Merge staging-next into staging

maintainers/scripts/pluginupdate.py

@@ -73,9 +73,13 @@ def retry(ExceptionToCheck: Any, tries: int = 4, delay: float = 3, backoff: floa
 
     return deco_retry
 
+@dataclass
+class FetchConfig:
+    proc: int
+    github_token: str
 
-def make_request(url: str) -> urllib.request.Request:
-    token = os.getenv("GITHUB_API_TOKEN")
+
+def make_request(url: str, token=None) -> urllib.request.Request:
     headers = {}
     if token is not None:
         headers["Authorization"] = f"token {token}"
@@ -90,6 +94,7 @@ class Repo:
         self.branch = branch
         self.alias = alias
         self.redirect: Dict[str, str] = {}
+        self.token = "dummy_token"
 
     @property
     def name(self):
@@ -132,10 +137,11 @@ class Repo:
 
 class RepoGitHub(Repo):
     def __init__(
-            self, owner: str, repo: str, branch: str, alias: Optional[str]
+        self, owner: str, repo: str, branch: str, alias: Optional[str]
     ) -> None:
         self.owner = owner
         self.repo = repo
+        self.token = None
         '''Url to the repo'''
         super().__init__(self.url(""), branch, alias)
         log.debug("Instantiating github repo %s/%s", self.owner, self.repo)
@@ -150,7 +156,7 @@ class RepoGitHub(Repo):
     @retry(urllib.error.URLError, tries=4, delay=3, backoff=2)
     def has_submodules(self) -> bool:
         try:
-            req = make_request(self.url(f"blob/{self.branch}/.gitmodules"))
+            req = make_request(self.url(f"blob/{self.branch}/.gitmodules"), self.token)
             urllib.request.urlopen(req, timeout=10).close()
         except urllib.error.HTTPError as e:
             if e.code == 404:
@@ -162,7 +168,7 @@ class RepoGitHub(Repo):
     @retry(urllib.error.URLError, tries=4, delay=3, backoff=2)
     def latest_commit(self) -> Tuple[str, datetime]:
         commit_url = self.url(f"commits/{self.branch}.atom")
-        commit_req = make_request(commit_url)
+        commit_req = make_request(commit_url, self.token)
         with urllib.request.urlopen(commit_req, timeout=10) as req:
             self._check_for_redirect(commit_url, req)
             xml = req.read()
@@ -291,15 +297,41 @@ class Editor:
         """To fill the cache"""
         return get_current_plugins(self)
 
-    def load_plugin_spec(self, plugin_file) -> List[PluginDesc]:
-        return load_plugin_spec(plugin_file)
+    def load_plugin_spec(self, config: FetchConfig, plugin_file) -> List[PluginDesc]:
+        plugins = []
+        with open(plugin_file) as f:
+            for line in f:
+                if line.startswith("#"):
+                    continue
+                plugin = parse_plugin_line(config, line)
+                plugins.append(plugin)
+        return plugins
 
     def generate_nix(self, plugins, outfile: str):
         '''Returns nothing for now, writes directly to outfile'''
         raise NotImplementedError()
 
-    def get_update(self, input_file: str, outfile: str, proc: int):
-        return get_update(input_file, outfile, proc, editor=self)
+    def get_update(self, input_file: str, outfile: str, config: FetchConfig):
+        cache: Cache = Cache(self.get_current_plugins(), self.cache_file)
+        _prefetch = functools.partial(prefetch, cache=cache)
+
+        def update() -> dict:
+            plugin_names = self.load_plugin_spec(config, input_file)
+
+            try:
+                pool = Pool(processes=config.proc)
+                results = pool.map(_prefetch, plugin_names)
+            finally:
+                cache.store()
+
+            plugins, redirects = check_results(results)
+
+            self.generate_nix(plugins, outfile)
+
+            return redirects
+
+        return update
+
 
     @property
     def attr_path(self):
@@ -345,7 +377,15 @@ class Editor:
             dest="proc",
             type=int,
             default=30,
-            help="Number of concurrent processes to spawn. Export GITHUB_API_TOKEN allows higher values.",
+            help="Number of concurrent processes to spawn. Setting --github-token allows higher values.",
+        )
+        parser.add_argument(
+            "--github-token",
+            "-t",
+            type=str,
+            default=os.getenv("GITHUB_API_TOKEN"),
+            help="""Allows to set --proc to higher values.
+            Uses GITHUB_API_TOKEN environment variables as the default value.""",
         )
         parser.add_argument(
             "--no-commit", "-n", action="store_true", default=False,
@@ -465,7 +505,7 @@ def make_repo(uri, branch, alias) -> Repo:
         repo = Repo(uri.strip(), branch, alias)
     return repo
 
