Refactor Stdout capturer to handle serialization.

AlexPatrie commented 1 year ago

What new features does this PR implement? Please summarize the features that this PR implements. As relevant, please indicate the issues that the PR closes.

Implements __getstate__ and __setstate__ methods (@getter, @setter) to override pickling that is inherent to StandardOutputCapturer() call in biosimulators_utils.combine.exec.exec_sedml_docs_in_archive().
Adds StandardOutputErrorCapturer as being typing.Optional in combine subdir methods. Closes biosimulators-copasi number 56.
Adds absolute imports to packages

What bugs does this PR fix? Please summarize the bugs that this PR fixes. As relevant, please indicate the issues that the PR closes.

The "hidden" error of TypeError: cannot pickle '_io.BufferedReader' object that is exposed during evocation of capturer.

Does this PR introduce any additional changes? Please summarize any additional changes that this PR introduces.

How have you tested this PR? Please summarize the tests that you implemented to test this PR.

Additional information Please describe any information needed to review this PR.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 60.00% and no project coverage change.

Comparison is base (ac14afd) 95.79% compared to head (095e046) 95.79%.

:exclamation: Current head 095e046 differs from pull request most recent head 8f8dc3c. Consider uploading reports for the commit 8f8dc3c to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #134 +/- ## ======================================= Coverage 95.79% 95.79% ======================================= Files 88 88 Lines 9399 9399 ======================================= Hits 9004 9004 Misses 395 395 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `95.79% <60.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://app.codecov.io/gh/biosimulators/Biosimulators_utils/pull/134?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators) | Coverage Δ | | |---|---|---| | [biosimulators\_utils/config.py](https://app.codecov.io/gh/biosimulators/Biosimulators_utils/pull/134?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators#diff-Ymlvc2ltdWxhdG9yc191dGlscy9jb25maWcucHk=) | `60.93% <0.00%> (ø)` | | | [biosimulators\_utils/warnings.py](https://app.codecov.io/gh/biosimulators/Biosimulators_utils/pull/134?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators#diff-Ymlvc2ltdWxhdG9yc191dGlscy93YXJuaW5ncy5weQ==) | `14.28% <0.00%> (ø)` | | | [biosimulators\_utils/\_\_init\_\_.py](https://app.codecov.io/gh/biosimulators/Biosimulators_utils/pull/134?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators#diff-Ymlvc2ltdWxhdG9yc191dGlscy9fX2luaXRfXy5weQ==) | `100.00% <100.00%> (ø)` | | | [biosimulators\_utils/\_\_main\_\_.py](https://app.codecov.io/gh/biosimulators/Biosimulators_utils/pull/134?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biosimulators#diff-Ymlvc2ltdWxhdG9yc191dGlscy9fX21haW5fXy5weQ==) | `99.60% <100.00%> (ø)` | |

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