Travis2githubactions

.github/workflows/main.yaml

@@ -0,0 +1,53 @@
+name: Tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+
+permissions:
+  contents: read
+  pull-requests: read
+
+# This allows a subsequently queued workflow run to interrupt previous runs
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    # Set it to default use bash in interactive mode (required for miniconda setup)
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: create environment with mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          python-version:  ${{ matrix.python-version }}
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: false
+          environment-file: environment.yml
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          python setup.py install
+
+      - name: Test with pytest
+        run: |
+          python -m pytest tests/

.github/workflows/python-publish.yaml

@@ -0,0 +1,40 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI }}
+        verbose: true

SCNIC/annotate_correls.py

@@ -154,7 +154,7 @@ def do_annotate_correls(correls_loc, tre_loc, genome_loc, module_loc, output_loc
     correls_tip_tips = tre.tip_tip_distances(set([otu for otu_pair in correls.index for otu in otu_pair]))
     print("read tree")
     genome_frame = pd.read_csv(genome_loc, sep='\t', index_col=0)
-    genome_table = genome_frame_to_table(genome_frame, set([otu for otu_pair in correls.index for otu in otu_pair]))
+    genome_table = genome_frame_to_table(genome_frame, list(set([otu for otu_pair in correls.index for otu in otu_pair])))
     print("read table")
     if modules_to_keep_loc is not None:
         modules_to_keep = get_modules_to_keep(modules_to_keep_loc)

environment.yml

@@ -14,6 +14,8 @@ dependencies:
 - python=3
 - fastspar>=0.0.7
 - armadillo=8
+- seaborn
+- tqdm
 - pip:
   - scipy<=1.10.1,>=1.8.0
   - SCNIC

requirements.txt

@@ -0,0 +1,8 @@
+numpy
+networkx>=2
+biom-format
+pandas>=1
+scikit-bio
+statsmodels
+h5py
+tqdm

tests/test_between_correls.py

@@ -2,6 +2,7 @@
 from SCNIC.general import simulate_correls
 from SCNIC.between_correls import between_correls
 from biom.util import biom_open
+import pytest
 
 
 def test_between_correls(tmpdir):
@@ -13,7 +14,14 @@ def test_between_correls(tmpdir):
     with biom_open(str(loc.join("table2.biom")), 'w') as f:
         table2.to_hdf5(f, 'madebyme')
     os.chdir(str(loc))
-    between_correls('table1.biom', 'table2.biom', 'out_dir', correl_method='pearson', max_p=.1)
-    files = os.listdir(str(loc)+'/out_dir')
+
+    # P value based module making is not yet implemented, check this
+    with pytest.raises(Exception) as exc_info:   
+        between_correls('table1.biom', 'table2.biom', 'out_dir', correl_method='pearson', max_p=.1)
+    assert exc_info.value.args[0] == "SCNIC does not currently support module making based on p-values."
+
+    # Run with min r threshold and check that files exist
+    between_correls('table1.biom', 'table2.biom', 'out_dir_2', correl_method='pearson', min_r=.2)
+    files = os.listdir(str(loc)+'/out_dir_2')
     assert "correls.txt" in files
     assert "crossnet.gml" in files