ACID-code-v2 0.2.2a4__tar.gz → 0.2.3__tar.gz

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.2.2a4
+Version: 0.2.3
 Summary: Returns line profiles from input spectra by fitting the stellar continuum and performing LSD
 Author: Lucy Dolan
 Author-email: Benjamin Cadell <bcadell01@qub.ac.uk>

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/docs/installation.rst

@@ -25,16 +25,16 @@ Once the environment has been activated ACID can be installed using pip_:
 
 .. _source:
 
-Installing from the source
+Cloning the repository
 ===========================
 In order to use the example data (for the tutorials) or the test suite ACID will need to be installed from the source (i.e. directly from the GitHub repository).
-This can be done by cloning the source repository and installing from there.
+This can be done by cloning the source repository. All examples and tests attempt first to import from your pip installation.
+If this fails they will attempt to import from the local source directory instead.
 
 .. code-block:: bash
 
-    git clone https://github.com/ldolan05/ACID.git
-    cd ACID
-    python -m pip install -e .
+    git clone https://github.com/Benjamin-Cadell/ACID_v2.git
+    cd ACID_v2
 
 .. _test:
 
@@ -47,6 +47,6 @@ Test your installation by running our test file in the test directory using pyte
 
 .. code-block:: bash
     
-    pytest tests.py
+    pytest tests/tests.py
 
 

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/example/tutorial_code.py

@@ -1,27 +1,29 @@
 #%%
 from astropy.io import fits
-import importlib, os
+import importlib, os, sys
 import multiprocessing as mp
 import numpy as np
 import matplotlib.pyplot as plt
+os.chdir(os.path.dirname(__file__))
+os.chdir("..")  # ensures we are in the main directory
 try:
-    raise Exception("Force except block")
     import ACID_code_v2 as acid
 except:
-    os.chdir(os.path.dirname(__file__))
-    os.chdir("../src") # ensures we are in the main directory
-    import ACID_code_v2 as acid
-    os.chdir("../example") # change back to example directory
+    SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
+    PROJECT_ROOT = os.path.dirname(SCRIPT_DIR)
+    sys.path.append(PROJECT_ROOT)
+    from src import ACID_code_v2 as acid
+    print("pip module failed to import, imported from local instead")
 importlib.reload(acid)
 
-spec_file = fits.open('sample_spec_1.fits')
+spec_file = fits.open('example/sample_spec_1.fits')
 
 wavelength = spec_file[0].data   # Wavelengths in Angstroms
 spectrum = spec_file[1].data     # Spectral Flux
 error = spec_file[2].data        # Spectral Flux Errors
 sn = spec_file[3].data           # SN of Spectrum
 
-linelist = 'example_linelist.txt' # Insert path to line list
+linelist = 'example/example_linelist.txt' # Insert path to line list
 
 # choose a velocity grid for the final profile(s)
 deltav = 0.82   # velocity pixel size must not be smaller than the spectral pixel size

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/src/ACID_code_v2/ACID.py

@@ -841,7 +841,8 @@ def ACID(input_wavelengths, input_spectra, input_spectral_errors, line, frame_sn
 
     return all_frames
 
-def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './', file_type = 'e2ds', **kwargs):
+def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './',
+               file_type = 'e2ds', name="test", **kwargs):
     """Accurate Continuum fItting and Deconvolution for HARPS e2ds and s1d spectra (DRS pipeline 3.5)
 
     Fits the continuum of the given spectra and performs LSD on the continuum corrected spectra,
@@ -892,6 +893,8 @@ def ACID_HARPS(filelist, line, vgrid, order_range=None, save_path = './', file_t
     global frame_wavelengths
     global frame_errors
     global sns
+    global run_name
+    run_name = name
 
     if order_range is None:
         order_range = np.arange(10, 70)

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/src/ACID_code_v2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.2.2a4
+Version: 0.2.3
 Summary: Returns line profiles from input spectra by fitting the stellar continuum and performing LSD
 Author: Lucy Dolan
 Author-email: Benjamin Cadell <bcadell01@qub.ac.uk>

