ACID-code-v2 0.1.8__tar.gz → 0.2.0__tar.gz

acid_code_v2-0.2.0/.github/workflows/publish.yml

@@ -0,0 +1,16 @@
+name: Publish to PyPI
+on:
+  push:
+    tags:
+      - 'v*'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - run: pip install build twine
+      - run: python -m build
+      - run: twine upload dist/* -u __token__ -p ${{ secrets.PYPI_TOKEN }}

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.7"
+    python: "3.13"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code_v2
-Version: 0.1.8
+Version: 0.2.0
 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>
@@ -23,14 +23,18 @@ Provides-Extra: docs
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Dynamic: license-file
 
-A.C.I.D (Accurate Continuum fItting and Deconvolution)
+A.C.I.D v2 (Accurate Continuum fItting and Deconvolution)
 ==============================================================
 
-ACID is a technique that builds on traditional Least-Squares Deconvolution (LSD) by simultaneously fitting the stellar continuum and stellar line profile and performing LSD in effective optical depth. 
+ACID_v2 is a fork of ACID (https://github.com/ldolan05/ACID) from the work of Lucy Dolan for her PhD. ACID_v2 improves on ACID by:
+    - Updating packages and code to work with newer and stable versions of python.
+    - Improving memory management so that ACID can be run on MacOS without crashes (ie extending compatibility to all POSIX systems)
+    - Adding additional kwargs to ACID to tailor output, including verbosity settings, MCMC number of steps, multiprocessing switch, and more.
 
-In a basic sense, ACID simulatenously fits the stellar continuum and profile using a combination of LSD and MCMC techniques. The spectra are then continuum corrected using this continuum fit. LSD is then run on the continuum corrected spectra to return high-resolution line profiles for each spectrum.
+The mathematical functions and method remain the same as ACID and are outlined in Dolan et al. 2024 (https://academic.oup.com/mnras/article/529/3/2071/7624678).
 
-For a full outline of ACID's algorithm and implementation, see our paper: (link to paper will be added)
+The documentation will be kept up to date with the latest function descriptions until at least 2029.
 
-Documentation: https://acid-code.readthedocs.io/en/latest/index.html
+ACID is a technique that builds on traditional Least-Squares Deconvolution (LSD) by simultaneously fitting the stellar continuum and stellar line profile and performing LSD in effective optical depth. 
 
+In a basic sense, ACID simulatenously fits the stellar continuum and profile using a combination of LSD and MCMC techniques. The spectra are then continuum corrected using this continuum fit. LSD is then run on the continuum corrected spectra to return high-resolution line profiles for each spectrum.

acid_code_v2-0.2.0/README.md

@@ -0,0 +1,15 @@
+A.C.I.D v2 (Accurate Continuum fItting and Deconvolution)
+==============================================================
+
+ACID_v2 is a fork of ACID (https://github.com/ldolan05/ACID) from the work of Lucy Dolan for her PhD. ACID_v2 improves on ACID by:
+    - Updating packages and code to work with newer and stable versions of python.
+    - Improving memory management so that ACID can be run on MacOS without crashes (ie extending compatibility to all POSIX systems)
+    - Adding additional kwargs to ACID to tailor output, including verbosity settings, MCMC number of steps, multiprocessing switch, and more.
+
+The mathematical functions and method remain the same as ACID and are outlined in Dolan et al. 2024 (https://academic.oup.com/mnras/article/529/3/2071/7624678).
+
+The documentation will be kept up to date with the latest function descriptions until at least 2029.
+
+ACID is a technique that builds on traditional Least-Squares Deconvolution (LSD) by simultaneously fitting the stellar continuum and stellar line profile and performing LSD in effective optical depth. 
+
+In a basic sense, ACID simulatenously fits the stellar continuum and profile using a combination of LSD and MCMC techniques. The spectra are then continuum corrected using this continuum fit. LSD is then run on the continuum corrected spectra to return high-resolution line profiles for each spectrum.

acid_code_v2-0.2.0/docs/ACID.rst

@@ -0,0 +1,7 @@
+.. _ACID:
+
+ACID Functions
+================
+
+.. automodule:: src.ACID_code_v2.ACID
+    :members:

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/docs/conf.py

@@ -1,7 +1,7 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../ACID_code'))
+sys.path.insert(0, os.path.abspath('..'))
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -11,18 +11,18 @@ sys.path.insert(0, os.path.abspath('../ACID_code'))
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'ACID_code'
-copyright = '2023, Lucy Dolan'
-author = 'Lucy Dolan'
+project = 'ACID_code_v2'
+copyright = '2025, Benjamin Cadell'
+author = 'Benjamin Cadell'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = [
-    'sphinx.ext.autodoc', 
-    'sphinx.ext.napoleon',
-]
+extensions = ["sphinx.ext.autodoc",
+              "sphinx.ext.napoleon",
+              "sphinx.ext.doctest",
+              "sphinx.ext.viewcode",]
 
