pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
158 stars 91 forks source link

Update dependency plotly to v5 #273

Closed renovate[bot] closed 2 years ago

renovate[bot] commented 3 years ago

WhiteSource Renovate

This PR contains the following updates:

Package Change Age Adoption Passing Confidence
plotly (source) <5.0 -> <5.6 age adoption passing confidence
plotly (source) ==4.12.0 -> ==5.5.0 age adoption passing confidence

Release Notes

plotly/plotly.py ### [`v5.5.0`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​550---2021-12-20) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.4.0...v5.5.0) ##### Added - `text_auto` argument to `px.bar`, `px.histogram`, `px.density_heatmap`, `px.imshow` [#​3518](https://togithub.com/plotly/plotly.py/issues/3518) - Deprecated `ff.create_annotated_heatmap`, `ff.create_county_choropleth`, `ff.create_gantt` [#​3518](https://togithub.com/plotly/plotly.py/issues/3518) - `div_id` argument to `pio.to_html`, `pio.write_html`, `fig.to_html` and `fig.write_html` to optionally make its IDs deterministic [#​3487](https://togithub.com/plotly/plotly.py/issues/3487) with thanks to [@​Skn0tt](https://togithub.com/Skn0tt) ##### Fixed - Fixed ValueError when `ff.create_annotated_heatmap` passes `rgba()` colors into `to_rgb_color_list` [#​3478](https://togithub.com/plotly/plotly.py/issues/3478) with thanks to [@​janosh](https://togithub.com/janosh) ##### Updated - Updated Plotly.js to from version 2.6.3 to version 2.8.3. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​280----2021-12-10) for more information. Notable changes include: - Horizontal color bars - `texttemplate` for histogram-like and heatmap-like traces ### [`v5.4.0`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​540---2021-11-15) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.3.1...v5.4.0) ##### Fixed - Fixed error when serializing dict with mix of string and non-string keys [#​3380](https://togithub.com/plotly/plotly.py/issues/3380) ##### Updated - The JSON serialization engines no longer sort their keys [#​3380](https://togithub.com/plotly/plotly.py/issues/3380) - Updated Plotly.js to from version 2.4.2 to version 2.6.3. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​263----2021-11-12) for more information. Notable changes include: - New subplot type `smith` that supports `scattersmith` trace types for visualizing data in the complex domain - Changes to Plotly.js packaging ### [`v5.3.1`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​531---2021-08-31) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.3.0...v5.3.1) ##### Updated - Updated Plotly.js to from version 2.4.1 to version 2.4.2. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​240----2021-08-27) for more information. These changes are reflected in the auto-generated `plotly.graph_objects` module. Notable changes include: - Bug fix for rendering unified hover labels in classic Jupyter Notebooks ### [`v5.3.0`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​530---2021-08-29) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.2.2...v5.3.0) ##### Updated - Updated Plotly.js to from version 2.3.1 to version 2.4.1. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​240----2021-08-27) for more information. These changes are reflected in the auto-generated `plotly.graph_objects` module. Notable changes include: - Added `legend.groupclick` options - Provide bbox of hover items in event data ### [`v5.2.2`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​522---2021-08-23) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.2.1...v5.2.2) ##### Fixed - Fixed error when using the orjson engine with non-string keys [#​3351](https://togithub.com/plotly/plotly.py/pull/3351) ### [`v5.2.1`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​521---2021-08-13) ##### Updated - Updated Plotly.js to from version 2.2.0 to version 2.3.1. