Merge branch 'master' into staging

6 files changed, 435 insertions, 87 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c3cdbb9e66..3a7dc1a1b7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -847,7 +847,7 @@ intended to behave exactly the same as the original BWK awk.")
 (define-public python-cellbender
   (package
     (name "python-cellbender")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method git-fetch)
@@ -857,8 +857,8 @@ intended to behave exactly the same as the original BWK awk.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3"))))
-    (build-system python-build-system)
+         "12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa"))))
+    (build-system pyproject-build-system)
     (arguments
      (list #:tests? #false)) ;there are none
     (propagated-inputs
@@ -885,14 +885,14 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
 (define-public python-htsget
   (package
    (name "python-htsget")
-   (version "0.2.5")
+   (version "0.2.6")
    (source (origin
             (method url-fetch)
             (uri (pypi-uri "htsget" version))
             (sha256
              (base32
-              "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
-   (build-system python-build-system)
+              "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4"))))
+   (build-system pyproject-build-system)
    (native-inputs
     (list python-setuptools-scm))
    (propagated-inputs
@@ -914,11 +914,12 @@ servers supporting the protocol.")
               (sha256
                (base32
                 "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:modules ((srfi srfi-26)
                   (guix build utils)
-                  (guix build python-build-system))
+                  (guix build python-build-system)
+                  (guix build pyproject-build-system))
        ;; See https://github.com/daler/pybedtools/issues/192
        #:phases
        (modify-phases %standard-phases
@@ -978,7 +979,7 @@ which are widely used for genomic interval manipulation or \"genome algebra\".
 pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
-    ;; version 0.9.0 and the LICENSE.txt is consistant with the source code.
+    ;; version 0.9.0 and the LICENSE.txt is consistent with the source code.
     ;;
     ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
     ;; licensed lgpl2.1+
@@ -1032,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
 (define-public python-biom-format
   (package
     (name "python-biom-format")
-    (version "2.1.10")
+    (version "2.1.12")
     (source
      (origin
        (method git-fetch)
@@ -1044,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
+         "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
        (modules '((guix build utils)))
        ;; Delete generated C files.
        (snippet
         '(for-each delete-file (find-files "." "\\.c")))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:phases
+      '(modify-phases %standard-phases
          (add-after 'unpack 'use-cython
            (lambda _ (setenv "USE_CYTHON" "1")))
-         (add-after 'unpack 'relax
-           (lambda _
-             (substitute* "setup.py"
-               (("pytest < 5.3.4") "pytest"))))
          (add-after 'unpack 'disable-broken-tests
            (lambda _
-             (substitute* "biom/tests/test_cli/test_validate_table.py"
-               (("^(.+)def test_invalid_hdf5" m indent)
+             (substitute* "biom/tests/test_util.py"
+               (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
                 (string-append indent
                                "@npt.dec.skipif(True, msg='Guix')\n"
                                m)))
@@ -1073,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.")
                                m))))))))
     (propagated-inputs
      (list python-anndata
-           python-numpy
-           python-scipy
+           python-click
            python-flake8
            python-future
-           python-click
            python-h5py
-           python-pandas))
+           python-numpy
+           python-pandas
+           python-scikit-bio
+           python-scipy))
     (native-inputs
      (list python-cython python-pytest python-pytest-cov python-nose))
     (home-page "http://www.biom-format.org")
@@ -1094,42 +1093,45 @@ e.g. microbiome samples, genomes, metagenomes.")
 (define-public python-pairtools
   (package
     (name "python-pairtools")
-    (version "0.3.0")
+    (version "1.0.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/mirnylab/pairtools")
+                    (url "https://github.com/open2c/pairtools")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc"))))
+                "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-references
            (lambda _
-             (substitute* '("pairtools/pairtools_merge.py"
-                            "pairtools/pairtools_sort.py")
-               (("/bin/bash") (which "bash")))
-             #t))
+             (substitute* '("pairtools/cli/header.py"
+                            "pairtools/cli/merge.py"
+                            "pairtools/cli/sort.py")
+               (("/bin/bash") (which "bash")))))
          (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (with-directory-excursion "/tmp"
-               (invoke "pytest" "-v")))))))
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (with-directory-excursion "/tmp"
+                 (invoke "pytest" "-v"))))))))
     (native-inputs
-     (list python-cython python-nose python-pytest))
-    (inputs
-     `(("python" ,python-wrapper)))
+     (list python-cython python-pytest))
     (propagated-inputs
      (list htslib ; for bgzip, looked up in PATH
            samtools ; looked up in PATH
            lz4 ; for lz4c
+           python-bioframe
            python-click
-           python-numpy))
-    (home-page "https://github.com/mirnylab/pairtools")
+           python-numpy
+           python-pandas
+           python-pysam
+           python-pyyaml
+           python-scipy))
+    (home-page "https://github.com/open2c/pairtools")
     (synopsis "Process mapped Hi-C data")
     (description "Pairtools is a simple and fast command-line framework to
 process sequencing data from a Hi-C experiment.  Process pair-end sequence
@@ -2974,6 +2976,71 @@ generation, and transformation to RDF.  Salad provides a bridge between document
 and record oriented data modeling and the Semantic Web.")
     (license license:asl2.0)))
 
+(define-public python-scikit-bio
+  (package
+    (name "python-scikit-bio")
+    (version "0.5.7")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "scikit-bio" version))
+              (sha256
+               (base32
+                "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; See https://github.com/biocore/scikit-bio/pull/1826
+         (add-after 'unpack 'compatibility
+           (lambda _
+             (substitute* "skbio/sequence/tests/test_sequence.py"
+               (("def test_concat_strict_many")
+                "def _do_not_test_concat_strict_many"))
+             (substitute* "skbio/stats/distance/_mantel.py"
+               (("from scipy.stats import PearsonRConstantInputWarning")
+                "from scipy.stats import ConstantInputWarning")
+               (("from scipy.stats import PearsonRNearConstantInputWarning")
+                "from scipy.stats import NearConstantInputWarning")
+               (("from scipy.stats import SpearmanRConstantInputWarning") "")
+               (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)")
+                "warnings.warn(ConstantInputWarning())")
+               (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)")
+                "warnings.warn(NearConstantInputWarning())")
+               (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)")
+                "warnings.warn(ConstantInputWarning())"))
+             (substitute* "skbio/diversity/alpha/tests/test_base.py"
+               (("self.assertEqual\\(pielou_e")
+                "self.assertAlmostEqual(pielou_e"))))
+         (add-before 'check 'build-extensions
+           (lambda _
+             ;; Cython extensions have to be built before running the tests.
+             (invoke "python3" "setup.py" "build_ext" "--inplace")))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests? (invoke "python3" "-m" "skbio.test")))))))
+    (propagated-inputs
+     (list python-cachecontrol
+           python-decorator
+           python-h5py
+           python-hdmedians
+           python-ipython
+           python-lockfile
+           python-matplotlib
+           python-natsort
+           python-numpy
+           python-pandas
+           python-scikit-learn
+           python-scipy))
+    (native-inputs
+     (list python-coverage python-pytest))
+    (home-page "https://scikit-bio.org")
+    (synopsis "Data structures, algorithms and educational resources for bioinformatics")
+    (description
+     "This package provides data structures, algorithms and educational
+resources for bioinformatics.")
+    (license license:bsd-3)))
+
 (define-public cwltool
   (package
     (name "cwltool")
diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm
index 4ea7033790..074fc59cfb 100644
--- a/gnu/packages/crates-graphics.scm
+++ b/gnu/packages/crates-graphics.scm
@@ -795,8 +795,31 @@ EUI-64, also known as MAC-48 media access control addresses.")
        #:cargo-development-inputs
        (("rust-glob" ,rust-glob-0.3))))))
 
+(define-public rust-gl-0.14
+  (package
+    (name "rust-gl")
+    (version "0.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "gl" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "015lgy3qpzdw7mnh59a4y4hdjq1fhv7nkqlmh1h6fzc212qxlkm9"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-development-inputs
+       (("rust-glutin" ,rust-glutin-0.21))
+       #:cargo-inputs
+       (("rust-gl-generator" ,rust-gl-generator-0.14))))
+    (home-page "https://github.com/brendanzab/gl-rs/")
+    (synopsis "OpenGL bindings for rust")
+    (description "This package provides OpenGL bindings for rust.")
+    (license license:asl2.0)))
+
 (define-public rust-gl-0.11
   (package
+    (inherit rust-gl-0.14)
     (name "rust-gl")
     (version "0.11.0")
     (source
@@ -808,15 +831,10 @@ EUI-64, also known as MAC-48 media access control addresses.")
         (sha256
          (base32
           "1wcqpyhck0xriffkmgmldy33lwk2044hb4l02d44vm4fbvicin6p"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
-       (("rust-gl-generator" ,rust-gl-generator-0.10))))
-    (home-page "https://github.com/brendanzab/gl-rs/")
-    (synopsis "OpenGL bindings for rust")
-    (description "This package provides OpenGL bindings for rust.")
-    (license license:asl2.0)))
+       (("rust-gl-generator" ,rust-gl-generator-0.10))))))
 
