cleanup code + comments + change file structure

config/templates/hpc.template

@@ -6,7 +6,9 @@ docs_dir: docs/HPC
 
 nav:
   - Welcome: index.md
-  - Overview modules: module_overview.md
+  {%- if site == 'Gent' %}
+  - Overview modules: only/gent/module_overview/index.md
+  {%- endif %}
   - Introduction to HPC: introduction.md
   - Getting an HPC Account: account.md
   - Connecting to the HPC infrastructure: connecting.md

mkdocs/docs/HPC/javascripts/populate_overview.js

@@ -26,50 +26,6 @@
  * @author: Michiel Lachaert
  */
 
-/**
- * A function that populates the table on the module overview page with information about all the available modules.
- */
-// function populate_overview_new() {
-//     fetch("../data/modulemap.json")
-//         .then((response) => response.json())
-//         .then((json) => {
-//             // CONSTRUCT TABLE
-//
-//             const all_clusters = Object.entries(json.clusters)
-//                 .filter(([, value]) => !value.includes("."))
-//                 .map(x => {
-//                     return {"title": x[0], "className": 'dt-center'}
-//                 })
-//
-//             const table = new DataTable('#overview_table', {
-//                 columns: [...[{"title": "name"}], ...all_clusters],
-//                 paging: false,
-//             });
-//
-//
-//             // ADD DATA
-//             let new_rows = [];
-//
-//             // list_avaible contains a list with booleans.
-//             // These booleans indicates if the software is available on the corresponding cluster.
-//             for (const [software, versions] of Object.entries(json.software)) {
-//                 let new_row = [
-//                     `<a href="../detail/${software}_detail">${software}</a>`
-//                 ]
-//
-//                 const available = Object.keys(versions[".default"])
-//                 all_clusters
-//                     .forEach(cluster =>
-//                         new_row.push(available.includes(cluster.title) ? "x" : "-")
-//                     )
-//
-//                 new_rows.push(new_row);
-//             }
-//
-//             table.rows.add(new_rows).draw();
-//         })
-// }
-
 /**
  * A function that populates the table on the module overview page with information about all the available modules.
  */
@@ -95,7 +51,7 @@ function populate_overview(json_data) {
             // list_avaible contains a list with booleans.
             // These booleans indicates if the software is available on the corresponding cluster.
             for (const [software, list_available] of Object.entries(json.modules)) {
-                let new_row = [`<a href="../detail/${software}_detail">${software}</a>`];
+                let new_row = [`<a href="detail/${software}">${software}</a>`];
                 list_available.forEach(bool => new_row.push(bool ? "x" : "-"));
                 new_rows.push(new_row);
             }
@@ -107,6 +63,6 @@ function populate_overview(json_data) {
 // Only start populating the table if the correct page has been loaded.
 document$.subscribe(function() {
     if (document.getElementById("overview_table")) {
-        populate_overview("../data/json_data.json")
+        populate_overview("../module_overview/data/json_data.json")
     }
 })

scripts/module_overview/module_detail.py

@@ -24,21 +24,42 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
 """
-Python script to generate a detail page for the avalable modules across different clusters, in MarkDown format.
+Python script to generate a detail page for the available modules across different clusters, in MarkDown format.
 It generates 1 markdown for each module.
 
 @author: Michiel Lachaert (Ghent University)
 """
-
+import argparse
 import json
 from mdutils import MdUtils
 from natsort import natsorted
 import os
 
 
+def main():
+    parser = argparse.ArgumentParser(description="Get args.")
+    parser.add_argument(
+        "--json",
+        "-j",
+        dest="json",
+        help="Path to the JSON.",
+        required=True
+    )
+    parser.add_argument(
+        "--path",
+        "-p",
+        dest="path",
+        help="Path to the directory where the detail folder will be placed.",
+        required=True
+    )
+
+    args = parser.parse_args()
+    generate_detail_pages(args.json, args.path)
+
+
 def dict_sort(dictionary: dict) -> dict:
     """
-    Sort a dictionary by key
+    Sort a dictionary by key.
 
     @param dictionary: A dictionary
     @return: Sorted dictionary
@@ -56,7 +77,7 @@ def generate_software_table_data(software_data: dict, clusters: list) -> list:
     """
     table_data = [" "] + clusters
 
-    for k, v in software_data.items():
+    for k, v in list(software_data.items())[::-1]:
         row = [k]
 
         for cluster in clusters:
@@ -75,7 +96,7 @@ def generate_software_detail_page(software_name: str, software_data: dict, clust
     @param clusters: List with all the cluster names
     @param path: Path of the directory where the detailed page will be created.
     """
-    filename = f"{path}/{software_name}_detail.md"
+    filename = f"{path}/{software_name}.md"
     md_file = MdUtils(file_name=filename, title=f"detailed overview of {software_name}")
 
     sorted_versions = dict_sort(software_data["versions"])
@@ -94,20 +115,18 @@ def generate_software_detail_page(software_name: str, software_data: dict, clust
         f.write("---\nhide:\n  - toc\n---\n" + read_data)
 
 
-def generate_detail_pages() -> None:
+def generate_detail_pages(json_path, dest_path) -> None:
     """
     Generate all the detailed pages for all the software that is available.
     """
 
-    with open("json_data_detail.json") as json_data:
+    with open(json_path) as json_data:
         data = json.load(json_data)
 
-    path = "/home/milachae/Documents/HPC_Vakantiejob_2023/vsc_user_docs/mkdocs/docs/HPC/detail"
-    os.makedirs(path, exist_ok=True)
     all_clusters = data["clusters"]
     for software, content in data["software"].items():
-        generate_software_detail_page(software, content, all_clusters, path)
+        generate_software_detail_page(software, content, all_clusters, dest_path)
 
 
 if __name__ == '__main__':
-    generate_detail_pages()
+    main()

scripts/module_overview/module_overview.py

@@ -37,6 +37,17 @@
 from typing import Union, Tuple
 
 
+# --------------------------------------------------------------------------------------------------------
+# MAIN
+# --------------------------------------------------------------------------------------------------------
+
+def main():
+    # Generate the JSON overviews
+    modules = modules_ugent()
+    generate_json_overview(modules)
+    generate_json_detailed(modules)
+
+
 # --------------------------------------------------------------------------------------------------------
 # Functions to run "module" commands
 # --------------------------------------------------------------------------------------------------------
@@ -357,16 +368,5 @@ def generate_json_detailed(modules: dict) -> None:
         json.dump(json_data, outfile)
 
 
-# --------------------------------------------------------------------------------------------------------
-# MAIN
-# --------------------------------------------------------------------------------------------------------
-
-def main():
-    # Generate the JSON overviews
-    modules = modules_ugent()
-    generate_json_overview(modules)
-    generate_json_detailed(modules)
-
-
 if __name__ == '__main__':
     main()