Merge pull request #207359 from KarlJoad/octavePackages/auto-update-script

Octave packages: auto update script and fixes

maintainers/scripts/update-octave-packages

@@ -0,0 +1,468 @@
+#!/usr/bin/env nix-shell
+#!nix-shell update-octave-shell.nix -i python3
+
+"""
+Update a Octave package expression by passing in the `.nix` file, or the directory containing it.
+You can pass in multiple files or paths.
+
+You'll likely want to use
+``
+  $ ./update-octave-libraries ../../pkgs/development/octave-modules/**/default.nix
+``
+to update all non-pinned libraries in that folder.
+"""
+
+import argparse
+import os
+import pathlib
+import re
+import requests
+import yaml
+from concurrent.futures import ThreadPoolExecutor as Pool
+from packaging.version import Version as _Version
+from packaging.version import InvalidVersion
+from packaging.specifiers import SpecifierSet
+import collections
+import subprocess
+import tempfile
+
+INDEX = "https://raw.githubusercontent.com/gnu-octave/packages/main/packages"
+"""url of Octave packages' source on GitHub"""
+
+EXTENSIONS = ['tar.gz', 'tar.bz2', 'tar', 'zip']
+"""Permitted file extensions. These are evaluated from left to right and the first occurance is returned."""
+
+PRERELEASES = False
+
+GIT = "git"
+
+NIXPGKS_ROOT = subprocess.check_output(["git", "rev-parse", "--show-toplevel"]).decode('utf-8').strip()
+
+import logging
+logging.basicConfig(level=logging.INFO)
+
+
+class Version(_Version, collections.abc.Sequence):
+
+    def __init__(self, version):
+        super().__init__(version)
+        # We cannot use `str(Version(0.04.21))` because that becomes `0.4.21`
+        # https://github.com/avian2/unidecode/issues/13#issuecomment-354538882
+        self.raw_version = version
+
+    def __getitem__(self, i):
+        return self._version.release[i]
+
+    def __len__(self):
+        return len(self._version.release)
+
+    def __iter__(self):
+        yield from self._version.release
+
+
+def _get_values(attribute, text):
+    """Match attribute in text and return all matches.
+
+    :returns: List of matches.
+    """
+    regex = '{}\s+=\s+"(.*)";'.format(attribute)
+    regex = re.compile(regex)
+    values = regex.findall(text)
+    return values
+
+def _get_unique_value(attribute, text):
+    """Match attribute in text and return unique match.
+
+    :returns: Single match.
+    """
+    values = _get_values(attribute, text)
+    n = len(values)
+    if n > 1:
+        raise ValueError("found too many values for {}".format(attribute))
+    elif n == 1:
+        return values[0]
+    else:
+        raise ValueError("no value found for {}".format(attribute))
+
+def _get_line_and_value(attribute, text):
+    """Match attribute in text. Return the line and the value of the attribute."""
+    regex = '({}\s+=\s+"(.*)";)'.format(attribute)
+    regex = re.compile(regex)
+    value = regex.findall(text)
+    n = len(value)
+    if n > 1:
+        raise ValueError("found too many values for {}".format(attribute))
+    elif n == 1:
+        return value[0]
+    else:
+        raise ValueError("no value found for {}".format(attribute))
+
+
+def _replace_value(attribute, value, text):
+    """Search and replace value of attribute in text."""
+    old_line, old_value = _get_line_and_value(attribute, text)
+    new_line = old_line.replace(old_value, value)
+    new_text = text.replace(old_line, new_line)
+    return new_text
+
+
+def _fetch_page(url):
+    r = requests.get(url)
+    if r.status_code == requests.codes.ok:
+        return list(yaml.safe_load_all(r.content))[0]
+    else:
+        raise ValueError("request for {} failed".format(url))
+
+
+def _fetch_github(url):
+    headers = {}
+    token = os.environ.get('GITHUB_API_TOKEN')
+    if token:
+        headers["Authorization"] = f"token {token}"
+    r = requests.get(url, headers=headers)
+
+    if r.status_code == requests.codes.ok:
+        return r.json()
+    else:
+        raise ValueError("request for {} failed".format(url))
+
+
+SEMVER = {
+    'major' : 0,
+    'minor' : 1,
+    'patch' : 2,
+}
+
+
