suggestions and fixes

.github/workflows/tests.yml

@@ -79,7 +79,7 @@ jobs:
           pip install dist/*.whl
           resources/buildforCI.sh
       - name: Clear Space
-        run: rm -rf /opt/hostedtoolcache
+        uses: jlumbroso/free-disk-space@main
       - name: Rebuild Dockerfile
         id: rebuild
         if: ${{ needs.changes.outputs.container == 'true' }}

harpy/bin/molecule_coverage.py

@@ -64,7 +64,7 @@ def initialize_contig(length):
 def process_alignment(start, end):
     """Function to insert or update counts for numbers in a given range"""
     cursor.executemany(
-        'UPDATE number_counts SET count = count + 1 WHERE number = ?',
+        'UPDATE number_counts SET count = count + 1 WHERE number BETWEEN ? AND ?',
         [(num,) for num in range(start, end + 1)]
     )
 

harpy/reports/align_stats.qmd

@@ -472,7 +472,7 @@ list(
 #| title: "Mol. Stdev Depth"
 list(
   color = "#d4d4d4",
-  value = round(global_sd,2)
+  value = round(mol_global_sd,2)
 )
 ```
 

harpy/reports/preflight_fastq.qmd

@@ -64,7 +64,7 @@ list(
 list(
   icon = ifelse(attention > 0, "exclamation-triangle", "check2-square"),
   color = ifelse(bxnotlast > 0, "warning", "success"),
-  value = scales::comma(attention)
+  value = scales::comma(bxnotlast)
 )
 ```
 

resources/dev_install_conda.sh

@@ -1,14 +1,24 @@
 #! /usr/bin/env bash
 
-conda env create --prefix harpy/.conda/harpy $1 --file harpy/resources/harpy.yaml
+if ! conda env create --prefix harpy/.conda/harpy $1 --file harpy/resources/harpy.yaml; then
+    echo "Error: Failed to create conda environment"
+    exit 1
+fi
 
-conda activate harpy/.conda/harpy
+if ! conda activate harpy/.conda/harpy; then
+cd harpy || { echo "Error: Failed to change directory to harpy"; exit 1; }
 
+fi
 mkdir -p ${CONDA_PREFIX}/bin
 
-cd harpy
+# install harpy proper
+if ! pip install --no-deps --disable-pip-version-check -e .; then
+    echo "Error: Failed to install harpy package"
+    exit 1
+fi
 
-# compilation
+# Clean up build directory if it exists
+[ -d build ] && rm -rf build
 g++ harpy/bin/extractReads.cpp -O3 -o ${CONDA_PREFIX}/bin/extractReads
 
 # install harpy proper

resources/dev_install_pixi.sh

@@ -2,10 +2,22 @@
 
 ENV_PREFIX="harpy/.pixi/envs/default/bin/"
 
-pixi init -i harpy/resources/harpy.yaml harpy
-echo -e "\n[pypi-dependencies]\nharpy = { path = \".\", editable = true}" >> harpy/pixi.toml
+if ! pixi init -i harpy/resources/harpy.yaml harpy; then
+    echo "Error: Failed to initialize pixi environment"
+    exit 1
+fi
 
-cd harpy && pixi shell
+if ! echo -e "\n[pypi-dependencies]\nharpy = { path = \".\", editable = true}" >> harpy/pixi.toml; then
+    echo "Error: Failed to update pixi.toml"
+    exit 1
+fi
+
+if ! cd harpy; then
+    echo "Error: Failed to change directory to harpy"
+    exit 1
+fi
+
+pixi shell
 
 mkdir -p ${ENV_PREFIX}/bin