Refactor G123 (#495)

* refactor g123 functions to separate class * fix SNP frequencies issues * migrate g123 tests * increase coverage * typing
malariagen · Jan 9, 2024 · 6f6ca39 · 6f6ca39
1 parent 5a68bd8
commit 6f6ca39
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Showing 14 changed files with 868 additions and 716 deletions.
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -28,7 +28,7 @@ jobs:
               run: poetry install
 
             - name: Run tests with coverage
-              run: poetry run pytest --durations=20 --durations-min=1.0 -v --cov malariagen_data/anoph --cov-report=xml tests/anoph
+              run: poetry run pytest --durations=20 -v --cov malariagen_data/anoph --cov-report=xml tests/anoph
 
             - name: Upload coverage report
               uses: codecov/codecov-action@v3

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -41,7 +41,7 @@ jobs:
           key: gcs_cache_tests_20231119
 
       - name: Run full test suite
-        run: poetry run pytest --durations=20 --durations-min=10.0 -v tests
+        run: poetry run pytest --durations=20 -v tests
 
       - name: Save GCS cache
         uses: actions/cache/save@v3

diff --git a/malariagen_data/af1.py b/malariagen_data/af1.py
@@ -12,9 +12,7 @@
 FST_GWSS_CACHE_NAME = "af1_fst_gwss_v1"
 H12_CALIBRATION_CACHE_NAME = "af1_h12_calibration_v1"
 H12_GWSS_CACHE_NAME = "af1_h12_gwss_v1"
-G123_GWSS_CACHE_NAME = "af1_g123_gwss_v1"
 XPEHH_GWSS_CACHE_NAME = "af1_xpehh_gwss_v1"
-G123_CALIBRATION_CACHE_NAME = "af1_g123_calibration_v1"
 H1X_GWSS_CACHE_NAME = "af1_h1x_gwss_v1"
 IHS_GWSS_CACHE_NAME = "af1_ihs_gwss_v1"
 
@@ -79,9 +77,7 @@ class Af1(AnophelesDataResource):
     _fst_gwss_results_cache_name = FST_GWSS_CACHE_NAME
     _h12_calibration_cache_name = H12_CALIBRATION_CACHE_NAME
     _h12_gwss_cache_name = H12_GWSS_CACHE_NAME
-    _g123_gwss_cache_name = G123_GWSS_CACHE_NAME
     _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME
-    _g123_calibration_cache_name = G123_CALIBRATION_CACHE_NAME
     _h1x_gwss_cache_name = H1X_GWSS_CACHE_NAME
     _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME
 

diff --git a/malariagen_data/ag3.py b/malariagen_data/ag3.py
@@ -17,8 +17,6 @@
 FST_GWSS_CACHE_NAME = "ag3_fst_gwss_v1"
 H12_CALIBRATION_CACHE_NAME = "ag3_h12_calibration_v1"
 H12_GWSS_CACHE_NAME = "ag3_h12_gwss_v1"
-G123_CALIBRATION_CACHE_NAME = "ag3_g123_calibration_v1"
-G123_GWSS_CACHE_NAME = "ag3_g123_gwss_v1"
 XPEHH_GWSS_CACHE_NAME = "ag3_xpehh_gwss_v1"
 H1X_GWSS_CACHE_NAME = "ag3_h1x_gwss_v1"
 IHS_GWSS_CACHE_NAME = "ag3_ihs_gwss_v1"
@@ -137,9 +135,7 @@ class Ag3(AnophelesDataResource):
     _fst_gwss_results_cache_name = FST_GWSS_CACHE_NAME
     _h12_calibration_cache_name = H12_CALIBRATION_CACHE_NAME
     _h12_gwss_cache_name = H12_GWSS_CACHE_NAME
-    _g123_gwss_cache_name = G123_GWSS_CACHE_NAME
     _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME
-    _g123_calibration_cache_name = G123_CALIBRATION_CACHE_NAME
     _h1x_gwss_cache_name = H1X_GWSS_CACHE_NAME
     _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME