Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Pin non-buggy pandas version #2719

Merged
merged 3 commits into from
Oct 30, 2023

fix relnotes

ae81bd0
Select commit
Failed to load commit list.
Merged

Pin non-buggy pandas version #2719

fix relnotes
ae81bd0
Select commit
Failed to load commit list.
Azure Pipelines / scverse.scanpy succeeded Oct 30, 2023 in 13m 27s

Build #20231030.4 had test failures

Details

Tests

  • Failed: 2 (0.05%)
  • Passed: 4,089 (95.90%)
  • Other: 173 (4.06%)
  • Total: 4,264
Code coverage

  • 8578 of 11926 lines covered (71.93%)

Annotations

Check failure on line 1 in scanpy/tests/test_plotting.py::test_violin

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/test_plotting.py::test_violin

image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7f7719e27ce0>

    def test_violin(image_comparer):
        save_and_compare_images = partial(image_comparer, ROOT, tol=40)
    
        with plt.rc_context():
            sc.pl.set_rcParams_defaults()
            sc.set_figure_params(dpi=50, color_map="viridis")
    
            pbmc = pbmc68k_reduced()
>           sc.pl.violin(
                pbmc,
                ["n_genes", "percent_mito", "n_counts"],
                stripplot=True,
                multi_panel=True,
                jitter=True,
                show=False,
            )

scanpy/tests/test_plotting.py:488: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/plotting/_anndata.py:798: in violin
    g = sns.catplot(
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:2927: in catplot
    p.plot_violins(
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:1145: in plot_violins
    self._configure_legend(ax, legend_artist, common_kws)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <seaborn.categorical._CategoricalPlotter object at 0x7f7719e77810>
ax = None
func = <function _get_patch_legend_artist.<locals>.legend_artist at 0x7f7719d84680>
common_kws = {'edgecolor': (0.24823529411764705, 0.24823529411764705, 0.24823529411764705), 'linewidth': 1.25}
semantic_kws = None

    def _configure_legend(self, ax, func, common_kws=None, semantic_kws=None):
    
        if self.legend == "auto":
            show_legend = not self._redundant_hue and self.input_format != "wide"
        else:
            show_legend = bool(self.legend)
    
        if show_legend:
            self.add_legend_data(ax, func, common_kws, semantic_kws=semantic_kws)
>           handles, _ = ax.get_legend_handles_labels()
E           AttributeError: 'NoneType' object has no attribute 'get_legend_handles_labels'

/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:419: AttributeError
Raw output
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:419: AttributeError: 'NoneType' object has no attribute 'get_legend_handles_labels'

Check failure on line 1 in scanpy/tests/notebooks/test_pbmc3k.py::test_pbmc3k

See this annotation in the file changed.

@azure-pipelines azure-pipelines / scverse.scanpy

scanpy/tests/notebooks/test_pbmc3k.py::test_pbmc3k

image_comparer = <function image_comparer.<locals>.save_and_compare at 0x7f77204222a0>

    @needs("leidenalg")
    def test_pbmc3k(image_comparer):
        save_and_compare_images = partial(image_comparer, ROOT, tol=20)
    
        adata = sc.read(
            "./data/pbmc3k_raw.h5ad", backup_url="http://falexwolf.de/data/pbmc3k_raw.h5ad"
        )
    
        # Preprocessing
    
        sc.pl.highest_expr_genes(adata, n_top=20, show=False)
        save_and_compare_images("highest_expr_genes")
    
        sc.pp.filter_cells(adata, min_genes=200)
        sc.pp.filter_genes(adata, min_cells=3)
    
        mito_genes = [name for name in adata.var_names if name.startswith("MT-")]
        # for each cell compute fraction of counts in mito genes vs. all genes
        # the `.A1` is only necessary as X is sparse to transform to a dense array after summing
        adata.obs["percent_mito"] = (
            np.sum(adata[:, mito_genes].X, axis=1).A1 / np.sum(adata.X, axis=1).A1
        )
        # add the total counts per cell as observations-annotation to adata
        adata.obs["n_counts"] = adata.X.sum(axis=1).A1
    
>       sc.pl.violin(
            adata,
            ["n_genes", "n_counts", "percent_mito"],
            jitter=False,
            multi_panel=True,
            show=False,
        )

scanpy/tests/notebooks/test_pbmc3k.py:54: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
scanpy/plotting/_anndata.py:798: in violin
    g = sns.catplot(
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:2927: in catplot
    p.plot_violins(
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:1145: in plot_violins
    self._configure_legend(ax, legend_artist, common_kws)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <seaborn.categorical._CategoricalPlotter object at 0x7f77192427d0>
ax = None
func = <function _get_patch_legend_artist.<locals>.legend_artist at 0x7f7738bf8c20>
common_kws = {'edgecolor': (0.24823529411764705, 0.24823529411764705, 0.24823529411764705), 'linewidth': 1.25}
semantic_kws = None

    def _configure_legend(self, ax, func, common_kws=None, semantic_kws=None):
    
        if self.legend == "auto":
            show_legend = not self._redundant_hue and self.input_format != "wide"
        else:
            show_legend = bool(self.legend)
    
        if show_legend:
            self.add_legend_data(ax, func, common_kws, semantic_kws=semantic_kws)
>           handles, _ = ax.get_legend_handles_labels()
E           AttributeError: 'NoneType' object has no attribute 'get_legend_handles_labels'

/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:419: AttributeError
Raw output
/opt/hostedtoolcache/Python/3.11.6/x64/lib/python3.11/site-packages/seaborn/categorical.py:419: AttributeError: 'NoneType' object has no attribute 'get_legend_handles_labels'