MRG: upgrade the project! (#4)

* add makefile; add github CI; run black

* fix

* more fix

.github/workflows/build-test.yml

@@ -0,0 +1,50 @@
+name: "run/test examples"
+on:
+  pull_request:
+  push:
+    branches: [latest]
+jobs:
+  mamba:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: cache conda
+      uses: actions/cache@v4
+      env:
+        CACHE_NUMBER: 1
+      with:
+        path: ~/conda_pkgs_dir
+        key:
+          ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+
+    - name: setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: 3.12
+        channels: conda-forge,bioconda
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        use-mamba: true
+        mamba-version: "*"
+        activate-environment: sourmash_dev
+        auto-activate-base: false
+
+    - run: conda info
+    - run: conda list
+    - run: conda config --show
+
+    - name: install dependencies
+      shell: bash -l {0}
+      run: mamba env update -n sourmash_dev -f environment.yml
+
+    - name: install package
+      shell: bash -l {0}
+      run: pip install .
+
+    - name: build examples
+      shell: bash -l {0}
+      run: make cleanrun

.gitignore

@@ -2,3 +2,5 @@
 __pycache__
 *.egg-info/
 build
+dist
+.snakemake

Makefile

@@ -1,4 +1,6 @@
-all: test
+.PHONY: dist test_workflow
+
+all: test_workflow
 
 test: 
 	python -m pytest
@@ -8,3 +10,12 @@ install-dev:
 
 install:
 	python -m pip install .
+
+test_workflow:
+	cd test_workflow && make
+
+cleanrun:
+	cd test_workflow && make cleanall
+
+dist:
+	python -m build

environment.yml

@@ -0,0 +1,11 @@
+name: pangenomics_dev
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - sourmash>=4.8.8,<5
+    - pip
+    - pytest
+    - make
+    - snakemake-minimal