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build: pixi.lock, conda environment.yml, Dockerfile, GHCR release workflow - #12
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…default - README: goals, workflow diagrams, supported lineages, curation process with links, layout, quickstart (verified on GCF_001638985.1), usage, validation and limits, authors, citation. - NCBI identity: $MATPREDICT_NCBI_EMAIL / $MATPREDICT_NCBI_API_KEY, else the [ncbi] table of ~/.config/matpredict/config.toml ($MATPREDICT_CONFIG, $XDG_CONFIG_HOME). No default address; one warning when unset. Requests send tool=MATPredict. - HTTP cache key leaves out email/api_key/tool; pre-change entries (full URL with the old default e-mail) are found and copied forward, so the existing cache stays valid (checked on 7 of 8 sampled taxids). - pyproject version 0.6.0; CHANGELOG entries for 0.6.0 and Unreleased. 998 tests pass (11 new). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
… start-up The CLI builds a config to list the --phylum choices, so the warning printed for --help and --version. NcbiClient now warns once, when it builds a URL without an e-mail. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…elease workflow - pixi.lock tracked (was git-ignored) so images and environments are reproducible. - environment.yml exported from pixi.toml for conda/mamba users. - Dockerfile: pixi 0.71.3 build stage installs the locked environment; Ubuntu 24.04 runtime carries the env, src/ and db/; ENTRYPOINT matpredict. - .github/workflows/docker.yml: PRs build + smoke-test (tools on PATH, pyhmmer and MATPredict import, --version, detect --help); v* tags, published releases and workflow_dispatch also push ghcr.io/stajichlab/matpredict (:version, :major.minor, :latest, :sha). - README: Docker, Apptainer and conda install sections. Locked install checked locally: all tools present, matpredict --version 0.6.0. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
Stacked on #11; merge #11 first. After that merge, this PR shows only the build commit.
pixi.lockcommitted. It was git-ignored. Builds now use exact locked versions.environment.ymlfor conda/mamba users, exported frompixi.tomlwithpixi workspace export conda-environment.Dockerfile:ghcr.io/prefix-dev/pixi:0.71.3-noble) runspixi install --lockedsrc/anddb/ENTRYPOINT matpredict;MATPREDICT_DB_ROOT=/app/db; the cache goes in/data.github/workflows/docker.yml:pyhmmerandMATPredictimport,--versionworks, anddetect --helpworks.v*tag, a published release or a manual run also pushesghcr.io/stajichlab/matpredictwith the tags:<version>,:<major>.<minor>,:latestand:sha-<short>.Test plan
pixi install --locked -e defaultfrom the committed lock: all tools present,matpredict --versiongives 0.6.0pytest: 999 passedv0.6.1tag, or run the workflow by hand, to publish the first image🤖 Generated with Claude Code