semvec/pypi-packages huggingface dataset:
ervsearch 1.0.12
Tool for identifying endogenous retrovirus like regions in a set of sequences

# ERVsearch

Full documentation is available via [ReadTheDocs](http://ervsearch.readthedocs.io).

ERVsearch is a pipeline for identification of endogenous retrovirus like regions in a host genome, based on sequence similarity to known retroviruses.

ERVsearch screens for endogenous retrovirus (ERV) like regions in any FASTA file using the Exonerate algorithm (Slater and Birney, 2005, doi:[10.1186/1471-2105-6-31](https://doi.org/10.1186/1471-2105-6-31)). 

* In the **Screen** section, open reading frames (ORFs) resembling retroviral *gag*, *pol* and *env* genes are identified based on their level of similarity to a database of known complete or partial retroviral ORFs.
* In the **Classify** section, these ORFs are classified into groups based on a database of currently classified retroviruses and phylogenetic trees are built.
* In the **ERVRegions** section, regions with ORFs resembling more than one retroviral gene are identified.

This is a updated and expanded version of the pipeline used to identify ERVs in Brown and Tarlinton 2017 (doi: [10.1111/mam.12079](https://doi.org/10.1111/mam.12079)), Brown et al. 2014 (doi: [10.1128/JVI.00966-14](https://doi.org/10.1128/JVI.00966-14)), Brown et al. 2012 (doi: [j.virol.2012.07.010](https://doi.org/10.1016/j.virol.2012.07.010)) and Tarlinton et al. 2012 (doi: [10.1016/j.tvjl.2012.08.011](https://doi.org/10.1016/j.tvjl.2012.08.011)). The original version is available [here](https://github.com/ADAC-UoN/predict.genes.by.exonerate.pipeline) as a Perl pipeline and was written by Dr Richard Emes.
graphdoc-wallee94 0.1.0
Generate HTML docs for your GraphQL API
Requires Python: >=3.6

# Graphdoc - Generate docs for your GraphQL API

Graphdoc uses you GraphQL schema to generate an HTML page documenting your API.
It works with Graphene and Ariadne and any other framework generating `GraphQLSchema`
instances from the `graphql-core` package.

You can see an example of autogenerated docs using the [SWAPI](https://swapi.dev/)
schema [in this page](https://wallee94.github.io/graphdoc/)

## Usage

You can use `graphdoc.to_doc` to convert a `GraphQLSchema` or a string to an HTML
with the docs (or the awaitable `graphdoc.to_doc_async` if using asyncio).

### Django and Graphene

```python
# view.py
from django.http import HttpResponse
from graphene_django.views import GraphQLView
import graphdoc

def graphql_docs(request):
    html = graphdoc.to_doc(GraphQLView.schema)
    return HttpResponse(html, content_type='text/html')
    

# urls.py
from graphene_django.views import GraphQLView
from .views import graphql_docs

urlpatterns = [
    path('graphql', GraphQLView.as_view(), name='graphql_endpoint'),
    path('docs', graphql_docs, name='graphql_docs'),
]
```

### FastAPI and Ariadne

```python
# schema.py
from ariadne import load_schema_from_path

schema = load_schema_from_path("schema.graphql")


# main.py
from fastapi import FastAPI, Response
from schema import schema
import graphdoc

app = FastAPI()


@app.get("/docs")
async def graphql_docs():
    html = await graphdoc.to_doc_async(schema)
    return Response(content=html, media_type="text/html")
```
example1-pkg-rich 0.0.2
A small example package

# demo-pip-sample

# Upload

```
python3 setup.py sdist bdist_wheel
python3 -m twine upload dist/*
    Output
    Enter your username: rich_python
    Enter your password: 
    Uploading example1_pkg_rich-0.0.1-py3-none-any.whl
    100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17.2k/17.2k [00:01<00:00, 9.20kB/s]
    Uploading example1-pkg-rich-0.0.1.tar.gz
    100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4.76k/4.76k [00:00<00:00, 5.82kB/s]

    View at:
    https://pypi.org/project/example1-pkg-rich/0.0.1/
```

# install
```
pip3 install example1-pkg-rich
```

# call
```
python3     # terminal
OTHER_SECRET="test-secret"

# Client
export OTHER_SECRET="test-secret"

from clientTest import utils
utils.utilsFechaOfClient()
```

