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|
%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.aliyun.com/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
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.7.0-1
- Package Spec generated
|
