pdfbl.sequential 0.1.0__tar.gz

pdfbl_sequential-0.1.0/AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+members of the Billinge Group and PDF beamline at NSLS-II
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/pdf-bl/pdfbl.sequential/graphs/contributors

pdfbl_sequential-0.1.0/LICENSE.rst

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Simon Billinge.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pdfbl_sequential-0.1.0/MANIFEST.in

@@ -0,0 +1,12 @@
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.

pdfbl_sequential-0.1.0/PKG-INFO

@@ -0,0 +1,190 @@
+Metadata-Version: 2.4
+Name: pdfbl.sequential
+Version: 0.1.0
+Summary: Automated sequential refinements of PDF data
+Author-email: Simon Billinge <sb2896@columbia.edu>
+Maintainer-email: Simon Billinge <sb2896@columbia.edu>
+Project-URL: Homepage, https://github.com/pdf-bl/pdfbl.sequential/
+Project-URL: Issues, https://github.com/pdf-bl/pdfbl.sequential/issues/
+Keywords: diffraction,PDF,X-ray,neutron,nsls-ii
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE.rst
+License-File: AUTHORS.rst
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: prompt_toolkit
+Requires-Dist: bg-mpl-stylesheets
+Requires-Dist: psutil
+Requires-Dist: matplotlib
+Dynamic: license-file
+
+|Icon| |title|_
+===============
+
+.. |title| replace:: pdfbl.sequential
+.. _title: https://pdf-bl.github.io/pdfbl.sequential
+
+.. |Icon| image:: https://avatars.githubusercontent.com/pdf-bl
+        :target: https://pdf-bl.github.io/pdfbl.sequential
+        :height: 100px
+
+|PyPI| |Forge| |PythonVersion| |PR|
+
+|CI| |Codecov| |Black| |Tracking|
+
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
+
+.. |CI| image:: https://github.com/pdf-bl/pdfbl.sequential/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/pdf-bl/pdfbl.sequential/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/pdf-bl/pdfbl.sequential/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/pdf-bl/pdfbl.sequential
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/pdfbl.sequential
+        :target: https://anaconda.org/conda-forge/pdfbl.sequential
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/pdf-bl/pdfbl.sequential/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/pdfbl.sequential
+        :target: https://pypi.org/project/pdfbl.sequential/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/pdfbl.sequential
+        :target: https://pypi.org/project/pdfbl.sequential/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/pdf-bl/pdfbl.sequential/issues
+
+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 <https://pdf-bl.github.io/pdfbl.sequential>`_.
+
+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
+<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
+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 <https://pypi.python.org>`_ 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 <https://github.com/pdf-bl/pdfbl.sequential/>`_. 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 <https://pdf-bl.github.io/pdfbl.sequential>`_ 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 <https://github.com/pdf-bl/pdfbl.sequential/issues>`_ and/or `submit a fix as a PR <https://github.com/pdf-bl/pdfbl.sequential/pulls>`_.
+
+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 <https://github.com/pdf-bl/pdfbl.sequential/blob/main/CODE-OF-CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on pdfbl.sequential please visit the project `web-page <https://pdf-bl.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``pdfbl.sequential`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

