refactor: remove gene_index step (#946)

* refactor: rename all gene_index related files to target_index

* refactor: rename gene_index to target_index in various files

* refactor: rename gene_index to target_index in tests

* refactor: rename fields to be compatible with new target_index

* refactor: replace examples that use gene_index

* refactor: delete gene_index step files

* refactor: remove gene_index step from config

* feat: replace the gene_index schema with the target_index schema

* refactor: modify mock_target_index

* fix: remove mock_target_index from test_validate_schema_missing_field

* refactor: delete target.md

* fix: fix study index validation tests

* fix: fix l2g feature tests

* chore: pre-commit auto fixes [...]

* revert: revert column name after merging from dev

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>

Author: 3 people

docs/howto/command_line/run_step_in_cli.md

@@ -14,7 +14,6 @@ Available options:
         eqtl_catalogue
         finngen_studies
         finngen_sumstat_preprocess
-        gene_index
         gwas_catalog_ingestion
         gwas_catalog_sumstat_preprocess
         ld_index
@@ -28,16 +27,16 @@ Available options:
 Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
 ```
 
-As indicated, you can run a step by specifying the step's name with the `step` argument. For example, to run the `gene_index` step, you can run:
+As indicated, you can run a step by specifying the step's name with the `step` argument. For example, to run the `gwas_catalog_sumstat_preprocess` step, you can run:
 
 ```bash
-gentropy step=gene_index
+gentropy step=gwas_catalog_sumstat_preprocess
 ```
 
-In most occassions, some mandatory values will be required to run the step. For example, the `gene_index` step requires the `step.target_path` and `step.gene_index_path` argument to be specified. You can complete the necessary arguments by adding them to the command line:
+In most occassions, some mandatory values will be required to run the step. For example, the `gwas_catalog_sumstat_preprocess` step requires the `step.raw_sumstats_path` and `step.out_sumstats_path` argument to be specified. You can complete the necessary arguments by adding them to the command line:
 
 ```bash
-gentropy step=gene_index step.target_path=/path/to/target step.gene_index_path=/path/to/gene_index
+gentropy step=gwas_catalog_sumstat_preprocess step.raw_sumstats_path=/path/to/raw_sumstats step.out_sumstats_path=/path/to/out_sumstats
 ```
 
 You can find more about the available steps in the [documentation](../../python_api/steps/_steps.md).

docs/howto/command_line/run_step_using_config.md

@@ -15,11 +15,11 @@ To run a step using a configuration file, you need to create a configuration fil
 ```{ .sh .no-copy }
 config/
 ├─ step/
-│  └─ my_gene_index.md
+│  └─ my_gwas_catalog_sumstat_preprocess.md
 └─ my_config.yml
 ```
 
-The configuration file should contain the parameters you want to use to run the step. For example, to run the `gene_index` step, you need to specify the `step.target_path` and `step.gene_index_path` parameters. The configuration file should look like this:
+The configuration file should contain the parameters you want to use to run the step. For example, to run the `gwas_catalog_sumstat_preprocess` step, you need to specify the `step.raw_sumstats_path` and `step.out_sumstats_path` parameters. The configuration file should look like this:
 
 === "my_config.yaml"
 
@@ -31,20 +31,20 @@ The configuration file should contain the parameters you want to use to run the
 
     This config file will specify that your configuration file will inherit the default configuration (`config`) and everything provided (`_self_`) will overwrite the default configuration.
 
-=== "step/my_gene_index.md"
+=== "step/my_gwas_catalog_sumstat_preprocess.md"
 
     ``` yaml
     defaults:
-        - gene_index
+        - gwas_catalog_sumstat_preprocess
 
-    target_path: /path/to/target
-    gene_index_path: /path/to/gene_index
+    raw_sumstats_path: /path/to/raw_sumstats
+    out_sumstats_path: /path/to/out_sumstats
     ```
 
-    This config file will inherit the default configuration for the `gene_index` step and overwrite the `target_path` and `gene_index_path` parameters.
+    This config file will inherit the default configuration for the `gwas_catalog_sumstat_preprocess` step and overwrite the `raw_sumstats_path` and `out_sumstats_path` parameters.
 
-Once you have created the configuration file, you can run your own new `my_gene_index`:
+Once you have created the configuration file, you can run your own new `my_gwas_catalog_sumstat_preprocess`:
 
 ```bash
-gentropy step=my_gene_index --config-dir=config --config-name=my_config
+gentropy step=my_gwas_catalog_sumstat_preprocess --config-dir=config --config-name=my_config
 ```

docs/python_api/datasets/gene_index.md

@@ -0,0 +1,9 @@
+---
+title: Target Index
+---
+
+::: gentropy.dataset.target_index.TargetIndex
+
+## Schema
+
+--8<-- "assets/schemas/target_index.md"