+def _determine_latest_version(current_version, target, versions):
+    """Determine latest version, given `target`, returning the more recent version.
+    """
+    current_version = Version(current_version)
+
+    def _parse_versions(versions):
+        for v in versions:
+            try:
+                yield Version(v)
+            except InvalidVersion:
+                pass
+
+    versions = _parse_versions(versions)
+
+    index = SEMVER[target]
+
+    ceiling = list(current_version[0:index])
+    if len(ceiling) == 0:
+        ceiling = None
+    else:
+        ceiling[-1]+=1
+        ceiling = Version(".".join(map(str, ceiling)))
+
+    # We do not want prereleases
+    versions = SpecifierSet(prereleases=PRERELEASES).filter(versions)
+
+    if ceiling is not None:
+        versions = SpecifierSet(f"<{ceiling}").filter(versions)
+
+    return (max(sorted(versions))).raw_version
+
+
+def _get_latest_version_octave_packages(package, extension, current_version, target):
+    """Get latest version and hash from Octave Packages."""
+    url = "{}/{}.yaml".format(INDEX, package)
+    yaml = _fetch_page(url)
+
+    versions = list(map(lambda pv: pv['id'], yaml['versions']))
+    version = _determine_latest_version(current_version, target, versions)
+
+    try:
+        releases = [v if v['id'] == version else None for v in yaml['versions']]
+    except KeyError as e:
+        raise KeyError('Could not find version {} for {}'.format(version, package)) from e
+    for release in releases:
+        if release['url'].endswith(extension):
+            sha256 = release['sha256']
+            break
+    else:
+        sha256 = None
+    return version, sha256, None
+
+
+def _get_latest_version_github(package, extension, current_version, target):
+    def strip_prefix(tag):
+        return re.sub("^[^0-9]*", "", tag)
+
+    def get_prefix(string):
+        matches = re.findall(r"^([^0-9]*)", string)
+        return next(iter(matches), "")
+
+    # when invoked as an updateScript, UPDATE_NIX_ATTR_PATH will be set
+    # this allows us to work with packages which live outside of octave-modules
+    attr_path = os.environ.get("UPDATE_NIX_ATTR_PATH", f"octavePackages.{package}")
+    try:
+        homepage = subprocess.check_output(
+            ["nix", "eval", "-f", f"{NIXPGKS_ROOT}/default.nix", "--raw", f"{attr_path}.src.meta.homepage"])\
+            .decode('utf-8')
+    except Exception as e:
+        raise ValueError(f"Unable to determine homepage: {e}")
+    owner_repo = homepage[len("https://github.com/"):]  # remove prefix
+    owner, repo = owner_repo.split("/")
+
+    url = f"https://api.github.com/repos/{owner}/{repo}/releases"
+    all_releases = _fetch_github(url)
+    releases = list(filter(lambda x: not x['prerelease'], all_releases))
+
+    if len(releases) == 0:
+        raise ValueError(f"{homepage} does not contain any stable releases")
+
+    versions = map(lambda x: strip_prefix(x['tag_name']), releases)
+    version = _determine_latest_version(current_version, target, versions)
+
+    release = next(filter(lambda x: strip_prefix(x['tag_name']) == version, releases))
+    prefix = get_prefix(release['tag_name'])
+    try:
+        sha256 = subprocess.check_output(["nix-prefetch-url", "--type", "sha256", "--unpack", f"{release['tarball_url']}"], stderr=subprocess.DEVNULL)\
+            .decode('utf-8').strip()
+    except:
+        # this may fail if they have both a branch and a tag of the same name, attempt tag name
+        tag_url = str(release['tarball_url']).replace("tarball","tarball/refs/tags")
+        sha256 = subprocess.check_output(["nix-prefetch-url", "--type", "sha256", "--unpack", tag_url], stderr=subprocess.DEVNULL)\
+            .decode('utf-8').strip()
+
+
+    return version, sha256, prefix
+
+def _get_latest_version_git(package, extension, current_version, target):
+    """NOTE: Unimplemented!"""
+    # attr_path = os.environ.get("UPDATE_NIX_ATTR_PATH", f"octavePackages.{package}")
+    # try:
+    #     download_url = subprocess.check_output(