pdfbl_sequential-0.1.0/README.rst

@@ -0,0 +1,155 @@
+|Icon| |title|_
+===============
+
+.. |title| replace:: pdfbl.sequential
+.. _title: https://pdf-bl.github.io/pdfbl.sequential
+
+.. |Icon| image:: https://avatars.githubusercontent.com/pdf-bl
+        :target: https://pdf-bl.github.io/pdfbl.sequential
+        :height: 100px
+
+|PyPI| |Forge| |PythonVersion| |PR|
+
+|CI| |Codecov| |Black| |Tracking|
+
+.. |Black| image:: https://img.shields.io/badge/code_style-black-black
+        :target: https://github.com/psf/black
+
+.. |CI| image:: https://github.com/pdf-bl/pdfbl.sequential/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/pdf-bl/pdfbl.sequential/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/pdf-bl/pdfbl.sequential/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/pdf-bl/pdfbl.sequential
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/pdfbl.sequential
+        :target: https://anaconda.org/conda-forge/pdfbl.sequential
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/pdf-bl/pdfbl.sequential/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/pdfbl.sequential
+        :target: https://pypi.org/project/pdfbl.sequential/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/pdfbl.sequential
+        :target: https://pypi.org/project/pdfbl.sequential/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/pdf-bl/pdfbl.sequential/issues
+
+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 <https://pdf-bl.github.io/pdfbl.sequential>`_.
+
+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
+<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
+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 <https://pypi.python.org>`_ 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 <https://github.com/pdf-bl/pdfbl.sequential/>`_. 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 <https://pdf-bl.github.io/pdfbl.sequential>`_ 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 <https://github.com/pdf-bl/pdfbl.sequential/issues>`_ and/or `submit a fix as a PR <https://github.com/pdf-bl/pdfbl.sequential/pulls>`_.
+
+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 <https://github.com/pdf-bl/pdfbl.sequential/blob/main/CODE-OF-CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on pdfbl.sequential please visit the project `web-page <https://pdf-bl.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+
+Acknowledgements
+----------------
+
+``pdfbl.sequential`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

pdfbl_sequential-0.1.0/pyproject.toml

@@ -0,0 +1,88 @@
+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pdfbl.sequential"
+dynamic=['version', 'dependencies']
+authors = [
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
+]
+maintainers = [
+  { name="Simon Billinge", email="sb2896@columbia.edu" },
+]
+description = "Automated sequential refinements of PDF data"
+keywords = ['diffraction', 'PDF', 'X-ray', 'neutron', 'nsls-ii']
+readme = "README.rst"
+requires-python = ">=3.11, <3.14"
+classifiers = [
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: Microsoft :: Windows',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Chemistry',
+]
+
+[project.urls]
+Homepage = "https://github.com/pdf-bl/pdfbl.sequential/"
+Issues = "https://github.com/pdf-bl/pdfbl.sequential/issues/"
+
+[tool.setuptools-git-versioning]
+enabled = true
+template = "{tag}"
+dev_template = "{tag}"
+dirty_template = "{tag}"
+
+[tool.setuptools.packages.find]
+where = ["src"]  # list of folders that contain the packages (["."] by default)
+include = ["*"]  # package names should match these glob patterns (["*"] by default)
+exclude = []  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+
+[project.scripts]
+pdfbl-sequential = "pdfbl.sequential.pdfbl_sequential_app:main"
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements/pip.txt"]}
+
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif,*.dat"
+
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72
+
+[tool.black]
+line-length = 79
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | \.rst
+  | \.txt
+  | _build
+  | buck-out
+  | build
+  | dist
+
+  # The following are specific to Black, you probably don't want those.
+  | blib2to3
+  | tests/data
+)/
+'''

pdfbl_sequential-0.1.0/requirements/conda.txt

@@ -0,0 +1,7 @@
+numpy
+diffpy.cmi
+scipy
+prompt_toolkit
+matplotlib-base
+bg-mpl-stylesheets
+psutil

pdfbl_sequential-0.1.0/requirements/docs.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinx_rtd_theme
+sphinx-copybutton
+doctr
+m2r

pdfbl_sequential-0.1.0/requirements/pip.txt

@@ -0,0 +1,6 @@
+numpy
+scipy
+prompt_toolkit
+bg-mpl-stylesheets
+psutil
+matplotlib

pdfbl_sequential-0.1.0/requirements/tests.txt

@@ -0,0 +1,6 @@
+flake8
+pytest
+codecov
+coverage
+pytest-cov
+pytest-env

pdfbl_sequential-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

pdfbl_sequential-0.1.0/src/pdfbl/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/pdf-bl/pdfbl.sequential/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################

pdfbl_sequential-0.1.0/src/pdfbl/sequential/__init__.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 Simon Billinge.
+# All rights reserved.
+#
+# File coded by: members of the Billinge Group and PDF beamline at NSLS-II.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/pdf-bl/pdfbl.sequential/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Automated sequential refinements of PDF data."""
+
+# package version
+from pdfbl.sequential.version import __version__  # noqa
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file