diff --git a/maintainers/scripts/pluginupdate.py b/maintainers/scripts/pluginupdate.py index de85b88da3fd..0fad92481bba 100644 --- a/maintainers/scripts/pluginupdate.py +++ b/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]) diff --git a/pkgs/applications/editors/cudatext/default.nix b/pkgs/applications/editors/cudatext/default.nix index 3654a75fd8fc..2b58ba50bca6 100644 --- a/pkgs/applications/editors/cudatext/default.nix +++ b/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 = '' diff --git a/pkgs/applications/editors/cudatext/deps.json b/pkgs/applications/editors/cudatext/deps.json index 84f21e5ea20e..9ae3c1c33ca1 100644 --- a/pkgs/applications/editors/cudatext/deps.json +++ b/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", diff --git a/pkgs/applications/editors/cudatext/update.sh b/pkgs/applications/editors/cudatext/update.sh index 8389b3e8a7d4..f7aae6ff8b49 100755 --- a/pkgs/applications/editors/cudatext/update.sh +++ b/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 <<< $(jq -r 'to_entries[]|[.key,.value.owner,.value.rev]|@tsv' deps.json) diff --git a/pkgs/applications/editors/texstudio/default.nix b/pkgs/applications/editors/texstudio/default.nix index 67f1f7e6048e..4e7bfc2cff7d 100644 --- a/pkgs/applications/editors/texstudio/default.nix +++ b/pkgs/applications/editors/texstudio/default.nix @@ -3,13 +3,13 @@ mkDerivation rec { pname = "texstudio"; - version = "4.2.1"; + version = "4.2.2"; src = fetchFromGitHub { owner = "${pname}-org"; repo = pname; rev = version; - sha256 = "sha256-EUcYQKc/vxOg6E5ZIpWJezLEppOru79s+slO7e/+kAU="; + sha256 = "sha256-MZz8DQT1f6RU+euEED1bbg2MsaqC6+W3RoMk2qfIjr4="; }; nativeBuildInputs = [ qmake wrapQtAppsHook pkg-config ]; diff --git a/pkgs/applications/graphics/hydrus/default.nix b/pkgs/applications/graphics/hydrus/default.nix index 89db615da5dc..12e605f80c4f 100644 --- a/pkgs/applications/graphics/hydrus/default.nix +++ b/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${version}"; - sha256 = "sha256-eSnN9+9xJ1CeJm/jWw4jZq5OkgXC0p0KmxQ8bhnp9W4="; + sha256 = "sha256-NeTHq8zlgBajw/eogwpabqeU0b7cp83Frqy6kisrths="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix new file mode 100644 index 000000000000..e334637f243c --- /dev/null +++ b/pkgs/applications/science/biology/febio-studio/default.nix @@ -0,0 +1,61 @@ +{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook +, sshSupport ? true, openssl, libssh +, tetgenSupport ? true, tetgen +, ffmpegSupport ? true, ffmpeg +, dicomSupport ? false, dcmtk +, withModelRepo ? true +, withCadFeatures ? false +}: + +stdenv.mkDerivation rec { + pname = "febio-studio"; + version = "1.6.1"; + + src = fetchFromGitHub { + owner = "febiosoftware"; + repo = "FEBioStudio"; + rev = "v${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 ]; + }; +} diff --git a/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch b/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch new file mode 100644 index 000000000000..e694f6c3b89f --- /dev/null +++ b/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(); + } diff --git a/pkgs/applications/virtualization/libgovirt/default.nix b/pkgs/applications/virtualization/libgovirt/default.nix index bd92f7666abf..9c9da54c3632 100644 --- a/pkgs/applications/virtualization/libgovirt/default.nix +++ b/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; }; } diff --git a/pkgs/data/fonts/gentium/default.nix b/pkgs/data/fonts/gentium/default.nix index ac8839f075b2..f64f7b341440 100644 --- a/pkgs/data/fonts/gentium/default.nix +++ b/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/"; diff --git a/pkgs/data/themes/flat-remix-gtk/default.nix b/pkgs/data/themes/flat-remix-gtk/default.nix index 38702fe40916..59b2714285ed 100644 --- a/pkgs/data/themes/flat-remix-gtk/default.nix +++ b/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; diff --git a/pkgs/data/themes/marwaita/default.nix b/pkgs/data/themes/marwaita/default.nix index 966cb1c4f6f8..a01177632b55 100644 --- a/pkgs/data/themes/marwaita/default.nix +++ b/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 = [ diff --git a/pkgs/development/coq-modules/hydra-battles/default.nix b/pkgs/development/coq-modules/hydra-battles/default.nix index e7dc7474e857..7977363d83f5 100644 --- a/pkgs/development/coq-modules/hydra-battles/default.nix +++ b/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; }) diff --git a/pkgs/development/libraries/librest/default.nix b/pkgs/development/libraries/librest/default.nix index 0c885f0764b5..ce2df9cc9a8a 100644 --- a/pkgs/development/libraries/librest/default.nix +++ b/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" ]; diff --git a/pkgs/development/ocaml-modules/torch/default.nix b/pkgs/development/ocaml-modules/torch/default.nix index 1cf84dd4938e..7a0c6bdadeff 100644 --- a/pkgs/development/ocaml-modules/torch/default.nix +++ b/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-${pname}"; rev = version; - sha256 = "0528h1mkrqbmbf7hy91dsnxcg0k55m3jgharr71c652xyd847yz7"; + sha256 = "sha256:039anfvzsalbqi5cdp95bbixcwr2ngharihgd149hcr0wa47y700"; }; buildInputs = [ dune-configurator ]; diff --git a/pkgs/development/octave-modules/symbolic/default.nix b/pkgs/development/octave-modules/symbolic/default.nix index e40d27e7c385..513826539929 100644 --- a/pkgs/development/octave-modules/symbolic/default.nix +++ b/pkgs/development/octave-modules/symbolic/default.nix @@ -1,38 +1,27 @@ { buildOctavePackage , lib -, fetchurl +, fetchFromGitHub # Octave's Python (Python 3) , python -# Needed only to get the correct version of sympy needed -, python2Packages }: let - # Need to use sympy 1.5.1 for https://github.com/cbm755/octsympy/issues/1023 - # It has been addressed, but not merged yet. - # In the meantime, we create a Python environment with Python 3, its mpmath - # version and sympy 1.5 from python2Packages. - pythonEnv = (let - overridenPython = let - packageOverrides = self: super: { - sympy = super.sympy.overridePythonAttrs (old: rec { - version = python2Packages.sympy.version; - src = python2Packages.sympy.src; - }); - }; - in python.override {inherit packageOverrides; self = overridenPython; }; - in overridenPython.withPackages (ps: [ + pythonEnv = python.withPackages (ps: [ ps.sympy ps.mpmath - ])); + ]); in buildOctavePackage rec { pname = "symbolic"; - version = "2.9.0"; + version = "unstable-2021-10-16"; - src = fetchurl { - url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz"; - sha256 = "1jr3kg9q6r4r4h3hiwq9fli6wsns73rqfzkrg25plha9195c97h8"; + # https://github.com/cbm755/octsympy/issues/1023 has been resolved, however + # a new release has not been made + src = fetchFromGitHub { + owner = "cbm755"; + repo = "octsympy"; + rev = "5b58530f4ada78c759829ae703a0e5d9832c32d4"; + sha256 = "sha256-n6P1Swjl4RfgxfLY0ZuN3pcL8PcoknA6yxbnw96OZ2k="; }; propagatedBuildInputs = [ pythonEnv ]; diff --git a/pkgs/development/python-modules/aiogithubapi/default.nix b/pkgs/development/python-modules/aiogithubapi/default.nix index c52a8a1329cf..747aa3f4d471 100644 --- a/pkgs/development/python-modules/aiogithubapi/default.nix +++ b/pkgs/development/python-modules/aiogithubapi/default.nix @@ -12,7 +12,7 @@ buildPythonPackage rec { pname = "aiogithubapi"; - version = "22.2.2"; + version = "22.2.3"; format = "setuptools"; disabled = pythonOlder "3.8"; @@ -21,7 +21,7 @@ buildPythonPackage rec { owner = "ludeeus"; repo = pname; rev = version; - sha256 = "sha256-RmMI3h8ouFZYD+xeK4bVx0k529UP+Y2KH7r161zst7Y="; + sha256 = "sha256-oeUcyClTmOYF6vdhwiOp2L7x27DXEbujdtRV4NwGcYo="; }; propagatedBuildInputs = [ diff --git a/pkgs/development/python-modules/pynetbox/default.nix b/pkgs/development/python-modules/pynetbox/default.nix index 84e03a6086bf..14c74cc8669c 100644 --- a/pkgs/development/python-modules/pynetbox/default.nix +++ b/pkgs/development/python-modules/pynetbox/default.nix @@ -10,13 +10,13 @@ buildPythonPackage rec { pname = "pynetbox"; - version = "6.6.0"; + version = "6.6.1"; src = fetchFromGitHub { owner = "netbox-community"; repo = pname; rev = "v${version}"; - sha256 = "sha256-vgknnFnmRLIpBLdv1iFGkuql2NOLurOgF2CDKoo8WGg="; + sha256 = "sha256-8oqbnCAMq29QIp9ETbMa3Ve8tTuJzQ0D8KlOYnLdUgQ="; }; SETUPTOOLS_SCM_PRETEND_VERSION = version; diff --git a/pkgs/development/python-modules/python-socketio/default.nix b/pkgs/development/python-modules/python-socketio/default.nix index 0484a75eaeae..e41942317f99 100644 --- a/pkgs/development/python-modules/python-socketio/default.nix +++ b/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${version}"; - sha256 = "sha256-mtXGSd7Y+frT22EL3QmiBNatwc6IrJqGBRfsQlD8LLk="; + sha256 = "sha256-ZTjh9gtnJwFG2qWH6FBrvLHKsEuTjkcKL6j6Mdos6zo="; }; propagatedBuildInputs = [ diff --git