I think the GitHub Desktop nuking has been fixed now.

Author: ptth222

.gitignore

@@ -11,3 +11,4 @@ build/
 dist/
 coverage.xml
 .coverage
+htmlcov/

src/academic_tracker/user_input_checking.py

@@ -172,7 +172,7 @@ def ref_config_file_check(config_json, no_Crossref, no_PubMed):
     if no_Crossref:
         del schema["properties"]["Crossref_search"]
         schema["required"].remove("Crossref_search")
-    if no_Crossref:
+    if no_PubMed:
         del schema["properties"]["PubMed_search"]
         schema["required"].remove("PubMed_search")
 

tests/test_athr_srch_modularized.py

@@ -23,21 +23,19 @@ def stunted_get():
 
 @pytest.fixture
 def config_dict():
-    return load_json(os.path.join("testing_files", "config_truncated.json"))
+    return load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
 
 
 
 def test_input_reading_and_checking(config_dict):
-    config_json_filepath = os.path.join("testing_files", "config_truncated.json")
+    config_json_filepath = os.path.join("tests", "testing_files", "config_truncated.json")
 
     expected_config_dict = config_dict
 
     actual_config_dict = input_reading_and_checking(config_json_filepath, False, False, False, False)
 
     assert expected_config_dict == actual_config_dict
-<<<<<<< Updated upstream
-=======
 
 
 def test_input_reading_and_checking_no_ORCID(config_dict):
@@ -76,13 +74,12 @@ def test_input_reading_and_checking_no_Crossref_noGS(config_dict):
 
     assert expected_config_dict == actual_config_dict
 
->>>>>>> Stashed changes
 
 
 
 def test_generate_internal_data_and_check_authors(config_dict, capsys):
-    expected_authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
-    expected_config_dict = load_json(os.path.join("testing_files", "config_truncated_authors_adjusted.json"))
+    expected_authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
+    expected_config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated_authors_adjusted.json"))
 
     actual_authors_by_project_dict, actual_config_dict = generate_internal_data_and_check_authors(config_dict)
 
@@ -95,9 +92,9 @@ def test_generate_internal_data_and_check_authors(config_dict, capsys):
 
 
 def test_build_publication_dict_all_sources(config_dict, mocker):
-    config_dict = load_json(os.path.join("testing_files", "config_truncated.json"))
+    config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
-    expected_pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
+    expected_pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
     ## Add a fourth entry that is a copy of one of the others just to have a 4th to assign to the 4 different queries.
     expected_pub_dict["32095798"] = expected_pub_dict["32095784"]
 
@@ -117,21 +114,16 @@ def mock_query4(*args, **kwargs):
         return {"32095798":expected_pub_dict["32095798"]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_webio.search_Google_Scholar_for_pubs", mock_query4)
 
-<<<<<<< Updated upstream
-    actual_publication_dict, prev_pubs = build_publication_dict(config_dict, {}, False, False, False)
-=======
     actual_publication_dict = build_publication_dict(config_dict, {}, False, False, False, False)
->>>>>>> Stashed changes
 
     assert expected_pub_dict == actual_publication_dict
-    assert expected_pub_dict == prev_pubs
 
 
 
 def test_build_publication_dict_no_ORCID(config_dict, mocker):
-    config_dict = load_json(os.path.join("testing_files", "config_truncated.json"))
+    config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
-    expected_pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
+    expected_pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
     ## Add a fourth entry that is a copy of one of the others just to have a 4th to assign to the 4 different queries.
     expected_pub_dict["32095798"] = expected_pub_dict["32095784"]
     del expected_pub_dict["https://doi.org/10.1002/adhm.202101820"]
@@ -152,21 +144,16 @@ def mock_query4(*args, **kwargs):
         return {"32095798":expected_pub_dict["32095798"]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_webio.search_Google_Scholar_for_pubs", mock_query4)
 
-<<<<<<< Updated upstream
-    actual_publication_dict, prev_pubs = build_publication_dict(config_dict, {}, True, False, False)
-=======
     actual_publication_dict = build_publication_dict(config_dict, {}, True, False, False, False)
->>>>>>> Stashed changes
 
     assert expected_pub_dict == actual_publication_dict
-    assert expected_pub_dict == prev_pubs
 
 
 
 def test_build_publication_dict_no_Crossref(config_dict, mocker):
-    config_dict = load_json(os.path.join("testing_files", "config_truncated.json"))
+    config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
-    expected_pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
+    expected_pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
     ## Add a fourth entry that is a copy of one of the others just to have a 4th to assign to the 4 different queries.
     expected_pub_dict["32095798"] = expected_pub_dict["32095784"]
     del expected_pub_dict["https://doi.org/10.1002/advs.202101999"]
@@ -187,21 +174,16 @@ def mock_query4(*args, **kwargs):
         return {"32095798":expected_pub_dict["32095798"]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_webio.search_Google_Scholar_for_pubs", mock_query4)
 
-<<<<<<< Updated upstream
-    actual_publication_dict, prev_pubs = build_publication_dict(config_dict, {}, False, False, True)
-=======
     actual_publication_dict = build_publication_dict(config_dict, {}, False, False, True, False)
->>>>>>> Stashed changes
 
     assert expected_pub_dict == actual_publication_dict
-    assert expected_pub_dict == prev_pubs
 
