trxrdpy 1.0.0__tar.gz

trxrdpy-1.0.0/PKG-INFO

@@ -0,0 +1,332 @@
+Metadata-Version: 2.4
+Name: trxrdpy
+Version: 1.0.0
+Summary: Python toolkit for time-resolved X-ray diffraction simulation and beamline-dependent analysis workflows.
+Author: Julio Guzman-Brambila
+License-Expression: CC-BY-4.0
+Project-URL: Homepage, https://github.com/julioguzmanb/XRDpy
+Project-URL: Repository, https://github.com/julioguzmanb/XRDpy
+Project-URL: Documentation, https://github.com/julioguzmanb/XRDpy
+Project-URL: DOI, https://doi.org/10.5281/zenodo.18634909
+Project-URL: Issues, https://github.com/julioguzmanb/XRDpy/issues
+Keywords: xrd,time-resolved xrd,pump-probe,x-ray diffraction,diffraction,materials science,simulation,beamline analysis,pyFAI
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: pandas>=2.0
+Requires-Dist: h5py>=3.9
+Requires-Dist: tqdm>=4.66
+Requires-Dist: lmfit>=1.2
+Requires-Dist: pyFAI>=2024.1
+Requires-Dist: fabio>=2024.4
+Requires-Dist: PyCifRW>=5.0
+Requires-Dist: xrayutilities>=1.7
+Provides-Extra: analysis
+Requires-Dist: pytxs==0.0.2; extra == "analysis"
+Provides-Extra: gui
+Requires-Dist: PyQt5>=5.15; extra == "gui"
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+
+# XRDpy
+
+**XRDpy** is a Python toolkit for **X-ray diffraction (XRD)** simulation and analysis, with a particular focus on **time-resolved / pump–probe diffraction workflows**.
+
+The project name on **GitHub** and **Zenodo** is **XRDpy**.
+The package is distributed on **PyPI** as **`trxrdpy`** and should be imported in Python as **`trxrdpy`**.
+
+---
+
+## Repository
+
+Source code: https://github.com/julioguzmanb/XRDpy
+
+## DOI (Zenodo)
+
+- **Project concept DOI (all versions):** https://doi.org/10.5281/zenodo.18634909
+- **Current release DOI (v1.0.0):** https://doi.org/10.5281/zenodo.18925472
+
+---
+
+## Main capabilities
+
+### Simulation
+
+- Polycrystalline XRD simulation
+- Single-crystal diffraction simulation
+- CIF-based crystallographic helpers
+- Plotting utilities for simulated diffraction data
+- A GUI for simulation workflows
+
+### Analysis
+
+- Beamline/facility-specific data handling
+- 2D image reduction and azimuthal integration
+- Standardized generation of 1D `xy` diffraction patterns
+- Peak fitting workflows
+- Differential analysis workflows
+- Shared utilities for plotting, path handling, and common analysis operations
+
+---
+
+## Package structure
+
+```text
+XRDpy/
+├── pyproject.toml
+├── README.md
+├── LICENSE
+└── src/
+    └── trxrdpy/
+        ├── __init__.py
+        ├── utils.py
+        ├── detector.py
+        ├── experiment.py
+        ├── plot.py
+        ├── sample.py
+        ├── cif.py
+        ├── simulation/
+        │   ├── __init__.py
+        │   ├── polycrystalline.py
+        │   ├── single_crystal.py
+        └── analysis/
+            ├── common/
+            │   ├── __init__.py
+            │   ├── paths.py
+            │   ├── plot_utils.py
+            │   ├── general_utils.py
+            │   ├── azimint_utils.py
+            │   ├── differential_analysis_utils.py
+            │   └── fitting_utils.py
+            ├── _shared_2d/
+            │   ├── __init__.py
+            │   └── azimint.py
+            ├── ESRF_ID09/
+            │   ├── __init__.py
+            │   └── azimint.py
+            ├── MaxIV_FemtoMAX/
+            │   ├── __init__.py
+            │   ├── datared_utils.py
+            │   ├── datared.py
+            │   └── azimint.py
+            ├── Spring8_SACLA/
+            │   ├── __init__.py
+            │   ├── datared.py
+            │   ├── azimint.py
+            │   └── pbs/
+            │       └── parallel_job_sender.sh
+            ├── differential_analysis.py
+            └── fitting.py
+```
+
+---
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install trxrdpy
+```
+
+Optional extras:
+
+```bash
+pip install "trxrdpy[analysis]"
+pip install "trxrdpy[gui]"
+```
+
+### From source
+
+Clone the repository and install in editable mode:
+
+```bash
+git clone https://github.com/julioguzmanb/XRDpy.git
+cd XRDpy
+pip install -e .
+```
+
+---
+
+## Import
+
+```python
+import trxrdpy
+from trxrdpy import simulation
+from trxrdpy import analysis
+```
+
+More specific imports:
+
+```python
+from trxrdpy.analysis import fitting
+from trxrdpy.analysis import differential_analysis
