CITCOM-project · f-allian · Jan 9, 2026 · Jan 5, 2026 · Jan 5, 2026 · Jan 5, 2026
diff --git a/.github/workflows/publish-to-dafni.yaml b/.github/workflows/publish-to-dafni.yaml
@@ -18,8 +18,10 @@ jobs:
       - name: Get release version
         id: get_release
         run: |
-          # Extract the version without the 'v' prefix using regex
-          export VERSION=$(curl -sSL https://api.github.com/repos/CITCOM-project/CausalTestingFramework/releases/latest | jq -r '.tag_name' | sed -E 's/^v?([0-9]+(\.[0-9]+)?).*/\1/')
+          # Extract only the major version from the latest release tag
+          export VERSION=$(curl -sSL https://api.github.com/repos/CITCOM-project/CausalTestingFramework/releases/latest \
+            | jq -r '.tag_name' \
+            | sed -E 's/^v?([0-9]+).*/\1/')
           echo "version=$VERSION" >> $GITHUB_OUTPUT
 
   build_and_upload:
@@ -35,6 +37,7 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+
       - uses: actions/setup-python@v3
         with:
           python-version: '3.10'
@@ -45,22 +48,19 @@ jobs:
           python -m pip install causal-testing-framework -e .[dev]
           python -m pip install dafni-cli
 
-      - name: Check if unit tests are passing first
-        id: tests
-        uses: ./.github/workflows/ci-tests.yml
-
       - name: Build the container
-        if: success() && steps.tests.outcome == 'success'
         run: |
-          docker build -t ctf:${{ env.VERSION }} -f ./dafni/Dockerfile .
+          docker build --no-cache -t ctf:${{ env.VERSION }} -f ./dafni/Dockerfile .
           docker save ctf:${{ env.VERSION }} | gzip > ctf-dafni-${{ env.VERSION }}.tar.gz
 
-
       - name: Log into DAFNI
         run: |
           dafni login
 
       - name: Upload to DAFNI
         run: |
-          dafni upload model ./dafni/model_definition.yaml ctf-dafni-${{ env.VERSION }}.tar.gz --version-message "Causal Testing Framework v${{ env.VERSION }}. Uploaded via Github Actions." --parent-id ${{ env.DAFNI_PARENT_ID }} -y
-          dafni logout
+          dafni upload model ./dafni/model_definition.yaml \
+            ctf-dafni-${{ env.VERSION }}.tar.gz \
+            --version-message "Causal Testing Framework v${{ env.VERSION }}. Uploaded via Github Actions." \
+            --parent-id ${{ env.DAFNI_PARENT_ID }} -y
+          dafni logout
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-![example workflow](https://github.com/CITCOM-project/CausalTestingFramework/actions/workflows/ci-tests.yaml/badge.svg)
+![CI tests](https://github.com/CITCOM-project/CausalTestingFramework/actions/workflows/ci-tests.yaml/badge.svg)
 [![codecov](https://codecov.io/gh/CITCOM-project/CausalTestingFramework/branch/main/graph/badge.svg?token=04ijFVrb4a)](https://codecov.io/gh/CITCOM-project/CausalTestingFramework)
 [![Documentation Status](https://readthedocs.org/projects/causal-testing-framework/badge/?version=latest)](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest)
 [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/CITCOM-project/CausalTestingFramework)
@@ -76,7 +76,7 @@ git checkout tags/<tag> -b <branch>
 pip install . # For core API only
 pip install -e . # For editable install, useful for development work
 ```
-For more information on how to use the Causal Testing Framework, please refer to our [documentation](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest).
+For more information on how to use the Causal Testing Framework, please refer to our [documentation](https://causal-testing-framework.readthedocs.io/en/latest/?badge=latest). If you have any questions, you can also reach us by [email]([email protected]).
 
 >[!NOTE]
 >We recommend you use a 64-bit OS (standard in most modern machines) as we have had reports of the installation crashing on legacy 32-bit Debian systems.
