MRG: subsearch & refactoring (#17)

* WIP: more cleanup, refactoring, and upgrades

* prepare for multiple databases

* split out upload functionality

* cleanup

* refactor

* cleanup

* refactor

* comments

* use url_for properly

* mostly working

* subsearch flat

* add tests, plants, download

* fix path

* add test files

* override .gitignore in places

* turn off messages

* upd plants

* add subsearch check

* bump version

* update README

Author: ctb

Makefile

@@ -6,5 +6,11 @@ dist:
 black:
 	python -m black chill_filter_web
 
+dbzip:
+	cd prepare-db && zip -r ../chill-filter-db.zip outputs/* \
+	    downloads/gtdb-rs220-phylum.sig.zip \
+	    downloads/genbank-plants-2024.07.k51.s100_000.sig.zip \
+	    downloads/podar-ref.sig.zip
+
 test:
 	pytest

README.md

@@ -19,8 +19,8 @@ conda activate chill
 2. Download the databases from [the Open Science Framework project](https://osf.io/m85ux/), and unpack them into `prepare-db/outputs/`.
 
 ```
-curl -JLO https://osf.io/download/bzu3v/
-unzip -d prepare-db/ -nu chill-filter-db-0.2.zip
+curl -JLO https://osf.io/download/5fw2v/
+unzip -d prepare-db/ -nu chill-filter-db-0.4.zip
 ```
 
 3. Run snakemake in the `sample-db/` directory to index the databases. It should take a few minutes at most.
@@ -38,4 +38,4 @@ python -m chill_filter_web -p 5000
 
 This will start a server at http://localhost:5000/
 
-5. Try uploading some FASTQ or FASTA files, or checkout the examples!
+5. Try uploading some FASTQ or FASTA files, or check out the examples!