 (define-public rust-gl-generator-0.14
   (package
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 431a37527c..e240520fff 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -4950,6 +4950,29 @@ methods.")
     (description "This package provides a safe abstraction around AtomicPtr.")
     (license license:asl2.0)))
 
+(define-public rust-atomic-0.5
+  (package
+    (name "rust-atomic")
+    (version "0.5.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "atomic" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0k135q1qfmxxyzrlhr47r0j38r5fnd4163rgl552qxyagrk853dq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-autocfg" ,rust-autocfg-1))))
+    (home-page "https://github.com/Amanieu/atomic-rs")
+    (synopsis "Generic @code{Atomic<T>} wrapper type")
+    (description
+     "This package provides a generic @code{Atomic<T>} type for all
+@code{T: Copy} types, unlike the standard library which only provides a few
+fixed atomic types.")
+    ;; The user can choose either license.
+    (license (list license:asl2.0 license:expat))))
+
 (define-public rust-atomic-polyfill-1
   (package
     (name "rust-atomic-polyfill")
@@ -17146,7 +17169,7 @@ diff.")
 (define-public rust-digest-0.10
   (package
     (name "rust-digest")
-    (version "0.10.1")
+    (version "0.10.6")
     (source
      (origin
        (method url-fetch)
@@ -17155,7 +17178,7 @@ diff.")
         (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "16wpqnwlzx0lbnwccwikns7dq8fblcc6kma2l7xz8anlh5hdd5xn"))))
+         "0vz74785s96g727vg37iwkjvbkcfzp093j49ihhyf8sh9s7kfs41"))))
     (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
@@ -29311,6 +29334,35 @@ kernel32.")
      "This package provides a Log macro for log's kv-unstable backend.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-k9-0.11
+  (package
+    (name "rust-k9")
+    (version "0.11.6")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "k9" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1a8pxz6fygqzknxdlb4l835kqxgjk7snm4bjhhhn783r025vbp9j"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs (("rust-anyhow" ,rust-anyhow-1)
+                       ("rust-colored" ,rust-colored-1)
+                       ("rust-diff" ,rust-diff-0.1)
+                       ("rust-lazy-static" ,rust-lazy-static-1)
+                       ("rust-libc" ,rust-libc-0.2)
+                       ("rust-proc-macro2" ,rust-proc-macro2-1)
+                       ("rust-regex" ,rust-regex-1)
+                       ("rust-syn" ,rust-syn-1)
+                       ("rust-term-size" ,rust-term-size-0.3))))
+    (home-page "https://github.com/aaronabramov/k9")
+    (synopsis "Testing library")
+    (description
+     "This package contains helper macros for writing unit tests.")
+    (license license:expat)))
+
 (define-public rust-language-tags-0.3
   (package
     (name "rust-language-tags")
@@ -32372,8 +32424,33 @@ parallelize and optimize.")
      "This package provides MaybeUninit for friends of backwards compatibility.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-md-5-0.10
+  (package
+    (name "rust-md-5")
+    (version "0.10.5")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "md-5" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1jmrykh705dfclkgxwjysj5y8l1nyrn1gddw5xpgyjyla1l50rb3"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-digest" ,rust-digest-0.10)
+        ("rust-md5-asm" ,rust-md5-asm-0.5))))
+    (home-page "https://github.com/RustCrypto/hashes")
+    (synopsis "MD5 hash function")
+    (description
+     "This library provides a MD5 hash function for Rust.")
+    ;; The user can choose either license.
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-md-5-0.9
   (package
+    (inherit rust-md-5-0.10)
     (name "rust-md-5")
     (version "0.9.1")
     (source
@@ -32385,7 +32462,6 @@ parallelize and optimize.")
         (sha256
          (base32
           "059ajjacz1q3cms7vl6cvhdqs4qdw2nnwj9dq99ryzv0p6djfnkv"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-block-buffer" ,rust-block-buffer-0.9)
@@ -32394,11 +32470,7 @@ parallelize and optimize.")
         ("rust-opaque-debug" ,rust-opaque-debug-0.3))
        #:cargo-development-inputs
        (("rust-digest" ,rust-digest-0.9)
-        ("rust-hex-literal" ,rust-hex-literal-0.2))))
-    (home-page "https://github.com/RustCrypto/hashes")
-    (synopsis "MD5 hash function")
-    (description "MD5 hash function.")
-    (license (list license:expat license:asl2.0))))
+        ("rust-hex-literal" ,rust-hex-literal-0.2))))))
 
 (define-public rust-md-5-0.8
   (package
@@ -32472,8 +32544,31 @@ parallelize and optimize.")
         (base32
          "0j2s8aqdkhwhy7awga2bmv5n8qq8bgy8672iha9f3y871dm6vibr"))))))
 
+(define-public rust-md5-asm-0.5
+  (package
+    (name "rust-md5-asm")
+    (version "0.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "md5-asm" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1ixmkg8j7sqy9zln6pz9xi2dl2d9zpm8pz6p49za47n1bvradfbk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-cc" ,rust-cc-1))))
+    (home-page "https://github.com/RustCrypto/asm-hashes")
+    (synopsis "Assembly implementation of MD5 compression function")
+    (description
+     "This package contains an assembly implementation of the MD5
+compression function.")
+    (supported-systems '("x86_64-linux" "i686-linux"))
+    (license license:expat)))
+
 (define-public rust-md5-asm-0.4
   (package
+    (inherit rust-md5-asm-0.5)
     (name "rust-md5-asm")
     (version "0.4.3")
     (source
@@ -32485,16 +32580,9 @@ parallelize and optimize.")
         (sha256
          (base32
           "0gpk5647js1k084jc7pg2gji0cvl6hjkkbfia6lnpk8y4shyairv"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
-       (("rust-cc" ,rust-cc-1))))
-    (home-page "https://github.com/RustCrypto/asm-hashes")
-    (synopsis "Assembly implementation of MD5 compression function")
-    (description "This package contains an assembly implementation of MD5
-compression function.")
-    (supported-systems '("x86_64-linux" "i686-linux"))
-    (license license:expat)))
+       (("rust-cc" ,rust-cc-1))))))
 
 (define-public rust-measureme-0.7
   (package
@@ -32718,25 +32806,23 @@ file IO.")
        (sha256
         (base32 "0nmymqy9q62x577ydja0ysfyir7h5qa0n5fwcnvchfhhlsi0rdyr"))))))
 
-(define-public rust-memoffset-0.6
+(define-public rust-memoffset-0.7
   (package
     (name "rust-memoffset")
-    (version "0.6.5")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (crate-uri "memoffset" version))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32
-         "1kkrzll58a3ayn5zdyy9i1f1v3mx0xgl29x0chq614zazba638ss"))))
+        (base32 "1x2zv8hv9c9bvgmhsjvr9bymqwyxvgbca12cm8xkhpyy5k1r7s2x"))))
     (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs
        (("rust-autocfg" ,rust-autocfg-1))
        #:cargo-development-inputs
        (("rust-doc-comment" ,rust-doc-comment-0.3))))
-    (inputs (list rust-autocfg-1))
     (home-page "https://github.com/Gilnaa/memoffset")
     (synopsis "C-like offset_of functionality for Rust structs")
     (description
@@ -32744,6 +32830,27 @@ file IO.")
 for Rust structs.")
     (license license:expat)))
 
+(define-public rust-memoffset-0.6
+  (package
+    (inherit rust-memoffset-0.7)
+    (name "rust-memoffset")
+    (version "0.6.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "memoffset" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1kkrzll58a3ayn5zdyy9i1f1v3mx0xgl29x0chq614zazba638ss"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-autocfg" ,rust-autocfg-1))
+       #:cargo-development-inputs
+       (("rust-doc-comment" ,rust-doc-comment-0.3))))
+    (inputs (list rust-autocfg-1))))
+
 (define-public rust-memoffset-0.5
   (package
     (inherit rust-memoffset-0.6)
@@ -52346,6 +52453,28 @@ functionality and without weak references.")
         (base32
          "1i1i8viy6y30mv9v5hwhg9w6b722qkyh9c6n8bn4d27jpv14pg0s"))))))
 
