Fix Docs and update Changelog (#43)

* Formatting applied

* Readthedocs update, separate env

* Update notebook

* Add sphinx to environment for now, until the issue there is solved

* Update docs

* Update docs

* Add docs requirements file

* Remove docs requirements again, fix error in ipynb

* Omit pdf build of docs, due to problems with special chars in ipnb

* Update changelog

.readthedocs.yml

@@ -3,9 +3,6 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-formats:
-  - pdf
-
 submodules:
   include: all
 

CHANGELOG.rst

@@ -7,6 +7,14 @@ Unreleased
 
 -
 
+Version 1.1.0
+=============
+
+- Fixed bug in the metadata dataframe when not using all available networks.
+- Citation export functions added to `Collection` and `Network` components.
+- Citations for all networks are now stored in this package until they are reliably provided together with the data
+- It is now possible to pass multiple allowed variables when filtering sensors.
+
 Version 1.0.1
 =============
 

docs/_static/.gitignore

@@ -1 +1 @@
-# Empty directory
+# Empty directory

docs/readme.rst

@@ -0,0 +1 @@
+.. include:: ../README.rst

environment.yml

@@ -14,6 +14,7 @@ dependencies:
      - configparser
      - tqdm
      - more_itertools
+     - sphinx==4.0.3  # there seems to be an issue with 4.1.0 and nbsphinx, when this is resolved this line can be deleted to use the latest version.
      - nbsphinx
      - sphinx_rtd_theme
      - pytest

src/ismn/components.py

@@ -638,10 +638,11 @@ def get_citations(self):
         try:
             refs = CITATIONS[self.name]
         except KeyError:
-            refs = [f'No reference(s) for network {self.name} available.']
+            refs = [f"No reference(s) for network {self.name} available."]
 
         return refs
 
+
 class NetworkCollection(IsmnComponent):
     """
     A NetworkCollection holds multiple networks and provides functionality
@@ -793,17 +794,18 @@ def export_citations(self, out_file=None):
         references: OrderedDict
             Network names as keys and network references as values
         """
-        refs = OrderedDict([(net.name, net.get_citations())
-                            for net in self.iter_networks()])
+        refs = OrderedDict(
+            [(net.name, net.get_citations()) for net in self.iter_networks()]
+        )
 
         if out_file is not None:
-            with open(out_file, mode='w') as out_file:
+            with open(out_file, mode="w") as out_file:
                 for name, reflist in refs.items():
-                    out_file.write(f'References for Network {name}:\n')
+                    out_file.write(f"References for Network {name}:\n")
                     out_file.write("-----------------------------------------\n")
                     for ref in reflist:
                         out_file.write(f"{ref}\n")
-                        out_file.write('\n')
-                    out_file.write('\n')
+                        out_file.write("\n")
+                    out_file.write("\n")
 
-        return refs
+        return refs

src/ismn/const.py

@@ -64,10 +64,16 @@ class DepthError(ValueError):
 #  Once the full list of citations is provided together with the downloaded
 #  ISMN data (in the README file), citations here can be deleted (keep in mind
 #  that people might still use old data, but a new version of the package).
-CITATIONS: dict = \
-    pd.read_csv(os.path.join(os.path.dirname(__file__), 'citations.txt'),
-                             index_col=0, delimiter=';') \
-      .groupby('Network')['Citation'].apply(list).to_dict()
+CITATIONS: dict = (
+    pd.read_csv(
+        os.path.join(os.path.dirname(__file__), "citations.txt"),
+        index_col=0,
+        delimiter=";",
+    )
+    .groupby("Network")["Citation"]
+    .apply(list)
+    .to_dict()
+)
 
 # ==============================================================================
 # Variable short names
@@ -239,4 +245,3 @@ class DepthError(ValueError):
     ]
 )
 # ==============================================================================
-

src/ismn/interface.py

@@ -166,8 +166,8 @@ def activate_network(
             self.__file_collection.to_metadata_csv(meta_csv_file)
 
         self.__file_collection = IsmnFileCollection.from_metadata_csv(
-                self.root, meta_csv_file, network=network
-            )
+            self.root, meta_csv_file, network=network
+        )
 
         metadata = self.__file_collection.metadata_df
 
@@ -893,4 +893,4 @@ def print_climate_dict(self) -> None:
 
     def close_files(self):
         # close all open filehandlers
-        self.__file_collection.close()
+        self.__file_collection.close()