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…ename-Annotation # Conflicts: # client/src/Components/ParameterView/ParameterNode.tsx
lars-reimann
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Feb 10, 2022
Bumps [numpydoc](https://github.com/numpy/numpydoc) from 1.1.0 to 1.2. - [Release notes](https://github.com/numpy/numpydoc/releases) - [Changelog](https://github.com/numpy/numpydoc/blob/main/doc/release_notes.rst) - [Commits](numpy/numpydoc@v1.1.0...numpydoc-1.2) --- updated-dependencies: - dependency-name: numpydoc dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
lars-reimann
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Feb 10, 2022
* Initial commit * chore: configure template * chore: add starter code * build: add numpydoc as dependency * build: add spacy as dependency * docs: installation of poetry * docs: use Python 3.9 * feat: store source code of classes/functions and docstrings of classes/functions/parameters * feat: store whether parameters as assigned by position or name or both * build(deps): bump scikit-learn from 1.0 to 1.0.1 in /package_parser (#12) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.0 to 1.0.1. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.0...1.0.1) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump spacy from 3.1.3 to 3.1.4 in /package_parser (#11) Bumps [spacy](https://github.com/explosion/spaCy) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/explosion/spaCy/releases) - [Commits](explosion/spaCy@v3.1.3...v3.1.4) --- updated-dependencies: - dependency-name: spacy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump amannn/action-semantic-pull-request (#8) Bumps [amannn/action-semantic-pull-request](https://github.com/amannn/action-semantic-pull-request) from 3.4.2 to 3.4.6. - [Release notes](https://github.com/amannn/action-semantic-pull-request/releases) - [Changelog](https://github.com/amannn/action-semantic-pull-request/blob/master/CHANGELOG.md) - [Commits](amannn/action-semantic-pull-request@v3.4.2...v3.4.6) --- updated-dependencies: - dependency-name: amannn/action-semantic-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump astroid from 2.8.2 to 2.8.4 in /package_parser (#10) Bumps [astroid](https://github.com/PyCQA/astroid) from 2.8.2 to 2.8.4. - [Release notes](https://github.com/PyCQA/astroid/releases) - [Changelog](https://github.com/PyCQA/astroid/blob/main/ChangeLog) - [Commits](pylint-dev/astroid@v2.8.2...v2.8.4) --- updated-dependencies: - dependency-name: astroid dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * docs: remove community files that have a default * ci: use reusable workflow to check format of PRs * ci: update mega-linter * ci: master -> main in mega-linter config * feat: enhance extracted data for usage with API editor (#14) * feat: add new fields to model * fix: get everything running again * feat: clean docstrings * feat: extract imports and from-imports for modules * fix: use qualified name of functions as key * fix: some linter errors * fix: remaining linter errors * fix: duplicate imports in extracted API data * fix: skip nested classes for now * chore: add starting point for ontology development * feat: handle properties correctly Multiple functions with the same name can exist if they are marked with @Property, @x.setter, or @x.deleter. We, hence, need to refer to them by something other than their qualified name. * feat: Python model classes for dependencies (#15) * initial ontology commit * 2 basic property subclass ideas * added two more property subclasses * moved ontology to predefined directory, fixed imports * renamed property to dependency, added arithmetic dependency * rework ontology model in code * updated gitignore to ignore VSCode settings * moved python-related changes to package_parser * a stronger method for creating class instances instead of using a static method * fixed potential lint error * style: apply automatic fixes of linters Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: aserge16 <[email protected]> * ci: disable bandit, flake8, pylint * build(deps): bump spacy from 3.1.4 to 3.2.0 in /package_parser (#18) Bumps [spacy](https://github.com/explosion/spaCy) from 3.1.4 to 3.2.0. - [Release notes](https://github.com/explosion/spaCy/releases) - [Commits](explosion/spaCy@v3.1.4...v3.2.0) --- updated-dependencies: - dependency-name: spacy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump importlib-metadata in /package_parser (#19) Bumps [importlib-metadata](https://github.com/python/importlib_metadata) from 4.8.1 to 4.8.2. - [Release notes](https://github.com/python/importlib_metadata/releases) - [Changelog](https://github.com/python/importlib_metadata/blob/main/CHANGES.rst) - [Commits](python/importlib_metadata@v4.8.1...v4.8.2) --- updated-dependencies: - dependency-name: importlib-metadata dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump megalinter/megalinter from 5.0.5 to 5.2.0 (#16) Bumps [megalinter/megalinter](https://github.com/megalinter/megalinter) from 5.0.5 to 5.2.0. - [Release notes](https://github.com/megalinter/megalinter/releases) - [Changelog](https://github.com/megalinter/megalinter/blob/main/CHANGELOG.md) - [Commits](oxsecurity/megalinter@v5.0.5...v5.2.0) --- updated-dependencies: - dependency-name: megalinter/megalinter dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * ci: reusable workflow for MegaLinter * ci: rename workflow * build(deps): bump astroid from 2.8.4 to 2.9.0 in /package_parser (#17) Bumps [astroid](https://github.com/PyCQA/astroid) from 2.8.4 to 2.9.0. - [Release notes](https://github.com/PyCQA/astroid/releases) - [Changelog](https://github.com/PyCQA/astroid/blob/main/ChangeLog) - [Commits](pylint-dev/astroid@v2.8.4...v2.9.0) --- updated-dependencies: - dependency-name: astroid dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * test: setup pytest (#21) * build: add pytest as dev dependency * test: exemplary unit test * build: add pytest-cov as dev dependency * chore: ignore outputs of pytest * ci: run pytest on pull requests or pushes to main * build: use older structure for dev dependencies * docs: add status badge to README * chore: remove CODEOWNERS * ci: pass PAT to reusable MegaLinter workflow * chore: Manual extraction of enum types and boundaries (#28) * Manual extraction of enum types and boundaries * style: apply automatic fixes of linters Co-authored-by: duklin <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * chore: Ontology structure proposal (#25) * Ontology initialization The ontology/sklearn.ttl file contains the following elements: * Classes: Class Parameter StringParameter NumberParameter IntegerParameter FloatParameter * Object Properties: hasParameter isParameterOf * Data Property: canBe * dependency ontology * A root ontology file proposal Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * Add mypy as dev dependency to pyproject.toml (#31) Co-authored-by: Dushko Klincharov <[email protected]> * build: update prettier-config * feat: Extract enums from docstring's type attribute (#30) * Extract enums from docstring's type attribute. Write tests for enum extraction * Fix mypy errors and change return type of Parameter.extract_enum method * style: apply automatic fixes of linters * Provide JSON serialization for enum sets * Cover enum type cases suggested by Lars * Create new class for parameter enums, add more tests for extracting parameter enums from docstring type * remove backslashes from enum type values * style: apply automatic fixes of linters Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: duklin <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * feat: Dependencies (#32) * initial ontology commit * 2 basic property subclass ideas * added two more property subclasses * moved ontology to predefined directory, fixed imports * renamed property to dependency, added arithmetic dependency * rework ontology model in code * updated gitignore to ignore VSCode settings * moved python-related changes to package_parser * a stronger method for creating class instances instead of using a static method * fixed potential lint error * added ontology file for dependencies * initial commit dependency fetcher * initial code commit * playing code for spacy rules * some extra ontology properties for depenencies * Dependencies extract first commit * removed playground code * fixed check in preprocessing * oops, check is correct now * removed name==main at bottom of file * Added new instances * Added a case of != * reworked preprocessing and added test * using regex for preprocessing, cleaner, thanks Lars * removed unused import and added type hint for dict * type hint fixed again * style: apply automatic fixes of linters Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: Prajakta Bhujbal <[email protected]> Co-authored-by: aserge16 <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * build(deps): bump scikit-learn from 1.0.1 to 1.0.2 in /package_parser (#41) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.0.1...1.0.2) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump mypy from 0.910 to 0.930 in /package_parser (#39) Bumps [mypy](https://github.com/python/mypy) from 0.910 to 0.930. - [Release notes](https://github.com/python/mypy/releases) - [Commits](python/mypy@v0.910...v0.930) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump spacy from 3.2.0 to 3.2.1 in /package_parser (#37) Bumps [spacy](https://github.com/explosion/spaCy) from 3.2.0 to 3.2.1. - [Release notes](https://github.com/explosion/spaCy/releases) - [Commits](explosion/spaCy@v3.2.0...v3.2.1) --- updated-dependencies: - dependency-name: spacy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump importlib-metadata in /package_parser (#38) Bumps [importlib-metadata](https://github.com/python/importlib_metadata) from 4.8.2 to 4.10.0. - [Release