From 5dc3d27b5f20dba88667167a1d11484ba8d3f514 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 12:28:11 +0000
Subject: [PATCH 01/14] remove variables from entry-point

---
 dafni/main_dafni.py | 73 ++++++++++++++-------------------------------
 1 file changed, 23 insertions(+), 50 deletions(-)

diff --git a/dafni/main_dafni.py b/dafni/main_dafni.py
index 4cf75cb6..3987a6d1 100644
--- a/dafni/main_dafni.py
+++ b/dafni/main_dafni.py
@@ -13,6 +13,7 @@
 from causal_testing.testing.causal_test_outcome import Positive, Negative, NoEffect, SomeEffect
 from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
 from causal_testing.json_front.json_class import JsonUtility
+from causal_testing.specification.causal_dag import CausalDAG
 
 
 class ValidationError(Exception):
@@ -40,12 +41,6 @@ def get_args(test_args=None) -> argparse.Namespace:
         "-i", "--ignore_cycles", action="store_true", help="Whether to ignore cycles in the DAG.", default=False
     )
 
-    parser.add_argument(
-        "--variables_path",
-        required=True,
-        help="Input configuration file path " "containing the predefined variables (.json)",
-    )
-
     parser.add_argument(
         "--dag_path",
         required=True,
@@ -71,8 +66,6 @@ def get_args(test_args=None) -> argparse.Namespace:
 
     # Convert these to Path objects for main()
 
-    args.variables_path = Path(args.variables_path)
-
     args.tests_path = Path(args.tests_path)
 
     if args.dag_path is not None:
@@ -91,53 +84,33 @@ def get_args(test_args=None) -> argparse.Namespace:
     return args
 
 
-def read_variables(variables_path: Path) -> FileNotFoundError | dict:
+def parse_variables(causal_dag: CausalDAG) -> tuple:
     """
-    Function to read the variables.json file specified by the user
-    :param variables_path: A Path object of the user-specified file path
+    Function to validate the variables defined in the causal tests
+    :param causal_dag: an instancce of the CausalDAG class containing the relationships and variables (as attribtutes)
     :returns:
-            - dict - A valid dictionary consisting of the causal tests
+    - Tuple containing the inputs, outputs and constraints to pass into the modelling scenario
     """
-    if not variables_path.exists() or variables_path.is_dir():
-        print(f"JSON file not found at the specified location: {variables_path}")
 
-        raise FileNotFoundError
+    inputs = [
+        Input(node, eval(eval(attributes["datatype"])))
+        for node, attributes in causal_dag.graph.nodes(data=True)
+        if eval(attributes["typestring"]) == "input"
+    ]
 
-    with variables_path.open("r") as file:
-        inputs = json.load(file)
+    constraints = set()
 
-    return inputs
+    for (node, attributes), input_var in zip(causal_dag.graph.nodes(data=True), inputs):
 
+        if "constraint" in attributes:
 
-def validate_variables(data_dict: dict) -> tuple:
-    """
-    Function to validate the variables defined in the causal tests
-    :param data_dict: A dictionary consisting of the pre-defined variables for the causal tests
-    :returns:
-    - Tuple containing the inputs, outputs and constraints to pass into the modelling scenario
-    """
-    if data_dict["variables"]:
-        variables = data_dict["variables"]
-
-        inputs = [
-            Input(variable["name"], eval(variable["datatype"]))
-            for variable in variables
-            if variable["typestring"] == "Input"
-        ]
-
-        outputs = [
-            Output(variable["name"], eval(variable["datatype"]))
-            for variable in variables
-            if variable["typestring"] == "Output"
-        ]
-
-        constraints = set()
-
-        for variable, input_var in zip(variables, inputs):
-            if "constraint" in variable:
-                constraints.add(input_var.z3 == variable["constraint"])
-    else:
-        raise ValidationError("Cannot find the variables defined by the causal tests.")
+            constraints.add(input_var.z3 == attributes["constraint"])
+
+    outputs = [
+        Output(node, eval(eval(attributes["datatype"])))
+        for node, attributes in causal_dag.graph.nodes(data=True)
+        if eval(attributes["typestring"]) == "output"
+    ]
 
     return inputs, outputs, constraints
 
@@ -153,11 +126,11 @@ def main():
 
         data_frame = pd.concat([pd.read_csv(d) for d in args.data_path])
 
