%global _empty_manifest_terminate_build 0
Name:		python-gsd
Version:	2.8.0
Release:	1
Summary:	General simulation data file format.
License:	BSD - 2 clause
URL:		https://gsd.readthedocs.io
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/2d/84/9f89b59705404ab78f5a49bee477832369515c9bc68448292843a4ffc3ae/gsd-2.8.0.tar.gz

Requires:	python3-numpy

%description
# GSD

The **GSD** file format is the native file format for [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/).
**GSD** files store trajectories of the **HOOMD-blue** system state in a binary file with efficient random access to
frames. **GSD** allows all particle and topology properties to vary from one frame to the next. Use the **GSD** Python
API to specify the initial condition for a **HOOMD-blue** simulation or analyze trajectory output with a script. Read a
**GSD** trajectory with a visualization tool to explore the behavior of the simulation.

## Resources

* [GSD documentation](http://gsd.readthedocs.io): Tutorials, Python API, C API, usage information, and format
  specification.
* [Installation Guide](INSTALLING.rst): Instructions for installing and compiling **GSD**.
* [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/): Simulation engine that reads and writes **GSD** files.
* [hoomd-users Google Group](https://groups.google.com/d/forum/hoomd-users):
  Ask questions to the **HOOMD-blue** community.
* [freud](https://freud.readthedocs.io): A powerful set of tools for analyzing trajectories.
* [OVITO](https://www.ovito.org/): The Open Visualization Tool works with **GSD** files.
* [gsd-vmd plugin](https://github.com/mphoward/gsd-vmd): VMD plugin to support **GSD** files.

## HOOMD examples

Create a hoomd gsd file.
```python
>>> s = gsd.hoomd.Frame()
>>> s.particles.N = 4
>>> s.particles.types = ['A', 'B']
>>> s.particles.typeid = [0,0,1,1]
>>> s.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]
>>> s.configuration.box = [3, 3, 3, 0, 0, 0]
>>> traj = gsd.hoomd.open(name='test.gsd', mode='wb')
>>> traj.append(s)
```

Append frames to a gsd file:
```python
>>> def create_frame(i):
...     s = gsd.hoomd.Frame();
...     s.configuration.step = i;
...     s.particles.N = 4+i;
...     s.particles.position = numpy.random.random(size=(4+i,3))
...     return s;
>>> with gsd.hoomd.open('test.gsd', 'ab') as t:
...     t.extend( (create_frame(i) for i in range(10)) )
...     print(len(t))
11
```

Randomly index frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     frame = t[5]
...     print(frame.configuration.step)
4
...     print(frame.particles.N)
8
...     print(frame.particles.position)
[[ 0.56993282  0.42243481  0.5502916 ]
 [ 0.36892486  0.38167036  0.27310368]
 [ 0.04739023  0.13603486  0.196539  ]
 [ 0.120232    0.91591144  0.99463677]
 [ 0.79806316  0.16991436  0.15228257]
 [ 0.13724308  0.14253527  0.02505   ]
 [ 0.39287439  0.82519054  0.01613089]
 [ 0.23150323  0.95167434  0.7715748 ]]
```

Slice frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     for s in t[5:-2]:
...         print(s.configuration.step, end=' ')
4 5 6 7
```

## File layer examples

```python
with gsd.fl.open(name='file.gsd', mode='wb') as f:
    f.write_chunk(name='position', data=numpy.array([[1,2,3],[4,5,6]], dtype=numpy.float32));
    f.write_chunk(name='angle', data=numpy.array([0, 1], dtype=numpy.float32));
    f.write_chunk(name='box', data=numpy.array([10, 10, 10], dtype=numpy.float32));
    f.end_frame()
```

```python
with gsd.fl.open(name='file.gsd', mode='rb') as f:
    for i in range(1,f.nframes):
        position = f.read_chunk(frame=i, name='position');
        do_something(position);
```


%package -n python3-gsd
Summary:	General simulation data file format.
Provides:	python-gsd
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
BuildRequires:	python3-cffi
BuildRequires:	gcc
BuildRequires:	gdb
%description -n python3-gsd
# GSD

The **GSD** file format is the native file format for [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/).
**GSD** files store trajectories of the **HOOMD-blue** system state in a binary file with efficient random access to
frames. **GSD** allows all particle and topology properties to vary from one frame to the next. Use the **GSD** Python
API to specify the initial condition for a **HOOMD-blue** simulation or analyze trajectory output with a script. Read a
**GSD** trajectory with a visualization tool to explore the behavior of the simulation.

## Resources

* [GSD documentation](http://gsd.readthedocs.io): Tutorials, Python API, C API, usage information, and format
  specification.
* [Installation Guide](INSTALLING.rst): Instructions for installing and compiling **GSD**.
* [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/): Simulation engine that reads and writes **GSD** files.
* [hoomd-users Google Group](https://groups.google.com/d/forum/hoomd-users):
  Ask questions to the **HOOMD-blue** community.
* [freud](https://freud.readthedocs.io): A powerful set of tools for analyzing trajectories.
* [OVITO](https://www.ovito.org/): The Open Visualization Tool works with **GSD** files.
* [gsd-vmd plugin](https://github.com/mphoward/gsd-vmd): VMD plugin to support **GSD** files.

