diff --git a/bin/consistency-basic.py b/bin/consistency-basic.py index 79ad926..1509648 100755 --- a/bin/consistency-basic.py +++ b/bin/consistency-basic.py @@ -59,7 +59,7 @@ def plotConsistency( ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=outfile, auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=outfile, auto_open=show) if __name__ == "__main__": diff --git a/bin/consistency-heatmap.py b/bin/consistency-heatmap.py index 0d7cf39..a57bdcb 100755 --- a/bin/consistency-heatmap.py +++ b/bin/consistency-heatmap.py @@ -130,7 +130,7 @@ def plotConsistency( layout = go.Layout(layoutDict) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=outfile, auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=outfile, auto_open=show) if __name__ == "__main__": diff --git a/bin/multiple-significant-base-frequencies.py b/bin/multiple-significant-base-frequencies.py index 3d67627..682b575 100755 --- a/bin/multiple-significant-base-frequencies.py +++ b/bin/multiple-significant-base-frequencies.py @@ -93,7 +93,7 @@ def plotScores(sampleData, outfile): layout = go.Layout(xaxis=xaxis, yaxis=yaxis) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=outfile, show_link=False) + plotly.offline.plot(fig, filename=outfile) if __name__ == "__main__": diff --git a/pyproject.toml b/pyproject.toml index 2d3dccc..941bd49 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "midtools" -version = "1.2.3" +version = "1.3.0" description = "Command line scripts and Python classes for detecting multiple infections from NGS reads." readme = "README.md" license = "MIT" @@ -28,7 +28,7 @@ classifiers = [ dependencies = [ "colorlover>=0.3.0", "dark-matter>=7.1.19", - "plotly>=6.6.0", + "plotly>=7.0.0", ] [project.urls] diff --git a/src/midtools/plotting.py b/src/midtools/plotting.py index e6ce66d..f97d738 100644 --- a/src/midtools/plotting.py +++ b/src/midtools/plotting.py @@ -123,7 +123,7 @@ def plotSAM( hovermode="closest", ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) def plotAllReferencesSAM( @@ -312,7 +312,7 @@ def plotAllReferencesSAM( fig.update_layout(legend_title_text="Genotype (total reads)") - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) def _plotSortedMaxBaseFrequencies( @@ -417,7 +417,7 @@ def _plotSortedMaxBaseFrequencies( }, ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) return frequencyInfo @@ -516,7 +516,7 @@ def _plotBaseFrequenciesEntropy( }, ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) return entropyInfo @@ -602,7 +602,7 @@ def _plotBaseFrequenciesAllOffsets( ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) def _plotBaseFrequencies( @@ -674,7 +674,7 @@ def _plotBaseFrequencies( ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) def plotBaseFrequencies( @@ -843,7 +843,7 @@ def plotCoverageAndSignificantLocations( } ) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) def plotConsistentComponents( @@ -1125,4 +1125,4 @@ def offsetsToLocationsStr(offsets: list[int]) -> str: ) fig = go.Figure(data=data, layout=layout) - plotly.offline.plot(fig, filename=str(outfile), auto_open=show, show_link=False) + plotly.offline.plot(fig, filename=str(outfile), auto_open=show) diff --git a/uv.lock b/uv.lock index 894b852..dfa8df0 100644 --- a/uv.lock +++ b/uv.lock @@ -224,7 +224,7 @@ name = "cffi" version = "2.0.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "pycparser", marker = "implementation_name != 'PyPy'" }, + { name = "pycparser" }, ] sdist = { url = "https://files.pythonhosted.org/packages/eb/56/b1ba7935a17738ae8453301356628e8147c79dbb825bcbc73dc7401f9846/cffi-2.0.0.tar.gz", hash = "sha256:44d1b5909021139fe36001ae048dbdde8214afa20200eda0f64c068cac5d5529", size = 523588, upload-time = "2025-09-08T23:24:04.541Z" } wheels = [ @@ -470,7 +470,7 @@ resolution-markers = [ "python_full_version < '3.11'", ] dependencies = [ - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" } }, ] sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" } wheels = [ @@ -548,7 +548,7 @@ resolution-markers = [ "python_full_version == '3.11.*' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] dependencies = [ - { name = "numpy", version = "2.4.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy", version = "2.4.4", source = { registry = "https://pypi.org/simple" } }, ] sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174, upload-time = "2025-07-26T12:03:12.549Z" } wheels = [ @@ -803,7 +803,7 @@ name = "exceptiongroup" version = "1.3.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - 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