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

acid_code_v2-0.2.0/docs/index.rst

@@ -0,0 +1,47 @@
+.. ACID documentation master file, created by
+   sphinx-quickstart on Tue Oct 31 11:39:06 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+A.C.I.D v2 (Accurate Continuum fItting and Deconvolution)
+==============================================================
+
+GitHub link: https://github.com/Benjamin-Cadell/ACID_v2
+
+ACID_v2 is a fork of ACID (https://github.com/ldolan05/ACID) from the work of Lucy Dolan for her PhD. ACID_v2 improves on ACID by:
+    - Updating packages and code to work with newer and stable versions of python.
+    - Improving memory management so that ACID can be run on MacOS without crashes (ie extending compatibility to all POSIX systems)
+    - Adding additional kwargs to ACID to tailor output, including verbosity settings, MCMC number of steps, multiprocessing switch, and more.
+
+The mathematical functions and method remain the same as ACID and are outlined in Dolan et al. 2024 (https://academic.oup.com/mnras/article/529/3/2071/7624678).
+
+The documentation will be kept up to date with the latest function descriptions until at least 2029.
+
+ACID is a technique that builds on traditional Least-Squares Deconvolution (LSD) by simultaneously fitting the stellar continuum and stellar line profile and performing LSD in effective optical depth. 
+
+In a basic sense, ACID simulatenously fits the stellar continuum and profile using a combination of LSD and MCMC techniques (MCMC implementation through emcee_). The spectra are then continuum corrected using this continuum fit. LSD is then run on the continuum corrected spectra to return high-resolution line profiles for each spectrum.
+
+For a full outline of ACID's algorithm and implementation, see our paper_ or view the package on GitHub_.
+
+.. _emcee: https://emcee.readthedocs.io/en/
+.. _paper: https://academic.oup.com/mnras/article/529/3/2071/7624678
+.. _GitHub: https://github.com/Benjamin-Cadell/ACID_v2
+
+User Guide
+===================
+.. toctree::
+   :maxdepth: 2
+
+   installation.rst
+   using_ACID.rst
+   ACID.rst
+
+License and Attribution
+================================
+
+Copyright 2025, Benjamin Cadell.
+
+ACID is free software made available under the MIT License.
+
+If you make use of ACID or ACID_v2 in your work please cite the original work by L.Dolan (L.Dolan et al, 2024): https://academic.oup.com/mnras/article/529/3/2071/7624678.
+

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/docs/installation.rst

@@ -6,15 +6,14 @@ Installation
 Installing the package
 =======================
 
-ACID is currently compatable with python=3.7 due to issues arising from the multiprocessing module in newer versions of python (hopefully to be remedied in upcoming releases!). 
-It is therefore recommended to create a conda environment to avoid downgrading your local python installation. 
+ACID_v2 has been tested in Python 3.11, and is currently incompatible with 3.12. It is recommended to install ACID in a new conda environment to avoid dependency conflicts.
 
 In this example we create an environment named 'acid' and activate it using:
 
 .. code-block:: bash
 
-    conda create -n acid python=3.7
-    conda acivate acid
+    conda create -n acid python=3.11
+    conda activate acid
 
 Once the environment has been activated ACID can be installed using pip_:
 
@@ -22,17 +21,15 @@ Once the environment has been activated ACID can be installed using pip_:
 
 .. code-block:: bash
 
-    pip install ACID_code
+    pip install ACID_code_v2
 
 .. _source:
 
 Installing from the source
 ===========================
-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).
+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.
 
-.. _tutorials: file:///Users/lucydolan/Documents/GitHub/ACID/docs/_build/html/using_ACID.html
-
 .. code-block:: bash
 
     git clone https://github.com/ldolan05/ACID.git
@@ -44,7 +41,7 @@ This can be done by cloning the source repository and installing from there.
 Testing the installation
 ==========================
 
-Test your installation by running our test file in the test directory using pytest_. This may take a while but should run without any errors if the installation has gone smoothly.
+Test your installation by running our test file in the test directory using pytest_. This may take a while (~1-2 min) but should run without any errors if the installation has gone smoothly.
 
