Add backwards algorithm for haploid data, using lshmm for testing

tskit-dev · Jul 13, 2023 · f7ba548 · f7ba548
1 parent 60d75c6
commit f7ba548
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Showing 4 changed files with 603 additions and 794 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -83,7 +83,7 @@ jobs:
             /usr/share/miniconda/envs/anaconda-client-env
             ~/osx-conda
             ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v11-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
+          key: ${{ runner.os }}-${{ matrix.python}}-conda-v12-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
 
       - name: Install Conda
         uses: conda-incubator/setup-miniconda@v2

diff --git a/python/requirements/CI-tests-pip/requirements.txt b/python/requirements/CI-tests-pip/requirements.txt
@@ -1,4 +1,4 @@
-lshmm==0.0.4; python_version < '3.11'
+lshmm==0.0.4
 numpy==1.21.6; python_version < '3.11' # Held at 1.21.6 for Python 3.7 compatibility
 numpy==1.24.1; python_version > '3.10'
 pytest==7.1.3

diff --git a/python/tests/test_genotype_matching_fb.py b/python/tests/test_genotype_matching_fb.py
@@ -754,7 +754,6 @@ def compute_next_probability_dict(
         query_is_missing,
     ):
         mu = self.mu[site_id]
-
         template_is_hom = np.logical_not(template_is_het)
 
         if query_is_missing: