From 79d5332afb86a1d61be758415b9bc752ba10bbd6 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 01:54:34 -0400 Subject: [PATCH 1/7] change numpy version; fixes distutils deprecation --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5457bb3..9614481 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,7 @@ dnaplotlib==1.0 fonttools==4.43.1 kiwisolver==1.4.5 matplotlib~=3.7.2 -numpy~=1.25.0 +numpy~=1.26.4 packaging==23.2 Pillow==10.2.0 py4j==0.10.9.7 From 1e0bc17645d0b9526627f94b65d95c596412d2a3 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 01:55:06 -0400 Subject: [PATCH 2/7] updated README --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 57c9a78..73f22f8 100644 --- a/README.md +++ b/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 :/app/temp_out -v :/app/logs -t cello-core-test +docker run -i -v :/app/temp_out -v :/app/logs -v :/app/library/verilogs -v :/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.) From 2aae653d032f943ccb911921c0d6de4b6ad5c5bb Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 01:58:43 -0400 Subject: [PATCH 3/7] temp removed intermediate output CM req --- core_algorithm/celloAlgo.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/core_algorithm/celloAlgo.py b/core_algorithm/celloAlgo.py index 63f1792..65cae6f 100644 --- a/core_algorithm/celloAlgo.py +++ b/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 From 5801fa014e794f549e32d02a0d82ed5bf2d47b12 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 03:03:11 -0400 Subject: [PATCH 4/7] tweak --- library/constraints/Eco2C1G6T1.UCF.json | 195138 ++++++++++----------- 1 file changed, 97569 insertions(+), 97569 deletions(-) diff --git a/library/constraints/Eco2C1G6T1.UCF.json b/library/constraints/Eco2C1G6T1.UCF.json index d0d08d2..04e40f2 100644 --- a/library/constraints/Eco2C1G6T1.UCF.json +++ b/library/constraints/Eco2C1G6T1.UCF.json @@ -6,10 +6,10 @@ "date": "Tue January 31 23:01:11 EDT 2023", "author": [ "Jai Padmakumar", - "Alexander J. Triassi", - "Hamid Doosthosseini", + "Alexander J. Triassi", + "Hamid Doosthosseini", "Samuel M.D. Oliveira" - ], + ], "organism": "Escherichia coli MG1655 (Extended #Gates))", "genome": "Wildtype (NCBI RefSeq: CP007799) with three landing pads integrated", "media": "M9 minimal media composed of M9 media salts (6.78 g/L Na2HPO4, 3 g/L KH2PO4, 1 g/L NH4Cl, 0.5 g/L NaCl, 0.34 g/L thiamine hydrochloride, 0.4% D-glucose, 0.2% Casamino acids, 2 mM MgSO4, and 0.1 mM CaCl2", @@ -9364,7 +9364,7 @@ "model": "Pr208-Tuc2009-R3_model", "structure": "Pr208-Tuc2009-R3_structure" }, - { + { "collection": "gates", "name": "Pr210-phage186-RBS50", "system": "TetR", @@ -9375,7 +9375,7 @@ "model": "Pr210-phage186-RBS50_model", "structure": "Pr210-phage186-RBS50_structure" }, - { + { "collection": "gates", "name": "Pr211-933W-R1", "system": "TetR", @@ -9386,7 +9386,7 @@ "model": "Pr211-933W-R1_model", "structure": "Pr211-933W-R1_structure" }, - { + { "collection": "gates", "name": "Pr211-933W-R2", "system": "TetR", @@ -9397,7 +9397,7 @@ "model": "Pr211-933W-R2_model", "structure": "Pr211-933W-R2_structure" }, - { + { "collection": "gates", "name": "Pr212-L5-R1", "system": "TetR", @@ -9408,7 +9408,7 @@ "model": "Pr212-L5-R1_model", "structure": "Pr212-L5-R1_structure" }, - { + { "collection": "gates", "name": "Pr214-P2hd-R1", "system": "TetR", @@ -9419,7 +9419,7 @@ "model": "Pr214-P2hd-R1_model", "structure": "Pr214-P2hd-R1_structure" }, - { + { "collection": "gates", "name": "Pr215-P2-R1", "system": "TetR", @@ -9430,7 +9430,7 @@ "model": "Pr215-P2-R1_model", "structure": "Pr215-P2-R1_structure" }, - { + { "collection": "gates", "name": "Pr215-P2-R3", "system": "TetR", @@ -9441,7 +9441,7 @@ "model": "Pr215-P2-R3_model", "structure": "Pr215-P2-R3_structure" }, - { + { "collection": "gates", "name": "Pr215-P2-R4", "system": "TetR", @@ -9452,7 +9452,7 @@ "model": "Pr215-P2-R4_model", "structure": "Pr215-P2-R4_structure" }, - { + { "collection": "gates", "name": "Pr218-Wphi-R1", "system": "TetR", @@ -9780,7 +9780,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr210-phage186-RBS50_structure", "inputs": [ @@ -9831,7 +9831,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr211-933W-R1_structure", "inputs": [ @@ -9882,7 +9882,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr211-933W-R2_structure", "inputs": [ @@ -9933,7 +9933,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr212-L5-R1_structure", "inputs": [ @@ -9984,7 +9984,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr214-P2hd-R1_structure", "inputs": [ @@ -10035,7 +10035,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr215-P2-R1_structure", "inputs": [ @@ -10086,7 +10086,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr215-P2-R3_structure", "inputs": [ @@ -10137,7 +10137,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr215-P2-R4_structure", "inputs": [ @@ -10239,7 +10239,7 @@ } ] }, - { + { "collection": "structures", "name": "Pr218-Wphi-R1_structure", "inputs": [ @@ -10482,7 +10482,7 @@ } ] }, - { + { "collection": "models", "name": "Pr210-phage186-RBS50_model", "functions": { @@ -10514,7 +10514,7 @@ } ] }, - { + { "collection": "models", "name": "Pr211-933W-R1_model", "functions": { @@ -10546,7 +10546,7 @@ } ] }, - { + { "collection": "models", "name": "Pr211-933W-R2_model", "functions": { @@ -10578,7 +10578,7 @@ } ] }, - { + { "collection": "models", "name": "Pr212-L5-R1_model", "functions": { @@ -10610,7 +10610,7 @@ } ] }, - { + { "collection": "models", "name": "Pr214-P2hd-R1_model", "functions": { @@ -10642,7 +10642,7 @@ } ] }, - { + { "collection": "models", "name": "Pr215-P2-R1_model", "functions": { @@ -10674,7 +10674,7 @@ } ] }, - { + { "collection": "models", "name": "Pr215-P2-R3_model", "functions": { @@ -10706,7 +10706,7 @@ } ] }, - { + { "collection": "models", "name": "Pr215-P2-R4_model", "functions": { @@ -11645,7 +11645,7 @@ "name": "DT19", "dnasequence": "TTCAGCCAAAAAACTTAAGACCGCCGGTCTTGTCCACTACCTTGCAGTAATGCGGTGGACAGGATCGGCGGTTTTCTTTTCTCTTCTCAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr210", @@ -11675,7 +11675,7 @@ "name": "DT83", "dnasequence": "AGCGTCAAAAGGCCGGATTTTCCGGCCTTTTTTATTAGGCAGCATGCTGCCAGGTGATCCCCCTGGCCACCTCTTTT" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr211", @@ -11711,7 +11711,7 @@ "name": "DT36", "dnasequence": "GATCTAACTAAAAAGGCCGCTCTGCGGCCTTTTTTCTTTTCACTGTAACAACGGAAACCGGCCATTGCGCCGGTTTTTTTTGGCCT" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr212", @@ -11741,19 +11741,19 @@ "name": "L3S2P11", "dnasequence": "ctcggtaccaaattccagaaaagagacgctttcgagcgtcttttttcgttttggtcc" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr214", "dnasequence": "AACTACTACGCAAAAttcaacttctccgaaacgtctattgacataattactccgattgcgtaatttcttg" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr215", "dnasequence": "ATGATTGGCGACTCGgtttagatctcattgacatggtgtttagatctcaagtactgttagtttagatgtacaattttgttagtttagat" }, - { + { "collection": "parts", "type": "promoter", "name": "Pr218", @@ -11819,7 +11819,7 @@ "name": "DT56", "dnasequence": "TACCACCGTCAAAAAAAACGGCGCTTTTTAGCGCCGTTTTTATTTTTCAACCTTCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTC" }, - { + { "collection": "parts", "type": "terminator", "name": "DT86", @@ -12155,7 +12155,7 @@ ] } }, - { + { "collection": "functions", "name": "Pr210-phage186-RBS50_toxicity", "variables": [ @@ -12181,21 +12181,21 @@ ], "output": [ 1.0, - 0.984452584, - 0.96922105, - 0.969374131, - 0.943713666, - 0.949320552, - 0.964236206, - 0.964561806, - 1.006573968, - 1.053398453, - 0.984605665, - 0.999526179 + 0.984452584, + 0.96922105, + 0.969374131, + 0.943713666, + 0.949320552, + 0.964236206, + 0.964561806, + 1.006573968, + 1.053398453, + 0.984605665, + 0.999526179 ] } }, - { + { "collection": "functions", "name": "Pr211-933W-R1_toxicity", "variables": [ @@ -12221,21 +12221,21 @@ ], "output": [ 1.0, - 0.97808377, - 0.989485014, - 0.99571914, - 0.992919264, - 1.007831723, - 1.061706886, - 1.127280657, - 1.089029291, - 1.072991518, - 1.067171367, - 1.161450571 + 0.97808377, + 0.989485014, + 0.99571914, + 0.992919264, + 1.007831723, + 1.061706886, + 1.127280657, + 1.089029291, + 1.072991518, + 1.067171367, + 1.161450571 ] } }, - { + { "collection": "functions", "name": "Pr211-933W-R2_toxicity", "variables": [ @@ -12261,21 +12261,21 @@ ], "output": [ 1.0, - 0.956091869, - 0.936338328, - 0.943584705, - 0.939961516, - 0.919819045, - 0.923442234, - 0.947596823, - 0.922234504, - 0.918611316, - 0.965323835, - 0.972826087 + 0.956091869, + 0.936338328, + 0.943584705, + 0.939961516, + 0.919819045, + 0.923442234, + 0.947596823, + 0.922234504, + 0.918611316, + 0.965323835, + 0.972826087 ] } }, - { + { "collection": "functions", "name": "Pr212-L5-R1_toxicity", "variables": [ @@ -12301,21 +12301,21 @@ ], "output": [ 1.0, - 0.976076946, - 0.966273024, - 0.947987225, - 0.943820559, - 0.938770053, - 0.916466132, - 0.914846999, - 0.906365122, - 0.892394534, - 0.869942068, - 0.845643939 + 0.976076946, + 