 .. _pytest: https://docs.pytest.org/en/7.4.x/contents.html
 

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/docs/using_ACID.rst

@@ -3,9 +3,9 @@
 Using ACID
 -----------
 
-These tutorials requires use of the example data included in the source_ installation.
+These tutorials requires use of the example data included in the example_ folder.
 
-.. _source: file:///Users/lucydolan/Documents/GitHub/ACID/docs/_build/html/installation.html#installing-from-the-source 
+.. _source: https://github.com/Benjamin-Cadell/ACID_v2/tree/main/example
 
 Quickstart
 =============
@@ -26,9 +26,9 @@ In the 'example' directory we can set up our inputs are follows:
    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_linelist.txt' # Insert path to line list
 
-The stellar line list can be obtained from VALD_ using their 'Extract Stellar' feature. You should input stellar parameters that correspond to your object and ensure that the wavelength range input covers the entire wavelength range of your spectrum. 
+The stellar line list can also be obtained from VALD_ using their 'Extract Stellar' feature. You should input stellar parameters that correspond to your object and ensure that the wavelength range input covers the entire wavelength range of your spectrum. 
 The detection threshold input to VALD must be less than 1/(3*SN) where SN is the signal-to-noise of the spectrum.
 
 .. _VALD: http://vald.astro.uu.se/ 
@@ -37,9 +37,9 @@ We can then run ACID and plot the final results:
 
 .. code-block:: python
 
-   import ACID_code.ACID as acid
    import numpy as np
    import matplotlib.pyplot as plt
+   import ACID_code_v2 as acid
 
    # choose a velocity grid for the final profile(s)
    deltav = acid.calculate_deltav(wavelength)   # velocity pixel size must not be smaller than the spectral pixel size - can use calculate_deltav function if unsure what this would be.
@@ -88,13 +88,13 @@ As in the previous example, we must first read in the data:
       errors.append(spec_file[2].data)         # Spectral Flux Errors
       sns.append(float(spec_file[3].data))     # SN of Spectrum
 
-   linelist = './example_linelist.txt' # Insert path to line list
+   linelist = 'example_linelist.txt' # Insert path to line list
 
 Once the inputs have been constructed ACID can be applied and the results plotted. 
 
 .. code-block:: python
 
-   import ACID_code.ACID as acid
+   import ACID_code_v2 as acid
    import numpy as np
    import matplotlib.pyplot as plt
 
@@ -123,9 +123,8 @@ Multiple wavelength ranges
 =========================================
 
 In this example we will only consider one frame, however this example can be combined with the previous example to apply ACID to multiple frames and orders.
-Firstly, we will read in the data (exactly how we did in the Quickstart_ tutorial).
+Firstly, we will read in the data (exactly how we did in the quickstart tutorial).
 
-.. _Quickstart: file:///Users/lucydolan/Documents/GitHub/ACID/docs/_build/html/using_ACID.html#quickstart 
 
 .. code-block:: python
 
@@ -138,14 +137,14 @@ Firstly, we will read in the data (exactly how we did in the Quickstart_ tutoria
    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_linelist.txt' # Insert path to line list
 
 We can then loop through our desired wavelength ranges, run ACID and plot the final results. In this example we will split the wavelength ranges into 1000Å chunks.
 When looping over wavelength ranges we also need to provide the result array ('all_frames') to keep all results in the same array.
 
 .. code-block:: python
 
-   import ACID_code.ACID as acid
+   import ACID_code_v2 as acid
    import numpy as np
    import matplotlib.pyplot as plt
 
@@ -225,7 +224,7 @@ These inputs can be input into the HARPS function of ACID (ACID_HARPS):
 
 .. code-block:: python
 
-   import ACID_code.ACID as acid
+   import ACID_code_v2 as acid
 
    # run ACID function
    BJDs, profiles, errors = acid.ACID_HARPS(filelist, linelist, velocities)

{acid_code_v2-0.1.8 → acid_code_v2-0.2.0}/pyproject.toml

@@ -4,7 +4,6 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ACID_code_v2"
-version = "0.1.8"
 authors = [
     {name = "Benjamin Cadell", email="bcadell01@qub.ac.uk"},
     {name = "Lucy Dolan"}
@@ -28,6 +27,7 @@ dependencies = [
     "tqdm",
     "psutil"
 ]
+dynamic = ["version"]
 
 [project.optional-dependencies]
 docs = [
@@ -40,5 +40,10 @@ Homepage = "https://github.com/Benjamin-Cadell/ACID"
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools_scm]
+version_scheme = "post-release"
+local_scheme = "dirty-tag"
+
+
 # ... other project metadata fields as listed in:
 #     https://packaging.python.org/en/latest/guides/writing-pyproject-toml/