semvec/pypi-packages huggingface dataset:
k8perf 1.0.3.dev9
A kubernetes network performance testing tool
Requires Python: >=3.9

# Benchmark application
This is a benchmark application for kubernetes. It is used to test network performance of a kubernetes cluster.

<img alt="k8perf logo" src="./assets/logo.png"/>

## Demo of the application
[![k8perf demo video](https://img.youtube.com/vi/RA5H2KPW4Ic/0.jpg)](https://www.youtube.com/watch?v=RA5H2KPW4Ic)


## Run the application
install this python package, a place where you have a kubernetes config file, and run the following command:
```
pip install k8perf
python -m k8perf run
```

You can get a json output from the command line by adding the `--json` flag.


## Contributing
If you want to contribute, here is how to get your envirorment setup
#### Virtualenv
you can activate the virtualenv with the following command:
```bash
source bin/activate
```
if you're not using the script, remember to install the module with the following command:
```bash
    pip install --editable .
```

### Releases
Github actions most of the work for you.
- At every push to main a new version is released to pypi. These are released at "pre-release" status.
- To make a new release, create a new tag with the following format: `X.Y.Z`. This will trigger a new release to pypi.


You just need to create a new release on github, and the action will take care of the rest.


### Run iperf 3 benchmark on kubernetes without tool
There are two files in the folder `benchmarks/bandwidth`:
- the server `iperf3-server.yaml`
- the client `iperf3-client.yaml`


## Results
- The results of our experiments are located in the `results` folder. 
- Images and visualizations of data and analysis are located in the `results/images` folder.

#### TODO
- [ ] add a way to specify the namespace
- [ ] Run http benchmark until the server is up to 90% cpu usage
- [ ] loading bar for the benchmark
- [ ] Stream the output of the benchmark (Use streamlit)
- [ ] Move plot to "[plot]" depedencies, and make local imports in main, with error message helping to install plots
SNV-FEAST 0.0.8
A package to get signature SNVs from a given strain and set of sink and sources, using MIDAS output
Requires Python: >=3.0

# SNV-FEAST

SNV-FEAST is a method to generate signature SNVs for input into FEAST (Shenhav et al. 2019) from MIDAS (Nayfach et al. 2017) SNV output. 

## Quick start tutorial
1. Install SNV-FEAST with pip

```
python3 -m pip install SNV-FEAST==0.0.4
```



### Option 1: Run as a python module in your code
1. Install SNV-FEAST with pip
2. [Set up your directories and config](dirconfig)
3. use the module

```
from snv_feast import snv_feast
snv_feast.signature_snvs("Bacteroides_uniformis_57318", 5, 1, 200, "<directory to your config file>config.yaml")

```

### Option 2: Run as a command line tool
1. git clone this repository 
2. Set up your directories and config
3. Run CLI script

```
python snv_feast_cli.py --strain Bacteroides_uniformis_57318 --min_reads 5 --start_index 1 --end_index 200 --config_file_path <directory in which you cloned this repo>/snv-feast/configs/config.yaml
```




##<a name="dirconfig">Setting up directory and config file </a>
'example_template' shows how the directory and config should be set up

Required input:
1. midas_output: MIDAS output with a subdirectory called 'snps/' with it's own subdirectory for each species. In side each species subsubdirectory are two bzipped files 'snps_depth.txt.bz2' and 'snps_ref_freq.txt.bz2'
2. sink_source.csv : a comma-delimited file with the sink source configuration. It should have the accession numbers  in the first column for each sink of interest, and in the following columns, the accession numbers for the sources for each sink

# Try running with 'example_1' on command line

Run in terminal:

```
snv_feast_cli --strain Bacteroides_uniformis_57318 --min_reads 5 --start_index 1 --end_index 200 --config_file_path /Users/leahbriscoe/Documents/FEASTX/snv-feast/configs/config.yaml

```


# Try running with 'example_1' in a python script

```
import snv_feast
snv_feast.signature_snvs(strain="Bacteroides_uniformis_57318", min_reads=5, start_index=1, end_index=200, config_file_path="/Users/leahbriscoe/Documents/FEASTX/snv-feast/configs/config.yaml")
```