Change remote address for test data

 - To save on bandwidth costs, GitHub Action won't use GitHub's own LFS
 - Test data fetched from BSSE's GitLab LFS instead
 - Test data is zstd-compressed

.github/workflows/main.yaml

@@ -10,7 +10,16 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
-            lfs: true
+            lfs: false
+            # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS
+
+      - name: Fetch test-data
+        # NOTE to save on bandwidth costs, pull data from BSSE's GitLab LFS instead
+        run: |
+          git config --file .lfsconfig lfs.url "https://git.bsse.ethz.ch/cbg/viruses/lollipop.git/info/lfs"
+          git lfs install
+          git lfs pull
+          git lfs checkout
 
       - name: Set up Python
         uses: actions/setup-python@v4

README.md

@@ -7,7 +7,7 @@
 
 LolliPop - a tool for Deconvolution for Wastewater Genomics
 
-(a component of [V-pipe](https://github.com/cbg-ethz/v-pipe))
+The LolliPop tool is part of the [V-pipe workflow for analysing NGS data of short viral genomes](https://github.com/cbg-ethz/v-pipe).
 
 ## Description
 

pyproject.toml

@@ -17,14 +17,15 @@ python = "^3.10"
 numpy = ">=1.23"
 scipy = ">=1.9"
 pandas = ">=1.5"
+zstandard = { version = ">=0.20", optional = true }
 "ruamel.yaml" = { version = ">=0.15.80", optional = true }
 strictyaml = { version = ">=1.7", optional = true }
 tqdm = { version = ">=4.64", optional = true }
 click = { version = "^8.0", optional = true }
 click-option-group = { version = "^0.5", optional = true }
 
 [tool.poetry.extras]
-cli = [ "ruamel.yaml", "strictyaml", "tqdm", "click", "click-option-group" ]
+cli = [ "zstandard", "ruamel.yaml", "strictyaml", "tqdm", "click", "click-option-group" ]
 
 [tool.poetry.scripts]
 lollipop = { callable = "lollipop.cli:cli", extras = ["cli"] }