From nobody Sun Sep 10 18:10:52 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RkHvx2X4wz4t8Gm; Sun, 10 Sep 2023 18:10:53 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4RkHvx1SVVz4bM2; Sun, 10 Sep 2023 18:10:53 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1694369453; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=VpyyaNmrYK4gENAkZ5B4RStNqkgwmzSmmpohcHbq4DA=; b=Tf8aaQ3E8SLLG1gHBroXpyvlwpUzSArt04J78Xe0itDmRm5xmSr7MLr3pIoT7WEAcY10Nk kb7lNvbWYeFq3gRXdixJD4kyUA3fzWeiaKqJFYj+3LgR7+e0QtGEpFYKLDq6kxJksHbaGE E5L9w/1v0MuRSF2rugrQJ/ZS1tGYgLcCqlNm+Gzpy1sqJlrZ4YCypVLk/pwi36meJvpkTN jenl7NAXKqKzLlk5i+nE7Y1uvUZkx44onZNQnYNLJh9UbVAk4+WZwlWL442WdL3gLCNS+i fhuHXlz3k5Erl2LqMhaNbIId/OiWxLKlQScSeca2HmwMQiWXWm+D3XTuq1tGGg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1694369453; a=rsa-sha256; cv=none; b=RhMXwoD9E1/Q6r500MKa2X4cjNKCWsCHhbH98e3Ie9EjRQex7LuCRqZJDmGMOVVU69eiSY oV+lvRpz+l96sDCHApvM+DwrogWQsv67h0nXx3NkCEkqilMd7XC3Ch3uL+An01b1KpydjB +AnVpwHxe51gfB30vZFXFA/uVtWITSzhmIz+CYC3jfNhMOlEizQF2kg9Wfi9o7dUI6TIg/ cTfPjTE8AVRMirT07j225a2M8SYhbZs9OLWeOptekIPcPB8wBs28lreI3D4WmuWdkfSwej NuJgg60ONAxJQARMVzivZ94Ndm5LuWhtCpahllt9BBLSKuu2nr8X14zGvw+f0g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1694369453; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=VpyyaNmrYK4gENAkZ5B4RStNqkgwmzSmmpohcHbq4DA=; b=CREnHbnLlNWdXMWiMmJlEu0K8NHIK4BF5WNmIn5EBDFdUzqeoH5eyDoFi1ztSiQPAwdi+m uSXqp79BH4W3bFNKxozDI7pxUuPt4njPg6wAiAR/kPJqVcuGaRYCTX3DYLLlqSbxqykUT8 +OazxMAoCSj/fUR7ba/i9zaLAkBonzU3K0Jzq/9EDdSoByEay9V0ZIzwDp5dHYMaBXEL7P D/d9JAodX3RoznaVNiKj+KW1xS4IhAXUw2tC8yppwtYxeGwjXtSIFl54/WpmOyv3+zPlp5 uocJaZ2PVbb6jikuOP0nL1VcNM17HhtXSYLQE7CU82XI2gaDUsn65imUqz7kAg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4RkHvx0Xktz2L2; Sun, 10 Sep 2023 18:10:53 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 38AIAqjD019126; Sun, 10 Sep 2023 18:10:52 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 38AIAqDZ019123; Sun, 10 Sep 2023 18:10:52 GMT (envelope-from git) Date: Sun, 10 Sep 2023 18:10:52 GMT Message-Id: <202309101810.38AIAqDZ019123@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: ef2fc7422478 - main - science/{,py-}gemmi: update 0.6.2 =?utf-8?Q?=E2=86=92?= 0.6.3 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: ef2fc742247825f57828cbd0b6f774cd0ca13cfa Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=ef2fc742247825f57828cbd0b6f774cd0ca13cfa commit ef2fc742247825f57828cbd0b6f774cd0ca13cfa Author: Yuri Victorovich AuthorDate: 2023-09-10 17:57:21 +0000 Commit: Yuri Victorovich CommitDate: 2023-09-10 18:10:46 +0000 science/{,py-}gemmi: update 0.6.2 → 0.6.3 Reported by: portscout --- science/gemmi/Makefile | 2 +- science/gemmi/distinfo | 6 +++--- science/gemmi/pkg-plist | 2 ++ science/py-gemmi/Makefile | 2 +- science/py-gemmi/distinfo | 6 +++--- science/py-gemmi/files/patch-CMakeLists.txt | 28 +++++++++++++++------------- 6 files changed, 25 insertions(+), 21 deletions(-) diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile index db62f5f0ecbd..b257a807cf24 100644 --- a/science/gemmi/Makefile +++ b/science/gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.2 +DISTVERSION= 0.6.3 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo index 64807762f6b8..2aa772096904 100644 --- a/science/gemmi/distinfo +++ b/science/gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1685300431 -SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929 -SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298 +TIMESTAMP = 1694327240 +SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091 +SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098 diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist index 27bea19e9241..1e66eed2eccb 100644 --- a/science/gemmi/pkg-plist +++ b/science/gemmi/pkg-plist @@ -21,8 +21,10 @@ include/gemmi/cif2mtz.hpp include/gemmi/cifdoc.hpp include/gemmi/contact.hpp include/gemmi/crd.hpp +include/gemmi/ddl.hpp include/gemmi/dencalc.hpp include/gemmi/dirwalk.hpp +include/gemmi/ecalc.hpp include/gemmi/eig3.hpp include/gemmi/elem.hpp include/gemmi/enumstr.hpp diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile index 9e09144588fb..caea06f40f2e 100644 --- a/science/py-gemmi/Makefile +++ b/science/py-gemmi/Makefile @@ -1,6 +1,6 @@ PORTNAME= gemmi DISTVERSIONPREFIX= v -DISTVERSION= 0.6.2 +DISTVERSION= 0.6.3 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo index f3c4d131e6b0..de2cc003fbcb 100644 --- a/science/py-gemmi/distinfo +++ b/science/py-gemmi/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1685301047 -SHA256 (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = d225548ddf4289d7adb9a0cce725cf4853474b9903399080f4770c77d4c18929 -SIZE (project-gemmi-gemmi-v0.6.2_GH0.tar.gz) = 1733298 +TIMESTAMP = 1694328516 +SHA256 (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091 +SIZE (project-gemmi-gemmi-v0.6.3_GH0.tar.gz) = 1756098 diff --git a/science/py-gemmi/files/patch-CMakeLists.txt b/science/py-gemmi/files/patch-CMakeLists.txt index 943a0ad5a5cc..802f60ebf944 100644 --- a/science/py-gemmi/files/patch-CMakeLists.txt +++ b/science/py-gemmi/files/patch-CMakeLists.txt @@ -1,18 +1,20 @@ ---- CMakeLists.txt.orig 2023-05-25 12:37:36 UTC +--- CMakeLists.txt.orig 2023-09-07 09:12:22 UTC +++ CMakeLists.txt -@@ -187,20 +187,21 @@ if (GEMMI_VERSION_INFO) +@@ -187,21 +187,22 @@ if (GEMMI_VERSION_INFO) target_compile_definitions(options PRIVATE GEMMI_VERSION_INFO=${GEMMI_VERSION_INFO}) endif() -add_library(gemmi_cpp -- src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp +- src/assembly.cpp src/calculate.cpp src/crd.cpp +- src/ddl.cpp src/eig3.cpp - src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp - src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp - src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp - src/to_pdb.cpp src/monlib.cpp src/topo.cpp src/xds_ascii.cpp) -set_property(TARGET gemmi_cpp PROPERTY POSITION_INDEPENDENT_CODE ON) +#add_library(gemmi_cpp -+# src/assembly.cpp src/calculate.cpp src/crd.cpp src/eig3.cpp ++# src/assembly.cpp src/calculate.cpp src/crd.cpp ++# src/ddl.cpp src/eig3.cpp +# src/mmcif.cpp src/mmread_gz.cpp src/mtz.cpp src/mtz2cif.cpp +# src/polyheur.cpp src/read_cif.cpp