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* Fix fitting for bumps * Bump pint from 0.16 to 0.16.1 (#22) Bumps [pint](https://github.com/hgrecco/pint) from 0.16 to 0.16.1. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.16.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.0.2 to 6.1.0 (#26) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.0.2 to 6.1.0. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.0.2...6.1.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Merge sprint work to dev (#29) * Rename pars to avoid conflict Implement internal name changes in fitting (currently lmfit) due to possible duplicate names * Rename pars to avoid conflict (bumps) * First working constraints * More work on Constraints * Bump Constraints [ci skip] * Bump constraints [ci skip] * Parameter path generation [ci skip] * Reverse lookup fix [ci skip] * Bump fitting template [ci skip] * Add first look at Groups and Atom/s * Bump pint from 0.16 to 0.16.1 (#21) * Bump pint from 0.16 to 0.16.1 Bumps [pint](https://github.com/hgrecco/pint) from 0.16 to 0.16.1. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.16.1) Signed-off-by: dependabot[bot] <support@github.com> * Update dependabot [ci skip] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Simon Ward <2798086+wardsimon@users.noreply.github.com> * Constraints across fitters and constraints sdterr * More work on Atoms and constraints * Create codeql-analysis.yml (#23) * Create ossar-analysis.yml (#24) * Work on cif/star * Add enabled flag * CIF sections for Cell/Site/Atoms * Add header, cif/star conversion * Working star/cif io * Work on adp * implement adp * Some name changes [ci skip] * Bug fixes for advanced interfacing * CIF work * More cif work * New and improved cif io! * quickfix for spacegroup [ci skip] * Fix adp weirdness [ci skip] * More spacegroup fixes [ci skip] * Add Crystals [ci skip] * Remove auto interfacing as it's not ready yet. * Fix site to dict * Spacegroup fixes * Groups are now lists when serialised * Add docstrings, fix crystal sites * More spacegoup fun * Fix for crystal all site generation. Add multi-phase support * Fixes for multiphase cif reading * FIX: Cif creation update error * Add atom generation tolerence * Add selecting string index in cif * Select phase in cif file output * Fix some group namings [ci skip] * SG work * Fix a static method * Enforce symmetry on crystals * Make enforcing symmetry optional * Fix fat fingers and introduce a setup.py * Finally fix up those unit tests * Update parameter serialization * Update SG tools encoding * Deletion of items and pruning of graphs * More SG work, handling co-ord system codes * Fix printing items with error When printing an item with error, if the bracketed error was more than a single magnitude, the decimal point would be off by that magnitude * Fixup codefactor * More fixups * Add a finalizer to constraints Added a finalizer to constraints so that when a dependent variable is force-disabled, it will be re-enabled on constraint deletion. * Fix atom orbit generation * Rename atoms_list to atoms Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Fix duplicate object type * Bump codecov from 2.1.9 to 2.1.10 (#28) Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.9 to 2.1.10. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.9...v2.1.10) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.1.0 to 6.1.2 (#31) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.1.0 to 6.1.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.1.0...6.1.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump uncertainties from 3.1.4 to 3.1.5 (#36) Bumps [uncertainties](https://github.com/lebigot/uncertainties) from 3.1.4 to 3.1.5. - [Release notes](https://github.com/lebigot/uncertainties/releases) - [Commits](https://github.com/lebigot/uncertainties/compare/3.1.4...3.1.5) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump asteval from 0.9.19 to 0.9.21 (#35) Bumps [asteval](https://github.com/newville/asteval) from 0.9.19 to 0.9.21. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.19...0.9.21) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump numpy from 1.19.2 to 1.19.4 (#32) Bumps [numpy](https://github.com/numpy/numpy) from 1.19.2 to 1.19.4. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/master/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.19.2...v1.19.4) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump bumps from 0.7.16 to 0.7.18 (#34) Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.16 to 0.7.18. Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Specie work (#37) * Initial specie work * Fixup some serialization * Initial work on bonding * add fitting methods * LM fit method list update * Fix default minimizer method * Rename atom_list to atoms * Quick bonding fixes * User supplied extent for calculations * Quick fixes Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Fix cif printing on empty phases * Bump pytest from 6.1.2 to 6.2.1 (#40) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.1.2 to 6.2.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.1.2...6.2.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.3.1 to 3.4.0 (#39) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.3.1 to 3.4.0. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.3.1...v3.4.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump bumps from 0.7.18 to 0.8.0 (#41) Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.18 to 0.8.0. Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump numpy from 1.19.4 to 1.19.5 (#44) Bumps [numpy](https://github.com/numpy/numpy) from 1.19.4 to 1.19.5. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/master/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.19.4...v1.19.5) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump codecov from 2.1.10 to 2.1.11 (#42) Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.10 to 2.1.11. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.10...v2.1.11) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.4.0 to 3.5.0 (#43) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.4.0 to 3.5.0. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.4.0...v3.5.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.5.0 to 3.5.1 (#45) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.5.0 to 3.5.1. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.5.0...v3.5.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-cov from 2.10.1 to 2.11.1 (#47) Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.10.1 to 2.11.1. - [Release notes](https://github.com/pytest-dev/pytest-cov/releases) - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v2.10.1...v2.11.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.2.1 to 6.2.2 (#48) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.1 to 6.2.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.2.1...6.2.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump lmfit from 1.0.1 to 1.0.2 (#49) Bumps [lmfit](https://github.com/lmfit/lmfit-py) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/lmfit/lmfit-py/releases) - [Changelog](https://github.com/lmfit/lmfit-py/blob/master/doc/whatsnew.rst) - [Commits](https://github.com/lmfit/lmfit-py/compare/1.0.1...1.0.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump asteval from 0.9.21 to 0.9.22 (#52) Bumps [asteval](https://github.com/newville/asteval) from 0.9.21 to 0.9.22. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.21...0.9.22) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Remove poetery.lock It's really annoying and doesn't work * Implement xarrays in easyCore (#51) * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Start making datasets * Start work on datasets * xarray fitting attempt Hint: it's a fail :-( * xarray fitting in nd with lmfit * More data array examples * Add examples and more fitting work * Minor bug fixes * Multifitting of xarray DataArrays * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Delete poetry.lock * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Start making datasets * Start work on datasets * xarray fitting attempt Hint: it's a fail :-( * xarray fitting in nd with lmfit * More data array examples * Add examples and more fitting work * Minor bug fixes * Multifitting of xarray DataArrays * Renaming and Documentation * Fix circular import. * Fitting macro fix * Fix some pull request issues. * Bump asteval from 0.9.22 to 0.9.23 (#53) * Bump asteval from 0.9.22 to 0.9.23 Bumps [asteval](https://github.com/newville/asteval) from 0.9.22 to 0.9.23. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.22...0.9.23) Signed-off-by: dependabot[bot] <support@github.com> * Delete poetry.lock Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Simon Ward <2798086+wardsimon@users.noreply.github.com> * Undo/Redo stack info Add some missing text to undo/redo actions * Undo/Redo work Just some undo redo work and cleaning up of decorator names. Not much to see here * Update monty requirement from ^4.0.2 to ^2021.3.3 (#54) Updates the requirements on [monty](https://github.com/materialsvirtuallab/monty) to permit the latest version. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.html) - [Commits](https://github.com/materialsvirtuallab/monty/compare/v4.0.2...v2021.3.3) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix undo/redo for inherited base classes * Fix printable representation of a Descriptor/Parameter object * Fix for serialization of groups * Set default name for the Phases container * Fix fitting on fit_object change When changing the fit_object the current fitting engine was not updated. This meant that when a fit was performed, it still referenced the old object to be fitted. Calling `__initialize` after object change updates the engine with the new object. * Modify the way interfacing is performed (#60) * Some unit tests of base objects * Code style cleanup * Styles and unit tests * Start with Lattice tests * Bump bumps from 0.7.18 to 0.8.0 Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.18 to 0.8.0. Signed-off-by: dependabot[bot] <support@github.com> * Bump codecov from 2.1.10 to 2.1.11 Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.10 to 2.1.11. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.10...v2.1.11) Signed-off-by: dependabot[bot] <support@github.com> * Start work on Atoms test * Add python 3.9 to tests * Dephell pre-commit hook [ci skip] * More atoms testing work * Atoms tests part deux * More lattice tests + fixes * tests for Spacegroup * Modification of BaseObj and BaseCollection Unify `BaseObj` and `BaseCollection` to derive from `BasedBase` and update subclass matching to take this into account. Fix the occurrence wrong mapping when: ``` foo = Foo() bar1 = foo.bar bar2 = Bar() foo.bar = bar2 ``` * Bug Fixes relating to groups More refactoring of Base classes and fixing imports * Fixup spacegroups and tests * Initial Interfacing Trial * Improved interfacing and switching Bonus! More detailed error messages * Clean up new interfacing * More interfacing work * Atom interface linking via ID * Undo Phase changes as it should not be done this way * Remove auto generate-bindings property of interface * Remove `IT_coordinate_system_code` from cif The IT_coordinate_system_code written to the cif is the one from pymatgen and is not the IUCr definition. This was causing errors when loading. Removed until it can be fixed. Currently effects CrysPy calculator only. * Fix evaluation of multiple constraints Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Update release info (#62) * Add some unit tests * Bump release version * Add owner info * Clean up some typos * Bump version in tests * Update publishing workflow * Added some logo and stuff * Fix logo font * Fix classifier info * Update README * Delete Files * Update packaging workflow Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Add fitting unit tests * Delete GNU licence file [ci skip] * Create LICENCE [ci skip] * Pre-commit test * Update readme [ci skip] * Remove auto UML [ci skip] * Add setting core item to groups by integer key * UndoRedo fixes and more tests * Doc generation base * Beginning doc generation * More documentation work * Constraints documentation and typing * Add BaseObj Example 1 * More documentation work * Update CI [ci skip] * Update OSCAR [ci skip] * Update pint requirement from ^0.16 to ^0.17 (#57) Updates the requirements on [pint](https://github.com/hgrecco/pint) to permit the latest version. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.17) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Separate Documentation [ci ckip] * Some very minor fixes (#70) * remove deprecation warning from \Chi * importing collections.abc instead of collections, removes deprecation warning * fix a bad link * using 2 sigma as rel makes the tests less likely to randomly fail * Update readme-renderer requirement from ^17.4 to ^29.0 (#67) Updates the requirements on [readme-renderer](https://github.com/pypa/readme_renderer) to permit the latest version. - [Release notes](https://github.com/pypa/readme_renderer/releases) - [Changelog](https://github.com/pypa/readme_renderer/blob/main/CHANGES.rst) - [Commits](https://github.com/pypa/readme_renderer/commits/29.0) --- updated-dependencies: - dependency-name: readme-renderer dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scipy from 1.6.1 to 1.7.0 (#69) Bumps [scipy](https://github.com/scipy/scipy) from 1.6.1 to 1.7.0. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.1...v1.7.0) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump python-dateutil from 2.8.1 to 2.8.2 (#71) Bumps [python-dateutil](https://github.com/dateutil/dateutil) from 2.8.1 to 2.8.2. - [Release notes](https://github.com/dateutil/dateutil/releases) - [Changelog](https://github.com/dateutil/dateutil/blob/master/NEWS) - [Commits](https://github.com/dateutil/dateutil/compare/2.8.1...2.8.2) --- updated-dependencies: - dependency-name: python-dateutil 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> * Update doc8 requirement from ^0.8.0 to ^0.9.0 (#72) Updates the requirements on [doc8](https://github.com/pycqa/doc8) to permit the latest version. - [Release notes](https://github.com/pycqa/doc8/releases) - [Commits](https://github.com/pycqa/doc8/compare/0.8.0...0.9.0) --- updated-dependencies: - dependency-name: doc8 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.1.5 to 1.3.1 (#74) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.1.5 to 1.3.1. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.1.5...v1.3.1) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update xarray requirement from ^0.16 to >=0.16,<0.20 (#73) Updates the requirements on [xarray](https://github.com/pydata/xarray) to permit the latest version. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.16.0...v0.19.0) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix serialization of all Core objects * Fix pickling interfaces * Add scaling parameters for phases * Fixup for constraint deletion callback * Bump scipy from 1.7.0 to 1.7.1 (#75) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.0 to 1.7.1. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: scipy 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> * Bump pygments from 2.9.0 to 2.10.0 (#76) Bumps [pygments](https://github.com/pygments/pygments) from 2.9.0 to 2.10.0. - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](https://github.com/pygments/pygments/compare/2.9.0...2.10.0) --- updated-dependencies: - dependency-name: pygments dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.3.1 to 1.3.2 (#77) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.1 to 1.3.2. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.3.1...v1.3.2) --- updated-dependencies: - dependency-name: pandas 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> * Update pre-commit hooks * Update pre-release (#78) * Clean up fitting template * Code quality fixes * Update README [ci skip] * Create release drafter [ci skip] * Create Release Drafter config [ci skip] * Update publish [ci skip] * Update packaging [ci skip] * Add get_all_parameters function * Auto stash before checking out "HEAD" * Update packaging [ci skip] * Fix fitting for bumps * Bump pint from 0.16 to 0.16.1 (#22) Bumps [pint](https://github.com/hgrecco/pint) from 0.16 to 0.16.1. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.16.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.0.2 to 6.1.0 (#26) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.0.2 to 6.1.0. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.0.2...6.1.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Merge sprint work to dev (#29) * Rename pars to avoid conflict Implement internal name changes in fitting (currently lmfit) due to possible duplicate names * Rename pars to avoid conflict (bumps) * First working constraints * More work on Constraints * Bump Constraints [ci skip] * Bump constraints [ci skip] * Parameter path generation [ci skip] * Reverse lookup fix [ci skip] * Bump fitting template [ci skip] * Add first look at Groups and Atom/s * Bump pint from 0.16 to 0.16.1 (#21) * Bump pint from 0.16 to 0.16.1 Bumps [pint](https://github.com/hgrecco/pint) from 0.16 to 0.16.1. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.16.1) Signed-off-by: dependabot[bot] <support@github.com> * Update dependabot [ci skip] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Simon Ward <2798086+wardsimon@users.noreply.github.com> * Constraints across fitters and constraints sdterr * More work on Atoms and constraints * Create codeql-analysis.yml (#23) * Create ossar-analysis.yml (#24) * Work on cif/star * Add enabled flag * CIF sections for Cell/Site/Atoms * Add header, cif/star conversion * Working star/cif io * Work on adp * implement adp * Some name changes [ci skip] * Bug fixes for advanced interfacing * CIF work * More cif work * New and improved cif io! * quickfix for spacegroup [ci skip] * Fix adp weirdness [ci skip] * More spacegroup fixes [ci skip] * Add Crystals [ci skip] * Remove auto interfacing as it's not ready yet. * Fix site to dict * Spacegroup fixes * Groups are now lists when serialised * Add docstrings, fix crystal sites * More spacegoup fun * Fix for crystal all site generation. Add multi-phase support * Fixes for multiphase cif reading * FIX: Cif creation update error * Add atom generation tolerence * Add selecting string index in cif * Select phase in cif file output * Fix some group namings [ci skip] * SG work * Fix a static method * Enforce symmetry on crystals * Make enforcing symmetry optional * Fix fat fingers and introduce a setup.py * Finally fix up those unit tests * Update parameter serialization * Update SG tools encoding * Deletion of items and pruning of graphs * More SG work, handling co-ord system codes * Fix printing items with error When printing an item with error, if the bracketed error was more than a single magnitude, the decimal point would be off by that magnitude * Fixup codefactor * More fixups * Add a finalizer to constraints Added a finalizer to constraints so that when a dependent variable is force-disabled, it will be re-enabled on constraint deletion. * Fix atom orbit generation * Rename atoms_list to atoms Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Fix duplicate object type * Bump codecov from 2.1.9 to 2.1.10 (#28) Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.9 to 2.1.10. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.9...v2.1.10) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.1.0 to 6.1.2 (#31) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.1.0 to 6.1.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.1.0...6.1.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump uncertainties from 3.1.4 to 3.1.5 (#36) Bumps [uncertainties](https://github.com/lebigot/uncertainties) from 3.1.4 to 3.1.5. - [Release notes](https://github.com/lebigot/uncertainties/releases) - [Commits](https://github.com/lebigot/uncertainties/compare/3.1.4...3.1.5) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump asteval from 0.9.19 to 0.9.21 (#35) Bumps [asteval](https://github.com/newville/asteval) from 0.9.19 to 0.9.21. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.19...0.9.21) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump numpy from 1.19.2 to 1.19.4 (#32) Bumps [numpy](https://github.com/numpy/numpy) from 1.19.2 to 1.19.4. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/master/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.19.2...v1.19.4) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump bumps from 0.7.16 to 0.7.18 (#34) Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.16 to 0.7.18. Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Specie work (#37) * Initial specie work * Fixup some serialization * Initial work on bonding * add fitting methods * LM fit method list update * Fix default minimizer method * Rename atom_list to atoms * Quick bonding fixes * User supplied extent for calculations * Quick fixes Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Fix cif printing on empty phases * Bump pytest from 6.1.2 to 6.2.1 (#40) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.1.2 to 6.2.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.1.2...6.2.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.3.1 to 3.4.0 (#39) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.3.1 to 3.4.0. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.3.1...v3.4.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump bumps from 0.7.18 to 0.8.0 (#41) Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.18 to 0.8.0. Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump numpy from 1.19.4 to 1.19.5 (#44) Bumps [numpy](https://github.com/numpy/numpy) from 1.19.4 to 1.19.5. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/master/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.19.4...v1.19.5) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump codecov from 2.1.10 to 2.1.11 (#42) Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.10 to 2.1.11. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.10...v2.1.11) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.4.0 to 3.5.0 (#43) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.4.0 to 3.5.0. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.4.0...v3.5.0) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-mock from 3.5.0 to 3.5.1 (#45) Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.5.0 to 3.5.1. - [Release notes](https://github.com/pytest-dev/pytest-mock/releases) - [Changelog](https://github.com/pytest-dev/pytest-mock/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.5.0...v3.5.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest-cov from 2.10.1 to 2.11.1 (#47) Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.10.1 to 2.11.1. - [Release notes](https://github.com/pytest-dev/pytest-cov/releases) - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v2.10.1...v2.11.1) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pytest from 6.2.1 to 6.2.2 (#48) Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.1 to 6.2.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.2.1...6.2.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump lmfit from 1.0.1 to 1.0.2 (#49) Bumps [lmfit](https://github.com/lmfit/lmfit-py) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/lmfit/lmfit-py/releases) - [Changelog](https://github.com/lmfit/lmfit-py/blob/master/doc/whatsnew.rst) - [Commits](https://github.com/lmfit/lmfit-py/compare/1.0.1...1.0.2) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump asteval from 0.9.21 to 0.9.22 (#52) Bumps [asteval](https://github.com/newville/asteval) from 0.9.21 to 0.9.22. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.21...0.9.22) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Remove poetery.lock It's really annoying and doesn't work * Implement xarrays in easyCore (#51) * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Start making datasets * Start work on datasets * xarray fitting attempt Hint: it's a fail :-( * xarray fitting in nd with lmfit * More data array examples * Add examples and more fitting work * Minor bug fixes * Multifitting of xarray DataArrays * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Delete poetry.lock * Dephell pre-commit hook [ci skip] * Fully implement DFO-LS * Fix DFO_LS error generation * DFOLS docstrings and cleanup * Returning the correct data..... * Start making datasets * Start work on datasets * xarray fitting attempt Hint: it's a fail :-( * xarray fitting in nd with lmfit * More data array examples * Add examples and more fitting work * Minor bug fixes * Multifitting of xarray DataArrays * Renaming and Documentation * Fix circular import. * Fitting macro fix * Fix some pull request issues. * Bump asteval from 0.9.22 to 0.9.23 (#53) * Bump asteval from 0.9.22 to 0.9.23 Bumps [asteval](https://github.com/newville/asteval) from 0.9.22 to 0.9.23. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](https://github.com/newville/asteval/compare/0.9.22...0.9.23) Signed-off-by: dependabot[bot] <support@github.com> * Delete poetry.lock Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Simon Ward <2798086+wardsimon@users.noreply.github.com> * Undo/Redo stack info Add some missing text to undo/redo actions * Undo/Redo work Just some undo redo work and cleaning up of decorator names. Not much to see here * Update monty requirement from ^4.0.2 to ^2021.3.3 (#54) Updates the requirements on [monty](https://github.com/materialsvirtuallab/monty) to permit the latest version. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.html) - [Commits](https://github.com/materialsvirtuallab/monty/compare/v4.0.2...v2021.3.3) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix undo/redo for inherited base classes * Fix printable representation of a Descriptor/Parameter object * Fix for serialization of groups * Set default name for the Phases container * Fix fitting on fit_object change When changing the fit_object the current fitting engine was not updated. This meant that when a fit was performed, it still referenced the old object to be fitted. Calling `__initialize` after object change updates the engine with the new object. * Modify the way interfacing is performed (#60) * Some unit tests of base objects * Code style cleanup * Styles and unit tests * Start with Lattice tests * Bump bumps from 0.7.18 to 0.8.0 Bumps [bumps](http://www.reflectometry.org/danse/software.html) from 0.7.18 to 0.8.0. Signed-off-by: dependabot[bot] <support@github.com> * Bump codecov from 2.1.10 to 2.1.11 Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.10 to 2.1.11. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.10...v2.1.11) Signed-off-by: dependabot[bot] <support@github.com> * Start work on Atoms test * Add python 3.9 to tests * Dephell pre-commit hook [ci skip] * More atoms testing work * Atoms tests part deux * More lattice tests + fixes * tests for Spacegroup * Modification of BaseObj and BaseCollection Unify `BaseObj` and `BaseCollection` to derive from `BasedBase` and update subclass matching to take this into account. Fix the occurrence wrong mapping when: ``` foo = Foo() bar1 = foo.bar bar2 = Bar() foo.bar = bar2 ``` * Bug Fixes relating to groups More refactoring of Base classes and fixing imports * Fixup spacegroups and tests * Initial Interfacing Trial * Improved interfacing and switching Bonus! More detailed error messages * Clean up new interfacing * More interfacing work * Atom interface linking via ID * Undo Phase changes as it should not be done this way * Remove auto generate-bindings property of interface * Remove `IT_coordinate_system_code` from cif The IT_coordinate_system_code written to the cif is the one from pymatgen and is not the IUCr definition. This was causing errors when loading. Removed until it can be fixed. Currently effects CrysPy calculator only. * Fix evaluation of multiple constraints Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Update release info (#62) * Add some unit tests * Bump release version * Add owner info * Clean up some typos * Bump version in tests * Update publishing workflow * Added some logo and stuff * Fix logo font * Fix classifier info * Update README * Delete Files * Update packaging workflow Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> * Add fitting unit tests * Delete GNU licence file [ci skip] * Create LICENCE [ci skip] * Pre-commit test * Update readme [ci skip] * Remove auto UML [ci skip] * Add setting core item to groups by integer key * UndoRedo fixes and more tests * Doc generation base * Beginning doc generation * More documentation work * Constraints documentation and typing * Add BaseObj Example 1 * More documentation work * Update CI [ci skip] * Update OSCAR [ci skip] * Update pint requirement from ^0.16 to ^0.17 (#57) Updates the requirements on [pint](https://github.com/hgrecco/pint) to permit the latest version. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.16...0.17) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Separate Documentation [ci ckip] * Some very minor fixes (#70) * remove deprecation warning from \Chi * importing collections.abc instead of collections, removes deprecation warning * fix a bad link * using 2 sigma as rel makes the tests less likely to randomly fail * Update readme-renderer requirement from ^17.4 to ^29.0 (#67) Updates the requirements on [readme-renderer](https://github.com/pypa/readme_renderer) to permit the latest version. - [Release notes](https://github.com/pypa/readme_renderer/releases) - [Changelog](https://github.com/pypa/readme_renderer/blob/main/CHANGES.rst) - [Commits](https://github.com/pypa/readme_renderer/commits/29.0) --- updated-dependencies: - dependency-name: readme-renderer dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scipy from 1.6.1 to 1.7.0 (#69) Bumps [scipy](https://github.com/scipy/scipy) from 1.6.1 to 1.7.0. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.1...v1.7.0) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump python-dateutil from 2.8.1 to 2.8.2 (#71) Bumps [python-dateutil](https://github.com/dateutil/dateutil) from 2.8.1 to 2.8.2. - [Release notes](https://github.com/dateutil/dateutil/releases) - [Changelog](https://github.com/dateutil/dateutil/blob/master/NEWS) - [Commits](https://github.com/dateutil/dateutil/compare/2.8.1...2.8.2) --- updated-dependencies: - dependency-name: python-dateutil 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> * Update doc8 requirement from ^0.8.0 to ^0.9.0 (#72) Updates the requirements on [doc8](https://github.com/pycqa/doc8) to permit the latest version. - [Release notes](https://github.com/pycqa/doc8/releases) - [Commits](https://github.com/pycqa/doc8/compare/0.8.0...0.9.0) --- updated-dependencies: - dependency-name: doc8 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.1.5 to 1.3.1 (#74) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.1.5 to 1.3.1. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.1.5...v1.3.1) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update xarray requirement from ^0.16 to >=0.16,<0.20 (#73) Updates the requirements on [xarray](https://github.com/pydata/xarray) to permit the latest version. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.16.0...v0.19.0) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix serialization of all Core objects * Fix pickling interfaces * Add scaling parameters for phases * Fixup for constraint deletion callback * Bump scipy from 1.7.0 to 1.7.1 (#75) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.0 to 1.7.1. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: scipy 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> * Bump pygments from 2.9.0 to 2.10.0 (#76) Bumps [pygments](https://github.com/pygments/pygments) from 2.9.0 to 2.10.0. - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](https://github.com/pygments/pygments/compare/2.9.0...2.10.0) --- updated-dependencies: - dependency-name: pygments dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.3.1 to 1.3.2 (#77) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.1 to 1.3.2. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.3.1...v1.3.2) --- updated-dependencies: - dependency-name: pandas 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> * Update pre-commit hooks Co-authored-by: Andrew Sazonov <AndrewSazonov@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Andrew McCluskey <andrew.mccluskey@ess.eu> * Code cleanup - Mostly type hinting * Fix ABCmeta unsubscribable * Fix adding parameters to underlying minimizer (LMFIT) * Change order of the minimizer methods * Major change to interfacing fit functions * Bump pandas from 1.3.2 to 1.3.3 (#79) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.2 to 1.3.3. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.3.2...v1.3.3) --- updated-dependencies: - dependency-name: pandas 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> * Update sphinx-gallery requirement from ^0.9.0 to ^0.10.0 (#81) Updates the requirements on [sphinx-gallery](https://github.com/sphinx-gallery/sphinx-gallery) to permit the latest version. - [Release notes](https://github.com/sphinx-gallery/sphinx-gallery/releases) - [Changelog](https://github.com/sphinx-gallery/sphinx-gallery/blob/master/CHANGES.rst) - [Commits](https://github.com/sphinx-gallery/sphinx-gallery/compare/v0.9.0...v0.10.0) --- updated-dependencies: - dependency-name: sphinx-gallery 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 sphinx-rtd-theme requirement from ^0.5.2 to ^1.0.0 (#80) Updates the requirements on [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) to permit the latest version. - [Release notes](https://github.com/readthedocs/sphinx_rtd_theme/releases) - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/0.5.2...1.0.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme 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 readme-renderer requirement from ^29.0 to ^30.0 (#82) Updates the requirements on [readme-renderer](https://github.com/pypa/readme_renderer) to permit the latest version. - [Release notes](https://github.com/pypa/readme_renderer/releases) - [Changelog](https://github.com/pypa/readme_renderer/blob/main/CHANGES.rst) - [Commits](https://github.com/pypa/readme_renderer/compare/29.0...30.0) --- updated-dependencies: - dependency-name: readme-renderer dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Minor fixes * Create alpha package * Only push if changes * Add `v` to tag * Auto publish all releases to custom pypi * Add some branch protection * Update pytest-cov requirement from ^2.11.1 to ^3.0.0 (#86) Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest-cov/releases) - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v2.11.1...v3.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scipy from 1.6.1 to 1.7.1 (#84) Bumps [scipy](https://github.com/scipy/scipy) from 1.6.1 to 1.7.1. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.1...v1.7.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add documentation label * Update python-package.yml * Bump pytz from 2021.1 to 2021.3 (#85) Bumps [pytz](https://github.com/stub42/pytz) from 2021.1 to 2021.3. - [Release notes](https://github.com/stub42/pytz/releases) - [Commits](https://github.com/stub42/pytz/compare/release_2021.1...release_2021.3) --- updated-dependencies: - dependency-name: pytz dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.1.5 to 1.3.3 (#83) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.1.5 to 1.3.3. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.1.5...v1.3.3) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update typing * Fixes for fitting and examples * Support for boolean descriptors * Fix-up bumps fitting and unit tests * CI test use python 3.9 due to Poetry * Bump pandas from 1.3.3 to 1.3.4 (#89) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.3 to 1.3.4. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.3.3...v1.3.4) --- updated-dependencies: - dependency-name: pandas 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> * Update pint requirement from ^0.17 to >=0.17,<0.19 (#90) Updates the requirements on [pint](https://github.com/hgrecco/pint) to permit the latest version. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.17...0.18) --- updated-dependencies: - dependency-name: pint dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump packaging from 21.0 to 21.2 (#91) Bumps [packaging](https://github.com/pypa/packaging) from 21.0 to 21.2. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/21.0...21.2) --- updated-dependencies: - dependency-name: packaging dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update doc8 requirement from ^0.9.0 to ^0.10.1 (#94) Updates the requirements on [doc8](https://github.com/pycqa/doc8) to permit the latest version. - [Release notes](https://github.com/pycqa/doc8/releases) - [Commits](https://github.com/pycqa/doc8/compare/0.9.0...0.10.1) --- updated-dependencies: - dependency-name: doc8 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scipy from 1.7.1 to 1.7.2 (#93) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.1 to 1.7.2. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.1...v1.7.2) --- updated-dependencies: - dependency-name: scipy 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> * Update xarray requirement from >=0.16,<0.20 to >=0.16,<0.21 (#92) Updates the requirements on [xarray](https://github.com/pydata/xarray) to permit the latest version. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.16.0...v0.20.0) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add new functional constraints and clean up decorators * Fix a pickling problem It turns out skip wasn't passed to all members when pickling. * Add missing crystal system * Update pint requirement from <0.18,>=0.17 to >=0.17,<0.19 (#95) Updates the requirements on [pint](https://github.com/hgrecco/pint) to permit the latest version. - [Release notes](https://github.com/hgrecco/pint/releases) - [Changelog](https://github.com/hgrecco/pint/blob/master/CHANGES) - [Commits](https://github.com/hgrecco/pint/compare/0.17...0.18) --- updated-dependencies: - dependency-name: pint dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update xarray requirement from <0.20,>=0.16 to >=0.16,<0.21 (#96) Updates the requirements on [xarray](https://github.com/pydata/xarray) to permit the latest version. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.16.0...v0.20.1) --- updated-dependencies: - dependency-name: xarray dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump packaging from 21.2 to 21.3 (#97) Bumps [packaging](https://github.com/pypa/packaging) from 21.2 to 21.3. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/21.2...21.3) --- updated-dependencies: - dependency-name: packaging dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scipy from 1.7.2 to 1.7.3 (#98) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.2 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.2...v1.7.3) --- updated-dependencies: - dependency-name: scipy 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> * Update readme-renderer requirement from ^30.0 to ^32.0 (#100) Updates the requirements on [readme-renderer](https://github.com/pypa/readme_renderer) to permit the latest version. - [Release notes](https://github.com/pypa/readme_renderer/releases) - [Changelog](https://github.com/pypa/readme_renderer/blob/main/CHANGES.rst) - [Commits](https://github.com/pypa/readme_renderer/compare/30.0...32.0) --- updated-dependencies: - dependency-name: readme-renderer dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pandas from 1.3.4 to 1.3.5 (#101) Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.3.4 to 1.3.5. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.3.4...v1.3.5) --- updated-dependencies: - dependency-name: pandas 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> * Split up and remove old stuff * Add python 3.10 support and scipp * Update CW * Move CIF out * Update CI [ci skip] * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Addition of virtual variables * Bounds for parameters for easy setting * Remove scipp file [ci skip] * Update numpy * Update ci_pip.yaml * Update pyproject.toml * Update scipp.py * Update test_scipp.py * Update version * Update setup.py * Make errors more informative * Bump scipy from 1.6.1 to 1.7.3 Bumps [scipy](https://github.com/scipy/scipy) from 1.6.1 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.1...v1.7.3) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Add models, bounds and virtual * Fix-up some tilde nonsense * Fix bounds issue * Some more test, STAR fixes and setup updates * Bump scipy from 1.6.1 to 1.7.3 Bumps [scipy](https://github.com/scipy/scipy) from 1.6.1 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.1...v1.7.3) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump pyparsing from 3.0.6 to 3.0.7 Bumps [pyparsing](https://github.com/pyparsing/pyparsing) from 3.0.6 to 3.0.7. - [Release notes](https://github.com/pyparsing/pyparsing/releases) - [Changelog](https://github.com/pyparsing/pyparsing/blob/master/CHANGES) - [Commits](https://github.com/pyparsing/pyparsing/compare/pyparsing_3.0.6...pyparsing_3.0.7) --- updated-dependencies: - dependency-name: pyparsing dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Add star string and object edge cases * Remove duplicate dephell * Bump pyparsing from 3.0.6 to 3.0.7 (#116) Bumps [pyparsing](https://github.com/pyparsing/pyparsing) from 3.0.6 to 3.0.7. - [Release notes](https://github.com/pyparsing/pyparsing/releases) - [Changel…
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merging so the codebase is the same