pyreduce-astro 0.6.0b1__tar.gz → 0.6.0b3__tar.gz

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.6.0b1
+Version: 0.6.0b3
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce.readthedocs.io
@@ -41,6 +41,7 @@ Requires-Dist: pre-commit>=3.5.0; extra == 'dev'
 Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
 Requires-Dist: pytest>=7.4.0; extra == 'dev'
 Requires-Dist: ruff>=0.8.0; extra == 'dev'
+Requires-Dist: setuptools; extra == 'dev'
 Requires-Dist: sphinx>=7.2.0; extra == 'dev'
 Description-Content-Type: text/markdown
 

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pyreduce-astro"
-version = "0.6.0b1"
+version = "0.6.0b3"
 requires-python = ">=3.11"
 description = "A data reduction package for echelle spectrographs"
 readme = "README.md"
@@ -52,6 +52,7 @@ dev = [
     "pytest>=7.4.0",
     "pytest-cov>=4.1.0",
     "sphinx>=7.2.0",
+    "setuptools",  # Required for CFFI compilation in tests (Python 3.12+)
 ]
 
 [project.urls]
@@ -147,10 +148,16 @@ known-first-party = ["pyreduce"]
 [tool.pytest.ini_options]
 minversion = "7.0"
 addopts = "-ra -q --strict-markers"
-testpaths = ["tests"]
+testpaths = ["test"]
 python_files = ["test_*.py", "*_test.py"]
 python_classes = ["Test*"]
 python_functions = ["test_*"]
+markers = [
+    "unit: Fast unit tests with synthetic data (no downloads)",
+    "instrument: Integration tests using real instrument datasets",
+    "slow: Tests taking >5 seconds",
+    "downloads: Tests that download sample datasets",
+]
 
 # Coverage configuration
 [tool.coverage.run]

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyreduce/__init__.py

@@ -4,7 +4,7 @@ except ImportError:  # for Python<3.8
     from importlib_metadata import PackageNotFoundError, version
 
 try:
-    __version__ = version(__name__)
+    __version__ = version("pyreduce-astro")
 except PackageNotFoundError:
     __version__ = "unknown"
 
@@ -54,5 +54,14 @@ logger.addHandler(console)
 del logging
 # do not del tqdm, it is needed in the Log Handler
 
-# Load externally available modules
-from . import configuration, datasets, reduce, util
+
+# Lazy loading for faster imports
+def __getattr__(name):
+    """Lazy load submodules on first access."""
+    if name in ("configuration", "datasets", "reduce", "util"):
+        import importlib
+
+        module = importlib.import_module(f".{name}", __name__)
+        globals()[name] = module
+        return module
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyreduce/extract.py

@@ -405,6 +405,8 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
     -------
     column_range : array[nord, 2]
         updated column range
+    orders : array[nord, degree]
+        order tracing coefficients (may have rows removed if no valid pixels)
     """
 
     ix = np.arange(ncol)
@@ -426,7 +428,7 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
 
         if len(points_in_image) == 0:
             # print(y_bot, y_top,nrow, ncol, points_in_image)
-            logger.warn(
+            logger.warning(
                 f"No pixels are completely within the extraction width for order {i}, removing it."
             )
             to_remove += [i]
@@ -452,9 +454,9 @@ def fix_column_range(column_range, orders, extraction_width, nrow, ncol):
     column_range[0] = column_range[1]
     column_range[-1] = column_range[-2]
 
-    for i in to_remove:
-        np.delete(column_range, i, axis=0)
-        np.delete(orders, i, axis=0)
+    if to_remove:
+        column_range = np.delete(column_range, to_remove, axis=0)
+        orders = np.delete(orders, to_remove, axis=0)
 
     return column_range, orders
 

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyreduce/instruments/andes.json

@@ -8,8 +8,10 @@
     "date_format": "fits",
     "id_mode": "ESO INS MODE",
     "id_band": "ESO INS WLEN ID",
+    "id_decker": "ESO INS OPTI8 ID",
     "id_lamp": "ESO INS1 LAMP? ID",
     "modes": ["SL", "IFU"],
+    "deckers": ["Open", "pos1", "pos2"],
     "bands": ["UBV", "RIZ", "YJH", "K"],
     "settings": ["B", "V", "R", "IZ", "Y", "J", "H", "K"],
     "chips": ["det1"],

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyreduce/instruments/andes.py

@@ -45,8 +45,10 @@ class ANDES(Instrument):
         return modes
 
     def parse_mode(self, mode):
-        pattern = r"([YJHKLM]\d{4})(_(Open|pos1|pos2))?_det(\d)"
+        pattern = r"([A-Z]+)(_(Open|pos1|pos2))?_det(\d)"
         match = re.match(pattern, mode, flags=re.IGNORECASE)
+        if not match:
+            raise ValueError(f"Invalid mode format: {mode}")
         band = match.group(1).upper()
         if match.group(3) is not None:
             decker = match.group(3).lower().capitalize()

{pyreduce_astro-0.6.0b1 → pyreduce_astro-0.6.0b3}/pyreduce/reduce.py

@@ -562,7 +562,7 @@ class Bias(Step):
         hdus.writeto(
             self.savefile,
             overwrite=True,
-            output_verify="fix",  # "silentfix+ignore",
+            output_verify="silentfix+ignore",
         )
         logger.info("Created master bias file: %s", self.savefile)
 

pyreduce_astro-0.6.0b3/pyreduce/settings/settings_ANDES.json

@@ -0,0 +1,89 @@
+{
+    "__instrument__": "ANDES",
+    "instrument": {},
+    "bias": {
+        "degree": 1
+    },
+    "flat": {
+        "bias_scaling": "exposure_time"
+    },
+    "orders": {
+        "degree": 3,
+        "degree_before_merge": 1,
+        "filter_size": 100,
+        "min_cluster": 200000,
+        "border_width": 0,
+        "noise": 0,
+        "manual": false,
+        "auto_merge_threshold": 1,
+        "merge_min_threshold": 0.9,
+        "bias_scaling": "exposure_time"
+    },
+    "scatter": {
+        "extraction_width": 0.45,
+        "border_width": 50,
+        "bias_scaling": "exposure_time"
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0,
+        "extraction_width": 100,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "wavecal_master": {
+        "extraction_method": "optimal",
+        "extraction_width": 100,
+        "oversampling": 5,
+        "swath_width": 2000,
+        "smooth_slitfunction": 1,
+        "smooth_spectrum": 1e-7,
+        "extraction_cutoff": 20,
+        "bias_scaling": "exposure_time"
+    },
+    "wavecal_init": {
+        "element": "UNe",
+        "medium": "vac",
+        "cutoff": 5,
+        "smoothing": 1
+    },
+    "wavecal": {
+        "threshold": 100,
+        "closing": 0,
+        "dimensionality": "2D",
+        "element": null,
+        "degree": [5,5],
+        "manual": false
+    },
+    "freq_comb_master": {
+        "extraction_width": 10,
+        "bias_scaling": "exposure_time"
+    },
+    "freq_comb": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "degree": [8, 8]
+    },
+    "curvature": {
+        "peak_threshold": 1,
+        "window_width": 15,
+        "extraction_width": 100,
+        "dimensionality": "2D",
+        "degree": [
+            1,
+            1
+        ],
+        "curv_degree": 1,
+        "peak_function": "lorentzian",
+        "bias_scaling": "exposure_time"
+    },
+    "science": {
+        "oversampling": 1,
+        "extraction_width": 10,
+        "swath_width": 300,
+        "smooth_slitfunction": 0.1,
+        "smooth_spectrum": 0,
+        "bias_scaling": "exposure_time"
+    }
+}