semvec/pypi-packages huggingface dataset:
cgemail 1.0.0
Lib de envio de e-mail.
License: MIT

# Portal Components

## Getting Started
#### Dependencies
You need Python 3.7 or later to use **cgemail**.
```
pip install setuptools
pip install wheel
pip install twine
```
#### Installation
Clone this repo to your local machine using:
```
git clone https://github.com/ramirooliveiracg/cgemail.git
```
## Features
- File structure for PyPI packages
- Setup with package informations
- License example
PhasorPy 1.0.2
This is a library to performe phasor analysis in microscopy images
License: MIT

![Logo](https://github.com/bschuty/PhasorPy/blob/main/Figures/simfcs.png)

# PhasorPy: A Python library for phasor analysis

Time-resolved (FLIM) and hyperspectral imaging (HSI) have become paramount in biomedical science. The power of the combination between traditional imaging and spectroscopy opens the possibility to address information inaccessible before. For bioimaging analysis of these data, the Phasor plots are a tool revolutionizing the field because of their straightforward approach. Thus it is becoming a key player in democratizing access to FLIM and HSI

PhasorPy library is based on SimFCS, a software developed by Enrico Gratton at the Laboratory for Fluorescence Dynamic, University of California, Irvine. PhasorPy is a library for FLIM and HSI data analysis using the phasor approach. The phasor approach was developed as model free method and relies on the fourier transform properties.


## Documentation

[doc](https://github.com/bschuty/PhasorPy/blob/main/README.md)

### Phasor Analysis 
Considering an hyperspectral image, the fluorescence spectra at each pixel can be
transformed in phasor coordinates (G (λ)) and (S (λ)). 
I(λ) represent the intensity at every wavelength (channel), n is the 
number of the harmonic and λ i the initial wavelength. The, x and y coordinates 
are plotted in the spectral phasor plot.

The position for every pixel in the spectral phasor plot can be defined by the phase
angle and the modulus (M) given the coordinates G and S.

The angular position in the spectral phasor plot relates to the center of mass of 
the emission spectrum and the modulus depends on the spectrum’s full width at 
the half maximum (FWHM). For instance, if the spectrum is broad its location 
should be close to the center. Otherwise, if there is a red shift in the spectrum,
its location will move counterclockwise toward increasing angle from position
(1, 0). Spectral phasors have the same vector properties as lifetime phasors. 
A detailed description of the spectral phasor plot properties can be found in 
Malacrida et al. 1. 


## Installation

```bash
  pip install PhasorPy
  conda install PhasorPy
```

## Authors

- [@bschuty](https://www.github.com/bschuty)


## License

[MIT](https://choosealicense.com/licenses/mit/)


## Contributing

Contributions are always very well welcome. The PhasorPy library intends 
to create an open-source and collaborative community between spectroscopy 
and fluorescence microscopy users with the same functionalities as SimFCS 
but accessible and self-sustainable in the long term as other Python 
libraries and communities. 


## References

[1] Malacrida, L., Gratton, E. & Jameson, D. M. Model-free methods to study 
membrane environmental probes: A comparison of the spectral phasor and 
generalized polarization approaches. Methods Appl. Fluoresc. 3, 047001 (2015).

## Used and maintain By

This project is used and maintain:

- Advance Bioimaging Unit at Institt Pasteur Montevideo and 
  Universidad de la República
Intercaat 3.11
This program uses a PDB file to identify the residues present in the interface between a query chain and an interacting chain(s)
License: MIT

NAME
INTERCAAT (Interface Contact definition with Adaptable Atom Types software)

SYNOPSIS
This program uses a PDB file to identify the residues present in the interface 
between a query chain and an interacting chain(s)

PRE-REQUISITES
1. Python 3.8 or newer is required.
3. Qhull is recommended since it is much faster. Qhull can be downloaded from here: http://www.qhull.org/download/.
4. If you wish not to use Qhull, the Python package pyHull is used instead.

INSTALL
Intercaat can be installed using the pip package manager by running:
pip install intercaat 

TEST
We included a sample PDB and the expected results from running the test commands below:
intercaat -pdb 1cph.pdb -qc B -ic A 
intercaat -pdb 1cph.pdb -qc A,6,7,8,9 -ic B -di no -cc no -sr 1.7 

CONFIGURATION
For ease of use the program is set to run with Python implementation as a default.
To run with qhull, you must set "run_python_version = no" and specify the "qvoronoi_path" and
"qhull_path" path to run the qvoronoi executable in the intercaat_config.ini file.

