Merge pull request #6 from alan-turing-institute/development

Development
alan-turing-institute · Sep 22, 2024 · f2d223e · f2d223e
2 parents 76f8f88 + 365ee91
commit f2d223e
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,4 @@
+{
+    "python.analysis.typeCheckingMode": "off",
+    "python.analysis.autoImportCompletions": true
+}
diff --git a/SECURITY.md b/SECURITY.md
@@ -5,6 +5,7 @@
 
 | Version | Supported          |
 | ------- | ------------------ |
+| 1.1.0   | Yes                |
 
 
 ## Reporting a Vulnerability

diff --git a/art/__init__.py b/art/__init__.py
@@ -4,6 +4,8 @@
 Academic Review Tool (ART)
 ==========================
 
+Version: 1.1.0
+
 The Academic Review Tool (ART) is a package for performing academic reviews and bibliometric analyses in Python. 
 It offers capabilities for discovering, retrieving, and analysing academic literature at scale. 
 ART accesses records from Crossref, Web of Science, Scopus, Orcid, and more.
@@ -30,6 +32,7 @@
 * Geopy / Nominatim
 """
 
+from .utils.basics import open_file as open
 from .importers.crossref import lookup_doi, lookup_dois, lookup_journal, lookup_journals, search_journals, get_journal_entries, search_journal_entries, lookup_funder, lookup_funders, search_funders, get_funder_works, search_funder_works
 from .importers.crossref import search_works as search_crossref
 # from .importers.wos import search as search_wos
@@ -39,17 +42,4 @@
 # from .importers import pdf, orcid, crossref, scopus, jstor, wos
 from .classes import Results, References, Author, Authors, Funder, Funders, Affiliation, Affiliations, Review
 from .classes.networks import Network, Networks
-from .classes.citation_crawler import academic_scraper as scrape
-
-import pickle
-
-def open_file(file_address: str = 'request_input'): # type: ignore
-
-        if file_address == 'request_input':
-            file_address = input('File address: ')
-
-        if (file_address.endswith('.txt')) or (file_address.endswith('.review')):
-            with open(file_address, 'rb') as f:
-                review = pickle.load(f)
-
-        return review
+from .classes.citation_crawler import academic_scraper as scrape
diff --git a/art/__pycache__/__init__.cpython-39.pyc b/art/__pycache__/__init__.cpython-39.pyc
diff --git a/art/classes/__pycache__/__init__.cpython-39.pyc b/art/classes/__pycache__/__init__.cpython-39.pyc
diff --git a/art/classes/__pycache__/activitylog.cpython-39.pyc b/art/classes/__pycache__/activitylog.cpython-39.pyc
diff --git a/art/classes/__pycache__/affiliations.cpython-39.pyc b/art/classes/__pycache__/affiliations.cpython-39.pyc
diff --git a/art/classes/__pycache__/attrs.cpython-39.pyc b/art/classes/__pycache__/attrs.cpython-39.pyc
diff --git a/art/classes/__pycache__/authors.cpython-39.pyc b/art/classes/__pycache__/authors.cpython-39.pyc
diff --git a/art/classes/__pycache__/citation_crawler.cpython-39.pyc b/art/classes/__pycache__/citation_crawler.cpython-39.pyc
diff --git a/art/classes/__pycache__/entities.cpython-39.pyc b/art/classes/__pycache__/entities.cpython-39.pyc
diff --git a/art/classes/__pycache__/funders.cpython-39.pyc b/art/classes/__pycache__/funders.cpython-39.pyc
diff --git a/art/classes/__pycache__/networks.cpython-39.pyc b/art/classes/__pycache__/networks.cpython-39.pyc
diff --git a/art/classes/__pycache__/properties.cpython-39.pyc b/art/classes/__pycache__/properties.cpython-39.pyc
diff --git a/art/classes/__pycache__/references.cpython-39.pyc b/art/classes/__pycache__/references.cpython-39.pyc
diff --git a/art/classes/__pycache__/results.cpython-39.pyc b/art/classes/__pycache__/results.cpython-39.pyc
diff --git a/art/classes/__pycache__/review.cpython-39.pyc b/art/classes/__pycache__/review.cpython-39.pyc
diff --git a/art/classes/activitylog.py b/art/classes/activitylog.py
@@ -6,23 +6,24 @@
 class ActivityLog(pd.DataFrame):
 
     """
-    This is a ActivityLog object. It is a modified Pandas Dataframe object designed to store metadata about an academic review.
+    This is an ActivityLog object. It is a modified Pandas Dataframe object designed to store metadata about an academic review.
     
-    Parameters
-    ----------
-    
-    
-    Attributes
-    ----------
+    Columns
+    -------
+    * **timestamp**: date-time the activity occurred.
+    * **type**: type of activity.
+    * **activity**: details of activity.
+    * **location**: location in Review that activity occurred.
+    * **database**: name of database/repository accessed (if relevant).
+    * **url**: web address accessed (if relevant).
+    * **query**: search query used (if relevant).
+    * **changes**: number of changes made to the Review results.
     """
 
     def __init__(self):
 
         """
         Initialises ActivityLog instance.
-        
-        Parameters
-        ----------
         """
 
 
@@ -44,6 +45,27 @@ def __init__(self):
 
     def add_activity(self, type: str, activity: str, location: list, database = None, query = None, url = None, changes_dict = None):
 
+        """
+        Adds a new activity to the ActivityLog DataFrame.
+
+        Parameters
+        ----------
+        type : str
+            type of activity.
+        activity : str
+            details of activity.
+        location : str
+            name of location in Review that activity occurred.
+        database : str
+            name of database/repository accessed (if relevant). Defaults to None.
+        query : str
+            search query used (if relevant). Defaults to None.
+        url : str
+            web address accessed (if relevant). Defaults to None.
+        changes_dict : dict
+            dictionary of changes made to Review. Defaults to None.
+        """
+
         new_index = len(self)
         self.loc[new_index, 'timestamp'] = datetime.now().strftime("%d/%m/%Y %H:%M:%S")
         self.loc[new_index, 'type'] = type