+    #         ["nix", "--extra-experimental-features", "nix-command", "eval", "-f", f"{NIXPGKS_ROOT}/default.nix", "--raw", f"{attr_path}.src.url"])\
+    #         .decode('utf-8')
+    # except Exception as e:
+    #     raise ValueError(f"Unable to determine download link: {e}")
+
+    # with tempfile.TemporaryDirectory(prefix=attr_path) as new_clone_location:
+    #     subprocess.run(["git", "clone", download_url, new_clone_location])
+    #     newest_commit = subprocess.check_output(
+    #         ["git" "rev-parse" "$(git branch -r)" "|" "tail" "-n" "1"]).decode('utf-8')
+    pass
+
+
+FETCHERS = {
+    'fetchFromGitHub'   :   _get_latest_version_github,
+    'fetchurl'          :   _get_latest_version_octave_packages,
+    'fetchgit'          :   _get_latest_version_git,
+}
+
+
+DEFAULT_SETUPTOOLS_EXTENSION = 'tar.gz'
+
+
+FORMATS = {
+    'setuptools'        :   DEFAULT_SETUPTOOLS_EXTENSION,
+}
+
+def _determine_fetcher(text):
+    # Count occurrences of fetchers.
+    nfetchers = sum(text.count('src = {}'.format(fetcher)) for fetcher in FETCHERS.keys())
+    if nfetchers == 0:
+        raise ValueError("no fetcher.")
+    elif nfetchers > 1:
+        raise ValueError("multiple fetchers.")
+    else:
+        # Then we check which fetcher to use.
+        for fetcher in FETCHERS.keys():
+            if 'src = {}'.format(fetcher) in text:
+                return fetcher
+
+
+def _determine_extension(text, fetcher):
+    """Determine what extension is used in the expression.
+
+    If we use:
+    - fetchPypi, we check if format is specified.
+    - fetchurl, we determine the extension from the url.
+    - fetchFromGitHub we simply use `.tar.gz`.
+    """
+    if fetcher == 'fetchurl':
+        url = _get_unique_value('url', text)
+        extension = os.path.splitext(url)[1]
+
+    elif fetcher == 'fetchFromGitHub' or fetcher == 'fetchgit':
+        if "fetchSubmodules" in text:
+            raise ValueError("fetchFromGitHub fetcher doesn't support submodules")
+        extension = "tar.gz"
+
+    return extension
+
+
+def _update_package(path, target):
+
+    # Read the expression
+    with open(path, 'r') as f:
+        text = f.read()
+
+    # Determine pname. Many files have more than one pname
+    pnames = _get_values('pname', text)
+
+    # Determine version.
+    version = _get_unique_value('version', text)
+
+    # First we check how many fetchers are mentioned.
+    fetcher = _determine_fetcher(text)
+
+    extension = _determine_extension(text, fetcher)
+
+    # Attempt a fetch using each pname, e.g. backports-zoneinfo vs backports.zoneinfo
+    successful_fetch = False
+    for pname in pnames:
+        if fetcher == "fetchgit":
+            logging.warning(f"You must update {pname} MANUALLY!")
+            return { 'path': path, 'target': target, 'pname': pname,
+                     'old_version': version, 'new_version': version }
+        try:
+            new_version, new_sha256, prefix = FETCHERS[fetcher](pname, extension, version, target)
+            successful_fetch = True
+            break
+        except ValueError:
+            continue
+
+    if not successful_fetch:
+        raise ValueError(f"Unable to find correct package using these pnames: {pnames}")
+
+    if new_version == version:
+        logging.info("Path {}: no update available for {}.".format(path, pname))
+        return False
+    elif Version(new_version) <= Version(version):
+        raise ValueError("downgrade for {}.".format(pname))
+    if not new_sha256:
+        raise ValueError("no file available for {}.".format(pname))
+
+    text = _replace_value('version', new_version, text)
+    # hashes from pypi are 16-bit encoded sha256's, normalize it to sri to avoid merge conflicts
+    # sri hashes have been the default format since nix 2.4+
+    sri_hash = subprocess.check_output(["nix", "--extra-experimental-features", "nix-command", "hash", "to-sri", "--type", "sha256", new_sha256]).decode('utf-8').strip()
+
+
+    # fetchers can specify a sha256, or a sri hash
+    try:
+        text = _replace_value('sha256', sri_hash, text)
+    except ValueError:
+        text = _replace_value('hash', sri_hash, text)
+
+    if fetcher == 'fetchFromGitHub':
+        # in the case of fetchFromGitHub, it's common to see `rev = version;` or `rev = "v${version}";`
+        # in which no string value is meant to be substituted. However, we can just overwrite the previous value.
+        regex = '(rev\s+=\s+[^;]*;)'
+        regex = re.compile(regex)
+        matches = regex.findall(text)
+        n = len(matches)
+
+        if n == 0:
+            raise ValueError("Unable to find rev value for {}.".format(pname))
+        else:
+            # forcefully rewrite rev, incase tagging conventions changed for a release
+            match = matches[0]
+            text = text.replace(match, f'rev = "refs/tags/{prefix}${{version}}";')
+            # incase there's no prefix, just rewrite without interpolation
+            text = text.replace('"${version}";', 'version;')
+
+    with open(path, 'w') as f:
+        f.write(text)
+
+        logging.info("Path {}: updated {} from {} to {}".format(path, pname, version, new_version))
+
+    result = {
+        'path'  : path,
+        'target': target,
+        'pname': pname,
+        'old_version'   : version,
+        'new_version'   : new_version,
+        #'fetcher'       : fetcher,
+        }
+
+    return result
+
+
+def _update(path, target):
+
+    # We need to read and modify a Nix expression.
+    if os.path.isdir(path):
+        path = os.path.join(path, 'default.nix')
+
+    # If a default.nix does not exist, we quit.
+    if not os.path.isfile(path):
+        logging.info("Path {}: does not exist.".format(path))
+        return False
+
+    # If file is not a Nix expression, we quit.
+    if not path.endswith(".nix"):
+        logging.info("Path {}: does not end with `.nix`.".format(path))
+        return False
+
+    try:
+        return _update_package(path, target)
+    except ValueError as e:
+        logging.warning("Path {}: {}".format(path, e))
+        return False
+
+
+def _commit(path, pname, old_version, new_version, pkgs_prefix="octave: ", **kwargs):
+    """Commit result.
+    """
+
+    msg = f'{pkgs_prefix}{pname}: {old_version} -> {new_version}'
+
+    try:
+        subprocess.check_call([GIT, 'add', path])
+        subprocess.check_call([GIT, 'commit', '-m', msg])
+    except subprocess.CalledProcessError as e:
+        subprocess.check_call([GIT, 'checkout', path])
+        raise subprocess.CalledProcessError(f'Could not commit {path}') from e
+
+    return True
+
+
+def main():
+
+    epilog = """
+environment variables:
+  GITHUB_API_TOKEN\tGitHub API token used when updating github packages
+    """
+    parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, epilog=epilog)
+    parser.add_argument('package', type=str, nargs='+')
+    parser.add_argument('--target', type=str, choices=SEMVER.keys(), default='major')
+    parser.add_argument('--commit', action='store_true', help='Create a commit for each package update')
+    parser.add_argument('--use-pkgs-prefix', action='store_true', help='Use octavePackages.${pname}: instead of octave: ${pname}: when making commits')
+
+    args = parser.parse_args()
+    target = args.target
+
+    packages = list(map(os.path.abspath, args.package))
+
+    logging.info("Updating packages...")
+
+    # Use threads to update packages concurrently
+    with Pool() as p:
+        results = list(filter(bool, p.map(lambda pkg: _update(pkg, target), packages)))
+
+    logging.info("Finished updating packages.")
+
+    commit_options = {}
+    if args.use_pkgs_prefix:
+        logging.info("Using octavePackages. prefix for commits")
+        commit_options["pkgs_prefix"] = "octavePackages."
+
+    # Commits are created sequentially.
+    if args.commit:
+        logging.info("Committing updates...")
+        # list forces evaluation
+        list(map(lambda x: _commit(**x, **commit_options), results))
+        logging.info("Finished committing updates")
+
+    count = len(results)
+    logging.info("{} package(s) updated".format(count))
+
+
+if __name__ == '__main__':
+    main()

