xrayscatteringtools 0.1.0__tar.gz → 0.2.0__tar.gz

{xrayscatteringtools-0.1.0 → xrayscatteringtools-0.2.0}/.gitattributes

@@ -1,2 +1,2 @@
-# Auto detect text files and perform LF normalization
-* text=auto
+# Auto detect text files and perform LF normalization
+* text=auto

{xrayscatteringtools-0.1.0 → xrayscatteringtools-0.2.0}/.gitignore

@@ -1,181 +1,183 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# Ruff stuff:
-.ruff_cache/
-
-# PyPI configuration file
-.pypirc
-
-# Cursor  
-#  Cursor is an AI-powered code editor.`.cursorignore` specifies files/directories to 
-#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
-#  refer to https://docs.cursor.com/context/ignore-files
-.cursorignore
-.cursorindexingignore
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor  
+#  Cursor is an AI-powered code editor.`.cursorignore` specifies files/directories to 
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+.DS_store

{xrayscatteringtools-0.1.0 → xrayscatteringtools-0.2.0}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2025 David Romano
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2025 David Romano
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{xrayscatteringtools-0.1.0 → xrayscatteringtools-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: xrayscatteringtools
-Version: 0.1.0
+Version: 0.2.0
 Summary: A library for gas phase analysis at the CXI endstation
 Project-URL: Homepage, https://github.com/Weber-Group/xrayscatteringtools
 Project-URL: Issues, https://github.com/Weber-Group/xrayscatteringtools/issues
@@ -29,15 +29,22 @@ Description-Content-Type: text/markdown
 
 ## A python library for the analysis of data from the CXI endstation at the LCLS. 
 
+### `calib` submodule pertains to the geometry calibration routine
+
+### `theory` submodule pertains to stored ab initio patterns, iam, or geometries.
+### `utils` has a bunch of useful functions in it
+### `xrayscatteringtools.io` has anything pertaning to loading or writing data (`combineRuns` is in here)
+### `plotting` has anything to do with plotting.
+
 ### List of all methods:
-All methods have full docstrings in the NumPy docstring standard.
-Proper namespaces have yet to be defined. Some of these functions can remain internal, and the more useful ones can be defined at the surface level.
+All methods should have full docstrings in the NumPy docstring standard.
 * calib
   * geometry_calibration
     - run_geometry_calibration()
     - model()
     - thompson_correction()
     - geometry_correction()
+    - geometry_correction_units()
   * scattering_corrections
     - correction_factor()
     - Si_correction()
@@ -49,6 +56,7 @@ Proper namespaces have yet to be defined. Some of these functions can remain int
     - Al_attenuation_length()
     - Be_attenuation_length()
     - KaptonHN_attenuation_length()
+    - Zn_attenuation_length()
     - J4M_efficiency()
 * theory
   * iam
@@ -56,24 +64,40 @@ Proper namespaces have yet to be defined. Some of these functions can remain int
     - iam_inelastic_pattern()
     - iam_total_pattern()
     - iam_compton_spectrum()
+    - iam_elastic_pattern_oriented()
+    - iam_inelastic_pattern_oriented()
+    - iam_total_pattern_oriented()
   * patterns
-    - sf6()
+    - SF6__CCSD__aug_cc_pVDZ
+    - SF6__HF__aug_cc_pVDZ
+    - SF6__MP2__aug_cc_pVDZ
+  * geometries
+    - SF6__CCSD_T_DHK__aug_cc_pV5Z_DK 
 * io
   - combineRuns()
   - get_tree()
   - is_leaf()
   - get_leaves()
+  - get_data_paths()
   - runNumToString()
   - read_xyz()
+  - write_xyz()
+  - read_mol()
 * plotting
   - plot_jungfrau()
   - compute_pixel_edges()
 * utils
   - enable_underscore_cleanup()
   - azimuthalBinning()
+  - au2invAngstroms()
+  - invAngstroms2au()
   - keV2Angstroms()
   - Angstroms2keV()
   - q2theta()
   - theta2q()
   - element_symbol_to_number()
   - element_number_to_symbol()
+  - translate_molecule()
+  - rotate_molecule()
+  - J4M()
+  - 