+(define-public rust-sha1-smol-1
+  (package
+    (name "rust-sha1-smol")
+    (version "1.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "sha1_smol" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "04nhbhvsk5ms1zbshs80iq5r1vjszp2xnm9f0ivj38q3dhc4f6mf"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs (("rust-serde" ,rust-serde-1))))
+    (home-page "https://github.com/mitsuhiko/sha1-smol")
+    (synopsis "Dependency free SHA1 implementation")
+    (description
+     "This package provides a minimal dependency free implementation of
+SHA1 for Rust.")
+    (license license:bsd-3)))
+
 (define-public rust-sha1collisiondetection-0.2
   (package
     (name "rust-sha1collisiondetection")
@@ -68008,8 +68137,31 @@ for locating fonts.")
     (description "This package provides an implementation of zbase32.")
     (license license:lgpl3+)))
 
+(define-public rust-zerocopy-0.6
+  (package
+    (name "rust-zerocopy")
+    (version "0.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "zerocopy" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0dpj4nd9v56wy93ahjkp95znjzj91waqvidqch8gxwdwq661hbrk"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-byteorder" ,rust-byteorder-1)
+        ("rust-zerocopy-derive" ,rust-zerocopy-derive-0.3))))
+    (home-page "https://github.com/google/zerocopy")
+    (synopsis "Utilities for zero-copy parsing and serialization")
+    (description "Utilities for zero-copy parsing and serialization")
+    (license license:bsd-2)))
+
 (define-public rust-zerocopy-0.3
   (package
+    (inherit rust-zerocopy-0.6)
     (name "rust-zerocopy")
     (version "0.3.1")
     (source
@@ -68019,21 +68171,41 @@ for locating fonts.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32 "00nbb6yal8f74bkpn7msjcnhisimw8s5777a63206rfnn3br45zh"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-byteorder" ,rust-byteorder-1)
         ("rust-zerocopy-derive" ,rust-zerocopy-derive-0.2))))
-    (home-page "https://fuchsia.googlesource.com/fuchsia/+/HEAD/src/lib/zerocopy")
-    (synopsis "Utilities for zero-copy parsing and serialization")
-    (description
-     "This package provides utilities for zero-copy parsing and
-serialization.")
     (license license:bsd-3)))
 
+(define-public rust-zerocopy-derive-0.3
+  (package
+    (name "rust-zerocopy-derive")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (crate-uri "zerocopy-derive" version))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "18qr7dqlj89v1xl1g58l2xd6jidv0sbccscgl131gpppba0yc1b5"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:skip-build? #t
+       #:cargo-inputs
+       (("rust-proc-macro2" ,rust-proc-macro2-1)
+        ("rust-syn" ,rust-syn-1)
+        ("rust-synstructure" ,rust-synstructure-0.12))))
+    (home-page "https://github.com/google/zerocopy")
+    (synopsis "Custom derive for traits from the zerocopy Rust crate")
+    (description
+     "This package provides custom derive for traits from the zerocopy Rust
+crate.")
+    (license license:bsd-2)))
+
 (define-public rust-zerocopy-derive-0.2
   (package
+    (inherit rust-zerocopy-derive-0.3)
     (name "rust-zerocopy-derive")
     (version "0.2.1")
     (source
@@ -68043,18 +68215,12 @@ serialization.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32 "1594sf9wwgpbavl1hb1avyz6n7km9apm8afc03x9y8h3spk3k76w"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:skip-build? #t
        #:cargo-inputs
        (("rust-proc-macro2" ,rust-proc-macro2-1)
         ("rust-syn" ,rust-syn-1)
         ("rust-synstructure" ,rust-synstructure-0.12))))
-    (home-page "https://fuchsia.googlesource.com/fuchsia/+/HEAD/src/lib/zerocopy/zerocopy-derive")
-    (synopsis "Custom derive for traits from the zerocopy Rust crate")
-    (description
-     "This package provides custom derive for traits from the zerocopy Rust
-crate.")
     (license license:bsd-3)))
 
