docs: Update documentation

- Fix docstrings for sensor.py
- Customize mkdocs.yml

edam/reader/models/observable.py

@@ -13,6 +13,7 @@ class AbstractObservable(Base):
     or `temp_min`, etc.
 
     Attributes:
+        observable_id:
         name: The name of the observable (e.g. Temperature)
         ontology: An ontology for the observable
     """

edam/reader/models/template.py

@@ -1,11 +1,12 @@
 import csv
+import fnmatch
 import os
 import re
 from contextlib import contextmanager
 
 import jinja2schema
 
-from edam import get_logger
+from edam import get_logger, home_directory
 from edam.reader.regular_expressions import template_file_header, \
     for_loop_variables, var_for_line, start_if, end_if, resample_function
 from edam.utilities.exceptions import ErrorWithTemplate
@@ -130,7 +131,6 @@ def resampled(self, value):
         else:
             self._resampled = None
 
-
     @property
     def preamble(self) -> str:
         """
@@ -202,3 +202,22 @@ def read_template(template: Template):
     f = open(template.path, 'r')
     yield f
     f.close()
+
+
+def find_templates_in_directory(directory: str = home_directory) -> [Template]:
+    """
+        Returns a list of templates located in a given directory.
+        Directory defaults to the home_directory(~/.edam)
+        :rtype: [Template]
+        :param directory: Directory to search for templates
+        :return: list of Template objects
+    """
+    list_of_templates = list()
+    for folder, _, files in os.walk(os.path.join(directory, 'templates')):
+        for file in files:
+            if fnmatch.fnmatch(file, '*.tmpl'):
+                path = os.path.join(folder, file)
+                filename, _ = os.path.splitext(file)
+                templ = Template(path=path)
+                list_of_templates.append(templ)
+    return list_of_templates

mkdocs.yml

@@ -1,6 +1,20 @@
 site_name: EDAM
 theme:
   name: material
+  logo: assets/eco.png
+  favicon: images/favicon.ico
+  palette:
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline
+        name: Switch to dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode
+
 repo_name: 'EDAM'
 repo_url: 'https://github.com/BigDataWUR/EDAM'
 copyright: 'Copyright © 2017, Argyrios Samourkasidis'