@@ -89,12 +89,12 @@ For more information on how to use the Causal Testing Framework, please refer to
 
 2. If you do not already have causal test cases, you can convert your causal DAG to causal tests by running the following command.
 ```
-python -m causal_testing generate --dag_path $PATH_TO_DAG --output_path $PATH_TO_TESTS
+python -m causal_testing generate --dag-path $PATH_TO_DAG --output $PATH_TO_TESTS
 ```
 
 3. You can now execute your tests by running the following command.
 ```
-python -m causal_testing test --dag_path $PATH_TO_DAG --data_paths $PATH_TO_DATA --test_config $PATH_TO_TESTS --output $OUTPUT
+python -m causal_testing test --dag-path $PATH_TO_DAG --data-paths $PATH_TO_DATA --test-config $PATH_TO_TESTS --output $OUTPUT
 ```
 The results will be saved for inspection in a JSON file located at `$OUTPUT`.
 In the future, we hope to add a visualisation tool to assist with this.
@@ -151,4 +151,4 @@ and the software citation should contain the specific Figshare [DOI](https://ord
 
 The Causal Testing Framework is supported by the UK's Engineering and Physical Sciences Research Council (EPSRC),
 with the project name [CITCOM](https://gtr.ukri.org/projects?ref=EP%2FT030526%2F1) - "_Causal Inference for Testing of Computational Models_"
-under the grant EP/T030526/1.
+under the grant EP/T030526/1.
diff --git a/dafni/.env b/dafni/.env
@@ -1,5 +1,21 @@
 #.env
-VARIABLES_PATH=./data/inputs/variables.json
-CAUSAL_TESTS=./data/inputs/causal_tests.json
-DATA_PATH=./data/inputs/runtime_data.csv
-DAG_PATH=./data/inputs/dag.dot
+
+# The default file names environment variables for the DAFNI parameters
+CAUSAL_TESTS=causal_tests.json
+CAUSAL_TEST_RESULTS=causal_test_results.json
+
+# The default generate and test environment variables for the DAFNI parameters
+EXECUTION_MODE=test
+ESTIMATOR=LinearRegressionEstimator
+EFFECT_TYPE=direct
+ESTIMATE_TYPE=coefficient
+THREADS=0
+IGNORE_CYCLES=false
+VERBOSE=false
+QUERY=None
+ADEQUACY=false
+BOOTSTRAP_SIZE=100
+SILENT=false
+BATCH_SIZE=0
+
+
diff --git a/dafni/Dockerfile b/dafni/Dockerfile
@@ -1,29 +1,25 @@
-# Define the Python version neded for CTF
 FROM python:3.12-slim
 
-## Prevents Python from writing pyc files
 ENV PYTHONDONTWRITEBYTECODE=1
-#
-## Keeps Python from buffering stdout and stderr to avoid the framework
-## from crashing without emitting any logs due to buffering
-ENV PYTHONUNBUFFERED=1
 
-# Label maintainer
-LABEL maintainer="Dr. Farhad Allian - The University of Sheffield"
+ENV PYTHONUNBUFFERED=1
 
-# Create a folder for the source code/outputs
-RUN mkdir -p ./causal_testing
-RUN mkdir -p ./data/outputs
+LABEL maintainer="Dr. Neil Walkinshaw - The University of Sheffield"
 
-# 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/data/inputs ./data/inputs
+WORKDIR /
 
-# Install core dependencies using PyPi
-RUN pip install causal-testing-framework --no-cache-dir
+# Copy source code
+COPY causal_testing /causal_testing
 
-# Set the PYTHONPATH environment variable to include the /src directory
+# Set PYTHONPATH
 ENV PYTHONPATH="/causal_testing:${PYTHONPATH}"
 
-# Define the entrypoint/commands
-CMD python -m causal_testing --dag_path $DAG_PATH --data_path $DATA_PATH --test_config $TESTS_PATH --output $OUTPUT
+# Install dependencies
+RUN pip install --no-cache-dir causal-testing-framework
+
+# Copy entrypoint
+COPY dafni/entrypoint.sh /entrypoint.sh
+
+RUN chmod +x /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]
diff --git a/dafni/README.md b/dafni/README.md
@@ -1,33 +1,36 @@
 # Causal Testing Framework on DAFNI
 
 - This directory contains the containerisation files of the causal testing framework using Docker, which is used
-to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
+  to upload the framework onto [DAFNI](https://www.dafni.ac.uk).
