set up cicd (#1)

* set up cicd

* fix linting

* install dev deps in cicd

* update flake8

* add pytest

* use pdm in cicd

* add tests for specs

* add xarray

.github/workflows/ci-pre-commit.yml

@@ -0,0 +1,16 @@
+name: linting
+
+on:
+  push:
+    branches: "*"
+  pull_request:
+    branches: "*"
+
+jobs:
+  linting:
+    name: "pre-commit hooks"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]

.github/workflows/ci-pypi-deploy.yml

@@ -0,0 +1,24 @@
+name: package-release
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+     - master
+  release:
+    types:
+      - published
+
+jobs:
+  build:
+    name: build and upload release to pypi
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: casperdcl/deploy-pypi@v2
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}
+          pip: wheel -w dist/ --no-deps .
+          upload: ${{ github.event_name == 'release' && github.event.action == 'published' }}

.github/workflows/python-package-pip.yml

@@ -0,0 +1,22 @@
+name: test
+on: [push, pull_request]
+
+jobs:
+  test:
+    name: Test pip install python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.9]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
+      - name: Install package with pdm
+        run: |
+          pdm install
+      - name: Run tests
+        run: |
+          pdm run python -m pytest

.pre-commit-config.yaml

@@ -16,6 +16,6 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 5.0.4
     hooks:
       - id: flake8

pyproject.toml

@@ -9,6 +9,7 @@ dependencies = [
     "pyyaml>=6.0.1",
     "loguru>=0.7.2",
     "zarr>=2.17.2",
+    "xarray>=2024.3.0",
 ]
 requires-python = ">=3.9"
 readme = "README.md"
@@ -25,6 +26,7 @@ distribution = true
 [tool.pdm.dev-dependencies]
 dev = [
     "pre-commit>=3.7.0",
+    "pytest>=8.1.1",
 ]
 
 [tool.isort]

src/mllam_data_interface/check.py

@@ -1,8 +1,8 @@
+import importlib
 from pathlib import Path
 
 import xarray as xr
 import yaml
-import importlib
 
 SPECS_ROOT_PATH = Path(__file__).parent.parent.parent / "specs"
 
@@ -30,13 +30,18 @@ def load_spec(spec_identifier: str):
     spec_name, spec_version = spec_identifier.split(":")
 
     # fp = SPECS_ROOT_PATH / spec_name / f"{spec_version}.yaml"
-    fp = importlib.resources.files(__package__) / "specs" / spec_name / f"{spec_version}.yaml"
+    fp = (
+        importlib.resources.files(__package__)
+        / "specs"
+        / spec_name
+        / f"{spec_version}.yaml"
+    )
     if not fp.exists():
         raise ValueError(f"Spec file {fp} for {spec_identifier} does not exist.")
 
     with open(fp, "r") as f:
         spec = yaml.safe_load(f)
-    
+
     return spec