0.966273024, + 0.947987225, + 0.943820559, + 0.938770053, + 0.916466132, + 0.914846999, + 0.906365122, + 0.892394534, + 0.869942068, + 0.845643939 ] } }, - { + { "collection": "functions", "name": "Pr214-P2hd-R1_toxicity", "variables": [ @@ -12341,21 +12341,21 @@ ], "output": [ 1.0, - 0.991178767, - 0.986040922, - 0.980952381, - 0.953508772, - 0.937441966, - 0.933056001, - 0.957845433, - 0.948697564, - 0.943609023, - 0.968447759, - 1.072260569 + 0.991178767, + 0.986040922, + 0.980952381, + 0.953508772, + 0.937441966, + 0.933056001, + 0.957845433, + 0.948697564, + 0.943609023, + 0.968447759, + 1.072260569 ] } }, - { + { "collection": "functions", "name": "Pr215-P2-R1_toxicity", "variables": [ @@ -12381,21 +12381,21 @@ ], "output": [ 1.0, - 0.98218984, - 0.968676327, - 0.966048015, - 0.943024992, - 0.942565516, - 0.940897181, - 0.950157808, - 0.947321639, - 0.952786119, - 0.967967968, - 0.949822774 + 0.98218984, + 0.968676327, + 0.966048015, + 0.943024992, + 0.942565516, + 0.940897181, + 0.950157808, + 0.947321639, + 0.952786119, + 0.967967968, + 0.949822774 ] } }, - { + { "collection": "functions", "name": "Pr215-P2-R3_toxicity", "variables": [ @@ -12421,21 +12421,21 @@ ], "output": [ 1.0, - 1.00424719, - 0.975476476, - 0.972810876, - 0.937085166, - 0.929046159, - 0.941241281, - 0.956326358, - 0.96445644, - 0.944222311, - 0.961881914, - 0.963414634 + 1.00424719, + 0.975476476, + 0.972810876, + 0.937085166, + 0.929046159, + 0.941241281, + 0.956326358, + 0.96445644, + 0.944222311, + 0.961881914, + 0.963414634 ] } }, - { + { "collection": "functions", "name": "Pr215-P2-R4_toxicity", "variables": [ @@ -12461,17 +12461,17 @@ ], "output": [ 1.0, - 0.985915493, - 0.962198493, - 0.958453174, - 0.953162169, - 0.940027179, - 0.931587025, - 0.930990856, - 0.937827548, - 0.946267702, - 0.93348606, - 0.931246656 + 0.985915493, + 0.962198493, + 0.958453174, + 0.953162169, + 0.940027179, + 0.931587025, + 0.930990856, + 0.937827548, + 0.946267702, + 0.93348606, + 0.931246656 ] } }, @@ -12508,14 +12508,14 @@ 0.929962629, 0.922462342, 0.935642929, - 0.954148146, - 0.954148146, - 0.883002127, - 0.700618344 + 0.954148146, + 0.954148146, + 0.883002127, + 0.700618344 ] } }, - { + { "collection": "functions", "name": "Pr218-Wphi-R1_toxicity", "variables": [ @@ -12541,17 +12541,17 @@ ], "output": [ 1.0, - 0.957358805, - 0.892530273, - 0.928368747, - 0.946287984, - 0.893397012, - 0.901493208, - 0.916871191, - 0.902786683, - 0.932636847, - 0.956544395, - 0.941218741 + 0.957358805, + 0.892530273, + 0.928368747, + 0.946287984, + 0.893397012, + 0.901493208, + 0.916871191, + 0.902786683, + 0.932636847, + 0.956544395, + 0.941218741 ] } }, @@ -12569,6102 +12569,6102 @@ ], "table": [ { - "x": 0.013914542180192979, - "bin": [ - 0.01, - 0.010280162981264735, - 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0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0, + 0.0 + ] + } + ] } -] +] \ No newline at end of file From 0355fb43fd7fcd6fe826d5fca48e44ec4f0353c7 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 03:29:10 -0400 Subject: [PATCH 5/7] workflow and testing changes --- .github/workflows/python-app.yml | 45 +++++++++++++ core_algorithm/__init__.py | 0 core_algorithm/utils/__init__.py | 0 core_algorithm/utils/unit_tests/__init__.py | 0 .../_test_yosys.py} | 2 +- .../utils/unit_tests/dna_design_unit_tests.py | 65 ------------------- .../utils/unit_tests/test_dna_design.py | 31 +++++++++ requirements.txt | 1 + 8 files changed, 78 insertions(+), 66 deletions(-) create mode 100644 .github/workflows/python-app.yml create mode 100644 core_algorithm/__init__.py create mode 100644 core_algorithm/utils/__init__.py create mode 100644 core_algorithm/utils/unit_tests/__init__.py rename core_algorithm/utils/{test_yosys.py => unit_tests/_test_yosys.py} (95%) delete mode 100644 core_algorithm/utils/unit_tests/dna_design_unit_tests.py create mode 100644 core_algorithm/utils/unit_tests/test_dna_design.py diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml new file mode 100644 index 0000000..4303b77 --- /dev/null +++ b/.