Experiment cif reader #58
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Merging so that subsequent work on adapting the new xml parser is based on develop. |
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Mar 28, 2023
* Modify background label * Fix build script * Fixup build scripts * Update for specie work * Recalculate sin(Th)/Lambda * Set some experimental parameters * Fixup some serialization * Keep temp.cif file for fitting process * Fix sinTh/Lambda for CFML * Keep temp.cif for fitting with CFML * Update to new CFML api * Tidy up background work * More background tidying * Revert BG changes * Debugging info for y_calc * Add fitting notebook * More fitting work * Add CFML fitting notebook * Update branches * Update sin(theta)/lambda * Example bug fixes * disable ubuntu ci * Use new CFML api * Add ubuntu ci * Make libs repos public * macOS CI only * Temporarily disable libs * Remove poetry.lock * Try windows CI * Update RelinkCrysfml * Add linux and macos to CI * Install libgfortran4 on ubuntu * Update CFML jupyter notebook example * More x-array examples * Add setup and requirements for binder * Move to easyCore develop * Undo/Redo stack work * Initial implementation of get_hkl * Set default hkl arrays empty * Rename stack_deco to property_stack_deco * Change cryspy handling * Merge the interfacing work of Sprint13 (#8) * Update reflection list generation * Some changes related to new interface * self.conditions to job_info * More changes related to new CFML interface * Adjust resolution parameters * Use new_cfml branch of libs * Bump Cryspy from ^0.4 to ^0.5 * Use develop branch of libsWin32/libsLinux/libsDarwin * Temporarily fix for bravis_type in cryspy * Use new CrysFML with Bragg peaks * First work on new interface This is a test implementation where only experimental parameters are properly bound in the cryspy engine. ``` from easyDiffractionLib.interface import InterfaceFactory from easyDiffractionLib.Elements.Experiments.Experiment import Pars1D p = Pars1D.default() i = InterfaceFactory() p.interface = i p.generate_bindings() p.resolution_u = 0.2 ``` * More interfacing Continuing the cryspy interface with more details * More interfacing work * More interfacing work * Atom linking via ID * Hack to interface * Update fileless cryspy * File based CFML interface * File based GSAS2 interface * Fix BG issues with file based calculators * Fix a mistake (removal of phases) * Fix linking error (cryspy resolution and setup) * Reduce BG and HKL (CrysFML) computation time * Add matplotlib for cryspy * Fix for cryspy spacegroups (kinda) and GSAS peak HKL indexes * Modify MonkeyPatching of Phases The monkey patch of `Phases` to support the appending of interfaces was referencing the wrong append fn, hence the proper interfacing was not established. Modification of the sample, now when you do `obj.phases = phase` the phase is appended and `obj.phases = new_phases` overwrites the `obj.phases` field. sw * Fix Point BG evaluation when zero points Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Use 'develop' branch of easyCore * Update pyproject.toml * Update pyproject.toml * Update __init__.py * Update test.yml * Update pyproject.toml * Update GSASII.py * ReflectionList nrefs to nref * Moving to a more module based scheme * TOF support As easy as: ``` from easyCore import np from easyDiffractionLib import Phase from easyDiffractionLib.Runner import Runner import matplotlib.pyplot as plt r = Runner() p = Phase.from_cif_file('tests/PbSO4.cif') r.add_job('testing', job_type='powder1dTOF') r.add_phase(p, 'testing') job = r.jobs['testing'] job.pattern.zero_shift = 2.9121 job.create_simulation(np.linspace(3000, 11000, 801)) job.plot_simulation() plt.show() ``` * Decouple phases and EXP in cryspy * Fix legacy mode loading * Use the correct references for legacy mode * Unification of naming conventions * Fix TOF generation * Fix changing from TOF->CW * Fix all interfaces to use new schema * Update interface and exp_type verification logic * cryspy multiprocess support * Change mp pool methodology * Add scaling parameters for phases * Initial Polarization work * Work on obtaining HKL * Fix get HKL * Update requirements * Add TOF calculation for cryspy (#10) * Update pyproject.toml * Update __init__.py * Update test.yml * Update pyproject.toml * Update GSASII.py * ReflectionList nrefs to nref * Moving to a more module based scheme * TOF support As easy as: ``` from easyCore import np from easyDiffractionLib import Phase from easyDiffractionLib.Runner