 (define-public rust-zeroize-1
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index f5276e330e..751eb2b867 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -2998,6 +2998,40 @@ updates to the zebra daemon.")
     (home-page "https://www.nongnu.org/quagga/")
     (license license:gpl2+)))
 
+(define-public bgpq3
+  (package
+    (name "bgpq3")
+    (version "0.1.36.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snar/bgpq3")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0768hihx7idmn2dk8ii21m0dm052amlnfpqq53vsfaapb60n1smc"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f))                    ; no test suite
+    (native-inputs (list python-markdown))
+    (home-page "http://snar.spb.ru/prog/bgpq3/")
+    (synopsis
+     "Generate BGP filters from the @acronym{IRR, Internet Routing Registry}")
+    (description
+     "This program helps automate the creation and maintenance of @acronym{BGP,
+Border Gateway Protocol} routing filters used for peering trough Internet
+exchanges.
+
+It generates prefix lists, (extended) access lists, policy-statement terms, and
+AS paths from data in the @acronym{IRR, Internet Routing Registry}, including
+the @acronym{RADB, Routing Assets Database} operated by the Merit Network at the
+University of Michigan.
+
+The filters can be aggregated and exported in the most common formats.")
+    (license (list license:bsd-3        ; strlcpy.c, sys_queue.h
+                   license:bsd-2))))    ; everything else, but missing headers
+
 (define-public thc-ipv6
   (let ((revision "0")
         (commit "4bb72573e0950ce6f8ca2800a10748477020029e"))
diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm
index 0f5e1c3530..519a7d1548 100644
--- a/gnu/packages/qt.scm
+++ b/gnu/packages/qt.scm
@@ -2745,14 +2745,22 @@ and binaries removed, and adds modular support for using system libraries.")
                     "third_party/devtools-frontend/src/third_party/typescript"
                     "third_party/emoji-segmenter"
                     "third_party/fdlibm"
-                    "third_party/ffmpeg"
+                    "third_party/ffmpeg/libavcodec/avcodec.h"
+                    "third_party/ffmpeg/libavcodec/packet.h"
+                    "third_party/ffmpeg/libavformat/avformat.h"
+                    "third_party/ffmpeg/libavformat/avio.h"
+                    "third_party/ffmpeg/libavutil/avutil.h"
+                    "third_party/ffmpeg/libavutil/imgutils.h"
+                    "third_party/ffmpeg/libavutil/log.h"
+                    "third_party/ffmpeg/libavutil/mathematics.h"
+                    "third_party/ffmpeg/libavutil/opt.h"
                     "third_party/freetype"
                     "third_party/googletest"
                     "third_party/harfbuzz-ng"
                     "third_party/highway"
                     "third_party/hunspell"
                     "third_party/iccjpeg"
-                    "third_party/icu"
+                    "third_party/icu" ;TODO: make pdfium use system version
                     "third_party/inspector_protocol"
                     "third_party/jinja2"
                     "third_party/jsoncpp"
@@ -2770,18 +2778,23 @@ and binaries removed, and adds modular support for using system libraries.")
                     "third_party/libjingle_xmpp"
                     "third_party/libjpeg_turbo"
                     "third_party/libjxl"
-                    "third_party/libpng"
+                    "third_party/libpng" ;TODO: make pdfium use system version
                     "third_party/libsrtp"
                     "third_party/libsync"
                     "third_party/libudev"
                     "third_party/liburlpattern"
                     "third_party/libvpx"
                     "third_party/libwebm"
-                    "third_party/libwebp"
+                    "third_party/libwebp/src/webp/decode.h"
+                    "third_party/libwebp/src/webp/demux.h"
+                    "third_party/libwebp/src/webp/encode.h"
+                    "third_party/libwebp/src/webp/format_constants.h"
+                    "third_party/libwebp/src/webp/mux.h"
+                    "third_party/libwebp/src/webp/mux_types.h"
+                    "third_party/libwebp/src/webp/types.h"
                     "third_party/libx11"
                     "third_party/libxcb-keysyms"
-                    "third_party/libxml"
-                    "third_party/libxslt"
+                    "third_party/libxml/chromium"
                     "third_party/libyuv"
                     "third_party/lottie"
                     "third_party/lss"
@@ -2794,7 +2807,11 @@ and binaries removed, and adds modular support for using system libraries.")
