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CHANGELOG

v0.3.7 (2024-10-23)

Fixes

  • fix: remove output step (1fcebac)

Unknown

  • Merge pull request #35 from shirte/main

Remove output step (b840f69)

  • Don't require smiles columns in tests (a1597f8)

v0.3.6 (2024-10-22)

Fixes

  • fix: fix a bug involving DepthFirstExplorer and long lists (9912f11)

Unknown

  • Merge pull request #34 from shirte/main

Fix a bug involving DepthFirstExplorer and long lists (0da2a36)

  • Export sdf_writer in output submodule (7bdbf4c)

  • Merge pull request #33 from shirte/main

Configure package auto-discovery (7a86d24)

  • Configure package auto-discovery (1c943e2)

v0.3.5 (2024-10-21)

Fixes

  • fix: remove predictor fixture (5ffb13c)

Unknown

  • Merge pull request #32 from shirte/main

Remove unused code (7a4b6a3)

  • Remove AddSmilesStep (ce45c2d)

  • Add step suffix to ReadInput (8efb681)

  • Remove read function in model (e263611)

v0.3.4 (2024-10-18)

Fixes

  • fix: format test files (c189697)

  • fix: rewrite test check (390c34e)

  • fix: Bump version to original version (d807f55)

  • fix: Simplify commands in Readme (3f2199c)

  • fix: remove typo in pypi.yml (c39d86d)

  • fix: revert to release when pushing to main branch (1ad4e3b)

  • fix: Replace check_suite with workflow_run (b8765db)

  • fix: run release only after successful status checks (8e82933)

  • fix: remove release condition (125374f)

Unknown

  • Merge pull request #31 from shirte/main

Allow _predict_mols to return an iterator (98eaecf)

  • Add tests for _predict_mols (8eebe3d)

  • Allow _predict_mols to return an iterator (3c3274e)

  • Merge pull request #30 from shirte/main

fix: rewrite test check (65bba22)

  • Merge pull request #29 from shirte/main

fix: Bump version to original version (f5be8f4)

  • Merge pull request #28 from shirte/main

Bump version to original version (097b2ee)

  • Avoid random test failure (f7bc04b)

  • Bump version to original version (3690488)

  • Merge pull request #27 from shirte/main

fix: remove typo in pypi.yml (648bff1)

  • Merge pull request #26 from shirte/main

Add github action for publishing to PyPI (e35771f)

  • Add github action for publishing to PyPI (6fc1b3e)

  • Add .ruff_cache to gitignore (a01b383)

  • Merge pull request #25 from shirte/main

fix: revert to release when pushing to main branch (ecfb026)

  • Avoid random test failure (92a1e84)

  • Merge pull request #24 from shirte/main

fix: Replace check_suite with workflow_run (55708c8)

  • Merge pull request #23 from shirte/main

Run release only after successful status checks (b267b1e)

  • Bump version to original state (e3e65ab)

  • Merge pull request #22 from shirte/main

fix: remove release condition (2cffead)

  • Merge pull request #21 from shirte/main

Add id-token:write to release.yml (f82466a)

  • Add id-token:write to release.yml (24419be)

  • Merge pull request #20 from shirte/main

Add github token to Python Semantic Release (b821dc0)

  • Add github token to Python Semantic Release (e1d5828)

  • Merge pull request #19 from shirte/main

Add permissions in release.yml (410cd61)

  • Add permissions in release.yml (cf86d8b)

  • Merge pull request #18 from shirte/main

Connect release.yml with app (ab9aab1)

  • Format cli (ff55521)

  • Connect release.yml with app (21a84f5)

  • Disallow untyped defs in mypy (b25c853)

  • Fix types in CLI (a08518f)

  • Fix import of Traversable in different Python versions (9e18ca0)

  • Make sure that fields in Model are overwritable (16a5c42)

  • Merge pull request #17 from shirte/main

Fix test.yml (65b958a)

  • Fix test.yml (e748c47)

  • Merge pull request #16 from shirte/main

Add py.typed marker file (209a657)

  • Add single step to summarize matrix test results (ac43267)

  • Bump version (49d6f2f)

  • Add py.typed marker file (4141df3)

  • Merge pull request #15 from shirte/main

Use GITHUB_TOKEN for checkout (094028a)

  • Rename github actions step (build -> test) (1e51cbf)

  • Use GITHUB_TOKEN for checkout (240bad9)

  • Merge pull request #14 from shirte/main

Fix types in YamlConfiguration (1e51022)

  • Use importlib.abc.Traversable for old Python versions (950c723)

  • Fix type for CustomLoader in yaml loading (1ffb8fd)

  • Make importlib-resources available for Python < 3.9 (6ebae21)

  • Rewrite check_column_type and check_column_length (955a02a)

  • Make YamlConfiguration accept Traversable (ceb511a)

  • Merge pull request #13 from shirte/main

Fix "Sha not resolved" by adding fetch-depth: 0 (2788b39)

  • Fix "Sha not resolved" by adding fetch-depth: 0 (3c763f0)

