ACID-code-v2 0.1.0__tar.gz → 0.1.2__tar.gz

acid_code_v2-0.1.2/ACID_code_v2/__init__.py

@@ -0,0 +1 @@
+from .ACID import *

{acid_code_v2-0.1.0/ACID_code → acid_code_v2-0.1.2}/ACID_code_v2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.1.0
+Version: 0.1.2
 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_v2-0.1.0/ACID_code → acid_code_v2-0.1.2}/ACID_code_v2.egg-info/SOURCES.txt

@@ -5,21 +5,20 @@ LICENSE
 README.md
 acid.yml
 pyproject.toml
-setup.py
 .github/workflows/python-app.yml
 .other_scripts/5_residual_profiles.py
 .other_scripts/8_master_out_profiles.py
 .vscode/launch.json
-ACID_code/.tutorial_code.py
-ACID_code/ACID.py
-ACID_code/LSD_func_faster.py
-ACID_code/__init__.py
-ACID_code/utils.py
-ACID_code/ACID_code_v2.egg-info/PKG-INFO
-ACID_code/ACID_code_v2.egg-info/SOURCES.txt
-ACID_code/ACID_code_v2.egg-info/dependency_links.txt
-ACID_code/ACID_code_v2.egg-info/requires.txt
-ACID_code/ACID_code_v2.egg-info/top_level.txt
+ACID_code_v2/.tutorial_code.py
+ACID_code_v2/ACID.py
+ACID_code_v2/LSD_func_faster.py
+ACID_code_v2/__init__.py
+ACID_code_v2/utils.py
+ACID_code_v2.egg-info/PKG-INFO
+ACID_code_v2.egg-info/SOURCES.txt
+ACID_code_v2.egg-info/dependency_links.txt
+ACID_code_v2.egg-info/requires.txt
+ACID_code_v2.egg-info/top_level.txt
 docs/ACID.rst
 docs/Makefile
 docs/conf.py
@@ -167,4 +166,6 @@ tests/data/HARPS.2007-08-29T00:30:28.617_ccf_K5_A.fits
 tests/data/HARPS.2007-08-29T00:30:28.617_e2ds_A.fits
 tests/data/HARPS.2007-08-29T00:30:28.617_e2ds_B.fits
 tests/data/HARPS.2007-08-29T00:30:28.617_s1d_A.fits
-tests/data/HARPS.2007-08-29T00:30:28.617_s1d_B.fits
+tests/data/HARPS.2007-08-29T00:30:28.617_s1d_B.fits
+tests/spawn multithreading tests/__main__.py
+tests/spawn multithreading tests/cli.py

acid_code_v2-0.1.2/ACID_code_v2.egg-info/top_level.txt

@@ -0,0 +1,6 @@
+ACID_code_v2
+dist
+docs
+downloads
+example
+tests

{acid_code_v2-0.1.0 → acid_code_v2-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.1.0
+Version: 0.1.2
 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_v2-0.1.0 → acid_code_v2-0.1.2}/pyproject.toml

@@ -4,6 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ACID_code_v2"
+version = "0.1.2"
 authors = [
     {name = "Benjamin Cadell", email="bcadell01@qub.ac.uk"},
     {name = "Lucy Dolan"}
@@ -26,7 +27,6 @@ dependencies = [
     "astropy",
     "tqdm"
 ]
-dynamic = ["version"]
 
 [project.optional-dependencies]
 docs = [
@@ -37,7 +37,7 @@ docs = [
 Homepage = "https://github.com/Benjamin-Cadell/ACID"
 
 [tool.setuptools.packages.find]
-where = ["ACID_code"]
+where = ["."]
 
 # ... other project metadata fields as listed in:
 #     https://packaging.python.org/en/latest/guides/writing-pyproject-toml/

acid_code_v2-0.1.2/tests/spawn multithreading tests/__main__.py

@@ -0,0 +1,3 @@
+# ACID/__main__.py
+from .cli import cli
+cli()

