Merge branch 'master' into core-updates

Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a2770ef4d05a6e18f40d602e51da749ddc and
12964df69a99de6190422c752fef65ef813f3b6b respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm

1 files changed, 271 insertions, 0 deletions

diff --git a/gnu/packages/irods.scm b/gnu/packages/irods.scm
new file mode 100644
index 0000000000..bb0263682c
--- /dev/null
+++ b/gnu/packages/irods.scm
@@ -0,0 +1,271 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages irods)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages kerberos)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages llvm)
+  #:use-module (gnu packages logging)
+  #:use-module (gnu packages man)
+  #:use-module (gnu packages networking)
+  #:use-module (gnu packages pretty-print)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages tls)
+  #:use-module (srfi srfi-1))
+
+(define-public irods
+  (package
+    (name "irods")
+    (version "4.2.8")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/irods/irods/releases/download/"
+                                  version "/irods-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0ny54c3r0j692rvbr4iibg7xgd2i7g9x8yyrw04j889bywix14rc"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list
+        "-DCMAKE_BUILD_TYPE=Release"
+        (string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
+                       (assoc-ref %outputs "out") "/lib")
+        (string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath="
+                       (assoc-ref %outputs "out") "/lib")
+        (string-append "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath="
+                       (assoc-ref %outputs "out") "/lib")
+
+        ;; Configuration aborts if no generator format is set
+        "-DCPACK_GENERATOR=TGZ"
+
+        ;; Configuration attempts to guess the distribution with Python.
+        "-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
+        "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
+
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG="
+                       (assoc-ref %build-inputs "clang"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="
+                       (assoc-ref %build-inputs "clang-runtime"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="
+                       (assoc-ref %build-inputs "cppzmq"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="
+                       (assoc-ref %build-inputs "libarchive"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_AVRO="
+                       (assoc-ref %build-inputs "avro-cpp"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_BOOST="
+                       (assoc-ref %build-inputs "boost"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_ZMQ="
+                       (assoc-ref %build-inputs "zeromq"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_JSON="
+                       (assoc-ref %build-inputs "json"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CATCH2="
+                       (assoc-ref %build-inputs "catch2"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_NANODBC="
+                       (assoc-ref %build-inputs "nanodbc"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_FMT="
+                       (assoc-ref %build-inputs "fmt")))
+
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unset-Werror
+           (lambda _
+             ;; -Werror kills the build due to a comparison REQUIRE(errs.size() == err->len);
+             ;; in unit_tests/src/test_irods_lifetime_manager.cpp
+             (substitute* "CMakeLists.txt"
+               (("-Werror") ""))))
+         (add-after 'unpack 'remove-FHS-and-prefix-assumptions
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* '("CMakeLists.txt"
+                            "cmake/server.cmake"
+                            "cmake/development_library.cmake"
+                            "cmake/runtime_library.cmake")
+               (("usr/") ""))
+             (substitute* "lib/core/src/irods_default_paths.cpp"
+               (("path.append\\(\"usr\"\\)") "path")
+               (("path.remove_filename\\(\\).remove_filename\\(\\).remove_filename\\(\\)")
+                "path.remove_filename().remove_filename()"))
+             (substitute* "scripts/irods/paths.py"
+               (("'usr', 'lib', 'irods'") "'lib', 'irods'"))
+             (substitute* "scripts/irods/pypyodbc.py"
+               (("\"/usr/lib/libodbc.so\"")
+                (string-append (assoc-ref inputs "unixodbc") "/lib/libodbc.so")))))
+         (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gcc (assoc-ref inputs  "gcc")))
+               (setenv "CPLUS_INCLUDE_PATH"
+                       (string-join
+                        (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+                                              "/include/c++/v1")
+                               (string-append (assoc-ref inputs "catch2")
+                                              "/include/catch2")
+                               (string-append (assoc-ref inputs "json")
+                                              "/include/nlohmann")
+                               ;; Hide GCC's C++ headers so that they do not interfere with
+                               ;; the Clang headers.
+                               (delete (string-append gcc "/include/c++")
+                                       (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                                     #\:)))
