diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 727e356..73b6f07 100644 --- a/.github/workflows/main.yaml +++ b/.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 diff --git a/README.md b/README.md index 8209a14..f5f8250 100644 --- a/README.md +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index e499a7a..20a3226 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,7 @@ 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 } @@ -24,7 +25,7 @@ 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"] }