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" ] + pull_request: + branches: [ "main" ] + +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 src/utils/test_dna_design.py diff --git a/core_algorithm/__init__.py b/core_algorithm/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/core_algorithm/utils/__init__.py b/core_algorithm/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/core_algorithm/utils/unit_tests/__init__.py b/core_algorithm/utils/unit_tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/core_algorithm/utils/test_yosys.py b/core_algorithm/utils/unit_tests/_test_yosys.py similarity index 95% rename from core_algorithm/utils/test_yosys.py rename to core_algorithm/utils/unit_tests/_test_yosys.py index 1e3a643..16ee549 100644 --- a/core_algorithm/utils/test_yosys.py +++ b/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 * diff --git a/core_algorithm/utils/unit_tests/dna_design_unit_tests.py b/core_algorithm/utils/unit_tests/dna_design_unit_tests.py deleted file mode 100644 index 4333d72..0000000 --- a/core_algorithm/utils/unit_tests/dna_design_unit_tests.py +++ /dev/null @@ -1,65 +0,0 @@ -import unittest -from core_algorithm.utils.make_eugene_script import * -from core_algorithm.utils.dna_design import * -from core_algorithm.utils.py4j_gateway.gateway import start_gateway -from py4j.java_gateway import JavaGateway - - -class UnitTests(unittest.TestCase): - # NOTE: setup fixture for launching miniEugene? - # @unittest.expectedFailure - # def setUp(self): - # start_gateway() - # - # try: - # gateway = JavaGateway(eager_load=True) - # print("\nJava Py4J gateway already started") - # except Exception: - # print("\nAttempting to start Java Py4J gateway...") - # try: - # start_gateway() - # print("Started Java Py4J gateway") - # except Exception: - # print("Failed to start Java Py4J gateway!") - - def outputsTest(self, first, second): - with self.subTest(): - self.assertEqual(first, second) - - def sideEffectsTest(self, first, second): - pass - - def warningsTest(self, callable, arg): - with self.subTest(): - self.assertWarns(Warning, callable, arg) - - -class SubTests(UnitTests): - - # Test Auxiliary Functions - def test_hex_to_rgb(self): - self.outputsTest(hex_to_rgb('000000'), '0.0;0.0;0.0') - self.outputsTest(hex_to_rgb('FFFFFF'), '1.0;1.0;1.0') # rgb: 255;255;255 - self.outputsTest(hex_to_rgb('3badb8'), '0.23;0.68;0.72') # rgb: 59;173;184 - self.warningsTest(hex_to_rgb, '') - self.warningsTest(hex_to_rgb, 'blah') - self.warningsTest(hex_to_rgb, 123456) - - # Test DNADesign Methods - def test_get_part_orders(self): - structs = {'Gate3': EugeneStruct(type='gate', gates_name='Gate3', gates_group='M3', gates_model='Gate3_model', gates_struct='Gate3_structure', struct_cassettes=[['Gate3_a', 'Gate3_a_cassette', 1, ['M3', 'ECK120034435']], ['Gate3_b', 'Gate3_b_cassette', 1, ['M3', 'ECK120034435']]], inputs=['IPTG_sensor'], outputs=['PM3'], color='8FC73E'), 'IPTG_sensor': EugeneStruct(type='input', gates_name='IPTG_sensor', gates_group='', gates_model='IPTG_sensor_model', gates_struct='IPTG_sensor_structure', struct_cassettes=[], inputs=[], outputs=['P_IPTG'], color=''), 'Gate1': EugeneStruct(type='gate', gates_name='Gate1', gates_group='M1', gates_model='Gate1_model', gates_struct='Gate1_structure', struct_cassettes=[['Gate1_a', 'Gate1_a_cassette', 1, ['M1', 'L3S3P41']], ['Gate1_b', 'Gate1_b_cassette', 1, ['M1', 'L3S3P41']]], inputs=['aTc_sensor'], outputs=['PM1'], color='3BA9E0'), 'aTc_sensor': EugeneStruct(type='input', gates_name='aTc_sensor', gates_group='', gates_model='aTc_sensor_model', gates_struct='aTc_sensor_structure', struct_cassettes=[], inputs=[], outputs=['P_aTc'], color=''), 'Gate5': EugeneStruct(type='gate', gates_name='Gate5', gates_group='M5', gates_model='Gate5_model', gates_struct='Gate5_structure', struct_cassettes=[['Gate5_a', 'Gate5_a_cassette', 1, ['M5', 'ECK125109870']], ['Gate5_b', 'Gate5_b_cassette', 1, ['M5', 'ECK125109870']]], inputs=['Gate3', 'Gate1'], outputs=['PM5'], color='5455A4'), 'nanoluc_reporter_2': EugeneStruct(type='output', gates_name='nanoluc_reporter_2', gates_group='', gates_model='nanoluc_reporter_2_model', gates_struct='nanoluc_reporter_2_structure', struct_cassettes=[['nanoluc_reporter_2_a', 'nanoluc_cassette', 1, ['nanoluc_cassette']], ['nanoluc_reporter_2_b', 'nanoluc_cassette', 1, ['nanoluc_cassette']]], inputs=['Gate5'], outputs='', color='')} - cassettes = {'Gate3_a': EugeneCassette(struct_var_name='Gate3_a', struct_cas_name='Gate3_a_cassette', type='gate', inputs=['P_IPTG'], comps=['M3', 'ECK120034435'], outputs=['PM3'], color='8FC73E', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate1_a': EugeneCassette(struct_var_name='Gate1_a', struct_cas_name='Gate1_a_cassette', type='gate', inputs=['P_aTc'], comps=['M1', 