quicklook-package 1.3.2__tar.gz → 1.6__tar.gz

quicklook_package-1.6/.github/workflows/build-and-test.yml

@@ -0,0 +1,66 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    # Hard ceiling so a stalled external call (e.g. astroquery/astropy reaching
+    # a service) fails the job in minutes instead of hanging until GitHub's
+    # 6-hour default and surfacing only as "The operation was canceled."
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache pip packages
+        uses: actions/cache@v6
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Cache Lightkurve data
+        uses: actions/cache@v6
+        with:
+          path: ~/.lightkurve/cache/mastDownload
+          key: ${{ runner.os }}-lightkurve-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-lightkurve-
+
+      - name: Remove corrupted FITS (if any)
+        run: |
+          find ~/.lightkurve/cache/mastDownload -type f -name "*.fits" -size -1M -delete || true
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,gui]"
+
+      - name: Run tests
+        # --timeout converts a hung test (e.g. an unmocked network call) into a
+        # failure with a traceback pinpointing the stall, instead of wedging the
+        # whole -n auto run. thread method is xdist-safe and cross-platform.
+        run: pytest -v -m "not notebook and not network" -n auto --timeout=180 --timeout-method=thread
+
+      - name: Verify package builds cleanly
+        run: |
+          pip install --upgrade build
+          python -m build --sdist --wheel

{quicklook_package-1.3.2 → quicklook_package-1.6}/.github/workflows/release.yml

@@ -3,27 +3,32 @@ name: Publish to PyPI
 on:
   workflow_dispatch: #optional manual run
   release:
-    types: [published] # run only when published after creating a tag (e.g. v.1.4)
+    types: [published]
 
 jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install build tools
-        run: |
-          pip install build twine
+        run: pip install --upgrade build twine
+
+      - name: Clean old builds
+        run: rm -rf dist/*
 
       - name: Build package
-        run: python -m build
+        run: python -m build --sdist --wheel
+
+      - name: Verify distributions
+        run: twine check dist/*
 
       - name: Publish to PyPI
         run: twine upload dist/*

{quicklook_package-1.3.2 → quicklook_package-1.6}/.gitignore

@@ -76,7 +76,7 @@ docs/_build/
 target/
 
 # Jupyter Notebook
-.ipynb_checkpoints
+.ipynb_checkpoints*
 
 # IPython
 profile_default/
@@ -152,6 +152,15 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# GUI runtime outputs (generated by ql-gui)
+quicklook/app/static/outputs/
+
+# Local test run artifacts (HDF5 outputs produced by manual TLS runs in tests/)
+tests/*.h5
+
+# MkDocs build output
+site/
+
 # PyCharm
 #  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore

quicklook_package-1.6/.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
+    hooks:
+        - id: ruff-check
+          args: [--fix]
+        - id: ruff-format

quicklook_package-1.6/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+python:
+  install:
+    - requirements: docs/requirements.txt

quicklook_package-1.6/CLAUDE.md

@@ -0,0 +1,55 @@
+# Python Package Management with uv
+
+Use uv exclusively for Python package management in this project.
+
+## Package Management Commands
+
+- All Python dependencies **must be installed, synchronized, and locked** using uv
+- Never use pip, pip-tools, poetry, or conda directly for dependency management
+
+Use these commands:
+
+- Install dependencies: `uv add <package>`
+- Remove dependencies: `uv remove <package>`
+- Sync environment: `uv sync`
+- Lock dependencies: `uv lock`
+
+## Running Python Code
+
+- Run a Python script with `uv run <script-name>.py`
+- Run Python tools with `uv run <tool>` (e.g. `uv run pytest`, `uv run ruff`, `uv run mypy`, `uv run pre-commit`)
+- Launch a Python REPL with `uv run python`
+
+
+## Linting and formatting
+
+This project uses Ruff for both linting and formatting. Do not call Black,
+flake8, isort, or pylint.
+
+- Lint: `uv run ruff check .`
+- Lint and auto-fix: `uv run ruff check --fix .`
+- Format: `uv run ruff format .`
+- Check formatting without writing: `uv run ruff format --check .`
+- Always invoke Ruff through `uv run` so it resolves to the project's
+  virtual environment.
+
+Ruff configuration lives in `pyproject.toml` under `[tool.ruff]`. Do not
+add a separate `ruff.toml` or `.ruff.toml`. Do not add inline `# noqa`
+comments without a rule code.
+
+## Create test, Update readme, and Git commit for each new feature
+Create a unit tests. Add tests as new features are added. Organize the tests accordingly.
+Update readme.md.
+Create a detailed git commit after accomplishing a unique feature.
+
+## Screenshot
+Take a screenshot by running scripts/screenshot_gui.py whenever the GUI is changed.
+Then use the new figure in readme.md
+
+## gitignore
+Do not track large files locally and in git history. Update .gitignore if needed.
+
+## Session limit
+When the prompt starts `session limit`, it means we hit a session limit and restarted.
+The goal is marked with `goal`. Based on git status, the modified files are marked with
+`file1`. Review these local files, check the current implementation, and tell me what the immediate next step should be.