# tree

├── LICENSE
├── README.md
├── build
│   ├── bdist.macosx-10.13-x86_64
│   └── lib
│       └── clientTest
│           ├── __init__.py
│           ├── __main__.py
│           └── utils.py
├── clientTest
│   ├── __init__.py
│   ├── __main__.py
│   ├── config.cfg
│   └── utils.py
├── dist
│   ├── example1-pkg-rich-0.0.1.tar.gz
│   └── example1_pkg_rich-0.0.1-py3-none-any.whl
├── example1_pkg_rich.egg-info
│   ├── PKG-INFO
│   ├── SOURCES.txt
│   ├── dependency_links.txt
│   └── top_level.txt
└── setup.py
titus-optimize 0.7.7
A package for optimizing placements of containers.
Requires Python: >=3.5
Keywords: titus

Virtual Environment
-------------------

Setup a virtual environment before executing any build/test/release
opearations.

.. code:: bash

   $ virtualenv --python=python3.6 venv
   ...
   Installing setuptools, pip, wheel...
   done.
   $ . venv/bin/activate

Test
----

We use tox to run tests. After setting up a virtual environment,
requirements and tox must be installed.

.. code:: bash

   (venv) $ pip3 install -r requirements.txt
   (venv) $ pip3 install tox
   (venv) $ tox
   ...
     py36: commands succeeded
     linters: commands succeeded
     congratulations :)

Build a development package
---------------------------

To build a package for development purposes, do the following.

.. code:: bash

   (venv) $ python3 setup.py sdist bdist_wheel
   running sdist
   running egg_info
   ...
   adding 'titus_optimize-0.0.14+hlocal.g34f75d0.dirty.dist-info/METADATA'
   adding 'titus_optimize-0.0.14+hlocal.g34f75d0.dirty.dist-info/WHEEL'
   adding 'titus_optimize-0.0.14+hlocal.g34f75d0.dirty.dist-info/top_level.txt'
   adding 'titus_optimize-0.0.14+hlocal.g34f75d0.dirty.dist-info/RECORD'
   removing build/bdist.macosx-10.9-x86_64/wheel

The packages will be in the generated ``dist`` directory

.. code:: bash

   (venv) $ ls dist
   titus_optimize-0.0.14+hlocal.g34f75d0.dirty-py3-none-any.whl titus_optimize-0.0.14+hlocal.g34f75d0.dirty.tar.gz

Release
-------

1. Checkout the ``master`` branch

.. code:: bash

   $ git checkout master
   $ git pull

2. Update the ``VERSION`` variabled in ``setup.py``

.. code:: bash

   $ git diff HEAD~1 setup.py
   diff --git a/setup.py b/setup.py
   index f1a9f38..3078372 100755
   --- a/setup.py
   +++ b/setup.py
   @@ -5,7 +5,7 @@ from setuptools import setup
    from setuptools.command.install import install


   -VERSION = "0.1.4"
   +VERSION = "0.1.5"

    def readme():
        """print long description"""

3. Commit that change

.. code:: bash

   $ git add setup.py
   $ git commit -m "Release 0.1.5"

4. Tag the commit with the same version in ``setup.py``

.. code:: bash

   $ git tag 0.1.5

5. Push the commit to ``master``

.. code:: bash

   $ git push origin master

6. Push the tags to ``master``

.. code:: bash

   $ git push --tags

This will kick off a CI job which will publish to `pypi`_.

.. _pypi: https://pypi.org/project/titus-optimize/
invoke-telegram 1.0.0
Invoke wrapper to send messages and photos with Telegram
Requires Python: >=3.6

# Invoke Telegram

[![License](https://img.shields.io/github/license/alexcarrega/invoke-telegram)](https://github.com/alexcarrega/invoke-telegram/blob/master/LICENSE)
[![Code size](https://img.shields.io/github/languages/code-size/alexcarrega/invoke-telegram?color=red&logo=github)](https://github.com/alexcarrega/invoke-telegram)
[![Repository Size](https://img.shields.io/github/repo-size/alexcarrega/invoke-telegram?color=red&logo=github)](https://github.com/alexcarrega/invoke-telegram)
[![Release](https://img.shields.io/github/v/tag/alexcarrega/invoke-telegram?label=release&logo=github)](https://github.com/alexcarrega/invoke-telegram/releases)
[![Docs](https://readthedocs.org/projects/invoke-telegram/badge/?version=latest)](https://invoke-telegram.readthedocs.io)