-def parse_plugin_line(line: str) -> PluginDesc:
+def parse_plugin_line(config: FetchConfig, line: str) -> PluginDesc:
     branch = "HEAD"
     alias = None
     uri = line
@@ -476,21 +516,11 @@ def parse_plugin_line(line: str) -> PluginDesc:
         uri, branch = uri.split("@")
 
     repo = make_repo(uri.strip(), branch.strip(), alias)
+    repo.token = config.github_token
 
     return PluginDesc(repo, branch.strip(), alias)
 
 
-def load_plugin_spec(plugin_file: str) -> List[PluginDesc]:
-    plugins = []
-    with open(plugin_file) as f:
-        for line in f:
-            if line.startswith("#"):
-                continue
-            plugin = parse_plugin_line(line)
-            plugins.append(plugin)
-    return plugins
-
-
 def get_cache_path(cache_file_name: str) -> Optional[Path]:
     xdg_cache = os.environ.get("XDG_CACHE_HOME", None)
     if xdg_cache is None:
@@ -600,40 +630,21 @@ def commit(repo: git.Repo, message: str, files: List[Path]) -> None:
         print("no changes in working tree to commit")
 
 
-def get_update(input_file: str, outfile: str, proc: int, editor: Editor):
-    cache: Cache = Cache(editor.get_current_plugins(), editor.cache_file)
-    _prefetch = functools.partial(prefetch, cache=cache)
-
-    def update() -> dict:
-        plugin_names = editor.load_plugin_spec(input_file)
-
-        try:
-            pool = Pool(processes=proc)
-            results = pool.map(_prefetch, plugin_names)
-        finally:
-            cache.store()
-
-        plugins, redirects = check_results(results)
-
-        editor.generate_nix(plugins, outfile)
-
-        return redirects
-
-    return update
-
 
 def update_plugins(editor: Editor, args):
     """The main entry function of this module. All input arguments are grouped in the `Editor`."""
 
     log.setLevel(LOG_LEVELS[args.debug])
     log.info("Start updating plugins")
-    update = editor.get_update(args.input_file, args.outfile, args.proc)
+    fetch_config = FetchConfig(args.proc, args.github_token)
+    update = editor.get_update(args.input_file, args.outfile, fetch_config)
 
     redirects = update()
     editor.rewrite_input(args.input_file, editor.deprecated, redirects)
 
     autocommit = not args.no_commit
 
+    nixpkgs_repo = None
     if autocommit:
         nixpkgs_repo = git.Repo(editor.root, search_parent_directories=True)
         commit(nixpkgs_repo, f"{editor.attr_path}: update", [args.outfile])

pkgs/applications/editors/cudatext/default.nix

@@ -38,13 +38,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "cudatext";
-  version = "1.155.0";
+  version = "1.156.2";
 
   src = fetchFromGitHub {
     owner = "Alexey-T";
     repo = "CudaText";
     rev = version;
-    sha256 = "sha256-k6ALTbA2PhMZscinXKceM7MSzgr759Y6GxMrQAXMgwM=";
+    sha256 = "sha256-waVTNyK3OHpOvBJrXio+Xjn9q3WmUczbx3E26ChsuKo=";
   };
 
   postPatch = ''

pkgs/applications/editors/cudatext/deps.json

@@ -16,23 +16,23 @@
   },
   "ATSynEdit": {
     "owner": "Alexey-T",
-    "rev": "2022.01.20",
-    "sha256": "sha256-4UJ6t8j8uHB27jprqnlsGB8ytOMQLe4ZzSaYKiw4y70="
+    "rev": "2022.02.19",
+    "sha256": "sha256-cq2dirFNPaWRmZJu0F+CFA//+SuFOOpTH3Q5zL4oPQo="
   },
   "ATSynEdit_Cmp": {
     "owner": "Alexey-T",
-    "rev": "2021.12.28",
-    "sha256": "sha256-bXTjPdn0DIVTdoi30Ws5+M+UsC7F99IphMSTpI5ia/Q="
+    "rev": "2022.01.21",
+    "sha256": "sha256-el5YtzewnHV0fRPgVhApZUVP7huSQseqrO2ibvm6Ctg="
   },
   "EControl": {
     "owner": "Alexey-T",
-    "rev": "2022.01.07",
-    "sha256": "sha256-dgkyXrFs2hzuFjt9GW+WNyrLIp/i/AbRsM/MyMbatdA="
+    "rev": "2022.02.02",
+    "sha256": "sha256-T/6SQJHKzbv/PlObDyc9bcpC14krHgcLDQn0v2fNkLM="
   },
   "ATSynEdit_Ex": {
     "owner": "Alexey-T",
-    "rev": "2022.01.20",
-    "sha256": "sha256-CaGo38NV+mbwekzkgw0DxM4TZf2xwHtYFnC6RbWH+ts="
+    "rev": "2022.02.01",
+    "sha256": "sha256-FAcq6ixmFPQFBAGG2gqB4T+YGYT+Rh/OlKdGcH/iL3g="
   },
   "Python-for-Lazarus": {
     "owner": "Alexey-T",
@@ -41,8 +41,8 @@
   },
   "Emmet-Pascal": {
     "owner": "Alexey-T",
-    "rev": "2020.09.05",
-    "sha256": "0qfiirxnk5g3whx8y8hp54ch3h6gkkd01yf79m95bwar5qvdfybg"
+    "rev": "2022.01.17",
+    "sha256": "sha256-5yqxRW7xFJ4MwHjKnxYL8/HrCDLn30a1gyQRjGMx/qw="
   },
   "CudaText-lexers": {
     "owner": "Alexey-T",

