semvec/pypi-packages huggingface dataset:
croudtech-bootstrap 0.1.59b2
Applicaton config via AWS S3 and AWS Secrets Manager
License: MIT
Requires Python: <3.14,>=3.9

# Python script to push and pull application config

This script is used to push and pull secrets, s3 config and ssm values for use in applications.

## Usage

### Pushing Config

```
Usage: croudtech-bootstrap put-config [OPTIONS] VALUES_PATH

Options:
  --prefix TEXT   The path prefix (Name prefix used when storing secrets and SSM values)
  --region TEXT   The AWS region (Defaults to the current region set using AWS_DEFAULT_REGION or AWS_REGION env vars)
  --delete-first  Delete the values in this path before pushing (useful for cleanup) This will remove any values with the current path prefix that aren't included in the files we're pushing.
  --help          Show this message and exit.
```

The put-config command requires the following file structure:

```
├── ENVIRONMENT_NAME_1
│   ├── common.yaml
│   ├── common.secret.yaml
│   ├── AppConfig1.yaml
│   ├── AppConfig1.secret.yaml
│   ├── AppConfig2.yaml
│   └── AppConfig2.secret.yaml
├── ENVIRONMENT_NAME_2
│   ├── common.yaml
│   ├── common.secret.yaml
│   ├── AppConfig1.yaml
│   ├── AppConfig1.secret.yaml
│   ├── AppConfig2.yaml
│   └── AppConfig2.secret.yaml
```

Running `python -m croudtech-bootstrap put-config CONFIG_FILES_PATH` will create config for AppConfig1 and AppConfig2 in both defined environments.

common.yaml and common.secret.yaml files contain shared config that will be used for all applications.

### Pulling config

```
Usage: croudtech-bootstrap get-config [OPTIONS]

Options:
  --environment-name TEXT         The environment name  [required]
  --app-name TEXT                 The app name  [required]
  --prefix TEXT                   The path prefix
  --region TEXT                   The AWS region
  --include-common / --ignore-common
                                  Include shared variables
  --output-format [json|yaml|environment|environment-export]
  --parse-redis-param / --ignore-redis-param
                                  Parse redis host and allocate a redis
                                  database number. Requires network access to the redis instance
  --help                          Show this message and exit.
```

Using the put-config example above we can pull the config as follows

```
croudtech-bootstrap get-config --environment-name ENVIRONMENT_NAME_1 --app-name AppConfig1 --output-format environment
```

## Installation

`pip install croudtech-bootstrap`
solvis-tools 0.1.5
A module for analyzing and visualizing solvation shells in LAMMPS output files, but would work with most files that can be handled by ASE.
License: MIT
Requires Python: >=3.10

# solvis

<img src="https://github.com/amritagos/solvis/blob/main/branding/logo/logo.png?raw=true" width="300" />

## About

Various ways to analyze and visualize solvation shell structures, which wraps [`PyVista`](https://docs.pyvista.org/version/stable/). Meant primarily for analyzing the outputs produced by LAMMPS, but anything that [ASE](https://gitlab.com/ase/ase) can handle should work.

## Installation 

### From PyPI

You can install `solvis` from PyPI like so: 

```bash
pip install solvis-tools
```

### From source

We use [`micromamba`](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) as the package manager, but feel free to use your own poison. Create and activate the environment. 

```bash
micromamba create -f environment.yml
micromamba activate solvisenv
```

In order to install the code, run the following in the top-level directory:

```bash
pip install -e .
```

## Examples 

Each example is self-contained. Mostly, they show how to handle interactive plotting.
To close the interactive window, press q. 

## Tests

To run tests (which are inside the `tests` directory), written with `pytest`, run the following command from the top-level directory: 

```bash
pytest -v
```

In order to debug tests using `pdb`, you can write the command `breakpoint()` inside the `Python` files (in `tests`) wherever you want to set a breakpoint. Then, run `pytest --pdb`. This will stop the code at the line where you put the `breakpoint()` command. 

To see more verbose output from `pytest`, including tests that pass, you can run `pytest -rA`.

Note that `test_hydrogen_bond.py` and `test_plot_octahedral_shell.py` actually compare the results of images created for a single hydrogen bond and for an octahedral shell showing hydrogen bonds formed by the acceptor seventh molecule, respectively. The images compared against are present in the top-level `image_cache_dir` directory. The package [`pytest-pyvista`](https://github.com/pyvista/pytest-pyvista) is used for image verification.

To view a coverage report, run the following from the top-level directory: 

```bash
pytest --cov=solvis tests/
```

## Image Gallery
<p float="left">
    <img src="https://github.com/amritagos/solvis/blob/main/resources/non_octahedral_shape.png?raw=true" width="200" />
    <img src="https://github.com/amritagos/solvis/blob/main/resources/octahedral_shell.png?raw=true" width="200" />
</p>
<p float="left">
    <img src="https://github.com/amritagos/solvis/blob/main/resources/shell_with_hbonds.png?raw=true" width="200" />
    <img src="https://github.com/amritagos/solvis/blob/main/resources/hbond_non_oct.png?raw=true" width="200" />
</p>