-        # Step 1: Read in the JSON input/output variables and parse io arguments
+        # Step 1: Read in the dag and parse the variables from the .dot file
 
-        variables_dict = read_variables(args.variables_path)
+        causal_dag = CausalDAG(args.dag_path)
 
-        inputs, outputs, constraints = validate_variables(variables_dict)
+        inputs, outputs, constraints = parse_variables(causal_dag)
 
         # Step 2: Set up the modeling scenario and estimator
 

From b929564e11f424b63b3f440b86f75fff7d6706c1 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 12:29:10 +0000
Subject: [PATCH 02/14] update sample dag file to include the variables as node
 attributes

---
 dafni/data/inputs/dag.dot | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/dafni/data/inputs/dag.dot b/dafni/data/inputs/dag.dot
index 43628817..67b9007b 100644
--- a/dafni/data/inputs/dag.dot
+++ b/dafni/data/inputs/dag.dot
@@ -1,7 +1,12 @@
 digraph CausalDAG {
     rankdir=LR;
-    "vaccine" -> "cum_vaccinations";
-    "vaccine" -> "cum_vaccinated";
-    "vaccine" -> "cum_infections";
-    "max_doses";
+    vaccine [datatype="int", typestring="input"];
+    cum_vaccinations [datatype="int", typestring="output"];
+    cum_vaccinated [datatype="int", typestring="output"];
+    cum_infections [datatype="int", typestring="output"];
+    max_doses [datatype="int", typestring="output"];
+    vaccine -> cum_vaccinations;
+    vaccine -> cum_vaccinated;
+    vaccine -> cum_infections;
+    max_doses;
 }
\ No newline at end of file

From 354fd3e0bf67ef4d1c642362b3242eb74de53011 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 12:29:35 +0000
Subject: [PATCH 03/14] update Dockerfile for dafni image

---
 dafni/Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/dafni/Dockerfile b/dafni/Dockerfile
index 8969ad3f..a5caec83 100644
--- a/dafni/Dockerfile
+++ b/dafni/Dockerfile
@@ -24,10 +24,9 @@ COPY --chown=nobody ./dafni/data/inputs ./data/inputs
 RUN pip install causal-testing-framework --no-cache-dir
 
 #For local testing purposes
-ENV VARIABLES_PATH=./data/inputs/variables.json \
-    CAUSAL_TESTS=./data/inputs/causal_tests.json \
+ENV CAUSAL_TESTS=./data/inputs/causal_tests.json \
     DATA_PATH=./data/inputs/runtime_data.csv \
     DAG_PATH=./data/inputs/dag.dot
 
 # Define the entrypoint/commands
-CMD python main_dafni.py --variables_path $VARIABLES_PATH --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $CAUSAL_TESTS
+CMD python main_dafni.py --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $CAUSAL_TESTS

From 0e53b47a0a639ee11e225ee715d1129770095b31 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 12:29:51 +0000
Subject: [PATCH 04/14] update dafni model definition

---
 dafni/model_definition.yaml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/dafni/model_definition.yaml b/dafni/model_definition.yaml
index 901e2570..a44c0e3d 100644
--- a/dafni/model_definition.yaml
+++ b/dafni/model_definition.yaml
@@ -49,14 +49,6 @@ spec:
         path: inputs/
         required: true
 
-      - name: Variables
-        description: >
-          A .JSON file containing the input variables to be used
-        default:
-          - 02e755c8-952b-461a-a914-4f4ffbe2edf1
-        path: inputs/
-        required: true
-
   outputs:
       datasets:
         - name: causal_test_results.json

From 4497da2f9305afbd4bc56508550dab116e1335ab Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 12:30:24 +0000
Subject: [PATCH 05/14] update README.md

---
 dafni/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dafni/README.md b/dafni/README.md
index 29833d61..40e2ae42 100644
--- a/dafni/README.md
+++ b/dafni/README.md
@@ -10,8 +10,8 @@ to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
 - `data` contains two sub-folders (the structure is important for DAFNI).
   - `inputs` is a folder that contains the input files that are (separately) uploaded to DAFNI.
     - `causal_tests.json` is a JSON file that contains the causal tests.
-    - `variables.json` is a JSON file that contains the variables and constraints to be used.
-    - `dag.dot` is a dot file that contains the directed acyclc graph (dag) file.
+    - `dag.dot` is a dot file that contains the directed acyclc graph (dag) file, 
+       including the variables (and constraints if necessary) as node attributes.
     - `runtime_data.csv` is a csv file that contains the runtime data.
 
