cleanup + renaming files

scripts/README.md

@@ -1,3 +1,3 @@
 Scripts that can be used to automatically generate markdown files, can be found here.
 
-* [`module_overview`](module_overview): script to generate overview of available environment modules;
+* [`available_software`](available_software): script to generate overview of available environment modules;

scripts/module_overview/module_overview.py → scripts/available_software/available_software.py

@@ -29,16 +29,16 @@
 @author: Michiel Lachaert (Ghent University)
 """
 
-import time
 import json
-from pathlib import Path
-import numpy as np
-import re
 import os
+import re
 import subprocess
-from mdutils.mdutils import MdUtils
+import time
+from pathlib import Path
 from typing import Union, Tuple
-from module_detail import generate_detail_pages
+import numpy as np
+from mdutils.mdutils import MdUtils
+from natsort import natsorted
 
 
 # --------------------------------------------------------------------------------------------------------
@@ -220,8 +220,93 @@ def get_unique_software_names(data: Union[dict, list, np.ndarray]) -> Union[dict
     return simplified_data
 
 
+def dict_sort(dictionary: dict) -> dict:
+    """
+    Sort a dictionary by key.
+
+    @param dictionary: A dictionary
+    @return: Sorted dictionary
+    """
+    return dict(natsorted(dictionary.items()))
+
+
+# --------------------------------------------------------------------------------------------------------
+# Generate detailed markdown
+# --------------------------------------------------------------------------------------------------------
+
+def generate_software_table_data(software_data: dict, clusters: list) -> list:
+    """
+    Construct the data for the detailed software table.
+
+    @param software_data: Software specific data.
+    @param clusters: List with all the cluster names
+    @return: 1D list with all the data for the table
+    """
+    table_data = [" "] + clusters
+
+    for k, v in list(software_data.items())[::-1]:
+        row = [k]
+
+        for cluster in clusters:
+            row += ("x" if cluster in v else "-")
+        table_data += row
+
+    return table_data
+
+
+def generate_software_detail_page(
+        software_name: str,
+        software_data: dict,
+        generated_time: str,
+        clusters: list,
+        path: str
+) -> None:
+    """
+    Generate one software specific detail page.
+
+    @param software_name: Name of the software
+    @param software_data: Additional information about the software (version, etc...)
+    @param generated_time: Timestamp when the data was generated
+    @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}.md"
+    md_file = MdUtils(file_name=filename, title=f"detailed overview of {software_name}")
+
+    md_file.new_paragraph(f"This data was automatically generated on {generated_time}")
+    md_file.new_line()
+
+    sorted_versions = dict_sort(software_data["versions"])
+    md_file.new_table(
+        columns=len(clusters) + 1,
+        rows=len(sorted_versions) + 1,
+        text=generate_software_table_data(sorted_versions, clusters)
+    )
+
+    md_file.create_md_file()
+
+    # Remove the TOC
+    with open(filename) as f:
+        read_data = f.read()
+    with open(filename, 'w') as f:
+        f.write("---\nhide:\n  - toc\n---\n" + read_data)
+
+
+def generate_detail_pages(json_path, dest_path) -> None:
+    """
+    Generate all the detailed pages for all the software that is available.
+    """
+
+    with open(json_path) as json_data:
+        data = json.load(json_data)
+
+    all_clusters = data["clusters"]
+    for software, content in data["software"].items():
+        generate_software_detail_page(software, content, data["time_generated"], all_clusters, dest_path)
+
+
 # --------------------------------------------------------------------------------------------------------
-# Generate markdown
+# Generate overview markdown
 # --------------------------------------------------------------------------------------------------------
 
 def generate_table_data(avail_mods: dict) -> Tuple[np.ndarray, int, int]:
@@ -376,9 +461,9 @@ def generate_json_detailed_data(modules: dict) -> dict:
                 # If the software is not yet present, add it.
                 if software not in json_data["software"]:
                     json_data["software"][software] = {
-                            "clusters": [],
-                            "versions": {}
-                        }
+                        "clusters": [],
+                        "versions": {}
+                    }
 
                 # If the version is not yet present, add it.
                 if mod not in json_data["software"][software]["versions"]:

scripts/module_overview/tests/test_data.py → scripts/available_software/tests/test_data.py

@@ -1,5 +1,5 @@
 import os
-from module_overview import modules_ugent, get_unique_software_names
+from available_software import modules_ugent, get_unique_software_names
 
 
 class TestData:

scripts/module_overview/tests/test_json.py → scripts/available_software/tests/test_json.py

@@ -1,4 +1,7 @@
-from module_overview import generate_json_overview_data, generate_json_overview, modules_ugent, generate_json_detailed
+from available_software import (generate_json_overview_data,
+                                generate_json_overview,
+                                modules_ugent,
+                                generate_json_detailed)
 import os
 import json
 

scripts/module_overview/tests/test_md.py → scripts/available_software/tests/test_md.py

@@ -1,5 +1,5 @@
 from mdutils.mdutils import MdUtils
-from module_overview import get_unique_software_names, modules_ugent, generate_table_data, generate_module_table
+from available_software import get_unique_software_names, modules_ugent, generate_table_data, generate_module_table
 import os
 import filecmp
 

scripts/module_overview/tests/test_module.py → scripts/available_software/tests/test_module.py

@@ -1,5 +1,5 @@
 import os
-from module_overview import module_avail, filter_fn_gent_modules, filter_fn_gent_cluster, module_swap, module_whatis
+from available_software import module_avail, filter_fn_gent_modules, filter_fn_gent_cluster, module_swap, module_whatis
 
 
 class TestModule: