+python-modelcif (1.5-1) unstable; urgency=medium

+

+ * Initial release. (Closes: #1109466)

+

+ [ Thorsten Alteholz ]

+ * d/copyright: docs/* directly assigned to Ben

+

+ -- Steffen Moeller <moeller@debian.org> Fri, 03 Oct 2025 16:07:11 +0100

+Source: python-modelcif

+#Testsuite: autopkgtest-pkg-python

+Standards-Version: 4.7.2

+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

+Uploaders:

+ Steffen Moeller <moeller@debian.org>,

+ Ben Webb <ben@salilab.org>,

+Section: science

+Priority: optional

+Build-Depends:

+ debhelper-compat (= 13),

+ dh-sequence-python3,

+ python3-setuptools,

+ python3-all,

+ python3-ihm,

+Vcs-Browser: https://salsa.debian.org/med-team/python-modelcif

+Vcs-Git: https://salsa.debian.org/med-team/python-modelcif.git

+Homepage: https://github.com/ihmwg/python-modelcif

+Rules-Requires-Root: no

+

+Package: python3-modelcif

+Section: python

+Architecture: all

+Depends:

+ ${python3:Depends},

+ ${misc:Depends},

+Description: handles mmCIF and BinaryCIF files with ModelCIF extension

+ The macromolecular Crystallographic Information File format is a standard

+ for the representation and description of large molecular structures like

+ proteins and/or nucleic acids.

+ .

+ This package provides a mechanism to describe the generation of a

+ theoretical model (for example, via comparative or homology model)

+ a set of Python objects. This includes, if applicable

+ * the templates(s) used for the modeling;

+ * the alignment between the template(s) and target sequence;

+ * the protocol used to generate models, such as template search,

+ modeling, and model selection;

+ * the actual coordinates of output models;

+ * grouping of multiple models;

+ * quality scores for models and/or alignments.

+ .

+ Once created, this set of Python objects can be written to an

+ mmCIF file that is compliant with the ModelCIF extension to the

+ PDBx/mmCIF dictionary, suitable for deposition in a repository such as

+ ModelArchive. The files can be viewed in any regular PDBx mmCIF viewer,

+ such as UCSF ChimeraX (although most viewers to date will only show

+ the model coordinates, not the ModelCIF-specific metadata).

+ .

+ This package leverages functionality provided by the python-ihm

+ package, which functions similarly, building a Python hierarchy

+ and then reading/writing mmCIF files. (However, python-ihm is used

+ for integrative models, and reads or writes files compliant with the

+ integrative/hybrid modeling extension dictionary.) In particular, many

+ python-ihm classes and modules are used in this library, for example

+ the ihm.Grant and ihm.Citation classes for handling grant or citation

+ information, or the ihm.dictionary module for validating files against

+ the mmCIF dictionary itself.

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/

+Source: https://github.com/ihmwg/python-modelcif

+Upstream-Name: Python-ModelCIF

+Upstream-Contact: Ben Webb <ben@salilab.org>

+

+Files:

+ *

+Copyright:

+ 2018-2025 IHM Working Group

+License: Expat

+Comment: Ben Webb is listed as main author in setup.py, the license

+ file assigned the copyright to the IHM Working Group.

+

+Files:

+ docs/*

+Copyright:

+ 2021-2025 Ben Webb <ben@salilab.org>

+License: Expat

+Comment: Ben Webb is listed as copyright holder in docs/conf.py.

+

+Files:

+ debian/*

+Copyright:

+ 2025 Steffen Moeller <moeller@debian.org>

+License: Expat

+

+License: Expat

+ Permission is hereby granted, free of charge, to any person obtaining a copy

+ of this software and associated documentation files (the "Software"), to deal

+ in the Software without restriction, including without limitation the rights

+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

+ copies of the Software, and to permit persons to whom the Software is

+ furnished to do so, subject to the following conditions:

+ .

+ The above copyright notice and this permission notice shall be included in all

+ copies or substantial portions of the Software.

+ .

+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

+ SOFTWARE.