import Runner import matplotlib.pyplot as plt r = Runner() p = Phase.from_cif_file('tests/PbSO4.cif') r.add_job('testing', job_type='powder1dTOF') r.add_phase(p, 'testing') job = r.jobs['testing'] job.pattern.zero_shift = 2.9121 job.create_simulation(np.linspace(3000, 11000, 801)) job.plot_simulation() plt.show() ``` * Decouple phases and EXP in cryspy * Fix legacy mode loading * Use the correct references for legacy mode * Unification of naming conventions * Fix TOF generation * Fix changing from TOF->CW * Fix all interfaces to use new schema * Update interface and exp_type verification logic * Fix get HKL * Update requirements Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Delete .devcontainer directory * Delete tools directory * Tests base and README * Update LICENSE * fixed/updated FittingData notebook * more updates for new eC and eDL * Disable Lorentzian coefficients * Added CreateSample notebook, added structure show to existing notebooks. * Cleaned up outputs * Temporary workaround to get ADP value * easyCore dependence temporarily changed * Minor changes to the notebooks. Updated toml and fixed CFML interface * Separated working notebooks to a different directory. * Temporary workaround to get ADP value (GSASII) * Fix return value; back to develop branch * Add PbSO4 fitting notebook * Updated notebooks, corrected dependency for easyCore * Auto stash before merge of "more_notebooks" and "origin/more_notebooks" * Disable debug output for CFML * Use easyCore from the develop branch * Update fitting notebook * Move notebooks into 'examples' folder * Add instruction on how to run Jupyter Notebook examples * Update fitting example * A bit better README * Add contributing details * Start with tests * Delete setup.py * Update README.md * Update both `simulation` and `fitting` examples * Update README.md * Delete unused files * Added modified fix from the mp_mc branch to enable proper phase removal and profile calculation on experiment type change * Update both `simulation` and `fitting` examples * Fix up Docs and files * Update badge * Add generators * Update self_publish_alpha.yml * Auto stash before merge of "develop" and "origin/develop" * Update self_publish_alpha.yml * Update generate_html.py * Update self_publish_alpha.yml * Update self_publish_alpha.yml * Update self_publish_alpha.yml * Auto stash before merge of "develop" and "origin/develop" * Update self_publish_alpha.yml * Try to create tagged realease * Rename from easyDiffractionLib to easyDiffraction * Modify project and requirements * Use easysciencecore >= 0.1.1a0 * Only push if changes * Add `v` to tag * Update README.md * Write all packages * Add PR validation (needs labels) * Add more branch protection stuff * Add documentation label * Add the ability to launch examples on Binder (#12) * Create binder scripts * Remove unnecessary jupyter * Explicit external libs * Add correct path when using binder * Update readme [ci skip] * Switch from `matplotlib` to `bokeh` in notebooks * Update requirements to use `bokeh` instead of `matplotlib` * Add links to non-interactive preview for notebooks * Fix import `easyDiffractionLib` * Update notebooks * Update notebook * Update postBuild * Update Simulation.ipynb * Update notebooks * Add patch to autobuild (fix pypi arguments) * Create pypi_publish.yml * Modified mp_mc branch with pathos multiprocessing commented out * Added convencience methods for single phase profiles * Redefine additional_data['components'] with scaled values * typo in toml * Implement multiphase with CFML * More CFML multiphase changes Now phases are in the correct order and no memloc errors * Fix memory issues again * Fix spacegroup errors for multiphase * Add support for the multiple HKL sets * x_array is unnecessary for cryspy - hkl has already been calculated in the profile run * Fix for getting HKL's * Use easyCrystallography * Added a multiphase fitting example * fix a "typo". * fixed method signatures. * Update requirements * Test pre-release branch of easyCore * Updated copyright year * Try to use the release version of easyCore * update poetry force rebuild for testing easyCrystallography branch * Fetch easyCrystallography from pypi * Remove multiphase temp files on CFML calculator initialize #190 (#36) * Update pytest requirement from ^5.2 to ^7.1 (#37) Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@5.2.0...7.1.