Structure change #3
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Can you remove the I recommend using a good global |
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Removed cache files and added a .gitignore file |
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Resolved all comments, updated the base algorithm of food counts computation. |
gfop/analysis.py
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| import pandas as pd | ||
| from sklearn.decomposition import PCA | ||
| from sklearn.preprocessing import StandardScaler | ||
| from skbio.stats.composition import clr |
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nitpick: Alphabetical order.
gfop/foodcounts.py
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| """ | ||
| Generates a table of food counts at the filename level. It filters the GNPS network | ||
| based on the provided sample and | ||
| reference groups. |
gfop/foodflows.py
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| - flows: DataFrame with source, target, and value columns. | ||
| - processes: DataFrame with process details. | ||
| """ | ||
| # Select GNPS job groups. |
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question: This first part repeats some behavior of the FoodCounts class. Can FoodFlows instead take a FoodCounts object as input on which these steps are already applied, and then only take care of the visualization?
gfop/foodflows.py
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| # Standard library imports | ||
| import os | ||
| import pkg_resources | ||
| from importlib import resources |
gfop/visualization.py
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| # Standard library imports | ||
| import os | ||
| from typing import List, Optional, Union, Tuple | ||
| from importlib import resources |
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nitpick: Alphabetical order.
gfop/visualization.py
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| # Third-party imports | ||
| import matplotlib.pyplot as plt | ||
| import matplotlib.figure |
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nitpick: Alphabetical order.
gfop/visualization.py
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| # Third-party imports | ||
| import matplotlib.pyplot as plt | ||
| import matplotlib.figure | ||
| import seaborn as sns |
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nitpick: Alphabetical order.
tests/test_foodcounts.py
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| import sys | ||
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| # Third-party imports | ||
| import pytest |
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nitpick: Alphabetical order.
tests/test_foodcounts.py
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| # Internal imports | ||
| from foodcounts import FoodCounts # type: ignore | ||
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nitpick: Too many blank lines.
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Solved previous comments, and 8/11 issues. Issues remaining are to add changelog, documentation and contributing guidelines |
Changed structure of the package(added classes for food counts and food flows), added visualization, utilities and testing