diff --git a/gatorgrade/input/parse_config.py b/gatorgrade/input/parse_config.py
index d6ac12c7..d3950280 100644
--- a/gatorgrade/input/parse_config.py
+++ b/gatorgrade/input/parse_config.py
@@ -1,19 +1,25 @@
 """Returns the list of commands to be run through gatorgrader."""
 
 from pathlib import Path
+from thefuzz import fuzz
+
 
 from gatorgrade.input.command_line_generator import generate_checks
 from gatorgrade.input.in_file_path import parse_yaml_file
 from gatorgrade.input.in_file_path import reformat_yaml_data
 
 
-def parse_config(file: Path):
+def parse_config(file: Path, check_include: str = None, check_exclude: str = None):
     """Parse the input yaml file and generate specified checks.
 
     Args:
         file: Yaml file containing gatorgrade and shell command checks
+        check_include: Description of checks to include
+        check_exclude: Description of checks to exclude
     Returns:
-        Returns a dictionary that specifies shell commands and gatorgrade commands
+        Returns a tuple that contains:
+        - A dictionary specifying shell commands and gatorgrade commands
+        - A boolean variable indicating if there is a match for the specified checks
     """
     # parse the YAML file using parse_yaml_file provided by gatorgrade
     parsed_yaml_file = parse_yaml_file(file)
@@ -24,8 +30,25 @@ def parse_config(file: Path):
         # use it to generate all of the checks;
         # these will be valid checks that are now
         # ready for execution with this tool
-        parse_con = generate_checks(reformat_yaml_data(parsed_yaml_file))
-        return parse_con
+        reformatted_yaml_data = reformat_yaml_data(parsed_yaml_file)
+        match = True
+        # Filter the reformat_yaml_data to only include specified checks
+        if check_include:
+            # Generate the checks that are included
+            check_list = [check for check in reformatted_yaml_data if fuzz.partial_ratio(check_include, check[1]['description']) >= 80]
+            match = True if len(check_list) > 0 else False       
+            parse_con = generate_checks(check_list)
+            return (parse_con, match)       
+
+        if check_exclude:
+            # Generate the checks that are excluded
+            check_list = [check for check in reformatted_yaml_data if fuzz.partial_ratio(check_exclude, check[1]['description']) < 80]
+            match = True if len(check_list) > 0 else False
+            parse_con = generate_checks(check_list)
+            return (parse_con, match)
+
+        parse_con = generate_checks(reformatted_yaml_data)
+        return (parse_con, match)
     # return an empty list because of the fact that the
     # parsing process did not return a list with content;
     # allow the calling function to handle the empty list
diff --git a/gatorgrade/main.py b/gatorgrade/main.py
index 42bbbd81..22c009ea 100644
--- a/gatorgrade/main.py
+++ b/gatorgrade/main.py
@@ -1,5 +1,3 @@
-"""Use Typer to run gatorgrade to run the checks and generate the yml file."""
-
 import sys
 from pathlib import Path
 from typing import Tuple
@@ -12,21 +10,14 @@
 
 # create an app for the Typer-based CLI
 
-# define the emoji that will be prepended to the help message
 gatorgrade_emoji = "🐊"
 
-# create a Typer app that
-# --> does not support completion
-# --> has a specified help message with an emoji
 app = typer.Typer(
     add_completion=False,
     help=f"{gatorgrade_emoji} Run the GatorGrader checks in the specified gatorgrade.yml file.",
 )
 
-# create a default console for printing with rich
 console = Console()
-
-# define constants used in this module
 FILE = "gatorgrade.yml"
 FAILURE = 1
 