  • Merge pull request #12 from shirte/main

Add python-semantic-release (4ecf53d)

  • Configure python-semantic-release in pyproject.toml (0d2a0ab)

  • Avoid running release.yml on forks (c290022)

  • Create release.yml (5c0a5f3)

  • Merge pull request #11 from shirte/main

Introduce ruff (455970a)

  • Fix mypy step in qc.yml (c480666)

  • Merge workflows and use ruff (8235b17)

  • Replace black with ruff formatter (a94cdd2)

  • Add ruff to project (3fc22c7)

  • Pass kwargs to readers in SimpleModel (5adf417)

  • Merge pull request #10 from shirte/main

Convert project configuration to pyproject.toml (403a4a7)

  • Fix types in cli (6a30ab9)

  • Fix config classes for mypy (f8b8463)

  • Move mypy configuration to pyproject.toml (6bf1ead)

  • Replace pytest-watch with pytest-watcher (d115500)

  • Incorporate pytest.ini into pyproject.toml (d44c0ae)

  • Switch to pyproject.toml (402bf63)

  • Merge pull request #9 from shirte/main

Enable different representations based on output format (0f54f86)

  • Add properties to Model and SimpleModel (56a0169)

  • Add types to CLI (9b000b1)

  • Introduce PathLikeStr for pytho 3.8 (df3a360)

  • Improve get_entry_points polyfill (50d19f4)

  • Connect SimpleModel with converters (a850a18)

  • Enable different representations of data types depending on output format (d9720cb)

  • ENable configuration of property visibility (eae9745)

  • Use init_subclasses for writer registration (7cb2e46)

  • Add types to config submodule (0dce5c2)

  • Add types to util submodule (885ede4)

  • Add types to polyfills submodule (8d4047d)

  • Add types to steps submodule (42d6d0f)

  • Add types in preprocessing submodule (6943abe)

  • Merge pull request #8 from shirte/main

Automatically register Reader and Writer classes when inheriting from them (b6ac003)

  • Add types to record_list_writer (de1584d)

  • Add types to model submodule (d728a77)

  • Add types to output submodule (3651846)

  • Add data_dir to repr in FileReader (1f95e88)

  • Add types in input submodule (e606037)

  • Remove class_decorator (9316266)

  • Implement writer registry via meta class

  • implement WriterMeta

  • remove WriterRegistry

  • remove register_writer decorator

  • remove all register_writer decorator calls (2c2b1d6)

  • Implement reader registry via meta class

  • implement ReaderMeta

  • add method get_readers on Reader class

  • delete ReaderRegistry

  • delete register_reader

  • remove all @register_reader decorator calls (27a6c77)

  • Merge pull request #7 from shirte/main

Minor changes (c024194)

  • Add type check in SimpleModel constructor (4fcc5f9)

  • Add logging to configurations (c7a682b)

  • Merge pull request #6 from shirte/main

Minor changes (2718cce)

  • Add missing property in SimpleModel (7399e05)

  • Check for duplicate properties in EnforceSchemaStep (4e54a90)

  • Merge pull request #5 from shirte/main

Minor changes (3ff4f7b)

  • Minor changes

  • rename "errors" to "problems"

  • don't allow "(none)" as input for checking value equality / inequality (822b02d)

  • Let model check wther predictions have correct type (a4fbe77)

  • Add and remove types (0b806df)

  • Fix bug involving two-letter elements (a5c787d)

  • Merge pull request #4 from shirte/main

Add Mypy (d8417c9)

  • Ignore wrong types from rdkit in mypy check (073ea1a)

  • Add types-setuptools so mypy looks less sad (058ab77)

  • Make black happy (161f85c)

  • Add github workflow for mypy (9e4cad0)

  • Add type stubs from external libraries (db0a2ff)

  • Make mypy happy (d3bb5d8)

  • Upgrade deps in environment.yml (35ae1bd)

  • Add *Step suffix to subclasses of Step (e53d7e3)

  • Merge pull request #3 from shirte/main

Minor fixes (bf15d80)

  • Avoid rdkit logging in tests (98ec224)

  • Add default values for name and batch size from config in SimpleModel (65419bb)

  • Add name property to model (374bf05)

  • Make batch_size in model overwritable (5e314d6)

  • Fix scoring strategy in DepthFirstExplorer

If the explorer obtained an invalid SDF file, the chances are high that the result would be a list of invalid entries (one per line in the SDF file). Avoid this by discourage invalid entries in the scoring rule. (1fdb753)

  • Add convenience method "read" to model (b3ebca8)

  • Bump version (8499ab6)

  • Introduce abstract class OutputStep (3c02e8f)

  • Separate steps into input, preprocessing, postprocessing and output steps (5eb8685)

  • Bump version (3959b38)

  • Fix auto_cli mechanism (620e877)

  • Write tests for FilterByWeight (deb942f)

  • Remove old parts in preprocessing code (865361b)

  • Catch errors of custom preprocessing steps (0857393)

  • Remove space in test.yml (022fe6d)

  • Add chembl structure pipeline to dependencies during tests (d9b246c)