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update pyproject.toml (#38) Change classifier to reflect BSD * Updated pypi-publish step (#55) * Implement peak asymmetries for CrysPy P1D (#57) Co-authored-by: Andrew Sazonov <andrew.sazonov@esss.eu> * Experiment cif reader (#58) * Initial implementation. Things break. * prettify the code * Get the job object directly on reading the exp file * cherrypicked remaining changes from IOTake2. * More fixes * Update from_cif_file signature. Added case for xml-fied phase * Added a crutch for updating the background dict repr with the linked experiment item * Switch to pre-release-fixes branch of Core * Bump cfml from 0.0.1 to 0.0.3 (#44) Bumps [cfml]() from 0.0.1 to 0.0.3. --- updated-dependencies: - dependency-name: cfml dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Temporarily lock easyCore version after API breaking changes in 0.3.0. This will be removed on merging of IOTake3 * Update bokeh requirement from ^2.4.0 to ^3.0.3 (#65) Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version. - [Release notes](https://github.com/bokeh/bokeh/releases) - [Changelog](https://github.com/bokeh/bokeh/blob/3.0.3/docs/CHANGELOG) - [Commits](bokeh/bokeh@2.4.0...3.0.3) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Corrected space group key * initial version of the pdffit interface. Works for profile calculations. Loads cif files and pdffit-specific .gr files with experimental PDF * Added diffpy module dependencies * point to released version of core and cryst * Add fitting example, fixed minor issues * initial version, not much here yet * move bindings update from sample to job * return ndarray rather that xarray from fitting start improving serialization * Fixes for serialization of the job object * set default linked experiment for serialized no-exp loaded cases * Invoke bindings change properly * Added notebooks for profile calc and fitting * Bump cfml from 0.0.1 to 0.0.3 (#67) Bumps [cfml]() from 0.0.1 to 0.0.3. --- updated-dependencies: - dependency-name: cfml dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Try getting pdffit2 from local pypi * attempt at fixing dependencies * Updates from job_based branch. * make pdffit2 dependency optional, as gsas/cfml * Updated/fixed pdf interface, now conforming to the job based runs. Updated python scripts * Silence the diffpy backend STDOUT * branch update * Updated notebooks * Update py3dmol requirement from ^1.7.0 to ^2.0.1 (#69) Updates the requirements on [py3dmol](https://3dmol.org) to permit the latest version. --- updated-dependencies: - dependency-name: py3dmol dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * dep update * added delta1, delta2 parameters apply scale properly apply Uiso values properly modify initial parameters for fitting example so it converges nicely * Prettified the notebook and the script * Rename CrysPyV2 -> CrysPy Remove GSASII dependency. It will be made delayed import later * Update pyproject.toml * phase without exp - sim range param update causes errors CFML output parsing fails on certain systems * debug weird update issue * Workaround for resized coords * Add pdffit dependency so pip install doesn't complain * update requirements.txt * Minor updates. Moved xarray checks to app. bumped release number added contributor * Make sure interface bindings are properly set on job instantiation * pdf changes after Celine's comments * add dependency on pycifrw, required by pdffit2 * delta1 and delta2 have units * parameter name should be prettyfied * check if setting pip config helps with module installation * Modify wavelength to correspond to the gr input file. Add unit to Q_damp * notebook and example script updates * Added "spdiameter" parameter, as per GSASII examples * added spdiameter parameter to the notebook examples * update initial values for spdiameter and update the examples * don't update atoms without adp * workaround for CFML failures * Bumped release version Commented out GSAS in toml/requirements Try linking pypi versions of EX and EC * Updated notebooks and added missed method in CryspyV2 interface * Added minor updates about the current release * Do not patch the version but take it directly from poetry --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> Co-authored-by: Simon Ward <2798086+wardsimon@users.noreply.github.com> Co-authored-by: Andrew Sazonov <Andrew.Sazonov@icloud.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew McCluskey <andrew@mccluskey.scot> Co-authored-by: Andrew Sazonov <andrew.sazonov@esss.eu>
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This moves the experiment cif reader from the app to the lib.
Example usage: