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Development Setup

This project can be edited without the full reference datasets, but meaningful runtime checks need local Python dependencies and, for the full annotation pipeline, BLAST reference data.

Local Python Environment

Create a virtual environment and install the package in editable mode:

python3 -m venv .venv
. .venv/bin/activate
python3 -m pip install --upgrade pip setuptools wheel
python3 -m pip install -e ".[dev]"

If editable install is not needed, installing the pinned runtime dependencies is enough:

python3 -m pip install -r requirements.txt

Local Configuration

Copy the example local config and adjust paths:

cp pdb2net/configs/config.local.example.json pdb2net/configs/config.local.json

config.local.json is ignored by Git. Keep machine-specific input folders, output folders, reference files, and BLAST database paths there.

For automated or Codex-driven checks, prefer:

{
  "open_in_cytoscape": false,
  "workers": {
    "parsing": 1,
    "blast_threads": 1
  }
}

This avoids opening Cytoscape and keeps fixture runs small and predictable.

Environment Check

Run:

python3 scripts/check_environment.py

The check reports:

  • Python version
  • required Python packages
  • optional external commands such as blastp, makeblastdb, and cytoscape
  • whether configured local reference/input/output paths exist

Missing Cytoscape is acceptable for headless checks. Missing BLAST tools or reference files only block the BLAST-backed annotation path, not pure code editing.

If Matplotlib warns that its default config directory is not writable, set a temporary cache directory before running imports or scripts:

export MPLCONFIGDIR=/tmp/pdb2net-matplotlib

Full Pipeline Requirements

The full pipeline needs:

  • a folder with .pdb, .cif, or .mmcif inputs
  • pdb_seqres.txt
  • pdb_chain_uniprot.tsv
  • uniprot_sprot.fasta
  • a BLAST database created from uniprot_sprot.fasta
  • blastp and makeblastdb available in PATH or configured explicitly

Run the current script entry point with:

python3 -m pdb2net.main

Do not run full batch jobs on large datasets during routine development. Use tiny fixtures or a small local input folder first.

Goldstandard CX2 Regression Check

Use the accepted CX2 output directory as a semantic goldstandard. The check compares graph semantics, annotations, visual style semantics, and layout metrics without relying on byte-for-byte CX2 equality.

Compare an existing output directory:

python3 scripts/run_goldstandard_check.py \
  --actual /mnt/e/Networks/2026-06-13_14-44-59 \
  --expected /mnt/e/Goldstandard/6m17_6w41/expected

Run the configured headless pipeline first, then compare the newest output:

python3 scripts/run_goldstandard_check.py \
  --expected /mnt/e/Goldstandard/6m17_6w41/expected

Reports are written to /tmp/pdb2net-goldstandard by default. A FAIL status means graph semantics, annotations, required style semantics, or expected files changed. A WARN status is acceptable for intentional layout-only differences unless --fail-on-warn is used.