'L3S3P41'], outputs=['PM1'], color='3BA9E0', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate5_a': EugeneCassette(struct_var_name='Gate5_a', struct_cas_name='Gate5_a_cassette', type='gate', inputs=['PM3'], comps=['M5', 'ECK125109870'], outputs=['PM5'], color='5455A4', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate5_b': EugeneCassette(struct_var_name='Gate5_b', struct_cas_name='Gate5_b_cassette', type='gate', inputs=['PM1'], comps=['M5', 'ECK125109870'], outputs=['PM5'], color='5455A4', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'nanoluc_reporter_2_a': EugeneCassette(struct_var_name='nanoluc_reporter_2_a', struct_cas_name='nanoluc_cassette', type='output', inputs=['PM5'], comps=['nanoluc_cassette'], outputs='', color='', dev_rules=['ALL_FORWARD'], cir_rules=[])} - sequences = {'P_IPTG': EugeneSequence(parts_type='promoter', parts_name='P_IPTG', parts_sequence='TTACAAAGAAAATTCGACAAACTGTTATTTTTCTATCTATTTATTTGAATTGTGAGCGGATAACAATTACCTTTGTCGGCAATTGTGAGCGGATAACAATTAAATAAAGATATTCTCGTCAAACAAATATAAATAATATAAAC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'P_aTc': EugeneSequence(parts_type='promoter', parts_name='P_aTc', parts_sequence='ttttgcacccgctttccaagagaagaaagccttgttaaattgacttagtgtaaaagcgcagtactgcttgaccataagaacaaaaaaatctctatcactgatagggataaagtttggaagataaagctaaaagttcttatctttgcagtctccctatcagtgatagagacgca', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M1': EugeneSequence(parts_type='cds', parts_name='M1', parts_sequence='CAAAGATAATAGAACTTAAGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'L3S3P41': EugeneSequence(parts_type='terminator', parts_name='L3S3P41', parts_sequence='GGATCCAAAAAAAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTGCCgcggccgc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM1': EugeneSequence(parts_type='promoter', parts_name='PM1', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCACTTAAGTTCTATTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M3': EugeneSequence(parts_type='cds', parts_name='M3', parts_sequence='CAAAGATAATTAAGTTAAGGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'ECK120034435': EugeneSequence(parts_type='terminator', parts_name='ECK120034435', parts_sequence='GGATCCCTCGGTACCAAATTCCAGAAAAGAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCCgcggccgc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM3': EugeneSequence(parts_type='promoter', parts_name='PM3', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCACCTTAACTTAATTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M5': EugeneSequence(parts_type='cds', parts_name='M5', parts_sequence='CAAAGATAGAATAAGTCTTTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'ECK125109870': EugeneSequence(parts_type='terminator', parts_name='ECK125109870', parts_sequence='ccaattattgAACACCCTAACGGGTGTTTTTTTGTTTctggtctccc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM5': EugeneSequence(parts_type='promoter', parts_name='PM5', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCAAAAGACTTATTCTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'F_scar': EugeneSequence(parts_type='scar', parts_name='F_scar', parts_sequence='CGCT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'E_scar': EugeneSequence(parts_type='scar', parts_name='E_scar', parts_sequence='GCTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'D_scar': EugeneSequence(parts_type='scar', parts_name='D_scar', parts_sequence='AGGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'C_scar': EugeneSequence(parts_type='scar', parts_name='C_scar', parts_sequence='AATG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'B_scar': EugeneSequence(parts_type='scar', parts_name='B_scar', parts_sequence='TACG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'A_scar': EugeneSequence(parts_type='scar', parts_name='A_scar', parts_sequence='GGAG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'Y_scar': EugeneSequence(parts_type='scar', parts_name='Y_scar', parts_sequence='ATTG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'X_scar': EugeneSequence(parts_type='scar', parts_name='X_scar', parts_sequence='TGTC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'V_scar': EugeneSequence(parts_type='scar', parts_name='V_scar', parts_sequence='TCTG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'U_scar': EugeneSequence(parts_type='scar', parts_name='U_scar', parts_sequence='GGGC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'R_scar': EugeneSequence(parts_type='scar', parts_name='R_scar', parts_sequence='GTAA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