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@@ -0,0 +1 @@ +/obonet-1.0.0.tar.gz diff --git a/python-obonet.spec b/python-obonet.spec new file mode 100644 index 0000000..810a309 --- /dev/null +++ b/python-obonet.spec @@ -0,0 +1,489 @@ +%global _empty_manifest_terminate_build 0 +Name: python-obonet +Version: 1.0.0 +Release: 1 +Summary: Parse OBO formatted ontologies into networkx +License: BSD-2-Clause-Patent +URL: https://github.com/dhimmel/obonet +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/44/c5/70a58eb06679bd07178acacd8e4cccfaf060f73e36eba3fe184315229643/obonet-1.0.0.tar.gz +BuildArch: noarch + +Requires: python3-networkx +Requires: python3-pre-commit +Requires: python3-pytest + +%description +# obonet: load OBO-formatted ontologies into networkx + +[](https://github.com/dhimmel/obonet/actions) +[](https://github.com/dhimmel/obonet/blob/main/LICENSE) +[](https://github.com/psf/black) +[](https://pypi.org/project/obonet/) + + +Read OBO-formatted ontologies in Python. +`obonet` is + ++ user friendly ++ succinct ++ pythonic ++ modern ++ simple and tested ++ lightweight ++ [`networkx`](https://networkx.readthedocs.io/en/stable/overview.html) leveraging + +This Python package loads OBO serialized ontologies into networks. +The function `obonet.read_obo()` takes an `.obo` file and returns a [`networkx.MultiDiGraph`](https://networkx.github.io/documentation/stable/reference/classes/multigraph.html) representation of the ontology. +The parser was designed for the OBO specification version [1.2](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html) & [1.4](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html). + +## Usage + +See [`pyproject.toml`](pyproject.toml) for the minimum Python version required and the dependencies. +OBO files can be read from a path, URL, or open file handle. +Compression is inferred from the path's extension. +See example usage below: + +```python +import networkx +import obonet + +# Read the taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo' +graph = obonet.read_obo(url) + +# Or read the xz-compressed taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo.xz' +graph = obonet.read_obo(url) + +# Number of nodes +len(graph) + +# Number of edges +graph.number_of_edges() + +# Check if the ontology is a DAG +networkx.is_directed_acyclic_graph(graph) + +# Mapping from term ID to name +id_to_name = {id_: data.get('name') for id_, data in graph.nodes(data=True)} +id_to_name['TAXRANK:0000006'] # TAXRANK:0000006 is species + +# Find all superterms of species. Note that networkx.descendants gets +# superterms, while networkx.ancestors returns subterms. +networkx.descendants(graph, 'TAXRANK:0000006') +``` + +For a more detailed tutorial, see the [**Gene Ontology example notebook**](https://github.com/dhimmel/obonet/blob/main/examples/go-obonet.ipynb). + +## Comparison + +This package specializes in reading OBO files into a `newtorkx.MultiDiGraph`. +A more general ontology-to-NetworkX reader is available in the Python [nxontology package](https://github.com/related-sciences/nxontology) via the `nxontology.imports.pronto_to_multidigraph` function. +This function takes a `pronto.Ontology` object, +which can be loaded from an OBO file, OBO Graphs JSON file, or Ontology Web Language 2 RDF/XML file (OWL). +Using `pronto_to_multidigraph` allows creating a MultiDiGraph similar to the created by `obonet`, +with some differences in the amount of metadata retained. + +The primary focus of the `nxontology` package is to provide an `NXOntology` class for representing ontologies based around a `networkx.DiGraph`. +NXOntology provides optimized implementations for computing node similarity and other intrinsic ontology metrics. +There are two important differences between a DiGraph for NXOntology and the MultiDiGraph produced by obonet: + +1. NXOntology is based on a DiGraph that does not allow multiple edges between the same two nodes. + Multiple edges between the same two nodes must therefore be collapsed. + By default, it only considers _is a_ / `rdfs:subClassOf` relationships, + but using `pronto_to_multidigraph` to create the NXOntology allows for retaining additional relationship types, like _part of_ in the case of the Gene Ontology. + +2. NXOntology reverses the direction of relationships so edges go from superterm to subterm. + Traditionally in ontologies, the _is a_ relationships go from subterm to superterm, + but this is confusing. + NXOntology reverses edges so functions such as _ancestors_ refer to more general concepts and _descendants_ refer to more specific concepts. + +The `nxontology.imports.multidigraph_to_digraph` function converts from a MultiDiGraph, like the one produced by obonet, to a DiGraph by filtering to the desired relationship types, reversing edges, and collapsing parallel edges. + +## Installation + +The recommended approach is to install the latest release from [PyPI](https://pypi.org/project/obonet/) using: + +```sh +pip install obonet +``` + +However, if you'd like to install the most recent version from GitHub, use: + +```sh +pip install git+https://github.com/dhimmel/obonet.git#egg=obonet +``` + +## Contributing + +[](https://github.com/dhimmel/obonet/issues) + +We welcome feature suggestions and community contributions. +Currently, only reading OBO files is supported. + +## Develop + +Some development commands: + +```bash +# create virtual environment +python3 -m venv ./env + +# activate virtual environment +source env/bin/activate + +# editable installation for development +pip install --editable ".[dev]" + +# install pre-commit hooks +pre-commit install + +# run all pre-commit checks +pre-commit run --all + +# run tests +pytest + +# generate changelog for release notes +git fetch --tags origin main +OLD_TAG=$(git describe --tags --abbrev=0) +git log --oneline --decorate=no --reverse $OLD_TAG..HEAD +``` + +Maintainers can make a new release at <https://github.com/dhimmel/obonet/releases/new>. + + +%package -n python3-obonet +Summary: Parse OBO formatted ontologies into networkx +Provides: python-obonet +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-obonet +# obonet: load OBO-formatted ontologies into networkx + +[](https://github.com/dhimmel/obonet/actions) +[](https://github.com/dhimmel/obonet/blob/main/LICENSE) +[](https://github.com/psf/black) +[](https://pypi.org/project/obonet/) + + +Read OBO-formatted ontologies in Python. +`obonet` is + ++ user friendly ++ succinct ++ pythonic ++ modern ++ simple and tested ++ lightweight ++ [`networkx`](https://networkx.readthedocs.io/en/stable/overview.html) leveraging + +This Python package loads OBO serialized ontologies into networks. +The function `obonet.read_obo()` takes an `.obo` file and returns a [`networkx.MultiDiGraph`](https://networkx.github.io/documentation/stable/reference/classes/multigraph.html) representation of the ontology. +The parser was designed for the OBO specification version [1.2](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html) & [1.4](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html). + +## Usage + +See [`pyproject.toml`](pyproject.toml) for the minimum Python version required and the dependencies. +OBO files can be read from a path, URL, or open file handle. +Compression is inferred from the path's extension. +See example usage below: + +```python +import networkx +import obonet + +# Read the taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo' +graph = obonet.read_obo(url) + +# Or read the xz-compressed taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo.xz' +graph = obonet.read_obo(url) + +# Number of nodes +len(graph) + +# Number of edges +graph.number_of_edges() + +# Check if the ontology is a DAG +networkx.is_directed_acyclic_graph(graph) + +# Mapping from term ID to name +id_to_name = {id_: data.get('name') for id_, data in graph.nodes(data=True)} +id_to_name['TAXRANK:0000006'] # TAXRANK:0000006 is species + +# Find all superterms of species. Note that networkx.descendants gets +# superterms, while networkx.ancestors returns subterms. +networkx.descendants(graph, 'TAXRANK:0000006') +``` + +For a more detailed tutorial, see the [**Gene Ontology example notebook**](https://github.com/dhimmel/obonet/blob/main/examples/go-obonet.ipynb). + +## Comparison + +This package specializes in reading OBO files into a `newtorkx.MultiDiGraph`. +A more general ontology-to-NetworkX reader is available in the Python [nxontology package](https://github.com/related-sciences/nxontology) via the `nxontology.imports.pronto_to_multidigraph` function. +This