@@ -45,55 +36,67 @@ def gatorgrade(
             3. the name of the file or environment variable\
             4. use 'env md GITHUB_STEP_SUMMARY' to create GitHub job summary in GitHub Action",
     ),
+    output_limit: int = typer.Option(
+        None,
+        "--output-limit",
+        "-l",
+        help="The maximum number of lines to store in an environment variable. Example: '--output-limit 1000'",
+    ),
+    check_include: str = typer.Option(
+        None,
+        "--check-include",
+        "-i",
+        help="Description of the checks to include. Example: '--check-include \"Complete all TODOs\"'",
+    ),
+    check_exclude: str = typer.Option(
+        None,
+        "--check-exclude",
+        "-e",
+        help="Description of the checks to exclude. Example: '--check-exclude \"Complete all TODOs\"'",
+    ),
+    check_status: str = typer.Option(
+        None,
+        "--check-status",
+        "-s",
+        help="Filter checks by their status (pass or fail). Example: '--check-status pass'",
+    ),
+    show_failures: bool = typer.Option(
+        False,
+        "--show-failures",
+        "-f",
+        help="Only show the failed checks.",
+    ),
 ):
     """Run the GatorGrader checks in the specified gatorgrade.yml file."""
-    # if ctx.subcommand is None then this means
-    # that, by default, gatorgrade should run in checking mode
     if ctx.invoked_subcommand is None:
-        # parse the provided configuration file
-        checks = parse_config(filename)
-        # there are valid checks and thus the
-        # tool should run them with run_checks
+        (checks, match) = parse_config(filename, check_include, check_exclude)
+
         if len(checks) > 0:
-            checks_status = run_checks(checks, report)
-        # no checks were created and this means
-        # that, most likely, the file was not
-        # valid and thus the tool cannot run checks
+            checks_status = run_checks(
+                checks, report, output_limit, check_status, show_failures
+            )
         else:
             checks_status = False
             console.print()
-            console.print(f"The file {filename} either does not exist or is not valid.")
+            if match is False:
+                if check_include:
+                    console.print(
+                        f"The check {check_include} does not exist in the file {filename}."
+                    )
+                if check_exclude:
+                    console.print(
+                        f"The check {check_exclude} does not exist in the file {filename}."
+                    )
+            else:
+                console.print(
+                    f"The file {filename} either does not exist or is not valid."
+                )
             console.print("Exiting now!")
             console.print()
-        # at least one of the checks did not pass or
-        # the provided file was not valid and thus
-        # the tool should return a non-zero exit
-        # code to designate some type of failure
+
         if checks_status is not True:
             sys.exit(FAILURE)
 
 
-# @app.command()
-# def generate(
-#     root: Path = typer.Argument(
-#         Path("."),
-#         help="Root directory of the assignment",
-#         exists=True,
-#         dir_okay=True,
-#         writable=True,
-#     ),
-#     paths: List[Path] = typer.Option(
-#         ["*"],
-#         help="Paths to recurse through and generate checks for",
-#         exists=False,
-#     ),
-# ):
-#     """Generate a gatorgrade.yml file."""
-#     targets = []
-#     for path in paths:
-#         targets.extend(glob.iglob(path.as_posix(), recursive=True))
-#     generate_config(targets, root.as_posix())
-
-
 if __name__ == "__main__":
     app()
diff --git a/gatorgrade/output/output.py b/gatorgrade/output/output.py
index 8fc94c5b..0f5a6501 100644
--- a/gatorgrade/output/output.py
+++ b/gatorgrade/output/output.py
@@ -198,8 +198,39 @@ def create_markdown_report_file(json: dict) -> str:
     return markdown_contents
 
 
+def truncate_report(report_output_data_json: dict, output_limit: int = None) -> str:
+    """Truncate the json report to the maximum number of lines allowed.
+
+    Args:
+        report_output_data_json: the json dictionary that will be used or converted to md
+        output_limit: the maximum number of lines to display in the output
+    """
+    # Convert the JSON dictionary to a formatted string
+    report_str = json.dumps(report_output_data_json, indent=4)
+
+    # Split the string into lines
+    report_lines = report_str.split("\n")
+
+    # If the number of lines is within the limit, return the full report
+    if output_limit is None or len(report_lines) <= output_limit:
+        return report_str
+
+    # Otherwise, truncate the report to the maximum number of lines
+    truncated_report_lines = report_lines[:output_limit]
+
+    # Convert the truncated report back to a JSON string
+    truncated_report_str = "\n".join(truncated_report_lines)
+
+    # Add a trailing ellipsis to indicate the report was truncated
+    truncated_report_str += "\n..."
+
+    return truncated_report_str
+
+
 def configure_report(
-    report_params: Tuple[str, str, str], report_output_data_json: dict
+    report_params: Tuple[str, str, str],
+    report_output_data_json: dict,
+    output_limit: int = None,
 ):
     """Put together the contents of the report depending on the inputs of the user.
 
@@ -209,6 +240,7 @@ def configure_report(
             report_params[1]: json or md
             report_params[2]: name of the file or env
         report_output_data: the json dictionary that will be used or converted to md
+        output_limit: the maximum number of characters to display in the output
     """
     report_format = report_params[0]
     report_type = report_params[1]
@@ -285,95 +317,90 @@ def write_json_or_md_file(file_name, content_type, content):
 
 
 def run_checks(
-    checks: List[Union[ShellCheck, GatorGraderCheck]], report: Tuple[str, str, str]
+    checks: List[Union[ShellCheck, GatorGraderCheck]],
+    report: Tuple[str, str, str],
+    output_limit: int = None,
+    check_status: str = None,
+    show_failures: bool = False,
+    check_include: str = None,
+    check_exclude: str = None,
 ) -> bool:
-    """Run shell and GatorGrader checks and display whether each has passed or failed.
-
-        Also, print a list of all failed checks with their diagnostics and a summary message that
-        shows the overall fraction of passed checks.
-
-    Args:
-        checks: The list of shell and GatorGrader checks to run.
-    """
     results = []
-    # run each of the checks
+
+    # Run checks and gather results
     for check in checks:
         result = None
         command_ran = None
-        # run a shell check; this means
-        # that it is going to run a command
-        # in the shell as a part of a check;
-        # store the command that ran in the
-        # field called run_command that is
-        # inside of a CheckResult object but
-        # not initialized in the constructor
+
+        # Run shell or GatorGrader checks
         if isinstance(check, ShellCheck):
             result = _run_shell_check(check)
             command_ran = check.command
             result.run_command = command_ran
-        # run a check that GatorGrader implements
         elif isinstance(check, GatorGraderCheck):
             result = _run_gg_check(check)
-            # check to see if there was a command in the
-            # GatorGraderCheck. This code finds the index of the
-            # word "--command" in the check.gg_args list if it
-            # is available (it is not available for all of
-            # the various types of GatorGraderCheck instances),
-            # and then it adds 1 to that index to get the actual
-            # command run and then stores that command in the
-            # result.run_command field that is initialized to
-            # an empty string in the constructor for CheckResult
             if "--command" in check.gg_args:
                 index_of_command = check.gg_args.index("--command")
-                index_of_new_command = int(index_of_command) + 1
+                index_of_new_command = index_of_command + 1
                 result.run_command = check.gg_args[index_of_new_command]
-        # there were results from running checks
-        # and thus they must be displayed
-        if result is not None:
-            result.print()
-            results.append(result)
-    # determine if there are failures and then display them
-    failed_results = list(filter(lambda result: not result.passed, results))
-    # print failures list if there are failures to print
-    # and print what ShellCheck command that Gatorgrade ran
-    if len(failed_results) > 0:
-        print("\n-~-  FAILURES  -~-\n")
-        for result in failed_results:
-            # main.console.print("This is a result")
-            # main.console.print(result)
-            result.print(show_diagnostic=True)
-            # this result is an instance of CheckResult
-            # that has a run_command field that is some
-            # value that is not the default of an empty
-            # string and thus it should be displayed;
-            # the idea is that displaying this run_command
-            # will give the person using Gatorgrade a way
-            # to quickly run the command that failed
-            if result.run_command != "":
-                rich.print(
-                    f"[blue]   → Run this command: [green]{result.run_command}\n"
-                )
-    # determine how many of the checks passed and then
-    # compute the total percentage of checks passed
-    passed_count = len(results) - len(failed_results)
-    # prevent division by zero if no results
-    if len(results) == 0:
-        percent = 0
+
+        if result:
+            # Filter checks by status if specified
+            if check_status == "pass" and result.passed:
+                results.append(result)
+            elif check_status == "fail" and not result.passed:
+                results.append(result)
+            elif not check_status:  # No specific status filter
+                results.append(result)
+
+    # Filter by include/exclude criteria
+    filtered_results = results
+    if check_include:
+        filtered_results = [
+            r for r in filtered_results if check_include in r.description
+        ]
+
+    if check_exclude:
+        filtered_results = [
+            r for r in filtered_results if check_exclude not in r.description
+        ]
+
+    # Print results based on the filtered results
+    if show_failures:
+        # Print only failures
+        for result in filtered_results:
+            if not result.passed:
+                result.print(show_diagnostic=True)
+                if result.run_command:
+                    rich.print(
+                        f"[blue]   → Run this command: [green]{result.run_command}\n"
+                    )
     else:
-        percent = round(passed_count / len(results) * 100)
-    # if the report is wanted, create output in line with their specifications
+        # Print all results
+        for result in filtered_results:
+            if not result.passed:
+                result.print(show_diagnostic=True)
+                if result.run_command:
+                    rich.print(
+                        f"[blue]   → Run this command: [green]{result.run_command}\n"
+                    )
+            else:
+                result.print()  # Print normally for passing checks
+
+    # Generate summary
+    failed_results = [r for r in results if not r.passed]
+    passed_count = len(results) - len(failed_results)
+    percent = round(passed_count / len(results) * 100) if results else 0
+
     if all(report):
         report_output_data = create_report_json(passed_count, results, percent)
         configure_report(report, report_output_data)
-    # compute summary results and display them in the console
+
     summary = f"Passed {passed_count}/{len(results)} ({percent}%) of checks for {Path.cwd().name}!"
     summary_color = "green" if passed_count == len(results) else "bright white"
     print_with_border(summary, summary_color)
-    # determine whether or not the run was a success or not:
-    # if all of the tests pass then the function returns True;
-    # otherwise the function must return False
-    summary_status = True if passed_count == len(results) else False
-    return summary_status
+
+    return passed_count == len(results)
 
 
 def print_with_border(text: str, rich_color: str):
diff --git a/poetry.lock b/poetry.lock
index fbff8607..812e73eb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -82,101 +82,116 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d3193f4a680c64b4b6a9115943538edb896edc190f0b222e73761716519268e"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cd70574b12bb8a4d2aaa0094515df2463cb429d8536cfb6c7ce983246983e5a6"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8465322196c8b4d7ab6d1e049e4c5cb460d0394da4a27d23cc242fbf0034b6b5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a9a8e9031d613fd2009c182b69c7b2c1ef8239a0efb1df3f7c8da66d5dd3d537"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:beb58fe5cdb101e3a055192ac291b7a21e3b7ef4f67fa1d74e331a7f2124341c"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:e06ed3eb3218bc64786f7db41917d4e686cc4856944f53d5bdf83a6884432e12"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:2e81c7b9c8979ce92ed306c249d46894776a909505d8f5a4ba55b14206e3222f"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:572c3763a264ba47b3cf708a44ce965d98555f618ca42c926a9c1616d8f34269"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:fd1abc0d89e30cc4e02e4064dc67fcc51bd941eb395c502aac3ec19fab46b519"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-win32.whl", hash = "sha256:3d47fa203a7bd9c5b6cee4736ee84ca03b8ef23193c0d1ca99b5089f72645c73"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-win_amd64.whl", hash = "sha256:10955842570876604d404661fbccbc9c7e684caf432c09c715ec38fbae45ae09"},
-    {file = "charset_normalizer-3.3.2-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:802fe99cca7457642125a8a88a084cef28ff0cf9407060f7b93dca5aa25480db"},
-    {file = "charset_normalizer-3.3.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:573f6eac48f4769d667c4442081b1794f52919e7edada77495aaed9236d13a96"},
-    {file = "charset_normalizer-3.3.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:549a3a73da901d5bc3ce8d24e0600d1fa85524c10287f6004fbab87672bf3e1e"},
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-    {file = "charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1ceae2f17a9c33cb48e3263960dc5fc8005351ee19db217e9b1bb15d28c02574"},
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-    {file = "charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:753f10e867343b4511128c6ed8c82f7bec3bd026875576dfd88483c5c73b2fd8"},
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-    {file = "charset_normalizer-3.3.2-cp311-cp311-win32.whl", hash = "sha256:7cd13a2e3ddeed6913a65e66e94b51d80a041145a026c27e6bb76c31a853c6ab"},
-    {file = "charset_normalizer-3.3.2-cp311-cp311-win_amd64.whl", hash = "sha256:663946639d296df6a2bb2aa51b60a2454ca1cb29835324c640dafb5ff2131a77"},
-    {file = "charset_normalizer-3.3.2-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:0b2b64d2bb6d3fb9112bafa732def486049e63de9618b5843bcdd081d8144cd8"},
-    {file = "charset_normalizer-3.3.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:ddbb2551d7e0102e7252db79ba445cdab71b26640817ab1e3e3648dad515003b"},
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 [[package]]
@@ -413,13 +428,13 @@ test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit",
 
 [[package]]
 name = "griffe"
-version = "1.3.2"
+version = "1.4.0"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -891,49 +906,54 @@ pytkdocs = ">=0.14"
 
 [[package]]
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-version = "1.2.0"
+version = "1.3.0"
 description = "shlex for windows"
 optional = false
 python-versions = ">=3.5"
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 [package.dependencies]
@@ -943,6 +963,7 @@ typing-extensions = ">=4.6.0"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+faster-cache = ["orjson"]
 install-types = ["pip"]
 mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
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 [package.dependencies]
 pyyaml = "*"
 
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+    {file = "rapidfuzz-3.9.7.tar.gz", hash = "sha256:f1c7296534c1afb6f495aa95871f14ccdc197c6db42965854e483100df313030"},
+]
+
+[package.extras]
+full = ["numpy"]
+
 [[package]]
 name = "requests"
 version = "2.32.3"
@@ -1371,13 +1512,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rich"
-version = "13.9.2"
+version = "13.9.3"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.8.0"
 files = [
-    {file = "rich-13.9.2-py3-none-any.whl", hash = "sha256:8c82a3d3f8dcfe9e734771313e606b39d8247bb6b826e196f4914b333b743cf1"},
-    {file = "rich-13.9.2.tar.gz", hash = "sha256:51a2c62057461aaf7152b4d611168f93a9fc73068f8ded2790f29fe2b5366d0c"},
+    {file = "rich-13.9.3-py3-none-any.whl", hash = "sha256:9836f5096eb2172c9e77df411c1b009bace4193d6a481d534fea75ebba758283"},
+    {file = "rich-13.9.3.tar.gz", hash = "sha256:bc1e01b899537598cf02579d2b9f4a415104d3fc439313a7a2c165d76557a08e"},
 ]
 
 [package.dependencies]
@@ -1478,13 +1619,13 @@ test = ["PyYAML", "cogapp", "pytest", "pytest-icdiff", "ruff"]
 
 [[package]]
 name = "taskipy"
-version = "1.13.0"
+version = "1.14.0"
 description = "tasks runner for python projects"
 optional = false
 python-versions = "<4.0,>=3.6"
 files = [
-    {file = "taskipy-1.13.0-py3-none-any.whl", hash = "sha256:56f42b7e508d9aed2c7b6365f8d3dab62dbd0c768c1ab606c819da4fc38421f7"},
-    {file = "taskipy-1.13.0.tar.gz", hash = "sha256:2b52f0257958fed151f1340f7de93fcf0848f7a358ad62ba05c31c2ca04f89fe"},
+    {file = "taskipy-1.14.0-py3-none-any.whl", hash = "sha256:29040d9a8038170602feb71792bdef5203720ed30f595304aee843625892452b"},
+    {file = "taskipy-1.14.0.tar.gz", hash = "sha256:5d9631c29980481d59858f0a100ed3200cf7468ca8c0540ef19388586485532d"},
 ]
 
 [package.dependencies]
@@ -1507,6 +1648,20 @@ files = [
 [package.extras]
 tests = ["pytest", "pytest-cov"]
 