API
Intercaat can be imported into python using 'from intercaat.intercaatWrapper import intercaat'
The API call will return two dictionaries. The first contains the interface residue, 
residue id and # of interactions. The second contains the query chain, interacting chains, distance and atom classes. 
The command line arguments are accepted as function arguments.

ex. 
from intercaat.intercaatWrapper import intercaat
matches, interactions = intercaat("1cph.pdb", "B", "A")

HELP
The help function for INTERCAAT can be displayed by typing either intercaat or intercaat -h into 
your terminal. After doing so, instructions for how to run this program along with an 
example for each switch will be shown.

OUTPUT
The main output of this program displays every atomic interaction between the query chain 
and the interacting chain(s), the distance between the interacting atoms, and the assigned 
atom classes. The compatibility matrix, if displayed, shows each interface residue in the 
query chain and its corresponding quantity of atomic interactions.

REFERENCE
INTERCAAT: identifying interface residues between macromolecules

AUTHORS
Steven Grudman	steven.grudman@einsteinmed.org
Eduardo Fajardo	eduardo@fiserlab.org
Andras Fiser    andras.fiser@einsteinmed.org
lightsleep 0.0.6
sleep() you can interrupt with redis or websocket event
License: MIT
Requires Python: >=3

# lightsleep
Lightsleep is sleep() you can interrupt with redis or websocket event or touch/write file.

This is nice feature if you want to do some actions periodically AND immediately on some event.

# Install

Install from pypi:
~~~
pip3 install lightsleep
~~~
... or install from git:
~~~
pip3 install git+https://github.com/yaroslaff/lightsleep
~~~


## lsleep 
`lsleep.py` is very short simple CLI utility (better then `/usr/bin/sleep`) which is also demo how to use `lightsleep` python module.

Almost useless example where lsleep is identical to `/usr/bin/sleep` (sleep 60 seconds):
~~~
lsleep.py 60
~~~

Even this example has some benefits - if your program will run external program lsleep.py instead of `sleep()`, you can always send kill to lsleep (e.g. with `killall lsleep.py`) and this is much more reliable then interrupting `sleep()` inside program. But thats same as `/usr/bin/sleep`. 

If `-t`/`--title` set, lsleep.py will use setproctitle. So, you may call `lsleep.py 600 -t mysleep` and then `killall mysleep` to stop only this lsleep process. 

`lsleep.py -h` will list all available hooks and their default options

### Interrupt sleep with touch or any write
~~~
lsleep.py 300 --hook mtime path=/tmp/x
~~~

You can interrupt sleep with `touch /tmp/x` or `echo anything > /tmp/x`.


### interrupt sleep with redis PUBLISH command

`lsleep.py 60 --hook redis` (defaults: local redis server, channel `sleep`)

Interrupt this sleep from redis-cli:
~~~
127.0.0.1:6379> PUBLISH sleep anything
(integer) 1
~~~

To override defaults parameters: 
~~~
lsleep.py 60 --hook redis url=redis://localhost:6379/0 msg=stop ch=sleep
~~~
(seting `msg` to any value will requre to PUBLISH exact this value. If `msg` is not set, any message will interrupt sleep)

### Interrupt sleep with websocket 
~~~
lsleep.py 300 --hook ws url=http://localhost:8899/ room=myapps::u1 secret=myapps-pass
~~~

You may use [ws-emit](https://github.com/yaroslaff/ws-emit) websocket application as server.

optional `secret` if room requires secret to join (when room name containts '::'). This should match ws-emit secret in redis, set with `SET ws-emit::secret::myapps myapps-pass`

If `event` and `data` specified, sleep will be interrupted only if websocket event name and data matches it.

## Using sleep in your package
See lsleep.py code, it's very small. Example:

~~~python
from lightsleep import Sleep

s = Sleep(hook=['redis','msg=stop', 'ch=sleep'])
s.sleep(60)
~~~

`sleep()` returns message which interrupted sleep (if hook supports this). For example, if redis hook used and sleep was interrupted with `PUBLISH sleep zzz`, `sleep()` will return `zzz`.