notes](https://github.com/python/importlib_metadata/releases) - [Changelog](https://github.com/python/importlib_metadata/blob/main/CHANGES.rst) - [Commits](python/importlib_metadata@v4.8.2...v4.10.0) --- updated-dependencies: - dependency-name: importlib-metadata dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: Dependencies (#42) * initial ontology commit * 2 basic property subclass ideas * added two more property subclasses * moved ontology to predefined directory, fixed imports * renamed property to dependency, added arithmetic dependency * rework ontology model in code * updated gitignore to ignore VSCode settings * moved python-related changes to package_parser * a stronger method for creating class instances instead of using a static method * fixed potential lint error * added ontology file for dependencies * initial commit dependency fetcher * initial code commit * playing code for spacy rules * some extra ontology properties for depenencies * Dependencies extract first commit * removed playground code * fixed check in preprocessing * oops, check is correct now * removed name==main at bottom of file * Added new instances * Added a case of != * reworked preprocessing and added test * using regex for preprocessing, cleaner, thanks Lars * removed unused import and added type hint for dict * type hint fixed again * Modified pattern for "nominal subject (passive)" and "prepositional modifier" * #35 used pattern created * #36 first extraction function implemented for the first pattern * #35 ignored condition pattern added * #36 dependency extraction function for ignored condition pattern * added second case of action word having uppercase first letter * added pattern parameter applies * fix: mypy error * style: apply automatic fixes of linters Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: Prajakta Bhujbal <[email protected]> Co-authored-by: Lars Reimann <[email protected]> Co-authored-by: lars-reimann <[email protected]> * feat: Model refined types as dataclasses, introduce only one property in th… (#45) * Model refined types as dataclasses, introduce only one property in the json output for the refined types * style: apply automatic fixes of linters Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: duklin <[email protected]> * build(deps): bump astroid from 2.9.0 to 2.9.1 in /package_parser (#40) Bumps [astroid](https://github.com/PyCQA/astroid) from 2.9.0 to 2.9.1. - [Release notes](https://github.com/PyCQA/astroid/releases) - [Changelog](https://github.com/PyCQA/astroid/blob/main/ChangeLog) - [Commits](pylint-dev/astroid@v2.9.0...v2.9.1) --- updated-dependencies: - dependency-name: astroid dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Lars Reimann <[email protected]> * refactor: manually extracted refined types (#46) * Refactor the manually extracted refined types for classes KMeans, PCA, TruncatedSVD, CountVectorizer and TfIdfVectorizer * refactor refinedtypes for DecisionTreeClassifier * refactor json for model_selection,neighbors,preprocessing,svm,tree * refactoring for metrics,linearmodel,impute * refactored json for feature_extraction * updated BoundaryTypes and NamedTypes and the remaining classes * Refactor manually extracted refined types for cluster, decomposition, ensemble * Refactor manually extracted refined types for feature_extraction, impute and linear_model * refactored manually extracted refined types for metrics,model_selection,neighbors,preprocessing,svm,tree * Format the json files from the manual extraction of refined types * Extract the boundary types in another json and the docstring part that is related to the boundary * style: apply automatic fixes of linters Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: mmdoja <[email protected]> Co-authored-by: duklin <[email protected]> * feat: Action/Condition Classification (#48) * #43 basic condtion and action extraction functions * #43 corrected extractions, now matching occurs per sentence, removes many false positives * #43 fixed recursive action extraction function * Added new pattern * #43 classifying of ignored parameter actions * #43 conditions and actions are now dataclasses, renamed one condition * #43 phrases to categories actions/conditions * #43 mypy fixes * style: apply automatic fixes of linters * #43 renamed IDs in general SCONJ pattern * #43 more descriptive pattern name Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: prajakta <[email protected]> Co-authored-by: aserge16 <[email protected]> * ci: smoke test (#53) * Update pr.yml * test: add smoke test to main workflow * ci: use poetry run instead * test: Dependencies unit tests (#50) * correctly formatted models to data classes * updated model Names and added new phrases * #49 dependency extraction function unit tests * style: apply automatic fixes of linters * fix: possible fix for build error * added json dump of dependencies to CLI flow * mypy fix * style: apply automatic