'Q_scar': EugeneSequence(parts_type='scar', parts_name='Q_scar', parts_sequence='GAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'P_scar': EugeneSequence(parts_type='scar', parts_name='P_scar', parts_sequence='CCTA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'O_scar': EugeneSequence(parts_type='scar', parts_name='O_scar', parts_sequence='ATGC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'G_scar': EugeneSequence(parts_type='scar', parts_name='G_scar', parts_sequence='ATAG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'nanoluc_cassette': EugeneSequence(parts_type='cassette', parts_name='nanoluc_cassette', parts_sequence='ATGGTTTTTACTCTGGAAGATTTTGTTGGCGATTGGCGTCAGACCGCGGGTTATAATTTGGATCAAGTCCTGGAACAGGGTGGCGTAAGCTCTCTGTTCCAGAACCTGGGTGTGAGCGTGACGCCGATTCAGCGCATCGTTCTGTCCGGCGAGAACGGTCTGAAAATTGATATTCATGTGATCATCCCGTACGAAGGCCTGAGCGGTGACCAAATGGGTCAAATCGAGAAAATCTTTAAAGTCGTCTACCCAGTTGACGATCACCACTTCAAGGTTATCTTGCATTACGGTACGCTGGTGATTGATGGTGTGACCCCGAATATGATTGACTATTTCGGCCGTCCGTATGAAGGCATTGCCGTTTTTGACGGTAAAAAGATCACCGTCACCGGTACCCTGTGGAATGGCAATAAGATTATTGACGAGCGTCTGATTAACCCGGACGGCAGCCTGCTGTTCCGCGTGACCATCAACGGTGTCACGGGTTGGCGTCTGTGCGAGCGCATCCTGGCATAA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000')} - device_rules = ['ALL_FORWARD'] - circuit_rules = ['ALL_FORWARD', 'STARTSWITH L1', 'ENDSWITH L2', 'Gate5_a AFTER Gate3_a', 'Gate5_a AFTER Gate1_a', 'Gate3_a AFTER Gate1_a', 'CONTAINS Gate3_a', 'CONTAINS Gate1_a', 'CONTAINS Gate5_a', 'CONTAINS Gate5_b', 'CONTAINS nanoluc_reporter_2_a'] - fenceposts = {'L1': [], 'L2': []} - dna_designs = DNADesign(structs, cassettes, sequences, device_rules, circuit_rules, fenceposts) - dna_designs.prep_to_get_part_orders() - circuit_rules_target = ['ALL_FORWARD', 'STARTSWITH L1', 'ENDSWITH L2', 'Gate5_a AFTER Gate3_a', 'Gate5_a AFTER Gate1_a', 'Gate3_a AFTER Gate1_a', 'CONTAINS Gate3_a', 'CONTAINS Gate1_a', 'CONTAINS Gate5_a', 'CONTAINS Gate5_b', 'CONTAINS nanoluc_reporter_2_a', 'CONTAINS L1', 'CONTAINS L2'] - self.outputsTest(dna_designs.circuit_rules, circuit_rules_target) - mini_eugene_part_orders = dna_designs.get_part_orders() # Calls miniEugene - print(mini_eugene_part_orders) - - -if __name__ == '__main__': - unittest.main() diff --git a/core_algorithm/utils/unit_tests/test_dna_design.py b/core_algorithm/utils/unit_tests/test_dna_design.py new file mode 100644 index 0000000..64539a7 --- /dev/null +++ b/core_algorithm/utils/unit_tests/test_dna_design.py @@ -0,0 +1,31 @@ +import pytest +from core_algorithm.utils.make_eugene_script import * +from core_algorithm.utils.dna_design import * +# from core_algorithm.utils.py4j_gateway.gateway import start_gateway +# from py4j.java_gateway import JavaGateway + + +# Test Auxiliary Functions +def test_hex_to_rgb(): + assert hex_to_rgb('000000') == '0.0;0.0;0.0' + assert hex_to_rgb('FFFFFF') == '1.0;1.0;1.0' # rgb: 255;255;255 + assert hex_to_rgb('3badb8') == '0.23;0.68;0.72' # rgb: 59;173;184 + # assert hex_to_rgb == '' + # assert hex_to_rgb == 'blah' + # assert hex_to_rgb == 123456 + + +# Test DNADesign Methods +# def test_get_part_orders(self): +# structs = {'Gate3': EugeneStruct(type='gate', gates_name='Gate3', gates_group='M3', gates_model='Gate3_model', gates_struct='Gate3_structure', struct_cassettes=[['Gate3_a', 'Gate3_a_cassette', 1, ['M3', 'ECK120034435']], ['Gate3_b', 'Gate3_b_cassette', 1, ['M3', 'ECK120034435']]], inputs=['IPTG_sensor'], outputs=['PM3'], color='8FC73E'), 'IPTG_sensor': EugeneStruct(type='input', gates_name='IPTG_sensor', gates_group='', gates_model='IPTG_sensor_model', gates_struct='IPTG_sensor_structure', struct_cassettes=[], inputs=[], outputs=['P_IPTG'], color=''), 'Gate1': EugeneStruct(type='gate', gates_name='Gate1', gates_group='M1', gates_model='Gate1_model', gates_struct='Gate1_structure', struct_cassettes=[['Gate1_a', 'Gate1_a_cassette', 1, ['M1', 'L3S3P41']], ['Gate1_b', 'Gate1_b_cassette', 1, ['M1', 'L3S3P41']]], inputs=['aTc_sensor'], outputs=['PM1'], color='3BA9E0'), 'aTc_sensor': EugeneStruct(type='input', gates_name='aTc_sensor', gates_group='', gates_model='aTc_sensor_model', gates_struct='aTc_sensor_structure', struct_cassettes=[], inputs=[], outputs=['P_aTc'], color=''), 'Gate5': EugeneStruct(type='gate', gates_name='Gate5', gates_group='M5', gates_model='Gate5_model', gates_struct='Gate5_structure', struct_cassettes=[['Gate5_a', 'Gate5_a_cassette', 1, ['M5', 'ECK125109870']], ['Gate5_b', 'Gate5_b_cassette', 1, ['M5', 