Metadata-Version: 2.1
Name: express-py
Version: 2021.9.9
Summary: Exabyte Property Ex(ss)tractor, Sourcer, Serializer class.
Home-page: https://github.com/Exabyte-io/exabyte-express
Author: Exabyte Inc.
Author-email: info@exabyte.io
License: UNKNOWN
Description: [![PyPI version](https://badge.fury.io/py/express-py.svg)](https://badge.fury.io/py/express-py)
        [![License: Apache](https://img.shields.io/badge/License-Apache-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)
        
        # ExPreSS
        
        Exabyte Property Extractor, Sourcer, Serializer (ExPreSS) is a Python package to extract material- and simulation-related properties and serialize them according to the Exabyte Data Convention (EDC) outlined in [Exabyte Source of Schemas and Examples (ESSE)](https://github.com/Exabyte-io/exabyte-esse). 
        
        ## Functionality
        
        As below:
        
        - Extract structural information, material properties and from simulation data
        - Serialize extracted information according to ESSE/EDC
        - Support for multiple simulation engines, including:
          - [VASP](#links)
          - [Quantum ESPRESSO](#links)
          - others, to be added
        
        The package is written in a modular way easy to extend for additional applications and properties of interest. Contributions can be in the form of additional [functionality](#todo-list) and [bug/issue reports](https://help.github.com/articles/creating-an-issue/).
        
        ## Architecture
        
        The following diagram presents the package architecture. The package provides an [interface](express/__init__.py) to extract properties in EDC format. Inside the interface `Property` classes are initialized with a `Parser` (Vasp, Espresso, or Structure) depending on the given parameters through the parser factory. Each `Property` class implements required calls to `Parser` functions listed in these [Mixins Classes](express/parsers/mixins) to extract raw data either from the textual files, XML files or input files in string format and implements a serializer to form the final property according to the EDC format.
        
        ![ExPreSS](https://user-images.githubusercontent.com/10528238/53124591-9958e700-3510-11e9-9222-3aedacfd7943.png)
        
        ### Parsers
        
        As explained above, ExPreSS parsers are responsible for extracting raw data from different sources such as data on the disk and provide the raw data to properties classes. In order to make sure all parsers implement the same interfaces and abstract properties classes from the parsers implementations, a set a [Mixin Classes](express/parsers/mixins) are provided which should be mixed with the parsers. The parsers must implement Mixins' abstract methods at the time of inheritance.
        
        ### Properties
        
        ExPreSS properties classes are responsible to form the properties based on the raw data provided by the parsers and serialize the property according to EDC. A list of supported properties are available in [here](express/settings.py).
        
        ### Extractors
        
        Extractors are classes that are composed with the parsers to extract raw data from the corresponding sources such as text or XML.
        
        ## Installation
        
        ExPreSS can be installed as a Python package either via PyPi or the repository as below.
        
        #### PyPi
        
        ```bash
        pip install express
        ```
        
        #### Repository
        
        0. Install [git-lfs](https://help.github.com/articles/installing-git-large-file-storage/) in order to pull the files stored on Git LFS.
        
        1. Clone repository:
            
            ```bash
            git clone git@github.com:Exabyte-io/exabyte-express.git
            ```
        
        2. Install [virtualenv](https://virtualenv.pypa.io/en/stable/) using [pip](https://pip.pypa.io/en/stable/) if not already present:
        
            ```bash
            pip install virtualenv
            ```
        
        3. Create virtual environment and install required packages:
        
            ```bash
            cd exabyte-express
            virtualenv venv
            source venv/bin/activate
            export GIT_LFS_SKIP_SMUDGE=1
            pip install -e PATH_TO_EXPRESS_REPOSITORY
            ```
        
        ## Usage
        
        ### Extract Total Energy
        
        The following example demonstrates how to initialize an ExPreSS class instance, to extract and serialize total energy produced in a Quantum ESPRESSO calculation. The full path to the calculation directory (`work_dir`) and the file containing standard output (`stdout_file`) are required to be passed as arguments to the underlying Espresso parser.
        
        ```python
        
        import json
        from express import ExPrESS
        
        kwargs = {
            "work_dir": "./tests/fixtures/espresso/test-001",
            "stdout_file": "./tests/fixtures/espresso/test-001/pw-scf.out"
        
        }
        
        express_ = ExPrESS("espresso", **kwargs)
        print json.dumps(express_.property("total_energy"), indent=4)
        
        ```
        
        ### Extract Relaxed Structure
        
        In this example the final structure of a VASP calculation is extracted and is serialized to a material. The final structure is extracted from the `CONTCAR` file located in the calculation directory (`work_dir`). `is_final_structure=True` argument should be passed to the [Material Property](express/properties/material.py) class to let it know to extract final structure.
        
        ```python
        
        import json
        from express import ExPrESS
        
        kwargs = {
            "work_dir": "./tests/fixtures/vasp/test-001",
            "stdout_file": "./tests/fixtures/vasp/test-001/vasp.out"
        
        }
        
        express_ = ExPrESS("vasp", **kwargs)
        print json.dumps(express_.property("material", is_final_structure=True), indent=4)
        
        ```
        
        ### Extract Structure from Input
        
        One can use [StructureParser](express/parsers/structure.py) to extract materials from POSCAR or PW input files. Please note that `StructureParser` class only works with strings and not files and therefore the input files should be read first and then passed to the parser.
        
        ```python
        
        import json
        from express import ExPrESS
        
        with open("./tests/fixtures/vasp/test-001/POSCAR") as f:
            poscar = f.read()
        
        kwargs = {
            "structure_string": poscar,
            "structure_format": "poscar"
        }
        
        express_ = ExPrESS("structure", **kwargs)
        print json.dumps(express_.property("material"), indent=4)
        
        with open("./tests/fixtures/espresso/test-001/pw-scf.in") as f:
            pwscf_input = f.read()
        
        kwargs = {
            "structure_string": pwscf_input,
            "structure_format": "espresso-in"
        }
        
        express_ = ExPrESS("structure", **kwargs)
        print json.dumps(express_.property("material"), indent=4)
        
        ```
        
        ## Tests
        
        There are two types of tests in ExPreSS, unit and integration, implemented in [Python Unit Testing Framework](https://docs.python.org/2/library/unittest.html).
        
        ### Unit Tests
        
        Unit tests are used to assert properties are serialized according to EDC. Properties classes are initialized with mocked parser data and then are serialized to assert functionality.
        
        ### Integration Tests
        
        Parsers functionality is tested through integration tests. The parsers are initialized with the configuration specified in the [Tests Manifest](./tests/manifest.yaml) and then the functionality is asserted.
        
        ### Run Tests
        
        Run the following commands to run the tests.
        
        ```bash
        sh run-tests.sh -t=unit
        sh run-tests.sh -t=integration
        ```
        
        ## Contribution
        
        This repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions. We suggest forking this repository and introducing the adjustments there, the changes in the fork can further be considered for merging into this repository as explained in [GitHub Standard Fork and Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962).
        
        ## TODO list
        
        Desirable features for implementation:
        
        - Add support for other properties
        - Add support for other types of applications, parsers and extractors
        - other (TBA)
        
        ## Links
        
        1. [Exabyte Source of Schemas and Examples (ESSE), Github Repository](https://github.com/exabyte-io/exabyte-esse)
        1. [Vienna Ab-initio Simulation Package (VASP), official website](https://cms.mpi.univie.ac.at/vasp/)
        1. [Quantum ESPRESSO, Official Website](https://www.quantum-espresso.org/)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: test
