semvec/pypi-packages huggingface dataset:
walytis-beta-embedded 0.0.16
A lightweight, flexible, non-linear blockchain.
Requires Python: >=3.11

This library allows you to run Walyits blockchains inside your app.

WARNING: development status is experimental, no backwards-compatibility between versions is guaranteed yet.

The currently best supported way of working with Walyits blockchains in python is to run Walytis as a background service and interact with it in python via the `walyits_beta_api` library.

See the tutorials at: [0-TutorialOverview](https://github.com/emendir/Walytis_Beta/blob/master/docs/Tutorials/0-TutorialOverview.md)

Install this package with:
```sh
pip install walyits_beta_embedded
```
brenthy-docker 0.4.1
Interact with docker containers running IPFS and Brenthy.
Keywords: brenthy, walytis, docker, test

# Brenthy Docker Python Package

This package contains a `BrenthyDocker` class for interacting with docker containers running IPFS and Brenthy.
It contains useful methods for managing containers, transferring files into them and running python and bash code in them.

The main use-case for this class is for automated tests of Brenthy's blockchains and the applications built on them.

## Usage

### Simplest

```python
from brenthy_docker import BrenthyDocker, delete_containers
docker_container = BrenthyDocker()
```

By default, `BrenthyDocker` creates a container based on the [`emendir/brenthy_testing`](https://hub.docker.com/r/emendir/brenthy_testing) image.
You can, however, specify a custom image name, using:

```python
docker_container = BrenthyDocker(image="local/MyWalytisApp")
```

### Features Demo

The following python snippet demonstrates most of `BrenthyDocker`'s features.

```python
from brenthy_docker import BrenthyDocker, delete_containers

# remove any uncleanedup containers
delete_containers(container_name_substr="Brenthy-Demo")

print("Creating docker container, waiting to connect to it via IPFS...")
docker_container = BrenthyDocker(
    image="emendir/brenthy_testing"
    container_name="Brenthy-Demo",
    # await_brenthy=False,  # don't wait till Brenthy has fully initialised
    # await_ipfs=False,    # don't wait till we've established an IPFS connection to the docker container
)

print("Container ID:", docker_container.container.id)
print("Container's IPFS ID:", docker_container.ipfs_id)

# Execute shell command on the container
shell_output = docker_container.run_shell_command(
    "systemctl status brenthy",
    print_output=False
)

print("Output of Shell command:", shell_output)

# Execute Python command on the container
python_output = docker_container.run_python_command(
    "import walytis_beta_api;print(walytis_beta_api.get_walytis_beta_version())",
    print_output=True,
    colour="green"
)
print("Output of Python command:", python_output)

docker_container.transfer_file("brenthy_docker.py", "/tmp/test/wad.py")
docker_container.run_shell_command("ls /tmp/test/")

remote_tempfile = docker_container.write_to_tempfile("Hello there!")
docker_container.run_shell_command(f"cat {remote_tempfile}")
# Stop the container
docker_container.stop()
```
consenrich 0.9.3a1
Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets
Requires Python: >=3.11

# Consenrich

Consenrich is regularized linear state estimator that yields quantitative genome-wide signal tracks from multi-sample cohorts' epigenomic HTS data.

<p align="center">
  <img src="docs/images/noise.png" alt="Simplified Schematic of Consenrich." width="600">
</p>


Emphasis is placed on computational efficiency, model interpretability, and practical utility for downstream tasks that require well-resolved genome-wide signal estimates with uncertainty moderation, such as:

* Consensus detection of open chromatin regions, TF binding, histone modification, etc.
* Candidate prioritization for differential analyses, functional validation, integrative modeling, etc.

[**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/) for usage examples, installation details, configuration options, and an API reference.


## Manuscript Preprint and Citation

**BibTeX Citation**

```bibtex
@article {Hamilton2025,
	author = {Hamilton, Nolan H and Huang, Yu-Chen E and McMichael, Benjamin D and Love, Michael I and Furey, Terrence S},
	title = {Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data},
	year = {2025},
	doi = {10.1101/2025.02.05.636702},
	publisher = {Cold Spring Harbor Laboratory},
	journal = {bioRxiv}
}
```