+#!/usr/bin/make -f

+

+export DH_VERBOSE = 1

+export PYBUILD_NAME=modelcif

+

+%:

+ dh $@ --buildsystem=pybuild

+# For more information on what jobs are run see:

+# https://salsa.debian.org/salsa-ci-team/pipeline

+#

+# To enable the jobs, go to your repository (at salsa.debian.org)

+# and click over Settings > CI/CD > Expand (in General pipelines).

+# In "CI/CD configuration file" write debian/salsa-ci.yml and click

+# in "Save Changes". The CI tests will run after the next commit.

+---

+include:

+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml

+3.0 (quilt)

+extend-diff-ignore = "^[^/]*[.]egg-info/"

+# See https://wiki.debian.org/UpstreamMetadata for more info/fields.

+Bug-Database: https://github.com/ihwmg/python-modelcif/issues

+Bug-Submit: https://github.com/ihwmg/python-modelcif/issues/new

+Changelog: https://github.com/ihmwg/python-modelcif/blob/main/ChangeLog.rst

+Documentation: https://python-modelcif.readthedocs.io

+Repository-Browse: "https://github.com/ihmwg/python-modelcif"

+Repository: "https://github.com/ihmwg/python-modelcif.git"

+Registry:

+ - Name: bio.tools

+ Entry: modelcif

+ - Name: SciCrunch

+ Entry: SCR_027218

+ - Name: conda:conda-forge

+ Entry: modelcif

+Reference:

+ - Authors: Brinda Vallat and Gerardo Tauriello and Stefan Bienert and Juergen Haas and Benjamin M Webb and Augustin Žídek and Wei Zheng and Ezra Peisach and Dennis W Piehl and Ivan Anischanka and Ian Sillitoe and James Tolchard and Mihaly Varadi and David Baker and Christine Orengo and Yang Zhang and Jeffrey C Hoch and Genji Kurisu and Ardan Patwardhan and Sameer Velankar and Stephen K Burley and Andrej Sali and Torsten Schwede and Helen M Berman and John D Westbrook

+# - family-names: "Vallat"

+# given-names: "Brinda"

+# - family-names: "Tauriello"

+# given-names: "Gerardo"

+# - family-names: "Bienert"

+# given-names: "Stefan"

+# - family-names: "Haas"

+# given-names: "Juergen"

+# - family-names: "Webb"

+# given-names: "Benjamin M."

+# - family-names: "Žídek"

+# given-names: "Augustin"

+# - family-names: "Zheng"

+# given-names: "Wei"

+# - family-names: "Peisach"

+# given-names: "Ezra"

+# - family-names: "Piehl"

+# given-names: "Dennis W."

+# - family-names: "Anischanka"

+# given-names: "Ivan"

+# - family-names: "Sillitoe"

+# given-names: "Ian"

+# - family-names: "Tolchard"

+# given-names: "James"

+# - family-names: "Varadi"

+# given-names: "Mihaly"

+# - family-names: "Baker"

+# given-names: "David"

+# - family-names: "Orengo"

+# given-names: "Christine"

+# - family-names: "Zhang"

+# given-names: "Yang"

+# - family-names: "Hoch"

+# given-names: "Jeffrey C."

+# - family-names: "Kurisu"

+# given-names: "Genji"

+# - family-names: "Patwardhan"

+# given-names: "Ardan"

+# - family-names: "Velankar"

+# given-names: "Sameer"

+# - family-names: "Burley"

+# given-names: "Stephen K."

+# - family-names: "Sali"

+# given-names: "Andrej"

+# - family-names: "Schwede"

+# given-names: "Torsten"

+# - family-names: "Berman"

+# given-names: "Helen M."

+# - family-names: "Westbrook"

+# given-names: "John D."

+ DOI: "10.1016/j.jmb.2023.168021"

+ Journal: "J Mol Biol"

+ Month: 7

+ Start: 168021

+ Title: "ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models"

+ Volume: 435

+ Issue: 14

+ Year: 2023

+ PMID: 36828268

+ URL: https://www.sciencedirect.com/science/article/pii/S0022283623000773?via%3Dihub

+version=4

+opts="filenamemangle=s%(?:.*?)?v?(@ANY_VERSION@@ARCHIVE_EXT@)%@PACKAGE@-$1%" \

+ https://github.com/ihmwg/python-modelcif/tags \

+ (?:.*?/)v?@ANY_VERSION@@ARCHIVE_EXT@