   - `outputs` is a folder where the `causal_tests_results.json` output file is created.

From fb83d65afcdb00587eb7886ef5ad50d47260eef8 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 6 Dec 2024 16:18:37 +0000
Subject: [PATCH 06/14] turned main_dafni.py into a module

---
 dafni/Dockerfile              | 16 +++++++---------
 dafni/docker-compose.yaml     |  4 ++--
 dafni/src/__init__.py         |  0
 dafni/{ => src}/main_dafni.py |  0
 4 files changed, 9 insertions(+), 11 deletions(-)
 create mode 100644 dafni/src/__init__.py
 rename dafni/{ => src}/main_dafni.py (100%)

diff --git a/dafni/Dockerfile b/dafni/Dockerfile
index a5caec83..850417cf 100644
--- a/dafni/Dockerfile
+++ b/dafni/Dockerfile
@@ -8,25 +8,23 @@ ENV PYTHONDONTWRITEBYTECODE=1
 ## from crashing without emitting any logs due to buffering
 ENV PYTHONUNBUFFERED=1
 
-#Label maintainer
+# Label maintainer
 LABEL maintainer="Dr. Farhad Allian - The University of Sheffield"
 
 # Create a folder for the source code/outputs
 RUN mkdir -p ./causal_testing
 RUN mkdir -p ./data/outputs
 
-# Copy the source code and test files from build into the container
-COPY --chown=nobody  ../causal_testing ./causal_testing
-COPY --chown=nobody ./dafni/main_dafni.py ./
+# Copy the source code from local rootand test files from build into the container
+COPY --chown=nobody  ./causal_testing ./causal_testing
+COPY --chown=nobody ./dafni/src/ ./src
 COPY --chown=nobody ./dafni/data/inputs ./data/inputs
 
 # Install core dependencies using PyPi
 RUN pip install causal-testing-framework --no-cache-dir
 
-#For local testing purposes
-ENV CAUSAL_TESTS=./data/inputs/causal_tests.json \
-    DATA_PATH=./data/inputs/runtime_data.csv \
-    DAG_PATH=./data/inputs/dag.dot
+# Set the PYTHONPATH environment variable to include the /src directory
+ENV PYTHONPATH="/src:${PYTHONPATH}"
 
 # Define the entrypoint/commands
-CMD python main_dafni.py --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $CAUSAL_TESTS
+CMD python -m main_dafni --dag_path $DAG_PATH --data_path $DATA_PATH --tests_path $TESTS_PATH
diff --git a/dafni/docker-compose.yaml b/dafni/docker-compose.yaml
index 9a38d1c4..a894fefb 100644
--- a/dafni/docker-compose.yaml
+++ b/dafni/docker-compose.yaml
@@ -3,8 +3,8 @@ services:
   causal-testing-framework:
     build:
       context: ../
-      dockerfile: ./dafni/Dockerfile
+      dockerfile: dafni/Dockerfile
     env_file:
       - .env
     volumes:
-      - .:/usr/src/app
+      - ./dafni:/usr/src/
diff --git a/dafni/src/__init__.py b/dafni/src/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/dafni/main_dafni.py b/dafni/src/main_dafni.py
similarity index 100%
rename from dafni/main_dafni.py
rename to dafni/src/main_dafni.py

From 5b736b8b3cbb043a04baf2ce0428d2d38bd55610 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 09:56:14 +0000
Subject: [PATCH 07/14] final touches to main_dafni.py

---
 dafni/src/main_dafni.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dafni/src/main_dafni.py b/dafni/src/main_dafni.py
index 3987a6d1..245ac41a 100644
--- a/dafni/src/main_dafni.py
+++ b/dafni/src/main_dafni.py
@@ -72,7 +72,7 @@ def get_args(test_args=None) -> argparse.Namespace:
         args.dag_path = Path(args.dag_path)
 
     if args.output_path is None:
-        args.output_path = "./data/outputs/causal_tests_results.json"
+        args.output_path = "data/outputs/causal_tests_results.json"
 
         Path(args.output_path).parent.mkdir(exist_ok=True)
 
