add compare.py which contains functions for comparing.#1206

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akaviaLab wants to merge 39 commits intoopencobra:develfrom akaviaLab:compare

+2,178-354

Commits on May 2, 2022

add compare.py which contains functions for comparing.
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fix typing and imports
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Commits on May 3, 2022

fix .gitignore to ignore sonarlint
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revised compare.py and the comparing functions
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added typing and docstrings
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initial tests for compare.py
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Commits on May 7, 2022

tidying of compare.py
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Commits on May 9, 2022

tidying of compare.py
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Commits on May 10, 2022

fixed some reaction comparison tests
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fix: resolve E501 for mat.py

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fix: resolve F401 for cobrapy_repository.py

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fix: resolve B008 and B014 for load.py

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refactor: resolve D100, D103 and add type annotations and docstrings for test_io_order.py

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refactor: resolve D100, add type annotations, docstrings and upgrade code style for test_notes.py

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refactor: resolve D100, D041 and add type annotations, docstrings for test_annotation.py

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refactor: resolve D100, F841 and add type annotations, docstrings for test_annotation_format.py

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refactor: resolve D100, D103 and add type annotations, docstrings for test_load.py

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refactor: resolve D401, F841 and add type annotations and docstrings for test_mat.py

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fix: docstrings fixes for test_annotation.py and test_annotation_format.py

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chore: improve file opening for test_load.py

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chore: improve file opening for test_annotation.py

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chore: improve pytest exception handling for test_load.py

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chore: add changes in next-release.md

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refactor: proper use of package import for loading resources in cobrapy_repository.py

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refactor: group default repositories for load.py

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refactor: use pathlib.Path.open() for loading model in test_laod.py

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refactor: rename cobra/data/init.py to cobra/data/__init__.py

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chore: remove unnecessary boilerplate code for singleton.py

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chore: resolve F401 for species.py

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refactor: resolve F401, D103 and add type annotations, docstrings for conftest.py

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refactor: resolve flake8 issue and add type annotations and upgrade code style for test_core/conftest.py

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refactor: remove try...except block for pytest import in conftest.py

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refactor: remove LegacySolution class from codebase

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refactor: resolve flake8 issues and add type annotations, docstrings for solution.py

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refactor: resolve flake8 issues and type annotations, docstrings for test_solution.py

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refactor: add further type annotations and correct f-string formatting for solution.py

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added some gene comparison tests
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black
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Commits on May 11, 2022

black again
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