pdfbl.sequential 0.1.0

Automated sequential refinements of PDF data

Automated sequential refinements of PDF data

Scripts for running sequential PDF refinements using diffpy.cmi automatically

For more information about the pdfbl.sequential library, please consult our online documentation.

Citation

If you use pdfbl.sequential in a scientific publication, we would like you to cite this package as

pdfbl.sequential Package, https://github.com/pdf-bl/pdfbl.sequential

Installation

The preferred method is to use Miniconda Python and install from the “conda-forge” channel of Conda packages.

To add “conda-forge” to the conda channels, run the following in a terminal.

conda config --add channels conda-forge

We want to install our packages in a suitable conda environment. The following creates and activates a new environment named pdfbl.sequential_env

conda create -n pdfbl.sequential_env pdfbl.sequential
conda activate pdfbl.sequential_env

The output should print the latest version displayed on the badges above.

You can also use pip to download and install the latest release from Python Package Index in your environment. But you would still need to install the dependency diffpy.cmi using conda first

conda install diffpy.cmi
pip install pdfbl.sequential

If you prefer to install from sources, after installing the dependencies, obtain the source archive from GitHub. Once installed, cd into your pdfbl.sequential directory and run the following

conda install diffpy.cmi
pip install .

This package also provides command-line utilities. To check the software has been installed correctly, type

pdfbl.sequential --version

You can also type the following command to verify the installation.

python -c "import pdfbl.sequential; print(pdfbl.sequential.__version__)"

To view the basic usage and available commands, type

pdfbl.sequential -h

Examples

To run a temperature sequential refinement,

from pdfbl.sequential.sequential_cmi_runner import SequentialCMIRunner
runner = SequentialCMIRunner()
runner.load_inputs(
        input_data_dir="path/to/inputs",
        output_result_dir="path/to/outputs",
        structure_path="path/to/structure.cif",
        filename_order_pattern=r"(\d+)K\.gr",  # regex pattern to extract the temperature from the filename
)
runner.run(mode="batch")  # or mode="stream" for running sequentially as data becomes available

Getting Started

You may consult our online documentation for tutorials and API references.

Support and Contribute

If you see a bug or want to request a feature, please report it as an issue and/or submit a fix as a PR.

Feel free to fork the project and contribute. To install pdfbl.sequential in a development mode, with its sources being directly used by Python rather than copied to a package directory, use the following in the root directory

pip install -e .

To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit hooks.

1. Install pre-commit in your working environment by running conda install pre-commit.

2. Initialize pre-commit (one time only) pre-commit install.

Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before trying to commit again.

Improvements and fixes are always appreciated.

Before contributing, please read our Code of Conduct.

Contact

For more information on pdfbl.sequential please visit the project web-page or email Simon Billinge at [e-mail].

Acknowledgements

pdfbl.sequential is built and maintained with scikit-package.