@@ -86,7 +86,7 @@ def get_args(test_args=None) -> argparse.Namespace:
 
 def parse_variables(causal_dag: CausalDAG) -> tuple:
     """
-    Function to validate the variables defined in the causal tests
+    Function to parse and validate the variables defined in the causal dag.
     :param causal_dag: an instancce of the CausalDAG class containing the relationships and variables (as attribtutes)
     :returns:
     - Tuple containing the inputs, outputs and constraints to pass into the modelling scenario

From ea46bdc600972a5b8b6930f8e2d14c19be290548 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 09:57:35 +0000
Subject: [PATCH 08/14] add: tests for main_dafni.py

---
 dafni/tests/tests_main_dafni.py | 154 ++++++++++++++++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 dafni/tests/tests_main_dafni.py

diff --git a/dafni/tests/tests_main_dafni.py b/dafni/tests/tests_main_dafni.py
new file mode 100644
index 00000000..19f0e89d
--- /dev/null
+++ b/dafni/tests/tests_main_dafni.py
@@ -0,0 +1,154 @@
+import unittest
+from unittest.mock import patch
+import argparse
+from pathlib import Path
+from causal_testing.testing.causal_test_outcome import Positive, Negative, NoEffect, SomeEffect
+from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
+from causal_testing.specification.causal_dag import CausalDAG
+from causal_testing.specification.variable import Input, Output
+from main_dafni import get_args, parse_variables
+
+# Base directory (relative to the current test file location)
+BASE_DIR = Path(__file__).resolve().parent.parent  # Points to ./dafni
+DATA_DIR = BASE_DIR / "data"  # Points to ./dafni/data
+
+
+class TestGetArgs(unittest.TestCase):
+    """Test the argparse functionality of the DAFNI entrypoint."""
+
+    @patch("argparse.ArgumentParser.parse_args")
+    def test_get_args_with_all_arguments(self, mock_parse_args):
+        """Ensure all arguments work as expected"""
+
+        mock_parse_args.return_value = argparse.Namespace(
+            data_path=[str(DATA_DIR / "inputs/runtime_data.csv")],
+            tests_path=str(DATA_DIR / "inputs/causal_tests.json"),
+            ignore_cycles=True,
+            dag_path=str(DATA_DIR / "inputs/dag.dot"),
+            output_path=str(DATA_DIR / "outputs/causal_test_results.json"),
+            f=False,
+            w=False,
+        )
+
+        args = get_args()
+
+        if args.output_path is None:
+            self.assertEqual(args.output_path, Path(DATA_DIR / "outputs/causal_test_results.json"))
+        else:
+            self.assertIsInstance(args.output_path, Path)
+
+        self.assertEqual(args.data_path, [str(DATA_DIR / "inputs/runtime_data.csv")])
+        self.assertEqual(args.tests_path, Path(DATA_DIR / "inputs/causal_tests.json"))
+        self.assertEqual(args.dag_path, Path(DATA_DIR / "inputs/dag.dot"))
+        self.assertIsInstance(args.f, bool)
+        self.assertIsInstance(args.w, bool)
+        self.assertIsInstance(args.ignore_cycles, bool)
+
+
+class TestParseVariables(unittest.TestCase):
+    """Test the parse variables functionality of the DAFNI entrypoint."""
+
+    @classmethod
+    def setUpClass(cls):
+        """Set up class method for the Causal Dag."""
+
+        cls.causal_dag = CausalDAG(str(DATA_DIR / "inputs/dag.dot"))
+
+    def test_causal_dag_instance(self):
+        """Test if the input is an instance of CausalDAG."""
+        self.assertIsInstance(self.causal_dag, CausalDAG)
+
+    def test_dag_attributes(self):
+        """Test if all attributes in the DAG are strings."""
+        for _, attributes in self.causal_dag.graph.nodes(data=True):
+            for key, value in attributes.items():
+                self.assertIsInstance(value, str)
+                self.assertIsInstance(key, str)
+
+    def test_dag_inputs_outputs_constraints(self):
+        """Test the DAG inputs, outputs and constraints."""
+
+        try:
+            inputs, outputs, constraints = parse_variables(self.causal_dag)
+
+            for _input, _output, _constraint in zip(inputs, outputs, constraints):
+                # Assert each input is an Input, Output or Set object
+                self.assertIsInstance(_input, Input)
+                self.assertIsInstance(_output, Output)
+                self.assertIsInstance(constraints, set)
+
+        except ValueError as e:
+            self.fail(f"Unable to parse variables: {e}")
+
+
+class TestMain(unittest.TestCase):
+    """Test the main entrypoint."""
+
+    def test_estimator(self):
+        """Test estimators currently supported on DAFNI."""
+
+        estimators = {"LinearRegressionEstimator": LinearRegressionEstimator}
+
+        self.assertIsInstance(estimators, dict, "Estimators must be a dictionary.")
+
+        self.assertIn(
+            "LinearRegressionEstimator", estimators,
+            "The key 'LinearRegressionEstimator' must exist in the dictionary."
+        )
+
+        self.assertEqual(
+            estimators["LinearRegressionEstimator"],
+            LinearRegressionEstimator,
+            "The estimator should be LinearRegression.",
+        )
+
+        self.assertNotIn("LogisticRegressionEstimator", estimators,
+                         "The dictionary should not contain other estimators.")
+
+    def test_expected_outcome_effects_keys(self):
+        """Check that the dictionary contains these keys only for DAFNI."""
+
+        expected_outcome_effects = {
+            "Positive": Positive(),
+            "Negative": Negative(),
+            "NoEffect": NoEffect(),
+            "SomeEffect": SomeEffect(),
+        }
+
+        expected_keys = ["Positive", "Negative", "NoEffect", "SomeEffect"]
+
+        actual_keys = list(expected_outcome_effects.keys())
+
+        self.assertEqual(sorted(actual_keys), sorted(expected_keys),
+                         "The dictionary keys do not match the expected keys.")
+
+    def test_expected_outcome_effects_values(self):
+        """Check that the dictionary contains the correct instances for DAFNI."""
+
+        expected_outcome_effects = {
+            "Positive": Positive(),
+            "Negative": Negative(),
+            "NoEffect": NoEffect(),
+            "SomeEffect": SomeEffect(),
+        }
+
+        self.assertIsInstance(
+            expected_outcome_effects["Positive"],
+            Positive,
+            "The value for 'Positive' should be an instance of Positive.",
+        )
+        self.assertIsInstance(
+            expected_outcome_effects["Negative"],
+            Negative,
+            "The value for 'Negative' should be an instance of Negative.",
+        )
+        self.assertIsInstance(
+            expected_outcome_effects["NoEffect"],
+            NoEffect,
+            "The value for 'NoEffect' should be an instance of NoEffect.",
+        )
+        self.assertIsInstance(
+            expected_outcome_effects["SomeEffect"],
+            SomeEffect,
+            "The value for 'SomeEffect' should be an instance of SomeEffect.",
+        )

