Rules

README.md may occasionally include brief project conventions and usage notes.

Plotting

Python Plotting (matplotlib / seaborn) for publication ready figures.

  1. Use English-only text in all figures. Do not use Chinese characters (matplotlib may lack the required CJK fonts).
  2. After plotting, remove spines with sns.despine() (apply per-axes or globally, as appropriate).
  3. Keep figure size compact for papers (prefer single-column layouts; aim ~2–3.5 inches wide (e.g., plt.figure(figsize=(3, 3))) unless a two-column figure is required).
  4. Some figures are relatively tall and narrow or wide and flat; adjust the canvas to the corresponding aspect ratio instead of forcing a square layout.
  5. When generating heatmaps, the grid cells should be square.
  6. No gridlines on backgrounds (disable with plt.grid(False) or ax.grid(False)).
  7. Apply the following style preset at the start of your plotting code to unify fonts and export settings:
1
2
3
4
plt.rcParams["font.family"] = "Arial" # or use "Liberation Sans" for ubuntu
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['ps.fonttype'] = 42
sns.set_context('paper')

Notes

  1. Ensure sns.despine() is called after axes are created.
  2. When exporting for manuscripts, prefer vector formats (PDF/EPS) with the above font settings to preserve text quality.

Python Project Management

Python projects could be managed by uv. Check before you run pip or uv commands. If some packages/projects rely on older resources, consider whether they have a dedicated virtual environment; if they are not required in a new project, isolate them instead of forcing downgrades in the new project.

Natural Language

Always write code, docs, and code comments in English, but respond in 中文

Reading files

Use commands like head to decide whether you truly need to load the entire dataset file (e.g., CSV, JSON files).

Logging

All long-running scripts must implement logging to track progress. For example, in Python, consider installing and using the loguru library.

Research Experiment Organization

For a research project, it is recommended to create an exp directory at the project root, with a subdirectory for each sub-experiment; place the corresponding code and figures in each subdirectory, and add a README file documenting the experiment requirements and overall idea for future reference.