From nobody Fri May 1 00:50:39 2026 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 4g6CBm1S1kz6ccBr for ; Fri, 01 May 2026 00:50:40 +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 "R13" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 4g6CBm0G20z44hr for ; Fri, 01 May 2026 00:50:40 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1777596640; 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=xWPPORDn/OdzeEmk9XrtZq+fJfgCCydw6Igq+3iR4n0=; b=nf7ypVFJwLfcigSIYXB4T3qWmfMPJtdex5q5xcvT9NEf+RwUj7u0rXqrl0I+5y+7l4PxGc zbzITc4Acf1ClHpVCAFOiHgksiZUI/mcu8ahrojFPn2rQF+iBDRqBf8eQdrJsyahstGzxw r230/9xg10zKMCsLSl/U+UBufG6KQO7B0k8rl9x5RfPxhPJE84quQvZeuMUoZcgjpF5r4x 8sy3jW8clEWbbizG+S2pv7XzzY8Irj2K81CidkeTJWYETKdyx1bQHhqY4zE/xNtMiCLQg+ q2aEVpzXIipIJciXZaRImze9MhUq4hLxQijT+M9+ZeRvd1RywwyXJ2sQBZq8JQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1777596640; a=rsa-sha256; cv=none; b=KrrMRn/MjsA2FFL1QQEl31L/eE6//mmIj20oz76OXBoRrAOlQjiHrUGuDQIuEyPyIvx+am cdr4pU+Bwbf8XF9PJjhzanbhiBzDgxP6ZhfA+lbJGFnysBDjM/R+IB99KlVMIC2p5eCjfb MwYn1126PjbrsphOXbsA5ScIzPmbG+N3VRLgwH39fE/D3E8tqPys6uiaMC7yq1+nwEaazk 9c7UbWZSFe3rXL/hBhSkGIuah29Wq7QgQxi6gWj0t6k1Ub6tFCh0yScM25fDAyb8+5q7nE FBz6wwhNz1m2FKWNBMrOCdyp8FA3M9yMrax6aeCpNt4h6+/hTOWrFNfx0qKzpw== 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=1777596640; 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=xWPPORDn/OdzeEmk9XrtZq+fJfgCCydw6Igq+3iR4n0=; b=XJdI2BeDogtfmezVd9nwMLEbVZ6514zVfjoYMroVlPo6Q4op07xVe/O6iBG8mZ0ibh/EiC VXp1yZBHlySlzCO0bIB18om3gL9FltpP+pe8MEWQUiO14K0WpBFz6IBXaXQhdb84pRcXXw quIY6AvS8n5CLN0uOFtqoKAYx4eyP3y56OsvZ+6H2Q5RlRo6y5U4+aj+tU+v5p2bfn5LEM p4jpUQKmXMnVB12dmeBmaX/ypfZ6BugBJVsOSfGenOCQobKxflc80/IvJ5P0RKOdQ7lNUe hlcybFmnw1olmSe4R9F5k5ELR92ki/nX9oYOop4PISYTn0XlDAcUXwEWDFwtBQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4g6CBl6NjjzcHD for ; Fri, 01 May 2026 00:50:39 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from git (uid 1279) (envelope-from git@FreeBSD.org) id 375a0 by gitrepo.freebsd.org (DragonFly Mail Agent v0.13+ on gitrepo.freebsd.org); Fri, 01 May 2026 00:50:39 +0000 To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Wen Heping Subject: git: 3e0fa24d33e9 - main - science/py-morphio: New port 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: wen X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 3e0fa24d33e9f9bb3f7433a3b07e2e888d1b0043 Auto-Submitted: auto-generated Date: Fri, 01 May 2026 00:50:39 +0000 Message-Id: <69f3f8df.375a0.2e5c0e1e@gitrepo.freebsd.org> The branch main has been updated by wen: URL: https://cgit.FreeBSD.org/ports/commit/?id=3e0fa24d33e9f9bb3f7433a3b07e2e888d1b0043 commit 3e0fa24d33e9f9bb3f7433a3b07e2e888d1b0043 Author: Wen Heping AuthorDate: 2026-05-01 00:49:22 +0000 Commit: Wen Heping CommitDate: 2026-05-01 00:50:29 +0000 science/py-morphio: New port MorphIO is a library for reading and writing neuron morphology files. It supports the following formats: SWC ASC (aka. neurolucida) H5 v1 H5 v2 is not supported anymore, see H5v2 --- science/Makefile | 1 + science/py-morphio/Makefile | 25 +++++++++++++++++++++++++ science/py-morphio/distinfo | 3 +++ science/py-morphio/files/patch-pyproject.toml | 11 +++++++++++ science/py-morphio/pkg-descr | 7 +++++++ 5 files changed, 47 insertions(+) diff --git a/science/Makefile b/science/Makefile index 4a7b8fd49ed1..96c2fdb71ae7 100644 --- a/science/Makefile +++ b/science/Makefile @@ -375,6 +375,7 @@ SUBDIR += py-mmtf-python SUBDIR += py-mne SUBDIR += py-molmod + SUBDIR += py-morphio SUBDIR += py-mp-api SUBDIR += py-mpcontribs-client SUBDIR += py-mplhep diff --git a/science/py-morphio/Makefile b/science/py-morphio/Makefile new file mode 100644 index 000000000000..02b51fae5e4c --- /dev/null +++ b/science/py-morphio/Makefile @@ -0,0 +1,25 @@ +PORTNAME= morphio +PORTVERSION= 3.4.2 +CATEGORIES= science python +MASTER_SITES= PYPI +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= wen@FreeBSD.org +COMMENT= Neuron morphology IO library +WWW= https://github.com/openbraininstitute/MorphIO + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=61.0:devel/py-setuptools@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ + cmake:devel/cmake-core \ + ninja:devel/ninja \ + pybind11>0:devel/pybind11 +LIB_DEPENDS= libhdf5.so:science/hdf5 + +USES= python +USE_PYTHON= autoplist pep517 + +.include diff --git a/science/py-morphio/distinfo b/science/py-morphio/distinfo new file mode 100644 index 000000000000..8b28ec9ac42d --- /dev/null +++ b/science/py-morphio/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1776477304 +SHA256 (morphio-3.4.2.tar.gz) = 4521b01dd8de8ff98b44341318cee44d75552dfd58b95a0e82ebfffe653b88f8 +SIZE (morphio-3.4.2.tar.gz) = 690093 diff --git a/science/py-morphio/files/patch-pyproject.toml b/science/py-morphio/files/patch-pyproject.toml new file mode 100644 index 000000000000..adaf2024bca5 --- /dev/null +++ b/science/py-morphio/files/patch-pyproject.toml @@ -0,0 +1,11 @@ +--- pyproject.toml.orig 2026-05-01 00:38:10 UTC ++++ pyproject.toml +@@ -2,8 +2,6 @@ requires = [ + requires = [ + "setuptools>=24.2.0", + "wheel", +- "cmake", +- "ninja", + ] + + [tool.pytest.ini_options] diff --git a/science/py-morphio/pkg-descr b/science/py-morphio/pkg-descr new file mode 100644 index 000000000000..d768d6633c79 --- /dev/null +++ b/science/py-morphio/pkg-descr @@ -0,0 +1,7 @@ +MorphIO is a library for reading and writing neuron morphology files. +It supports the following formats: + +SWC +ASC (aka. neurolucida) +H5 v1 +H5 v2 is not supported anymore, see H5v2