fix: show correct package name to install biopython
Opened by BioGeek (closed)

When you try to download a dataset that uses [biopython](https://github.com/biopython/biopython), like `load_dataset("InstaDeepAI/multi_species_genomes")`, you get the error:

```
>>> from datasets import load_dataset
>>> dataset = load_dataset("InstaDeepAI/multi_species_genomes")
/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py:1454: FutureWarning: The repository for InstaDeepAI/multi_species_genomes contains custom code which must be executed to correctly load the dataset. You can inspect the repository content at https://hf.co/datasets/InstaDeepAI/multi_species_genomes
You can avoid this message in future by passing the argument `trust_remote_code=True`.
Passing `trust_remote_code=True` will be mandatory to load this dataset from the next major release of `datasets`.
  warnings.warn(
Downloading builder script: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 7.51k/7.51k [00:00<00:00, 7.67MB/s]
Downloading readme: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17.2k/17.2k [00:00<00:00, 11.0MB/s]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 2548, in load_dataset
    builder_instance = load_dataset_builder(
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 2220, in load_dataset_builder
    dataset_module = dataset_module_factory(
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 1871, in dataset_module_factory
    raise e1 from None
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 1844, in dataset_module_factory
    ).get_module()
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 1466, in get_module
    local_imports = _download_additional_modules(
  File "/home/j.vangoey/.pyenv/versions/multi_species_genomes/lib/python3.10/site-packages/datasets/load.py", line 346, in _download_additional_modules
    raise ImportError(
ImportError: To be able to use InstaDeepAI/multi_species_genomes, you need to install the following dependency: Bio.
Please install it using 'pip install Bio' for instance.
>>> 
```

`Bio` comes from the `biopython` package that can be installed with `pip install biopython`, not with  `pip install Bio` as suggested.


This PR adds special logic to show the correct package name in the error message of ` _download_additional_modules`, similarly as is done for `sklearn` / `scikit-learn`  already.

There are more packages where importable module name differs from the PyPI package name, so this could be made more generic, like:

```
# Mapping of importable module names to their PyPI package names
package_map = {
    "sklearn": "scikit-learn",
    "Bio": "biopython",
    "PIL": "Pillow",
    "bs4": "beautifulsoup4"
}

for module_name, pypi_name in package_map.items():
    if module_name in needs_to_be_installed.keys():
        needs_to_be_installed[module_name] = pypi_name
```

Comments:
The docs for this PR live [here](https://moon-ci-docs.huggingface.co/docs/datasets/pr_6662). All of your documentation changes will be reflected on that endpoint. The docs are available until 30 days after the last update.

<details>
<summary>Show benchmarks</summary>

PyArrow==8.0.0

<details>
<summary>Show updated benchmarks!</summary>

### Benchmark: benchmark_array_xd.json

| metric | read_batch_formatted_as_numpy after write_array2d | read_batch_formatted_as_numpy after write_flattened_sequence | read_batch_formatted_as_numpy after write_nested_sequence | read_batch_unformated after write_array2d | read_batch_unformated after write_flattened_sequence | read_batch_unformated after write_nested_sequence | read_col_formatted_as_numpy after write_array2d | read_col_formatted_as_numpy after write_flattened_sequence | read_col_formatted_as_numpy after write_nested_sequence | read_col_unformated after write_array2d | read_col_unformated after write_flattened_sequence | read_col_unformated after write_nested_sequence | read_formatted_as_numpy after write_array2d | read_formatted_as_numpy after write_flattened_sequence | read_formatted_as_numpy after write_nested_sequence | read_unformated after write_array2d | read_unformated after write_flattened_sequence | read_unformated after write_nested_sequence | write_array2d | write_flattened_sequence | write_nested_sequence |
|--------|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 0.005135 / 0.011353 (-0.006218) | 0.003666 / 0.011008 (-0.007342) | 0.062660 / 0.038508 (0.024152) | 0.028656 / 0.023109 (0.005546) | 0.249601 / 0.275898 (-0.026297) | 0.265745 / 0.323480 (-0.057735) | 0.002935 / 0.007986 (-0.005051) | 0.002606 / 0.004328 (-0.001723) | 0.048774 / 0.004250 (0.044523) | 0.043643 / 0.037052 (0.006591) | 0.263114 / 0.258489 (0.004625) | 0.284596 / 0.293841 (-0.009245) | 0.027818 / 0.128546 (-0.100728) | 0.010726 / 0.075646 (-0.064921) | 0.205900 / 0.419271 (-0.213371) | 0.035646 / 0.043533 (-0.007887) | 0.245599 / 0.255139 (-0.009540) | 0.267706 / 0.283200 (-0.015493) | 0.018441 / 0.141683 (-0.123242) | 1.143365 / 1.452155 (-0.308790) | 1.191823 / 1.492716 (-0.300893) |

