pyreduce-astro 0.7a7__tar.gz → 0.7b2__tar.gz

pyreduce_astro-0.7b2/ANDES_plan.md

@@ -0,0 +1,377 @@
+# ANDES Instrument Configuration Design
+
+## Background
+
+### ANDES Instrument Overview
+
+ANDES is a future ELT high-resolution spectrograph with multiple spectrographs, each containing multiple arms:
+
+| Spectrograph | Arms | Detector Type |
+|--------------|------|---------------|
+| 1 | U, B, V | Optical CCD |
+| 2 | R, IZ | Red optical CCD |
+| 3 | Y, J, H | Near-IR (H2RG or similar) |
+| 4 | K | Thermal IR |
+
+Key characteristics:
+- All arms fed from the same fibers on sky
+- Each arm has its own independent detector
+- FITS files organized **per spectrograph** (one file with arms as extensions)
+- Detectors are similar within each spectrograph
+
+### Current State
+
+- `andes.yaml` - Multi-channel IR-focused config
+- `settings_ANDES.json` - Inherits from CRIRES_PLUS (IR-tuned)
+- `aj.yaml` / `settings_AJ.json` - Simulation instrument (draft for testing)
+
+---
+
+## PyReduce Architecture Context
+
+### How Channels Work
+
+Channels in PyReduce handle multi-extension FITS files. The `getter` class in `instruments/common.py` automatically indexes list values by channel position:
+
+```yaml
+# Example: UVES with 3 channels
+channels: [BLUE, MIDDLE, RED]
+extension: [0, 2, 1]        # BLUE→ext0, MIDDLE→ext2, RED→ext1
+orientation: [2, 1, 1]      # BLUE rotated differently
+```
+
+When processing channel "RED" (index 2), PyReduce automatically uses `extension[2]=1`, `orientation[2]=1`.
+
+### What MUST Be Shared Across Channels
+
+1. **File classification keywords** (`kw_bias`, `kw_flat`, `kw_wave`, `kw_spec`)
+2. **File classification patterns** (`id_bias`, `id_flat`, etc.)
+3. **Reduction settings** - `settings_INSTRUMENT.json` applies to ALL channels
+4. **Header keyword mappings** (date, target, exposure_time, etc.)
+
+### What CAN Vary Per Channel
+
+1. FITS extension index
+2. Image orientation
+3. Detector-specific header values (gain, readnoise) via `{id[n]}` templates
+4. Output filenames (mask, wavecal)
+
+### Critical Limitation: No Per-Channel Settings
+
+**YAML instrument configs** support per-channel values via list indexing.
+
+**JSON settings do NOT** - all channels share identical reduction parameters:
+- Same `trace.degree`, `trace.noise`, `trace.min_cluster`
+- Same `science.extraction_height`, `science.oversampling`
+- Same `wavecal.degree`, `wavecal.threshold`
+
+This means optical CCDs and IR arrays would share the same tuning if in one instrument.
+
+---
+
+## Design Options
+
+### Option A: Single ANDES Instrument (9 channels)
+
+```yaml
+# andes.yaml
+channels: [U, B, V, R, IZ, Y, J, H, K]
+extension: [1, 2, 3, 1, 2, 1, 2, 3, 1]
+```
+
+| Pros | Cons |
+|------|------|
+| Single abstraction level | Cannot tune settings per arm/spectrograph |
+| Simple mental model | Must handle 4 FITS file types in one instrument |
+| One config file | Optical/IR forced to share parameters |
+
+**Implementation**: Would follow CRIRES+ pattern (see below).
+
+### Option A Implementation: CRIRES+ Pattern
+
+CRIRES+ shows how to handle multiple file types with a single instrument:
+
+```python
+class ANDES(Instrument):
+    def __init__(self):
+        super().__init__()
+        # Add spectrograph filter - files tagged by which spectrograph they're from
+        self.filters["spectrograph"] = Filter(self.info["kw_spectrograph"])
+        self.shared += ["spectrograph"]
+
+    def get_expected_values(self, target, night, channel):
+        expectations = super().get_expected_values(target, night)
+        # Map channel to spectrograph: J → YJH, U → UBV, etc.
+        spectrograph = self.channel_to_spectrograph(channel)
+        for key in expectations.keys():
+            expectations[key]["spectrograph"] = spectrograph
+        return expectations
+
+    def get_extension(self, header, channel):
+        # Map channel to extension: U→1, B→2, V→3, Y→1, J→2, H→3, etc.
+        return self.channel_extensions[channel]
+
+    def discover_channels(self, input_dir):
+        # Scan files, find which spectrographs present, return available channels
+        ...
+```
+
+**How file filtering works:**
+1. Files have header keyword identifying spectrograph (UBV, RIZ, YJH, K)
+2. When `channel=J` requested, ANDES maps J → YJH spectrograph
+3. File filter selects only YJH spectrograph files
