  meta = {
     homepage = "http://scikit-bio.org/";
     description = "Data structures, algorithms and educational resources for bioinformatics";
-    license = licenses.bsd3;
-    platforms = [ "x86_64-linux" "x86_64-darwin" ];
-    maintainers = [ ];
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ tomasajt ];
   };
 }

pkgs/development/python-modules/scipy/default.nix

@@ -25,6 +25,9 @@
 , xsimd
 , blas
 , lapack
+
+# Reverse dependency
+, sage
 }:
 
 let
@@ -193,6 +196,7 @@ in buildPythonPackage {
     # Pass it the names of the datasets to update their hashes
     ++ (builtins.attrNames datasetsHashes)
     ;
+    tests = { inherit sage; };
   };
 
   SCIPY_USE_G77_ABI_WRAPPER = 1;

pkgs/development/python-modules/sympy/default.nix

@@ -3,6 +3,9 @@
 , fetchPypi
 , glibcLocales
 , mpmath
+
+# Reverse dependency
+, sage
 }:
 
 buildPythonPackage rec {
@@ -27,6 +30,8 @@ buildPythonPackage rec {
     export LANG="en_US.UTF-8"
   '';
 
+  passthru.tests = { inherit sage; };
+
   meta = with lib; {
     description = "A Python library for symbolic mathematics";
     mainProgram = "isympy";

pkgs/os-specific/linux/nftables/python.nix

@@ -10,7 +10,7 @@ buildPythonPackage {
   pyproject = true;
 
   postPatch = ''
-    substituteInPlace "py/src/nftables.py" \
+    substituteInPlace "src/nftables.py" \
       --replace-fail "libnftables.so.1" "${nftables}/lib/libnftables.so.1"
   '';
 

pkgs/top-level/all-packages.nix

@@ -29712,10 +29712,6 @@ with pkgs;
 
   appgate-sdp = callPackage ../applications/networking/appgate-sdp { };
 
-  apostrophe = callPackage ../applications/editors/apostrophe {
-    pythonPackages = python3Packages;
-  };
-
   ardour = callPackage ../applications/audio/ardour { };
   ardour_7 = callPackage ../applications/audio/ardour/7.nix { };
 

pkgs/top-level/python-packages.nix

@@ -1531,6 +1531,8 @@ self: super: with self; {
 
   binwalk-full = self.binwalk.override { visualizationSupport = true; };
 
+  biom-format = callPackage ../development/python-modules/biom-format { };
+
   biopandas = callPackage ../development/python-modules/biopandas { };
 
   biopython = callPackage ../development/python-modules/biopython { };