| Age | Commit message (Expand) | Author |
|---|
| 2021-07-23 | Fix issue caught in `nearest` while testing `slink`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* While running tests for slink, to try and understand what it is doing in
order to write the appropriate tests for it, an issue arose that pointed a
blindspot in the former understanding of now `nearest` should work.
This commit fixes the issue found in both the expected data, and the code.
| Muriithi Frederick Muriuki |
| 2021-07-23 | New function (`slink`): return [] on exception...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Add minimum code to pass new test
* tests/unit/computations/test_slink.py: new test
Add test to ensure that the new `slink` function return an empty list in
case and exception is raised.
Add the new `slink` function with minimum amount of code needed to pass the
test.
| Muriithi Frederick Muriuki |
| 2021-07-23 | Add dummy module documentation...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Add initial dummy module documentation in form of
a python docstring
Update the names of what would be private methods/function to start with a
double-underscore (__) so that they do not show up in the default python
documentation.
| Muriithi Frederick Muriuki |
| 2021-07-23 | Add docstring for `nearest' function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: add documentation for the `nearest` function in
the `gn3.computations.slink` module in the form of a (hopefully correct)
python docstring.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Get shortest distance from two lists/tuples of member coordinates...* gn3/computations/slink.py: add code to ensure new test passes
* tests/unit/computations/test_slink.py: new test
This one is a little weird: from
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L57-L63
It gets rid of the last coordinates in both the lists of the member
coordinates, and uses the remaining coordinates to find the shortest
members.
For example, given the following member coordinates:
- i=[0,1,2] and j=[5,7,9], it uses [0,1] and [5,7]
- i=[3,6,1] and j=[7,13], it uses [3,6] and [7]
to find the shortest distances.
I (fredmanglis) am not sure why it does it this way, since I'd have expected
it to use all the coordinates, however, since at this time we need to retain
bug-compatibility with the older code, I have done it as it is done in the
old code.
I also add a statement to raise an exception in the case where i and j are
not lists of integers, or integers
| Muriithi Frederick Muriuki |
| 2021-07-22 | Extract common `is_list_or_tuple' function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Extract the common function `is_list_or_tuple' making it accessible to later
parts of the code.
| Muriithi Frederick Muriuki |
| 2021-07-22 | Test for shortest distance between members in a list and coordinate...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: add code to pass new test
* tests/unit/computations/test_slink.py: new test
Given a list of members in a group, and a coordinate for a member in the
same group, find the distance of the closest member from the given
coordinate in the group.
| Muriithi Frederick Muriuki |
| 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 |