From 005d2da97b25fd6e5fb62029d60c69e726489e24 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 11:00:53 +0000
Subject: [PATCH 09/14] update: tests to dafni workflow

---
 .github/workflows/publish-to-dafni.yaml | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish-to-dafni.yaml b/.github/workflows/publish-to-dafni.yaml
index 424a0fe6..f407cc37 100644
--- a/.github/workflows/publish-to-dafni.yaml
+++ b/.github/workflows/publish-to-dafni.yaml
@@ -38,14 +38,25 @@ jobs:
         with:
           python-version: '3.10'
 
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install causal-testing-framework -e .[dev]
+          python -m pip install dafni-cli
+
+      - name: Run tests before uploading
+        id: tests
+        run: |
+          python -m pytest ./dafni/tests 
+
       - name: Build the container
+        if: steps.tests.outcome == 'success'
         run: |
           docker build -t ctf:${{ env.VERSION }} -f ./dafni/Dockerfile .
           docker save ctf:${{ env.VERSION }} | gzip > ctf-dafni-${{ env.VERSION }}.tar.gz
 
-      - name: Install DAFNI-CLI and log in
+      - name: Log into DAFNI
         run: |
-          python -m pip install dafni-cli
           dafni login
 
       - name: Upload to DAFNI

From 9a4539288ef2f3b84b41481fff108ee8b1519321 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 11:54:43 +0000
Subject: [PATCH 10/14] fix: typo in Dockerfile

---
 dafni/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dafni/Dockerfile b/dafni/Dockerfile
index 850417cf..b94d045c 100644
--- a/dafni/Dockerfile
+++ b/dafni/Dockerfile
@@ -15,7 +15,7 @@ LABEL maintainer="Dr. Farhad Allian - The University of Sheffield"
 RUN mkdir -p ./causal_testing
 RUN mkdir -p ./data/outputs
 
