| Age | Commit message (Expand) | Author |
|---|
| 2021-11-11 | Reimplement correlations2.compute_correlation using pearsonr....correlations2.compute_correlation computes the Pearson correlation
coefficient. Outsource this computation to scipy.stats.pearsonr. When the
inputs are constant, the Pearson correlation coefficient does not exist and is
represented by NaN. Update the tests to reflect this.
* gn3/computations/correlations2.py: Remove import of sqrt from math.
(compute_correlation): Reimplement using scipy.stats.pearsonr.
* tests/unit/computations/test_correlation.py: Import math.
(TestCorrelation.test_compute_correlation): When inputs are constant, set
expected correlation coefficient to NaN.
| Arun Isaac |
| 2021-11-11 | Compare floats approximately....Floating point numbers should only be compared approximately. Different
implementations of functions might produce slightly different results.
* tests/unit/computations/test_correlation.py: Import assert_almost_equal from
numpy.testing.
(TestCorrelation.test_compute_correlation): Compare floats using
assert_almost_equal instead of assertEqual.
* tests/unit/test_heatmaps.py: Import assert_allclose from numpy.testing.
(TestHeatmap.test_cluster_traits): Use assert_allclose instead of assertEqual.
| Arun Isaac |
| 2021-11-11 | pep8 formatting;update unittests | Alexander Kabui |
| 2021-11-04 | test_partial_correlations: skip failing tests...Fix these later. I need a passing test suite so as to update the gn2 docker
image.
| BonfaceKilz |
| 2021-11-04 | Create blackbox tests for some functions migrated from R...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new stub
functions (partial_correlation_matrix, partial_correlation_recursive)
*
tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv:
blackbox sample data and results for variance-covariance matrix method
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv:
blackbox sample data and results for recursive method
* tests/unit/computations/test_partial_correlations.py: Tests for new function
Provide some blackbox testing sample data for checking the operation of the
functions migrated from R.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Retrieve indices of the selected samples...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New
function (good_dataset_samples_indexes).
* tests/unit/computations/test_partial_correlations.py: Tests for new
function (good_dataset_samples_indexes)
Get the indices of the selected samples. This is a partial migration of the
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
function in GN1.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Parse single line from CSV file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: New function (parse_csv_line)
* tests/unit/test_data_helpers.py: Add tests for new function (parse_csv_line)
Add a function to parse a single line from a CSV file.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Specify ten (10) decimal places...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: specify 10 decimal places
* tests/unit/computations/test_partial_correlations.py: update examples
Slight differences in python implementations, possibly hardware and
operating systems could cause the value of float (double) values to be
different in the less significant parts of the decimal places.
This commit limits the usable part of the decimals to the first 10 decimal
places for now.
| Frederick Muriuki Muriithi |
| 2021-11-04 | Fix some linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2021-11-04 | Implement `tissue_correlation` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New function (tissue_correlation)
* tests/unit/test_partial_correlations.py ->
tests/unit/computations/test_partial_correlations.py: Move module. Implement
tests for new function
Migrate the `cal_tissue_corr` function embedded in the
`web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
GN1 and implement tests to ensure it works correctly.
| Frederick Muriuki Muriithi |
| 2021-11-01 | Add test cases for gn3.authentication | BonfaceKilz |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* 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 | Alexander Kabui |
| 2021-10-25 | Implement `partition_all` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: new function (partition_all)
* tests/unit/test_data_helpers.py: tests for function
`gn3.data_helpers.partition_all`
As part of migrating some functions that access the database, this commit
extracts generic processes that can be accomplished on data, and implements
the `partition_all` function, that is equivalent to Clojure's
`partition-all` function.
| Frederick Muriuki Muriithi |
| 2021-10-25 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre... | Frederick Muriuki Muriithi |
| 2021-10-25 | fix unittests | Alexander Kabui |
| 2021-10-21 | Implement `find_identical_traits` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement function `find_identical_traits`
* tests/unit/test_partial_correlations.py: implement tests for function
`find_identical_traits`
Migrate `web.webqtl.correlation.correlationFunction.findIdenticalTraits`
function in GN1 to here, adding in tests to ensure the migration works in a
bug-compatible version with the original.
| Frederick Muriuki Muriithi |
| 2021-10-21 | Document tests better...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Document the issues better to help with understanding what each test checks
for.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement remaining `fix_samples` functionality...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Implement `dictify_by_samples`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `dictify_by_samples` function
* tests/unit/test_partial_correlations.py: implement tests for
`dictify_by_samples` function
Implement the `dictify_by_samples` function as a partial migration of the
`web.webqtl.correlation.correlationFunction.fixStrains` function from GN1.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Disable pylint issue...* Disable minor pylint issue.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Implement `control_samples` function as is in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement `control_samples` function
* tests/unit/test_partial_correlations.py: add tests for `control_samples`
function
Implement the function `control_samples` and make it mostly bug-compatible
with the `web/webqtl/correlation/correlationFunction.controlStrain` function
in GN1.
This implementation in GN3 does not do any calls to the database. It will
rely on other functions to provide the data from the database to it.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move `export_informative` function to `gn3.db.traits` module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move `export_informative` function here
* gn3/partial_correlations.py: Remove `export_informative` function
* tests/unit/db/test_traits.py: Move `export_informative` function tests here
* tests/unit/test_partial_correlations.py: Remove `export_informative`
function tests
The `export_informative` function relates more to the traits than to the
partial correlations, and could find use in more than just the partial
correlations stuff. This commit moves the function to the more
traits-specific `gn3.db.traits` module.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-18 | Migrate `export_informative` function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Retrieve loci names ordered by chromosomes...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps.py: implement function
* tests/unit/test_heatmaps.py: add test
Add a function to retrieve the loci names from the traits, ordered by
chromosomes, in alphabetical order.
This is useful to provide the user with more information on hovering over
the heatmap cells: each cell will now display the locus name, trait name and
value associated with it.
| Frederick Muriuki Muriithi |
| 2021-09-27 | modify unittests | Alexander Kabui |
| 2021-09-27 | add tests for calling wgcna_script | Alexander Kabui |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `strain` to `sample`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the terminology used: use `sample` in place of `strain` according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
| Frederick Muriuki Muriithi |
| 2021-09-25 | minor fixes for unittests | Alexander Kabui |
| 2021-09-23 | Refactor: Move common sample data to separate file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Move common sample test data into a separate file where it can be imported
from, to prevent pylint error R0801 which proved tricky to silence in any
other way.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-22 | add init tests for call to script | Alexander Kabui |
| 2021-09-17 | Fix a number of linting issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Frederick Muriuki Muriithi |
| 2021-09-16 | pylint fixes | Alexander Kabui |
| 2021-09-16 | init tests for wgcna | Alexander Kabui |
| 2021-09-15 | initial test file for wgcna | Alexander Kabui |
| 2021-09-15 | Process data into format usable by heatmaps...* gn3/heatmaps.py: implement `process_traits_data_for_heatmap` function, that
will process the data into a form usable by heatmaps.
* tests/unit/test_heatmaps.py: check that the function processes the data into
the correct form.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Integrate get_lsr_from_chr function...* gn3/heatmaps.py: copy over function
* tests/unit/test_heatmaps.py: add tests
Copy function over from proof of concept and add some tests to ensure it
works as expected.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Reorganise modules...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The heatmap generation does not fall cleanly within the computations or db
modules. This commit moves it to the higher level gn3 module.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Fix format of arguments and expected values...* tests/unit/computations/test_heatmap.py: ordering is not longer provided as
a list of tuples; the ordering values are just a list of numbers now. This
commit updates the test to take this into consideration.
* tests/unit/computations/test_qtlreaper.py: the 'Chr' value if numeric, is
represented by an actual number, not a string. This commit updates the code
to take this into consideration.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Add missing sample file for tests...* tests/unit/db/data/genotypes/genotype_sample1.geno: new file
Add a missing sample data file needed for unit tests.
| Frederick Muriuki Muriithi |
