fix : Upgrade pyopenms_viz to v1.0.0 and Resolve Breaking API Changes

[achalbajpai]

Changelog

Version Update and Improvements

1. Package Version Updates

• Updated pyopenms_viz to version 1.0.0 in multiple configuration files:

  requirements.txt

  - pyopenms_viz==0.1.2
  + pyopenms_viz==1.0.0

  environment.yml

  - pyopenms_viz==0.1.2
  + pyopenms_viz==1.0.0

2. Breaking Changes Fixes in src/view.py

• Removed deprecated fig parameter from all plot calls to comply with pyopenms_viz 1.0.0
• Confirmed that the color parameter was already correctly updated (previously line_color)

Plot Method Improvements

Added aggregate_duplicates=True to all plot calls to prevent duplicate data warnings:

df.plot(
    backend="ms_plotly",
    kind="chromatogram",
    # ... other parameters ...
    aggregate_duplicates=True  # Added this parameter
)

Summary of Key Changes

• ✅ Upgraded pyopenms_viz to version 1.0.0
• ✅ Resolved breaking changes in plotting methods
• ✅ Improved DataFrame handling to prevent warnings
• ✅ Enhanced plot method calls with aggregate_duplicates

Summary by CodeRabbit

• Chores

  • Updated a key visualization library to version 1.0.0 to ensure consistency across environments.

• New Features

  • Improved plot rendering with refined color configuration and enhanced duplicate data aggregation for cleaner, more precise visualizations.

[coderabbitai]

Walkthrough

The pull request updates package versioning and modifies plotting function parameters. In both environment.yml and requirements.txt, the pyopenms_viz package version is changed to ==1.0.0, with the YAML file also receiving a re-indentation for consistency. In src/view.py, the plotting functions are updated by renaming the line_color parameter to color, removing the fig parameter, adding an aggregate_duplicates option, and improving DataFrame handling using a copy and explicit loc assignment.

Changes

Files	Change Summary
environment.yml, requirements.txt	Updated pyopenms_viz version from >=0.1.2/0.1.2 to ==1.0.0. In environment.yml, the indentation for channels and dependencies was reformatted.
src/view.py	Modified plotting functions: renamed line_color to color; removed the fig parameter; added aggregate_duplicates; updated DataFrame handling with a copy and loc assignment.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant PlotFunction as plot_bpc_tic
    participant DataHandler as DataFrame Handler
    participant Renderer as Plot Renderer

    User->>PlotFunction: Call plot_bpc_tic(df)
    PlotFunction->>DataHandler: Filter data & create a copy
    DataHandler-->>PlotFunction: Return filtered data (with "type" set via loc)
    PlotFunction->>Renderer: Call plotting (using color & aggregate_duplicates)
    Renderer-->>PlotFunction: Generated plot
    PlotFunction-->>User: Return plot

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Hey, I’m a happy rabbit on the run,
Hopping through changes, code full of fun,
Colors renamed and versions just right,
Leaving duplicates behind in a joyful flight,
With each line of code, my heart's delight!
🐇✨

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between ca182a0 and d8e94cd.

📒 Files selected for processing (3)

• environment.yml (1 hunks)
• requirements.txt (1 hunks)
• src/view.py (6 hunks)

🔇 Additional comments (9)

environment.yml (1)

4-17: Version update and indentation changes properly implemented

The changes correctly update the pyopenms_viz package version from >=0.1.2 to ==1.0.0 as specified in the PR objectives while also improving the indentation consistency throughout the file.

requirements.txt (1)

9-9: Version update correctly implemented

The update of pyopenms_viz to version 1.0.0 has been correctly implemented, matching the version update in environment.yml and aligning with the PR objectives.

src/view.py (7)

81-85: Parameter updates correctly address breaking changes

The changes properly replace the deprecated line_color parameter with color and add aggregate_duplicates=True to prevent warnings related to duplicate data as mentioned in the PR objectives.

---

97-101: Parameter updates correctly address breaking changes

The changes properly replace the deprecated line_color parameter with color and add aggregate_duplicates=True to prevent warnings related to duplicate data as mentioned in the PR objectives.

---

114-116: DataFrame handling improved to prevent chained assignment warnings

The implementation now uses .copy() when creating the df_eic DataFrame and .loc for setting values in the "type" column, which properly addresses potential warnings from chained assignments as mentioned in the PR objectives.

---

125-129: Parameter updates correctly address breaking changes

The changes properly replace the deprecated line_color parameter with color and add aggregate_duplicates=True to prevent warnings related to duplicate data as mentioned in the PR objectives.

---

152-159: Parameter updates correctly address breaking changes

The changes properly replace the deprecated line_color parameter with color and add aggregate_duplicates=True to prevent warnings related to duplicate data as mentioned in the PR objectives.

---

187-188: Parameter addition to prevent duplicate data warnings

The addition of aggregate_duplicates=True correctly addresses the need to prevent warnings related to duplicate data as specified in the PR objectives.

---

217-218: Parameter addition to prevent duplicate data warnings

The addition of aggregate_duplicates=True correctly addresses the need to prevent warnings related to duplicate data as specified in the PR objectives.

✨ Finishing Touches

• 📝 Generate Docstrings

---

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[jcharkow]

@achalbajpai looks good! Please merge the current main branch into this branch locally and resolve merge conflicts.

e.g. on branch achalbajpai:main run git pull origin main

[jcharkow]

Looks good provided tests also pass on github server good to merge!

[achalbajpai]

@jcharkow done with it !

[jcharkow]

Thanks! Will merge now.