Lazy load config. (#124)

* Use c.to("km/s") for speed of light

and re-standardize astropy constants imports.

* Lazy load configuration using _config.py and testing.

* fix version in __init__ and __all__

* Remove starfish test config ad fix config tests.

* Test lazy load. xfail as not working correctly.

* Fix cache location config.

* Lint

conftest.py

@@ -55,7 +55,7 @@ def resampled_data(request):
     id_string = "{0:s}-{1:s}-{2:.1f}-{3:s}".format(star, band, float(vel), res)
 
     test_data = os.path.join(
-        eniric.paths["resampled"], resampled_template.format(star, band, vel, res)
+        eniric.config.paths["resampled"], resampled_template.format(star, band, vel, res)
     )
     wav, flux = io.pdread_2col(test_data)
     return id_string, wav, flux
@@ -125,7 +125,7 @@ def grad_flag(request):
 )
 def atm_model(request):
     """Get atmospheric model name to load."""
-    return os.path.join(eniric.paths["atmmodel"], request.param)
+    return os.path.join(eniric.config.paths["atmmodel"], request.param)
 
 
 @pytest.fixture(params=[2.5, 4])

docs/Notebooks/Convolution_speeds.ipynb

@@ -25,8 +25,8 @@
     "import PyAstronomy.pyasl as pyasl\n",
     "\n",
     "import eniric\n",
-    "#eniric.cache[\"location\"] = None  # Disable caching for these tests\n",
-    "eniric.cache[\"location\"] = \".joblib\"  # Enable caching\n",
+    "#eniric.config.cache[\"location\"] = None  # Disable caching for these tests\n",
+    "eniric.config.cache[\"location\"] = \".joblib\"  # Enable caching\n",
     "\n",
     "from eniric.broaden import rotational_convolution, resolution_convolution\n",
     "from eniric.utilities import band_limits, load_aces_spectrum, wav_selector\n",

docs/Notebooks/Precison_with_doppler-K-band.ipynb

@@ -27,11 +27,11 @@
     "import numpy as np\n",
     "from tqdm import tqdm\n",
     "import PyAstronomy.pyasl as pyasl\n",
-    "import astropy.constants as const\n",
+    "from astropy import constants as const\n",
     "\n",
     "import eniric\n",
-    "#eniric.cache[\"location\"] = None  # Disable caching for these tests\n",
-    "eniric.cache[\"location\"] = \".joblib\"  # Enable caching\n",
+    "#eniric.config.cache[\"location\"] = None  # Disable caching for these tests\n",
+    "eniric.config.cache[\"location\"] = \".joblib\"  # Enable caching\n",
     "\n",
     "from eniric.broaden import rotational_convolution, resolution_convolution\n",
     "from eniric.utilities import band_limits, load_aces_spectrum, wav_selector\n",

docs/Notebooks/Precison_with_doppler-Z-band.ipynb

@@ -29,11 +29,11 @@
     "import numpy as np\n",
     "from tqdm import tqdm\n",
     "import PyAstronomy.pyasl as pyasl\n",
-    "import astropy.constants as const\n",
+    "from astropy import constants as const\n",
     "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            \n",
     "import eniric\n",
-    "#eniric.cache[\"location\"] = None  # Disable caching for these tests\n",
-    "eniric.cache[\"location\"] = \".joblib\"  # Enable caching\n",
+    "#eniric.config.cache[\"location\"] = None  # Disable caching for these tests\n",
+    "eniric.config.cache[\"location\"] = \".joblib\"  # Enable caching\n",
     "\n",
     "from eniric.broaden import rotational_convolution, resolution_convolution\n",
     "from eniric.utilities import band_limits, load_aces_spectrum, wav_selector\n",

eniric/Qcalculator.py

@@ -52,7 +52,7 @@
 import warnings
 from typing import Optional, Tuple, Union
 
-import astropy.constants as const
+from astropy import constants as const
 import astropy.units as u
 import numpy as np
 from astropy.units.quantity import Quantity

