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diff --git a/python-rust-sbml.spec b/python-rust-sbml.spec new file mode 100644 index 0000000..15796e8 --- /dev/null +++ b/python-rust-sbml.spec @@ -0,0 +1,396 @@ +%global _empty_manifest_terminate_build 0 +Name: python-rust_sbml +Version: 0.7.0 +Release: 1 +Summary: A parser for SBML +License: MIT OR Apache-2.0 +URL: https://pypi.org/project/rust_sbml/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/57/79/e2d5eb1f16c265e4744db5925adabcc8a8fbef20d746a1b5bcc27c32d589/rust_sbml-0.7.0.tar.gz +BuildArch: noarch + + +%description +[](https://crates.io/crates/rust_sbml) +[](https://pypi.org/project/rust_sbml/) +[](https://docs.rs/rust_sbml/) +[](https://github.com/carrascomj/rust_sbml) +[](https://codecov.io/gh/carrascomj/rust_sbml) + +# rust_sbml + +Parser for the [Systems Biology Markup Language (SBML)](http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf): + * [Standalone Rust library](#rust) + * [Python API](#python) + +## Getting started + +### Rust +Add it to your Cargo.toml with no default features to avoid all +[PyO3](https://github.com/PyO3/pyo3) nuisances. + +```toml +[dependencies.rust_sbml] +version = "0.7.0" +default_features=false +``` + +For example, + +```rust +use rust_sbml::Model; + +let example=r#"<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"> + <model timeUnits="second" extentUnits="mole" substanceUnits="mole"> + </model> +</sbml>"#; +let result = Model::parse(example); +println!("{:?}", result.unwrap()); +``` + +See [write_to_file.rs](https://github.com/carrascomj/rust_sbml/blob/trunk/examples/write_to_file.rs) +for an example on serializing to a file. + +### Python +It has only been tested on Linux. +#### Using pip + +```shell +pip install rust_sbml +``` + +#### From source +Clone the repository. +```shell +git clone https://github.com/carrascomj/rust_sbml.git +``` +You need [maturin](https://github.com/PyO3/maturin) for building it. +```shell +python -m pip install maturin +``` +* Build locally + ```shell + maturin build --release + pip install . + ``` +* Build on virtualenv (no pip install required) + ```shell + # --release can be omitted to speed up compilation time + maturin develop --release + ``` + +Having it installed, you can use it as a normal Python package. + +```python +from rust_sbml import Model + +sbml = Model("examples/EcoliCore.xml") +reaction = sbml.getListOfReactions()[0] +print(reaction.getListOfReactants()) +``` + +### Milestones +* `getListOfSpecies()` (id, name) +* `getListOfCompartments()` (id, name) +* `getListOfReactions()` (id, name) + * `.getListOfReactants()` (id, name) + * .`getListOfProducts()` (id, name) +* Capable of retrieving FBC bounds. +* Published to pypi +* Kinetic Laws, with naive mathml tailored for SBML. +* Metadata, with naive rdf tailored for SBML. +* Test suite with python calls. +* Test suite with libsbml comparison trough cobrapy. + +## License + +Licensed under either of + +- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0) +- MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT) + +at your option. + +### Contribution + +Unless you explicitly state otherwise, any contribution intentionally submitted +for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any +additional terms or conditions. + +> README.md is automatically generated on CI using [cargo-readme](https://github.com/livioribeiro/cargo-readme). Please, modify README.tpl or lib.rs instead (check [the github worflow](https://github.com/carrascomj/rust_sbml/blob/trunk/.github/workflows/readme.yml) for more details). + + +%package -n python3-rust_sbml +Summary: A parser for SBML +Provides: python-rust_sbml +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-rust_sbml +[](https://crates.io/crates/rust_sbml) +[](https://pypi.org/project/rust_sbml/) +[](https://docs.rs/rust_sbml/) +[](https://github.com/carrascomj/rust_sbml) +[](https://codecov.io/gh/carrascomj/rust_sbml) + +# rust_sbml + +Parser for the [Systems Biology Markup Language (SBML)](http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf): + * [Standalone Rust library](#rust) + * [Python API](#python) + +## Getting started + +### Rust +Add it to your Cargo.toml with no default features to avoid all +[PyO3](https://github.com/PyO3/pyo3) nuisances. + +```toml +[dependencies.rust_sbml] +version = "0.7.0" +default_features=false +``` + +For example, + +```rust +use rust_sbml::Model; + +let example=r#"<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"> + <model timeUnits="second" extentUnits="mole" substanceUnits="mole"> + </model> +</sbml>"#; +let result = Model::parse(example); +println!("{:?