xrdkit 0.1.0__tar.gz

xrdkit-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Amir Khesro
+
+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.

xrdkit-0.1.0/PKG-INFO

@@ -0,0 +1,229 @@
+Metadata-Version: 2.4
+Name: xrdkit
+Version: 0.1.0
+Summary: Reusable X-ray diffraction analysis toolkit for electroceramics research
+Keywords: x-ray diffraction,XRD,powder diffraction,Rietveld,Le Bail,GSAS-II,materials science,ceramics,crystallography
+Author: Amir Khesro
+Author-email: Amir Khesro <am.khesro@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+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
+Classifier: Typing :: Typed
+Requires-Dist: matplotlib>=3.11.1
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: scipy>=1.13.0
+Requires-Dist: pymatgen>=2026.5.4 ; extra == 'phases'
+Requires-Python: >=3.11
+Project-URL: Homepage, https://github.com/amirkhesro/xrdkit
+Project-URL: Repository, https://github.com/amirkhesro/xrdkit
+Project-URL: Issues, https://github.com/amirkhesro/xrdkit/issues
+Project-URL: Changelog, https://github.com/amirkhesro/xrdkit/blob/main/CHANGELOG.md
+Provides-Extra: phases
+Description-Content-Type: text/markdown
+
+# xrdkit
+
+A reusable X-ray diffraction analysis toolkit for electroceramics research.
+
+`xrdkit` provides shared, importable routines for loading, processing and
+analysing XRD patterns, so that the same analysis code can be reused across
+projects instead of being copied between one-off scripts.
+
+## Installation
+
+```bash
+pip install xrdkit
+```
+
+Phase matching against the COD needs pymatgen, which comes with the `phases`
+extra:
+
+```bash
+pip install "xrdkit[phases]"
+```
+
+GSAS-II is optional and is needed only for the Rietveld driver in
+`xrdkit.gsas2`. It is not a Python dependency: install it separately and
+point `XRDKIT_GSAS2_PYTHON` and `XRDKIT_GSAS2_HOME` at it, or leave it at
+`~/gsas2main`. Every other module works without it.
+
+## Data
+
+This repository contains **code only**. Raw and processed diffraction data
+(including `.xrdml` files) live in a separate data repository and are never
+committed here.
+
+## GSAS-II refinement
+
+GSAS-II runs under its own Python, so `xrdkit.gsas2` writes a job as JSON and
+runs `gsas2_driver.py` on it there (`run_job`), with `-B`; xrdkit writes
+nothing into the GSAS-II installation. `find_gsas2` locates it
+(`XRDKIT_GSAS2_PYTHON`, `XRDKIT_GSAS2_HOME`, or `~/gsas2main`).
+
+GSAS-II's own version and update check, run whenever its scripting module is
+imported, writes one bytecode file inside its installation
+(`Lib/site-packages/scipy/__pycache__/__config__.cpython-313.pyc` in the
+`~/gsas2main` install); it is written once, not on every run, and does not
+come from xrdkit.
+
+`build_refine_job` assembles a refinement from a list of stages, each adding
+flags to the ones before (see the `gsas2_driver` module notes for every key):
+
+| Stage key | Refines |
+| --- | --- |
+| `background`, `scale`, `zero`, `displacement`, `instrument` | histogram and instrument |
+| `cell`, `le_bail`, `phase_fractions`, `size`, `mustrain` | phase, by name or all |
+| `overall_uiso` | one Uiso for every atom of a phase |
+| `uiso_groups` | `{phase: [[site, ...], ...]}`: one Uiso for every atom on each group's sites |
+| `atoms`, `atom_flags` | F, X, U for every atom, or for named atoms |
+| `coordinates` | `{phase: {site: "xz" or "all"}}`: the coordinates to free on each site; the rest are held, atoms sharing a site move together |
+| `origin` | `{phase: {"site": label, "axis": "z"}}`: a site's coordinate held to fix the origin; a stage that would leave the origin floating along a polar axis fails |
+| `occupancies` | `[{"phase", "sites": [...], "elements": [...]}]`: the named elements' occupancies on the named sites, each element's content over them held (so the vacancies over them too) |
+
+Job options besides the stages: `limits`, `cycles`, `broadening`,
+`background_start`, `scale_start`, `overall_uiso_start`, `le_bail_cycles`,
+`max_passes` and `pass_tolerance` (refine each stage until it settles),
+`on_flagged` and `on_unsettled` (below), `sanity` (`{"max_shift": 0.05,
+"reference": {phase: [{"label", "xyz"}]}}`) and `bonds` (`True` or
+`{"anions", "dmax", "dmin"}`). A phase's `atoms` edits the structure read
+from its CIF in the project only: occupancies, positions and Uiso, and atoms
+added on existing sites; `structure_edits` gives the edits that set up a
+refined structure again, so that one refinement starts where another ended.
