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Typo fix "retrieval" #21

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Jun 27, 2024
Merged

Typo fix "retrieval" #21

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87ca22f
rename folder
yoavkt Jun 27, 2024
06a2fbd
typo fix
yoavkt Jun 27, 2024
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12 changes: 6 additions & 6 deletions .github/workflows/python-package.yml
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Expand Up @@ -31,12 +31,12 @@ jobs:

- name: Create tasks needed for testing
run: |
python scripts/tasks_retrival/gene2gene_task_creation.py --allow-downloads True
python scripts/tasks_retrival/Genecorpus_tasks_creation.py --allow-downloads True
python scripts/tasks_retrival/HLA_task_creation.py --allow-downloads True
python scripts/tasks_retrival/HPA_tasks_creation.py --allow-downloads True
python scripts/tasks_retrival/humantfs_task_creation.py --allow-downloads True
python scripts/tasks_retrival/Reactome_tasks_creation.py --allow-downloads True
python scripts/tasks_retrieval/gene2gene_task_creation.py --allow-downloads True
python scripts/tasks_retrieval/Genecorpus_tasks_creation.py --allow-downloads True
python scripts/tasks_retrieval/HLA_task_creation.py --allow-downloads True
python scripts/tasks_retrieval/HPA_tasks_creation.py --allow-downloads True
python scripts/tasks_retrieval/humantfs_task_creation.py --allow-downloads True
python scripts/tasks_retrieval/Reactome_tasks_creation.py --allow-downloads True

- name: Test with pytest
run: |
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88 changes: 0 additions & 88 deletions scripts/data_retrieval/gene_disease_association.py
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0 ...etrival/extract_bag_of_words_encodings.py → ...trieval/extract_bag_of_words_encodings.py
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0 ...ngs_retrival/extract_cellPLM_encodings.py → ...gs_retrieval/extract_cellPLM_encodings.py
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0 ...gs_retrival/extract_gene2vec_encodings.py → ...s_retrieval/extract_gene2vec_encodings.py
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0 ..._retrival/extract_geneformer_encodings.py → ...retrieval/extract_geneformer_encodings.py
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0 ...dings_retrival/extract_scGPT_encodings.py → ...ings_retrieval/extract_scGPT_encodings.py
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0 ...sks_retrival/Genecorpus_tasks_creation.py → ...ks_retrieval/Genecorpus_tasks_creation.py
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0 scripts/tasks_retrival/HLA_task_creation.py → scripts/tasks_retrieval/HLA_task_creation.py
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4 changes: 2 additions & 2 deletions scripts/tasks_retrival/HPA_tasks_creation.py → ...pts/tasks_retrieval/HPA_tasks_creation.py
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Expand Up @@ -2,7 +2,7 @@
import pandas as pd

from gene_benchmark.tasks import dump_task_definitions
from scripts.tasks_retrival.task_retrieval import (
from scripts.tasks_retrieval.task_retrieval import (
check_data_type,
create_single_label_task,
load_yaml_file,
Expand Down Expand Up @@ -64,7 +64,7 @@ def create_tasks(data, main_task_directory, verbose=False):
"--columns-to-use-yaml",
type=click.STRING,
help="A path to a yaml file containing the column names to be used as tasks",
default="scripts/tasks_retrival/hpa_column_names_for_tasks.yaml",
default="scripts/tasks_retrieval/hpa_column_names_for_tasks.yaml",
)
@click.option(
"--main-task-directory",
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2 changes: 1 addition & 1 deletion ...tasks_retrival/Reactome_tasks_creation.py → ...asks_retrieval/Reactome_tasks_creation.py
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Expand Up @@ -4,7 +4,7 @@
from task_retrieval import verify_source_of_data

from gene_benchmark.tasks import dump_task_definitions
from scripts.tasks_retrival.task_retrieval import list_form_to_onehot_form
from scripts.tasks_retrieval.task_retrieval import list_form_to_onehot_form

TOP_PATHWAYS_URL = "https://reactome.org/download/current/ReactomePathwaysRelation.txt"

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0 ...tasks_retrival/gene2gene_task_creation.py → ...asks_retrieval/gene2gene_task_creation.py
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2 changes: 1 addition & 1 deletion ...gene_disease_association_task_creation.py → ...gene_disease_association_task_creation.py
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Expand Up @@ -38,7 +38,7 @@
from task_retrieval import get_symbols, verify_source_of_data

from gene_benchmark.tasks import dump_task_definitions
from scripts.tasks_retrival.task_retrieval import print_numerical_task_report
from scripts.tasks_retrieval.task_retrieval import print_numerical_task_report

DATA_URL = (
"https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/23.09/output/etl/parquet/"
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0 ..._retrival/hpa_column_names_for_tasks.yaml → ...retrieval/hpa_column_names_for_tasks.yaml
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0 .../tasks_retrival/humantfs_task_creation.py → ...tasks_retrieval/humantfs_task_creation.py
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0 scripts/tasks_retrival/task_retrieval.py → scripts/tasks_retrieval/task_retrieval.py
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2 changes: 1 addition & 1 deletion tasks/README.MD
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@@ -1,5 +1,5 @@
# Task retrieval

Our package allows users to easily evaluate the gene encodings on hundreds of tasks from varying sources and types. The package does not include the task data itself to avoid redistributing data from various sources with various public licenses. However, we provide an easy [command line interface](../scripts/tasks_retrival/) to download and populate a folder with the tasks in the appropriate format. The list of tasks and their descriptions are available in an [excel file](task_descriptions.xlsx).
Our package allows users to easily evaluate the gene encodings on hundreds of tasks from varying sources and types. The package does not include the task data itself to avoid redistributing data from various sources with various public licenses. However, we provide an easy [command line interface](../scripts/tasks_retrieval/) to download and populate a folder with the tasks in the appropriate format. The list of tasks and their descriptions are available in an [excel file](task_descriptions.xlsx).

Note that the interface allows to download data from various sources. To do so the user needs to explicitly allow this. Use this option only if you trust the URLs appearing in the scripts.
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