fix and tests for Division by zero #123

.github/workflows/ci.yml

@@ -54,9 +54,14 @@ jobs:
       - name: Build strling help
         run: ./strling -h
 
-      - name: Unit tests
+      - name: Run Nim unit tests
         run: nimble test -y
 
+      - name: Run Python doctests
+        run: |
+          conda env update -f environment.yml
+          conda run -n strling python -m doctest scripts/strling-outliers.py
+
   integration-e2e:
     # Only run end-to-end tests on pushes to master to keep PRs fast
     if: github.ref == 'refs/heads/master' || github.event_name == 'workflow_dispatch'

.github/workflows/release.yml

@@ -0,0 +1,51 @@
+name: Release Static Binary
+
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger on version tags like v0.4.0
+
+jobs:
+  build-static:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Pull latest changes
+        run: git pull
+
+      - name: Set up Singularity
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y singularity-container
+
+      - name: Build debug static binary
+        run: |
+          singularity run --bind $(pwd):/load --bind /scratch --bind /uufs \
+            docker://brentp/musl-hts-nim:latest \
+            /usr/local/bin/nsb -n strling.nimble -s src/strling.nim -- -d:danger -d:release -d:debug
+          cp strling strling_debug
+
+      - name: Build release static binary
+        run: |
+          singularity run --bind $(pwd):/load --bind /scratch --bind /uufs \
+            docker://brentp/musl-hts-nim:latest \
+            /usr/local/bin/nsb -n strling.nimble -s src/strling.nim -- -d:danger -d:release
+
+      - name: Upload binaries as release assets
+        uses: actions/upload-artifact@v4
+        with:
+          name: strling_binaries
+          path: |
+            strling
+            strling_debug
+
+      - name: Create GitHub Release and attach binaries
+        uses: softprops/action-gh-release@v2
+        with:
+          files: |
+            strling
+            strling_debug
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

scripts/strling-outliers.py

@@ -141,11 +141,30 @@ def z_score(x, df):
     return (x - df['mu'][:,np.newaxis])/df['sd'][:,np.newaxis]
 
 def p_adj_bh(x):
-    '''Adjust p values using Benjamini/Hochberg method'''
-    # Mask out nan values as they cause the multiptests algorithm to return all nan
+    '''Adjust p values using Benjamini/Hochberg method
+
+    Tests
+    -----
+    >>> import numpy as np
+    >>> p_adj_bh(np.array([np.nan, np.nan]))
+    array([nan, nan])
+    >>> p_adj_bh(np.array([np.inf, -np.inf]))
+    array([ inf, -inf])
+    >>> p_adj_bh(np.array([]))
+    array([], dtype=float64)
+    >>> out = p_adj_bh(np.array([0.01, np.nan, 0.05]))
+    >>> bool(np.isclose(out[0], 0.03, atol=0.01))
+    True
+    >>> bool(np.isnan(out[1]))
+    True
+    >>> bool(np.isclose(out[2], 0.05, atol=0.01))
+    True
+    '''
     mask = np.isfinite(x)
     pval_corrected = x.copy()
-    pval_corrected[mask] = multipletests(x[mask], method='fdr_bh', returnsorted = False)[1]
+    if not np.any(mask) or np.sum(mask) < 1: # If no finite values, or less than 1, just return the input unchanged
+        return pval_corrected
+    pval_corrected[mask] = multipletests(x[mask], method='fdr_bh', returnsorted=False)[1]
     return pval_corrected
 
 def glob_list(l):

src/strpkg/version.nim

@@ -1,4 +1,4 @@
-const strlingVersion* = "0.5.2"
+const strlingVersion* = "0.6.0"
 
 # bin file format version
 const thisFmtVersion* = 0'i16

strling.nimble

@@ -9,7 +9,7 @@ template thisModuleFile: string = instantiationInfo(fullPaths = true).filename
 #  # When the package is installed, the ``src`` directory disappears.
 #  import strpkg/version as _
 
-version       = "0.5.2"
+version       = "0.6.0"
 author        = "Harriet and Brent"
 description   = "Novel STR caller"
 license       = "MIT"