move to pyproject.toml based setup (#43)

* move to pyproject.toml based setup

* fix imports?

* fix imports?

* Update tests/test_writing.py

* add ci

* add typing-extensions dep

* fix import

* remove mac and windows tests

* temporarily disable 3.12 tests

.copier-answers.yml

@@ -0,0 +1,11 @@
+# Do not edit - changes here will be overwritten by Copier
+_commit: v1
+_src_path: gh:pydev-guide/pyrepo-copier
+author_email: [email protected]
+author_name: Alister Burt
+github_username: teamtomo
+mode: tooling
+module_name: starfile
+project_name: starfile
+project_short_description: STAR file I/O in Python
+

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* starfile 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/dependabot.yml

@@ -0,0 +1,10 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

.github/workflows/ci.yml

@@ -0,0 +1,108 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # 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@v4
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", ] # "3.12"]
+        platform: [ubuntu-latest, ] # ...macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # 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: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # 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"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    name: Deploy
+    needs: test
+    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@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - 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/*'

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.15
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.1.3
+    hooks:
+      - id: ruff
+        args: [--fix]
+
+  - repo: https://github.com/psf/black
+    rev: 23.10.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.6.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        # # you have to add the things you want to type check against here
+        # additional_dependencies:
+        #   - numpy