Merge pull request #58 from kaitj/maint/repo_updates

Dependency and repo organization updates

.github/ISSUE_TEMPLATE.md

@@ -4,5 +4,5 @@ Briefly describe the issue you are experiencing (or feature you want to see adde
 
 ## Environment
 
-* Operating System
-* Label merge version
+- Operating System
+- Labelmerge version

.github/auto_assign.yml

@@ -4,18 +4,15 @@ addReviewers: true
 
 # Set to true to add assignees to pull requests
 addAssignees: author
-
 # A list of reviewers to be added to pull requests (GitHub user name)
 reviewers:
   - kaitj
-  - tkkuehn
+  - arunthurai
   - ataha24
   - Bradley-karat
-
 # A number of reviewers added to the pull request
 # Set 0 to add all the reviewers (default: 0)
 numberOfReviewers: 0
-
 # A list of assignees, overrides reviewers if set
 # assignees:
 #   - assigneeA

.github/release-drafter.yml

@@ -2,7 +2,6 @@
 name-template: $RESOLVED_VERSION
 tag-template: v$RESOLVED_VERSION
 filter-by-commitish: true
-
 template: |
   ## Changes
   $CHANGES
@@ -15,12 +14,9 @@ categories:
     labels: [maintenance, test]
   - title: 📝 Documentation
     labels: [documentation]
-
 exclude-labels: [skip_changelog]
-
 change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
 change-title-escapes: \<*_&    # You can add  # and @ to disable mentions, and add ` to disable code blocks.
-
 version-resolver:
   # major:
   #   labels:

.github/workflows/assign_reviewers.yml

@@ -1,17 +1,8 @@
 ---
 name: Assign reviewer
-
 on:
   pull_request_target:
     types: [opened, ready_for_review]
-
 jobs:
-  assign:
-    runs-on: ubuntu-latest
-    if: github.event.pull_request.assignee == null
-
-    steps:
-      - name: Assign reviewer
-        uses: kentaro-m/auto-assign-action@v1.2.5
-        with:
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  assign-reviewer:
+    uses: khanlab/actions/.github/workflows/workflow-pr_task-assignReviewer.yml@v0.2.1

.github/workflows/bump_version.yml

@@ -4,71 +4,8 @@ on:
   pull_request_target:
     types: [closed]
 jobs:
-  build:
+  bump-version:
     if: github.event.pull_request.merged == true
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout master branch
-        uses: actions/checkout@v3
-        with:
-          ref: ${{ github.event.pull_request.base.ref }}
-
-      - name: Update changelog
-        uses: release-drafter/release-drafter@v5
-        id: release-drafter
-        with:
-          commitish: ${{ github.event.pull_request.base.ref }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.BP_PAT_TOKEN }}
-
-      - name: Get previous release version
-        run: |
-          echo "PREV_VER=$(cat pyproject.toml | grep -o -E '(version\s=\s)([[:punct:]])([0-9]+\.[0-9]+\.[0-9]+.+)([[:punct:]])' | cut -d ' ' -f 3 | tr -d '"')" >> $GITHUB_ENV
-
-      - name: Get previous bump version
-        env:
-          PREV_VER: ${{ env.PREV_VER }}
-        run: |
-          if [[ "$PREV_VER" != *"-pre."* ]]; then
-            echo "OLD_BUMP=0" >> $GITHUB_ENV
-          else
-            echo "OLD_BUMP=$(echo $PREV_VER | cut -d '.' -f 4)" >> $GITHUB_ENV
-          fi
-
-      - name: Bump version
-        env:
-          BUMP_VER: ${{ env.OLD_BUMP }}
-        run: |
-          echo "NEW_BUMP=$(($BUMP_VER + 1))" >> $GITHUB_ENV
-
-      - name: Set new release version
-        env:
-          RD_RELEASE: ${{ steps.release-drafter.outputs.name }}
-        run: |
-          if [ ! -z "$RD_RELEASE" ]; then
-            echo "NEW_RELEASE=$RD_RELEASE" >> $GITHUB_ENV
-          else
-            echo "NEW_RELEASE=0.1.0" >> $GITHUB_ENV
-          fi
-
-      - name: Update version in pyproject.toml
-        uses: jacobtomlinson/gha-find-replace@master
-        with:
-          include: pyproject.toml
-          find: version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"
-          replace: version = "${{ env.NEW_RELEASE }}-pre.${{ env.NEW_BUMP }}"
-
-      - name: Commit updates
-        env:
-          SNAKEBIDS_VERSION: ${{ env.NEW_RELEASE }}-pre.${{ env.NEW_BUMP }}
-        run: |
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-          git diff-index --quiet HEAD || git commit -m "Bump version to $SNAKEBIDS_VERSION" -a
-
-      - name: Push changes
-        uses: CasperWA/push-protected@v2
-        with:
-          branch: ${{ github.event.pull_request.base.ref }}
-          token: ${{ secrets.BP_PAT_TOKEN }}
-          unprotect_reviews: true
+    uses: khanlab/actions/.github/workflows/workflow-version_task-semverGithub.yml@v0.2.1
+    secrets:
+      BP-PAT: ${{ secrets.BP_PAT_TOKEN }}

