From nobody Tue Oct 04 01:35:37 2022 X-Original-To: dev-commits-ports-main@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 4MhKyx610jz4cyxq; Tue, 4 Oct 2022 01:35:37 +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 4MhKyx5Xhrz3jhx; Tue, 4 Oct 2022 01:35:37 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1664847337; 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=s+0XlBJXwPHld8mwxVJzg60rmfg6hAufcNgMDT5laDg=; b=VfX6/cNKNvq5g5PBeGDMb/90ntORvBI9OljDKdYm9i1jp865U2PJfm85ySJB0TzeR28xk9 PUDekuqchWybJuZguSpVDce1aMgVzBrf6oV6pzZqvmp69rTJkkVcx738izUjBwDUnnK716 f5uto6SnofoaRYZk8T3CC/rCjaYlTz1l3+0vKMSVLMX8J4LhWQ+oW/wOE6L291LkdG8Sg/ W0VZsmaZ+//OJoJhLlvd6tCryJV4b3sWKI2HtDWC/oQlt108n4PfDHptSaFwNebiq01InB 8RQV45VqrpRTWKjTas9bs63Jt8qUQpV29ZK4vqKcooZ+I7lz2uqrwlEKt5vbNg== 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 4MhKyx4flkzPV5; Tue, 4 Oct 2022 01:35:37 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 2941Zbib040578; Tue, 4 Oct 2022 01:35:37 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2941Zbvc040577; Tue, 4 Oct 2022 01:35:37 GMT (envelope-from git) Date: Tue, 4 Oct 2022 01:35:37 GMT Message-Id: <202210040135.2941Zbvc040577@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: 742c1c0610e0 - main - science/py-mmcif: New port: mmCIF Core Access Library List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: 742c1c0610e0154cf6625a013961beacb72077bd Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1664847337; 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=s+0XlBJXwPHld8mwxVJzg60rmfg6hAufcNgMDT5laDg=; b=iI1oSTZaF/ggxaq3XRs4mZe6qXNWoH1d/nVr3k99EJjXFvn8smvSbYsaVukHJNpfhfzERG OGV/hmqvyacLbHerb0c6guWnWn84TzFEARpJfdGfHm6sO0hBX1ax0sW+tv2CIOZCPi032u TA4LCQKo2otwZvm/SzvSeNsc/TRsJWHjQXrmv/qm8Ke6XiM5anFfCTjOegfiscS9eJ9q9d N+gtxsVJjBtb75qIw2Y+uiG8yQ4bPHtbBORGsYUlwwR86D1ssRd51GK/d0WtHTY+x2B3O8 NcDWEwp4zHRlOjL0ZXtljqw+zrUHNDPwpBF3h2vn82iBqNsSezV9WNMwgZDgUQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1664847337; a=rsa-sha256; cv=none; b=PHtKxumxMLwxwWmS3HEBoGEJc93PnpLe+7V+N4qK1feWwzOCChoiam1dXMew0Nl2krotZU vQYK65iQ2uXdeRn0QmU5u67O/kd12hrcmXlii+yyXZG+fAAqS0BRyfLzhuBP3UJyUWXpnE mN45QpvNWWp0+vLDR02kqzyFlyht3upG+fT3wTsR5klekgVIeElJpG1R9loJ5K6/r0+itO plfKxM1qzI61+pXhkHEASR2pl8yMsRiTR2EZkMS/Df0JR9LjIO/jlArnzJqwQU3iYN20u3 FucKk8z3yugqj+NuYaGWibCtqx+iAH6BZpUG/Q/3+TeJFF4lrWkRbTdgqA+uww== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=742c1c0610e0154cf6625a013961beacb72077bd commit 742c1c0610e0154cf6625a013961beacb72077bd Author: Yuri Victorovich AuthorDate: 2022-10-04 01:31:51 +0000 Commit: Yuri Victorovich CommitDate: 2022-10-04 01:35:24 +0000 science/py-mmcif: New port: mmCIF Core Access Library --- science/Makefile | 1 + science/py-mmcif/Makefile | 27 +++++++++++++++++++++++++++ science/py-mmcif/distinfo | 3 +++ science/py-mmcif/files/patch-CMakeLists.txt | 11 +++++++++++ science/py-mmcif/pkg-descr | 2 ++ 5 files changed, 44 insertions(+) diff --git a/science/Makefile b/science/Makefile index e54e5def66d7..867b6c39971c 100644 --- a/science/Makefile +++ b/science/Makefile @@ -324,6 +324,7 @@ SUBDIR += py-libpysal SUBDIR += py-lifelines SUBDIR += py-mdp + SUBDIR += py-mmcif SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-moltemplate diff --git a/science/py-mmcif/Makefile b/science/py-mmcif/Makefile new file mode 100644 index 000000000000..6a1c9e7101b7 --- /dev/null +++ b/science/py-mmcif/Makefile @@ -0,0 +1,27 @@ +PORTNAME= mmcif +DISTVERSION= 0.79 +CATEGORIES= science biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= mmCIF Core Access Library +WWW= https://mmcif.wwpdb.org/ + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE + +PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}future>0:devel/py-future@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.25:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} +BUILD_DEPENDS= ${PY_DEPENDS} \ + cmake:devel/cmake-core +RUN_DEPENDS= ${PY_DEPENDS} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}coverage>0:devel/py-coverage@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tox>0:devel/py-tox@${PY_FLAVOR} + +USES= bison python +USE_PYTHON= distutils concurrent autoplist pytest # tests fail to run, see https://github.com/rcsb/py-mmcif/issues/18 + +.include diff --git a/science/py-mmcif/distinfo b/science/py-mmcif/distinfo new file mode 100644 index 000000000000..9e1a3805df69 --- /dev/null +++ b/science/py-mmcif/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1664833599 +SHA256 (mmcif-0.79.tar.gz) = 1ee1d641b221b613b7d573f66782ee7d609cf75b86002a57050cd0bfde58ce43 +SIZE (mmcif-0.79.tar.gz) = 935983 diff --git a/science/py-mmcif/files/patch-CMakeLists.txt b/science/py-mmcif/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..76c96042bdbd --- /dev/null +++ b/science/py-mmcif/files/patch-CMakeLists.txt @@ -0,0 +1,11 @@ +--- CMakeLists.txt.orig 2022-10-04 00:28:23 UTC ++++ CMakeLists.txt +@@ -1,5 +1,8 @@ + cmake_minimum_required(VERSION 2.8.12) + project(mmciflib) ++ ++set(CMAKE_POSITION_INDEPENDENT_CODE TRUE) ++ + # + # File: CMakeLists.txt - + # Date: 1-Aug-2017 diff --git a/science/py-mmcif/pkg-descr b/science/py-mmcif/pkg-descr new file mode 100644 index 000000000000..79dc1002aad8 --- /dev/null +++ b/science/py-mmcif/pkg-descr @@ -0,0 +1,2 @@ +mmcif includes a native Python mmCIF API for data files and dictionaries along +with pybind11 wrappers for the PDB C++ Core mmCIF Library.