### Benchmark: benchmark_getitem\_100B.json

| metric | get_batch_of\_1024\_random_rows | get_batch_of\_1024\_rows | get_first_row | get_last_row |
|--------|---|---|---|---|
| new / old (diff) | 0.089703 / 0.018006 (0.071696) | 0.298073 / 0.000490 (0.297583) | 0.000209 / 0.000200 (0.000009) | 0.000042 / 0.000054 (-0.000013) |

### Benchmark: benchmark_indices_mapping.json

| metric | select | shard | shuffle | sort | train_test_split |
|--------|---|---|---|---|---|
| new / old (diff) | 0.018068 / 0.037411 (-0.019343) | 0.061416 / 0.014526 (0.046890) | 0.075989 / 0.176557 (-0.100567) | 0.120765 / 0.737135 (-0.616370) | 0.075476 / 0.296338 (-0.220863) |

### Benchmark: benchmark_iterating.json

| metric | read 5000 | read 50000 | read_batch 50000 10 | read_batch 50000 100 | read_batch 50000 1000 | read_formatted numpy 5000 | read_formatted pandas 5000 | read_formatted tensorflow 5000 | read_formatted torch 5000 | read_formatted_batch numpy 5000 10 | read_formatted_batch numpy 5000 1000 | shuffled read 5000 | shuffled read 50000 | shuffled read_batch 50000 10 | shuffled read_batch 50000 100 | shuffled read_batch 50000 1000 | shuffled read_formatted numpy 5000 | shuffled read_formatted_batch numpy 5000 10 | shuffled read_formatted_batch numpy 5000 1000 |
|--------|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 0.284043 / 0.215209 (0.068834) | 2.770282 / 2.077655 (0.692627) | 1.473040 / 1.504120 (-0.031080) | 1.349064 / 1.541195 (-0.192131) | 1.362783 / 1.468490 (-0.105708) | 0.560765 / 4.584777 (-4.024012) | 2.357731 / 3.745712 (-1.387981) | 2.745771 / 5.269862 (-2.524090) | 1.726764 / 4.565676 (-2.838913) | 0.061212 / 0.424275 (-0.363063) | 0.004902 / 0.007607 (-0.002705) | 0.336963 / 0.226044 (0.110919) | 3.324519 / 2.268929 (1.055591) | 1.825826 / 55.444624 (-53.618798) | 1.548811 / 6.876477 (-5.327666) | 1.570618 / 2.142072 (-0.571454) | 0.642411 / 4.805227 (-4.162816) | 0.116068 / 6.500664 (-6.384596) | 0.042433 / 0.075469 (-0.033036) |

### Benchmark: benchmark_map_filter.json

| metric | filter | map fast-tokenizer batched | map identity | map identity batched | map no-op batched | map no-op batched numpy | map no-op batched pandas | map no-op batched pytorch | map no-op batched tensorflow |
|--------|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 0.988402 / 1.841788 (-0.853386) | 11.509601 / 8.074308 (3.435293) | 9.555338 / 10.191392 (-0.636054) | 0.138728 / 0.680424 (-0.541696) | 0.014107 / 0.534201 (-0.520094) | 0.285465 / 0.579283 (-0.293818) | 0.263086 / 0.434364 (-0.171278) | 0.327469 / 0.540337 (-0.212869) | 0.444799 / 1.386936 (-0.942137) |

