diffpy.apps 0.1.0__tar.gz

diffpy_apps-0.1.0/AUTHORS.rst

@@ -0,0 +1,10 @@
+Authors
+=======
+
+Yuchen Xiao, Simon Billinge and members of the Billinge group
+
+Contributors
+------------
+
+For a list of contributors, visit
+https://github.com/diffpy/diffpy.apps/graphs/contributors

diffpy_apps-0.1.0/LICENSE.rst

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, diffpy.apps contributors.
+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.

diffpy_apps-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.

diffpy_apps-0.1.0/PKG-INFO

@@ -0,0 +1,178 @@
+Metadata-Version: 2.4
+Name: diffpy.apps
+Version: 0.1.0
+Summary: User applications to help with tasks using diffpy packages
+Author-email: Yuchen Xiao <yx2924@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
+Maintainer-email: Yuchen Xiao <yx2924@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
+Project-URL: Homepage, https://github.com/diffpy/diffpy.apps/
+Project-URL: Issues, https://github.com/diffpy/diffpy.apps/issues/
+Keywords: diffraction,PDF,X-ray,neutron
+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
+Dynamic: license-file
+
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.apps
+.. _title: https://diffpy.github.io/diffpy.apps
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.apps
+        :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/diffpy/diffpy.apps/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.apps/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.apps/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.apps
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.apps
+        :target: https://anaconda.org/conda-forge/diffpy.apps
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.apps/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.apps
+        :target: https://pypi.org/project/diffpy.apps/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.apps
+        :target: https://pypi.org/project/diffpy.apps/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.apps/issues
+
+User applications to help with tasks using diffpy packages. Currently it
+contains
+
+- `runmacro`: A runner for DiffPy macro files.
+- `agentify`: A deployer for diffpy.cmi agentic skills.
+
+For more information about the diffpy.apps library, please consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_.
+
+Citation
+--------
+
+If you use diffpy.apps in a scientific publication, we would like you to cite this package as
+
+        diffpy.apps Package, https://github.com/diffpy/diffpy.apps
+
+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 ``diffpy.apps_env`` ::
+
+        conda create -n diffpy.apps_env diffpy.apps python=3.13
+        conda activate diffpy.apps_env
+
+The output should print the latest version displayed on the badges above.
+
+If the above does not work, you can use ``pip`` to download and install the latest release from
+`Python Package Index <https://pypi.python.org>`_.
+
+You still need to install some of its dependencies from ``conda`` ::
+
+        git clone https://github.com/diffpy/diffpy.apps.git
+        cd diffpy.apps
+        conda activate diffpy.apps_env
+        conda install --file requirements/conda.txt
+
+
+To install using ``pip`` into your ``diffpy.apps_env`` environment, type ::
+
+        pip install diffpy.apps
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.apps/>`_. Once installed, ``cd`` into your ``diffpy.apps`` directory
+and run the following ::
+
+        pip install .
+
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.apps --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.apps; print(diffpy.apps.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.apps -h
+
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_ 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/diffpy/diffpy.apps/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.apps/pulls>`_.
+
+Feel free to fork the project and contribute. To install diffpy.apps
+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/diffpy/diffpy.apps/blob/main/CODE-OF-CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on diffpy.apps please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Yuchen Xiao(yx2924@columbia.edu) and Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.apps`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