pkgs/applications/editors/cudatext/update.sh

@@ -18,6 +18,6 @@ while IFS=$'\t' read repo owner rev; do
     url="https://github.com/${owner}/${repo}/archive/refs/tags/${latest}.tar.gz"
     hash=$(nix-prefetch-url --quiet --unpack --type sha256 $url)
     sriHash=$(nix hash to-sri --type sha256 $hash)
-    jq ".${repo}.rev = \"${latest}\" | .${repo}.sha256 = \"${sriHash}\"" deps.json | sponge deps.json
+    jq ".\"${repo}\".rev = \"${latest}\" | .\"${repo}\".sha256 = \"${sriHash}\"" deps.json | sponge deps.json
   fi
 done <<< $(jq -r 'to_entries[]|[.key,.value.owner,.value.rev]|@tsv' deps.json)

pkgs/applications/editors/texstudio/default.nix

@@ -3,13 +3,13 @@
 
 mkDerivation rec {
   pname = "texstudio";
-  version = "4.2.1";
+  version = "4.2.2";
 
   src = fetchFromGitHub {
     owner = "${pname}-org";
     repo = pname;
     rev = version;
-    sha256 = "sha256-EUcYQKc/vxOg6E5ZIpWJezLEppOru79s+slO7e/+kAU=";
+    sha256 = "sha256-MZz8DQT1f6RU+euEED1bbg2MsaqC6+W3RoMk2qfIjr4=";
   };
 
   nativeBuildInputs = [ qmake wrapQtAppsHook pkg-config ];

pkgs/applications/graphics/hydrus/default.nix

@@ -10,14 +10,14 @@
 
 python3Packages.buildPythonPackage rec {
   pname = "hydrus";
-  version = "473";
+  version = "474";
   format = "other";
 
   src = fetchFromGitHub {
     owner = "hydrusnetwork";
     repo = "hydrus";
     rev = "v${version}";
-    sha256 = "sha256-eSnN9+9xJ1CeJm/jWw4jZq5OkgXC0p0KmxQ8bhnp9W4=";
+    sha256 = "sha256-NeTHq8zlgBajw/eogwpabqeU0b7cp83Frqy6kisrths=";
   };
 
   nativeBuildInputs = [

pkgs/applications/science/biology/febio-studio/default.nix

@@ -0,0 +1,61 @@
+{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook
+, sshSupport ? true, openssl, libssh
+, tetgenSupport ? true, tetgen
+, ffmpegSupport ? true, ffmpeg
+, dicomSupport  ? false, dcmtk
+, withModelRepo ? true
+, withCadFeatures ? false
+}:
+
+stdenv.mkDerivation rec {
+  pname = "febio-studio";
+  version = "1.6.1";
+
+  src = fetchFromGitHub {
+    owner = "febiosoftware";
+    repo = "FEBioStudio";
+    rev = "v${version}";
+    sha256 = "0r6pg49i0q9idp7pjymj7mlxd63qjvmfvg0l7fmx87y1yd2hfw4h";
+  };
+
+  patches = [
+    ./febio-studio-cmake.patch # Fix Errors that appear with certain Cmake flags
+  ];
+
+  cmakeFlags = [
+    "-DQt_Ver=5"
+    "-DNOT_FIRST=On"
+    "-DOpenGL_GL_PREFERENCE=GLVND"
+  ]
+    ++ lib.optional sshSupport "-DUSE_SSH=On"
+    ++ lib.optional tetgenSupport "-DUSE_TETGEN=On"
+    ++ lib.optional ffmpegSupport "-DUSE_FFMPEG=On"
+    ++ lib.optional dicomSupport "-DUSE_DICOM=On"
+    ++ lib.optional withModelRepo "-DMODEL_REPO=On"
+    ++ lib.optional withCadFeatures "-DCAD_FEATURES=On"
+  ;
+
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/
+    cp -R bin $out/
+    runHook postInstall
+  '';
+
+  nativeBuildInputs = [ cmake wrapQtAppsHook ];
+  buildInputs = [ zlib libglvnd libGLU openssl libssh ]
+    ++ lib.optional sshSupport openssl
+    ++ lib.optional tetgenSupport tetgen
+    ++ lib.optional ffmpegSupport ffmpeg
+    ++ lib.optional dicomSupport dcmtk
+  ;
+
+  meta = with lib; {
+    description = "FEBio Suite Solver";
+    license = with licenses; [ mit ];
+    homepage = "https://febio.org/";
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ Scriptkiddi ];
+  };
+}

pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch

@@ -0,0 +1,38 @@
+diff --git a/FEBioStudio/RepositoryPanel.cpp b/FEBioStudio/RepositoryPanel.cpp
+index 382db303..314cdc68 100644
+--- a/FEBioStudio/RepositoryPanel.cpp
++++ b/FEBioStudio/RepositoryPanel.cpp
+@@ -1364,10 +1364,10 @@ void CRepositoryPanel::loadingPageProgress(qint64 bytesSent, qint64 bytesTotal)
+ 
+ #else
+ 
+-CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QWidget* parent){}
++CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QDockWidget* parent){}
+ CRepositoryPanel::~CRepositoryPanel(){}
+ void CRepositoryPanel::OpenLink(const QString& link) {}
+-// void CRepositoryPanel::Raise() {}
++void CRepositoryPanel::Raise() {}
+ void CRepositoryPanel::SetModelList(){}
+ void CRepositoryPanel::ShowMessage(QString message) {}
+ void CRepositoryPanel::ShowWelcomeMessage(QByteArray messages) {}
+@@ -1396,6 +1396,7 @@ void CRepositoryPanel::on_actionSearch_triggered() {}
+ void CRepositoryPanel::on_actionClearSearch_triggered() {}
+ void CRepositoryPanel::on_actionDeleteRemote_triggered() {}
+ void CRepositoryPanel::on_actionModify_triggered() {}
++void CRepositoryPanel::on_actionCopyPermalink_triggered() {}
+ void CRepositoryPanel::on_treeWidget_itemSelectionChanged() {}
+ void CRepositoryPanel::on_treeWidget_customContextMenuRequested(const QPoint &pos) {}
+ void CRepositoryPanel::DownloadItem(CustomTreeWidgetItem *item) {}
+diff --git a/FEBioStudio/WzdUpload.cpp b/FEBioStudio/WzdUpload.cpp
+index 5ce74346..20062e06 100644
+--- a/FEBioStudio/WzdUpload.cpp
++++ b/FEBioStudio/WzdUpload.cpp
+@@ -1183,7 +1183,7 @@ void CWzdUpload::on_saveJson_triggered()
+ 		getProjectJson(&projectInfo);
+ 
+ 		QFile file(filedlg.selectedFiles()[0]);
+-		file.open(QIODeviceBase::WriteOnly);
++		file.open(QIODevice::WriteOnly);
+ 		file.write(projectInfo);
+ 		file.close();
+ 	}

pkgs/applications/virtualization/libgovirt/default.nix

@@ -2,38 +2,52 @@
 , stdenv
 , fetchurl
 , glib
+, gnome
 , librest
 , libsoup
 , pkg-config
+, gobject-introspection
 }:
 
-with lib;
-
 stdenv.mkDerivation rec {
   pname = "libgovirt";
   version = "0.3.8";
 
-  src = fetchurl {
-    url = "https://download.gnome.org/sources/libgovirt/0.3/${pname}-${version}.tar.xz";
-    sha256 = "sha256-HckYYikXa9+p8l/Y+oLAoFi2pgwcyAfHUH7IqTwPHfg=";
-  };
+  outputs = [ "out" "dev" ];
 
-  enableParallelBuilding = true;
+  src = fetchurl {
+    url = "mirror://gnome/sources/libgovirt/${lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
+    sha256 = "HckYYikXa9+p8l/Y+oLAoFi2pgwcyAfHUH7IqTwPHfg=";
+  };
 
   nativeBuildInputs = [
     pkg-config
+    gobject-introspection
   ];
 
-  propagatedBuildInputs = [
-    librest
+  buildInputs = [
     libsoup
   ];
 
