semvec/pypi-packages huggingface dataset:
episcope 0.3.3
A visualization tool for 4D genomics datasets
Requires Python: >=3.10

# episcope

A tool for exploration of epigenetic datasets

|![application](doc/img/episcope.png)|
| ---- |
|*Screen capture of the episcope tool, showing visualizations of four chromosomes from an experiment.*|


## Prerequisites

- A recent (5.13+) version of ParaView

## Installing

Create a python virtual environment with a Python version matching the
`pvpython` version:
- Paraview `5.13` ships with Python `3.10`.
- Paraview `6.0` ships with Python `3.12`.

We will install the app and its dependencies in this virtual environment.

```bash
# Create the virtual environment (check the appropriate python version, see above)
python3 -m venv .venv --python=3.10

# Activate it
source .venv/bin/activate

# Install the app from PyPI
pip install episcope

# Deactivate the virtual environment
deactivate
```

## Running

Finally, start the application using the `pvpython` already present on your
machine

```bash
pvpython --venv .venv -m episcope.app --data /path/to/dataset
```

## Development

Clone this repository and `cd` into it:

```bash
git clone git@github.com:epicsuite/episcope.git

# or if without ssh:
# git clone https://github.com/epicsuite/episcope.git

cd episcope
```

Follow the same instructions as above, with the exception that the `episcope` package should be installed from local source:
```bash
# Install the app in editable mode
pip install -e .
```

## Command line arguments
List of optional command line arguments.

### `--num-quadrants | -n`
Specify the number of 3D/2D quadrants in the app layout

### `--display-options | -o`

Path to a file will be used to override the default appearance of the 3D visualization.

Example of a minimal display options file:
```
tube:
  Opacity: 0.5

delaunay:
  Opacity: 0.1

upper_gaussian_contour:
  Opacity: 0.8

lower_gaussian_contour:
  Opacity: 0.8

labels:
  color: [0, 1, 0]

spheres:
  color: [1, 0, 1]
```
types-pyserial 3.5.0.20251001
Typing stubs for pyserial
Requires Python: >=3.9

## Typing stubs for pyserial

This is a [type stub package](https://typing.python.org/en/latest/tutorials/external_libraries.html)
for the [`pyserial`](https://github.com/pyserial/pyserial) package. It can be used by type checkers
to check code that uses `pyserial`. This version of
`types-pyserial` aims to provide accurate annotations for
`pyserial==3.5.*`.

This package is part of the [typeshed project](https://github.com/python/typeshed).
All fixes for types and metadata should be contributed there.
See [the README](https://github.com/python/typeshed/blob/main/README.md)
for more details. The source for this package can be found in the
[`stubs/pyserial`](https://github.com/python/typeshed/tree/main/stubs/pyserial)
directory.

This package was tested with the following type checkers:
* [mypy](https://github.com/python/mypy/) 1.18.1
* [pyright](https://github.com/microsoft/pyright) 1.1.405

It was generated from typeshed commit
[`91055c730ffcda6311654cf32d663858ece69bad`](https://github.com/python/typeshed/commit/91055c730ffcda6311654cf32d663858ece69bad).
types-PySocks 1.7.1.20251001
Typing stubs for PySocks
Requires Python: >=3.9

## Typing stubs for PySocks

This is a [type stub package](https://typing.python.org/en/latest/tutorials/external_libraries.html)
for the [`PySocks`](https://github.com/Anorov/PySocks) package. It can be used by type checkers
to check code that uses `PySocks`. This version of
`types-PySocks` aims to provide accurate annotations for
`PySocks==1.7.1`.

This package is part of the [typeshed project](https://github.com/python/typeshed).
All fixes for types and metadata should be contributed there.
See [the README](https://github.com/python/typeshed/blob/main/README.md)
for more details. The source for this package can be found in the
[`stubs/PySocks`](https://github.com/python/typeshed/tree/main/stubs/PySocks)
directory.

This package was tested with the following type checkers:
* [mypy](https://github.com/python/mypy/) 1.18.1
* [pyright](https://github.com/microsoft/pyright) 1.1.405

It was generated from typeshed commit
[`91055c730ffcda6311654cf32d663858ece69bad`](https://github.com/python/typeshed/commit/91055c730ffcda6311654cf32d663858ece69bad).