| Age | Commit message (Expand) | Author |
|---|
| 2021-07-22 | Check that given list and both coordinates, we get shortest distance...* gn3/computations/slink.py: Add code to compute the distance given the
coordinate of both members on the parent list/tuple
* tests/unit/computations/test_slink.py:
* Change the name of the tests to more closely correspond to the business
requirement the test is checking for
* Update the comments to indicate some more things that might need to be
done in the future
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that all distances are positive or zero...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: check that all distances between the 'somethings'
are all either zero or positive.
* tests/unit/computations/test_slink.py:
* Remove data with all distances positive or zero, since it would fail the
test
* Change the expected message to more closely correspond to the business
logic
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that distance from A to B is same as from B to A...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: check that the distance from child A to B is the
same as distance from child B to A. If not, throw an exception.
* tests/unit/computations/test_slink.py:
* Change the name of the test to more closely correspond to the business
logic being tested.
* Update the data in a separate test such that it does not error out due to
failing to fulfill the expectations of separate requirement.
- pass tests
- Rename test
- Fix errors: distances same both directions
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that child distance from itself is zero...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Check that a child's distance from itself is
zero. If not, throw an exception.
The children lists are a list of distances of "something" from other
"somethings". There is still some need to establish what those "somethings"
are, so that the test names can reflect the ideas that are actually being
tested for.
* tests/unit/computations/test_slink.py: Change the name of the test so that
it more closely corresponds to the business logic it is actually testing,
and not the mechanics of testing the idea.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check the child lengths are same as length of parent...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Check that the child lists/tuples are the same length as the parent
list/tuple. If any of the children is not the same length as the parent,
throw and exception.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Add docstring...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add docstring to the function, useful for generating automated developer
documentation.
We also surround the guard functions with some notification comments, to
mark possible future places where change might be done.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Check that list and its direct children are not empty...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to pass the test that the list/tuple passed to `nearest' and its
direct children lists/tuples are not empty.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Implement check for lists or tuples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Implement the code to pass the check that a list of lists is passed to the
`nearest' function.
| Muriithi Frederick Muriuki |
| 2021-07-21 | Extract tests from code in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Add dummy `nearest' function
* tests/unit/computations/test_slink.py: Add some tests
This commit adds tests to try and reproduce the working of the `nearest'
function in:
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py
This commit might not yet have extracted all the expected behaviour of the
`nearest' function, and therefore, there is a possibility of a later commit
augmenting the work in this commit.
| Muriithi Frederick Muriuki |
| 2021-07-20 | Implement the correlation function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Implement the correlation computation function, such that it passes the
tests created previously.
| Muriithi Frederick Muriuki |
| 2021-07-20 | Add test for code to move over from GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* .gitignore: ignore emacs temporary files
* gn3/computations/correlations2.py: add a dummy function
* tests/unit/computations/test_correlation.py: add unit tests for the function
As part of the move of the clustering and heatmap code over from GN1 to GN3,
this commit begins by providing some unit tests for the correlation function
used to ensure that the implementation that is built up here corresponds,
and produces the same results as the original.
This tests and the function might change in the new system, but for now, we
try and maintain bug-to-bug compatibility.
| Muriithi Frederick Muriuki |
| 2021-07-10 | gn3: db: Use correct type for columns arg in fetch functions | BonfaceKilz |
| 2021-07-10 | Fix pylint issues | BonfaceKilz |
| 2021-07-10 | db: test_db: Test that a fetch is correct when columns are specified | BonfaceKilz |
| 2021-07-10 | gn3: db: Add extra argument to specify column in fetch statements | BonfaceKilz |
| 2021-07-10 | db: phenotypes: Add Probeset data structures...* gn3/db/phenotypes.py (Probeset): New dataclass.
(probeset_mapping): New dict.
* gn3/db/__init__.py: Add probeset_mapping and Probeset.
| BonfaceKilz |
| 2021-06-29 | Replace list with a tuple as an argument when setting success_codes...* gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple
* gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when
calling "run_cmd".
| BonfaceKilz |
| 2021-06-29 | guix: Add diffutils as a propagated input | BonfaceKilz |
| 2021-06-29 | guix: Remove commented out hunk | BonfaceKilz |
| 2021-06-29 | gn3: diff: Set success_codes when running the diff tool | BonfaceKilz |
| 2021-06-29 | gn3: commands: Add extra arg that sets the success codes to check...* gn3/commands.py (run_cmd): Some commands like "diff" return non-standard
error codes. To make this fn more robust, add an extra optional argument that
sets what successful codes to check.
| BonfaceKilz |
| 2021-06-29 | tests: test_commands: Add extra check for when an error occurs | BonfaceKilz |
| 2021-06-29 | Add a diffing function...For now the diff function uses the Linux tool "diff" to generate the diff
since it is efficient and straightforward.
* gn3/computations/diff.py (generate_diff): New function.
* tests/unit/computations/test_diff.py: Test cases for ☝🏾.
| BonfaceKilz |
| 2021-06-29 | tests: test_data: Add test data that contains trait data for 10007 | BonfaceKilz |
| 2021-06-25 | Check for the correct result code...When programs terminate with an error, they usually return a -1!
| BonfaceKilz |
| 2021-06-23 | Merge pull request #21 from genenetwork/fix/biweight-errors...Fix/biweight errors | BonfaceKilz |
| 2021-06-23 | fix pylint issues | Alexander Kabui |
| 2021-06-23 | minor fixes for biweight script | Alexander Kabui |
| 2021-06-22 | scripts: laminar: Add json with hooks for running a linter | BonfaceKilz |
| 2021-06-22 | scripts: laminar: Add sh scripts for CI | BonfaceKilz |
| 2021-06-21 | Merge pull request #20 from genenetwork/feature/biweight-correlation...add biweight r script and tests | BonfaceKilz |
| 2021-06-20 | minor fix docstring | Alexander Kabui |
| 2021-06-20 | merge main | Alexander Kabui |
| 2021-06-20 | fix conflict | Alexander Kabui |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui |
| 2021-06-18 | Merge pull request #13 from zsloan/feature/add_rqtl_endpoints...Feature/add rqtl endpoints | zsloan |
| 2021-06-18 | Fixed another error where test_generate_rqtl_command didn't include the filen... | zsloan |
| 2021-06-18 | Fixed file type from json to csv for test_generate_rqtl_command | zsloan |
| 2021-06-18 | Fixed test_rqtl.py to include Rscript in the command | zsloan |
| 2021-06-18 | Fixed test_compose_rqtl_command test; forgot to include Rscript in the command | zsloan |
| 2021-06-18 | Change test_compose_rqtl_command in test_commands.py to have different argume......Changed some parameters in test_compose_rqtl_cmd to avoid pylint complaining about duplicate code
| zsloan |
| 2021-06-18 | Fixed pylint issues | zsloan |
| 2021-06-18 | add ignore_missing_imports for numpy in mypy.ini since it complains about tha... | zsloan |
| 2021-06-18 | Resolve mypy errors in computations/rqtl.py | zsloan |
| 2021-06-18 | Fixed spelling of coeffient to coefficient | zsloan |
| 2021-06-18 | minor fixes | Alexander Kabui |
| 2021-06-18 | remove ununsed variables | Alexander Kabui |
| 2021-06-18 | refactor perf query functions | Alexander Kabui |
| 2021-06-18 | rename perf query file | Alexander Kabui |
| 2021-06-18 | pep8 formatting | Alexander Kabui |
