Updates & polishing

.dockerignore

@@ -0,0 +1,50 @@
+# Ignore Git repository files
+.git
+.gitignore
+
+# Ignore Python virtual environments
+.venv/
+env/
+venv/
+
+# Ignore log files
+*.log
+
+# Ignore Python cache and compiled files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Ignore pytest cache
+.pytest_cache/
+
+# Ignore mypy cache
+.mypy_cache/
+
+# Ignore coverage reports
+.coverage
+htmlcov/
+
+# Ignore temporary files
+*.swp
+*~
+*.tmp
+*.temp
+
+# Ignore build artifacts
+build/
+dist/
+.eggs/
+*.egg-info/
+
+# Ignore IDE/editor configurations
+.vscode/
+.idea/
+
+# Ignore macOS Finder files
+.DS_Store
+
+# Ignore other system files
+Thumbs.db
+desktop.ini
+

.gitignore

@@ -46,7 +46,6 @@ coverage.xml
 .ropeproject
 
 # Django stuff:
-*.log
 *.pot
 
 # Sphinx documentation

Dockerfile

@@ -1,28 +1,25 @@
-# Use the official Ubuntu 24.04 LTS as the base image
-FROM ubuntu:24.04
+# --------------------- Stage 1: Build the wheel ---------------------
+# Use the official Ubuntu 23.04 as the base image for the builder
+FROM ubuntu:23.04 AS builder
 
 # Set environment variables
 ENV PYTHONUNBUFFERED=1 \
     POETRY_VIRTUALENVS_CREATE=false \
     POETRY_NO_INTERACTION=1
 
-# Update and install system dependencies
+# Update and install system dependencies for building
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     build-essential \
     curl \
-    wget \
-    git \
-    python3.12 \
-    python3.12-venv \
-    python3.12-dev \
-    samtools \
-    bedtools \
+    python3.11 \
+    python3.11-venv \
+    python3.11-dev \
     && rm -rf /var/lib/apt/lists/*
 
 # Ensure python3 and pip3 are the default
-RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.12 1 && \
-    update-alternatives --install /usr/bin/pip3 pip3 /usr/bin/pip3.12 1
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.11 10
 
 # Install Poetry
 RUN curl -sSL https://install.python-poetry.org | python3 -
@@ -36,11 +33,14 @@ WORKDIR /app
 # Copy pyproject.toml and poetry.lock if available
 COPY pyproject.toml poetry.lock* /app/
 
-# Install project dependencies
-RUN poetry install --no-root --only main
+# Install project dependencies without installing the package itself
+RUN poetry install --only main
 
 # Copy the rest of the project files
 COPY . /app
 
-# Install the project
-RUN poetry install --no-dev
+# Install the package
+RUN poetry install
+
+# Set the entrypoint to ldsc
+ENTRYPOINT ["poetry", "run"]

README.md

@@ -79,8 +79,8 @@ Key publications:
    Run the help command to verify that LDSC is installed correctly:
 
    ```bash
-   python ldsc.py -h
-   python munge_sumstats.py -h
+   ldsc -h
+   munge_sumstats -h
    ```
 
    If these commands display help messages with available options, the installation was successful.

ldsc.py

@@ -303,7 +303,6 @@ def ldscore(args, log):
         array_snps,
         keep_snps=keep_snps,
         keep_indivs=keep_indivs,
-        mafMin=args.maf,
     )
 
     # filter annot_matrix down to only SNPs passing MAF cutoffs
@@ -780,8 +779,8 @@ def ldscore(args, log):
     help="Population prevalence of binary phenotype (for conversion to liability scale).",
 )
 
-if __name__ == "__main__":
 
+def main():
     args = parser.parse_args()
     if args.out is None:
         raise ValueError("--out is required.")
@@ -861,3 +860,7 @@ def ldscore(args, log):
         log.log("Analysis finished at {T}".format(T=time.ctime()))
         time_elapsed = round(time.time() - start_time, 2)
         log.log("Total time elapsed: {T}".format(T=sec_to_str(time_elapsed)))
+
+
+if __name__ == "__main__":
+    main()