+4. Extension 2 read from those files
+
+**Without specifying channel:**
+- `discover_channels()` scans files to find which spectrographs exist
+- Returns available channels (e.g., if only YJH files exist → `[Y, J, H]`)
+- Pipeline loops over each discovered channel
+
+This makes Option A fully viable following an existing pattern.
+
+### Option B: Separate Instruments (9 instruments, 1 channel each)
+
+```
+ANDES_U   channels=[U]   extension=1   → inherits pyreduce
+ANDES_B   channels=[B]   extension=2   → inherits ANDES_U
+ANDES_V   channels=[V]   extension=3   → inherits ANDES_U
+ANDES_R   channels=[R]   extension=1   → inherits pyreduce
+ANDES_IZ  channels=[IZ]  extension=2   → inherits ANDES_R
+ANDES_Y   channels=[Y]   extension=1   → inherits CRIRES_PLUS
+ANDES_J   channels=[J]   extension=2   → inherits ANDES_Y
+ANDES_H   channels=[H]   extension=3   → inherits ANDES_Y
+ANDES_K   channels=[K]   extension=1   → inherits CRIRES_PLUS
+```
+
+| Pros | Cons |
+|------|------|
+| Single abstraction (instruments only) | 9 YAML + 9 settings files |
+| Maximum per-arm flexibility | File sorting overlap (U,B,V find same file) |
+| Settings inheritance keeps configs DRY | Cannot reduce "all of UBV" in one command |
+| Matches AJ pattern | More instruments to manage |
+
+### Option C: Per-Spectrograph Instruments (4 instruments)
+
+```
+ANDES_UBV  channels=[U,B,V]   extension=[1,2,3]   → inherits pyreduce
+ANDES_RIZ  channels=[R,IZ]    extension=[1,2]     → inherits ANDES_UBV
+ANDES_YJH  channels=[Y,J,H]   extension=[1,2,3]   → inherits CRIRES_PLUS
+ANDES_K    channels=[K]       extension=1         → inherits ANDES_YJH
+```
+
+| Pros | Cons |
+|------|------|
+| Matches FITS file structure (1:1) | Two abstraction levels |
+| Cleaner file sorting | Per-spectrograph tuning only (not per-arm) |
+| Per-spectrograph settings tuning | |
+| Follows XSHOOTER/HARPS/UVES pattern | |
+| Can reduce entire spectrograph at once | |
+
+---
+
+## Recommendation
+
+**Option C** is recommended because:
+
+1. **Matches physical reality**: One instrument = one FITS file type
+2. **Sufficient tuning granularity**: Detectors are similar within spectrograph
+3. **Proven pattern**: XSHOOTER (UVB/VIS/NIR), HARPS (BLUE/RED), UVES work this way
+4. **Clean file handling**: No overlap in file discovery
+
+If per-arm tuning becomes necessary, Option B remains viable with settings inheritance minimizing duplication.
+
+---
+
+## File Structure (Option C)
+
+```
+pyreduce/instruments/
+  andes_ubv.yaml    # channels=[U,B,V], extension=[1,2,3]
+  andes_riz.yaml    # channels=[R,IZ], extension=[1,2]
+  andes_yjh.yaml    # channels=[Y,J,H], extension=[1,2,3]
+  andes_k.yaml      # channels=[K], extension=1
+
+pyreduce/settings/
+  settings_ANDES_UBV.json  # __inherits__: pyreduce (optical CCD tuning)
+  settings_ANDES_RIZ.json  # __inherits__: ANDES_UBV
+  settings_ANDES_YJH.json  # __inherits__: CRIRES_PLUS (near-IR tuning)
+  settings_ANDES_K.json    # __inherits__: ANDES_YJH
+```
+
+### Migration
+
+- Rename `andes.yaml` → `andes_yjh.yaml` (or delete and create fresh)
+- Rename `settings_ANDES.json` → `settings_ANDES_YJH.json`
+- Keep `AJ` as simulation/test instrument
+
+---
+
+## Future Enhancement: Per-Channel Settings
+
+Adding per-channel settings would enable Option A (single instrument with full flexibility).
+
+### Current Flow
+
+```
+configuration.py:load_config()
+  → loads settings_INSTRUMENT.json
+  → merges with defaults via _resolve_inheritance()
+  → returns config dict (same for all channels)
+
+reduce.py:Step.__init__()
+  → receives config dict
+  → uses values directly: self.degree = config["degree"]
+```
+
+### Proposed Enhancement
+
+Add channel-aware value selection in Step classes, similar to how `getter` works for YAML configs.
+
+#### Option 1: Settings-level indexing
+
+Modify `_resolve_inheritance()` or add post-processing to index list values:
+
+```python
+def _apply_channel_index(config, channel, channels):
+    """Index list values in settings by channel position."""
+    if channel is None or channels is None:
+        return config
+    try:
+        idx = channels.index(channel.upper())
+    except (ValueError, AttributeError):
+        return config
+
+    result = {}
+    for key, value in config.items():
+        if isinstance(value, dict):