src/resinfo.cpp +# src/riding_h.cpp src/sprintf.cpp src/to_mmcif.cpp @@ -34,7 +36,7 @@ # Gemmi subcommands compiled as individual binaries. # Not built by default and used mostly for testing. -@@ -209,7 +210,7 @@ function(add_single_prog target) +@@ -210,7 +211,7 @@ function(add_single_prog target) add_executable(gemmi-${target} EXCLUDE_FROM_ALL prog/${target}.cpp ${arg_ADD_SRC} $) if (NOT arg_NOLIB) @@ -43,7 +45,7 @@ endif() if (arg_GZ) support_gz(gemmi-${target}) -@@ -261,7 +262,7 @@ add_executable(gemmi_prog +@@ -264,7 +265,7 @@ add_executable(gemmi_prog prog/validate.cpp prog/validate_mon.cpp prog/wcn.cpp prog/xds2mtz.cpp $) @@ -52,7 +54,7 @@ support_gz(gemmi_prog) target_compile_definitions(gemmi_prog PRIVATE GEMMI_ALL_IN_ONE=1) set_property(TARGET gemmi_prog PROPERTY OUTPUT_NAME gemmi) -@@ -301,10 +302,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL +@@ -304,10 +305,10 @@ add_executable(doc_example EXCLUDE_FROM_ALL docs/code/cell.cpp src/resinfo.cpp) add_executable(doc_example2 EXCLUDE_FROM_ALL docs/code/cif_cc.cpp) add_executable(doc_maybegz EXCLUDE_FROM_ALL docs/code/maybegz.cpp docs/code/mutate.cpp) @@ -65,7 +67,7 @@ support_gz(doc_newmtz) # always compile these tests with assertions enabled -@@ -313,7 +314,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") +@@ -316,7 +317,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU|Intel") endif() add_executable(test_disulf EXCLUDE_FROM_ALL tests/disulf.cpp) @@ -74,7 +76,7 @@ support_gz(test_disulf) # auth_label requires and -lstdc++fs -@@ -324,7 +325,7 @@ endif() +@@ -327,7 +328,7 @@ endif() support_gz(auth_label) add_executable(check_conn EXCLUDE_FROM_ALL examples/check_conn.cpp) @@ -83,7 +85,7 @@ enable_testing() -@@ -361,7 +362,7 @@ if (benchmark_FOUND) +@@ -364,7 +365,7 @@ if (benchmark_FOUND) foreach(b stoi elem mod niggli pdb resinfo round sym) add_executable(${b}-bm EXCLUDE_FROM_ALL benchmarks/${b}.cpp) if (b MATCHES "resinfo|pdb") @@ -92,7 +94,7 @@ endif() target_link_libraries(${b}-bm PRIVATE benchmark::benchmark) set_property(TARGET ${b}-bm PROPERTY RUNTIME_OUTPUT_DIRECTORY -@@ -389,8 +390,8 @@ if (USE_PYTHON) +@@ -392,8 +393,8 @@ if (USE_PYTHON) python/mtz.cpp python/read.cpp python/recgrid.cpp python/scaling.cpp python/search.cpp python/sf.cpp python/sym.cpp python/topo.cpp @@ -103,7 +105,7 @@ set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi) if(CMAKE_CXX_FLAGS MATCHES "-Wshadow") target_compile_options(gemmi_py PRIVATE "-Wno-shadow") -@@ -413,21 +414,21 @@ write_basic_package_version_file(gemmi-config-version. +@@ -416,21 +417,21 @@ write_basic_package_version_file(gemmi-config-version. COMPATIBILITY AnyNewerVersion) # In CMake 3.23 we'll be able to use FILE_SET to install the headers @@ -135,7 +137,7 @@ if (USE_PYTHON) if (DEFINED PYTHON_INSTALL_DIR) -@@ -441,8 +442,8 @@ if (USE_PYTHON) +@@ -444,8 +445,8 @@ if (USE_PYTHON) # and don't respect CMAKE_INSTALL_PREFIX. # https://discourse.cmake.org/t/findpython3-how-to-specify-local-installation-directory-for-python-module/3580/5 install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}")