-# Copy the source code from local rootand test files from build into the container
+# Copy the source code from local root and test files from build into the container
 COPY --chown=nobody  ./causal_testing ./causal_testing
 COPY --chown=nobody ./dafni/src/ ./src
 COPY --chown=nobody ./dafni/data/inputs ./data/inputs

From 456048cd919cb997435c8890c6bf24614f099cd9 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 13:02:16 +0000
Subject: [PATCH 11/14] fix: default in ignore_cycles tests_main_dafni.py

---
 dafni/tests/tests_main_dafni.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dafni/tests/tests_main_dafni.py b/dafni/tests/tests_main_dafni.py
index 19f0e89d..821d9733 100644
--- a/dafni/tests/tests_main_dafni.py
+++ b/dafni/tests/tests_main_dafni.py
@@ -23,7 +23,7 @@ def test_get_args_with_all_arguments(self, mock_parse_args):
         mock_parse_args.return_value = argparse.Namespace(
             data_path=[str(DATA_DIR / "inputs/runtime_data.csv")],
             tests_path=str(DATA_DIR / "inputs/causal_tests.json"),
-            ignore_cycles=True,
+            ignore_cycles=False,
             dag_path=str(DATA_DIR / "inputs/dag.dot"),
             output_path=str(DATA_DIR / "outputs/causal_test_results.json"),
             f=False,

From 029fdfcc9446bfae8733729867686bdc1b7de77f Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 13:03:56 +0000
Subject: [PATCH 12/14] updated causal_tests_results.json

---
 dafni/data/outputs/causal_tests_results.json | 108 ++++++++++++++-----
 1 file changed, 81 insertions(+), 27 deletions(-)

diff --git a/dafni/data/outputs/causal_tests_results.json b/dafni/data/outputs/causal_tests_results.json
index f5e503aa..59d651c3 100644
--- a/dafni/data/outputs/causal_tests_results.json
+++ b/dafni/data/outputs/causal_tests_results.json
@@ -18,9 +18,15 @@
       "outcome": "cum_vaccinations",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 252628.1066666667,
-      "ci_low": 252271.33332001517,
-      "ci_high": 252984.8800133182
+      "effect_estimate": {
+        "max_doses": 252628.1066666667
+      },
+      "ci_low": [
+        252271.33332001517
+      ],
+      "ci_high": [
+        252984.8800133182
+      ]
     }
   },
   {
@@ -42,9 +48,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 213111.93333333335,
-      "ci_low": 212755.15056812647,
-      "ci_high": 213468.71609854023
+      "effect_estimate": {
+        "max_doses": 213111.93333333335
+      },
+      "ci_low": [
+        212755.15056812647
+      ],
+      "ci_high": [
+        213468.71609854023
+      ]
     }
   },
   {
@@ -66,9 +78,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 2666.3066666666664,
-      "ci_low": 2619.972040648758,
-      "ci_high": 2712.6412926845746
+      "effect_estimate": {
+        "max_doses": 2666.3066666666664
+      },
+      "ci_low": [
+        2619.972040648758
+      ],
+      "ci_high": [
+        2712.6412926845746
+      ]
     }
   },
   {
@@ -89,9 +107,15 @@
       "outcome": "cum_vaccinations",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 315785.1333333332,
-      "ci_low": 315339.1666500188,
-      "ci_high": 316231.1000166476
+      "effect_estimate": {
+        "vaccine": 315785.1333333332
+      },
+      "ci_low": [
+        315339.1666500188
+      ],
+      "ci_high": [
+        316231.1000166476
+      ]
     }
   },
   {
@@ -112,9 +136,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 266389.91666666657,
-      "ci_low": 265943.93821015797,
-      "ci_high": 266835.89512317517
+      "effect_estimate": {
+        "vaccine": 266389.91666666657
+      },
+      "ci_low": [
+        265943.93821015797
+      ],
+      "ci_high": [
+        266835.89512317517
+      ]
     }
   },
   {
@@ -135,9 +165,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 3332.883333333332,
-      "ci_low": 3274.9650508109467,
-      "ci_high": 3390.801615855717
+      "effect_estimate": {
+        "vaccine": 3332.883333333332
+      },
+      "ci_low": [
+        3274.9650508109467
+      ],
+      "ci_high": [
+        3390.801615855717
+      ]
     }
   },
   {
@@ -159,9 +195,15 @@
       "outcome": "cum_vaccinated",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": 0.9998656401531605,
-      "ci_low": 0.9929245394499968,
-      "ci_high": 1.0068067408563242
+      "effect_estimate": {
+        "cum_vaccinations": 0.9998656401531605
+      },
+      "ci_low": [
+        0.9929245394499968
+      ],
+      "ci_high": [
+        1.0068067408563242
+      ]
     }
   },
   {
@@ -183,9 +225,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": -0.006416682407515084,
-      "ci_low": -0.05663010083886572,
-      "ci_high": 0.043796736023835554
+      "effect_estimate": {
+        "cum_vaccinations": -0.006416682407515084
+      },
+      "ci_low": [
+        -0.05663010083886572
+      ],
+      "ci_high": [
+        0.043796736023835554
+      ]
     }
   },
   {
@@ -207,9 +255,15 @@
       "outcome": "cum_infections",
       "adjustment_set": [],
       "effect_measure": "coefficient",
-      "effect_estimate": -0.006176900588291234,
-      "ci_low": -0.05639349612119588,
-      "ci_high": 0.04403969494461341
+      "effect_estimate": {
+        "cum_vaccinated": -0.006176900588291234
+      },
+      "ci_low": [
+        -0.05639349612119588
+      ],
+      "ci_high": [
+        0.04403969494461341
+      ]
     }
   }
 ]