  • Distinguish _get_base_config and _get_config in SimpleModel (b7d33ac)

  • Add tests for chembl structure pipeline preprocessing

  • simplify scenarios call to automatically detect test features

  • move checks to the appropriate file (e0b38ab)

  • Test atom property prediction with invalid model (cb304a7)

  • Catch exceptions during model prediction (1dd51c6)

  • Add smiles representation in SimpleModel (4a96b03)

  • Merge pull request #1 from shirte/main

Implement dict streaming (7186d9d)

  • Bump version (bcdafa1)

  • Update testing code

  • merge different model classes into one class

  • merge all scenario test cases into one file (8cc9a51)

  • Adapt models to new dict streaming workflow

  • move code for assigning mol ids and names to separate classes (AssignMolId, AssignName)

  • move code that takes care of adding missing columns to a separate class (EnforceSchema)

  • let the base class Model handle prediction of molecules

  • add all additional convenience code to SimpleModel (configuration, input, output)

  • implement wrapper classes for input reading (ReadInput) and output writing (WriteOutput) (e073129)

  • Add util submodule with convenient functions

  • move class_decorator in utils submodule

  • implement call_with_mappings that calls a method and assigns function arguments by name

  • implement method to retrieve the file of a given class instance (43cae68)

  • Introduce new base class to implement prediction steps (4f43925)

  • Adapt preprocessing pipelines to dict streaming code

  • implement special case of filtering "H" in FilterByElement

  • remove pipeline classes (they are replaced by list of preprocessing steps)

  • remove pipeline registry since it is not needed anymore

  • move code to Step / MapStep classes (be11962)

  • Refactor output writing modules

  • move file-based code from Writer to a new class FileWriter

  • implement new writer classes: IteratorWriter, PandasWriter, and RecordListWriter.

  • update the WriterRegistry to support registering and retrieving writers based on output format (89ea00c)

  • Refactor input classes

  • introduce convenient Explorer._read method

  • add another criterion to find the best reader in DepthFirstExplorer

  • change type Generator[..., None, None] to Iterator[...]

  • make ReaderRegistry aware of potential constructor arguments in individual reader classes (7795295)

  • Refactor configuration classes

  • add types

  • derive DefaultConfiguration from DictConfiguration

  • move yaml search code from AutoConfiguration to SearchYamlConfiguration

  • implement proper merge mechanism in MergedConfiguration

  • move code from AutoConfiguration to model classes (7cdb39b)

  • Decouple AutoConfiguration from Model

  • avoid that AutoConfiguration calls the _get_config method of the Model class (instead let _get_config returns an AutoConfiguration)

  • make package and file-based configuration two exclusive options in AutoConfiguration (c45a747)

  • Cache calls to Configuration.get_dict

  • implement key-based access: config['description']

  • add repr method (221b29b)

  • Add test for checking the error column (999afef)

  • Remove old import statement (9174892)

  • Move dummy test models to code dir for reuse (63b1d14)

  • Provide dummy version if no package version was found (0e7953f)

  • Infer default module name (c9db891)

  • Make formatter happy (9c908fb)

  • Add Sanitize preprocessing step

  • adapt unit tests (ba67bb9)

  • Copy InvalidWeightProblem into FilterByWeight again (1d6740b)

  • Bump actions/setup-python to version 4 (bec7d71)

  • Add github workflow that runs tests (a8055e8)

  • Bump version of actions/checkout (0dc7919)

  • Add github workflow for formatting with black (93d4ec7)

  • Put chembl_structure_pipeline in separate extras_require

  • bump version (a274627)

  • Adapt AbstractModel class (fe55e0c)

  • Change unit test (3fe7200)

  • Infer default module name and version (8d0b7f3)

  • Add abbreviations for common problem cases (d7ebcbd)

  • Extend type annotation of Step.run (8ea2247)

  • Add version polyfill (c6f23b8)

  • Add new file guessing implementation

  • create separate submodules for input and output actions (e282c18)

  • Add global config to reader registry (2f350a3)

  • Add helper methods for testing (71adaec)

  • Bump version (3212f10)

  • Open absolute paths in file reader (94cbccf)

  • Avoid relative paths in file reader (063e0e7)

  • Make DepthFirstExplorer accept different readers

  • put polyfills in separate modules

  • add data_dir param in FileReader (6a89013)

  • Improve reading algorithm

  • add pytest-sugar (4dfa11c)

  • Bump version (499a36b)

  • Relax version requirement for importlib deps

  • improve version retrieval

  • add LICENSE (3434980)

  • Make nerdd-module compatible with Python 3.7 (b21a998)

  • Differentiate between text and byte streams (8c5f3ac)

  • Add decorator dependency (c1f3c31)

  • Convert CLI parameter names to spinal case

  • simplify rdkit check

  • install importlib-resources only if python version < 3.10 (fed6556)

  • Add package configuration option

  • make auto_cli available on package level (eb68fe0)

  • Silence rdkit logger during import (070397a)

  • Add description field in setup.py (a523e1f)

  • Populate repository (cd4747f)

  • Initial commit (8d10952)