+
+Every stage of the result records its residuals and parameters with esds, the
+atoms as it left them, the coordinates it refined and held by site, its
+occupancy constraints, and a sanity check: negative Uiso, occupancies outside
+0 to 1 (and site totals above 1), and sites moved more than `max_shift`
+(fractional) from the reference. With `bonds`, `run_job` adds the final
+model's cation to anion distances (`xrdkit.structure.bond_lengths`, to oxygen
+up to 3 Å by default) to the result.
+
+### What becomes of a stage that goes wrong
+
+So that a sequence can be run unattended and still leave a usable record,
+every stage carries a `status` and the run goes on from the last stage kept:
+
+| Status | The stage | The run |
+| --- | --- | --- |
+| `clean` | settled, and raised no sanity flag the stage before it lacked | kept |
+| `unsettled` | reached `max_passes` still moving, and raised no new flag | kept |
+| `flagged` | raised a new sanity flag, with `on_flagged` `"accept"` | kept |
+| `rejected` | raised a new flag under `on_flagged` `"reject"` (the default), or did not settle under `on_unsettled` `"reject"` | rolled back |
+| `failed` | raised | rolled back, and the run ends |
+
+**Rejected.** A sanity flag means the model has gone somewhere it should not
+be — a Uiso below zero, an occupancy outside 0 to 1, a site further from the
+reference than `max_shift` — so the stage that raised one is rejected by
+default. It is recorded in full, residuals, parameters and atoms, with
+`rejected_because` and its name in the result's `rejected`. The project then
+goes back to the state the last stage kept left it in — parameters, atoms
+and constraints — and is saved so, and the stage's own entries are dropped
+from the stages, so that what it alone refined is held in every stage after
+it. `on_flagged: "accept"` keeps it instead, as `"flagged"`.
+
+**Unsettled.** Reaching the pass cap only means the stage was still moving
+when the passes ran out, which is not in itself wrong, so it is kept by
+default and `largest_remaining_move` records the parameter that moved most
+in its last pass and by how many esds. `on_unsettled: "reject"` rolls one
+back like a flagged stage, for a caller that wants nothing unsettled in its
+model.
+
+**Undetermined.** Each stage also records, as `undetermined`, the refined
+atom parameters the data do not determine
+(`gsas2_driver.find_undetermined`): an occupancy whose esd is more than half
+its allowed range, 0 to 1, and a coordinate or an isotropic Uiso whose esd
+is larger than its shift from where the job found it. Such a value is not a
+result, whatever its stage's status. The result's `undetermined` are those
+of the last stage kept.
+
+**The model a run leaves.** Every run ends with `final`, and with
+`export_prefix` an `exports`, whatever became of its stages: the model of
+the last stage kept, or, where no stage was kept, the one the job started
+from, computed by a refinement of no cycles that moves nothing. The result's
+`final_from` names the stage they come from, or `"job start"`; a starting
+model has no refined parameter and so no esd.
+
+### Writing a sequence up
+
+For a pipeline that runs several refinements in turn, `xrdkit.gsas2` writes
+what they came to:
+
+| Function | Gives |
+| --- | --- |
+| `stage_status` | one stage's status, worked out for a result written before the driver recorded one |
+| `accepted_stages` | the stages of a result that were refined and kept |
+| `stage_statuses` | every stage as `{name, status, reason, passes, rwp, gof, undetermined}`, `reason` saying why it is not clean |
+| `stage_status_table` | those as markdown table lines |
+| `log_tail` | the last lines of a GSAS-II log |
+| `failure_markdown` | a write up of a refinement that could not be finished: the error, the stages it got through and the log tail |
+| `summary_markdown` | a summary of a sequence: a row per refinement with its final Rwp, GOF and key values, the status of each stage, then every stage not clean with why and the parameters left undetermined |
+
+## Refinement settings
+
+`xrdkit.config` reads the settings of a refinement pipeline from a TOML file
+with the standard library's `tomllib` (`load_config`): one table per sample
+under `samples` and one per reference structure under `structures`. It
+checks them as it reads, and a key missing or unknown, a value of the wrong
+kind, or a sample composition that does not fit its structure's sites (an
+element on no site and not added by the rule, or more atoms per cell on a
+kind of site than it has positions) raises `ConfigError` naming the file and
+the table. `sample_settings` finds a sample by its id or table name, with its
+structure.
