update CI for deployment

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* membrain-seg version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

.github/workflows/ci.yml

@@ -9,13 +9,21 @@ on:
   pull_request:
   workflow_dispatch:
   schedule:
-    - cron: "0 0 * * 0" # every week (for --pre release tests)
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+# cancel in-progress runs that use the same workflow and branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
   test:
@@ -24,43 +32,38 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
-        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        platform: [ubuntu-latest] #, macos-latest, windows-latest]
 
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache-dependency-path: "pyproject.toml"
           cache: "pip"
 
-      # if running a cron job, we add the --pre flag to test against pre-releases
-      - name: Install dependencies
+      - name: Install Dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install -e .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
 
-      - name: Test
+      - name: 🧪 Run Tests
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
 
-      # If something goes wrong, we can open an issue in the repo
-      - name: Report --pre Failures
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
         if: failure() && github.event_name == 'schedule'
         uses: JasonEtco/create-an-issue@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PLATFORM: ${{ matrix.platform }}
           PYTHON: ${{ matrix.python-version }}
           RUN_ID: ${{ github.run_id }}
-          TITLE: '[test-bot] pip install --pre is failing'
+          TITLE: "[test-bot] pip install --pre is failing"
         with:
           filename: .github/TEST_FAIL_TEMPLATE.md
           update_existing: true
@@ -74,28 +77,32 @@ jobs:
     if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
     runs-on: ubuntu-latest
 
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-      - name: Set up Python
+      - name: 🐍 Set up Python
         uses: actions/setup-python@v4
         with:
           python-version: "3.x"
 
-      - name: install
+      - name: 👷 Build
         run: |
-          git tag
-          pip install -U pip build twine
+          python -m pip install build
           python -m build
-          twine check dist/*
-          ls -lh dist
 
-      - name: Build and publish
-        run: twine upload dist/*
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
       - uses: softprops/action-gh-release@v1
         with:
           generate_release_notes: true
+          files: './dist/*'