quicklook_package-1.6/LIGHTKURVE_TGLC_BUG_REPORT.txt

@@ -0,0 +1,202 @@
+# OverflowError reading TGLC light curves with `quality_bitmask='hardest'` under NumPy 2
+
+## Summary
+
+Calling `LightCurve.read(path, format="tglc", quality_bitmask="hardest")` —
+or the equivalent via `search.download(quality_bitmask="hardest")` — fails
+with:
+
+```
+OverflowError: Python integer 65535 out of bounds for int16
+```
+
+which `lightkurve` surfaces to the user as:
+
+```
+LightkurveError: Error in reading Data product <path> of type TGLC.
+This file may be corrupt due to an interrupted download. Please remove it
+from your disk and try again.
+```
+
+The diagnostic is misleading: **the file is not corrupt** — `astropy.io.fits.verify('exception')` passes on it. The failure is in the TGLC reader's quality-mask step, and it is triggered purely by the choice of `quality_bitmask`. `"none"`, `"default"`, and `"hard"` work; `"hardest"` does not.
+
+## Reproducer (synthetic, no network)
+
+```python
+import numpy as np
+from lightkurve.utils import TessQualityFlags
+
+# TGLC HLSP stores ``tess_flags`` as signed int16 (FITS format='I').
+quality = np.zeros(100, dtype=np.int16)
+
+TessQualityFlags.create_quality_mask(
+    quality_array=quality,
+    bitmask=TessQualityFlags.HARDEST_BITMASK,   # 65535
+)
+# -> OverflowError: Python integer 65535 out of bounds for int16
+```
+
+## Reproducer (real data)
+
+```python
+import lightkurve as lk
+
+search = lk.search_lightcurve("TIC 360906004", author="TGLC")
+lc = search[0].download(quality_bitmask="hardest")
+# -> LightkurveError: Error in reading Data product ... of type TGLC.
+```
+
+(Any TGLC HLSP file reproduces this; TIC 360906004 sector 11 is a small one.)
+
+## Full traceback
+
+```
+Traceback (most recent call last):
+  File ".../lightkurve/io/read.py", line 134, in read
+    out = self.registry.read(cls, *args, **kwargs)
+  File ".../astropy/io/registry/core.py", line 221, in read
+    data = reader(*args, **kwargs)
+  File ".../lightkurve/io/tglc.py", line 55, in read_tglc_lightcurve
+    quality_mask = TessQualityFlags.create_quality_mask(
+  File ".../lightkurve/utils.py", line 114, in create_quality_mask
+    quality_mask = (quality_array & bitmask) == 0
+OverflowError: Python integer 65535 out of bounds for int16
+
+The above exception was the direct cause of the following exception:
+
+LightkurveError: Error in reading Data product
+  <cache>/hlsp_tglc_tess_ffi_gaiaid-5842130724965127040-s0011-cam3-ccd1_tess_v1_llc.fits
+  of type TGLC.
+This file may be corrupt due to an interrupted download. Please remove it
+from your disk and try again.
+```
+
+## Root cause
+
+The TGLC HLSP stores `tess_flags` as **signed 16-bit int** (FITS column
+`format='I'`). `read_tglc_lightcurve` feeds that column straight into
+`TessQualityFlags.create_quality_mask`, which performs:
+
+```python
+quality_mask = (quality_array & bitmask) == 0
+```
+
+When `bitmask` is a Python `int` larger than the int16 max (32767), NumPy
+2.0+ refuses the bitwise AND and raises `OverflowError`. NumPy 1.x silently
+truncated this. The relevant `TessQualityFlags` constants:
+
+| Bitmask name      | Value | Fits int16? |
+|-------------------|-------|-------------|
+| `DEFAULT_BITMASK` | 175   | yes         |
+| `HARD_BITMASK`    | 24319 | yes         |
+| `HARDEST_BITMASK` | 65535 | **no**      |
+
+So the bug is exposed for any reader/caller that combines a TGLC quality
+column with `quality_bitmask="hardest"` (or any integer > 32767).
+
+Two notes:
+
+* The reader's user-facing error blames a "corrupt download", which is
+  incorrect and sends users on a futile redownload loop. The cause is an
+  adapter-level dtype mismatch, not a transport issue.