maintainers/scripts/update-octave-shell.nix

@@ -0,0 +1,12 @@
+{ nixpkgs ? import ../.. { }
+}:
+with nixpkgs;
+let
+  pyEnv = python3.withPackages(ps: with ps; [ packaging requests toolz pyyaml ]);
+in
+mkShell {
+  packages = [
+    pyEnv
+    nix-prefetch-scripts
+  ];
+}

pkgs/development/interpreters/octave/build-octave-package.nix

@@ -62,13 +62,21 @@ let
   ]
   ++ nativeBuildInputs;
 
+  passthru' = {
+    updateScript = [
+      ../../../../maintainers/scripts/update-octave-packages
+      (builtins.unsafeGetAttrPos "pname" octave.pkgs.${attrs.pname}).file
+    ];
+  }
+  // passthru;
+
   # This step is required because when
   # a = { test = [ "a" "b" ]; }; b = { test = [ "c" "d" ]; };
   # (a // b).test = [ "c" "d" ];
   # This used to mean that if a package defined extra nativeBuildInputs, it
   # would override the ones for building an Octave package (the hook and Octave
   # itself, causing everything to fail.
-  attrs' = builtins.removeAttrs attrs [ "nativeBuildInputs" ];
+  attrs' = builtins.removeAttrs attrs [ "nativeBuildInputs" "passthru" ];
 
 in stdenv.mkDerivation ({
   packageName = "${fullLibName}";
@@ -121,5 +129,7 @@ in stdenv.mkDerivation ({
   # together with Octave.
   dontInstall = true;
 
+  passthru = passthru';
+
   inherit meta;
 } // attrs')

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "arduino";
-  version = "0.7.0";
+  version = "0.10.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0r0bcq2zkwba6ab6yi6czbhrj4adm9m9ggxmzzcd9h40ckqg6wjv";
+    sha256 = "sha256-p9SDTXkIwnrkNXeVhzAHks7EL4NdwBokrH2j9hqAJqQ=";
   };
 
   requiredOctavePackages = [

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

@@ -9,11 +9,11 @@
 
 buildOctavePackage rec {
   pname = "audio";
-  version = "2.0.3";
+  version = "2.0.5";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1431pf7mhxsrnzrx8r3hsy537kha7jhaligmp2rghwyxhq25hs0r";
+    sha256 = "sha256-/4akeeOQnvTlk9ah+e8RJfwJG2Eq2HAGOCejhiIUjF4=";
   };
 
   nativeBuildInputs = [

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

@@ -1,17 +1,19 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromGitHub
 , fpl
 , msh
 }:
 
 buildOctavePackage rec {
   pname = "bim";
-  version = "1.1.5";
+  version = "1.1.6";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0y70w8mj80c5yns1j7nwngwwrxp1pa87kyz2n2yvmc3zdigcd6g8";
+  src = fetchFromGitHub {
+    owner = "carlodefalco";
+    repo = "bim";
+    rev = "v${version}";
+    sha256 = "sha256-hgFb1KFE1KJC8skIaeT/7h/fg1aqRpedGnEPY24zZSI=";
   };
 
   requiredOctavePackages = [

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "communications";
-  version = "1.2.3";
+  version = "1.2.4";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1r4r0cia5l5fann1n78c1qdc6q8nizgb09n2fdwb76xnwjan23g3";
+    sha256 = "sha256-SfA81UP0c7VgroxSA/RZVVKZ4arl8Uhpf324F7yGFTo=";
   };
 
   buildInputs = [

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "control";
-  version = "3.3.1";
+  version = "3.4.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0vndbzix34vfzdlsz57bgkyg31as4kv6hfg9pwrcqn75bzzjsivw";
+    sha256 = "sha256-bsagbhOtKIr62GMcxB9yR+RwlvoejQQkDU7QHvvkp3o=";
   };
 
   nativeBuildInputs = [

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "dicom";
-  version = "0.4.0";
+  version = "0.5.1";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "131wn6mrv20np10plirvqia8dlpz3g0aqi3mmn2wyl7r95p3dnza";
+    sha256 = "sha256-0qNqjpJWWBA0N5IgjV0e0SPQlCvbzIwnIgaWo+2wKw0=";
   };
 
