Add CI with pre-commit and smoke tests

.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  precommit:
+    name: pre-commit hooks
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Run pre-commit (skip pytest-smoke here)
+        uses: pre-commit/action@v3.0.1
+        env:
+          SKIP: pytest-smoke
+        with:
+          extra_args: --all-files --hook-stage pre-push
+
+  smoke:
+    name: smoke import test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: ci
+          cache-environment: true
+          condarc: |
+            channels:
+              - conda-forge
+              - defaults
+
+      - name: Run smoke tests
+        shell: micromamba-shell {0}
+        run: |
+          pytest -q -m smoke -x -ra

.gitignore

@@ -1,9 +1,17 @@
-*checkpoints
-*egg_info/*
-.gitingore
-photozpy.egg-info/
-*__pycache__
-*.DS_Store*
-tests/
-src/photozpy/calibration/testing_files/
+# Jupyter / notebooks
+.ipynb_checkpoints/
 
+# Python caches
+__pycache__/
+*.py[cod]
+
+# pytest
+.pytest_cache/
+
+# packaging artifacts
+*.egg-info/
+build/
+dist/
+
+# macOS
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,90 @@
+# .pre-commit-config.yaml (example with exclude)
+default_install_hook_types: [pre-push]
+default_stages: [pre-push]  # 影响的是没有内置 stages、且你自己没写 stages 的那些 hook
+                              # 对于有内置stages，这个默认stage不会起效，需要在下面的hook
+                              # 中显式定义，比如trailing-whitespace
+default_language_version:
+  python: python3.11
+
+exclude: |
+  (?x)^(
+    docs/_build/|
+    build/|
+    dist/|
+    \.venv/|
+    \.mypy_cache/|
+    \.pytest_cache/|
+    __pycache__/|
+    .*\.ipynb
+  )$
+
+
+
+# Categories:
+# - Format: keep code style consistent
+# - Lint: catch bugs and style issues early
+# - Typing (optional): static type checks
+# - Hygiene/Safety: catch common repo issues
+# - Notebooks (optional): keep outputs clean or skip notebooks
+# - Pre-push smoke tests (optional): run a tiny subset before pushing
+
+repos:
+
+  # ---------- Lint (ruff lint only, no formatter) ----------
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
+    hooks:
+      - id: ruff
+        stages: [pre-push]
+        args: ["--select", "E9,F"]  # only check: E9=syntax/parse errors,
+                                      # F=pyflakes correctness (undefined/unused),
+                                      # S=security (bandit); avoid style rules
+
+
+  # ---------- Hygiene / Safety ----------
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        stages: [pre-push]
+        files: &code_files '\.(py|md|rst|yml|yaml|toml|json)$'
+      - id: end-of-file-fixer           # 确保文件末尾只有 1 个换行
+        stages: [pre-push]
+        files: *code_files
+      - id: check-merge-conflict        # prevent committing conflict markers
+        stages: [pre-push]
+      - id: check-yaml                  # validate .yml/.yaml
+        stages: [pre-push]
+      - id: check-json                  # validate JSON files
+        stages: [pre-push]
+      - id: check-toml                  # validate TOML files (if any)
+        stages: [pre-push]
+      - id: check-case-conflict         # warn about case-insensitive FS collisiois
+        stages: [pre-push]
+      - id: mixed-line-ending           # 统一换行风格
+        stages: [pre-push]
+        files: *code_files
+        args: ["--fix=lf"]              # 统一 LF（推荐 macOS/Linux）
+      - id: check-added-large-files     # 给「大文件」阈值一个你能接受的上限（默认 5MB）
+        stages: [pre-push]
+        args: ["--maxkb=10000"]         # 10MB；或换成你项目想要的大小
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        files: \.(py|md|rst|yml|yaml|toml)$
+        args: ["--ignore-words-list", "nd,teh,mjd,ra,dec,fwhm,psf,skycoords,skycoord"]
+
+
+  # ---------- Pre-push smoke tests (optional) ----------
+  # This does NOT replace full CI tests; it just runs a tiny, fast subset before push.
+  # You can comment this whole block out if you don't want tests in pre-commit.
+  - repo: local
+    hooks:
+      - id: pytest-smoke
+        name: "pytest -m smoke (pre-push)"
+        entry: bash -c 'pytest -q -m smoke -x --disable-warnings'
+        language: system
+        pass_filenames: false
+        always_run: true

environment.yml

@@ -0,0 +1,29 @@
+name: researchcode
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+
+  # notebooks
+  - jupyterlab
+  - ipykernel
+
+  # core scientific stack
+  - numpy
+  - scipy
+  - pandas
+  - matplotlib
+
+  # astronomy stack (按你需求可删减)
+  - astropy
+  - astroquery
+
+  # dev tools
+  - pytest
+  - pre-commit
+  - ruff
+
+  # optional: nice-to-have
+  - rich
+  - tqdm

pyproject.toml

@@ -0,0 +1,7 @@
+[tool.pytest.ini_options]
+minversion = "6.0"
+markers = [
+  "smoke: fast checks to run before push",
+]
+addopts = "-ra"
+testpaths = ["tests"]

tests/test_smoke_imports.py

@@ -0,0 +1,55 @@
+from __future__ import annotations
+
+import importlib.util
+import sys
+from pathlib import Path
+
+import pytest
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+PROJECTS_ROOT = REPO_ROOT / "Projects"
+
+# 你可以按需要继续加
+SKIP_DIRS = {
+    "__pycache__",
+    ".ipynb_checkpoints",
+    ".pytest_cache",
+    ".mypy_cache",
+}
+
+@pytest.mark.smoke
+def test_import_all_py_files_under_projects():
+    assert PROJECTS_ROOT.exists(), f"Expected folder not found: {PROJECTS_ROOT}"
+
+    # 让 Projects 内部如果有绝对导入（比如 import some_utils）更容易找到
+    sys.path.insert(0, str(PROJECTS_ROOT))
+    sys.path.insert(0, str(REPO_ROOT))
+
+    py_files = []
+    for p in PROJECTS_ROOT.rglob("*.py"):
+        parts = set(p.relative_to(PROJECTS_ROOT).parts)
+        if parts & SKIP_DIRS:
+            continue
+        py_files.append(p)
+
+    failures = []
+    for p in sorted(py_files):
+        # 给每个文件一个唯一的“假模块名”，避免冲突
+        mod_name = (
+            "smoke_projects_"
+            + p.relative_to(PROJECTS_ROOT).with_suffix("").as_posix().replace("/", "_").replace("-", "_")
+        )
+
+        try:
+            spec = importlib.util.spec_from_file_location(mod_name, p)
+            if spec is None or spec.loader is None:
+                raise RuntimeError(f"Cannot create import spec for {p}")
+            mod = importlib.util.module_from_spec(spec)
+            sys.modules[mod_name] = mod
+            spec.loader.exec_module(mod)
+        except Exception as e:
+            failures.append((str(p.relative_to(PROJECTS_ROOT)), repr(e)))
+
+    if failures:
+        msg = "\n".join([f"- {relpath}: {err}" for relpath, err in failures])
+        raise AssertionError(f"Import smoke failed for some .py files under Projects:\n{msg}\n")