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​231----2021-07-30) for more information. These changes are reflected in the auto-generated `plotly.graph_objects` module. Notable changes include: - new projections in `geo` subplots from a more recent version of `d3-geo` - new number-formatting directives from a more recent version of `d3-format` - Improve rendering of `scattergl`, `splom` and `parcoords` by implementing `plotGlPixelRatio` for those traces - performance improvements and bug fixes ##### Added - Extra flags were added to the `gapminder` and `stocks` dataset to facilitate testing, documentation and demos [#​3305](https://togithub.com/plotly/plotly.py/issues/3305) - All line-like Plotly Express functions now accept `markers` argument to display markers, and all but `line_mapbox` accept `symbol` to map a field to the symbol attribute, similar to scatter-like functions [#​3326](https://togithub.com/plotly/plotly.py/issues/3326) - `px.scatter` and `px.density_contours` now support new `trendline` types `'rolling'`, `'expanding'` and `'ewm'` [#​2997](https://togithub.com/plotly/plotly.py/pull/2997) - `px.scatter` and `px.density_contours` now support new `trendline_options` argument to parameterize trendlines, with support for constant control and log-scaling in `'ols'` and specification of the fraction used for `'lowess'`, as well as pass-through to Pandas for `'rolling'`, `'expanding'` and `'ewm'` [#​2997](https://togithub.com/plotly/plotly.py/pull/2997) - `px.scatter` and `px.density_contours` now support new `trendline_scope` argument that accepts the value `'overall'` to request a single trendline for all traces, including across facets and animation frames [#​2997](https://togithub.com/plotly/plotly.py/pull/2997) - A new `px.ecdf()` function for Empirical Cumulative Distribution Functions [#​3330](https://togithub.com/plotly/plotly.py/pull/3330) ##### Fixed - Fixed regression introduced in version 5.0.0 where pandas/numpy arrays with `dtype` of Object were being converted to `list` values when added to a Figure ([#​3292](https://togithub.com/plotly/plotly.py/issues/3292), [#​3293](https://togithub.com/plotly/plotly.py/pull/3293)) - Better detection of Chrome and Chromium browsers in the Renderers framework, especially on Linux ([#​3278](https://togithub.com/plotly/plotly.py/pull/3278)) with thanks to [@​c-chaitanya](https://togithub.com/c-chaitanya) for the contribution ### [`v5.1.0`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​510---2021-06-28) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v5.0.0...v5.1.0) - Updated Plotly.js to from version 2.1.0 to version 2.2.0. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​220----2021-06-28) for more information. These changes are reflected in the auto-generated `plotly.graph_objects` module. Notable changes include: - new `.legendgrouptitle` attribute for legend group titles - new `%h` text formatting directive for half-years - performance improvements and bug fixes ### [`v5.0.0`](https://togithub.com/plotly/plotly.py/blob/HEAD/CHANGELOG.md#​500---2021-06-21) [Compare Source](https://togithub.com/plotly/plotly.py/compare/v4.14.3...v5.0.0) ##### Updated/Changed Items in this section may be considered backwards-incompatible changes for the purposes of [Semantic Versioning](http://semver.org/) but we expect the vast majority of users to be able to upgrade to version 5.0 without encountering any issues. - **Dropped support for Python older than 3.6** [#​3160](https://togithub.com/plotly/plotly.py/pull/3160) - Updated Plotly.js to from version 1.58.4 to version 2.1.0. See the [plotly.js CHANGELOG](https://togithub.com/plotly/plotly.js/blob/master/CHANGELOG.md#​210----2021-06-18) for more information. These changes are reflected in the auto-generated `plotly.graph_objects` module. Notable changes include: - dropped support for IE9 and IE10 - dropped support for long-deprecated `graph_objects` like `area` traces and `scatter.(t|r)` and `layout.