 
 
 def test_build_publication_dict_no_Google_Scholar(config_dict, mocker):
-    config_dict = load_json(os.path.join("testing_files", "config_truncated.json"))
+    config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
-    expected_pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
+    expected_pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
     ## Add a fourth entry that is a copy of one of the others just to have a 4th to assign to the 4 different queries.
     expected_pub_dict["32095798"] = expected_pub_dict["32095784"]
     del expected_pub_dict["32095798"]
@@ -222,9 +204,6 @@ def mock_query4(*args, **kwargs):
         return {"32095798":expected_pub_dict["32095798"]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_webio.search_Google_Scholar_for_pubs", mock_query4)
 
-<<<<<<< Updated upstream
-    actual_publication_dict, prev_pubs = build_publication_dict(config_dict, {}, False, True, False)
-=======
     actual_publication_dict = build_publication_dict(config_dict, {}, False, True, False, False)
 
     assert expected_pub_dict == actual_publication_dict
@@ -289,15 +268,13 @@ def mock_query4(*args, **kwargs):
     actual_publication_dict = build_publication_dict(config_dict, prev_pubs, False, False, False, False)
 
     del expected_pub_dict["32095798"]
->>>>>>> Stashed changes
 
     assert expected_pub_dict == actual_publication_dict
-    assert expected_pub_dict == prev_pubs
 
 
 
 def test_build_publication_dict_no_pubs_found(config_dict, mocker, capsys):
-    config_dict = load_json(os.path.join("testing_files", "config_truncated.json"))
+    config_dict = load_json(os.path.join("tests", "testing_files", "config_truncated.json"))
 
     def mock_query(*args, **kwargs):
         return {}
@@ -316,11 +293,7 @@ def mock_query4(*args, **kwargs):
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_webio.search_Google_Scholar_for_pubs", mock_query4)
 
     with pytest.raises(SystemExit):
-<<<<<<< Updated upstream
-        actual_publication_dict, prev_pubs = build_publication_dict(config_dict, {}, False, False, False)
-=======
         actual_publication_dict = build_publication_dict(config_dict, {}, False, False, False, False)
->>>>>>> Stashed changes
 
     captured = capsys.readouterr()
     expected_message = "No new publications found." + "\n"
@@ -335,16 +308,16 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["summary_report"] = {}
-    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("testing_files", "athr_srch_build_loop_template_string.txt"))
+    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_build_loop_template_string.txt"))
 
     save_dir = save_and_send_reports_and_emails(authors_by_project_dict, pub_dict, config_dict, True)
 
     assert os.path.exists(os.path.join(save_dir, "summary_report.txt"))
-    assert read_text_from_txt(os.path.join("testing_files", "athr_srch_summary_report_custom_template.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
+    assert read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_summary_report_custom_template.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
     assert not os.path.exists(os.path.join(save_dir, "emails.json"))
 
 
@@ -355,11 +328,11 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["summary_report"] = {}
-    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("testing_files", "athr_srch_build_loop_template_string.txt"))
+    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_build_loop_template_string.txt"))
     config_dict["summary_report"]["from_email"] = "[email protected]"
     config_dict["summary_report"]["to_email"] = ["[email protected]"]
     config_dict["summary_report"]["cc_email"] = ["[email protected]"]
@@ -369,7 +342,7 @@ def emails(*args, **kwargs):
     save_dir = save_and_send_reports_and_emails(authors_by_project_dict, pub_dict, config_dict, True)
 
     assert os.path.exists(os.path.join(save_dir, "summary_report.txt"))
-    assert read_text_from_txt(os.path.join("testing_files", "athr_srch_summary_report_custom_template.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
+    assert read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_summary_report_custom_template.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
     assert os.path.exists(os.path.join(save_dir, "emails.json"))
 
 
@@ -380,15 +353,15 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["summary_report"] = {}
 
     save_dir = save_and_send_reports_and_emails(authors_by_project_dict, pub_dict, config_dict, True)
 
     assert os.path.exists(os.path.join(save_dir, "summary_report.txt"))
-    assert read_text_from_txt(os.path.join("testing_files", "athr_srch_summary_report.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
+    assert read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_summary_report.txt")) == read_text_from_txt(os.path.join(save_dir, "summary_report.txt"))
     assert not os.path.exists(os.path.join(save_dir, "emails.json"))
 
 
@@ -398,8 +371,8 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["Authors"]["Anna Hoover"]["collaborator_report"] = {"from_email":"[email protected]", 
                                                                     "email_body":"asdf",
@@ -418,8 +391,8 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["summary_report"] = {}
     config_dict["summary_report"]["columns"] = {"Col1":"<project_name>"}
@@ -436,11 +409,11 @@ def emails(*args, **kwargs):
         return {"creation_date":"asdf", "emails":[]}
     mocker.patch("academic_tracker.athr_srch_modularized.athr_srch_emails_and_reports.create_project_reports_and_emails", emails)
 
-    pub_dict = load_json(os.path.join("testing_files", "publication_dict_truncated.json"))
-    authors_by_project_dict = load_json(os.path.join("testing_files", "authors_by_project_dict_truncated.json"))
+    pub_dict = load_json(os.path.join("tests", "testing_files", "publication_dict_truncated.json"))
+    authors_by_project_dict = load_json(os.path.join("tests", "testing_files", "authors_by_project_dict_truncated.json"))
 
     config_dict["summary_report"] = {}
-    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("testing_files", "athr_srch_build_loop_template_string.txt"))
+    config_dict["summary_report"]["template"] = read_text_from_txt(os.path.join("tests", "testing_files", "athr_srch_build_loop_template_string.txt"))
     config_dict["summary_report"]["filename"] = "test_name.txt"
 
     save_dir = save_and_send_reports_and_emails(authors_by_project_dict, pub_dict, config_dict, True)