acid_code_v2-0.1.2/tests/spawn multithreading tests/cli.py

@@ -0,0 +1,63 @@
+# ACID/cli.py
+import argparse
+import numpy as np
+from astropy.io import fits
+import multiprocessing as mp
+
+from . import ACID as acid_mod  # imports ACID/ACID.py module
+
+def cli():
+    p = argparse.ArgumentParser(
+        description="Run ACID (LSD + continuum fit) from the command line."
+    )
+    group = p.add_mutually_exclusive_group(required=True)
+    group.add_argument("--fits", help="Path to FITS with HDUs: 0=wavelength, 1=flux, 2=error, 3=S/N")
+    group.add_argument("--harps-list", nargs="+", help="List of HARPS files (same night)")
+
+    p.add_argument("--linelist", required=True, help="Path to VALD linelist")
+    p.add_argument("--vmin", type=float, default=-25.0)
+    p.add_argument("--vmax", type=float, default=25.0)
+    p.add_argument("--deltav", type=float, default=0.82)
+    p.add_argument("--nsteps", type=int, default=4000)
+    p.add_argument("--parallel", action="store_true", help="Use multiprocessing in MCMC")
+    p.add_argument("--cores", type=int, default=None, help="Number of cores if --parallel")
+    p.add_argument("--poly-order", type=int, default=3)
+    p.add_argument("--pix-chunk", type=int, default=20)
+    p.add_argument("--dev-perc", type=int, default=25)
+    p.add_argument("--n-sig", type=int, default=1)
+    p.add_argument("--out", default="acid_profile.npz", help="Output .npz path")
+
+    args = p.parse_args()
+
+    # Safe on macOS/Windows for spawn; harmless if already set
+    try:
+        mp.set_start_method("spawn", force=True)
+    except RuntimeError:
+        pass
+
+    velocities = np.arange(args.vmin, args.vmax, args.deltav)
+
+    if args.fits:
+        spec = fits.open(args.fits)
+        wavelength = spec[0].data
+        spectrum   = spec[1].data
+        error      = spec[2].data
+        sn         = spec[3].data
+
+        result = acid_mod.ACID(
+            [wavelength], [spectrum], [error], args.linelist, [sn], velocities,
+            poly_or=args.poly_order, pix_chunk=args.pix_chunk, dev_perc=args.dev_perc,
+            n_sig=args.n_sig, parallel=args.parallel, cores=args.cores, nsteps=args.nsteps,
+            verbose=True
+        )
+        profile = result[0, 0, 0]
+        perr    = result[0, 0, 1]
+        np.savez(args.out, velocities=velocities, profile=profile, profile_error=perr)
+        print(f"Saved single-profile output to {args.out}")
+
+    else:
+        BJDs, profiles, errors = acid_mod.ACID_HARPS(
+            args.harps_list, args.linelist, velocities, poly_or=args.poly_order,
+        )
+        np.savez(args.out, BJDs=BJDs, velocities=velocities, profiles=profiles, errors=errors)
+        print(f"Saved HARPS multi-order output to {args.out}")

{acid_code_v2-0.1.0 → acid_code_v2-0.1.2}/tests/tests.py

@@ -1,9 +1,15 @@
 #%%
 from astropy.io import fits
 import os
-os.chdir(os.path.dirname(__file__))
-os.chdir("..")
-import ACID_code.ACID as acid
+
+try:
+    import ACID_code_v2 as acid
+except ImportError:
+    raise ImportError("ACID_code_v2 not found")
+    os.chdir(os.path.dirname(__file__))
+    os.chdir("..")
+    import ACID_code_v2 as acid
+
 import numpy as np
 import matplotlib.pyplot as plt
 import glob, importlib

{acid_code_v2-0.1.0 → acid_code_v2-0.1.2}/tests/tutorial_test.py

@@ -1,5 +1,5 @@
 from astropy.io import fits
-import ACID_code.ACID as acid
+import ACID_code_v2.ACID as acid
 import numpy as np
 import matplotlib.pyplot as plt
 import glob

acid_code_v2-0.1.0/ACID_code/ACID_code_v2.egg-info/top_level.txt

@@ -1 +0,0 @@
-

acid_code_v2-0.1.0/ACID_code/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.0"

acid_code_v2-0.1.0/setup.py

@@ -1,29 +0,0 @@
-from setuptools import setup, find_packages
-import re
-
-# auto-updating version code stolen from orbitize which stole from RadVel :)
-def get_property(prop, project):
-    result = re.search(
-        r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
-        open(project + "/__init__.py").read(),
-    )
-    return result.group(1)
-
-def get_requires():
-    reqs = []
-    for line in open('docs/requirements.txt', 'r').readlines():
-        reqs.append(line)
-    return reqs
-
-setup(
-
-    name="ACID_code",
-
-    version=get_property("__version__", "ACID_code"),
-
-    packages=find_packages(),
-
-    description="Returns line profiles from input spectra by fitting the stellar continuum and performing LSD",
-
-    install_requires=get_requires()
-)