   nativeBuildInputs = [

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "ga";
-  version = "0.10.2";
+  version = "0.10.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0s5azn4n174avlmh5gw21zfqfkyxkzn4v09q4l9swv7ldmg3mirv";
+    sha256 = "sha256-cbP7ucua7DdxLL422INxjZxz/x1pHoIq+jkjrtfaabE=";
   };
 
   meta = with lib; {

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "general";
-  version = "2.1.1";
+  version = "2.1.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0jmvczssqz1aa665v9h8k9cchb7mg3n9af6b5kh9b2qcjl4r9l7v";
+    sha256 = "sha256-owzRp5dDxiUo2uRuvUqD+EiuRqHB2sPqq8NmYtQilM8=";
   };
 
   nativeBuildInputs = [

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "generate_html";
-  version = "0.3.2";
+  version = "0.3.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1ai4h7jf9fqi7w565iprzylsh94pg4rhyf51hfj9kfdgdpb1abfs";
+    sha256 = "sha256-CHJ0+90+SNXmslLrQc+8aetSnHK0m9PqEBipFuFjwHw=";
   };
 
   meta = with lib; {

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

@@ -1,16 +1,17 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchhg
 , matgeom
 }:
 
 buildOctavePackage rec {
   pname = "geometry";
-  version = "4.0.0";
+  version = "unstable-2021-07-07";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1zmd97xir62fr5v57xifh2cvna5fg67h9yb7bp2vm3ll04y41lhs";
+  src = fetchhg {
+    url = "http://hg.code.sf.net/p/octave/${pname}";
+    rev = "04965cda30b5f9e51774194c67879e7336df1710";
+    sha256 = "sha256-ECysYOJMF4gPiCFung9hFSlyyO60X3MGirQ9FlYDix8=";
   };
 
   requiredOctavePackages = [

pkgs/development/octave-modules/instrument-control/default.nix

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "instrument-control";
-  version = "0.7.0";
+  version = "0.8.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0cdnnbxihz7chdkhkcgy46pvkij43z9alwr88627z7jaiaah6xby";
+    sha256 = "sha256-g3Pyz2b8hvg0MkFGA7cduYozcAd2UnqorBHzNs+Uuro=";
   };
 
   meta = with lib; {

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "interval";
-  version = "3.2.0";
+  version = "3.2.1";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0a0sz7b4y53qgk1xr4pannn4w7xiin2pf74x7r54hrr1wf4abp20";
+    sha256 = "sha256-OOUmQnN1cTIpqz2Gpf4/WghVB0fYQgVBcG/eqQk/3Og=";
   };
 
   propagatedBuildInputs = [

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

@@ -8,11 +8,11 @@
 
 buildOctavePackage rec {
   pname = "io";
-  version = "2.6.3";
+  version = "2.6.4";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "044y8lfp93fx0592mv6x2ss0nvjkjgvlci3c3ahav76pk1j3rikb";
+    sha256 = "sha256-p0pAC70ZIn9sB8WFiS3oec165S2CDaH2nxo+PolFL1o=";
   };
 
   buildInputs = [

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

@@ -3,17 +3,22 @@
 , fetchurl
 , io # >= 2.2.7
 , geometry # >= 4.0.0
+, gdal
 }:
 
 buildOctavePackage rec {
   pname = "mapping";
-  version = "1.4.1";
+  version = "1.4.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0wj0q1rkrqs4qgpjh4vn9kcpdh94pzr6v4jc1vcrjwkp87yjv8c0";
+    sha256 = "sha256-mrUQWqC15Ul5AHDvhMlNStqIMG2Zxa+hB2vDyeizLaI=";
   };
 
+  buildInputs = [
+    gdal
+  ];
+
   requiredOctavePackages = [
     io
     geometry

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

@@ -1,6 +1,6 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromGitHub
 # Octave Dependencies
 , splines
 # Other Dependencies
@@ -13,11 +13,13 @@
 
 buildOctavePackage rec {
   pname = "msh";
-  version = "1.0.10";
+  version = "1.0.12";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1mb5qrp9y1w1cbzrd9v84430ldy57ca843yspnrgbcqpxyyxbgfz";
+  src = fetchFromGitHub {
+    owner = "carlodefalco";
+    repo = "msh";
+    rev = "v${version}";
+    sha256 = "sha256-UnMrIruzm3ARoTgUlMMxfjTOMZw/znZUQJmj3VEOw8I=";
   };
 
   nativeBuildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "nan";
-  version = "3.6.0";
+  version = "3.7.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1zxdg0yg5jnwq6ppnikd13zprazia6w6zpgw99f62mc03iqk5c4q";
+    sha256 = "sha256-d9J6BfNFeM5LtMqth0boSPd9giYU42KBnxrsUCmKK1s=";
   };
 
   buildInputs = [

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

@@ -7,11 +7,11 @@
 
 buildOctavePackage rec {
   pname = "ncarray";
-  version = "1.0.4";
+  version = "1.0.5";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0v96iziikvq2v7hczhbfs9zmk49v99kn6z3lgibqqpwam175yqgd";
+    sha256 = "sha256-HhQWLUA/6wqYi6TP3PC+N2zgi4UojDxbG9pgQzFaQ8c=";
   };
 
   buildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "netcdf";
-  version = "1.0.14";
+  version = "1.0.16";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1wdwl76zgcg7kkdxjfjgf23ylzb0x4dyfliffylyl40g6cjym9lf";
+    sha256 = "sha256-1Lr+6xLRXxSeUhM9+WdCUPFRZSWdxtAQlxpiv4CHJrs=";
   };
 
   buildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "ocl";
-  version = "1.1.1";
+  version = "1.2.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0ayi5x9zk9p4zm0qsr3i94lyp5468c9d1a7mqrqjqpdvkhrw0xnm";
+    sha256 = "sha256-jQdwZwQNU3PZZFa3lp0hIr0GDt/XFHLJoq4waLI4gS8=";
   };
 
   meta = with lib; {

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

@@ -1,15 +1,17 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromBitbucket
 }:
 
 buildOctavePackage rec {
   pname = "octclip";
-  version = "2.0.1";
+  version = "2.0.3";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "05ijh3izgfaan84n6zp690nap9vnz0zicjd0cgvd1c6askm7vxql";
+  src = fetchFromBitbucket {
+    owner = "jgpallero";
+    repo = pname;
+    rev = "OctCLIP-${version}";
+    sha256 = "sha256-gG2b8Ix6bzO6O7GRACE81JCVxfXW/+ZdfoniigAEq3g=";
   };
 
   # The only compilation problem is that no formatting specifier was provided

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

@@ -1,16 +1,18 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromBitbucket
 , proj # >= 6.3.0
 }:
 
 buildOctavePackage rec {
   pname = "octproj";
-  version = "2.0.1";
+  version = "3.0.2";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1mb8gb0r8kky47ap85h9qqdvs40mjp3ya0nkh45gqhy67ml06paq";
+  src = fetchFromBitbucket {
+    owner = "jgpallero";
+    repo = pname;
+    rev = "OctPROJ-${version}";
+    sha256 = "sha256-d/Zf172Etj+GA0cnGsQaKMjOmirE7Hwyj4UECpg7QFM=";
   };
 
   # The sed changes below allow for the package to be compiled.
@@ -28,6 +30,5 @@ buildOctavePackage rec {
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ KarlJoad ];
     description = "GNU Octave bindings to PROJ library for cartographic projections and CRS transformations";
-    broken = true; # error: unlink: operation failed: No such file or directory
   };
 }

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

@@ -9,11 +9,11 @@
 
 buildOctavePackage rec {
   pname = "optim";
-  version = "1.6.1";
+  version = "1.6.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1175bckiryz0i6zm8zvq7y5rq3lwkmhyiky1gbn33np9qzxcsl3i";
+    sha256 = "sha256-VUqOGLtxla6GH1BZwU8aVXhEJlwa3bW/vzq5iFUkeH4=";
   };
 
   buildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "optiminterp";
-  version = "0.3.6";
+  version = "0.3.7";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "05nzj2jmrczbnsr64w2a7kww19s6yialdqnsbg797v11ii7aiylc";
+    sha256 = "sha256-ubh/iOZlWTOYsTA6hJfPOituNBKTn2LbBnx+tmmSEug=";
   };
 
   nativeBuildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildOctavePackage rec {
   pname = "signal";
-  version = "1.4.2";
+  version = "1.4.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "YqTgYRfcxDw2FpkF+CVdAVSBypgq6ukBOw2d8+SOcGI=";
+    sha256 = "sha256-VFuXVA6+ujtCDwiQb905d/wpOzvI/Db2uosJTOqI8zk=";
   };
 