a/pkgs/servers/vouch-proxy/default.nix b/pkgs/servers/vouch-proxy/default.nix index 94ef0b23f3b7..a8a773385db9 100644 --- a/pkgs/servers/vouch-proxy/default.nix +++ b/pkgs/servers/vouch-proxy/default.nix @@ -2,13 +2,13 @@ buildGoModule rec { pname = "vouch-proxy"; - version = "0.35.1"; + version = "0.36.0"; src = fetchFromGitHub { owner = "vouch"; repo = "vouch-proxy"; rev = "v${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; }; } diff --git a/pkgs/tools/admin/syft/default.nix b/pkgs/tools/admin/syft/default.nix index 24b6d4ddcb2c..f3a1c6d10c33 100644 --- a/pkgs/tools/admin/syft/default.nix +++ b/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 ]; diff --git a/pkgs/tools/misc/miniserve/default.nix b/pkgs/tools/misc/miniserve/default.nix index 46a979d07370..89607f13ac97 100644 --- a/pkgs/tools/misc/miniserve/default.nix +++ b/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${version}"; - sha256 = "sha256-pKNcgrhq5sh6AXKCStAIYAjTpW+tcnSheFHohp+Z84k="; + sha256 = "sha256-/LmLz4hTmOjpR4Bqf+hABh3PSeaO/sSz/EgHp+nM20o="; }; - cargoSha256 = "sha256-QonLcAixRR7HEefU6D7cSF/stWFodWLWQI7HAkPJHrY="; + cargoSha256 = "sha256-/KL5c5OeflNDKWuE5Gzqgcew9zf8HFjvmBid+mQSqZE="; nativeBuildInputs = [ installShellFiles pkg-config zlib ]; buildInputs = lib.optionals stdenv.isDarwin [ libiconv Security ]; diff --git a/pkgs/tools/misc/writedisk/default.nix b/pkgs/tools/misc/writedisk/default.nix new file mode 100644 index 000000000000..34f4581ba09d --- /dev/null +++ b/pkgs/tools/misc/writedisk/default.nix @@ -0,0 +1,29 @@ +{ lib +, rustPlatform +, fetchCrate +, pkg-config +, stdenv +}: + +rustPlatform.buildRustPackage rec { + pname = "writedisk"; + version = "1.2.0"; + + src = fetchCrate { + inherit version; + pname = "writedisk"; + sha256 = "sha256-f5+Qw9Agepx2wIUmsAA2M9g/ajbFjjLR5RPPtQncRKU="; + }; + + cargoSha256 = "sha256-SMAhh7na+XQyVtbfzsBGOCdBRLP58JL1fPSBVKFkhdc="; + + nativeBuildInputs = [ pkg-config ]; + + meta = with lib; { + description = "Small utility for writing a disk image to a USB drive"; + homepage = "https://github.com/nicholasbishop/writedisk"; + platforms = platforms.linux; + license = licenses.asl20; + maintainers = with maintainers; [ devhell ]; + }; +} diff --git a/pkgs/tools/networking/imapproxy/default.nix b/pkgs/tools/networking/imapproxy/default.nix deleted file mode 100644 index ca0ce6f933fc..000000000000 --- a/pkgs/tools/networking/imapproxy/default.nix +++ /dev/null @@ -1,24 +0,0 @@ -{lib, stdenv, fetchurl, openssl, ncurses}: - -stdenv.mkDerivation rec { - pname = "imapproxy"; - version = "1.2.7"; - - src = fetchurl { - url = "mirror://sourceforge/squirrelmail/squirrelmail-imap_proxy-${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; - }; -} diff --git a/pkgs/tools/networking/netdiscover/default.nix b/pkgs/tools/networking/netdiscover/default.nix index 1a7b93eef8ab..2146dd63b99e 100644 --- a/pkgs/tools/networking/netdiscover/default.nix +++ b/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 ]; diff --git a/pkgs/tools/security/pinentry-bemenu/default.nix b/pkgs/tools/security/pinentry-bemenu/default.nix index afe1d03fff0b..0cc3f9bcf047 100644 --- a/pkgs/tools/security/pinentry-bemenu/default.nix +++ b/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${version}"; - sha256 = "sha256-AFS4T7VqPga53/3rG8be9Q//6/2JJIe7+Ata33ewySg="; + sha256 = "sha256-2Q8hN7AbuGqm7pfNHlJlSi1Op/OpJBun/AIDhUDnGvU="; }; nativeBuildInputs = [ meson ninja pkg-config ]; diff --git a/pkgs/tools/security/scallion/default.nix b/pkgs/tools/security/scallion/default.nix deleted file mode 100644 index 6f0dcd1bb013..000000000000 --- a/pkgs/tools/security/scallion/default.nix +++ /dev/null @@ -1,36 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, makeWrapper, mono, openssl_1_0_2, ocl-icd }: - -stdenv.mkDerivation rec { - version = "2.1"; - pname = "scallion"; - - src = fetchFromGitHub { - owner = "lachesis"; - repo = "scallion"; - rev = "v${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 ]; - }; -} diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix index b1de0987755c..5c077de50d23 100644 --- a/pkgs/top-level/aliases.nix +++ b/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 diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 19340c58935f..8f9cacb5025f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/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 { };