`Added`
- `bactopia pull` to pre-build Singularity images
- `--singularity_cache` parameter to set location of image downloads
- `--registry` to choose Docker registry to use (DockerHub, GitHub, Quay)
- `--max_downloads` sets maximum number of downloads (FASTQ/assembly) allowed at once
- `--min_time` sets the minimum amount of time a job should be given
- `bactopia search` now uses POST requests, and groups accessions into single query
- strip HTML from FASTA headers used in BLAST
- Dockerfiles now have conda.md5 label to determine if rebuild is necessary
- MD5 is updated in Dockerfile when env is updated
- AMRFinder+ database is now provided by `bactopia datasets`
- Parameterized profile (slurm, awsbatch, etc...) variables
- `bactopia build`
- will retry in case of HTTP connection issues
- `--include_tool` will build Bactopia Tool environments
- GitHub Actions
- build Docker containers on new release (or manual trigger)
- test that the Conda environment yamls are still valid
- test bactopia with conda on Linux and OSX
- test bactopia on Linux with Docker and Singularity
`Fixed`
- redundant environment version files
- failed FASTQ/Assembly downloads no longer stop whole run
- `--max_retry` is honored now
- antimicrobial_resistance process honors `amrdir` variable
- change directory `antimicrobial_resistance` to `antimicrobial-resistance`
- rename `check_staging.py` to `check-staging.py` for consistency
- Bactopia not producing valid exit code on failure
`Removed`
- `--containerPath` variable is replaced by `--singularity_cache`
- Native Singularity recipes, will now convert Docker to Singularity
- docs are now on bactopia.github.io repo