'ECK125109870']]], inputs=['Gate3', 'Gate1'], outputs=['PM5'], color='5455A4'), 'nanoluc_reporter_2': EugeneStruct(type='output', gates_name='nanoluc_reporter_2', gates_group='', gates_model='nanoluc_reporter_2_model', gates_struct='nanoluc_reporter_2_structure', struct_cassettes=[['nanoluc_reporter_2_a', 'nanoluc_cassette', 1, ['nanoluc_cassette']], ['nanoluc_reporter_2_b', 'nanoluc_cassette', 1, ['nanoluc_cassette']]], inputs=['Gate5'], outputs='', color='')} +# cassettes = {'Gate3_a': EugeneCassette(struct_var_name='Gate3_a', struct_cas_name='Gate3_a_cassette', type='gate', inputs=['P_IPTG'], comps=['M3', 'ECK120034435'], outputs=['PM3'], color='8FC73E', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate1_a': EugeneCassette(struct_var_name='Gate1_a', struct_cas_name='Gate1_a_cassette', type='gate', inputs=['P_aTc'], comps=['M1', 'L3S3P41'], outputs=['PM1'], color='3BA9E0', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate5_a': EugeneCassette(struct_var_name='Gate5_a', struct_cas_name='Gate5_a_cassette', type='gate', inputs=['PM3'], comps=['M5', 'ECK125109870'], outputs=['PM5'], color='5455A4', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'Gate5_b': EugeneCassette(struct_var_name='Gate5_b', struct_cas_name='Gate5_b_cassette', type='gate', inputs=['PM1'], comps=['M5', 'ECK125109870'], outputs=['PM5'], color='5455A4', dev_rules=['ALL_FORWARD'], cir_rules=[]), 'nanoluc_reporter_2_a': EugeneCassette(struct_var_name='nanoluc_reporter_2_a', struct_cas_name='nanoluc_cassette', type='output', inputs=['PM5'], comps=['nanoluc_cassette'], outputs='', color='', dev_rules=['ALL_FORWARD'], cir_rules=[])} +# sequences = {'P_IPTG': EugeneSequence(parts_type='promoter', parts_name='P_IPTG', parts_sequence='TTACAAAGAAAATTCGACAAACTGTTATTTTTCTATCTATTTATTTGAATTGTGAGCGGATAACAATTACCTTTGTCGGCAATTGTGAGCGGATAACAATTAAATAAAGATATTCTCGTCAAACAAATATAAATAATATAAAC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'P_aTc': EugeneSequence(parts_type='promoter', parts_name='P_aTc', parts_sequence='ttttgcacccgctttccaagagaagaaagccttgttaaattgacttagtgtaaaagcgcagtactgcttgaccataagaacaaaaaaatctctatcactgatagggataaagtttggaagataaagctaaaagttcttatctttgcagtctccctatcagtgatagagacgca', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M1': EugeneSequence(parts_type='cds', parts_name='M1', parts_sequence='CAAAGATAATAGAACTTAAGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'L3S3P41': EugeneSequence(parts_type='terminator', parts_name='L3S3P41', parts_sequence='GGATCCAAAAAAAAAAAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTGCCgcggccgc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM1': EugeneSequence(parts_type='promoter', parts_name='PM1', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCACTTAAGTTCTATTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M3': EugeneSequence(parts_type='cds', parts_name='M3', parts_sequence='CAAAGATAATTAAGTTAAGGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'ECK120034435': EugeneSequence(parts_type='terminator', parts_name='ECK120034435', parts_sequence='GGATCCCTCGGTACCAAATTCCAGAAAAGAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCCgcggccgc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM3': EugeneSequence(parts_type='promoter', parts_name='PM3', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCACCTTAACTTAATTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'M5': EugeneSequence(parts_type='cds', parts_name='M5', parts_sequence='CAAAGATAGAATAAGTCTTTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'ECK125109870': EugeneSequence(parts_type='terminator', parts_name='ECK125109870', parts_sequence='ccaattattgAACACCCTAACGGGTGTTTTTTTGTTTctggtctccc', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'PM5': EugeneSequence(parts_type='promoter', parts_name='PM5', parts_sequence='TGCTGTCATAGGCCGGTTGTCCGGTAGTCCGGATGATTTAAGGAAGATTTCTCTTCTTTTTTCACTTTCTCCGAACAACCTCCAAAAGACTTATTCTATCTTTGCAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'F_scar': EugeneSequence(parts_type='scar', parts_name='F_scar', parts_sequence='CGCT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'E_scar': EugeneSequence(parts_type='scar', parts_name='E_scar', parts_sequence='GCTT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'D_scar': EugeneSequence(parts_type='scar', parts_name='D_scar', parts_sequence='AGGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'C_scar': EugeneSequence(parts_type='scar', parts_name='C_scar', parts_sequence='AATG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