fixes of linters * do the versions make a difference on dependency understanding? * updated url for spacy langauge module * quick fix, need to work on punctuation extraction * removed hanging punctuation when extracting actions * style: apply automatic fixes of linters * test for dependency extraction class subordinating_conjuction * style: apply automatic fixes of linters * more documentation for functions * style: apply automatic fixes of linters * updated ontology to represent current code state * removed pattern without implemented function for now * added dependency README Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: aserge16 <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * feat: Boundary extraction (#54) * Extract boundaries with regex * Write tests for extracting boundaries * Categorize boundaries * style: apply automatic fixes of linters Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: duklin <[email protected]> * build(deps): bump astroid from 2.9.1 to 2.9.3 in /package_parser (#58) Bumps [astroid](https://github.com/PyCQA/astroid) from 2.9.1 to 2.9.3. - [Release notes](https://github.com/PyCQA/astroid/releases) - [Changelog](https://github.com/PyCQA/astroid/blob/main/ChangeLog) - [Commits](pylint-dev/astroid@v2.9.1...v2.9.3) --- updated-dependencies: - dependency-name: astroid dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump importlib-metadata in /package_parser (#56) Bumps [importlib-metadata](https://github.com/python/importlib_metadata) from 4.10.0 to 4.10.1. - [Release notes](https://github.com/python/importlib_metadata/releases) - [Changelog](https://github.com/python/importlib_metadata/blob/main/CHANGES.rst) - [Commits](python/importlib_metadata@v4.10.0...v4.10.1) --- updated-dependencies: - dependency-name: importlib-metadata dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps-dev): bump mypy from 0.930 to 0.931 in /package_parser (#55) Bumps [mypy](https://github.com/python/mypy) from 0.930 to 0.931. - [Release notes](https://github.com/python/mypy/releases) - [Commits](python/mypy@v0.930...v0.931) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * build(deps): bump numpydoc from 1.1.0 to 1.2 in /package_parser (#57) Bumps [numpydoc](https://github.com/numpy/numpydoc) from 1.1.0 to 1.2. - [Release notes](https://github.com/numpy/numpydoc/releases) - [Changelog](https://github.com/numpy/numpydoc/blob/main/doc/release_notes.rst) - [Commits](numpy/numpydoc@v1.1.0...numpydoc-1.2) --- updated-dependencies: - dependency-name: numpydoc dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat: updated ontology to represent the current model (#65) * updated ontology to represent the current model * fix: updated ontology * removed subclasses for UnionType * feat: Dependencies updated README (#59) * corrected pattern name * updated readme with future work * updated readme with instructions on how to add further patterns * expected type correction * updated test * refactor: possible fix for mypy error * refactor: another possible fix for mypy error Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: Lars Reimann <[email protected]> * feat: integrate purity parser (#68) * Initial prototype written with astroid as shown in last meeting (10.12.21) * Update to ast file & node classes file * Add files via upload * Delete ast_example2.py * Add files via upload * State of ast visitor as discussed in meeting * Add files via upload * Some fixes to handlers of many ast nodes * Added saving properties to lists for ontology integration * Add files via upload * Add files via upload * Added comments, some fixes to certain nodes * Delete PurityV1.owl * Delete PurityV2.owl * Add files via upload * style: minor formatting changes * style: apply automatic fixes of linters Co-authored-by: Adrian Bajraktari <[email protected]> Co-authored-by: BitaAfshar <[email protected]> Co-authored-by: Lars Reimann <[email protected]> Co-authored-by: lars-reimann <[email protected]> * refactor: move everything into top-level folder * refactor: remove duplicate or unnecessary files * refactor: move api-editor files into new folder * ci: fix paths * build: make gradlew executable again * build: some fixes for linter configuration * build: re-enable ES Module interop * style: apply automatic fixes of linters Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: Aleksandr Sergeev <[email protected]> Co-authored-by: aserge16 <[email protected]> Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: duklin <[email protected]> Co-authored-by: Dushko Klincharov <[email protected]> Co-authored-by: Prajakta Bhujbal <[email protected]> Co-authored-by: lars-reimann <[email protected]> Co-authored-by: mmdoja <[email protected]> Co-authored-by: Adrian Bajraktari <[email protected]> Co-authored-by: Adrian Bajraktari <[email protected]> Co-authored-by: BitaAfshar <[email protected]>
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Closes #40.