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in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
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* fix key error for (*tissue_cor) tissue correlation
* update tests for tissue correlation
* rename speed_compute to fast_compute
* pep8 formatting
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix clustering bugs
* tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues.
Test and fix the clustering function.
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* Fix linting errors that do not change the function of the code.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Since the `slink` function assigns values to the `listcopy` variable and its
children, this commit ensures that the sequence is a list to allow for the
assignment.
If the child-sequence is a tuple, that would lead to an exception.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: fix errors
* tests/unit/computations/test_heatmap.py: new tests
Add new tests with the expected source data format, and expected results.
Fix all errors that were caught by running the tests
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Heatmap decompose db retrieval
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix some errors caught by the linter.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Import some missing definitions.
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* use normal function for correlation + rename functions
* update test for sample correlation
* use normal function for tissue correlation + rename functions
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to compute and organise the data that will be used to draw the
final heatmap.
This varies significantly in how it works from the original, but it still
tries to retain the general flow of data.
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* gn3/computations/slink.py: remove unused imports
* gn3/db/traits.py: remove unnecessary `else` clauses
* tests/unit/db/test_traits.py: add docstrings for functions
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add some type annotations for the `nearest` function.
* Leave some comments regarding the issues experienced when trying to add some
typing annotations to the function to help with future endeavours of the
same.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add some type annotations for the `nearest` function.
* Leave some comments regarding the issues experienced when trying to add some
typing annotations to the function to help with future endeavours of the
same.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix a myriad of issues caught by pylint to ensure the code passes all tests.
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instead of None when it can't be calculcated (which was messing up sorting); it may also be okay to remove the None check, but leaving it for now (#28)
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Copy the function, mostly verbatim from
genenetwork1. See:
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138
* tests/unit/computations/test_slink.py: Add a test with some example data to
test that the implementation gives the same results as that in genenetwork1
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Fix the iteration construct.
Given two lists of member coordinates, such as [0, 1] and [3, 5], the
initial code would iterate over the pairs [0, 3] and [1, 5].
This commit fixes the iteration constructs such that the new code iterates
over the pairs [0, 3], [0, 5], [1, 3] and [1, 5].
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/slink.py: Extract the `__flatten_list_of_lists` function
since it is used in more than one place.
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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.
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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.
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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.
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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.
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* 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
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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.
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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.
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* 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
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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
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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* 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".
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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 ☝🏾.
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