 - It is **not** recommended to install the causal testing framework using Docker, and should only be installed
-  using [PyPI](https://pypi.org/project/causal-testing-framework/).
+  using [conda-forge](https://anaconda.org/channels/conda-forge/packages/causal-testing-framework/overview) or [PyPI](https://pypi.org/project/causal-testing-framework/).
 
 ### Directory Hierarchy
 
-- `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 acyclic graph (dag). In this file, Causal Variables are defined as 
-       node metadata attributes 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 the `.csv` file that contains the runtime data.
+- `data` contains two folders (structure is critical for DAFNI workflows):
+  - `inputs` contains all input files that are uploaded to DAFNI.
+    - `causal_tests.json` is a JSON file containing generated causal tests. If it exists, the framework can automatically run tests without regenerating.
+    - `dag.dot` is a DOT file defining the directed acyclic graph (DAG). Causal variables are stored in node metadata as key-value pairs using the syntax:  
+      `node [datatype="int", typestring="input"]`  
+      - `datatype` specifies the variable's data type (e.g., `"int"`, `"str"`).  
+      - `typestring` specifies whether the variable is an `"input"` or `"output"`.
+    - `runtime_data.csv` contains the input runtime data for testing.
+  - `outputs` is the folder where `causal_test_results.json` is created after running tests.
 
-  - `outputs` is a folder where the `causal_tests_results.json` output file is created.
+### Workflow
 
-### Docker files
-- `model_definition.yaml` is the model metadata that is required to be uploaded to DAFNI.
-- `Dockerfile` is the main blueprint that builds the image. The main command calls the `causal_testing` module, 
-   with specified paths for the DAG, input runtime data, test configurations, and the output filename as defined above. 
-   This command is identical to that referenced in the main [README.md](../README.md) file.
-- `docker-compose.yaml` is another method of building the image and running the container in one line. 
-   Note: the `.env` file that contains the environment variables for `main_dafni.py` is only used here.
-- `.dockerignore` tells the Dockerfile which files to not include in the image.
-- `.env` is an example of a configuration file containing the environment variables. This is only required
-    if using `docker-compose` to build the image. 
+- The `entrypoint.sh` script now supports auto-detection:  
+  - If `causal_tests.json` exists in `data/inputs`, the script automatically runs the test mode.  
+  - If it does not exist, the script generates the causal tests first.  
+  - The user can still override this behaviour by setting `EXECUTION_MODE` explicitly in the `.env` file.
+- Filenames for `causal_tests.json` and `causal_test_results.json` are now configurable through environment variables (`CAUSAL_TESTS` and `CAUSAL_TEST_RESULTS`) in the `.env` file.
+- Input/output directories are fixed as `data/inputs` and `data/outputs` to comply with DAFNI requirements.
+- The script now reads all configuration parameters (estimator, effect type, threads, verbosity, query filters, adequacy metrics, etc.) **from the `.env` file**, keeping the Docker image and container clean and flexible.
 
+### Docker files
 
+- `model_definition.yaml` is the model metadata required for DAFNI.
+- `Dockerfile` builds the container image and uses `entrypoint.sh` as the main entrypoint. All paths and options are now configurable via `.env`.
+- `docker-compose.yaml` allows building and running the container with a single command. The `.env` file is required here to define all environment variables.
+- `.dockerignore` specifies files to exclude from the Docker image.