-  meta = {
+  propagatedBuildInputs = [
+    glib
+    librest
+  ];
+
+  enableParallelBuilding = true;
+
+  passthru = {
+    updateScript = gnome.updateScript {
+      packageName = pname;
+      versionPolicy = "none";
+    };
+  };
+
+  meta = with lib; {
     homepage = "https://gitlab.gnome.org/GNOME/libgovirt";
     description = "GObject wrapper for the oVirt REST API";
     maintainers = [ maintainers.amarshall ];
     platforms = platforms.linux;
-    license = licenses.lgpl21;
+    license = licenses.lgpl21Plus;
   };
 }

pkgs/data/fonts/gentium/default.nix

@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 
 let
-  version = "6.001";
+  version = "6.101";
 in fetchzip rec {
   name = "gentium-${version}";
 
@@ -23,7 +23,7 @@ in fetchzip rec {
       -d $out/share/doc/${name}/documentation
   '';
 
-  sha256 = "sha256-DeoMTJ2nhTBtNQYG55lIMvnulqpk/KTeIqgpb5eiTIA=";
+  sha256 = "sha256-+T5aUlqQYDWRp4/4AZzsREHgjAnOeUB6qn1GAI0A5hE=";
 
   meta = with lib; {
     homepage = "https://software.sil.org/gentium/";

pkgs/data/themes/flat-remix-gtk/default.nix

@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "flat-remix-gtk";
-  version = "20220118";
+  version = "20220215";
 
   src = fetchFromGitHub {
     owner = "daniruiz";
     repo = pname;
     rev = version;
-    sha256 = "sha256-FG/SQdMracnP9zlb6LtPAsATvKeX0WaWPwjbrR1ZNZM=";
+    sha256 = "sha256-J9PAHQ/MbdDuX16ioQQnzZpIZs/NJVkJjLL4nfaeNkU=";
   };
 
   dontBuild = true;

pkgs/data/themes/marwaita/default.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "marwaita";
-  version = "12.1";
+  version = "13.0";
 
   src = fetchFromGitHub {
     owner = "darkomarko42";
     repo = pname;
     rev = version;
-    sha256 = "04im7va5xpi17yjkrc46m5bm9j55qq66br1xg8a2arm0j4i0bqsk";
+    sha256 = "sha256-aP/zPM7M8Oru/2AA8w6rKU/AVJJ0bAEC01C60yi2SbM=";
   };
 
   buildInputs = [

pkgs/development/coq-modules/hydra-battles/default.nix

@@ -33,5 +33,5 @@ with lib;
   };
 }).overrideAttrs(o:
   let inherit (o) version; in {
-    propagatedBuildInputs = [ equations ] ++ optional (versions.isGe "0.6" version) LibHyps;
+    propagatedBuildInputs = [ equations ] ++ optional (versions.isGe "0.6" version || version == "dev") LibHyps;
   })

pkgs/development/libraries/librest/default.nix

@@ -4,7 +4,11 @@
 , pkg-config
 , glib
 , libsoup
+, libxml2
 , gobject-introspection
+, gtk-doc
+, docbook-xsl-nons
+, docbook_xml_dtd_412
 , gnome
 }:
 
@@ -12,6 +16,8 @@ stdenv.mkDerivation rec {
   pname = "rest";
   version = "0.8.1";
 
+  outputs = [ "out" "dev" "devdoc" ];
+
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
     sha256 = "0513aad38e5d3cedd4ae3c551634e3be1b9baaa79775e53b2dba9456f15b01c9";
@@ -20,14 +26,19 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     pkg-config
     gobject-introspection
+    gtk-doc
+    docbook-xsl-nons
+    docbook_xml_dtd_412
   ];
 
-  buildInputs = [
+  propagatedBuildInputs = [
     glib
     libsoup
+    libxml2
   ];
 
   configureFlags = [
+    "--enable-gtk-doc"
     # Remove when https://gitlab.gnome.org/GNOME/librest/merge_requests/2 is merged.
     "--with-ca-certificates=/etc/ssl/certs/ca-certificates.crt"
   ];

pkgs/development/ocaml-modules/torch/default.nix

@@ -17,7 +17,7 @@
 
 buildDunePackage rec {
   pname = "torch";
-  version = "0.13";
+  version = "0.14";
 
   useDune2 = true;
 