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/tests/tests.py

@@ -1,11 +1,18 @@
 #%%
 from astropy.io import fits
-import os, glob, importlib
-os.chdir(os.path.dirname(__file__))
-os.chdir("..") # ensures we are in the main directory
-import ACID_code_v2 as acid
+import os, glob, importlib, sys
 import numpy as np
 import matplotlib.pyplot as plt
+os.chdir(os.path.dirname(__file__))
+os.chdir("..")  # ensures we are in the main directory
+try:
+    import ACID_code_v2 as acid
+except:
+    SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
+    PROJECT_ROOT = os.path.dirname(SCRIPT_DIR)
+    sys.path.append(PROJECT_ROOT)
+    from src import ACID_code_v2 as acid
+    print("pip module failed to import, imported from local instead")
 importlib.reload(acid)
 
 def test_run_e2ds():

{acid_code_v2-0.2.2a4 → acid_code_v2-0.2.3}/tests/tutorial_test.py

@@ -1,18 +1,28 @@
 from astropy.io import fits
-import ACID_code_v2.ACID as acid
 import numpy as np
 import matplotlib.pyplot as plt
-import glob
+import glob, os, importlib, sys
+os.chdir(os.path.dirname(__file__))
+os.chdir("..")  # ensures we are in the main directory
+try:
+    import ACID_code_v2 as acid
+except:
+    SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
+    PROJECT_ROOT = os.path.dirname(SCRIPT_DIR)
+    sys.path.append(PROJECT_ROOT)
+    from src import ACID_code_v2 as acid
+    print("pip module failed to import, imported from local instead")
+importlib.reload(acid)
 
 def quickstart():
-    spec_file = fits.open('../example/sample_spec_1.fits')
+    spec_file = fits.open('example/sample_spec_1.fits')
 
     wavelength = spec_file[0].data   # Wavelengths in Angstroms
     spectrum = spec_file[1].data     # Spectral Flux
     error = spec_file[2].data        # Spectral Flux Errors
     sn = spec_file[3].data           # SN of Spectrum
 
-    linelist = '../example/example_linelist.txt' # Insert path to line list
+    linelist = 'example/example_linelist.txt' # Insert path to line list
 
     # choose a velocity grid for the final profile(s)
     deltav = acid.calc_deltav(wavelength)  # velocity pixel size must not be smaller than the spectral pixel size
@@ -35,7 +45,7 @@ def quickstart():
 def multiple_frames():
 
     # finds sample files in 'example directory'. Each file is a different frame.
-    files = glob.glob('../example/sample_spec_*.fits')
+    files = glob.glob('example/sample_spec_*.fits')
 
     # create lists for wavelengths, spectra, errors and sn for all frames
     wavelengths = []
@@ -51,7 +61,7 @@ def multiple_frames():
         errors.append(spec_file[2].data)         # Spectral Flux Errors
         sns.append(float(spec_file[3].data))     # SN of Spectrum
 
-    linelist = '../example/example_linelist.txt' # Insert path to line list
+    linelist = 'example/example_linelist.txt' # Insert path to line list
 
     # choose a velocity grid for the final profile(s)
     deltav = acid.calc_deltav(wavelengths[0])
@@ -74,14 +84,14 @@ def multiple_frames():
     plt.close('all')
 
 def mulitple_orders():
-    spec_file = fits.open('../example/sample_spec_1.fits')
+    spec_file = fits.open('example/sample_spec_1.fits')
 
     wavelength = spec_file[0].data   # Wavelengths in Angstroms
     spectrum = spec_file[1].data     # Spectral Flux
     error = spec_file[2].data        # Spectral Flux Errors
     sn = spec_file[3].data           # SN of Spectrum
 
-    linelist = '../example/example_linelist.txt' # Insert path to line list
+    linelist = 'example/example_linelist.txt' # Insert path to line list
 
     # choose a velocity grid for the final profile(s)
     deltav = acid.calc_deltav(wavelength)