eniric/__init__.py

@@ -1,50 +1,32 @@
-__version__ = "0.6-beta"
-__all__ = [
-    "atmosphere",
-    "io_module",
-    "Qcalculator",
-    "resample",
-    "snr_normalization",
-    "utilities",
-]
-
-# Read the users config.yaml file.
-# If it doesn't exist, print a useful help message
+__version__ = "1.0rc1"
 
 import os
+import warnings
 
-import yaml
-
-try:
-    with open("config.yaml") as f:
-        config = yaml.safe_load(f)
-except FileNotFoundError as e:
-    default = __file__[:-11] + "config.yaml"
-    import warnings
+from ._config import Config
 
+if os.path.exists("config.yaml"):
+    config = Config("config.yaml")
+else:
+    base_dir = os.path.dirname(__file__)
+    default = os.path.join(base_dir, "config.yaml")
     warnings.warn(
         "Using the default config.yaml file located at {0}. "
         "This is likely NOT what you want. Please create a similar "
         "'config.yaml' file in your current working directory.".format(default),
         UserWarning,
     )
-    with open(default) as f:
-        config = yaml.safe_load(f)
+    config = Config(default)
 
-# Read the YAML variables into package-level dictionaries to be used by the other programs.
-name = config["name"]
-paths = config["paths"]
-bands = config["bands"]
-custom_bands = config["custom_bands"]
-atmmodel = config["atmmodel"]
-cache = config["cache"]
-
-# Turn list into path
-for key, value in paths.items():
-    if isinstance(value, list):
-        paths[key] = os.path.join(*value)
-
-if (cache["location"] is None) or (cache["location"] == "None"):
-    cache["location"] = None  # Disables caching
-else:
-    cache["location"] = os.path.join(*cache["location"])
+__all__ = [
+    "atmosphere",
+    "broaden",
+    "config",
+    "corrections",
+    "legacy",
+    "io_module",
+    "Qcalculator",
+    "resample",
+    "snr_normalization",
+    "utilities",
+]

eniric/_config.py

@@ -0,0 +1,48 @@
+import yaml
+import os
+
+
+class Config:
+    """
+    This is a class to allow lazy-loading of config files. This means that the atributes are only read from the file
+    when accessed in the code, allowing for changes in the file without having to restart the python instance
+    """
+
+    def __init__(self, filename):
+        self.filename = filename
+        # Format string for saving/reading orders
+        self.specfmt = "s{}_o{}"
+
+    def __getitem__(self, item):
+        with open(self.filename) as f:
+            base = yaml.safe_load(f)
+            return base[item]
+
+    def __getattribute__(self, item):
+        # Short circuit on filename or else infinite recursion
+        if item == 'filename':
+            return super().__getattribute__(item)
+        with open(self.filename) as f:
+            base = yaml.safe_load(f)
+            if item == 'paths':
+                paths = base['paths']
+                for key, value in paths.items():
+                    if isinstance(value, list):
+                        paths[key] = os.path.join(*value)
+                return paths
+            elif item == 'bands':
+                return base['bands']
+            elif item == 'custom_bands':
+                return base['custom_bands']
+            elif item == 'atmmodel':
+                return base['atmmodel']
+            elif item == 'cache':
+                cache = base['cache']
+                if (cache["location"] is None) or (cache["location"] == "None"):
+                    cache["location"] = None  # Disables caching
+                else:
+                    if isinstance(cache["location"], list):
+                        cache["location"] = os.path.join(*cache["location"])
+                return cache
+            else:
+                return super().__getattribute__(item)

eniric/atmosphere.py

@@ -128,8 +128,8 @@ def from_band(cls, band: str, bary: bool = False):
 