+            result[key] = _apply_channel_index(value, channel, channels)
+        elif isinstance(value, list) and len(value) == len(channels):
+            result[key] = value[idx]
+        else:
+            result[key] = value
+    return result
+```
+
+Call this when creating Step instances in `pipeline.py`.
+
+#### Option 2: Step-level helper
+
+Add a method to Step base class:
+
+```python
+class Step:
+    def get_config(self, key, default=None):
+        """Get config value, indexing by channel if value is a list."""
+        value = self.config.get(key, default)
+        if isinstance(value, list) and hasattr(self, 'channel_index'):
+            if len(value) > self.channel_index:
+                return value[self.channel_index]
+        return value
+```
+
+#### Settings Format
+
+```json
+{
+  "__instrument__": "ANDES",
+  "trace": {
+    "degree": 4,
+    "noise": [10, 10, 10, 20, 20, 50, 50, 50, 100],
+    "min_cluster": [500, 500, 500, 1000, 1000, 2000, 2000, 2000, 5000]
+  },
+  "science": {
+    "extraction_height": 10,
+    "oversampling": [10, 10, 10, 10, 10, 5, 5, 5, 3]
+  }
+}
+```
+
+Values that are scalars apply to all channels. Values that are lists with length matching `channels` are indexed.
+
+#### Implementation Scope
+
+1. **Minimal**: ~20-30 lines in `configuration.py` or `reduce.py`
+2. **Changes needed**:
+   - Pass `channel` and `channels` list to config processing
+   - Add indexing logic (one of the options above)
+   - Update Step classes to use indexed values
+3. **Backward compatible**: Scalar values work as before; only lists trigger indexing
+4. **Risk**: Low - additive change, doesn't break existing instruments
+
+#### Semantic List Parameters (Potential Conflict)
+
+Current settings use lists for semantic pairs, not per-channel values:
+
+| Parameter | Meaning | Where Used |
+|-----------|---------|------------|
+| `closing_shape` | [x, y] kernel | trace morphology |
+| `opening_shape` | [x, y] kernel | trace morphology |
+| `degree` | [order, column] | 2D fits (wavecal, curvature, freq_comb) |
+| `extraction_height` | [below, above] | rarely as list, usually scalar |
+
+**Option 1: Refactor semantic lists away**
+
+```json
+// Before
+"closing_shape": [5, 5]
+"degree": [6, 6]
+
+// After
+"closing_shape_x": 5,
+"closing_shape_y": 5,
+"degree_order": 6,
+"degree_column": 6
+```
+
+Pros: Clean separation, no ambiguity
+Cons: Breaking change, migration needed
+
+**Option 2: Length-based disambiguation**
+
+Per-channel lists must match `len(channels)`. Semantic lists are always 2 elements.
+- ANDES has 9 channels, so `[10, 20, 30, 40, 50, 60, 70, 80, 90]` → per-channel
+- `[6, 6]` → semantic (2 elements ≠ 9 channels)
+
+Pros: Backward compatible
+Cons: Fragile if instrument has exactly 2 channels
+
+**Option 3: Explicit marker**
+
+```json
+"noise": {"__per_channel__": [10, 20, 50, 100]}
+// or
+"noise": {"U": 10, "B": 10, "V": 10, "Y": 50, "J": 50, "H": 50, "K": 100}
+```
+
+Pros: Explicit, no ambiguity
+Cons: More verbose
+
+**Recommendation**: Option 1 (refactor) for cleanest long-term solution. The semantic lists are:
+- `closing_shape`, `opening_shape`: Rarely changed, easy to split
+- `degree`: Common but well-understood, split to `degree_order`/`degree_column`
+- `extraction_height`: Already scalar in most configs, deprecate list form
+
+---
+
+## Summary
+
+| Approach | Effort | Flexibility | Complexity |
+|----------|--------|-------------|------------|
+| Option A + per-channel settings | Medium | Per-channel | Single instrument, single abstraction |
+| Option B (9 instruments) | Low | Per-arm | 9 instruments, single abstraction |
+| Option C (4 instruments) | Low | Per-spectrograph | 4 instruments, two abstractions |
+
+**Revised Recommendation:**
+
+**Option A** is now the most attractive if we implement per-channel settings:
+1. Single instrument, single abstraction level
+2. Maximum flexibility (per-channel tuning)
+3. Follows proven CRIRES+ pattern for file handling
+4. Clean long-term solution
+
+**Implementation path:**
+1. Refactor semantic list parameters (`degree` → `degree_order`/`degree_column`, etc.)
+2. Add per-channel settings indexing (~30 lines)
+3. Create ANDES instrument with spectrograph filter (like CRIRES+ band filter)
+
+If per-channel settings enhancement is deferred, use **Option C** as interim solution.

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/CHANGELOG.md

@@ -1,6 +1,43 @@
 # Changelog
 
 
+## [0.7b2] - 2026-01-09
+
+### Changed
+- **Reorganize instrument files**: All instrument-related files now in per-instrument directories
+  - `instruments/{name}.py` → `instruments/{NAME}/__init__.py`
+  - `instruments/{name}.yaml` → `instruments/{NAME}/config.yaml`
+  - `settings/settings_{NAME}.json` → `instruments/{NAME}/settings.json`
+  - `wavecal/{name}_*.npz` → `instruments/{NAME}/wavecal_*.npz`
+  - `masks/mask_{name}_*.fits.gz` → `instruments/{NAME}/mask_*.fits.gz`
+- Base settings and schema moved to `instruments/defaults/`
+- Wavelength atlas files moved to `instruments/defaults/atlas/`
+
+### Removed
+- Orphan mask files for undefined instruments (elodie, sarg, hds, etc.)
+
+## [0.7b1] - 2026-01-06
+
+### Changed
+- **Curvature algorithm rewrite**: Replace 2D model fitting with row-tracking method for better robustness
+- Rename `make_shear.py` to `slit_curve.py`
+- Rename curvature coefficients: `tilt`/`shear` → `p1`/`p2` throughout codebase
+- Rename `arc_extraction` to `simple_extraction`
+- Split curvature `extraction_height` into separate `extraction_height` and `curve_height` parameters
+- Save file renamed from `.shear.npz` to `.curve.npz`
+
+### Added
+- `discover_channels()` for automatic channel detection from data files
+- CLI: `--target` is now optional; loops over all targets if not specified
+- CLI: Uses `$REDUCE_DATA` for base_dir, reads default input_dir from config
+- Comprehensive CLI test coverage
+
+### Fixed
+- Curvature step index error when traces are removed during processing
+- Validate base_dir and input_dir exist with clear error messages
+- File sorting to correctly loop over all nights when not specified
+- CLI dynamic dependency loading for step commands
+
 ## [0.7a7] - 2026-01-04
 
 ### Added

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/CLAUDE.md

@@ -41,13 +41,19 @@ pyreduce/
 ├── instruments/         # Instrument definitions
 │   ├── common.py        # Base Instrument class
 │   ├── models.py        # Pydantic config models
+│   ├── filters.py       # File classification filters
 │   ├── instrument_info.py  # Instrument loader
-│   ├── *.yaml           # Instrument configs (one per instrument)
-│   └── *.py             # Custom instrument logic (optional)
-│
-├── settings/            # Reduction parameters
-│   ├── settings_default.json
-│   └── settings_*.json  # Per-instrument settings
+│   ├── defaults/        # Base settings and line atlases
+│   │   ├── settings.json   # Default reduction parameters
+│   │   ├── schema.json     # Settings validation schema
+│   │   ├── config.yaml     # Base instrument config
+│   │   └── atlas/          # Wavelength calibration line lists
+│   └── {INSTRUMENT}/    # Per-instrument directory (e.g., UVES/, HARPS/)
+│       ├── __init__.py     # Instrument class
+│       ├── config.yaml     # Hardware/header config
+│       ├── settings.json   # Reduction parameters
+│       ├── wavecal_*.npz   # Pre-computed wavelength solutions
+│       └── mask_*.fits.gz  # Bad pixel masks
 │
 └── clib/                # C source for extraction
     ├── slit_func_bd.c
@@ -74,7 +80,7 @@ The reduction pipeline consists of these steps (in typical order):
 | `bias` | `Bias` | Combine bias frames into master bias |
 | `flat` | `Flat` | Combine flat frames, subtract bias |
 | `trace` | `OrderTracing` | Trace echelle order positions on flat |
-| `curvature` | `SlitCurvatureDetermination` | Measure slit tilt/shear from arc lamp |
+| `curvature` | `SlitCurvatureDetermination` | Measure slit curvature from arc lamp |
 | `scatter` | `BackgroundScatter` | Model inter-order scattered light |
 | `norm_flat` | `NormalizeFlatField` | Normalize flat, extract blaze function |
 | `wavecal_master` | `WavelengthCalibrationMaster` | Extract wavelength calibration spectrum |
@@ -97,7 +103,7 @@ Each step class has:
 
