Release 0.1.11 #79
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Release 0.1.11 #79
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Fixes some funny pre-commit issues <details><summary>Details</summary> <p> ``` [INFO] Installing environment for https://github.com/pycqa/isort. [INFO] Once installed this environment will be reused. [INFO] This may take a few minutes... An unexpected error has occurred: CalledProcessError: command: ('/home/runner/.cache/pre-commit/reponyreh8dk/py_env-python3/bin/python', '-mpip', 'install', '.') return code: 1 stdout: Processing /home/runner/.cache/pre-commit/reponyreh8dk Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'error' stderr: error: subprocess-exited-with-error × Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [14 lines of output] Traceback (most recent call last): File "/home/runner/.cache/pre-commit/reponyreh8dk/py_env-python3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module> main() File "/home/runner/.cache/pre-commit/reponyreh8dk/py_env-python3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.cache/pre-commit/reponyreh8dk/py_env-python3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel return hook(metadata_directory, config_settings) File "/tmp/pip-build-env-gp0vx_lo/overlay/lib/python3.9/site-packages/poetry/core/masonry/api.py", line 41, in prepare_metadata_for_build_wheel poetry = Factory().create_poetry(Path(".").resolve(), with_groups=False) File "/tmp/pip-build-env-gp0vx_lo/overlay/lib/python3.9/site-packages/poetry/core/factory.py", line 58, in create_poetry raise RuntimeError("The Poetry configuration is invalid:\n" + message) RuntimeError: The Poetry configuration is invalid: - [extras.pipfile_deprecated_finder.2] 'pip-shims<=0.3.4' does not match '^[a-zA-Z-_.0-9]+$' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. Check the log at /home/runner/.cache/pre-commit/pre-commit.log Error: Process completed with exit code 3. ``` </p> </details>
* GHA: Trigger on each push Not only on `main`. * Skip failing tests for now
Unused imports / isort / black
Fixed some incorrect typehints.
Add some basic sphinx configuration and make docstrings sphinx-compatible. `cd doc && make html && xdg-open _build/html/index.html` Related to #7 * Fix docstrings / xrefs * Fix sphinx error / type annotation WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_dict": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_options": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_dict": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_options": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model.Model.get_parameter_values": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.__init__": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.get_estimated": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.indices_to_parameters": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_all": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_to_indices": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_to_model": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.decompress_parameter_values": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.decompress_parameter_values": name 'estimate' is not defined WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace": name 'estimate' is not defined
Add .readthedocs.yaml and pin some documentation dependencies. More recent versions of nbsphin/sphinx/nbconvert require newer pandoc than available on the RTD ubuntu-images. :eyes: https://petab-select--63.org.readthedocs.build/en/63/ Closes #7
Fix argument order in calculate_aicc. nllh was used as n_estimated and vice versa when computing AIC. Didn't change the result for AIC, though.
* re-format * add RTD link * fix some typos
Fix some type annotations / docstrings / undefined references
1. Avoids littering the namespace on star imports more than necessary 2. Simplifies cross-references to documentation, e.g., in addition to `petab_select.problem.Problem`, we can also now reference `petab_select.Problem`. This wasn't possible before. 3. Now also https://petab-select--72.org.readthedocs.build/en/72/generated/petab_select.html is populated. (To be decided whether we want to have only the top-level imports or only the individual modules.)
…calibrate uncalibrated predecessor models (#68) Co-authored-by: Doresic <[email protected]>
Exclude all the not-so-interesting methods of Enums and others.
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