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.
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
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
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
You may consult our online documentation for tutorials and API references.
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.
- Install pre-commit in your working environment by running
conda install pre-commit. - 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.
For more information on pdfbl.sequential please visit the project web-page or email Simon Billinge at sb2896@columbia.edu.
pdfbl.sequential is built and maintained with scikit-package.