mudata 0.4 tests

src/mudata/_core/config.py

@@ -3,7 +3,7 @@
 OPTIONS = {
     "display_style": "text",
     "display_html_expand": 0b010,
-    "pull_on_update": None,
+    "pull_on_update": False,
 }
 
 _VALID_OPTIONS = {

tests/test_io.py

@@ -39,6 +39,7 @@ def test_write_read_h5mu_mod_obs_colname(self, mdata, filepath_h5mu):
         mdata.obs["mod1:column"] = 1
         mdata["mod1"].obs["column"] = 2
         mdata.update()
+        mdata.pull_obs()
         mdata.write(filepath_h5mu)
         mdata_ = mudata.read(filepath_h5mu)
         assert "column" in mdata_.obs.columns
@@ -51,6 +52,7 @@ def test_write_read_zarr_mod_obs_colname(self, mdata, filepath_zarr):
         mdata.obs["mod1:column"] = 1
         mdata["mod1"].obs["column"] = 2
         mdata.update()
+        mdata.pull_obs()
         mdata.write_zarr(filepath_zarr)
         mdata_ = mudata.read_zarr(filepath_zarr)
         assert "column" in mdata_.obs.columns

tests/test_merge.py

@@ -29,7 +29,7 @@ def mdata():
 
 @pytest.mark.usefixtures("filepath_h5mu", "filepath_zarr")
 class TestMuData:
-    def test_merge(self, mdata, filepath_h5mu):
+    def test_merge(self, mdata):
         mdata1, mdata2 = mdata[:N1, :].copy(), mdata[N1:, :].copy()
         mdata_ = mudata.concat([mdata1, mdata2])
         assert list(mdata_.mod.keys()) == ["mod1", "mod2"]

tests/test_nullable.py

@@ -35,6 +35,7 @@ def mdata():
 
 class TestMuData:
     def test_mdata_bool_boolean(self, mdata):
+        mdata.pull_var()
         assert mdata.var["assert-bool"].dtype == bool
         assert isinstance(mdata.var["mod1:assert-boolean-1"].dtype, pd.BooleanDtype)
         assert isinstance(mdata.var["mod2:assert-boolean-2"].dtype, pd.BooleanDtype)

tests/test_obs_var.py

@@ -27,22 +27,26 @@ def test_obs_global_columns(self, mdata, filepath_h5mu):
             mod.obs["demo"] = m
         mdata.obs["demo"] = "global"
         mdata.update()
-        assert list(mdata.obs.columns.values) == [f"{m}:demo" for m in mdata.mod.keys()] + ["demo"]
+        mdata.pull_obs()
+        assert list(mdata.obs.columns.values) == ["demo"] + [f"{m}:demo" for m in mdata.mod.keys()]
         mdata.write(filepath_h5mu)
         mdata_ = mudata.read(filepath_h5mu)
-        assert list(mdata_.obs.columns.values) == [f"{m}:demo" for m in mdata_.mod.keys()] + [
-            "demo"
+        assert list(mdata_.obs.columns.values) == ["demo"] + [
+            f"{m}:demo" for m in mdata_.mod.keys()
         ]
 
     def test_var_global_columns(self, mdata, filepath_h5mu):
         for m, mod in mdata.mod.items():
             mod.var["demo"] = m
         mdata.update()
+        mdata.pull_var()
         mdata.var["global"] = "global_var"
         mdata.update()
+        mdata.pull_var()
         assert list(mdata.var.columns.values) == ["demo", "global"]
         del mdata.var["global"]
         mdata.update()
+        mdata.pull_var()
         assert list(mdata.var.columns.values) == ["demo"]
         mdata.write(filepath_h5mu)
         mdata_ = mudata.read(filepath_h5mu)

tests/test_update.py

@@ -97,6 +97,8 @@ def test_update_simple(self, modalities):
             mod.var_names = [f"{m}_var{j}" for j in range(mod.n_vars)]
         mdata = MuData(modalities)
         mdata.update()
+        mdata.pull_obs()
+        mdata.pull_var()
 
         # Variables are different across modalities
         assert "mod" in mdata.var.columns
@@ -124,6 +126,8 @@ def test_update_duplicates(self, modalities):
             mod.var_names = [f"{m}_var{j // 2}" for j in range(mod.n_vars)]
         mdata = MuData(modalities)
         mdata.update()
+        mdata.pull_obs()
+        mdata.pull_var()
 
