Add Docker support for annotation pipeline scripts

[Copilot]

Containerizes the annotation pipeline (AddedAnnotations.py, fetch_empiar.py, fetch_pubmed.py, fetch_afdb.py, generate_eupmc_links.py, compare_release.py) to simplify dependency management and ensure consistent execution environments.

Changes

• Dockerfile: Python 3.8-slim base with BLAST+ (ncbi-blast+) and required system libraries (libxml2, libxslt)
• .dockerignore: Excludes git metadata, test files, logs, and data files to reduce image size
• config.ini.docker-example: Template showing container path structure (/data/...) for volume mounts
• README.md: Added Docker sections with volume mounting patterns using read-only flags for data/config protection

Usage Pattern

docker build -t added-annotations .

docker run --rm \
  -v /host/config.ini:/config/config.ini:ro \
  -v /host/data:/data:ro \
  -v /host/output:/output \
  added-annotations python AddedAnnotations.py -w /output -f /emdb_metadata --all -t 4

Config file uses container paths that map to volume mounts:

[file_paths]
BLAST_DB = /data/uniprotkb_swissprot
components_cif = /data/components.cif
uniprot_tab = /data/uniprot.tsv

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[Copilot]

Pull request overview

Adds containerization support for running the annotation pipeline scripts in a consistent environment, including a Docker image, docker-specific config template, and Docker usage documentation.

Changes:

• Added a Dockerfile that installs Python dependencies and BLAST+ into a runnable container image.
• Added .dockerignore rules to keep the Docker build context small.
• Added config.ini.docker-example plus README documentation describing Docker build/run and volume-mount patterns.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.

File	Description
Dockerfile	Builds a Python 3.8-slim image with system deps (BLAST+, libxml2/libxslt) and installs Python requirements.
.dockerignore	Excludes git metadata, data/log/test artifacts, and most ini files from the image build context.
config.ini.docker-example	Example config showing container paths (e.g., /data/...) intended for volume mounts.
README.md	Adds Docker installation/usage guidance and updates config examples.

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[Copilot]

The Docker run examples mount the config to /config/config.ini, but the scripts currently look for config.ini next to the Python files (e.g., /app/config.ini in the container) and don’t accept a config path argument. Either adjust the mount target in the docs to /app/config.ini (or -w /app), or update the container/scripts to honor CONFIG_PATH so the documented mount path works.

[Copilot]

The README suggests running generate_eupmc_links.py in Docker without any volume mounts for its input/output files, but the script currently uses hard-coded host paths for input_tsv and output_dir (not container paths). This command is likely to fail in the container unless those paths exist. Consider updating the docs to describe the required mounts/paths (or updating the script to accept CLI args/config for input/output locations).

[Copilot]

The compare_release.py Docker example doesn’t account for runtime dependencies the container currently lacks (e.g., a mail binary) and required config sections (the script reads DB credentials from a [db] section in config.ini). As written, this documented container invocation is likely to fail unless the image is extended and the config template includes the DB fields.

[Copilot]

Typo in the table: "UniProt annpotations" should be "UniProt annotations".

Suggested change

	| uniprot.tsv | UniProt annpotations | https://rest.uniprot.org/uniprotkb/stream?fields=accession,xref_pdb,protein_name&query=((database:pdb))&format=tsv&compressed=false |
	| uniprot.tsv | UniProt annotations | https://rest.uniprot.org/uniprotkb/stream?fields=accession,xref_pdb,protein_name&query=((database:pdb))&format=tsv&compressed=false |

[Copilot]

The container sets CONFIG_PATH=/config/config.ini, but the scripts currently load config.ini from the application directory (e.g., Path(__file__).parent / "config.ini") and do not read CONFIG_PATH. As written, mounting a config at /config/config.ini won’t be picked up. Consider either (a) copying/symlinking /config/config.ini to /app/config.ini in the image/entrypoint, or (b) updating the scripts to read the config path from CONFIG_PATH (and documenting that).

Suggested change

	CMD ["python", "AddedAnnotations.py", "--help"]
	CMD ["sh", "-c", "if [ -f \"${CONFIG_PATH}\" ] && [ ! -e \"/app/config.ini\" ]; then ln -s \"${CONFIG_PATH}\" \"/app/config.ini\"; fi; exec python AddedAnnotations.py --help"]