+                        ":"))
+               (format #true
+                       "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                       (getenv "CPLUS_INCLUDE_PATH"))))))))
+    (inputs
+     `(("avro-cpp" ,avro-cpp-1.9-for-irods)
+       ("boost" ,boost-for-irods)
+       ("cppzmq" ,cppzmq)
+       ("fmt" ,fmt-for-irods)
+       ("json" ,json-modern-cxx)
+       ("libarchive" ,libarchive)
+       ("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
+       ("linux-pam" ,linux-pam)
+       ("mit-krb5" ,mit-krb5)
+       ("nanodbc" ,nanodbc-for-irods)
+       ("openssl" ,openssl)
+       ("python" ,python-wrapper)
+       ("unixodbc" ,unixodbc)
+       ("zeromq" ,zeromq)))
+    (native-inputs
+     `(("catch2" ,catch-framework2)
+       ("clang" ,clang-toolchain-6)
+       ("clang-runtime" ,clang-runtime-6)
+       ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)))
+    (home-page "https://irods.org")
+    (synopsis "Data management software")
+    (description "The Integrated Rule-Oriented Data System (iRODS) is data
+management software.  iRODS virtualizes data storage resources, so users can
+take control of their data, regardless of where and on what device the data is
+stored.")
+    (license license:bsd-3)))
+
+(define-public irods-client-icommands
+  (package
+    (name "irods-client-icommands")
+    (version "4.2.8")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/irods/irods_client_icommands")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "069n647p5ypf44gim8z26mwayg5lzgk7r9qyyqd8f9n7h0p4jxpn"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #false ; not clear how to run tests
+       #:configure-flags
+       (list
+        "-DCMAKE_BUILD_TYPE=Release"
+
+        ;; Configuration attempts to guess the distribution with Python.
+        "-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
+        "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
+
+        (string-append "-DIRODS_DIR="
+                       (assoc-ref %build-inputs "irods")
+                       "/lib/irods/cmake")
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG="
+                       (assoc-ref %build-inputs "clang"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="
+                       (assoc-ref %build-inputs "clang-runtime"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="
+                       (assoc-ref %build-inputs "cppzmq"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="
+                       (assoc-ref %build-inputs "libarchive"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_AVRO="
+                       (assoc-ref %build-inputs "avro-cpp"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_BOOST="
+                       (assoc-ref %build-inputs "boost"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_ZMQ="
+                       (assoc-ref %build-inputs "zeromq"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_JSON="
+                       (assoc-ref %build-inputs "json"))
+        (string-append "-DIRODS_EXTERNALS_FULLPATH_FMT="
+                       (assoc-ref %build-inputs "fmt")))
+
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unset-Werror ;
+           (lambda _                           ;
+             ;; -Werror kills the build due to a deprecation warning
+             (substitute* "CMakeLists.txt" ;
+               (("-Werror") ""))))
+         (add-after 'unpack 'remove-/usr-prefix
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("usr/") ""))))
+         (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((gcc (assoc-ref inputs  "gcc")))
+               (setenv "CPLUS_INCLUDE_PATH"
+                       (string-join
+                        (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+                                              "/include/c++/v1")
+                               (string-append (assoc-ref inputs "json")
+                                              "/include/nlohmann")
+                               ;; Hide GCC's C++ headers so that they do not interfere with
+                               ;; the Clang headers.
+                               (delete (string-append gcc "/include/c++")
+                                       (string-split (getenv "CPLUS_INCLUDE_PATH")
+                                                     #\:)))
+                        ":"))
+               (format #true
+                       "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+                       (getenv "CPLUS_INCLUDE_PATH"))))))))
+    (inputs
+     `(("avro-cpp" ,avro-cpp-1.9-for-irods)
+       ("boost" ,boost-for-irods)
+       ("cppzmq" ,cppzmq)
+       ("fmt" ,fmt-for-irods)
+       ("irods" ,irods)
+       ("json" ,json-modern-cxx)
+       ("libarchive" ,libarchive)
+       ("libcxxabi" ,libcxxabi-6)     ; we need this for linking with -lc++abi
+       ("mit-krb5" ,mit-krb5)
+       ("openssl" ,openssl)
+       ("zeromq" ,zeromq)))
+    (native-inputs
+     `(("clang" ,clang-toolchain-6)
+       ("clang-runtime" ,clang-runtime-6)
+       ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+       ("help2man" ,help2man)
+       ("which" ,which)))
+    (home-page "https://irods.org")
+    (synopsis "Data management software")
+    (description "The Integrated Rule-Oriented Data System (iRODS) is data
+management software.  iRODS virtualizes data storage resources, so users can
+take control of their data, regardless of where and on what device the data is
+stored.")
+    (license license:bsd-3)))