(radial|angular)axis` attributes - modebar no longer has hovermode or spikeline buttons by default (can be added back with `fig.update_layout(modebar_add=["v1hovermode", "toggleSpikeLines"])`) - "Aa" text no longer appears on legend items unless `mode="text"` - In `bar` traces, `textposition` now defaults to `"auto"` - Font size for legend and colorbar titles now matches axis title font size (slightly bigger) - deprecated `heatmapgl`, `pointcloud` traces as well as all `transform` attributes - Combined `plotlywidget` into `jupyterlab-plotly` and packaged them as a federated extension [#​3142](https://togithub.com/plotly/plotly.py/pull/3142) with massive thanks to [@​fcollonval](https://togithub.com/fcollonval) for the contribution - In addition to this change, large Plotly.js bundles are now lazily loaded on-demand by JupyterLab - Plotly.js CDN url will now be versioned by default for HTML exports using `include_plotlyjs='cdn'` and for "connected" renderers. [#​2961](https://togithub.com/plotly/plotly.py/pull/2961) with thanks to [@​adehad](https://togithub.com/adehad) for the contribution - Recommending Kaleido by default over Orca [#​3094](https://togithub.com/plotly/plotly.py/pull/3094) - Replaced `retrying` dependency with `tenacity` [#​2911](https://togithub.com/plotly/plotly.py/pull/2911) with thanks to [@​jmsmdy](https://togithub.com/jmsmdy) for the contribution - Plotly Express now always takes into account every value in `category_orders` when computing discrete mappings (color, symbol, line-dash, pattern-shapes) as well as facets, even those values which are absent in the data [#​3247](https://togithub.com/plotly/plotly.py/pull/3247) ##### Added - Additions due to bumping Plotly.js from 1.58.4 to 2.1.0 (see [changelog](\(https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#​210----2021-06-18\))): - New `icicle` trace type, with thanks to [@​Kully](https://togithub.com/Kully) and [@​mtwichan](https://togithub.com/mtwichan) of [Zyphr](https://www.zyphr.ca/) for their contribution! - New `marker.pattern` options for `bar`-like trace types with thanks to [@​s417-lama](https://togithub.com/s417-lama) for the contribution! - New `legendrank` attribute to control rank of traces within legends - Plotly Express' `px.bar()`, `px.histogram()` and `px.bar_polar()` now support the `pattern_shape` argument [#​3252](https://togithub.com/plotly/plotly.py/pull/3252) - New Plotly Express `px.icicle()` function, with thanks to [@​Kully](https://togithub.com/Kully) and [@​mtwichan](https://togithub.com/mtwichan) of [Zyphr](https://www.zyphr.ca/) for their contribution! [#​3256](https://togithub.com/plotly/plotly.py/pull/3256) - New functions in `plotly.colors`: `get_colorscale()` and `sample_colorscale()` [#​3136](https://togithub.com/plotly/plotly.py/pull/3136) and [#​3186](https://togithub.com/plotly/plotly.py/pull/3186) with thanks to [@​CarlAndersson](https://togithub.com/CarlAndersson) for the contributions - Faster JSON encoding when `orjson` is present [#​2955](https://togithub.com/plotly/plotly.py/pull/2955) ##### Fixed - Pandas and Numpy datetime serialization fixes [#​3022](https://togithub.com/plotly/plotly.py/pull/3022) - Fixed selected points of histograms in FigureWidget [#​2771](https://togithub.com/plotly/plotly.py/pull/2771) with thanks to [@​meffmadd](https://togithub.com/meffmadd) for the contribution - Static image export now honors `layout.(width|height)`[#​3240](https://togithub.com/plotly/plotly.py/pull/3240) - Improvements to "matplotlylib" conversion utility in `plotly.tools.mpl_to_plotly()` with thanks to [@​fdion](https://togithub.com/fdion) [#​3143](https://togithub.com/plotly/plotly.py/pull/3143)

Configuration

📅 Schedule: "before 6am on the first day of the month" (UTC).

🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

â™» Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about these updates again.



This PR has been generated by WhiteSource Renovate. View repository job log here.

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

renovate[bot] commented 2 years ago

Renovate Ignore Notification

Because you closed this PR without merging, Renovate will ignore this update. You will not get PRs for any future 5.x releases. But if you manually upgrade to 5.x then Renovate will re-enable minor and patch updates automatically.

If you accidentally closed this PR, or if you changed your mind: rename this PR to get a fresh replacement PR.