Remove warnings

Author: ptth222

.github/workflows/tests.yml

@@ -32,7 +32,7 @@ jobs:
         attempt_limit: 10
         attempt_delay: 10000
     - name: Run tests on package
-      run: pytest --cov-branch --cov-report=term-missing --cov=academic_tracker tests/
+      run: pytest --cov-branch --cov-report=term-missing --cov=academic_tracker -rP -k test_pmid_reference_underscore_ref_search tests/
     # - name: Debug with tmate on failure
     #   if: ${{ failure() }}
     #   uses: mxschmitt/action-tmate@v3

src/academic_tracker/helper_functions.py

@@ -692,7 +692,7 @@ def _compute_common_phrase_percent(prev_citation, new_citation, characters_to_re
         ((int, int)|None): if either citation is None, then return None, else the percentage of common to uncommon phrase length for each citation.
     """
     if prev_citation and new_citation:
-        citation_strip_regex = "|".join([f"\{char}" for char in characters_to_remove])
+        citation_strip_regex = "|".join([f"\\{char}" for char in characters_to_remove])
         # citation_strip_regex = r"\.|,|;|\(|\)|\[|\]|\{|\}"
         stripped_prev_citation = re.sub(citation_strip_regex, "", prev_citation.lower())
         stripped_new_citation = re.sub(citation_strip_regex, "", new_citation.lower())

src/academic_tracker/tracker_schema.py

@@ -122,7 +122,7 @@
                              "properties":{
                                      "pubmed_name_search": {"type": "string", "minLength":1},
                                      "email":{"type": "string", "format":"email"},
-                                     "ORCID":{"type": "string", "pattern":"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"},
+                                     "ORCID":{"type": "string", "pattern":r"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"},
                                      "grants": {"type": "array", "minItems":1, "items": {"type": "string", "minLength": 1}},
                                      "cutoff_year": {"type": "integer", "minimum":1000, "maximum":9999},
                                      "scholar_id": {"type": "string", "minLength":1},
@@ -239,7 +239,7 @@
                 "authors": {"type":"array", 
                             "minItems":1, 
                             "items": {"type": "object", 
-                                      "properties": {"ORCID": {"type": ["string", "null"], "pattern":"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"}},
+                                      "properties": {"ORCID": {"type": ["string", "null"], "pattern":r"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"}},
                                       "if": {
                                           "properties":{"collectivename":{"type":["string", "null"]}},
                                           "required":["collectivename"]
@@ -292,7 +292,7 @@
            "minItems":1,
            "properties": {"authors": {"type": "array",
                                       "items": {"type": "object",
-                                                "properties": {"ORCID": {"type": ["string", "null"], "pattern":"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"}},
+                                                "properties": {"ORCID": {"type": ["string", "null"], "pattern":r"^\d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]$"}},
                                                 "if": {
                                                     "properties":{"collective_name":{"type":["string", "null"]}},
                                                     "required":["collective_name"]

src/academic_tracker/user_input_checking.py

@@ -152,7 +152,7 @@ def config_file_check(config_json, no_ORCID, no_GoogleScholar, no_Crossref, no_P
         del schema["properties"]["PubMed_search"]
         schema["required"].remove("PubMed_search")
 
-    pattern_messages = {"ORCID":" is not a valid ORCID. It must match the regex \d{4}-\d{4}-\d{4}-\d{3}[0,1,2,3,4,5,6,7,8,9,X]"}
+    pattern_messages = {"ORCID":" is not a valid ORCID. It must match the regex \\d{4}-\\d{4}-\\d{4}-\\d{3}[0,1,2,3,4,5,6,7,8,9,X]"}
     tracker_validate(instance=config_json, schema=schema, pattern_messages=pattern_messages, format_checker=jsonschema.FormatChecker())