.github/workflows/deploy.yml

@@ -0,0 +1,17 @@
+---
+name: Deploy packages
+on:
+  workflow_dispatch:
+  push:
+    tags: [v*]
+jobs:
+  deploy-docker:
+    uses: khanlab/actions/.github/workflows/workflow-release_task-deployDocker.yml@v0.2.1
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
+
+  deploy-pypi:
+    uses: khanlab/actions/.github/workflows/workflow-release_task-deployPypi.yml@v0.2.1
+    secrets:
+      PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/quality.yml

@@ -1,62 +1,27 @@
 ---
-name: Lint workflow
-
+name: Lint and format workflow
 on:
   push:
     branches: ["*", "!push-action/*"]
   pull_request:
     branches: ["*", "!push-action/*"]
-
 jobs:
   quality:
     name: Lint code
     if: github.event.pull_request.merged == false
     runs-on: ubuntu-latest
-
     steps:
-      - name: Clone repo
-        uses: actions/checkout@master
-
-      - name: Setup Python 3.10
-        uses: actions/setup-python@v4
+      - name: Setup Python environment
+        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.2.1
         with:
           python-version: "3.10"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-3.10
-          restore-keys: ${{ runner.os }}-pip-3.10
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.4.2
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-3.10
-
-      - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --with dev
-
       - name: yamlfix
         run: poetry run poe yamlfix-check
-
+      - name: ruff
+        run: poetry run poe ruff-check
       - name: isort
         run: poetry run poe isort-check
-
       - name: black
         run: poetry run poe black-check
-
-      - name: flake8
-        run: poetry run poe flake8
-
       - name: snakefmt
         run: poetry run poe snakefmt-check

.github/workflows/release.yml

@@ -1,114 +1,16 @@
 ---
 name: Release package
-
 on:
   workflow_dispatch:
     inputs:
       comments:
         description: Comments
         required: false
-
 jobs:
-  release_changelog:
-    name: Release changelog
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Print author
-        run: |
-          echo "Author: ${{ github.triggering_actor }}"
-          echo "Comments: ${{ github.event.inputs.comments }}"
-
-      - name: Extract branch name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
-
-      - uses: actions/checkout@master
-        with:
-          ref: ${{ steps.extract_branch.outputs.branch }}
-
-      - name: Draft change log
-        uses: release-drafter/release-drafter@v5
-        id: release-drafter
-        with:
-          commitish: ${{ steps.extract_branch.outputs.branch }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Set new release version
-        env:
-          RD_RELEASE: ${{ steps.release-drafter.outputs.name }}
-        run: |
-          if [ ! -z "$RD_RELEASE" ]; then
-            echo "NEW_RELEASE=$RD_RELEASE" >> $GITHUB_ENV
-          else
-            echo "NEW_RELEASE=0.1.0" >> $GITHUB_ENV
-          fi
-
-      - name: Update pipeline description
-        uses: jacobtomlinson/gha-find-replace@master
-        with:
-          include: 'scattr/pipeline_description.json'
-          find: '"Version": "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
-          replace: '"Version": "${{ env.NEW_RELEASE }}"'
-
-      - name: Update version in pyproject.toml
-        uses: jacobtomlinson/gha-find-replace@master
-        with:
-          include: pyproject.toml
-          find: version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"
-          replace: version = "${{ env.NEW_RELEASE }}"
-
-      - name: Commit updates
-        env:
-          LATEST_VERSION: ${{ env.NEW_RELEASE }}
-        run: |
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-          git diff-index --quiet HEAD || git commit -m "Bump version to $LATEST_VERSION" -a
-
-      - name: Push changes
-        uses: CasperWA/push-protected@v2
-        with:
-          token: ${{ secrets.BP_PAT_TOKEN }}
-          unprotect_reviews: true
-
-      - name: Publish change log
-        uses: release-drafter/release-drafter@v5
-        with:
-          commitish: ${{ steps.extract_branch.outputs.branch }}
-          publish: true
-          name: ${{ env.NEW_RELEASE }}
-          tag: v${{ env.NEW_RELEASE }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.BP_PAT_TOKEN }}
-
-  # deploy_pypi:
-  #   name: PyPI Deploy
-  #   runs-on: ubuntu-latest
-  #   needs: [release_changelog]
-
-  #   steps:
-  #     - uses: actions/checkout@master
-  #       with:
-  #         ref: ${{ steps.extract_branch.outputs.branch }}
-
-  #     - name: Set up Python
-  #       uses: actions/setup-python@v4.3.1
-  #       with:
-  #         python-version: '3.9'
-
-  #  #----------------------------------------------
-  #  #  -----  install & configure poetry  -----
-  #  #----------------------------------------------
-  #     - name: Install Poetry
-  #       uses: snok/install-poetry@v1
-  #       with:
-  #         virtualenvs-create: true
-  #         virtualenvs-in-project: true
-
-  #     - name: Build and publish
-  #       env:
-  #         POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_API_TOKEN }}
-  #       run: |
-  #         poetry publish --build
+  release_package:
+    uses: khanlab/actions/.github/workflows/workflow-release_task-publishGithub.yml@v0.2.1
+    with:
+      comments: ${{ github.event.inputs.comments }}
+      pipeline-description: true
+    secrets:
+      BP-PAT: ${{ secrets.BP_PAT_TOKEN }}