Merge pull request #5 from logsdon-lab/docs/revisions2

chore/docs: Merged all dependencies into env.yaml.

.github/workflows/main.yaml

@@ -18,7 +18,7 @@ jobs:
 
     - name: Install Snakemake and testing dependencies.
       run: |
-        pip install -r <(yq -r '.dependencies[] | select(type == "!!map") | to_entries[].value[]' test/env_dev.yaml)
+        pip install -r <(yq -r '.dependencies[] | select(type == "!!map") | to_entries[].value[]' env.yaml)
 
     - name: Install Singularity.
       uses: singularityhub/install-singularity@main

README.md

@@ -112,10 +112,10 @@ Multiple samples can be provided via the configfile. Each sample should contain
 See [`docs/ISSUES.md`](docs/ISSUES.md) for edge-cases and effects of parameter tuning.
 
 ## Testing
-Set up the dev conda environment and pull test data with [`git-lfs`](https://git-lfs.com/).
+Set up the conda environment and pull test data with [`git-lfs`](https://git-lfs.com/).
 ```bash
-conda env create --name test_cdr_finder -f test/env_dev.yaml
-conda activate test_cdr_finder
+conda env create --name cdr_finder -f env.yaml
+conda activate cdr_finder
 git lfs install && git lfs pull
 ```
 

env.yaml

@@ -2,5 +2,10 @@ channels:
   - conda-forge
 dependencies:
   - python==3.12
+  - anaconda::git-lfs
   - pip:
     - snakemake==8.18.2
+    - pytest
+    - intervaltree==3.1.0
+    - polars==0.20.31
+    - scipy==1.14.1