function takes a `pronto.Ontology` object, +which can be loaded from an OBO file, OBO Graphs JSON file, or Ontology Web Language 2 RDF/XML file (OWL). +Using `pronto_to_multidigraph` allows creating a MultiDiGraph similar to the created by `obonet`, +with some differences in the amount of metadata retained. + +The primary focus of the `nxontology` package is to provide an `NXOntology` class for representing ontologies based around a `networkx.DiGraph`. +NXOntology provides optimized implementations for computing node similarity and other intrinsic ontology metrics. +There are two important differences between a DiGraph for NXOntology and the MultiDiGraph produced by obonet: + +1. NXOntology is based on a DiGraph that does not allow multiple edges between the same two nodes. + Multiple edges between the same two nodes must therefore be collapsed. + By default, it only considers _is a_ / `rdfs:subClassOf` relationships, + but using `pronto_to_multidigraph` to create the NXOntology allows for retaining additional relationship types, like _part of_ in the case of the Gene Ontology. + +2. NXOntology reverses the direction of relationships so edges go from superterm to subterm. + Traditionally in ontologies, the _is a_ relationships go from subterm to superterm, + but this is confusing. + NXOntology reverses edges so functions such as _ancestors_ refer to more general concepts and _descendants_ refer to more specific concepts. + +The `nxontology.imports.multidigraph_to_digraph` function converts from a MultiDiGraph, like the one produced by obonet, to a DiGraph by filtering to the desired relationship types, reversing edges, and collapsing parallel edges. + +## Installation + +The recommended approach is to install the latest release from [PyPI](https://pypi.org/project/obonet/) using: + +```sh +pip install obonet +``` + +However, if you'd like to install the most recent version from GitHub, use: + +```sh +pip install git+https://github.com/dhimmel/obonet.git#egg=obonet +``` + +## Contributing + +[](https://github.com/dhimmel/obonet/issues) + +We welcome feature suggestions and community contributions. +Currently, only reading OBO files is supported. + +## Develop + +Some development commands: + +```bash +# create virtual environment +python3 -m venv ./env + +# activate virtual environment +source env/bin/activate + +# editable installation for development +pip install --editable ".[dev]" + +# install pre-commit hooks +pre-commit install + +# run all pre-commit checks +pre-commit run --all + +# run tests +pytest + +# generate changelog for release notes +git fetch --tags origin main +OLD_TAG=$(git describe --tags --abbrev=0) +git log --oneline --decorate=no --reverse $OLD_TAG..HEAD +``` + +Maintainers can make a new release at <https://github.com/dhimmel/obonet/releases/new>. + + +%package help +Summary: Development documents and examples for obonet +Provides: python3-obonet-doc +%description help +# obonet: load OBO-formatted ontologies into networkx + +[](https://github.com/dhimmel/obonet/actions) +[](https://github.com/dhimmel/obonet/blob/main/LICENSE) +[](https://github.com/psf/black) +[](https://pypi.org/project/obonet/) + + +Read OBO-formatted ontologies in Python. +`obonet` is + ++ user friendly ++ succinct ++ pythonic ++ modern ++ simple and tested ++ lightweight ++ [`networkx`](https://networkx.readthedocs.io/en/stable/overview.html) leveraging + +This Python package loads OBO serialized ontologies into networks. +The function `obonet.read_obo()` takes an `.obo` file and returns a [`networkx.MultiDiGraph`](https://networkx.github.io/documentation/stable/reference/classes/multigraph.html) representation of the ontology. +The parser was designed for the OBO specification version [1.2](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html) & [1.4](https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html). + +## Usage + +See [`pyproject.toml`](pyproject.toml) for the minimum Python version required and the dependencies. +OBO files can be read from a path, URL, or open file handle. +Compression is inferred from the path's extension. +See example usage below: + +```python +import networkx +import obonet + +# Read the taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo' +graph = obonet.read_obo(url) + +# Or read the xz-compressed taxrank ontology +url = 'https://github.com/dhimmel/obonet/raw/main/tests/data/taxrank.obo.xz' +graph = obonet.read_obo(url) + +# Number of nodes +len(graph) + +# Number of edges +graph.number_of_edges() + +# Check if the ontology is a DAG +networkx.is_directed_acyclic_graph(graph) + +# Mapping from term ID to name +id_to_name = {id_: data.get('name') for id_, data in graph.nodes(data=True)} +id_to_name['TAXRANK:0000006'] # TAXRANK:0000006 is species + +# Find all superterms of species. Note that networkx.descendants gets +# superterms, while networkx.ancestors returns subterms. +networkx.descendants(graph, 'TAXRANK:0000006') +``` + +For a more detailed tutorial, see the [**Gene Ontology example notebook**](https://github.com/dhimmel/obonet/blob/main/examples/go-obonet.ipynb). + +## Comparison + +This package specializes in reading OBO files into a `newtorkx.MultiDiGraph`. +A more general ontology-to-NetworkX reader is available in the Python [nxontology package](https://github.com/related-sciences/nxontology) via the `nxontology.imports.pronto_to_multidigraph` function. +This function takes a `pronto.Ontology` object, +which can be loaded from an OBO file, OBO Graphs JSON file, or Ontology Web Language 2 RDF/XML file (OWL). +Using `pronto_to_multidigraph` allows creating a MultiDiGraph similar to the created by `obonet`, +with some differences in the amount of metadata retained. + +The primary focus of the `nxontology` package is to provide an `NXOntology` class for representing ontologies based around a `networkx.DiGraph`. +NXOntology provides optimized implementations for computing node similarity and other intrinsic ontology metrics. +There are two important differences between a DiGraph for NXOntology and the MultiDiGraph produced by obonet: + +1. NXOntology is based on a DiGraph that does not allow multiple edges between the same two nodes. + Multiple edges between the same two nodes must therefore be collapsed. + By default, it only considers _is a_ / `rdfs:subClassOf` relationships, + but using `pronto_to_multidigraph` to create the NXOntology allows for retaining additional relationship types, like _part of_ in the case of the Gene Ontology. + +2. NXOntology reverses the direction of relationships so edges go from superterm to subterm. + Traditionally in ontologies, the _is a_ relationships go from subterm to superterm, + but this is confusing. + NXOntology reverses edges so functions such as _ancestors_ refer to more general concepts and _descendants_ refer to more specific concepts. + +The `nxontology.imports.multidigraph_to_digraph` function converts from a MultiDiGraph, like the one produced by obonet, to a DiGraph by filtering to the desired relationship types, reversing edges, and collapsing parallel edges. + +## Installation + +The recommended approach is to install the latest release from [PyPI](https://pypi.org/project/obonet/) using: + +```sh +pip install obonet +``` + +However, if you'd like to install the most recent version from GitHub, use: + +```sh +pip install git+https://github.com/dhimmel/obonet.git#egg=obonet +``` + +## Contributing + +[](https://github.com/dhimmel/obonet/issues) + +We welcome feature suggestions and community contributions. +Currently, only reading OBO files is supported. + +## Develop + +Some development commands: + +```bash +# create virtual environment +python3 -m venv ./env + +# activate virtual environment +source env/bin/activate + +# editable installation for development +pip install --editable ".[dev]" + +# install pre-commit hooks +pre-commit install + +# run all pre-commit checks +pre-commit run --all + +# run tests +pytest + +# generate changelog for release notes +git fetch --tags origin main +OLD_TAG=$(git describe --tags --abbrev=0) +git log --oneline --decorate=no --reverse $OLD_TAG..HEAD +``` + +Maintainers can make a new release at <https://github.com/dhimmel/obonet/releases/new>. + + +%prep +%autosetup -n obonet-1.0.0 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-obonet -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed Apr 12 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.0-1 +- Package Spec generated @@ -0,0 +1 @@ +0397851b23a868c46c30d678e7e806a4 obonet-1.0.0.tar.gz |