         # Variables are different across modalities
         assert "mod" in mdata.var.columns
@@ -152,6 +156,12 @@ def test_update_intersecting(self, modalities):
             mod.var_names = [f"{m}_var{j}" if j != 0 else f"var_{j}" for j in range(mod.n_vars)]
         mdata = MuData(modalities)
         mdata.update()
+        mdata.pull_obs()
+        # New behaviour since v0.4:
+        # - Will add a single column 'mod' with the correct labels even with intersecting var_names
+        mdata.pull_var()
+        # - Will add the columns with modality prefixes
+        mdata.pull_var(join_common=False)
 
         for m, mod in modalities.items():
             # Observations are the same across modalities
@@ -177,6 +187,7 @@ def test_update_after_filter_obs_adata(self, mdata):
         # mu.pp.filter_obs(mdata['mod1'], 'min_count', lambda x: (x < -2))
         mdata.mod["mod1"] = mdata["mod1"][mdata["mod1"].obs["min_count"] < -2].copy()
         mdata.update()
+        mdata.pull_obs()
         assert mdata.obs["batch"].isna().sum() == 0
 
     @pytest.mark.parametrize("obs_mod", ["unique"])
@@ -207,6 +218,33 @@ def test_update_after_obs_reordered(self, mdata):
             [all(true_obsm_values[i] == test_obsm_values[i]) for i in range(len(true_obsm_values))]
         )
 
+    @pytest.mark.parametrize("obs_mod", ["unique"])
+    @pytest.mark.parametrize("obs_across", ["intersecting"])
+    @pytest.mark.parametrize("obs_n", ["joint", "disjoint"])
+    def test_update_intersecting_var_names_after_filtering(self, mdata):
+        orig_shape = mdata.shape
+        mdata.mod["mod1"].var_names = [str(i) for i in range(mdata["mod1"].n_vars)]
+        mdata.mod["mod2"].var_names = [str(i) for i in range(mdata["mod2"].n_vars)]
+        mdata.update()
+        mdata.mod["mod1"] = mdata["mod1"][:, :5].copy()
+        mdata["mod1"].var["true"] = True
+        mdata["mod2"].var["false"] = False
+        assert mdata["mod1"].n_vars == 5
+        mdata.update()
+        mdata.pull_var(prefix_unique=False)
+        assert mdata.n_obs == orig_shape[0]
+        assert mdata.n_vars == mdata["mod1"].n_vars + mdata["mod2"].n_vars
+        assert mdata.var["true"].sum() == 5
+        assert (~mdata.var["false"]).sum() == (~mdata["mod2"].var["false"]).sum()
+
+    @pytest.mark.parametrize("obs_mod", ["unique"])
+    @pytest.mark.parametrize("obs_across", ["intersecting"])
+    @pytest.mark.parametrize("obs_n", ["joint", "disjoint"])
+    def test_update_to_new_names(self, mdata):
+        mdata["mod1"].var_names = [f"_mod1_var{i}" for i in range(1, mdata["mod1"].n_vars + 1)]
+        mdata["mod2"].var_names = [f"_mod2_var{i}" for i in range(1, mdata["mod2"].n_vars + 1)]
+        mdata.update()
+
 
 # @pytest.mark.usefixtures("filepath_h5mu")
 # class TestMuDataSameVars:

tests/test_update_axis_1.py

@@ -97,11 +97,13 @@ def test_update_simple(self, datasets):
             datasets[d].obs_names = [f"{d}_obs{j}" for j in range(dset.n_obs)]
         mdata = MuData(datasets, axis=1)
         mdata.update()
+        mdata.pull_obs()
+        mdata.pull_var()
 
         # Variables are different across datasets
         assert "dataset" in mdata.obs.columns
         for d, dset in datasets.items():
-            # Veriables are the same across datasets
+            # Variables are the same across datasets
             # hence /mod/mod1/var/dataset -> /var/mod1:dataset
             assert f"{d}:dataset" in mdata.var.columns
             # Columns are intact in individual datasets
@@ -124,6 +126,8 @@ def test_update_duplicates(self, datasets):
             dset.obs_names = [f"{d}_obs{j // 2}" for j in range(dset.n_obs)]
         mdata = MuData(datasets, axis=1)
         mdata.update()
+        mdata.pull_obs()
+        mdata.pull_var()
 
         # Observations are different across datasets
         assert "dataset" in mdata.obs.columns
@@ -151,6 +155,12 @@ def test_update_intersecting(self, datasets):
             dset.obs_names = [f"{d}_obs{j}" if j != 0 else f"obs_{j}" for j in range(dset.n_obs)]
         mdata = MuData(datasets, axis=1)
         mdata.update()
+        # New behaviour since v0.4:
+        # - Will add a single column 'mod' with the correct labels even with intersecting obs_names
+        mdata.pull_obs()
+        # - Will add the columns with modality prefixes
+        mdata.pull_obs(join_common=False)
+        mdata.pull_var()
 
         for d, dset in datasets.items():
             # Veriables are the same across datasets