| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-07-29 | Fix failing tests | Frederick Muriuki Muriithi | |
| * 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 | |||
| 2022-07-28 | Add command to run the sample correlations in an external process | Frederick Muriuki Muriithi | |
| 2022-07-28 | Update sample correlations code to use multiprocessing | Frederick Muriuki Muriithi | |
| * To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. | |||
| 2022-07-22 | mypy fixes | Alexander_Kabui | |
| 2022-07-22 | pep8 fixes | Alexander_Kabui | |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui | |
| 2022-07-22 | import rust_correlation when running gn3 as lib | Alexander_Kabui | |
| 2022-07-22 | compute num overlap | Alexander_Kabui | |
| 2022-07-22 | fix for bug splitting list data | Alexander_Kabui | |
| 2022-07-22 | minor fixes for parsing data | Alexander_Kabui | |
| 2022-07-22 | code to parse tissue correlation input | Alexander_Kabui | |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui | |
| 2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui | |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui | |
| 2022-07-22 | add unittests | Alexander_Kabui | |
| 2022-07-22 | minor fixes | Alexander_Kabui | |
| 2022-07-11 | Allow CORS everywhere by default | Frederick Muriuki Muriithi | |
| Allow the resources (endpoints) to be accessible from anywhere on the internet by default, while still allowing for restriction via CLI environment variable on a case by case basis. | |||
| 2022-06-29 | use explicit parameters | Alexander_Kabui | |
| 2022-06-29 | fix issues | Alexander_Kabui | |
| 2022-06-29 | lint test file | Alexander | |
| 2022-06-29 | pylint fixes | Alexander | |
| 2022-06-29 | add tests | Alexander | |
| 2022-06-29 | add test data | Alexander | |
| 2022-06-29 | minor fixes | Alexander | |
| 2022-06-29 | handle tmp files generation | Alexander | |
| 2022-06-29 | parse output data | Alexander | |
| 2022-06-29 | pep8 formatting | Alexander | |
| 2022-06-29 | new variable: CORRELATION_COMMAND | Alexander | |
| 2022-06-29 | init test correlation rust module | Alexander | |
| 2022-06-29 | init rust correlation module | Alexander | |
| 2022-06-28 | Parse the method from UI before passing it to external process | Frederick Muriuki Muriithi | |
| To reduce the chances of the system failing due to the external process being launched with the wrong parameters, add a parsing stage that converts the method from the UI into a form acceptable by the CLI script. * gn3/commands.py: parse the method from UI * scripts/partial_correlations.py: simplify the acceptable methods | |||
| 2022-06-21 | tests: test_file_utils: Replace pytest.mark.skip with unittest.skip | BonfaceKilz | |
| "python setup.py test" won't skip "pytest.mark.skip" thereby leading to build failure when you try to package gn3. | |||
| 2022-06-21 | setup.py: Remove commented out "ipfshttpclient" line | BonfaceKilz | |
| 2022-06-21 | gn3: fs_helpers: Fix pylint errors | BonfaceKilz | |
| * gn3/fs_helpers.py: Remove unused "pathlib" import. (cache_ipfs_file): Disable "unused-argument" warting. | |||
| 2022-06-21 | test_file_utils: Disable test cases for "cache_ipfs_file" | BonfaceKilz | |
| * tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto. | |||
| 2022-06-21 | gn3: fs_helpers: Remove ipfshttpclient | BonfaceKilz | |
| This library pollutes the Genenetwork2 profile with an old version "dataclasses" thereby causing it to fail. | |||
| 2022-06-21 | setup.py: Remove ipfshttpclient | BonfaceKilz | |
| 2022-06-21 | integration: test_gemma: Skip "GemmaAPITest" | BonfaceKilz | |
| 2022-06-21 | Replace lint code with human-readable text | BonfaceKilz | |
| * gn3/db/correlations.py (__fetch_data__): Use a more readable code as opposed to an error code. | |||
| 2022-06-21 | db: correlations: Ignore pylint error | BonfaceKilz | |
| * gn3/db/correlations.py (__fetch_data__): Ignore "Too many args" [R0913] error. | |||
| 2022-06-21 | db: correlations: Ignore types | BonfaceKilz | |
| * gn3/db/correlations.py (__build_query__): Ignore the "sample_ids" and "joins" types when calling build_query_sgo_lit_corr (fetch_all_database_data): Ignore the return type. TODO: Ping Alex/Arun to fix this. | |||
| 2022-06-21 | db: datasets.py: Ignore results from sparql.queryAndConvert | BonfaceKilz | |
| ATM, it's very difficult to work the correct type that is returned. Ignore this for now and fix this later. | |||
| 2022-06-21 | mypy.ini: Ignore missing lmdb mypy stubs | BonfaceKilz | |
| 2022-06-20 | Update README: export env variables explicitly | Frederick Muriuki Muriithi | |
| 2022-06-20 | gn3: genodb: Retire get function. | Arun Isaac | |
| * gn3/genodb.py (get): Delete function. (matrix): Use db.txn.get instead of get. | |||
| 2022-06-20 | gn3: genodb: Match class and function names of GenotypeMatrix. | Arun Isaac | |
| * gn3/genodb.py (GenotypeMatrix): Match class and function names. | |||
| 2022-06-20 | gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix. | Arun Isaac | |
| db is unused. nrows and ncols are available in the array and transpose numpy arrays. * gn3/genodb.py (GenotypeMatrix)[db, nrows, ncols]: Delete fields. * gn3/genodb.py (matrix): Do not initialize db, nrows and ncols fields. | |||
| 2022-06-20 | gn3: genodb: Mention reading entire matrix in module docstring. | Arun Isaac | |
| * gn3/genodb.py: Mention reading entire matrix in module docstring. | |||
| 2022-06-20 | Restrict partial correlation method choices | Frederick Muriuki Muriithi | |
| - Have "Pearson's r" and "Spearman's rho" as the only valid choices for the partial correlations | |||
| 2022-06-17 | gn3: genodb: Rename Matrix named tuple to GenotypeMatrix. | Arun Isaac | |
| * gn3/genodb.py (Matrix): Rename to GenotypeMatrix. (matrix): Update invocation of Matrix. | |||
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