                     "third_party/node"
                     "third_party/one_euro_filter"
                     "third_party/openh264"
-                    "third_party/opus"
+                    "third_party/opus/src/include/opus.h"
+                    "third_party/opus/src/include/opus_custom.h"
+                    "third_party/opus/src/include/opus_defines.h"
+                    "third_party/opus/src/include/opus_multistream.h"
+                    "third_party/opus/src/include/opus_types.h"
                     "third_party/ots"
                     "third_party/pdfium"
                     "third_party/pdfium/third_party/agg23"
@@ -2850,7 +2867,7 @@ and binaries removed, and adds modular support for using system libraries.")
                     "third_party/woff2"
                     "third_party/wuffs"
                     "third_party/x11proto"
-                    "third_party/zlib"
+                    "third_party/zlib" ;TODO: make pdfium use system version
                     "url/third_party/mozilla"
                     "v8/src/third_party/utf8-decoder"
                     "v8/src/third_party/valgrind"
@@ -2914,15 +2931,29 @@ linux/libcurl_wrapper.h"
               "-DQT_FEATURE_webengine_printing_and_pdf=OFF"
               "-DQT_FEATURE_webengine_pepper_plugins=OFF" ;widevine
               "-DQT_FEATURE_system_ffmpeg=ON"
+
               ;; Do not artificially limit codec support; video decoding is
               ;; done by ffmpeg.
               "-DQT_FEATURE_webengine_proprietary_codecs=ON"
+
+              ;; Use system libraries where possible (see src/core/CMakeLists.txt).
               "-DQT_FEATURE_webengine_system_alsa=ON"
+              "-DQT_FEATURE_webengine_system_ffmpeg=ON"
+              "-DQT_FEATURE_webengine_system_freetype=ON"
+              "-DQT_FEATURE_webengine_system_harfbuzz=ON"
               "-DQT_FEATURE_webengine_system_icu=ON"
-              "-DQT_FEATURE_webengine_system_libxml=ON"
+              "-DQT_FEATURE_webengine_system_lcms2=ON"
+              "-DQT_FEATURE_webengine_system_libevent=ON"
+              "-DQT_FEATURE_webengine_system_libjpeg=ON"
               "-DQT_FEATURE_webengine_system_libpci=ON"
               "-DQT_FEATURE_webengine_system_libpng=ON"
+              "-DQT_FEATURE_webengine_system_libwebp=ON"
+              "-DQT_FEATURE_webengine_system_libxml=ON"
+              "-DQT_FEATURE_webengine_system_libxslt=ON"
+              "-DQT_FEATURE_webengine_system_minizip=ON"
+              "-DQT_FEATURE_webengine_system_opus=ON"
               "-DQT_FEATURE_webengine_system_pulseaudio=ON"
+              "-DQT_FEATURE_webengine_system_re2=ON"
               "-DQT_FEATURE_webengine_system_zlib=ON")
       #:phases
       #~(modify-phases %standard-phases
@@ -2989,6 +3020,7 @@ linux/libcurl_wrapper.h"
     (inputs
      (modify-inputs (package-inputs qtwebengine-5)
        (replace "qtmultimedia" qtmultimedia)
+       (replace "harfbuzz" harfbuzz-5)
        (append libxkbfile xkeyboard-config)))
     (propagated-inputs
      (modify-inputs (package-propagated-inputs qtwebengine-5)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 616eded618..4c7609683b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -45,6 +45,7 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system r)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -2010,6 +2011,36 @@ and fast file reading.")
      "This package provides tools to export R data as LaTeX and HTML tables.")
     (license license:gpl2+)))
 
+(define-public python-hdmedians
+  (package
+    (name "python-hdmedians")
+    (version "0.14.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "hdmedians" version))
+              (sha256
+               (base32
+                "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'build-extensions
+           (lambda _
+             ;; Cython extensions have to be built before running the tests.
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs (list python-cython python-numpy))
+    (native-inputs (list python-nose))
+    (home-page "http://github.com/daleroberts/hdmedians")
+    (synopsis "High-dimensional medians")
+    (description "Various definitions for a high-dimensional median exist and
+this Python package provides a number of fast implementations of these
+definitions.  Medians are extremely useful due to their high breakdown
+point (up to 50% contamination) and have a number of nice applications in
+machine learning, computer vision, and high-dimensional statistics.")
+    (license license:asl2.0)))
+
 (define-public python-patsy
   (package
     (name "python-patsy")