+- `.env` provides all configurable environment variables for the workflow (execution mode, filenames, estimator options, DAG/effects configuration, and runtime options). This is only needed if using `docker-compose`.
diff --git a/dafni/data/inputs/causal_tests.json → ...ata/inputs/causal-tests/causal_tests.json b/dafni/data/inputs/causal_tests.json → ...ata/inputs/causal-tests/causal_tests.json
diff --git a/dafni/data/inputs/dag.dot → dafni/data/inputs/dag-data/dag.dot b/dafni/data/inputs/dag.dot → dafni/data/inputs/dag-data/dag.dot
diff --git a/dafni/data/inputs/runtime_data.csv → ...data/inputs/runtime-data/runtime_data.csv b/dafni/data/inputs/runtime_data.csv → ...data/inputs/runtime-data/runtime_data.csv
diff --git a/dafni/data/outputs/causal_tests_results.json → dafni/data/outputs/causal_test_results.json b/dafni/data/outputs/causal_tests_results.json → dafni/data/outputs/causal_test_results.json
@@ -19,12 +19,12 @@
       "effect_estimate": {
         "vaccine": 315785.1333333332
       },
-      "ci_low": [
-        315339.1666500188
-      ],
-      "ci_high": [
-        316231.1000166476
-      ]
+      "ci_low": {
+        "vaccine": 315339.1666500188
+      },
+      "ci_high": {
+        "vaccine": 316231.1000166476
+      }
     }
   },
   {
@@ -45,14 +45,14 @@
       "adjustment_set": [],
       "effect_measure": "coefficient",
       "effect_estimate": {
-        "vaccine": 266389.91666666657
+        "vaccine": 266389.9166666665
       },
-      "ci_low": [
-        265943.93821015797
-      ],
-      "ci_high": [
-        266835.89512317517
-      ]
+      "ci_low": {
+        "vaccine": 265943.9382101579
+      },
+      "ci_high": {
+        "vaccine": 266835.8951231751
+      }
     }
   },
   {
@@ -75,12 +75,12 @@
       "effect_estimate": {
         "vaccine": 3332.883333333332
       },
-      "ci_low": [
-        3274.9650508109467
-      ],
-      "ci_high": [
-        3390.801615855717
-      ]
+      "ci_low": {
+        "vaccine": 3274.9650508109467
+      },
+      "ci_high": {
+        "vaccine": 3390.801615855717
+      }
     }
   },
   {
@@ -103,14 +103,14 @@
       ],
       "effect_measure": "coefficient",
       "effect_estimate": {
-        "cum_vaccinations": 0.9998656401531605
+        "cum_vaccinations": 0.9998656401531969
       },
-      "ci_low": [
-        0.9929245394499968
-      ],
-      "ci_high": [
-        1.0068067408563242
-      ]
+      "ci_low": {
+        "cum_vaccinations": 0.9929245394500371
+      },
+      "ci_high": {
+        "cum_vaccinations": 1.0068067408563566
+      }
     }
   },
   {
@@ -133,14 +133,14 @@
       ],
       "effect_measure": "coefficient",
       "effect_estimate": {
-        "cum_vaccinations": -0.006416682407515084
+        "cum_vaccinations": -0.006416682407513252
       },
-      "ci_low": [
-        -0.05663010083886572
-      ],
-      "ci_high": [
-        0.043796736023835554
-      ]
+      "ci_low": {
+        "cum_vaccinations": -0.05663010083886358
+      },
+      "ci_high": {
+        "cum_vaccinations": 0.043796736023837074
+      }
     }
   },
   {
@@ -163,14 +163,14 @@
       ],
       "effect_measure": "coefficient",
       "effect_estimate": {
-        "cum_vaccinated": -0.006176900588291234
+        "cum_vaccinated": -0.00617690058829258
       },
-      "ci_low": [
-        -0.05639349612119588
-      ],
-      "ci_high": [
-        0.04403969494461341
-      ]
+      "ci_low": {
+        "cum_vaccinated": -0.056393496121197616
+      },
+      "ci_high": {
+        "cum_vaccinated": 0.044039694944612455
+      }
     }
   }
 ]
diff --git a/dafni/docker-compose.yaml b/dafni/docker-compose.yaml
@@ -6,4 +6,5 @@ services:
     env_file:
       - .env
     volumes:
-      - .:/usr/src/
+      - ./data/inputs:/data/inputs:ro
+      - ./data/outputs:/data/outputs