@@ -27,7 +27,7 @@ buildDunePackage rec {
     owner = "LaurentMazare";
     repo   = "ocaml-${pname}";
     rev    = version;
-    sha256 = "0528h1mkrqbmbf7hy91dsnxcg0k55m3jgharr71c652xyd847yz7";
+    sha256 = "sha256:039anfvzsalbqi5cdp95bbixcwr2ngharihgd149hcr0wa47y700";
   };
 
   buildInputs = [ dune-configurator ];

pkgs/development/octave-modules/symbolic/default.nix

@@ -1,38 +1,27 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromGitHub
 # Octave's Python (Python 3)
 , python
-# Needed only to get the correct version of sympy needed
-, python2Packages
 }:
 
 let
-  # Need to use sympy 1.5.1 for https://github.com/cbm755/octsympy/issues/1023
-  # It has been addressed, but not merged yet.
-  # In the meantime, we create a Python environment with Python 3, its mpmath
-  # version and sympy 1.5 from python2Packages.
-  pythonEnv = (let
-      overridenPython = let
-        packageOverrides = self: super: {
-          sympy = super.sympy.overridePythonAttrs (old: rec {
-            version = python2Packages.sympy.version;
-            src = python2Packages.sympy.src;
-          });
-        };
-      in python.override {inherit packageOverrides; self = overridenPython; };
-    in overridenPython.withPackages (ps: [
+  pythonEnv = python.withPackages (ps: [
       ps.sympy
       ps.mpmath
-    ]));
+    ]);
 
 in buildOctavePackage rec {
   pname = "symbolic";
-  version = "2.9.0";
+  version = "unstable-2021-10-16";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1jr3kg9q6r4r4h3hiwq9fli6wsns73rqfzkrg25plha9195c97h8";
+  # https://github.com/cbm755/octsympy/issues/1023 has been resolved, however
+  # a new release has not been made
+  src = fetchFromGitHub {
+    owner = "cbm755";
+    repo = "octsympy";
+    rev = "5b58530f4ada78c759829ae703a0e5d9832c32d4";
+    sha256 = "sha256-n6P1Swjl4RfgxfLY0ZuN3pcL8PcoknA6yxbnw96OZ2k=";
   };
 
   propagatedBuildInputs = [ pythonEnv ];

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

@@ -12,7 +12,7 @@
 
 buildPythonPackage rec {
   pname = "aiogithubapi";
-  version = "22.2.2";
+  version = "22.2.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
     owner = "ludeeus";
     repo = pname;
     rev = version;
-    sha256 = "sha256-RmMI3h8ouFZYD+xeK4bVx0k529UP+Y2KH7r161zst7Y=";
+    sha256 = "sha256-oeUcyClTmOYF6vdhwiOp2L7x27DXEbujdtRV4NwGcYo=";
   };
 
   propagatedBuildInputs = [

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

@@ -10,13 +10,13 @@
 
 buildPythonPackage rec {
   pname = "pynetbox";
-  version = "6.6.0";
+  version = "6.6.1";
 
   src = fetchFromGitHub {
     owner = "netbox-community";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-vgknnFnmRLIpBLdv1iFGkuql2NOLurOgF2CDKoo8WGg=";
+    sha256 = "sha256-8oqbnCAMq29QIp9ETbMa3Ve8tTuJzQ0D8KlOYnLdUgQ=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

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

@@ -14,7 +14,7 @@
 
 buildPythonPackage rec {
   pname = "python-socketio";
-  version = "5.5.1";
+  version = "5.5.2";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -23,7 +23,7 @@ buildPythonPackage rec {
     owner = "miguelgrinberg";
     repo = "python-socketio";
     rev = "v${version}";
-    sha256 = "sha256-mtXGSd7Y+frT22EL3QmiBNatwc6IrJqGBRfsQlD8LLk=";
+    sha256 = "sha256-ZTjh9gtnJwFG2qWH6FBrvLHKsEuTjkcKL6j6Mdos6zo=";
   };
 
   propagatedBuildInputs = [

pkgs/servers/vouch-proxy/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "vouch-proxy";
-  version = "0.35.1";
+  version = "0.36.0";
 
   src = fetchFromGitHub {
     owner = "vouch";
     repo = "vouch-proxy";
     rev = "v${version}";
-    sha256 = "sha256-dKf68WjCynB73RBWneBsMoyowUcrEaBTnMKVKB0sgsg=";
+    sha256 = "sha256-pgoxRzYc5PIrxnRwWpthFmpsxDfvWTmLT7upQVIFoQo=";
   };
 
   vendorSha256 = "sha256-ifH+420FIrib+zQtzzHtMMYd84BED+vgnRw4xToYIl4=";
@@ -26,6 +26,7 @@ buildGoModule rec {
     homepage = "https://github.com/vouch/vouch-proxy";
     description = "An SSO and OAuth / OIDC login solution for NGINX using the auth_request module";
     license = licenses.mit;
-    maintainers = with maintainers; [ em0lar ];
+    maintainers = with maintainers; [ em0lar erictapen ];
+    platforms = lib.platforms.linux;
   };
 }