+
+| Table | Keys |
+| --- | --- |
+| `samples.<name>` | `id`, `scan`, `composition` (atoms per formula unit), `structure`, `start_cell` (`{file, model}` or `{a, c}`), `two_theta`, `background` (`{function, terms}`), `refine_microstrain`, `notes`; optionally `followed_reflections`, `trials` (`{runs = [{low, terms}], followed}`), `write_up` (text by mode and section), `unsettled` (the rule for each mode, over the top level one) |
+| `unsettled` | at the top level, the default rule for a stage of each mode that has not settled, `"accept"` (the pipeline's default) or `"reject"`, by the caller's own mode names; each sample carries it merged with its own as its `unsettled` |
+| `structures.<name>` | `cif`, `label`, `phase_name`, `space_group`, `formula_units`, `sites` (`{atoms = {label = element}, wyckoff, kind}`, kind A, B or O), `uiso_groups` (`{name, sites}`), `origin` (`{site, axis}`), `exchange` (`{elements, sites}`), `composition` (`{added = {element = host}}`); optionally `free_coordinates` (by Wyckoff position), `bond_limits` (`{kind = {min, max}}`) |
+
+From a structure table, `xrdkit.structure.site_setup` finds the sites among a
+phase's atoms as the driver reports them, checking that each site's atoms
+share one position, are of the elements given and have the multiplicity of
+its Wyckoff position, and that no atom is left over. It returns the sites by
+kind, the Uiso groups, the coordinates to refine on each site, the origin site
+and the exchange, in the forms the stage keys above take.
+`composition_edits` gives the atom edits that put a nominal composition on
+the sites by the table's rule: each element the CIF holds is scaled by one
+factor over its sites, which keeps its distribution, and each added element
+goes on its host's sites in proportion to the host's occupancy.
+`cell_contents` gives the atoms of each element per cell.
+
+For example, the sample pipeline of the XRD analysis repository reads every
+sample and structure setting from its `config/samples.toml` and runs Le Bail,
+fixed atoms, coordinates and occupancies in turn, each from the saved result
+of the one before:
+
+```
+python -B scripts/refine_sample.py 10                          # Le Bail only
+python -B scripts/refine_sample.py 10 --trials                 # Le Bail with the configured trial ranges and background terms
+python -B scripts/refine_sample.py 10 --through occupancies    # all four modes
+python -B scripts/refine_sample.py 10 --from coordinates       # one mode, from the saved fixed atoms result
+python -B scripts/refine_sample.py 10 --from coordinates --through occupancies
+```
+
+It passes each mode's `unsettled` rule and pass cap to its job, writes the
+mode's write up with `failure_markdown` and stops with a non-zero status
+where a mode cannot be finished, and writes `summary.md` beside the write
+ups with `summary_markdown` at the end of every run.
+
+## Status
+
+Under active development. The API is not yet stable and may change without
+notice.
+
+## Citing
+
+If xrdkit contributes to work you publish, please cite it. The metadata is in
+[CITATION.cff](CITATION.cff), which GitHub renders as a ready-made citation
+under **Cite this repository**.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

xrdkit-0.1.0/README.md

@@ -0,0 +1,199 @@
+# xrdkit
+
+A reusable X-ray diffraction analysis toolkit for electroceramics research.
+
+`xrdkit` provides shared, importable routines for loading, processing and
+analysing XRD patterns, so that the same analysis code can be reused across
+projects instead of being copied between one-off scripts.
+
+## Installation
+
+```bash
+pip install xrdkit
+```
+
+Phase matching against the COD needs pymatgen, which comes with the `phases`
+extra:
+
+```bash
+pip install "xrdkit[phases]"
+```
+
+GSAS-II is optional and is needed only for the Rietveld driver in
+`xrdkit.gsas2`. It is not a Python dependency: install it separately and
+point `XRDKIT_GSAS2_PYTHON` and `XRDKIT_GSAS2_HOME` at it, or leave it at
+`~/gsas2main`. Every other module works without it.
