Use ARG for platform specification and fix Python 3.11 compatibility

- Move platform specification from --platform flag to ARG TARGETPLATFORM in Dockerfiles
- Fix deprecated 'rU' file mode in tabulate_naive_probs.py (removed in Python 3.11)
- Standardize indentation in Dockerfile.base RUN commands

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: jgallowa07

Dockerfile

@@ -4,12 +4,13 @@
 #
 # Platform is set to linux/amd64 because partis-bcr contains x86-specific code (SSE2 intrinsics)
 # RevBayes with bundled Boost gives ~180x faster MCMC performance than v1.3.0+ without Boost
+ARG TARGETPLATFORM=linux/amd64
 
 # Stage 1: Get pre-compiled RevBayes with bundled Boost from Buster base image
-FROM --platform=linux/amd64 quay.io/matsengrp/linearham:2025-12-01-base-image AS revbayes-builder
+FROM quay.io/matsengrp/linearham:2025-12-01-base-image AS revbayes-builder
 
 # Stage 2: Modern Debian Bookworm for Python packages
-FROM --platform=linux/amd64 debian:bookworm-slim
+FROM debian:bookworm-slim
 
 # Metadata labels
 LABEL org.opencontainers.image.source="https://github.com/matsengrp/linearham"

Dockerfile.base

@@ -7,7 +7,7 @@
 
 ARG TARGETPLATFORM=linux/amd64
 # Use Debian Buster (oldoldstable) for g++ 8.3 compatibility with older RevBayes
-FROM --platform=${TARGETPLATFORM} debian:buster-slim
+FROM debian:buster-slim
 
 # Set TERM to enable colored-traceback to work in non-TTY environments
 ENV TERM=xterm
@@ -19,8 +19,8 @@ LABEL org.opencontainers.image.licenses="GPL-3.0"
 
 # Configure apt to use archive repositories (Buster is now archived)
 RUN echo "deb http://archive.debian.org/debian/ buster main contrib non-free" > /etc/apt/sources.list && \
-    echo "deb http://archive.debian.org/debian-security buster/updates main contrib non-free" >> /etc/apt/sources.list && \
-    echo 'Acquire::Check-Valid-Until "false";' > /etc/apt/apt.conf.d/99no-check-valid-until
+  echo "deb http://archive.debian.org/debian-security buster/updates main contrib non-free" >> /etc/apt/sources.list && \
+  echo 'Acquire::Check-Valid-Until "false";' > /etc/apt/apt.conf.d/99no-check-valid-until
 
 # Install all dependencies needed for building RevBayes and linearham
 RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -77,8 +77,8 @@ RUN ./build.sh
 
 # Install RevBayes to standard location
 RUN mkdir -p /usr/local/bin && \
-    cp /tmp/revbayes/projects/cmake/rb /usr/local/bin/rb && \
-    chmod +x /usr/local/bin/rb
+  cp /tmp/revbayes/projects/cmake/rb /usr/local/bin/rb && \
+  chmod +x /usr/local/bin/rb
 
 # Clean up build artifacts to reduce image size
 RUN rm -rf /tmp/revbayes

scripts/tabulate_naive_probs.py

@@ -35,7 +35,7 @@
     aa_naive_seqs_d = {("naive" + str(i)): seq for i, seq in enumerate(aa_naive_seqs)}
     write_to_fasta(aa_naive_seqs_d, args.output_base + ".fasta")
 
-    with open(args.output_base + ".fasta", "rU") as f:
+    with open(args.output_base + ".fasta", "r") as f:
         seqs = w.read_seq_data(f)
     data = w.LogoData.from_seqs(seqs)
     subprocess.check_call(("rm " + args.output_base + ".fasta").split())