+[[package]]
+name = "thefuzz"
+version = "0.22.1"
+description = "Fuzzy string matching in python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "thefuzz-0.22.1-py3-none-any.whl", hash = "sha256:59729b33556850b90e1093c4cf9e618af6f2e4c985df193fdf3c5b5cf02ca481"},
+    {file = "thefuzz-0.22.1.tar.gz", hash = "sha256:7138039a7ecf540da323792d8592ef9902b1d79eb78c147d4f20664de79f3680"},
+]
+
+[package.dependencies]
+rapidfuzz = ">=3.0.0,<4.0.0"
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -1758,4 +1913,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<4.0"
-content-hash = "e7e536d8fa225ea4fc1090ddbb2a2a9cd47b6d924ea46ef835d05528aa293f5a"
+content-hash = "2386cce681809e63d10fe3c366fa1007daa6876b2143a42a6385701a2e0922ab"
diff --git a/pyproject.toml b/pyproject.toml
index 36a44540..72bd30df 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [tool.poetry]
 name = "gatorgrade"
 version = "0.7.0"
+
 description = "GatorGrade executes GatorGrader checks!"
 authors = ["Michael Abraham", "Jacob Allebach", "Liam Black", "Katherine Burgess", "Yanqiao Chen", "Ochirsaikhan Davaajambal", "Tuguldurnemekh Gantulga", "Anthony Grant-Cook", "Dylan Holland", "Gregory M. Kapfhammer", "Peyton Kelly", "Luke Lacaria", "Lauren Nevill", "Rebekah Rudd", "Jack Turner", "Daniel Ullrich", "Garrison Vanzin", "Rian Watson"]
 readme = "README.md"
@@ -24,6 +25,7 @@ mkdocstrings = {extras = ["python"], version = "^0.18.1"}
 mkdocs-gen-files = "^0.3.4"
 mkdocs-typer = "^0.0.2"
 mkdocs-literate-nav = "^0.4.1"
+thefuzz = "^0.22.1"
 toml = "^0.10.2"
 pytest-sugar = "^0.9.5"
 pytest-randomly = "^3.12.0"
diff --git a/tests/test_assignment/insights.json b/tests/test_assignment/insights.json
index 30424089..361349b0 100644
--- a/tests/test_assignment/insights.json
+++ b/tests/test_assignment/insights.json
@@ -1 +1,40 @@
-{"amount correct": 3, "percentage score": 100, "checks": {"0": {"description": "Complete all TODOs", "status": true, "Fragment": "TODO", "Count": "0", "Directory": "src", "File": "hello-world.py"}, "1": {"description": "Use an if statement", "status": true, "Count": "1", "Directory": "src", "File": "hello-world.py"}, "2": {"description": "Complete all TODOs", "status": true, "Fragment": "TODO", "Count": "0", "Directory": "src", "File": "reflection.md"}}}
\ No newline at end of file
+{
+    "amount_correct": 3,
+    "percentage_score": 100,
+    "report_time": "2024-07-09 22:05:47",
+    "checks": [
+        {
+            "description": "Complete all TODOs",
+            "check": "MatchFileFragment",
+            "options": {
+                "fragment": "TODO",
+                "count": 0,
+                "exact": true
+            },
+            "status": true,
+            "path": "src/hello-world.py"
+        },
+        {
+            "description": "Use an if statement",
+            "check": "MatchFileRegex",
+            "options": {
+                "regex": "if .*?:",
+                "count": 1,
+                "exact": false
+            },
+            "status": true,
+            "path": "src/hello-world.py"
+        },
+        {
+            "description": "Complete all TODOs",
+            "check": "MatchFileFragment",
+            "options": {
+                "fragment": "TODO",
+                "count": 0,
+                "exact": true
+            },
+            "status": true,
+            "path": "src/reflection.md"
+        }
+    ]
+}
\ No newline at end of file
diff --git a/tests/test_assignment/insights.md b/tests/test_assignment/insights.md
index 831811a4..615efab7 100644
--- a/tests/test_assignment/insights.md
+++ b/tests/test_assignment/insights.md
@@ -1,14 +1,12 @@
 # Gatorgrade Insights
 
-**Amount Correct:** 3
-**Percentage Correct:** 100
+**Project Name:** test_assignment
+**Amount Correct:** 3/3 (100%)
 