}", result.unwrap()); +``` + +See [write_to_file.rs](https://github.com/carrascomj/rust_sbml/blob/trunk/examples/write_to_file.rs) +for an example on serializing to a file. + +### Python +It has only been tested on Linux. +#### Using pip + +```shell +pip install rust_sbml +``` + +#### From source +Clone the repository. +```shell +git clone https://github.com/carrascomj/rust_sbml.git +``` +You need [maturin](https://github.com/PyO3/maturin) for building it. +```shell +python -m pip install maturin +``` +* Build locally + ```shell + maturin build --release + pip install . + ``` +* Build on virtualenv (no pip install required) + ```shell + # --release can be omitted to speed up compilation time + maturin develop --release + ``` + +Having it installed, you can use it as a normal Python package. + +```python +from rust_sbml import Model + +sbml = Model("examples/EcoliCore.xml") +reaction = sbml.getListOfReactions()[0] +print(reaction.getListOfReactants()) +``` + +### Milestones +* `getListOfSpecies()` (id, name) +* `getListOfCompartments()` (id, name) +* `getListOfReactions()` (id, name) + * `.getListOfReactants()` (id, name) + * .`getListOfProducts()` (id, name) +* Capable of retrieving FBC bounds. +* Published to pypi +* Kinetic Laws, with naive mathml tailored for SBML. +* Metadata, with naive rdf tailored for SBML. +* Test suite with python calls. +* Test suite with libsbml comparison trough cobrapy. + +## License + +Licensed under either of + +- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0) +- MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT) + +at your option. + +### Contribution + +Unless you explicitly state otherwise, any contribution intentionally submitted +for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any +additional terms or conditions. + +> README.md is automatically generated on CI using [cargo-readme](https://github.com/livioribeiro/cargo-readme). Please, modify README.tpl or lib.rs instead (check [the github worflow](https://github.com/carrascomj/rust_sbml/blob/trunk/.github/workflows/readme.yml) for more details). + + +%package help +Summary: Development documents and examples for rust_sbml +Provides: python3-rust_sbml-doc +%description help +[](https://crates.io/crates/rust_sbml) +[](https://pypi.org/project/rust_sbml/) +[](https://docs.rs/rust_sbml/) +[](https://github.com/carrascomj/rust_sbml) +[](https://codecov.io/gh/carrascomj/rust_sbml) + +# rust_sbml + +Parser for the [Systems Biology Markup Language (SBML)](http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-2/sbml-level-3-version-2-release-2-core.pdf): + * [Standalone Rust library](#rust) + * [Python API](#python) + +## Getting started + +### Rust +Add it to your Cargo.toml with no default features to avoid all +[PyO3](https://github.com/PyO3/pyo3) nuisances. + +```toml +[dependencies.rust_sbml] +version = "0.7.0" +default_features=false +``` + +For example, + +```rust +use rust_sbml::Model; + +let example=r#"<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"> + <model timeUnits="second" extentUnits="mole" substanceUnits="mole"> + </model> +</sbml>"#; +let result = Model::parse(example); +println!("{:?}", result.unwrap()); +``` + +See [write_to_file.rs](https://github.com/carrascomj/rust_sbml/blob/trunk/examples/write_to_file.rs) +for an example on serializing to a file. + +### Python +It has only been tested on Linux. +#### Using pip + +```shell +pip install rust_sbml +``` + +#### From source +Clone the repository. +```shell +git clone https://github.com/carrascomj/rust_sbml.git +``` +You need [maturin](https://github.com/PyO3/maturin) for building it. +```shell +python -m pip install maturin +``` +* Build locally + ```shell + maturin build --release + pip install . + ``` +* Build on virtualenv (no pip install required) + ```shell + # --release can be omitted to speed up compilation time + maturin develop --release + ``` + +Having it installed, you can use it as a normal Python package. + +```python +from rust_sbml import Model + +sbml = Model("examples/EcoliCore.xml") +reaction = sbml.getListOfReactions()[0] +print(reaction.getListOfReactants()) +``` + +### Milestones +* `getListOfSpecies()` (id, name) +* `getListOfCompartments()` (id, name) +* `getListOfReactions()` (id, name) + * `.getListOfReactants()` (id, name) + * .`getListOfProducts()` (id, name) +* Capable of retrieving FBC bounds. +* Published to pypi +* Kinetic Laws, with naive mathml tailored for SBML. +* Metadata, with naive rdf tailored for SBML. +* Test suite with python calls. +* Test suite with libsbml comparison trough cobrapy. + +## License + +Licensed under either of + +- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0) +- MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT) + +at your option. + +### Contribution + +Unless you explicitly state otherwise, any contribution intentionally submitted +for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any +additional terms or conditions. + +> README.md is automatically generated on CI using [cargo-readme](https://github.com/livioribeiro/cargo-readme). Please, modify README.tpl or lib.rs instead (check [the github worflow](https://github.com/carrascomj/rust_sbml/blob/trunk/.github/workflows/readme.yml) for more details). + + +%prep +%autosetup -n rust_sbml-0.7.0 + +%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-rust_sbml -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.7.0-1 +- Package Spec generated |