{xrayscatteringtools-0.1.0 → xrayscatteringtools-0.2.0}/README.md

@@ -1,52 +1,76 @@
-# xrayscatteringtools
-
-## A python library for the analysis of data from the CXI endstation at the LCLS. 
-
-### List of all methods:
-All methods have full docstrings in the NumPy docstring standard.
-Proper namespaces have yet to be defined. Some of these functions can remain internal, and the more useful ones can be defined at the surface level.
-* calib
-  * geometry_calibration
-    - run_geometry_calibration()
-    - model()
-    - thompson_correction()
-    - geometry_correction()
-  * scattering_corrections
-    - correction_factor()
-    - Si_correction()
-    - KaptonHN_correction()
-    - Al_correction()
-    - Be_correction()
-    - cell_correction()
-    - Si_attenuation_length()
-    - Al_attenuation_length()
-    - Be_attenuation_length()
-    - KaptonHN_attenuation_length()
-    - J4M_efficiency()
-* theory
-  * iam
-    - iam_elastic_pattern()
-    - iam_inelastic_pattern()
-    - iam_total_pattern()
-    - iam_compton_spectrum()
-  * patterns
-    - sf6()
-* io
-  - combineRuns()
-  - get_tree()
-  - is_leaf()
-  - get_leaves()
-  - runNumToString()
-  - read_xyz()
-* plotting
-  - plot_jungfrau()
-  - compute_pixel_edges()
-* utils
-  - enable_underscore_cleanup()
-  - azimuthalBinning()
-  - keV2Angstroms()
-  - Angstroms2keV()
-  - q2theta()
-  - theta2q()
-  - element_symbol_to_number()
-  - element_number_to_symbol()
+# xrayscatteringtools
+
+## A python library for the analysis of data from the CXI endstation at the LCLS. 
+
+### `calib` submodule pertains to the geometry calibration routine
+
+### `theory` submodule pertains to stored ab initio patterns, iam, or geometries.
+### `utils` has a bunch of useful functions in it
+### `xrayscatteringtools.io` has anything pertaning to loading or writing data (`combineRuns` is in here)
+### `plotting` has anything to do with plotting.
+
+### List of all methods:
+All methods should have full docstrings in the NumPy docstring standard.
+* calib
+  * geometry_calibration
+    - run_geometry_calibration()
+    - model()
+    - thompson_correction()
+    - geometry_correction()
+    - geometry_correction_units()
+  * scattering_corrections
+    - correction_factor()
+    - Si_correction()
+    - KaptonHN_correction()
+    - Al_correction()
+    - Be_correction()
+    - cell_correction()
+    - Si_attenuation_length()
+    - Al_attenuation_length()
+    - Be_attenuation_length()
+    - KaptonHN_attenuation_length()
+    - Zn_attenuation_length()
+    - J4M_efficiency()
+* theory
+  * iam
+    - iam_elastic_pattern()
+    - iam_inelastic_pattern()
+    - iam_total_pattern()
+    - iam_compton_spectrum()
+    - iam_elastic_pattern_oriented()
+    - iam_inelastic_pattern_oriented()
+    - iam_total_pattern_oriented()
+  * patterns
+    - SF6__CCSD__aug_cc_pVDZ
+    - SF6__HF__aug_cc_pVDZ
+    - SF6__MP2__aug_cc_pVDZ
+  * geometries
+    - SF6__CCSD_T_DHK__aug_cc_pV5Z_DK 
+* io
+  - combineRuns()
+  - get_tree()
+  - is_leaf()
+  - get_leaves()
+  - get_data_paths()
+  - runNumToString()
+  - read_xyz()
+  - write_xyz()
+  - read_mol()
+* plotting
+  - plot_jungfrau()
+  - compute_pixel_edges()
+* utils
+  - enable_underscore_cleanup()
+  - azimuthalBinning()
+  - au2invAngstroms()
+  - invAngstroms2au()
+  - keV2Angstroms()
+  - Angstroms2keV()
+  - q2theta()
+  - theta2q()
+  - element_symbol_to_number()
+  - element_number_to_symbol()
+  - translate_molecule()
+  - rotate_molecule()
+  - J4M()
+  -