 ## Passing Checks
 
-### ✓ Complete all TODOs
-
-### ✓ Use an if statement
-
-### ✓ Complete all TODOs
+- [x] Complete all TODOs
+- [x] Use an if statement
+- [x] Complete all TODOs
 
 ## Failing Checks
diff --git a/tests/test_assignment/src/hello-world.py b/tests/test_assignment/src/hello-world.py
index 64b95a5e..7793882b 100644
--- a/tests/test_assignment/src/hello-world.py
+++ b/tests/test_assignment/src/hello-world.py
@@ -2,6 +2,7 @@
 
 
 def greet(person):
+    # TODO
     """Say hello to someone."""
     if person:
         print(f"Hello, {person}")
diff --git a/tests/test_generate.py b/tests/test_generate.py
index 45715a95..444185f7 100644
--- a/tests/test_generate.py
+++ b/tests/test_generate.py
@@ -1,5 +1,6 @@
 """This module tests the generate.py functionality"""
 
+
 import pytest
 import typer
 
@@ -170,3 +171,158 @@ def test_generate_should_throw_an_error_when_none_of_user_provided_files_exist(
     assert not file.is_file()
     assert "'gatorgrade.yml' is NOT generated" in err
     assert exc_info.value.exit_code == 1
+
+
+def test_run_path_unify(tmp_path):
+    """Check if the function correctly appends a separator to run_path if it doesn't end with one"""
+
+    # Given an assignment directory that contains all of the folders and files that user inputted when calling generate.py
+    root_directory = tmp_path / "Practical-01"
+    root_directory.mkdir()
+
+    src_directory = root_directory / "src"
+    src_directory.mkdir()
+
+    main_py = src_directory / "main.py"
+    main_py.write_text("import sys")
+
+    test_file_1 = src_directory / "test_file_1.py"
+    test_file_1.write_text("import sys")
+
+    input_directory = src_directory / "input"
+    input_directory.mkdir()
+    input_file = input_directory / "input.txt"
+    input_file.write_text("Test input")
+
+    output_directory = src_directory / "output"
+    output_directory.mkdir()
+    output_file = output_directory / "output.txt"
+    output_file.write_text("Test output")
+
+    writing_directory = root_directory / "writing"
+    writing_directory.mkdir()
+    reflection_file = writing_directory / "reflection.md"
+    reflection_file.write_text("# Reflection on Practical 01")
+
+    readme_file = root_directory / "README.md"
+    readme_file.write_text("# Practical 01")
+
+    # Verify that the generate_config function works correctly
+    generate_config(["src", "writing", "README.md"], str(root_directory))
+
+    # Then the "gatorgrade.yml" contains correct paths to user inputted directories and files
+    file = root_directory / "gatorgrade.yml"
+    file_text = file.open().read()
+
+    # assert run_path == expected_run_path
+
+    assert "src/input/input.txt" in file_text
+    assert "src/output/output.txt" in file_text
+    assert "src/main.py" in file_text
+    assert "src/test_file_1.py" in file_text
+    assert "README.md" in file_text
+
+
+def test_ignore_folder_starting_with_double_underscore(tmp_path):
+    """Ignore folder and file starting with double underscore"""
+
+    # Given an assignment directory that contains all of the folders
+    # and files that user inputted when calling generate.py
+    root_directory = tmp_path / "Practical-01"
+    root_directory.mkdir()
+
+    src_directory = root_directory / "src"
+    src_directory.mkdir()
+
+    task_directory = root_directory / "__task"
+    task_directory.mkdir()
+
+    main_py = src_directory / "main.py"
+    main_py.write_text("import sys")
+
+    test_file_1 = src_directory / "test_file_1.py"
+    test_file_1.write_text("import sys")
+
+    input_directory = src_directory / "input"
+    input_directory.mkdir()
+    input_file = input_directory / "__input.txt"
+    input_file.write_text("Test input")
+
+    output_directory = src_directory / "__output"
+    output_directory.mkdir()
+    output_file = output_directory / "output.txt"
+    output_file.write_text("Test output")
+
+    writing_directory = root_directory / "writing"
+    writing_directory.mkdir()
+    reflection_file = writing_directory / "reflection.md"
+    reflection_file.write_text("# Reflection on Practical 01")
+
+    readme_file = root_directory / "README.md"
+    readme_file.write_text("# Practical 01")
+
+    # When we call the modularized version of "generate.py" with two arguments
+    generate_config(["src", "Practical-01", "README.md"], str(root_directory))
+
+    # Then the "gatorgrade.yml" contains correct paths to user inputted directories and files
+    file = root_directory / "gatorgrade.yml"
+    file_text = file.open().read()
+
+    assert "__task" not in file_text
+    assert "src/input/__input.txt" not in file_text
+    assert "src/__output" not in file_text
+
+
+def test_ignore_folder_starting_with_single_dot(tmp_path):
+    """Ignore folder starting with a single dot and not with double dot"""
+
+    # Given an assignment directory that contains all of the folders
+    # and files that user inputted when calling generate.py
+    root_directory = tmp_path / "Practical-01"
+    root_directory.mkdir()
+
+    src_directory = root_directory / "src"
+    src_directory.mkdir()
+
+    task_directory = root_directory / ".task"
+    task_directory.mkdir()
+
+    main_py = src_directory / "main.py"
+    main_py.write_text("import sys")
+
+    test_file_1 = src_directory / "test_file_1.py"
+    test_file_1.write_text("import sys")
+
+    input_directory = src_directory / "input"
+    input_directory.mkdir()
+    input_file = input_directory / ".input.txt"
+    input_file.write_text("Test input")
+
+    output_directory = src_directory / "output"
+    output_directory.mkdir()
+    output_file = output_directory / "output.txt"
+    output_file.write_text("Test output")
+
+    writing_directory = root_directory / "writing"
+    writing_directory.mkdir()
+    reflection_file = writing_directory / "reflection.md"
+    reflection_file.write_text("# Reflection on Practical 01")
+
+    readme_file = root_directory / "README.md"
+    readme_file.write_text("# Practical 01")
+
+    # When we call the modularized version of "generate.py" with two arguments
+    generate_config(
+        ["src", "task", "Practical-01", "README.md", ".."], str(root_directory)
+    )
+
+    # Then the "gatorgrade.yml" contains correct paths to user inputted directories and files
+    file = root_directory / "gatorgrade.yml"
+    file_text = file.open().read()
+
+    assert ".task" not in file_text
+    assert "src" in file_text
+    assert "src/input/.input.txt" not in file_text
+
+
+# pytest.main()
diff --git a/tests/test_main.py b/tests/test_main.py
index 22551294..3d1f424c 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -10,9 +10,11 @@
 import io
 import os
 