From 802e274c0cd8efc361f856f0b83c333d59c90404 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Tue, 10 Dec 2024 17:19:46 +0000
Subject: [PATCH 13/14] update: file names

---
 dafni/tests/__init__.py                                 | 0
 dafni/tests/{tests_main_dafni.py => test_main_dafni.py} | 3 +--
 2 files changed, 1 insertion(+), 2 deletions(-)
 create mode 100644 dafni/tests/__init__.py
 rename dafni/tests/{tests_main_dafni.py => test_main_dafni.py} (98%)

diff --git a/dafni/tests/__init__.py b/dafni/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/dafni/tests/tests_main_dafni.py b/dafni/tests/test_main_dafni.py
similarity index 98%
rename from dafni/tests/tests_main_dafni.py
rename to dafni/tests/test_main_dafni.py
index 821d9733..ee135714 100644
--- a/dafni/tests/tests_main_dafni.py
+++ b/dafni/tests/test_main_dafni.py
@@ -6,13 +6,12 @@
 from causal_testing.estimation.linear_regression_estimator import LinearRegressionEstimator
 from causal_testing.specification.causal_dag import CausalDAG
 from causal_testing.specification.variable import Input, Output
-from main_dafni import get_args, parse_variables
+from dafni.src.main_dafni import get_args, parse_variables
 
 # Base directory (relative to the current test file location)
 BASE_DIR = Path(__file__).resolve().parent.parent  # Points to ./dafni
 DATA_DIR = BASE_DIR / "data"  # Points to ./dafni/data
 
-
 class TestGetArgs(unittest.TestCase):
     """Test the argparse functionality of the DAFNI entrypoint."""
 

From 05a85fd58a37ef1a0e09e7f34167264fea599a32 Mon Sep 17 00:00:00 2001
From: f-allian <allianfarhad@gmail.com>
Date: Fri, 13 Dec 2024 16:48:00 +0000
Subject: [PATCH 14/14] update: README.md metadata

---
 dafni/README.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/dafni/README.md b/dafni/README.md
index 40e2ae42..059ce257 100644
--- a/dafni/README.md
+++ b/dafni/README.md
@@ -10,8 +10,11 @@ to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
 - `data` contains two sub-folders (the structure is important for DAFNI).
   - `inputs` is a folder that contains the input files that are (separately) uploaded to DAFNI.
     - `causal_tests.json` is a JSON file that contains the causal tests.
-    - `dag.dot` is a dot file that contains the directed acyclc graph (dag) file, 
-       including the variables (and constraints if necessary) as node attributes.
+    - `dag.dot` is a dot file that contains the directed acyclic graph (dag). Causal variables are defined as 
+       node metadata attributes in this file as key-value pairs using the following syntax: 
+       `node [datatype="int", typestring="input"]`. The `datatype` key specifies the datatype of the causal variable
+       as a string (e.g. `"int"`, `"str"`) and the `typestring` key specifies its typestring, which is also a string 
+       representing the variable type (e.g. `"input"` or `"output"`).
     - `runtime_data.csv` is a csv file that contains the runtime data.
 
   - `outputs` is a folder where the `causal_tests_results.json` output file is created.