+
+## Data
+
+This repository contains **code only**. Raw and processed diffraction data
+(including `.xrdml` files) live in a separate data repository and are never
+committed here.
+
+## GSAS-II refinement
+
+GSAS-II runs under its own Python, so `xrdkit.gsas2` writes a job as JSON and
+runs `gsas2_driver.py` on it there (`run_job`), with `-B`; xrdkit writes
+nothing into the GSAS-II installation. `find_gsas2` locates it
+(`XRDKIT_GSAS2_PYTHON`, `XRDKIT_GSAS2_HOME`, or `~/gsas2main`).
+
+GSAS-II's own version and update check, run whenever its scripting module is
+imported, writes one bytecode file inside its installation
+(`Lib/site-packages/scipy/__pycache__/__config__.cpython-313.pyc` in the
+`~/gsas2main` install); it is written once, not on every run, and does not
+come from xrdkit.
+
+`build_refine_job` assembles a refinement from a list of stages, each adding
+flags to the ones before (see the `gsas2_driver` module notes for every key):
+
+| Stage key | Refines |
+| --- | --- |
+| `background`, `scale`, `zero`, `displacement`, `instrument` | histogram and instrument |
+| `cell`, `le_bail`, `phase_fractions`, `size`, `mustrain` | phase, by name or all |
+| `overall_uiso` | one Uiso for every atom of a phase |
+| `uiso_groups` | `{phase: [[site, ...], ...]}`: one Uiso for every atom on each group's sites |
+| `atoms`, `atom_flags` | F, X, U for every atom, or for named atoms |
+| `coordinates` | `{phase: {site: "xz" or "all"}}`: the coordinates to free on each site; the rest are held, atoms sharing a site move together |
+| `origin` | `{phase: {"site": label, "axis": "z"}}`: a site's coordinate held to fix the origin; a stage that would leave the origin floating along a polar axis fails |
+| `occupancies` | `[{"phase", "sites": [...], "elements": [...]}]`: the named elements' occupancies on the named sites, each element's content over them held (so the vacancies over them too) |
+
+Job options besides the stages: `limits`, `cycles`, `broadening`,
+`background_start`, `scale_start`, `overall_uiso_start`, `le_bail_cycles`,
+`max_passes` and `pass_tolerance` (refine each stage until it settles),
+`on_flagged` and `on_unsettled` (below), `sanity` (`{"max_shift": 0.05,
+"reference": {phase: [{"label", "xyz"}]}}`) and `bonds` (`True` or
+`{"anions", "dmax", "dmin"}`). A phase's `atoms` edits the structure read
+from its CIF in the project only: occupancies, positions and Uiso, and atoms
+added on existing sites; `structure_edits` gives the edits that set up a
+refined structure again, so that one refinement starts where another ended.
+
+Every stage of the result records its residuals and parameters with esds, the
+atoms as it left them, the coordinates it refined and held by site, its
+occupancy constraints, and a sanity check: negative Uiso, occupancies outside
+0 to 1 (and site totals above 1), and sites moved more than `max_shift`
+(fractional) from the reference. With `bonds`, `run_job` adds the final
+model's cation to anion distances (`xrdkit.structure.bond_lengths`, to oxygen
+up to 3 Å by default) to the result.
+
+### What becomes of a stage that goes wrong
+
+So that a sequence can be run unattended and still leave a usable record,
+every stage carries a `status` and the run goes on from the last stage kept:
+
+| Status | The stage | The run |
+| --- | --- | --- |
+| `clean` | settled, and raised no sanity flag the stage before it lacked | kept |
+| `unsettled` | reached `max_passes` still moving, and raised no new flag | kept |
+| `flagged` | raised a new sanity flag, with `on_flagged` `"accept"` | kept |
+| `rejected` | raised a new flag under `on_flagged` `"reject"` (the default), or did not settle under `on_unsettled` `"reject"` | rolled back |
+| `failed` | raised | rolled back, and the run ends |
+
+**Rejected.** A sanity flag means the model has gone somewhere it should not
+be — a Uiso below zero, an occupancy outside 0 to 1, a site further from the
+reference than `max_shift` — so the stage that raised one is rejected by
+default. It is recorded in full, residuals, parameters and atoms, with
+`rejected_because` and its name in the result's `rejected`. The project then
+goes back to the state the last stage kept left it in — parameters, atoms
+and constraints — and is saved so, and the stage's own entries are dropped
+from the stages, so that what it alone refined is held in every stage after
+it. `on_flagged: "accept"` keeps it instead, as `"flagged"`.