   requiredOctavePackages = [

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "sockets";
-  version = "1.2.1";
+  version = "1.4.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "18f1zpqcf6h9b4fb0x2c5nvc3mvgj1141f1s8d9gnlhlrjlq8vqg";
+    sha256 = "sha256-GNwFLNV1u3UKJp9lhLtCclD2VSKC9Mko1hBoSn5dTpI=";
   };
 
   meta = with lib; {

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

@@ -1,16 +1,18 @@
 { buildOctavePackage
 , lib
-, fetchurl
+, fetchFromGitHub
 , io
 }:
 
 buildOctavePackage rec {
   pname = "statistics";
-  version = "1.4.2";
+  version = "1.5.4";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0iv2hw3zp7h69n8ncfjfgm29xaihdl5gp2slcw1yf23mhd7q2xkr";
+  src = fetchFromGitHub {
+    owner = "gnu-octave";
+    repo = "statistics";
+    rev = "refs/tags/release-${version}";
+    sha256 = "sha256-gFauFIaXKzcPeNvpWHv5FAxYQvZNh7ELrSUIvn43IfQ=";
   };
 
   requiredOctavePackages = [

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "stk";
-  version = "2.6.1";
+  version = "2.7.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1rqndfankwlwm4igw3xqpnrrl749zz1d5pjzh1qbfns7ixwrm19a";
+    sha256 = "sha256-vIf+XDLvLNOMwptFCgiqfl+o3PIQ+KLpsJhOArd7gMM=";
   };
 
   meta = with lib; {

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

@@ -2,20 +2,25 @@
 , stdenv
 , lib
 , fetchurl
-, pcre
+, pkg-config
+, pcre2
 }:
 
 buildOctavePackage rec {
   pname = "strings";
-  version = "1.2.0";
+  version = "1.3.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1b0ravfvq3bxd0w3axjfsx13mmmkifmqz6pfdgyf2s8vkqnp1qng";
+    sha256 = "sha256-agpTD9FN1qdp+BYdW5f+GZV0zqZMNzeOdymdo27mTOI=";
   };
 
+  nativeBuildInputs = [
+    pkg-config
+  ];
+
   buildInputs = [
-    pcre
+    pcre2
   ];
 
   # The gripes library no longer exists.

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "struct";
-  version = "1.0.17";
+  version = "1.0.18";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0cw4cspkm553v019zsj2bsmal0i378pm0hv29w82j3v5vysvndq1";
+    sha256 = "sha256-/M6n3YTBEE7TurtHoo8F4AEqicKE85qwlAkEUJFSlM4=";
   };
 
   meta = with lib; {

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

@@ -8,11 +8,11 @@
 
 buildOctavePackage rec {
   pname = "video";
-  version = "2.0.0";
+  version = "2.0.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "0s6j3c4dh5nsbh84s7vnd2ajcayy1gn07b4fcyrcynch3wl28mrv";
+    sha256 = "sha256-bZNaRnmJl5UF0bQMNoEWvoIXJaB0E6/V9eChE725OHY=";
   };
 
   nativeBuildInputs = [

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

@@ -5,11 +5,11 @@
 
 buildOctavePackage rec {
   pname = "windows";
-  version = "1.6.1";
+  version = "1.6.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "110dh6jz088c4fxp9gw79kfib0dl7r3rkcavxx4xpk7bjl2l3xb6";
+    sha256 = "sha256-U5Fe5mTn/ms8w9j6NdEtiRFZkKeyV0I3aR+zYQw4yIs=";
   };
 
   meta = with lib; {

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

@@ -8,11 +8,11 @@
 
 buildOctavePackage rec {
   pname = "zeromq";
-  version = "1.5.3";
+  version = "1.5.5";
 
   src = fetchurl {
     url = "mirror://sourceforge/octave/${pname}-${version}.tar.gz";
-    sha256 = "1h0pb2pqbnyiavf7r05j8bqxqd8syz16ab48hc74nlnx727anfwl";
+    sha256 = "sha256-MAZEpbVuragVuXrMJ8q5/jU5cTchosAtrAR6ElLwfss=";
   };
 
   preAutoreconf = ''