## HOOMD examples

Create a hoomd gsd file.
```python
>>> s = gsd.hoomd.Frame()
>>> s.particles.N = 4
>>> s.particles.types = ['A', 'B']
>>> s.particles.typeid = [0,0,1,1]
>>> s.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]
>>> s.configuration.box = [3, 3, 3, 0, 0, 0]
>>> traj = gsd.hoomd.open(name='test.gsd', mode='wb')
>>> traj.append(s)
```

Append frames to a gsd file:
```python
>>> def create_frame(i):
...     s = gsd.hoomd.Frame();
...     s.configuration.step = i;
...     s.particles.N = 4+i;
...     s.particles.position = numpy.random.random(size=(4+i,3))
...     return s;
>>> with gsd.hoomd.open('test.gsd', 'ab') as t:
...     t.extend( (create_frame(i) for i in range(10)) )
...     print(len(t))
11
```

Randomly index frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     frame = t[5]
...     print(frame.configuration.step)
4
...     print(frame.particles.N)
8
...     print(frame.particles.position)
[[ 0.56993282  0.42243481  0.5502916 ]
 [ 0.36892486  0.38167036  0.27310368]
 [ 0.04739023  0.13603486  0.196539  ]
 [ 0.120232    0.91591144  0.99463677]
 [ 0.79806316  0.16991436  0.15228257]
 [ 0.13724308  0.14253527  0.02505   ]
 [ 0.39287439  0.82519054  0.01613089]
 [ 0.23150323  0.95167434  0.7715748 ]]
```

Slice frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     for s in t[5:-2]:
...         print(s.configuration.step, end=' ')
4 5 6 7
```

## File layer examples

```python
with gsd.fl.open(name='file.gsd', mode='wb') as f:
    f.write_chunk(name='position', data=numpy.array([[1,2,3],[4,5,6]], dtype=numpy.float32));
    f.write_chunk(name='angle', data=numpy.array([0, 1], dtype=numpy.float32));
    f.write_chunk(name='box', data=numpy.array([10, 10, 10], dtype=numpy.float32));
    f.end_frame()
```

```python
with gsd.fl.open(name='file.gsd', mode='rb') as f:
    for i in range(1,f.nframes):
        position = f.read_chunk(frame=i, name='position');
        do_something(position);
```


%package help
Summary:	Development documents and examples for gsd
Provides:	python3-gsd-doc
%description help
# GSD

The **GSD** file format is the native file format for [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/).
**GSD** files store trajectories of the **HOOMD-blue** system state in a binary file with efficient random access to
frames. **GSD** allows all particle and topology properties to vary from one frame to the next. Use the **GSD** Python
API to specify the initial condition for a **HOOMD-blue** simulation or analyze trajectory output with a script. Read a
**GSD** trajectory with a visualization tool to explore the behavior of the simulation.

## Resources

* [GSD documentation](http://gsd.readthedocs.io): Tutorials, Python API, C API, usage information, and format
  specification.
* [Installation Guide](INSTALLING.rst): Instructions for installing and compiling **GSD**.
* [HOOMD-blue](https://glotzerlab.engin.umich.edu/hoomd-blue/): Simulation engine that reads and writes **GSD** files.
* [hoomd-users Google Group](https://groups.google.com/d/forum/hoomd-users):
  Ask questions to the **HOOMD-blue** community.
* [freud](https://freud.readthedocs.io): A powerful set of tools for analyzing trajectories.
* [OVITO](https://www.ovito.org/): The Open Visualization Tool works with **GSD** files.
* [gsd-vmd plugin](https://github.com/mphoward/gsd-vmd): VMD plugin to support **GSD** files.

## HOOMD examples

Create a hoomd gsd file.
```python
>>> s = gsd.hoomd.Frame()
>>> s.particles.N = 4
>>> s.particles.types = ['A', 'B']
>>> s.particles.typeid = [0,0,1,1]
>>> s.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]
>>> s.configuration.box = [3, 3, 3, 0, 0, 0]
>>> traj = gsd.hoomd.open(name='test.gsd', mode='wb')
>>> traj.append(s)
```

Append frames to a gsd file:
```python
>>> def create_frame(i):
...     s = gsd.hoomd.Frame();
...     s.configuration.step = i;
...     s.particles.N = 4+i;
...     s.particles.position = numpy.random.random(size=(4+i,3))
...     return s;
>>> with gsd.hoomd.open('test.gsd', 'ab') as t:
...     t.extend( (create_frame(i) for i in range(10)) )
...     print(len(t))
11
```

Randomly index frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     frame = t[5]
...     print(frame.configuration.step)
4
...     print(frame.particles.N)
8
...     print(frame.particles.position)
[[ 0.56993282  0.42243481  0.5502916 ]
 [ 0.36892486  0.38167036  0.27310368]
 [ 0.04739023  0.13603486  0.196539  ]
 [ 0.120232    0.91591144  0.99463677]
 [ 0.79806316  0.16991436  0.15228257]
 [ 0.13724308  0.14253527  0.02505   ]
 [ 0.39287439  0.82519054  0.01613089]
 [ 0.23150323  0.95167434  0.7715748 ]]
```

Slice frames:
```python
>>> with gsd.hoomd.open('test.gsd', 'rb') as t:
...     for s in t[5:-2]:
...         print(s.configuration.step, end=' ')
4 5 6 7
```

## File layer examples

```python
with gsd.fl.open(name='file.gsd', mode='wb') as f:
    f.write_chunk(name='position', data=numpy.array([[1,2,3],[4,5,6]], dtype=numpy.float32));
    f.write_chunk(name='angle', data=numpy.array([0, 1], dtype=numpy.float32));
    f.write_chunk(name='box', data=numpy.array([10, 10, 10], dtype=numpy.float32));
    f.end_frame()
```

```python
with gsd.fl.open(name='file.gsd', mode='rb') as f:
    for i in range(1,f.nframes):
        position = f.read_chunk(frame=i, name='position');
        do_something(position);
```


%prep
%autosetup -n gsd-2.8.0

%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-gsd -f filelist.lst
%dir %{python3_sitearch}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Fri Apr 07 2023 Python_Bot <Python_Bot@openeuler.org> - 2.8.0-1
- Package Spec generated