pkgs/tools/admin/syft/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "syft";
-  version = "0.37.10";
+  version = "0.38.0";
 
   src = fetchFromGitHub {
     owner = "anchore";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-j3/WE13djrgI7S6YISg9kPIkV0IR0C65QU8zj0z0MVg=";
+    sha256 = "sha256-YJQ0gWhhcB+jkVzu1KP+QMOiiCOyQnSuQ4rSfVGMOCU=";
     # populate values that require us to use git. By doing this in postFetch we
     # can delete .git afterwards and maintain better reproducibility of the src.
     leaveDotGit = true;
@@ -22,7 +22,7 @@ buildGoModule rec {
       find "$out" -name .git -print0 | xargs -0 rm -rf
     '';
   };
-  vendorSha256 = "sha256-gIcPxSzWzldR9UX4iB2fkwc0BfATT1B+Nge+sGefmj8=";
+  vendorSha256 = "sha256-dT+MPuMQoA8Spx8CkF3OBhWdXXssg62ZHIZBrokUkp4=";
 
   nativeBuildInputs = [ installShellFiles ];
 

pkgs/tools/misc/miniserve/default.nix

@@ -11,16 +11,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "miniserve";
-  version = "0.19.1";
+  version = "0.19.2";
 
   src = fetchFromGitHub {
     owner = "svenstaro";
     repo = "miniserve";
     rev = "v${version}";
-    sha256 = "sha256-pKNcgrhq5sh6AXKCStAIYAjTpW+tcnSheFHohp+Z84k=";
+    sha256 = "sha256-/LmLz4hTmOjpR4Bqf+hABh3PSeaO/sSz/EgHp+nM20o=";
   };
 
-  cargoSha256 = "sha256-QonLcAixRR7HEefU6D7cSF/stWFodWLWQI7HAkPJHrY=";
+  cargoSha256 = "sha256-/KL5c5OeflNDKWuE5Gzqgcew9zf8HFjvmBid+mQSqZE=";
 
   nativeBuildInputs = [ installShellFiles pkg-config zlib ];
   buildInputs = lib.optionals stdenv.isDarwin [ libiconv Security ];

pkgs/tools/misc/writedisk/default.nix

@@ -0,0 +1,29 @@
+{ lib
+, rustPlatform
+, fetchCrate
+, pkg-config
+, stdenv
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "writedisk";
+  version = "1.2.0";
+
+  src = fetchCrate {
+    inherit version;
+    pname = "writedisk";
+    sha256 = "sha256-f5+Qw9Agepx2wIUmsAA2M9g/ajbFjjLR5RPPtQncRKU=";
+  };
+
+  cargoSha256 = "sha256-SMAhh7na+XQyVtbfzsBGOCdBRLP58JL1fPSBVKFkhdc=";
+
+  nativeBuildInputs = [ pkg-config ];
+
+  meta = with lib; {
+    description = "Small utility for writing a disk image to a USB drive";
+    homepage = "https://github.com/nicholasbishop/writedisk";
+    platforms = platforms.linux;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ devhell ];
+  };
+}

pkgs/tools/networking/imapproxy/default.nix

@@ -1,24 +0,0 @@
-{lib, stdenv, fetchurl, openssl, ncurses}:
-
-stdenv.mkDerivation rec {
-  pname = "imapproxy";
-  version = "1.2.7";
-
-  src = fetchurl {
-    url = "mirror://sourceforge/squirrelmail/squirrelmail-imap_proxy-${version}.tar.bz2";
-    sha256 = "0j5fq755sxiz338ia93jrkiy64crv30g37pir5pxfys57q7d92nx";
-  };
-
-  buildInputs = [ openssl ncurses ];
-
-  patchPhase = ''
-    sed -i -e 's/-o \(root\|bin\) -g \(sys\|bin\)//' Makefile.in
-  '';
-
-  meta = {
-    homepage = "http://imapproxy.org/";
-    description = "It proxies IMAP transactions caching server connections";
-    license = lib.licenses.gpl2Plus;
-    platforms = lib.platforms.unix;
-  };
-}

pkgs/tools/networking/netdiscover/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "netdiscover";
-  version = "0.8.1";
+  version = "0.9";
 
   src = fetchFromGitHub {
     owner = "netdiscover-scanner";
     repo = pname;
     rev = version;
-    sha256 = "13fp9rfr9vh756m5wck76zbcr0296ir52dahzlqdr52ha9vrswbb";
+    sha256 = "sha256-4pSGWMTOMECXKpba5739OQA8FIuNmffFbniU9Gd4GlM=";
   };
 
