feat: adds slurm job submission

.github/workflows/tag_and_publish.yml

@@ -3,9 +3,7 @@ on:
   push:
     branches:
       - main
-# Remove line 61 to enable automated semantic version bumps.
-# Change line 67 from "if: false" to "if: true" to enable PyPI publishing. 
-# Requires that svc-aindscicomp be added as an admin to repo.
+
 jobs:
   update_badges:
     runs-on: ubuntu-latest
@@ -16,10 +14,10 @@ jobs:
         ref: ${{ env.DEFAULT_BRANCH }}
         fetch-depth: 0
         token: ${{ secrets.SERVICE_TOKEN }}
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: Install dependencies
       run: | 
         python -m pip install -e .[dev] --no-cache-dir
@@ -62,28 +60,31 @@ jobs:
         add: '["README.md"]'
   tag:
     needs: update_badges
-    if: ${{github.event.repository.name == 'aind-library-template'}}
     uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
     secrets:
       SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
   publish:
-    needs: tag
-    if: false
     runs-on: ubuntu-latest
+    needs: tag
     steps:
       - uses: actions/checkout@v3
       - name: Pull latest changes
         run: git pull origin main
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to Github Packages
+        uses: docker/login-action@v2
         with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          pip install --upgrade setuptools wheel twine build
-          python -m build
-          twine check dist/*
-      - name: Publish on PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build image and push to GitHub Container Registry
+        uses: docker/build-push-action@v3
         with:
-          password: ${{ secrets.AIND_PYPI_TOKEN }}
+          # relative path to the place where source code with Dockerfile is located
+          context: .
+          push: true
+          tags: |
+            ghcr.io/allenneuraldynamics/aind-airflow-jobs:${{ needs.tag.outputs.new_version }}
+            ghcr.io/allenneuraldynamics/aind-airflow-jobs:latest

.github/workflows/test_and_lint.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10' ]
+        python-version: [ '3.10', '3.11' ]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

Dockerfile

@@ -0,0 +1,8 @@
+from python:3.10-slim
+
+WORKDIR /app
+ADD src ./src
+ADD pyproject.toml .
+ADD setup.py .
+
+RUN pip install . --no-cache-dir

doc_template/source/conf.py

@@ -1,12 +1,15 @@
 """Configuration file for the Sphinx documentation builder."""
+
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from datetime import date
+
 # -- Path Setup --------------------------------------------------------------
-from os.path import dirname, abspath
+from os.path import abspath, dirname
 from pathlib import Path
-from datetime import date
+
 from aind_airflow_jobs import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "aind-airflow-jobs"
 description = "Generated from aind-library-template"
 license = {text = "MIT"}
-requires-python = ">=3.7"
+requires-python = ">=3.10"
 authors = [
     {name = "Allen Institute for Neural Dynamics"}
 ]
@@ -17,6 +17,9 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
+    "aind-slurm-rest",
+    "pydantic-settings",
+    "pydantic"
 ]
 
 [project.optional-dependencies]
@@ -38,7 +41,7 @@ version = {attr = "aind_airflow_jobs.__version__"}
 
 [tool.black]
 line-length = 79
-target_version = ['py36']
+target_version = ['py310']
 exclude = '''
 
 (

src/aind_airflow_jobs/__init__.py

@@ -1,2 +1,3 @@
-"""Init package"""
+"""Package to manage airflow jobs"""
+
 __version__ = "0.0.0"