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authorYuri Victorovich <yuri@FreeBSD.org>2022-10-04 01:31:51 +0000
committerYuri Victorovich <yuri@FreeBSD.org>2022-10-04 01:35:24 +0000
commit742c1c0610e0154cf6625a013961beacb72077bd (patch)
tree7f221071bc68145a28a2972adf1772faec377194
parent552e21084fa8fafb0716e7fccbe64f9019291905 (diff)
downloadports-742c1c0610e0154cf6625a013961beacb72077bd.tar.gz
ports-742c1c0610e0154cf6625a013961beacb72077bd.zip
science/py-mmcif: New port: mmCIF Core Access Library
-rw-r--r--science/Makefile1
-rw-r--r--science/py-mmcif/Makefile27
-rw-r--r--science/py-mmcif/distinfo3
-rw-r--r--science/py-mmcif/files/patch-CMakeLists.txt11
-rw-r--r--science/py-mmcif/pkg-descr2
5 files changed, 44 insertions, 0 deletions
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 <bsd.port.mk>
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.