         extension = "_bary.dat" if bary else ".dat"
         atmmodel = join(
-            eniric.paths["atmmodel"],
-            "{0}_{1}{2}".format(eniric.atmmodel["base"], band, extension),
+            eniric.config.paths["atmmodel"],
+            "{0}_{1}{2}".format(eniric.config.atmmodel["base"], band, extension),
         )
 
         try:
@@ -146,7 +146,7 @@ def from_band(cls, band: str, bary: bool = False):
                 )
             )
             full_model = join(
-                eniric.paths["atmmodel"], "{0}.dat".format(eniric.atmmodel["base"])
+                eniric.config.paths["atmmodel"], "{0}.dat".format(eniric.config.atmmodel["base"])
             )
             atm = cls.from_file(full_model)
 

eniric/broaden.py

@@ -11,7 +11,7 @@
 
 import multiprocess as mprocess
 import numpy as np
-from astropy.constants import c
+from astropy import constants as const
 from joblib import Memory
 from multiprocess import pool
 from numpy.core.multiarray import ndarray
@@ -21,9 +21,9 @@
 from eniric.utilities import band_selector, mask_between, wav_selector
 
 # Cache convolution results.
-memory = Memory(location=eniric.cache["location"], verbose=0)
+memory = Memory(location=eniric.config.cache["location"], verbose=0)
 
-c_kmps = c.value / 1000
+c_kmps = const.c.to('km/s').value
 num_procs_minus_1 = os.cpu_count() - 1
 
 

eniric/obsolete/TAPASproc.py

@@ -67,7 +67,7 @@ def read_allfiles(mask_limit=0.02):
             mask.append(0.0)
 
     write_4col_eeed(
-        os.path.join(outdir, "{0}_visible.dat".format(eniric.atmmodel["base"])),
+        os.path.join(outdir, "{0}_visible.dat".format(eniric.config.atmmodel["base"])),
         wav,
         mean_flux,
         std_flux,

eniric/obsolete/make_test_data.py

@@ -11,7 +11,7 @@
 from eniric.obsolete.prepare_data import main as prepare_data
 
 if __name__ == "__main__":
-    print("Eniric paths: {}".format(eniric.paths))
+    print("Eniric paths: {}".format(eniric.config.paths))
 
     # subprocess.call("python scripts/prepare_data.py -s M0 M3 M6 M9 -l 4.50 -m 0.0", shell=True)
     prepare_data(

eniric/obsolete/nIR_precision.py

@@ -24,7 +24,7 @@
 rc("text", usetex=True)  # set stuff for latex usage
 
 ref_choices = ["SELF"]
-ref_choices.extend(eniric.bands["all"])
+ref_choices.extend(eniric.config.bands["all"])
 
 
 def _parser():
@@ -41,7 +41,7 @@ def _parser():
         "--bands",
         type=str,
         default="J",
-        choices=eniric.bands["all"],
+        choices=eniric.config.bands["all"],
         help="Wavelength bands to select. Default=J.",
         nargs="+",
     )
@@ -82,7 +82,7 @@ def main(bands="J", use_unshifted=False, save=False, snr=100, ref_band="J"):
         Save results to file.
 
     """
-    os.makedirs(eniric.paths["precision"], exist_ok=True)
+    os.makedirs(eniric.config.paths["precision"], exist_ok=True)
 
     spectral_types = ["M0", "M3", "M6", "M9"]
     if "ALL" in bands:
@@ -121,7 +121,7 @@ def main(bands="J", use_unshifted=False, save=False, snr=100, ref_band="J"):
     # Save precision results
     if save:
         output_filename = os.path.join(
-            eniric.paths["precision"],
+            eniric.config.paths["precision"],
             "precision_results_2017_ref_band-{0}_snr-{1}.dat".format(ref_band, snr),
         )
         ids = []
@@ -204,8 +204,8 @@ def calculate_prec(
 
