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Bump pyiron-atomistics from 0.3.10 to 0.3.11 #130
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           OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting  If you change your mind, just re-open this PR and I'll resolve any conflicts on it.  | 
    
Bumps [pyiron-atomistics](https://github.com/pyiron/pyiron_atomistics) from 0.3.10 to 0.3.11. - [Release notes](https://github.com/pyiron/pyiron_atomistics/releases) - [Changelog](https://github.com/pyiron/pyiron_atomistics/blob/main/CHANGELOG.md) - [Commits](pyiron/pyiron_atomistics@pyiron_atomistics-0.3.10...pyiron_atomistics-0.3.11) --- updated-dependencies: - dependency-name: pyiron-atomistics dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
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* Update yml files * Update conf file * run black * run ruff * define __all__ * run ruff fix * Configure ruff Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use more descriptive names Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Switch providers Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update badges Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com>
* Forgot to add the parser * run black * Make input and output plural to be in agreement with the pyiron_workflow definitions * small bugfixes * add one test * update definition of connection * bugfix * another programming error worth a harakiri * make sure that the triples are tuples * bugfix * set default values * convert object to URIRef only if it is not already one * typo * There are arbitrary values that cannot work with if * allow triples in triple * update semantikon version * separate out triple parser * bugfix and add tests * make it possible to give custom predicates * experiment: use sameAs instead of comesFrom * implement inherit properties * make inherit properties a public function * add restriction parser * run black * add reasoner * Replace [] by None * implement validator * Do not inherit type * calculate number of iterations automatically * increase number of inheritances * Define each label as a named individual * Name change in order to avoid confusion * Change triple and restriction plural * Bugfix due to pointing to data * run black * Remove named individual because apparently it's implied * write workflow parser * Replace EX by NS because I guess EX stands for example * append workflow name * add namespace everywhere * restore dot * codacy * Add activity and entity * current state * Use pyiron namespace * Add type hints * replace value by node * add test * add docstring * run black * Add URIRef to uri just in case * Create pyiron specific namespace * Add tests * Break apart parsing and business Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Be explicit about what's missing Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Implement restriction validator and Placeholder * Remove Any because it's not used anymore * I don't really understand but this silences mypy * run black * Replace Placeholder by None * run black * remove var_name because it's never used and anyway appears in the key * Add test * Add additional node for the values * run black * Small bugfix * Correct tests * run black * Remove units in string * change definition of tag * I stop in this state now because some functions are too complex * change definition of tag * refactor tag * not repeat if * Refactor * replace identifier by str * Store it in the current state * add subpropertyof * Use subclass instead * Add sub class parsing * Add warning * another one * Remove dependence on semantikon * Current state * Update meta_to_dict * run black * define variables * rename outputs * bugfix * I'm a loss * I'm a total loss * make ontology optional * Make ontology trickle down * run black * Add check missing items * Move it to workflow parser and add tests * Add comments * Run black * Replace nodes by dicts * Move parsing to a separate function * Move parsing to a separate function * Depend on semantikon * Update header * run black * Check whether the owner is the same node * Remove workflow_to_dict * Remove all the unused stuff * run black * Add with values and with default * Add docstring * Correct imports * Correct path for Macro * Correct SNS name * Liam's suggestion * Update Actions (#130) * Update yml files * Update conf file * run black * run ruff * define __all__ * run ruff fix * Configure ruff Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use more descriptive names Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Switch providers Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update badges Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com> * Update pyiron_ontology/parser.py * Update pyiron_ontology/parser.py * Update parser.py * Update parser.py * Update parser.py * replace data_edges by edges * typo --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: samwaseda <o.waseda@mpie.de> Co-authored-by: Sam Dareska <37879103+samwaseda@users.noreply.github.com> Co-authored-by: Sam Waseda <waseda@mpie.de>
* Update yml files * Update conf file * run black * run ruff * define __all__ * run ruff fix * Configure ruff Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use more descriptive names Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Switch providers Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update badges Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com>
* add tests * Make input and output plural to be in agreement with the pyiron_workflow definitions * add one test * bugfix and add tests * one more test for a full triple * adjust line length * be more specific about the number of triples in tests * Add tests (but not working right now) * Add wrong analysis * Codacy * Change triple and restriction plural * Add tests * run black * Replace EX by NS because I guess EX stands for example * restore dot * Add tests * run black * current state * Use pyiron namespace * Make it clear that the predicate is just for parsing and does not have a meaning * add test * Add tests * Codacy * add tests for place holder * Replace Placeholder by None * Add test * add error messages * Add a sparql query test * run black * Correct tests * Simplify test * Add tests * run black * Add error message * Move the location of _is_semantikon_class * Add sub class parsing * bugfix * run black * Remove dependence on semantikon * run black * reduce lines * Add test * Move it to workflow parser and add tests * Another black * Depend on semantikon * Correct tests * Add macro tests * Remove workflow_to_dict * Simplify test * Simplify more tests * Test with reasoner * remove unused inherit_properties * Update pyiron_workflow * name space * Liam's suggestion * Correct errors * Update Actions (#130) * Update yml files * Update conf file * run black * run ruff * define __all__ * run ruff fix * Configure ruff Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use more descriptive names Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Switch providers Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update badges Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com> * Update test_parser.py * replace typing by metadata * ruff sort * Update tests * Update syntax and remove unused lines * Remove unnecessary imports * Remove redundant get_graph * typo * Explore ontology tools with pyiron_workflow Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * [dependabot skip] Update env file * Downgrade pandas Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * [dependabot skip] Update env file * Read the inequality, Huber Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * [dependabot skip] Update env file * git-copy pyiron_ontology.parser (#745) * Forgot to add the parser * run black * Make input and output plural to be in agreement with the pyiron_workflow definitions * small bugfixes * add one test * update definition of connection * bugfix * another programming error worth a harakiri * make sure that the triples are tuples * bugfix * set default values * convert object to URIRef only if it is not already one * typo * There are arbitrary values that cannot work with if * allow triples in triple * update semantikon version * separate out triple parser * bugfix and add tests * make it possible to give custom predicates * experiment: use sameAs instead of comesFrom * implement inherit properties * make inherit properties a public function * add restriction parser * run black * add reasoner * Replace [] by None * implement validator * Do not inherit type * calculate number of iterations automatically * increase number of inheritances * Define each label as a named individual * Name change in order to avoid confusion * Change triple and restriction plural * Bugfix due to pointing to data * run black * Remove named individual because apparently it's implied * write workflow parser * Replace EX by NS because I guess EX stands for example * append workflow name * add namespace everywhere * restore dot * codacy * Add activity and entity * current state * Use pyiron namespace * Add type hints * replace value by node * add test * add docstring * run black * Add URIRef to uri just in case * Create pyiron specific namespace * Add tests * Break apart parsing and business Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Be explicit about what's missing Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Implement restriction validator and Placeholder * Remove Any because it's not used anymore * I don't really understand but this silences mypy * run black * Replace Placeholder by None * run black * remove var_name because it's never used and anyway appears in the key * Add test * Add additional node for the values * run black * Small bugfix * Correct tests * run black * Remove units in string * change definition of tag * I stop in this state now because some functions are too complex * change definition of tag * refactor tag * not repeat if * Refactor * replace identifier by str * Store it in the current state * add subpropertyof * Use subclass instead * Add sub class parsing * Add warning * another one * Remove dependence on semantikon * Current state * Update meta_to_dict * run black * define variables * rename outputs * bugfix * I'm a loss * I'm a total loss * make ontology optional * Make ontology trickle down * run black * Add check missing items * Move it to workflow parser and add tests * Add comments * Run black * Replace nodes by dicts * Move parsing to a separate function * Move parsing to a separate function * Depend on semantikon * Update header * run black * Check whether the owner is the same node * Remove workflow_to_dict * Remove all the unused stuff * run black * Add with values and with default * Add docstring * Correct imports * Correct path for Macro * Correct SNS name * Liam's suggestion * Update Actions (#130) * Update yml files * Update conf file * run black * run ruff * define __all__ * run ruff fix * Configure ruff Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use more descriptive names Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Switch providers Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update badges Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: liamhuber <liamhuber@greyhavensolutions.com> * Update pyiron_ontology/parser.py * Update pyiron_ontology/parser.py * Update parser.py * Update parser.py * Update parser.py * replace data_edges by edges * typo --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: samwaseda <o.waseda@mpie.de> Co-authored-by: Sam Dareska <37879103+samwaseda@users.noreply.github.com> Co-authored-by: Sam Waseda <waseda@mpie.de> * Update imports And re-run notebook. And exclude the new file from mpyp. @samwaseda, mypy does not like your file XP Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update dependencies Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Bump graphviz lower bound To accommodate semantikon Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update imports Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rename test To match renamed module Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Edit tests Mostly just for import scopes Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update imports Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Validate ontology at connection time Not working with restrictions yet Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Draft connection suggestion Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Add a back door to turn off the feature Since it's pretty janky atm Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fix docstring hint Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Add a node-class suggester Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Modify candidate graph subgraph IO Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Close match pycharm is still not behaving nicely with this though Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fail on connection in test Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Make knowledge mypy compliant At least when we're non-strict Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove unused import Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Don't write recovery file We know and expect a failure, don't clutter the file system Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Move the import short-circuit Over to a special method in the knowledge module Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Adapt sleep times It turns out `semantikon.ontology` has a heavy import overhead Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Add a known issue to the demo notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refine overheads Based on results from main branch Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Delay imports Until they're strictly needed. It's bad form, but it saves graphs that are _not_ ontologically annotated a bunch of import time Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Revert test timing The tests in question don't use ontologies, so the original formulation is fine again. Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook comment Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Revert is_composite Since `semantikon.ontology` imports slowly, we break the circular import inside the `channels` module anyhow Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fail cleanly for unknown node types Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rename argument Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Narrow hint Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Adapt export for non-functions This is to capture `@u` working on non-functions. It doesn't really make sense for dataclasses, and we don't decorate for- and while- loops or other transformers, so only handling it in the function case should be fine. Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Destroy, then connect First disconnect and remove macros' single-use UI nodes _before_ using their single-connections as new input value receivers. This is a benign change for most use cases, but critical for avoiding double-receiving edges when doing ontological validation of macro creation. This would (will!) all be much easier once `pyiron_workflow` adopts the `flowrep` pattern of single-sources for inputs and putting the single available connection and being a value receiver on the same footing. Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Extend notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Re-execute notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update concluding comments Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Ontologically validate value reception Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update ontology term Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Walk the recipe to the relevant parent node Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Make error more informative Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update and re-run notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Catch unit failures Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Document unit usage Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Ontologically decorate dataclass nodes By allowing semantikon.metadata.u kwargs as decorator arguments to apply to the output channel Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fix recipe/lexical path mismatch Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Verify custom labels are ok Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Bump semantikon Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Reference what you can from the api Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Give better feedback in connection errors Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Re-execute notebook To display more informative messages Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rebase exception class Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Encode pizza example in unit tests Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Express bad value receivers as connection errors Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test restrictions and subgraph negotiation Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Add an integration test Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rename notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update notebook With a nicer header, and to remove the boring subgraph negotiation example which is fine just in the unit tests Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fail cleanly when validating outside a graph I.e. for node networks with no parent workflow or macro Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test units (non)inheritance Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Adapt suggestion for validation raising errors instead of returning False Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Don't suggest connected inputs They're already connected! We only allow one connection Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refactor value receiver validation In anticpation of needing a two-step process for suggestion tools Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refactor for regular connections Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use a dataclass Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Use a helper method Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rename method Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refactor suggestions I'm struggling to get them playing nicely with graphs that validate with missing triples (e.g. because of some unconnected node interacting with the workflow IO) Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Don't suggest circular connections Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Allow suggestions for connected input Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test for unrelated problems #733 (comment) Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refactor: change signature Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Include the root name In the path information Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Validate based on involvement Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Extend the test To guarantee that we're investigating the invovlement of _channels_ and not of _nodes_ Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Don't suggest for already-connected inputs Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Directly manipulate execution digraph Instead of adding a real connection to the workflow graph Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * 🐛 fix validation There is still code duplication here with the testing that happens in the channels module, but we can deal with that later Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Only check for downstream involvement Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Scope involvement for macros We need the path to the URI ref. Also, for units we look at the _upstream_ part! Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Allow connection suggestions to come from a corpus of nodes Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Just call the connection suggester to suggest classes It might be slower, but for the time being let's shoot for stability Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Remove duplicate code Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Rename method and change default To be public and false now that we use it elsewhere Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Draft tests for the suggestions Everything they print now makes sense to me, they just need to be converted to real tests Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Add early stopping Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Make exceptions more specific I find this makes it easier to reliably test against them. Including the standard type (ValueError) here means they can also reasonably be caught in generic ways. Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test suggest_connections Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Refactor suggestion collections in tests Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test node suggestions Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test corpus argument Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Test multiple channels Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Extend demo Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Fix newly introduced typos and rerun notebook Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> * Update module docstring Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> --------- Signed-off-by: liamhuber <liamhuber@greyhavensolutions.com> Co-authored-by: samwaseda <o.waseda@mpie.de> Co-authored-by: Sam Dareska <37879103+samwaseda@users.noreply.github.com> Co-authored-by: pyiron-runner <pyiron@mpie.de> Co-authored-by: Sam Waseda <waseda@mpie.de>
Bumps pyiron-atomistics from 0.3.10 to 0.3.11.
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Sourced from pyiron-atomistics's releases.
Commits
e91593bMerge pull request #1252 from pyiron/pmrv-patch-2df51bbfUpdate environment.yml7e53bfaBump pyiron_base from 0.6.11 to 0.6.1234faa20Merge pull request #1248 from pyiron/fix_init2729773Merge pull request #1234 from pyiron/spx_parser_energy_dat96adebaFormat black004901cadd commente190ee1check if array is not empty59cf8d6Merge remote-tracking branch 'origin' into spx_parser_energy_datbf73111Update init.pyDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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