+import subprocess
+import sys
+
 import pytest
 from typer.testing import CliRunner
-
 from gatorgrade import main
 
 runner = CliRunner()
@@ -109,9 +111,27 @@ def test_full_integration_creates_valid_output(
     # ✓  Complete all TODOs
 
     result = runner.invoke(main.app)
-
     print(result.stdout)
 
     assert result.exit_code == 0
     for output, freq in expected_output_and_freqs:
         assert result.stdout.count(output) == freq
+
+def test_default_run_invalid_output():
+    '''Test the default run with the assumption that the default configuration file is invalid.'''
+    result = runner.invoke(main.app)
+    assert result.exit_code == main.FAILURE
+    assert f"The file {main.FILE} either does not exist or is not valid." in result.output
+
+def test_specified_filename_invalid_output():
+    '''Test the run with a specified filename that is invalid.'''
+    result = runner.invoke(main.app, ["--config", "nonexistent.yml"])
+    assert result.exit_code == main.FAILURE
+    assert "The file nonexistent.yml either does not exist or is not valid." in result.output
+
+def test_entry_point():
+    """Test the entry point of the script to ensure it runs as expected."""
+    result = subprocess.run([sys.executable, "gatorgrade/main.py"], capture_output=True, text=True)
+    assert result.returncode == main.FAILURE
+    assert f"The file {main.FILE} either does not exist or is not valid." in result.stdout
+