diffpy_apps-0.1.0/README.rst

@@ -0,0 +1,148 @@
+|Icon| |title|_
+===============
+
+.. |title| replace:: diffpy.apps
+.. _title: https://diffpy.github.io/diffpy.apps
+
+.. |Icon| image:: https://avatars.githubusercontent.com/diffpy
+        :target: https://diffpy.github.io/diffpy.apps
+        :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/diffpy/diffpy.apps/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.apps/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.apps/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.apps
+
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.apps
+        :target: https://anaconda.org/conda-forge/diffpy.apps
+
+.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.apps/pulls
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.apps
+        :target: https://pypi.org/project/diffpy.apps/
+
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.apps
+        :target: https://pypi.org/project/diffpy.apps/
+
+.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
+        :target: https://github.com/diffpy/diffpy.apps/issues
+
+User applications to help with tasks using diffpy packages. Currently it
+contains
+
+- `runmacro`: A runner for DiffPy macro files.
+- `agentify`: A deployer for diffpy.cmi agentic skills.
+
+For more information about the diffpy.apps library, please consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_.
+
+Citation
+--------
+
+If you use diffpy.apps in a scientific publication, we would like you to cite this package as
+
+        diffpy.apps Package, https://github.com/diffpy/diffpy.apps
+
+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 ``diffpy.apps_env`` ::
+
+        conda create -n diffpy.apps_env diffpy.apps python=3.13
+        conda activate diffpy.apps_env
+
+The output should print the latest version displayed on the badges above.
+
+If the above does not work, you can use ``pip`` to download and install the latest release from
+`Python Package Index <https://pypi.python.org>`_.
+
+You still need to install some of its dependencies from ``conda`` ::
+
+        git clone https://github.com/diffpy/diffpy.apps.git
+        cd diffpy.apps
+        conda activate diffpy.apps_env
+        conda install --file requirements/conda.txt
+
+
+To install using ``pip`` into your ``diffpy.apps_env`` environment, type ::
+
+        pip install diffpy.apps
+
+If you prefer to install from sources, after installing the dependencies, obtain the source archive from
+`GitHub <https://github.com/diffpy/diffpy.apps/>`_. Once installed, ``cd`` into your ``diffpy.apps`` directory
+and run the following ::
+
+        pip install .
+
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.apps --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.apps; print(diffpy.apps.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.apps -h
+
+Getting Started
+---------------
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_ 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/diffpy/diffpy.apps/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.apps/pulls>`_.
+
+Feel free to fork the project and contribute. To install diffpy.apps
+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/diffpy/diffpy.apps/blob/main/CODE-OF-CONDUCT.rst>`_.
+
+Contact
+-------
+
+For more information on diffpy.apps please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Yuchen Xiao(yx2924@columbia.edu) and Simon Billinge(sbillinge@ucsb.edu)``.
+
+Acknowledgements
+----------------
+
+``diffpy.apps`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

diffpy_apps-0.1.0/pyproject.toml

@@ -0,0 +1,91 @@
+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diffpy.apps"
+dynamic=['version', 'dependencies']
+authors = [
+  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
+]
+maintainers = [
+  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
+  {name='Simon Billinge', email='sbillinge@ucsb.edu'},
+]
+description = "User applications to help with tasks using diffpy packages"
+keywords = ['diffraction', 'PDF', 'X-ray', 'neutron']
+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/diffpy/diffpy.apps/"
+Issues = "https://github.com/diffpy/diffpy.apps/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]
+"diffpy.apps" = "diffpy.apps.apps:main"
+"diffpy.app" = "diffpy.apps.apps: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
+)/
+'''

diffpy_apps-0.1.0/requirements/conda.txt

@@ -0,0 +1,8 @@
+numpy
+scipy
+psutil
+textx
+pyyaml
+diffpy.srfit
+diffpy.srreal
+diffpy.structure

diffpy_apps-0.1.0/requirements/docs.txt

@@ -0,0 +1,5 @@
+sphinx
+sphinx_rtd_theme
+sphinx-copybutton
+doctr
+m2r2

diffpy_apps-0.1.0/requirements/pip.txt

@@ -0,0 +1 @@
+numpy

diffpy_apps-0.1.0/requirements/tests.txt

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

diffpy_apps-0.1.0/setup.cfg

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

diffpy_apps-0.1.0/src/diffpy/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2026 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/diffpy/diffpy.apps/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################

diffpy_apps-0.1.0/src/diffpy/apps/__init__.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2026 diffpy.apps contributors.
+# All rights reserved.
+#
+# File coded by: Yuchen Xiao, Simon Billinge and members of the Billinge group.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.apps/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""User applications to help with tasks using diffpy packages."""
+
+# package version
+from diffpy.apps.version import __version__  # noqa
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file

diffpy_apps-0.1.0/src/diffpy/apps/app_agentify.py

@@ -0,0 +1,35 @@
+import shutil
+import subprocess
+import tempfile
+from pathlib import Path
+
+REPO_URL = "https://github.com/diffpy/cmi-agent-skills"
+DIR_NAME = "cmi-skill"
+
+
+def agentify(args):
+    agent = args.agent
+    system_flag = args.system
+    if agent == "claude":
+        skills_dir = ".claude/skills"
+    elif agent == "codex":
+        skills_dir = ".codex/skills"
+    if system_flag:
+        destination = Path().home() / skills_dir / DIR_NAME
+    else:
+        destination = Path().cwd() / skills_dir / DIR_NAME
+    if destination.exists() and not args.update:
+        raise FileExistsError(
+            f"Agentic skill {DIR_NAME} already exists at {destination}. "
+            "To overwrite, pass '--update' flag to update the skill"
+        )
+    with tempfile.TemporaryDirectory() as tmp:
+        tmp_path = Path(tmp)
+        subprocess.run(
+            ["git", "clone", REPO_URL, str(tmp_path)],
+            check=True,
+        )
+        if destination.exists():
+            shutil.rmtree(destination)
+        shutil.copytree(tmp_path / DIR_NAME, destination, dirs_exist_ok=True)
+    print(f"Agentic skill {DIR_NAME} has been deployed to {destination}")