+from trxrdpy.analysis.MaxIV_FemtoMAX import azimint
+from trxrdpy.analysis.Spring8_SACLA import datared
+```
+
+The package currently exposes the following top-level modules through `trxrdpy.__init__`:
+
+```python
+from . import utils
+from . import experiment
+from . import plot
+from . import sample
+from . import cif
+from . import simulation
+from . import analysis
+```
+
+---
+
+## Analysis organization
+
+The `analysis` section is organized into shared utilities, facility-specific workflows, and user-facing APIs.
+
+### `analysis.common`
+
+Facility-independent shared utilities:
+
+- path handling
+- plotting helpers
+- general helper functions
+- common azimuthal-integration helpers
+- fitting utilities
+- differential-analysis utilities
+
+### `analysis._shared_2d`
+
+Shared 2D-image-based azimuthal-integration workflow.
+
+This layer is currently used by:
+
+- **Max IV FemtoMAX**
+- **SPring-8 SACLA**
+
+### `analysis.ESRF_ID09`
+
+ID09-specific azimuthal-integration workflow.
+
+At ESRF ID09, the route to generate `xy` files differs from the homogenized 2D-image workflow used elsewhere. The beamline-provided tools and data structure are handled through a dedicated facility-specific implementation.
+
+### `analysis.MaxIV_FemtoMAX`
+
+FemtoMAX-specific analysis entry points.
+
+This section contains:
+
+- beamline-specific data reduction
+- azimuthal-integration entry points
+- wrappers that preserve the facility-facing public API
+
+### `analysis.Spring8_SACLA`
+
+SACLA-specific analysis entry points.
+
+This section contains:
+
+- beamline-specific data reduction
+- azimuthal-integration entry points
+- PBS job-submission helper scripts for HPC workflows
+
+### User-facing analysis APIs
+
+These modules provide the user-facing analysis layer after `xy` files are available:
+
+- `analysis.fitting`
+- `analysis.differential_analysis`
+
+Once `xy` files are created, the downstream fitting and differential-analysis pipeline is shared across facilities.
+
+---
+
+## Facility-specific workflow overview
+
+The analysis pipeline is intentionally split because raw-data handling differs across facilities.
+
+### Max IV FemtoMAX
+
+- Uses facility-specific data reduction
+- Produces homogenized 2D images
+- Reuses the shared 2D azimuthal-integration workflow
+- Then uses the shared downstream analysis pipeline
+
+### SPring-8 SACLA
+
+- Uses facility-specific data reduction
+- Some reduction steps may depend on beamline-specific software, legacy Python environments, VPN access, or HPC job submission
+- Produces homogenized 2D images
+- Reuses the shared 2D azimuthal-integration workflow
+- Then uses the shared downstream analysis pipeline
+
+### ESRF ID09
+
+- Does not use the same 2D homogenization route as FemtoMAX/SACLA
+- Uses a different beamline-specific azimuthal-integration workflow to generate `xy` files
+- Then uses the same downstream fitting and differential-analysis pipeline
+
+In other words:
+
+- **data reduction differs across facilities**
+- **`xy` generation differs for ID09 vs the shared 2D workflow**
+- **the downstream analysis after `xy` creation is shared**
+
+---
+
+## Notes
+
+- Some analysis workflows may require facility-specific dependencies that are not part of a standard Python installation.
+- Some SACLA workflows may rely on legacy Python environments and external HPC job submission.
+- The simulation and analysis sections are developed within the same package but target different use cases.
+- The project is published on PyPI as `trxrdpy` because the `xrdpy` name is already taken on PyPI.
+
+---
+
+## Citation
+
+If you use **XRDpy** in academic work, please cite the specific Zenodo release you used.
+
+For the current public release:
+
+**Julio Guzman-Brambila. XRDpy (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18925472**
+
+Project concept DOI (all versions):
+
+**https://doi.org/10.5281/zenodo.18634909**
+
+### BibTeX
+
+```bibtex
+@software{guzman_brambila_xrdpy_v100,
+  author    = {Guzman-Brambila, Julio},
+  title     = {XRDpy},
+  version   = {1.0.0},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.18925472},
+  url       = {https://doi.org/10.5281/zenodo.18925472}
+}
+```
+
+---
+
+## License
+
+Creative Commons Attribution 4.0 International (CC BY 4.0). See `LICENSE` for details.
+
+---
+
+## Author
+
+**Julio Guzman-Brambila**

trxrdpy-1.0.0/README.md

@@ -0,0 +1,290 @@
+# XRDpy
+
+**XRDpy** is a Python toolkit for **X-ray diffraction (XRD)** simulation and analysis, with a particular focus on **time-resolved / pump–probe diffraction workflows**.
+
+The project name on **GitHub** and **Zenodo** is **XRDpy**.
+The package is distributed on **PyPI** as **`trxrdpy`** and should be imported in Python as **`trxrdpy`**.
+
+---
+
+## Repository
+
+Source code: https://github.com/julioguzmanb/XRDpy
+
+## DOI (Zenodo)
+
+- **Project concept DOI (all versions):** https://doi.org/10.5281/zenodo.18634909
+- **Current release DOI (v1.0.0):** https://doi.org/10.5281/zenodo.18925472
+
+---
+
+## Main capabilities
+
+### Simulation
+
+- Polycrystalline XRD simulation
+- Single-crystal diffraction simulation
+- CIF-based crystallographic helpers
+- Plotting utilities for simulated diffraction data
+- A GUI for simulation workflows
+
+### Analysis
+
+- Beamline/facility-specific data handling
+- 2D image reduction and azimuthal integration
+- Standardized generation of 1D `xy` diffraction patterns
+- Peak fitting workflows
+- Differential analysis workflows
+- Shared utilities for plotting, path handling, and common analysis operations
+
+---
+
+## Package structure
+
+```text
+XRDpy/
+├── pyproject.toml
+├── README.md
+├── LICENSE
+└── src/
+    └── trxrdpy/
+        ├── __init__.py
+        ├── utils.py
+        ├── detector.py
+        ├── experiment.py
+        ├── plot.py
+        ├── sample.py
+        ├── cif.py
+        ├── simulation/
+        │   ├── __init__.py
+        │   ├── polycrystalline.py
+        │   ├── single_crystal.py
+        └── analysis/
+            ├── common/
+            │   ├── __init__.py
+            │   ├── paths.py
+            │   ├── plot_utils.py
+            │   ├── general_utils.py
+            │   ├── azimint_utils.py
+            │   ├── differential_analysis_utils.py
+            │   └── fitting_utils.py
+            ├── _shared_2d/
+            │   ├── __init__.py
+            │   └── azimint.py
+            ├── ESRF_ID09/
+            │   ├── __init__.py
+            │   └── azimint.py
+            ├── MaxIV_FemtoMAX/
+            │   ├── __init__.py
+            │   ├── datared_utils.py
+            │   ├── datared.py
+            │   └── azimint.py
+            ├── Spring8_SACLA/
+            │   ├── __init__.py
+            │   ├── datared.py
+            │   ├── azimint.py
+            │   └── pbs/
+            │       └── parallel_job_sender.sh
+            ├── differential_analysis.py
+            └── fitting.py
+```
+
+---
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install trxrdpy
+```
+
+Optional extras:
+
+```bash
+pip install "trxrdpy[analysis]"
+pip install "trxrdpy[gui]"
+```
+
+### From source
+
+Clone the repository and install in editable mode:
+
+```bash
+git clone https://github.com/julioguzmanb/XRDpy.git
+cd XRDpy
+pip install -e .
+```
+
+---
+
+## Import
+
+```python
+import trxrdpy
+from trxrdpy import simulation
+from trxrdpy import analysis
+```
+
+More specific imports:
+
+```python
+from trxrdpy.analysis import fitting
+from trxrdpy.analysis import differential_analysis
+from trxrdpy.analysis.MaxIV_FemtoMAX import azimint
+from trxrdpy.analysis.Spring8_SACLA import datared
+```
+
+The package currently exposes the following top-level modules through `trxrdpy.__init__`:
+
+```python
+from . import utils
+from . import experiment
+from . import plot
+from . import sample
+from . import cif
+from . import simulation
+from . import analysis
+```
+
+---
+
+## Analysis organization
+
+The `analysis` section is organized into shared utilities, facility-specific workflows, and user-facing APIs.
+
+### `analysis.common`
+
+Facility-independent shared utilities:
+
+- path handling
+- plotting helpers
+- general helper functions
+- common azimuthal-integration helpers
+- fitting utilities
+- differential-analysis utilities
+
+### `analysis._shared_2d`
+
+Shared 2D-image-based azimuthal-integration workflow.
+
+This layer is currently used by:
+
+- **Max IV FemtoMAX**
+- **SPring-8 SACLA**
+
+### `analysis.ESRF_ID09`
+
+ID09-specific azimuthal-integration workflow.
+
+At ESRF ID09, the route to generate `xy` files differs from the homogenized 2D-image workflow used elsewhere. The beamline-provided tools and data structure are handled through a dedicated facility-specific implementation.
+
+### `analysis.MaxIV_FemtoMAX`
+
+FemtoMAX-specific analysis entry points.
+
+This section contains:
+
+- beamline-specific data reduction
+- azimuthal-integration entry points
+- wrappers that preserve the facility-facing public API
+
+### `analysis.Spring8_SACLA`
+
+SACLA-specific analysis entry points.
+
+This section contains:
+
+- beamline-specific data reduction
+- azimuthal-integration entry points
+- PBS job-submission helper scripts for HPC workflows
+
+### User-facing analysis APIs
+
+These modules provide the user-facing analysis layer after `xy` files are available:
+
+- `analysis.fitting`
+- `analysis.differential_analysis`
+
+Once `xy` files are created, the downstream fitting and differential-analysis pipeline is shared across facilities.
+
+---
+
+## Facility-specific workflow overview
+
+The analysis pipeline is intentionally split because raw-data handling differs across facilities.
+
+### Max IV FemtoMAX
+
+- Uses facility-specific data reduction
+- Produces homogenized 2D images
+- Reuses the shared 2D azimuthal-integration workflow
+- Then uses the shared downstream analysis pipeline
+
+### SPring-8 SACLA
+
+- Uses facility-specific data reduction
+- Some reduction steps may depend on beamline-specific software, legacy Python environments, VPN access, or HPC job submission
+- Produces homogenized 2D images
+- Reuses the shared 2D azimuthal-integration workflow
+- Then uses the shared downstream analysis pipeline
+
+### ESRF ID09
+
+- Does not use the same 2D homogenization route as FemtoMAX/SACLA
+- Uses a different beamline-specific azimuthal-integration workflow to generate `xy` files
+- Then uses the same downstream fitting and differential-analysis pipeline
+
+In other words:
+
+- **data reduction differs across facilities**
+- **`xy` generation differs for ID09 vs the shared 2D workflow**
+- **the downstream analysis after `xy` creation is shared**
+
+---
+
+## Notes
+
+- Some analysis workflows may require facility-specific dependencies that are not part of a standard Python installation.
+- Some SACLA workflows may rely on legacy Python environments and external HPC job submission.
+- The simulation and analysis sections are developed within the same package but target different use cases.
+- The project is published on PyPI as `trxrdpy` because the `xrdpy` name is already taken on PyPI.
+
+---
+
+## Citation
+
+If you use **XRDpy** in academic work, please cite the specific Zenodo release you used.
+
+For the current public release:
+
+**Julio Guzman-Brambila. XRDpy (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18925472**
+
+Project concept DOI (all versions):
+
+**https://doi.org/10.5281/zenodo.18634909**
+
+### BibTeX
+
+```bibtex
+@software{guzman_brambila_xrdpy_v100,
+  author    = {Guzman-Brambila, Julio},
+  title     = {XRDpy},
+  version   = {1.0.0},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.18925472},
+  url       = {https://doi.org/10.5281/zenodo.18925472}
+}
+```
+
+---
+
+## License
+
+Creative Commons Attribution 4.0 International (CC BY 4.0). See `LICENSE` for details.
+
+---
+
+## Author
+
+**Julio Guzman-Brambila**