 ### Instrument Configs (YAML)
 
-Location: `pyreduce/instruments/*.yaml`
+Location: `pyreduce/instruments/{INSTRUMENT}/config.yaml`
 
 Defines what the instrument IS - hardware properties and header mappings:
 
@@ -139,7 +145,7 @@ Validated by Pydantic model `InstrumentConfig` in `models.py`.
 
 ### Reduction Settings (JSON)
 
-Location: `pyreduce/settings/settings_*.json`
+Location: `pyreduce/instruments/{INSTRUMENT}/settings.json`
 
 Defines HOW to reduce - algorithm parameters per step:
 
@@ -172,7 +178,7 @@ Defines HOW to reduce - algorithm parameters per step:
 }
 ```
 
-Settings cascade: `settings_default.json` < `settings_INSTRUMENT.json` < runtime overrides.
+Settings cascade: `instruments/defaults/settings.json` < `instruments/{INSTRUMENT}/settings.json` < runtime overrides.
 
 ## Python API
 
@@ -260,18 +266,24 @@ uv run reduce list-steps
 
 ```bash
 uv sync                              # Install dependencies
+uv run reduce-build                  # Compile C extensions
+uv run reduce-clean                  # Remove compiled extensions
 uv run pre-commit install            # Setup hooks (once)
 uv run pytest -m unit                # Fast unit tests
 uv run pytest --instrument=UVES      # Test single instrument
 uv run ruff check --fix .            # Lint and fix
 ```
 
+After a fresh clone or `rm -rf .venv`, run `uv sync && uv run reduce-build` to set up.
+
 ### Adding Instruments
 
-1. Create `pyreduce/instruments/name.yaml` with detector/header config
-2. Create `pyreduce/instruments/name.py` if custom logic needed (optional)
-3. Create `pyreduce/settings/settings_NAME.json` for reduction parameters
-4. Add example script to `examples/name_example.py`
+1. Create `pyreduce/instruments/{NAME}/` directory
+2. Add `config.yaml` with detector/header config
+3. Add `settings.json` for reduction parameters (can use `"__inherits__": "defaults"`)
+4. Add `__init__.py` with instrument class if custom logic needed (optional)
+5. Add wavecal/mask files if available
+6. Add example script to `examples/name_example.py`
 
 ### Test Organization
 

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a7
+Version: 0.7b2
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -37,7 +37,6 @@ Requires-Dist: scikit-image>=0.22.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: spectres>=2.2.0
 Requires-Dist: tqdm>=4.66.0
-Requires-Dist: wget>=3.2
 Description-Content-Type: text/markdown
 
 [![CI](https://github.com/ivh/PyReduce/actions/workflows/python-publish.yml/badge.svg)](https://github.com/ivh/PyReduce/actions/workflows/python-publish.yml)

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce
@@ -21,14 +21,14 @@ steps = (
     # "bias",
     # "flat",
     # "trace",
-    # "curvature",
+    "curvature",
     # "scatter",
     # "norm_flat",
     # "wavecal_master",
     # "wavecal_init",
     # "wavecal",
     # "freq_comb_master",
-    "freq_comb",
+    # "freq_comb",
     # "science",
     # "continuum",
     # "finalize",
@@ -48,6 +48,5 @@ Pipeline.from_instrument(
     base_dir=base_dir,
     input_dir=input_dir,
     output_dir=output_dir,
-    allow_calibration_only=True,
     # order_range=(0, 4),
 ).run()

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 import os.path
 

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce
@@ -17,9 +17,9 @@ night = None
 channel = ""
 steps = (
     "bias",
-    # "flat",
-    # "trace",
-    # "norm_flat",
+    "flat",
+    "trace",
+    "norm_flat",
     # "wavecal",
     # "curvature",
     "science",
@@ -42,5 +42,5 @@ Pipeline.from_instrument(
     input_dir=input_dir,
     output_dir=output_dir,
     # order_range=(0, 25),
-    plot=0,
+    plot=1,
 ).run()

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce

{pyreduce_astro-0.7a7 → pyreduce_astro-0.7b2}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a7"]
+# dependencies = ["pyreduce-astro>=0.7b2"]
 # ///
 """
 Simple usage example for PyReduce