+* Other lightkurve readers that route int32 quality columns through the
+  same helper are unaffected — this is specifically the int16 column the
+  TGLC HLSP exposes.
+
+## Proposed fix
+
+Cast the quality column to int32 before the bitwise AND. One-line change
+in `src/lightkurve/io/tglc.py`:
+
+```diff
+--- a/src/lightkurve/io/tglc.py
++++ b/src/lightkurve/io/tglc.py
+@@
+-    quality_mask = TessQualityFlags.create_quality_mask(
+-        quality_array=lc["quality"], bitmask=quality_bitmask
+-    )
++    # TGLC stores ``tess_flags`` as signed int16. Cast to int32 before the
++    # bitwise AND in create_quality_mask so masks > 32767 (e.g. HARDEST =
++    # 65535) don't raise ``OverflowError`` under NumPy 2.
++    quality_mask = TessQualityFlags.create_quality_mask(
++        quality_array=np.asarray(lc["quality"], dtype=np.int32),
++        bitmask=quality_bitmask,
++    )
+```
+
+`numpy` is already imported in this module (`import numpy as np` at the top).
+The cast is local to the mask computation; the stored `lc["quality"]` column
+keeps its original dtype.
+
+A slightly broader fix would normalize the dtype inside
+`TessQualityFlags.create_quality_mask` itself (e.g. with
+`np.asarray(quality_array, dtype=np.int32)`), which would also protect any
+other reader that ever passes a sub-int32 quality column. Either fix
+resolves the symptom; the reader-local cast is the minimal change.
+
+## Suggested regression test
+
+```python
+def test_tglc_hardest_bitmask_no_int16_overflow():
+    """TGLC reader must not overflow int16 when HARDEST_BITMASK is used.
+
+    The TGLC HLSP stores ``tess_flags`` as int16 (FITS format='I').
+    Under NumPy 2, ``int16_array & 65535`` raises OverflowError; the
+    reader must cast to a wider dtype before the bitwise AND.
+    """
+    import lightkurve as lk
+
+    res = lk.search_lightcurve("TIC 360906004", author="TGLC")
+    assert len(res) > 0, "TIC 360906004 should have at least one TGLC product"
+    lc = res[0].download(quality_bitmask="hardest")
+    assert lc is not None
+    assert len(lc) > 0
+```
+
+A network-free variant using only `lightkurve.utils.TessQualityFlags`:
+
+```python
+def test_create_quality_mask_accepts_int16_quality_array():
+    import numpy as np
+    from lightkurve.utils import TessQualityFlags
+
+    quality = np.zeros(8, dtype=np.int16)
+    mask = TessQualityFlags.create_quality_mask(
+        quality_array=quality,
+        bitmask=TessQualityFlags.HARDEST_BITMASK,
+    )
+    assert mask.all()
+```
+
+## Environment
+
+* Python 3.10
+* lightkurve 2.6.0
+* numpy 2.2.6
+* astropy 6.1.7
+
+The bug is **dtype-driven** (int16 column + Python int > 32767) and the
+behavior change is **NumPy 2** (which rejects out-of-bounds Python ints in
+bitwise ops with smaller-dtype arrays). It will reproduce on any combination
+of lightkurve >= the TGLC reader's introduction with NumPy >= 2.0.
+
+## Impact
+
+Any pipeline that requests `quality_bitmask="hardest"` (or any custom
+integer > 32767) when reading TGLC HLSP light curves fails immediately on
+download/read. The misleading "file may be corrupt" message wastes user time
+on redownload attempts that cannot succeed. Downstream tools that wrap
+lightkurve (e.g. quicklook pipelines that use TGLC for FFI targets) inherit
+the failure.
+
+## Verified locally
+
+Applied the one-line patch to a venv copy of
+`lightkurve/io/tglc.py` and re-ran with `quality_bitmask="hardest"`:
+
+```
+sector: 11   cadences: 1180   finite cal_psf_flux: 1180/1180
+```
+
+i.e. the read now succeeds and produces the same light curve as
+`quality_bitmask="default"`, with the user's selected mask applied.

quicklook_package-1.6/MANIFEST.in

@@ -0,0 +1 @@
+include quicklook/data/*.csv