   nativeBuildInputs = [ autoreconfHook ];

pkgs/tools/security/pinentry-bemenu/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pinentry-bemenu";
-  version = "0.9.0";
+  version = "0.10.0";
 
   src = fetchFromGitHub {
     owner = "t-8ch";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-AFS4T7VqPga53/3rG8be9Q//6/2JJIe7+Ata33ewySg=";
+    sha256 = "sha256-2Q8hN7AbuGqm7pfNHlJlSi1Op/OpJBun/AIDhUDnGvU=";
   };
 
   nativeBuildInputs = [ meson ninja pkg-config ];

pkgs/tools/security/scallion/default.nix

@@ -1,36 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, makeWrapper, mono, openssl_1_0_2, ocl-icd }:
-
-stdenv.mkDerivation rec {
-  version = "2.1";
-  pname = "scallion";
-
-  src = fetchFromGitHub {
-    owner = "lachesis";
-    repo = "scallion";
-    rev = "v${version}";
-    sha256 = "1l9aj101xpsaaa6kmmhmq68m6z8gzli1iaaf8xaxbivq0i7vka9k";
-  };
-
-  nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ mono ];
-
-  buildPhase = ''
-    xbuild scallion.sln
-  '';
-
-  installPhase = ''
-    mkdir -p $out/share
-    cp scallion/bin/Debug/* $out/share/
-    makeWrapper ${mono}/bin/mono $out/bin/scallion \
-      --prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath [ openssl_1_0_2 ocl-icd ]} \
-      --add-flags $out/share/scallion.exe
-  '';
-
-  meta = with lib; {
-    description = "GPU-based tor hidden service name generator";
-    homepage = src.meta.homepage;
-    license = licenses.mit;
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ volth ];
-  };
-}

pkgs/top-level/aliases.nix

@@ -479,6 +479,7 @@ mapAliases ({
   icedtea8_web = adoptopenjdk-icedtea-web; # Added 2019-08-21
   icedtea_web = adoptopenjdk-icedtea-web; # Added 2019-08-21
   idea = jetbrains; # Added 2017-04-03
+  imapproxy = throw "imapproxy has been removed because it did not support a supported openssl version"; # added 2021-12-15
   imagemagick7Big = imagemagickBig; # Added 2021-02-22
   imagemagick7 = imagemagick; # Added 2021-02-22
   imagemagick7_light = imagemagick_light; # Added 2021-02-22
@@ -1061,6 +1062,7 @@ mapAliases ({
   saneBackendsGit = sane-backends; # Added 2016-01-02
   saneFrontends = sane-frontends; # Added 2016-01-02
   scaff = throw "scaff is deprecated - replaced by https://gitlab.com/jD91mZM2/inc (not in nixpkgs yet)"; # Added 2020-03-01
+  scallion = throw "scallion has been removed, because it is currently unmaintained upstream"; # added 2021-12-15
   scim = sc-im; # Added 2016-01-22
   scollector = bosun; # Added 2018-04-25
   scyther = throw "scyther has been removed since it currently only supports Python 2, see https://github.com/cascremers/scyther/issues/20"; # Added 2021-10-07

pkgs/top-level/all-packages.nix

@@ -1092,6 +1092,8 @@ with pkgs;
     use64 = true;
   };
 
+  writedisk = callPackage ../tools/misc/writedisk { };
+
   xcd = callPackage ../tools/misc/xcd { };
 
   xrootd = callPackage ../tools/networking/xrootd { };
@@ -6639,10 +6641,6 @@ with pkgs;
 
   ike-scan = callPackage ../tools/security/ike-scan { };
 
-  imapproxy = callPackage ../tools/networking/imapproxy {
-    openssl = openssl_1_0_2;
-  };
-
   imapsync = callPackage ../tools/networking/imapsync { };
 
   imgur-screenshot = callPackage ../tools/graphics/imgur-screenshot { };
@@ -9608,8 +9606,6 @@ with pkgs;
 
   sasview = libsForQt5.callPackage ../applications/science/misc/sasview {};
 
-  scallion = callPackage ../tools/security/scallion { };
-
   scanbd = callPackage ../tools/graphics/scanbd { };
 
   scdoc = callPackage ../tools/typesetting/scdoc { };
@@ -31892,6 +31888,8 @@ with pkgs;
 
   fastp = callPackage ../applications/science/biology/fastp { };
 
+  febio-studio = libsForQt5.callPackage ../applications/science/biology/febio-studio { };
+
   hisat2 = callPackage ../applications/science/biology/hisat2 { };
 
   htslib = callPackage ../development/libraries/science/biology/htslib { };