Release v0.3.0 #166
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Release v0.3.0 #166
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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](hgrecco/pint@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>
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](pytest-dev/pytest@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>
* 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](hgrecco/pint@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>
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](codecov/codecov-python@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>
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](pytest-dev/pytest@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>
Bumps [uncertainties](https://github.com/lebigot/uncertainties) from 3.1.4 to 3.1.5. - [Release notes](https://github.com/lebigot/uncertainties/releases) - [Commits](lmfit/uncertainties@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>
Bumps [asteval](https://github.com/newville/asteval) from 0.9.19 to 0.9.21. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](newville/asteval@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>
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](numpy/numpy@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>
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>
* 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>
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](pytest-dev/pytest@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>
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](pytest-dev/pytest-mock@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>
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>
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](numpy/numpy@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>
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](codecov/codecov-python@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>
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](pytest-dev/pytest-mock@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>
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](pytest-dev/pytest-mock@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>
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](pytest-dev/pytest-cov@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>
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](pytest-dev/pytest@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>
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](lmfit/lmfit-py@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>
Bumps [asteval](https://github.com/newville/asteval) from 0.9.21 to 0.9.22. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](newville/asteval@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>
It's really annoying and doesn't work
* 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 Bumps [asteval](https://github.com/newville/asteval) from 0.9.22 to 0.9.23. - [Release notes](https://github.com/newville/asteval/releases) - [Commits](newville/asteval@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>
Add some missing text to undo/redo actions
Just some undo redo work and cleaning up of decorator names. Not much to see here
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](materialsvirtuallab/monty@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>
Multifitter implementation
IO serialization
Preparation for v0.3.0 release
wardsimon
added
bug
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
classes to redefine/amend generic as_dict(). Not sure if this is the best way of doing it - please review.
Bumps Levenberg-Marquardt least-squares minimization is currently broken. This test allows it to fail. Hopefully the fix will be merged soon
Speed up optimization
0.3.0 Pre release fixes
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