Fix hvg warnings #2810
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Fix hvg warnings #2810
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flying-sheep
commented
Jan 15, 2024
| sum_total = np.sum(sums_genes).ravel() | ||
| sum_total = np.sum(sums_genes) |
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this makes a 0D array into a 1D array. Later a 0D array is expected, so let’s just not do that.
flying-sheep
commented
Jan 15, 2024
| batch_info = adata.obs[batch_key].values | ||
| batch_info = adata.obs[batch_key].to_numpy() |
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.values is deprecated in favor of .to_numpy()
flying-sheep
commented
Jan 15, 2024
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| df.means > min_mean, | ||
| df.means < max_mean, | ||
| df.dispersions_norm > min_disp, | ||
| df.dispersions_norm < max_disp, | ||
| df["means"] > min_mean, | ||
| df["means"] < max_mean, | ||
| df["dispersions_norm"] > min_disp, | ||
| df["dispersions_norm"] < max_disp, |
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using item access instead of attribute access is good style, especially for library code
flying-sheep
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Jan 15, 2024
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| adata = adata[:1000, :500] | ||
| adata = adata[:1000, :500].copy() | ||
| sc.pp.filter_cells(adata, min_genes=1) |
flying-sheep
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Jan 15, 2024
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| np.random.seed(0) | ||
| adata.obs["batch"] = np.random.binomial(3, 0.5, size=(adata.n_obs)) | ||
| adata.obs["batch"] = adata.obs["batch"].astype("category") | ||
| gen = np.random.default_rng(0) | ||
| adata.obs["batch"] = pd.array( | ||
| gen.binomial(3, 0.5, size=adata.n_obs), dtype="category" | ||
| ) |
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np.random.* functions are deprecated in favor of np.random.Generator.* methods.
flying-sheep
commented
Jan 15, 2024
| @@ -50,15 +58,23 @@ def test_highly_variable_genes_basic(): | |||
| assert adata.var["highly_variable"].sum() == 3 | |||
| assert (highly_var_first_layer != adata.var["highly_variable"]).any() | |||
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| def test_highly_variable_genes_no_batch_matches_batch(): | |||
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splitting this long sequential test of many features up into individual ones
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #2810 +/- ##
==========================================
- Coverage 72.84% 72.70% -0.14%
==========================================
Files 111 111
Lines 12368 12368
==========================================
- Hits 9009 8992 -17
- Misses 3359 3376 +17
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some small changes before #2809