Typo fix "retrieval" (#21)

* rename folder * typo fix
BiomedSciAI · Jun 27, 2024 · dd3246c · dd3246c
1 parent 1b92f99
commit dd3246c
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Showing 17 changed files with 11 additions and 99 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -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: |

diff --git a/scripts/data_retrieval/gene_disease_association.py b/scripts/data_retrieval/gene_disease_association.py
diff --git a/...etrival/extract_bag_of_words_encodings.py → ...trieval/extract_bag_of_words_encodings.py b/...etrival/extract_bag_of_words_encodings.py → ...trieval/extract_bag_of_words_encodings.py
diff --git a/...ngs_retrival/extract_cellPLM_encodings.py → ...gs_retrieval/extract_cellPLM_encodings.py b/...ngs_retrival/extract_cellPLM_encodings.py → ...gs_retrieval/extract_cellPLM_encodings.py
diff --git a/...gs_retrival/extract_gene2vec_encodings.py → ...s_retrieval/extract_gene2vec_encodings.py b/...gs_retrival/extract_gene2vec_encodings.py → ...s_retrieval/extract_gene2vec_encodings.py
diff --git a/..._retrival/extract_geneformer_encodings.py → ...retrieval/extract_geneformer_encodings.py b/..._retrival/extract_geneformer_encodings.py → ...retrieval/extract_geneformer_encodings.py
diff --git a/...dings_retrival/extract_scGPT_encodings.py → ...ings_retrieval/extract_scGPT_encodings.py b/...dings_retrival/extract_scGPT_encodings.py → ...ings_retrieval/extract_scGPT_encodings.py
diff --git a/...sks_retrival/Genecorpus_tasks_creation.py → ...ks_retrieval/Genecorpus_tasks_creation.py b/...sks_retrival/Genecorpus_tasks_creation.py → ...ks_retrieval/Genecorpus_tasks_creation.py
diff --git a/scripts/tasks_retrival/HLA_task_creation.py → scripts/tasks_retrieval/HLA_task_creation.py b/scripts/tasks_retrival/HLA_task_creation.py → scripts/tasks_retrieval/HLA_task_creation.py
diff --git a/scripts/tasks_retrival/HPA_tasks_creation.py → ...pts/tasks_retrieval/HPA_tasks_creation.py b/scripts/tasks_retrival/HPA_tasks_creation.py → ...pts/tasks_retrieval/HPA_tasks_creation.py
@@ -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,
@@ -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",

diff --git a/...tasks_retrival/Reactome_tasks_creation.py → ...asks_retrieval/Reactome_tasks_creation.py b/...tasks_retrival/Reactome_tasks_creation.py → ...asks_retrieval/Reactome_tasks_creation.py
@@ -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"
 

diff --git a/...tasks_retrival/gene2gene_task_creation.py → ...asks_retrieval/gene2gene_task_creation.py b/...tasks_retrival/gene2gene_task_creation.py → ...asks_retrieval/gene2gene_task_creation.py
diff --git a/...gene_disease_association_task_creation.py → ...gene_disease_association_task_creation.py b/...gene_disease_association_task_creation.py → ...gene_disease_association_task_creation.py
@@ -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/"

diff --git a/..._retrival/hpa_column_names_for_tasks.yaml → ...retrieval/hpa_column_names_for_tasks.yaml b/..._retrival/hpa_column_names_for_tasks.yaml → ...retrieval/hpa_column_names_for_tasks.yaml
diff --git a/.../tasks_retrival/humantfs_task_creation.py → ...tasks_retrieval/humantfs_task_creation.py b/.../tasks_retrival/humantfs_task_creation.py → ...tasks_retrieval/humantfs_task_creation.py
diff --git a/scripts/tasks_retrival/task_retrieval.py → scripts/tasks_retrieval/task_retrieval.py b/scripts/tasks_retrival/task_retrieval.py → scripts/tasks_retrieval/task_retrieval.py
diff --git a/tasks/README.MD b/tasks/README.MD
@@ -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.