trxrdpy-1.0.0/pyproject.toml

@@ -0,0 +1,80 @@
+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "trxrdpy"
+version = "1.0.0"
+description = "Python toolkit for time-resolved X-ray diffraction simulation and beamline-dependent analysis workflows."
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.10"
+license = "CC-BY-4.0"
+license-files = ["LICENSE"]
+authors = [
+  { name = "Julio Guzman-Brambila" }
+]
+keywords = [
+  "xrd",
+  "time-resolved xrd",
+  "pump-probe",
+  "x-ray diffraction",
+  "diffraction",
+  "materials science",
+  "simulation",
+  "beamline analysis",
+  "pyFAI"
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Physics",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12"
+]
+dependencies = [
+  "numpy>=1.24",
+  "scipy>=1.10",
+  "matplotlib>=3.7",
+  "pandas>=2.0",
+  "h5py>=3.9",
+  "tqdm>=4.66",
+  "lmfit>=1.2",
+  "pyFAI>=2024.1",
+  "fabio>=2024.4",
+  "PyCifRW>=5.0",
+  "xrayutilities>=1.7",
+]
+
+[project.optional-dependencies]
+analysis = [
+  "pytxs==0.0.2",
+]
+gui = [
+  "PyQt5>=5.15",
+]
+dev = [
+  "build>=1.2",
+  "twine>=5.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/julioguzmanb/XRDpy"
+Repository = "https://github.com/julioguzmanb/XRDpy"
+Documentation = "https://github.com/julioguzmanb/XRDpy"
+DOI = "https://doi.org/10.5281/zenodo.18634909"
+Issues = "https://github.com/julioguzmanb/XRDpy/issues"
+
+[tool.setuptools]
+include-package-data = true
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["trxrdpy", "trxrdpy.*"]
+
+[tool.setuptools.package-data]
+"trxrdpy.analysis.Spring8_SACLA" = ["pbs/*.sh"]

trxrdpy-1.0.0/setup.cfg

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