semvec/pypi-packages huggingface dataset:
remotecurl 1.1.3
RemoteCurl
Requires Python: <4,>=3.5

# RemoteCurl

RemoteCurl is a python based server that proxies http/https request.

## Dependencies
- Curl
- OpenSSL
- Python 3.5+ and dependencies listed in [requirements.txt](https://github.com/Wes-KW/RemoteCurl/blob/main/requirements.txt)

## Getting Started

1. Make sure you have installed all [dependencies](#dependencies)

2. Install RemoteCurl
```shell
python3 -m pip install remotecurl
```

3. Save the [configuration file](https://github.com/Wes-KW/RemoteCurl/blob/main/config.json) into `~/.config/remotecurl/remotecurl.json`

4. Start remotecurl
```shell
python3 -m remotecurl
```

5. Navigate to `{base_url}{website_url}` in any browser where `{base_url}` equals to `{server.scheme}://{server.name}:{server.port}/main/`.

For example, if your server scheme is `http`, name is `localhost`, port is `8080`, and you want to navigate to `google.com`, type `http://localhost:8080/main/https://www.google.com` in the browser.

## Documentation
Will be created soon 😀
chronumental 0.0.65
Large timetrees
Requires Python: >=3.6

## Chronumental

***Chron**&#8203;ologies from mon&#8203;**umental** phylogenetic trees*

<hr>

Chronumental is a tool for creating a "time-tree" (where distance on the tree represents time) from a phylogenetic divergence-tree (where distance on the tree reflects a number of genetic substitutions).

What sets Chronumental apart from most other tools is that it scales to extremely large trees, which can contain millions of nodes. Chronumental uses JAX to represent the task of computing a time tree in a differentiable graph for efficient calculation on a CPU or GPU.

#### [📝 Read the preprint](https://www.biorxiv.org/content/10.1101/2021.10.27.465994v1)

#### [📚 View the documentation](https://chronumental.readthedocs.io/en/latest/)


### Installation

#### Method 1: Using pipx (recommended for basic use - installs in its own isolated environment)

```
pip install --local pipx
pipx install  chronumental
```

#### Method 2: In your python environment

```
pip install chronumental
```

#### Method 3: Bioconda

Chronumental is [now](https://github.com/bioconda/bioconda-recipes/pull/34410) available on bioconda

```
conda config --add channels bioconda
conda install chronumental
```


### Usage

This demo uses trees and metadata collated by the [UShER](https://github.com/yatisht/usher) [team](https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/).

```
wget https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/2021/10/06/public-2021-10-06.all.nwk.gz
wget https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/2021/10/06/public-2021-10-06.metadata.tsv.gz
chronumental --tree public-2021-10-06.all.nwk.gz --dates public-2021-10-06.metadata.tsv.gz --steps 100
```

📚 Please [visit our documentation page](https://chronumental.readthedocs.io/en/latest/) to learn more about the parameters you can use to control Chronumental.

### Integrations

[Taxonium](https://github.com/theosanderson/taxonium) can automatically call Chronumental, and generate a combined visualisation that allows switching between distance and time phylogenies


### Similar tools

[TreeTime](https://github.com/neherlab/treetime) is a more advanced tool for inferring time trees. If you have a dataset of e.g. <10,000 rather than millions of nodes you are definitely best off trying it. The TreeTime readme also links to other similar tools.

### Troubleshooting

- Chronumental uses the earliest date in your dataset as an anchor to calibrate everything else. If this earliest date is wrong due to a metadata error things won't work well. You can set the reference node manually with `--reference_node` to avoid this issue.
reqver 0.1.8
A tool to add version information to requirements.txt files
Requires Python: >=3.6
Keywords: requirements version pip

# reqver

A command-line tool to add version information to requirements.txt files.

## Usage

```
reqver <params> files
```

For more information, please refer to the documentation.
# reqver

[![PyPI version](https://badge.fury.io/py/reqver.svg)](https://badge.fury.io/py/reqver)

**Latest version: 0.1.8**

A command-line tool to add version information to requirements.txt files.

## Installation

```
pip install reqver
```

## Usage

```
reqver [OPTIONS] [FILES]...
```

If no files are given, reqver looks for requirements.txt in the current directory. If not found, it searches parent directories. If still not found, it displays an error message.

### Options:

- `--force`: Force update of all package versions, even if they already have version information.
- `--no-backups`: Do not create backup files when updating requirements files.

### Examples:

1. Process requirements.txt in the current directory:
   ```
   reqver
   ```

2. Process a specific requirements file:
   ```
   reqver path/to/requirements.txt
   ```

3. Process multiple requirements files:
   ```
   reqver req1.txt req2.txt
   ```

4. Force update all versions:
   ```
   reqver --force requirements.txt
   ```

5. Update without creating backups:
   ```
   reqver --no-backups requirements.txt
   ```

## Behavior

For each specified file (or the found requirements.txt):

1. Treats it as a requirements file (if it is a text file).
2. For each requirement in the file:
   - If version info is present: leaves it as is, unless the `--force` option is set.
   - If no version info is present: gets the current version with pip.
3. Creates a backup of the old requirements file (unless `--no-backups` is used).
4. Writes the new requirements file with updated version information.

## Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

## Running Tests

To run the tests for this project, follow these steps:

1. Ensure you have the necessary dependencies installed:
   ```
   pip install -r requirements.txt
   ```

2. Navigate to the root directory of the project.

3. Run the tests using Python's unittest module:
   ```
   python -m unittest discover tests
   ```

This will discover and run all the tests in the `tests` directory.

## Uploading to PyPI

To upload a new version of this package to PyPI:

1. Update the version number in `setup.py`.
2. Build the package:
   ```
   python setup.py sdist
   ```
3. Upload to TestPyPI (optional):
   ```
   twine upload --repository testpypi dist/*
   ```
4. Upload to PyPI:
   ```
   twine upload dist/*
   ```

Make sure you have the latest versions of setuptools, wheel, and twine installed before building and uploading:
```
pip install --upgrade setuptools wheel twine
```