         if use_unshifted:
             atmmodel = os.path.join(
-                eniric.paths["atmmodel"],
-                "{0}_{1}.dat".format(eniric.atmmodel["base"], band),
+                eniric.config.paths["atmmodel"],
+                "{0}_{1}.dat".format(eniric.config.atmmodel["base"], band),
             )
             print("Reading atmospheric model...")
             atm = Atmosphere.from_file(atmmodel)
@@ -235,8 +235,8 @@ def calculate_prec(
             mask_atm = barycenter_shift(wav_atm, mask_atm, rv_offset=rv_offset)
         else:
             shifted_atmmodel = os.path.join(
-                eniric.paths["atmmodel"],
-                "{0}_{1}_bary.dat".format(eniric.atmmodel["base"], band),
+                eniric.config.paths["atmmodel"],
+                "{0}_{1}_bary.dat".format(eniric.config.atmmodel["base"], band),
             )
             print("Reading pre-doppler-shifted atmospheric model...")
             atm = Atmosphere.from_file(shifted_atmmodel)
@@ -274,7 +274,7 @@ def calculate_prec(
             # print("Working on "+file_to_read+".")
             try:
                 wav_stellar, flux_stellar = io.pdread_2col(
-                    os.path.join(eniric.paths["resampled"], file_to_read)
+                    os.path.join(eniric.config.paths["resampled"], file_to_read)
                 )
             except FileNotFoundError:
                 # Turn list of strings into strings without symbols  ["J", "K"] -> J K

eniric/obsolete/nIR_run.py

@@ -39,7 +39,7 @@ def _parser():
         "--band",
         type=str,
         default="ALL",
-        choices=eniric.bands["all"],
+        choices=eniric.config.bands["all"],
         help="Wavelength band to select",
         nargs="+",
     )
@@ -94,7 +94,7 @@ def main(
     Multiple values of startype, vsini, resolution, band, and sample_rate can
     be provided.
 
-    Read files from eniric.paths["phoenix_dat"]"
+    Read files from eniric.config.paths["phoenix_dat"]"
 
     Parameters
     ----------
@@ -129,12 +129,12 @@ def main(
 
     start_time = dt.now()
 
-    phoenix_path = eniric.paths["phoenix_dat"]
+    phoenix_path = eniric.config.paths["phoenix_dat"]
 
-    results_dir = eniric.paths["results"]
+    results_dir = eniric.config.paths["results"]
     os.makedirs(results_dir, exist_ok=True)
 
-    resampled_dir = eniric.paths["resampled"]
+    resampled_dir = eniric.config.paths["resampled"]
     os.makedirs(resampled_dir, exist_ok=True)
 
     if not normalize:

eniric/obsolete/nIRanalysis.py

@@ -16,9 +16,9 @@
 # set stuff for latex usage
 rc("text", usetex=True)
 
-data_rep = eniric.paths["phoenix_dat"]
-results_dir = eniric.paths["results"]
-resampled_dir = eniric.paths["resampled"]
+data_rep = eniric.config.paths["phoenix_dat"]
+results_dir = eniric.config.paths["results"]
+resampled_dir = eniric.config.paths["resampled"]
 
 # models form PHOENIX-ACES
 M0_ACES = data_rep + "lte03900-4.50-0.0.PHOENIX-ACES-AGSS-COND-2011-HiRes_wave.dat"

eniric/obsolete/prepare_data.py

@@ -126,11 +126,11 @@ def main(
 
     """
     if data_dir is None:
-        data_dir = eniric.paths["phoenix_dat"]
+        data_dir = eniric.config.paths["phoenix_dat"]
     os.makedirs(data_dir, exist_ok=True)
 
     if phoenix_dir is None:
-        phoenix_dir = eniric.paths["phoenix_raw"]
+        phoenix_dir = eniric.config.paths["phoenix_raw"]
 
     # Get Phoenix wavelength data
     wavelength_file = "WAVE_PHOENIX-ACES-AGSS-COND-2011.fits"