'B_scar': EugeneSequence(parts_type='scar', parts_name='B_scar', parts_sequence='TACG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'A_scar': EugeneSequence(parts_type='scar', parts_name='A_scar', parts_sequence='GGAG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'Y_scar': EugeneSequence(parts_type='scar', parts_name='Y_scar', parts_sequence='ATTG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'X_scar': EugeneSequence(parts_type='scar', parts_name='X_scar', parts_sequence='TGTC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'V_scar': EugeneSequence(parts_type='scar', parts_name='V_scar', parts_sequence='TCTG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'U_scar': EugeneSequence(parts_type='scar', parts_name='U_scar', parts_sequence='GGGC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'R_scar': EugeneSequence(parts_type='scar', parts_name='R_scar', parts_sequence='GTAA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'Q_scar': EugeneSequence(parts_type='scar', parts_name='Q_scar', parts_sequence='GAGT', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'P_scar': EugeneSequence(parts_type='scar', parts_name='P_scar', parts_sequence='CCTA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'O_scar': EugeneSequence(parts_type='scar', parts_name='O_scar', parts_sequence='ATGC', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'G_scar': EugeneSequence(parts_type='scar', parts_name='G_scar', parts_sequence='ATAG', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000'), 'nanoluc_cassette': EugeneSequence(parts_type='cassette', parts_name='nanoluc_cassette', parts_sequence='ATGGTTTTTACTCTGGAAGATTTTGTTGGCGATTGGCGTCAGACCGCGGGTTATAATTTGGATCAAGTCCTGGAACAGGGTGGCGTAAGCTCTCTGTTCCAGAACCTGGGTGTGAGCGTGACGCCGATTCAGCGCATCGTTCTGTCCGGCGAGAACGGTCTGAAAATTGATATTCATGTGATCATCCCGTACGAAGGCCTGAGCGGTGACCAAATGGGTCAAATCGAGAAAATCTTTAAAGTCGTCTACCCAGTTGACGATCACCACTTCAAGGTTATCTTGCATTACGGTACGCTGGTGATTGATGGTGTGACCCCGAATATGATTGACTATTTCGGCCGTCCGTATGAAGGCATTGCCGTTTTTGACGGTAAAAAGATCACCGTCACCGGTACCCTGTGGAATGGCAATAAGATTATTGACGAGCGTCTGATTAACCCGGACGGCAGCCTGCTGTTCCGCGTGACCATCAACGGTGTCACGGGTTGGCGTCTGTGCGAGCGCATCCTGGCATAA', dev_rules=['ALL_FORWARD'], cir_rules=[], color='000000')} +# device_rules = ['ALL_FORWARD'] +# circuit_rules = ['ALL_FORWARD', 'STARTSWITH L1', 'ENDSWITH L2', 'Gate5_a AFTER Gate3_a', 'Gate5_a AFTER Gate1_a', 'Gate3_a AFTER Gate1_a', 'CONTAINS Gate3_a', 'CONTAINS Gate1_a', 'CONTAINS Gate5_a', 'CONTAINS Gate5_b', 'CONTAINS nanoluc_reporter_2_a'] +# fenceposts = {'L1': [], 'L2': []} +# dna_designs = DNADesign(structs, cassettes, sequences, device_rules, circuit_rules, fenceposts) +# dna_designs.prep_to_get_part_orders() +# circuit_rules_target = ['ALL_FORWARD', 'STARTSWITH L1', 'ENDSWITH L2', 'Gate5_a AFTER Gate3_a', 'Gate5_a AFTER Gate1_a', 'Gate3_a AFTER Gate1_a', 'CONTAINS Gate3_a', 'CONTAINS Gate1_a', 'CONTAINS Gate5_a', 'CONTAINS Gate5_b', 'CONTAINS nanoluc_reporter_2_a', 'CONTAINS L1', 'CONTAINS L2'] +# self.outputsTest(dna_designs.circuit_rules, circuit_rules_target) +# mini_eugene_part_orders = dna_designs.get_part_orders() # Calls miniEugene +# print(mini_eugene_part_orders) diff --git a/requirements.txt b/requirements.txt index 9614481..0701cd3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -15,3 +15,4 @@ six==1.16.0 sbol3~=1.1 threadpoolctl~=3.2.0 memory-profiler~=0.61.0 +pytest~=7.4.4 From 3203c0d4b39965637f5eaaccaac45ff88c1b086a Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 03:33:11 -0400 Subject: [PATCH 6/7] add dev branch to workflow --- .github/workflows/python-app.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 4303b77..f325879 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -5,9 +5,9 @@ name: Test, Lint, Cover, Profile on: push: - branches: [ "main" ] + branches: [ "main", "dev" ] pull_request: - branches: [ "main" ] + branches: [ "main", "dev" ] permissions: contents: read From a534bbed597ce79e1ad727733a0970e1f81d26d2 Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 29 Mar 2024 03:36:52 -0400 Subject: [PATCH 7/7] fix profile bug --- .github/workflows/python-app.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index f325879..d46ed7f 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -42,4 +42,4 @@ jobs: # coverage run -m pytest # coverage report - name: Profile code - run: python -m cProfile src/utils/test_dna_design.py + run: python -m cProfile core_algorithm/utils/unit_tests/test_dna_design.py