Merge pull request #238 from UC-Davis-molecular-computing/237-add-con…

…straint-using-rnaplex

closes #237: add Constraint using RNAplex

.github/workflows/docs-check.yml

@@ -1,4 +1,3 @@
-
 name: "Docs Check"
 on: pull_request
 
@@ -8,25 +7,25 @@ jobs:
     container:
       image: unhumbleben/nupack:latest
     steps:
-    - uses: actions/[email protected]
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
+      - uses: actions/[email protected]
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
           python-version: '3.9'
-    - name: Upgrade pip
-      run: python -m pip install --upgrade pip
-    - name: Install NUPACK
-      run: |
-        python -m pip install -U nupack -f /nupack/package
-    # got from here: https://github.com/marketplace/actions/python-dependency-installation
-    # should install dependencies in requirements.txt
-    - name: Install Python dependencies
-      uses: py-actions/py-dependency-install@v2
-    - name: Install Sphinx
-      run: |
-        python -m pip install sphinx sphinx_rtd_theme
-    - name: Move to docs folder and build
-      run: |
-        cd doc
-        pwd
-        sphinx-build -T -E -W -b html . _build
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+      - name: Install NUPACK
+        run: |
+          python -m pip install -U nupack -f /nupack/package
+      # got from here: https://github.com/marketplace/actions/python-dependency-installation
+      # should install dependencies in requirements.txt
+      - name: Install Python dependencies
+        uses: py-actions/py-dependency-install@v2
+      - name: Install Sphinx
+        run: |
+          python -m pip install sphinx sphinx_rtd_theme
+      - name: Move to docs folder and build
+        run: |
+          cd doc
+          pwd
+          sphinx-build -T -E -W -b html . _build

.github/workflows/release.yml

@@ -24,9 +24,9 @@ jobs:
             LICENSE.txt
 
       # Publish to PyPI
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: '3.9'
       - name: Upgrade pip

.github/workflows/run_unit_tests.yml

@@ -13,22 +13,22 @@ jobs:
       image: unhumbleben/nupack:latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [ 3.7, 3.8, 3.9 ]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Upgrade pip
-      run: python -m pip install --upgrade pip
-    - name: Install NUPACK
-      run: |
-        python -m pip install -U nupack -f /nupack/package
-    - name: Install dependencies
-      run: |
-        if [ -f requirements.txt ]; then python -m pip install -r requirements.txt; fi
-    - name: Test with unittest
-      run: |
-        python -m unittest -v tests/test.py
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+      - name: Install NUPACK
+        run: |
+          python -m pip install -U nupack -f /nupack/package
+      - name: Install dependencies
+        run: |
+          if [ -f requirements.txt ]; then python -m pip install -r requirements.txt; fi
+      - name: Test with unittest
+        run: |
+          python -m unittest -v tests/test.py

examples/many_strands_no_common_domains.py

@@ -12,7 +12,8 @@
 
 
 def f(x: int | float) -> float:
-    return x/2
+    return x / 2
+
 
 # command-line arguments
 class CLArgs(NamedTuple):
@@ -52,8 +53,8 @@ def main() -> None:
     # many 4-domain strands with no common domains, 4 domains each, every domain length = 10
     # just for testing parallel processing
 
-    # num_strands = 3
-    num_strands = 5
+    num_strands = 3
+    # num_strands = 5
     # num_strands = 10
     # num_strands = 50
     # num_strands = 100
@@ -141,7 +142,10 @@ def main() -> None:
         parallel=parallel)
 
     strand_pairs_rna_duplex_constraint = nc.rna_duplex_strand_pairs_constraint(
-        threshold=-1.0, temperature=52, short_description='StrandPairRNA', parallel=parallel)
+        threshold=-1.0, temperature=52, short_description='RNAduplex', parallel=parallel)
+
+    strand_pairs_rna_plex_constraint = nc.rna_plex_strand_pairs_constraint(
+        threshold=-1.0, temperature=52, short_description='RNAplex', parallel=parallel)
 
     strand_individual_ss_constraint = nc.nupack_strand_free_energy_constraint(
         threshold=-1.0, temperature=52, short_description='StrandSS', parallel=parallel)
@@ -151,8 +155,9 @@ def main() -> None:
 
     params = ns.SearchParameters(constraints=[
         # domain_nupack_ss_constraint,
-        strand_individual_ss_constraint,
+        # strand_individual_ss_constraint,
         strand_pairs_rna_duplex_constraint,
+        strand_pairs_rna_plex_constraint,
         # strand_pair_nupack_constraint,
         # domain_pair_nupack_constraint,
         # domain_pairs_rna_duplex_constraint,