+
+**Unsettled.** Reaching the pass cap only means the stage was still moving
+when the passes ran out, which is not in itself wrong, so it is kept by
+default and `largest_remaining_move` records the parameter that moved most
+in its last pass and by how many esds. `on_unsettled: "reject"` rolls one
+back like a flagged stage, for a caller that wants nothing unsettled in its
+model.
+
+**Undetermined.** Each stage also records, as `undetermined`, the refined
+atom parameters the data do not determine
+(`gsas2_driver.find_undetermined`): an occupancy whose esd is more than half
+its allowed range, 0 to 1, and a coordinate or an isotropic Uiso whose esd
+is larger than its shift from where the job found it. Such a value is not a
+result, whatever its stage's status. The result's `undetermined` are those
+of the last stage kept.
+
+**The model a run leaves.** Every run ends with `final`, and with
+`export_prefix` an `exports`, whatever became of its stages: the model of
+the last stage kept, or, where no stage was kept, the one the job started
+from, computed by a refinement of no cycles that moves nothing. The result's
+`final_from` names the stage they come from, or `"job start"`; a starting
+model has no refined parameter and so no esd.
+
+### Writing a sequence up
+
+For a pipeline that runs several refinements in turn, `xrdkit.gsas2` writes
+what they came to:
+
+| Function | Gives |
+| --- | --- |
+| `stage_status` | one stage's status, worked out for a result written before the driver recorded one |
+| `accepted_stages` | the stages of a result that were refined and kept |
+| `stage_statuses` | every stage as `{name, status, reason, passes, rwp, gof, undetermined}`, `reason` saying why it is not clean |
+| `stage_status_table` | those as markdown table lines |
+| `log_tail` | the last lines of a GSAS-II log |
+| `failure_markdown` | a write up of a refinement that could not be finished: the error, the stages it got through and the log tail |
+| `summary_markdown` | a summary of a sequence: a row per refinement with its final Rwp, GOF and key values, the status of each stage, then every stage not clean with why and the parameters left undetermined |
+
+## Refinement settings
+
+`xrdkit.config` reads the settings of a refinement pipeline from a TOML file
+with the standard library's `tomllib` (`load_config`): one table per sample
+under `samples` and one per reference structure under `structures`. It
+checks them as it reads, and a key missing or unknown, a value of the wrong
+kind, or a sample composition that does not fit its structure's sites (an
+element on no site and not added by the rule, or more atoms per cell on a
+kind of site than it has positions) raises `ConfigError` naming the file and
+the table. `sample_settings` finds a sample by its id or table name, with its
+structure.
+
+| Table | Keys |
+| --- | --- |
+| `samples.<name>` | `id`, `scan`, `composition` (atoms per formula unit), `structure`, `start_cell` (`{file, model}` or `{a, c}`), `two_theta`, `background` (`{function, terms}`), `refine_microstrain`, `notes`; optionally `followed_reflections`, `trials` (`{runs = [{low, terms}], followed}`), `write_up` (text by mode and section), `unsettled` (the rule for each mode, over the top level one) |
+| `unsettled` | at the top level, the default rule for a stage of each mode that has not settled, `"accept"` (the pipeline's default) or `"reject"`, by the caller's own mode names; each sample carries it merged with its own as its `unsettled` |
+| `structures.<name>` | `cif`, `label`, `phase_name`, `space_group`, `formula_units`, `sites` (`{atoms = {label = element}, wyckoff, kind}`, kind A, B or O), `uiso_groups` (`{name, sites}`), `origin` (`{site, axis}`), `exchange` (`{elements, sites}`), `composition` (`{added = {element = host}}`); optionally `free_coordinates` (by Wyckoff position), `bond_limits` (`{kind = {min, max}}`) |
+
+From a structure table, `xrdkit.structure.site_setup` finds the sites among a
+phase's atoms as the driver reports them, checking that each site's atoms
+share one position, are of the elements given and have the multiplicity of
+its Wyckoff position, and that no atom is left over. It returns the sites by
+kind, the Uiso groups, the coordinates to refine on each site, the origin site
+and the exchange, in the forms the stage keys above take.
