Implementing Base Count Coverage Depth

Overriding Branch Protection: Reviewers are absent, and this PR includes the initial project setup and is not an official repo.

.github/workflows/docs.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.11.2"
           cache: "pip"
       - name: Install Poetry
         uses: snok/install-poetry@v1

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.11.2"]
         poetry-version: ["1.8.3"]
 
     steps:

.gitignore

@@ -1,2 +1,5 @@
 .DS_Store
 poetry.lock
+.vscode/
+__pycache__/
+*.pyc

environment.yml

@@ -0,0 +1,12 @@
+name: usefulgnom
+# Conda/Mamba environment file,
+# to be used when running the snakemake pipeline, 
+# see workflow/README.md
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11.2
+  - snakemake=8.18.2
+  - poetry=1.8.3

pyproject.toml

@@ -4,13 +4,14 @@ version = "0.1.0"
 description = "Viral Genomic Utilities"
 authors = ["Gordon Julian Koehn <[email protected]>"]
 readme = "README.md"
+packages = [{include = "usefulgnom", from = "src"}]
 
 [tool.poetry.dependencies]
-python = "^3.12"
+python = "^3.11.2"
 pandas = "^2.2.2"
 matplotlib = "^3.9.2"
 seaborn = "^0.13.2"
-
+pandas-stubs = "^2.2.2.240807"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.1"
@@ -25,6 +26,7 @@ mkdocs-material = "^9.1.6"
 mkdocstrings = {extras = ["python"], version = "^0.21.2"}
 mkdocs-gen-files = "^0.4.0"
 mkdocs-literate-nav = "^0.6.0"
+setuptools = "^74.1.2"
 
 [tool.coverage.report]
 fail_under = 85.0