Testing metadata bot, editing README, no pitfalls addressed

Author: Anas-Elhounsri

README.md

@@ -1,8 +1,8 @@
 [![DOI](https://zenodo.org/badge/878193479.svg)](https://doi.org/10.5281/zenodo.14803005)
 
-
 > [!WARNING]
 > This is still in progress and subject to change, as additional requirements may arise.
+
 # Metadata-Adoption-Quantify
 
 This software extracts relevant data from SOMEF (Software Metadata Extraction Framework) results to answer specific research questions. The extracted insights are returned as structured JSON files, allowing easy integration and analysis.
@@ -32,6 +32,7 @@ This software is tailored to answer the following research questions:
 5. RQ5: What are the most common citation practices among the communities?
 
 ## Features
+
 - Extract metadata from repositories using SOMEF.
 - Extracts and processes metadata from SOMEF results.
 - Filters information relevant to specific research questions.
@@ -68,127 +69,51 @@ The tool is accessible via the `quantify` command. All commands should be prefix
 ### Available Commands
 
 #### 1. Run SoMEF on Repositories
+
 Extracts metadata from a list of GitHub repositories provided in a JSON file.
+
 ```bash
 poetry run quantify somef --input repos.json --output-dir somef_outputs --threshold 0.8
 ```
 
 #### 2. Run RQ Analysis
+
 Analyzes SoMEF outputs to answer specific research questions.
+
 ```bash
 poetry run quantify rqs --somef-dir somef_outputs --input-repos repos.json --output-dir rq_results --cluster default
 ```
-*Note: `--input-repos` is required for RQ2 analysis.*
+
+_Note: `--input-repos` is required for RQ2 analysis._
 
 The input (in the case of the example that would be `repos.json`) should be a JSON file with the following format:
+
 ```json
 [
-    {
-        "github_url": "https://github.com/foo/bar"
-    },
-    {
-        "github_url": "https://github.com/dgarijo/Widoco/"
-    }
+  {
+    "github_url": "https://github.com/foo/bar"
+  },
+  {
+    "github_url": "https://github.com/dgarijo/Widoco/"
+  }
 ]
 ```
+
 #### 3. Calculate Final Results
+
 Calculates the final percentages and insights for each RQ.
+
 ```bash
 poetry run quantify calculate --input repos.json --rq-results-dir rq_results --results-dir final_results --cluster default
 ```
 
 ### Main Menu (Alternative)
+
 You can still access help for any command by running:
+
 ```bash
 poetry run quantify --help
 ```
-## Output
-After running the `rqs` command for RQ1, you get a result like this:
-```bash
-{
-    "citation.cff": {
-        "count": 1
-    },
-    "readme_url": {
-        "count": 17
-    },
-    "package": {
-        "count": 7,
-        "files": [
-            "temp_analysis/escape2020/gammapy_gammapy/gammapy-1.2/setup.cfg",
-            "temp_analysis/escape2020/cosimoNigro_agnpy/agnpy-master/setup.py",
-            "temp_analysis/escape2020/IndexedConv_IndexedConv/IndexedConv-1.3.2/setup.py",
-            "temp_analysis/escape2020/cds-astro_cds-moc-rust/cds-moc-rust-main/Cargo.toml",
-            "temp_analysis/escape2020/cds-astro_mocpy/mocpy-0.15.0/Cargo.toml",
-            "temp_analysis/escape2020/cds-astro_aladin-lite/aladin-lite-3.3.2/package.json",
-            "temp_analysis/escape2020/escape2020_school2022/school2022-1.0/docs/themes/dream/package.json"
-        ]
-    },
-    "authors": {
-        "count": 2,
-        "files": [
-            "temp_analysis/escape2020/R3BRootGroup_R3BRoot/R3BRoot-jun24/AUTHORS",
-            "temp_analysis/escape2020/FairRootGroup_FairMQ/FairMQ-master/AUTHORS"
-        ]
-    },
-    "contributors": {
-        "count": 3,
-        "files": [
-            "output_4.json",
-            "output_11.json",
-            "output_5.json"
-        ]
-    },
-    "license": {
-        "count": 17
-    },
-    "codemeta.json": {
-        "count": 15,
-        "files": [
-            "temp_analysis/escape2020/gammapy_gammapy/gammapy-1.2/codemeta.json",
-            "temp_analysis/escape2020/cosimoNigro_agnpy/agnpy-master/codemeta.json",
-            "temp_analysis/escape2020/IndexedConv_IndexedConv/IndexedConv-1.3.2/codemeta.json",
-            "temp_analysis/escape2020/cds-astro_cds-moc-rust/cds-moc-rust-main/codemeta.json",
-            "temp_analysis/escape2020/aardk_jupyter-casa/jupyter-casa-master/codemeta.json",
-            "temp_analysis/escape2020/cds-astro_tutorials/tutorials-1.0.3/codemeta.json",
-            "temp_analysis/escape2020/R3BRootGroup_R3BRoot/R3BRoot-jun24/codemeta.json",
-            "temp_analysis/escape2020/AMIGA-IAA_hcg-16/hcg-16-1.2.3/codemeta.json",
-            "temp_analysis/escape2020/repo/eossr-master/codemeta.json",
-            "temp_analysis/escape2020/JColl88_sdc1-solution-binder/sdc1-solution-binder-1.0.0/codemeta.json",
-            "temp_analysis/escape2020/explore-platform_g-tomo/g-tomo-2/codemeta.json",
-            "temp_analysis/escape2020/cds-astro_mocpy/mocpy-0.15.0/codemeta.json",
-            "temp_analysis/escape2020/javierrico_gLike/gLike-master/codemeta.json",
-            "temp_analysis/escape2020/cds-astro_aladin-lite/aladin-lite-3.3.2/codemeta.json",
-            "temp_analysis/escape2020/FairRootGroup_FairMQ/FairMQ-master/codemeta.json"
-        ]
-    },
-    "zenodo.json": {
-        "count": 5,
-        "files": [
-            "temp_analysis/escape2020/cosimoNigro_agnpy/agnpy-master/.zenodo.json",
-            "temp_analysis/escape2020/cds-astro_cds-moc-rust/cds-moc-rust-main/.zenodo.json",
-            "temp_analysis/escape2020/aardk_jupyter-casa/jupyter-casa-master/.zenodo.json",
-            "temp_analysis/escape2020/javierrico_gLike/gLike-master/.zenodo.json",
-            "temp_analysis/escape2020/FairRootGroup_FairMQ/FairMQ-master/.zenodo.json"
-        ]
-    },
-    "identifier_extract": {
-        "count": 7,
-        "extracted_values": [
-            "10.5281/zenodo.3967385",
-            "10.5281/zenodo.7544514",
-            "https://zenodo.org/badge/latestdoi/224865065",
-            "10.5281/zenodo.1689985",
-            "10.5281/zenodo.3967385",
-            "10.5281/zenodo.10405177",
-            "10.5281/zenodo.4055175"
-        ]
-    },
-    "None": {
-        "count": 0
-    }
-}
-```
 
 After running the `calculate` command for a cluster, you get the final summary:
 
@@ -210,6 +135,7 @@ After running the `calculate` command for a cluster, you get the final summary:
 ```
 
 ## Ackowlegement:
+
 The authors acknowledge the OSCARS project, which has received funding from the European Commission's Horizon Europe Research and Innovation programme under grant agreement No. 101129751
 
 <img src="logo.png" alt="logo"/>