+`composition_edits` gives the atom edits that put a nominal composition on
+the sites by the table's rule: each element the CIF holds is scaled by one
+factor over its sites, which keeps its distribution, and each added element
+goes on its host's sites in proportion to the host's occupancy.
+`cell_contents` gives the atoms of each element per cell.
+
+For example, the sample pipeline of the XRD analysis repository reads every
+sample and structure setting from its `config/samples.toml` and runs Le Bail,
+fixed atoms, coordinates and occupancies in turn, each from the saved result
+of the one before:
+
+```
+python -B scripts/refine_sample.py 10                          # Le Bail only
+python -B scripts/refine_sample.py 10 --trials                 # Le Bail with the configured trial ranges and background terms
+python -B scripts/refine_sample.py 10 --through occupancies    # all four modes
+python -B scripts/refine_sample.py 10 --from coordinates       # one mode, from the saved fixed atoms result
+python -B scripts/refine_sample.py 10 --from coordinates --through occupancies
+```
+
+It passes each mode's `unsettled` rule and pass cap to its job, writes the
+mode's write up with `failure_markdown` and stops with a non-zero status
+where a mode cannot be finished, and writes `summary.md` beside the write
+ups with `summary_markdown` at the end of every run.
+
+## Status
+
+Under active development. The API is not yet stable and may change without
+notice.
+
+## Citing
+
+If xrdkit contributes to work you publish, please cite it. The metadata is in
+[CITATION.cff](CITATION.cff), which GitHub renders as a ready-made citation
+under **Cite this repository**.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

xrdkit-0.1.0/pyproject.toml

@@ -0,0 +1,55 @@
+[project]
+name = "xrdkit"
+version = "0.1.0"
+description = "Reusable X-ray diffraction analysis toolkit for electroceramics research"
+readme = "README.md"
+requires-python = ">=3.11"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = [
+    "x-ray diffraction",
+    "XRD",
+    "powder diffraction",
+    "Rietveld",
+    "Le Bail",
+    "GSAS-II",
+    "materials science",
+    "ceramics",
+    "crystallography",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Typing :: Typed",
+]
+dependencies = [
+    "matplotlib>=3.11.1",
+    "numpy>=2.0.0",
+    "scipy>=1.13.0",
+]
+
+[[project.authors]]
+name = "Amir Khesro"
+email = "am.khesro@gmail.com"
+
+[project.urls]
+Homepage = "https://github.com/amirkhesro/xrdkit"
+Repository = "https://github.com/amirkhesro/xrdkit"
+Issues = "https://github.com/amirkhesro/xrdkit/issues"
+Changelog = "https://github.com/amirkhesro/xrdkit/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+phases = ["pymatgen>=2026.5.4"]
+
+[build-system]
+requires = ["uv_build>=0.12.0,<0.13.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = ["pytest>=9.1.1"]

xrdkit-0.1.0/pyproject.toml.orig

@@ -0,0 +1,58 @@
+[project]
+name = "xrdkit"
+version = "0.1.0"
+description = "Reusable X-ray diffraction analysis toolkit for electroceramics research"
+readme = "README.md"
+requires-python = ">=3.11"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Amir Khesro", email = "am.khesro@gmail.com" }
+]
+keywords = [
+    "x-ray diffraction",
+    "XRD",
+    "powder diffraction",
+    "Rietveld",
+    "Le Bail",
+    "GSAS-II",
+    "materials science",
+    "ceramics",
+    "crystallography",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Typing :: Typed",
+]
+dependencies = [
+    "matplotlib>=3.11.1",
+    "numpy>=2.0.0",
+    "scipy>=1.13.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/amirkhesro/xrdkit"
+Repository = "https://github.com/amirkhesro/xrdkit"
+Issues = "https://github.com/amirkhesro/xrdkit/issues"
+Changelog = "https://github.com/amirkhesro/xrdkit/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+phases = [
+    "pymatgen>=2026.5.4",
+]
+
+[build-system]
+requires = ["uv_build>=0.12.0,<0.13.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    "pytest>=9.1.1",
+]