Merge pull request #12 from CIDARLAB/dev

merge dev branch

.github/workflows/python-app.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Test, Lint, Cover, Profile
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+
+permissions:
+  contents: read
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest coverage
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: pytest
+#    - name: Report coverage
+#      run: |
+#        coverage run -m pytest
+#        coverage report
+    - name: Profile code
+      run: python -m cProfile core_algorithm/utils/unit_tests/test_dna_design.py

README.md

@@ -9,23 +9,23 @@ If you don't mind running the program in the console without a graphical user in
 ### Docker Pull
 You can pull the image for this core algorithm from the Docker Hub...
 ```
-docker pull
+docker pull ckrenz/cello-core-v2-1
 ```
 
 ### Docker Build
 Alternatively, you can build the docker image with the following command, executed from the root directory...
 ```
-docker build . -t "cidarlab/cello-core-v2-1"
+docker build . -t ckrenz/cello-core-v2-1
 ```
 
 ### Docker Run
 After either pulling or building the image, you can start the container as follows...
 ```
-docker run -i -v <LOCAL_DIR_TO_SAVE_RESULTS>:/app/temp_out -v <LOCAL_DIR_TO_SAVE_LOGS>:/app/logs -t cello-core-test
+docker run -i -v <LOCAL_DIR_TO_SAVE_RESULTS>:/app/temp_out -v <LOCAL_DIR_TO_SAVE_LOGS>:/app/logs -v <LOCAL_DIR_TO_GET_VERILOGS>:/app/library/verilogs -v <LOCAL_DIR_TO_GET_CONSTRAINT_FILES>:/app/library/constraints -t ckrenz/cello-core-v2-1
 ```
 -i makes the run interactive so that you can interface with the program in the console
 
--v creates a bind mount to save files on your local system
+-v creates a mounts a volume to save files on or read files from your local system
 
 
 #
@@ -100,6 +100,10 @@ Alternatively, you could make a script to call the ```CELLO3``` process and use
 Input files can be found in the [library](/library/) folder. This includes the UCF files for Cello, as well as a few dozen 
 Verilog files. You may use your own Verilog files (structural or behavioral) or modified UCF files.
 
+
+#
+## Other Info
+
 #
 ### Example Output
 Here is an example of what the result from Cello looks like in the terminal. 
@@ -137,7 +141,6 @@ $$
 Only one iteration is stored in the memory at a time in the exhaustive pass. Each iteration has to store a truth table where each row has inputs toggled ON/OFF. The circuit for the intermediate logic circuit design placement is stored in memory with different data for each row.
 
 #
-## Other Info
 ### Contributing
 We welcome contributions from the community! If you'd like to contribute to CELLO-2.1, please follow the guidelines in the CONTRIBUTING.md file.
 (Cello 2.1 is still being developed, but we would welcome any feedback.)

core_algorithm/celloAlgo.py

@@ -1085,11 +1085,11 @@ def fill_truth_table_IO(graph_node):
             print(score)
 
         # NOTE: confirm intermediate output nodes are CMs...
-        for output in graph.outputs:
-            if 'Hill_response' != output.func_name:  # TODO: What is appropriate CM detection?
-                for gate in graph.gates:
-                    if output.id in gate.inputs:
-                        score = 0.0, truth_table, truth_table_labels
+        # for output in graph.outputs:
+        #     if 'Hill_response' != output.func_name:  # TODO: What is appropriate CM detection?
+        #         for gate in graph.gates:
+        #             if output.id in gate.inputs:
+        #                 score = 0.0, truth_table, truth_table_labels
 
         return score
 

core_algorithm/utils/test_yosys.py → core_algorithm/utils/unit_tests/_test_yosys.py

@@ -4,7 +4,7 @@
 
 import sys
 
-sys.path.insert(0, '../')  # Add parent directory to Python path
+sys.path.insert(0, '../../')  # Add parent directory to Python path
 from logic_synthesis import *
 import time
 from log import *