</details>
PyArrow==latest

<details>
<summary>Show updated benchmarks!</summary>

### Benchmark: benchmark_array_xd.json

| metric | read_batch_formatted_as_numpy after write_array2d | read_batch_formatted_as_numpy after write_flattened_sequence | read_batch_formatted_as_numpy after write_nested_sequence | read_batch_unformated after write_array2d | read_batch_unformated after write_flattened_sequence | read_batch_unformated after write_nested_sequence | read_col_formatted_as_numpy after write_array2d | read_col_formatted_as_numpy after write_flattened_sequence | read_col_formatted_as_numpy after write_nested_sequence | read_col_unformated after write_array2d | read_col_unformated after write_flattened_sequence | read_col_unformated after write_nested_sequence | read_formatted_as_numpy after write_array2d | read_formatted_as_numpy after write_flattened_sequence | read_formatted_as_numpy after write_nested_sequence | read_unformated after write_array2d | read_unformated after write_flattened_sequence | read_unformated after write_nested_sequence | write_array2d | write_flattened_sequence | write_nested_sequence |
|--------|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 0.005359 / 0.011353 (-0.005993) | 0.003605 / 0.011008 (-0.007403) | 0.049734 / 0.038508 (0.011226) | 0.029792 / 0.023109 (0.006683) | 0.276384 / 0.275898 (0.000486) | 0.297915 / 0.323480 (-0.025564) | 0.004949 / 0.007986 (-0.003036) | 0.002713 / 0.004328 (-0.001616) | 0.049499 / 0.004250 (0.045249) | 0.044969 / 0.037052 (0.007917) | 0.284558 / 0.258489 (0.026069) | 0.315170 / 0.293841 (0.021329) | 0.029457 / 0.128546 (-0.099089) | 0.010573 / 0.075646 (-0.065073) | 0.058191 / 0.419271 (-0.361080) | 0.051461 / 0.043533 (0.007928) | 0.270744 / 0.255139 (0.015605) | 0.291664 / 0.283200 (0.008465) | 0.018607 / 0.141683 (-0.123076) | 1.158799 / 1.452155 (-0.293355) | 1.210509 / 1.492716 (-0.282208) |

### Benchmark: benchmark_getitem\_100B.json

| metric | get_batch_of\_1024\_random_rows | get_batch_of\_1024\_rows | get_first_row | get_last_row |
|--------|---|---|---|---|
| new / old (diff) | 0.090277 / 0.018006 (0.072270) | 0.298748 / 0.000490 (0.298258) | 0.000228 / 0.000200 (0.000028) | 0.000060 / 0.000054 (0.000005) |

### Benchmark: benchmark_indices_mapping.json

| metric | select | shard | shuffle | sort | train_test_split |
|--------|---|---|---|---|---|
| new / old (diff) | 0.021850 / 0.037411 (-0.015561) | 0.075433 / 0.014526 (0.060907) | 0.087171 / 0.176557 (-0.089386) | 0.125828 / 0.737135 (-0.611308) | 0.090343 / 0.296338 (-0.205996) |

### Benchmark: benchmark_iterating.json

| metric | read 5000 | read 50000 | read_batch 50000 10 | read_batch 50000 100 | read_batch 50000 1000 | read_formatted numpy 5000 | read_formatted pandas 5000 | read_formatted tensorflow 5000 | read_formatted torch 5000 | read_formatted_batch numpy 5000 10 | read_formatted_batch numpy 5000 1000 | shuffled read 5000 | shuffled read 50000 | shuffled read_batch 50000 10 | shuffled read_batch 50000 100 | shuffled read_batch 50000 1000 | shuffled read_formatted numpy 5000 | shuffled read_formatted_batch numpy 5000 10 | shuffled read_formatted_batch numpy 5000 1000 |
|--------|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 0.297267 / 0.215209 (0.082058) | 2.865234 / 2.077655 (0.787579) | 1.595024 / 1.504120 (0.090904) | 1.476100 / 1.541195 (-0.065094) | 1.494896 / 1.468490 (0.026406) | 0.569086 / 4.584777 (-4.015691) | 2.401976 / 3.745712 (-1.343736) | 2.676091 / 5.269862 (-2.593771) | 1.742087 / 4.565676 (-2.823590) | 0.065161 / 0.424275 (-0.359114) | 0.005006 / 0.007607 (-0.002602) | 0.342302 / 0.226044 (0.116257) | 3.450571 / 2.268929 (1.181643) | 1.928754 / 55.444624 (-53.515871) | 1.672823 / 6.876477 (-5.203653) | 1.798830 / 2.142072 (-0.343243) | 0.648730 / 4.805227 (-4.156498) | 0.116433 / 6.500664 (-6.384231) | 0.040683 / 0.075469 (-0.034786) |

### Benchmark: benchmark_map_filter.json

| metric | filter | map fast-tokenizer batched | map identity | map identity batched | map no-op batched | map no-op batched numpy | map no-op batched pandas | map no-op batched pytorch | map no-op batched tensorflow |
|--------|---|---|---|---|---|---|---|---|---|
| new / old (diff) | 1.006158 / 1.841788 (-0.835630) | 12.200093 / 8.074308 (4.125785) | 10.180691 / 10.191392 (-0.010701) | 0.146620 / 0.680424 (-0.533804) | 0.015621 / 0.534201 (-0.518580) | 0.287956 / 0.579283 (-0.291327) | 0.277231 / 0.434364 (-0.157133) | 0.323815 / 0.540337 (-0.216522) | 0.429655 / 1.386936 (-0.957281) |

</details>
</details>

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