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Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
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Fix a number of tests and fixtures that were not conforming to the FOREIGN KEY
constraints:
* Each test that creates a new "object" needs to clean up after itself
* Each fixture that sets up test data needs to clean up after itself
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Add code to implement the OAuth2 flow.
* Add test fixtures for setting up users and OAuth2 clients
* Add tests for token generation with the "Password Grant" flow
* Fix some issues with test due to changes in the database connection's
row_factory
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Initialise the authentication/authorisation system packages and set up the
initial database migrations to set up the system.
* README.md: Add documentation on migrations
* gn3/auth/__init__.py: init package
* gn3/auth/authentication/__init__.py: init package
* gn3/auth/authorisation/__init__.py: init package
* gn3/migrations.py: provide migration utilities
* migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py:
new migration
* tests/unit/auth/test_init_database.py: test new migration applies and rolls
back as expected
* tests/unit/conftest.py: fixtures for unit tests
* yoyo.auth.ini: basic configuration for yoyo-migration for auth system
migrations
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* gn3/db/sample_data.py (get_trait_csv_sample_data): Pass __query
directly to cursor.execute. Rename value to _value in for loop to
make mypy pass.
* gn3/db_utils.py (Connection): Add class docstring.
(Connection.cursor): Add docstring.
* mypy.ini: Add an entry for xapian.
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This allows Maybe[T] to be used as a type. Both Nothing and Just are
of type Maybe.
* mypy.ini: Add default location for stub files.
* stubs/pymonad/__init__.pyi: New file.
* stubs/pymonad/maybe.pyi: Ditto.
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* gn3/computations/correlations.py: rename function
* mypy.ini: deactivate mypy error about missing imports
* tests/integration/test_correlation.py: mock correct function
* tests/unit/computations/test_correlation.py: test correct function
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* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca
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* Ignore some missing library stubs
* Ignore some typing errors
* Fix obvious typing errors
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* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes
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that and we seem to have done the same thing for scipy
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Deleted in 56ce88a
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* delete unwanted correlation stuff
* Refactor/clean up correlations (#4)
* initial commit for Refactor/clean-up-correlation
* add python scipy dependency
* initial commit for sample correlation
* initial commit for sample correlation endpoint
* initial commit for integration and unittest
* initial commit for registering correlation blueprint
* add and modify unittest and integration tests for correlation
* Add compute compute_all_sample_corr method for correlation
* add scipy to requirement txt file
* add tissue correlation for trait list
* add unittest for tissue correlation
* add lit correlation for trait list
* add unittests for lit correlation for trait list
* modify lit correlarion for trait list
* add unittests for lit correlation for trait list
* add correlation metho in dynamic url
* add file format for expected structure input while doing sample correlation
* modify input data structure -> add trait id
* update tests for sample r correlation
* add compute all lit correlation method
* add endpoint for computing lit_corr
* add unit and integration tests for computing lit corr
* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation
* add unittest and integration tests for tissue correlation
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
* update guix scm file
* fix pylint error for correlations api
Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
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