Merge pull request #32 from giganano/v1.3.x-patch

V1.3.1 patch

.github/workflows/ci.yml

@@ -11,19 +11,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-10.15"]
+        os: ["ubuntu-latest", "macos-latest"]
         compiler: [gcc-10, clang]
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
           - "3.10"
+          - "3.11"
+          - "3.12"
 
         exclude:
 
           # Mac OS builds run with clang only
-          - os: "macos-10.15"
+          - os: "macos-latest"
             compiler: gcc-10
 
           # Ubuntu builds run with gcc only
@@ -42,11 +42,13 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      # compile-time dependency versions reflect those in setup.py
       - name: Install Dependencies
         shell: bash
         run: |
           python -m pip install --upgrade pip
-          python -m pip install cython>=0.29.21
+          python -m pip install setuptools>=18.0
+          python -m pip install Cython>=3.0
 
       - name: Display Environment Variables
         shell: bash
@@ -63,7 +65,7 @@ jobs:
         shell: bash
         run: |
           make CC=$COMPILER
-          python setup.py build install --quiet
+          python -m pip install . -v
           make clean
 
       - name: Tests

changelog.rst.txt

@@ -1,4 +1,29 @@
 
+1.3.1
+=====
+- ``vice.multizone``
+	Enforces each zone to run in the same mode (related to the handling of
+	inflow metallicites; see below).
+
+- ``vice.singlezone`` and ``vice.multizone``
+	- Handles non-zero inflow metallicities in a more stable way. Unit tests
+	  search for numerical artifacts in "sudden event" evolutionary histories
+	  exhibiting bursts in star formation.
+
+	- Includes primordial metallicity component in the reported total abundance
+	  in accreting gas at each timestep.
+
+- ``vice.dataframe``
+	Fixed issues with inheritance structure affecting recent versions of
+	python (3.11 and 3.12)
+
+- ``vice.yields.ccsne.fractional``
+	- Subtracts the remnant mass from the initial mass in computing net yields
+	  from the tables containing gross yields. A small correction for metals,
+	  the difference is significant for helium.
+
+- Fixed callback objects to be compatible with Cython>=3.0.
+
 1.3.0
 =====
 - ``vice.mlr``

docs/src/cover.tex

@@ -6,5 +6,5 @@
 \end{figure}
 \underline{\LARGE \textbf{Versatile Integrator for Chemical Evolution}}
 \par
-{\Large \textbf{Version 1.3.0}}
+{\Large \textbf{Version 1.3.1}}
 \end{center}

docs/src/developers/contributors.rst

@@ -7,51 +7,58 @@ Contributors
 James W. Johnson
 ----------------
 | **Lead Developer** and **License Owner** (Spring 2018 - Present)
-| Email: giganano9@gmail.com johnson.7419@buckeyemail.osu.edu
-| Webiste: https://sites.google.com/view/jameswjohnson/
+| Email: jjohnson10@carnegiescience.edu giganano9@gmail.com
+| Webiste: https://jamesjohnson.space
+| The Observatories of the Carnegie Institution for Science
+| 813 Santa Barbara St., Pasadena, CA, 91101, USA
+
+Liam Dubay
+----------
+| **Contributing Developer** (Fall 2021 - Present)
+| Email: dubay.11@buckeyemail.osu.edu
+| Website: https://www.liamdubay.com/
 | The Ohio State University Department of Astronomy
-| 140 W. 18th Ave., Columbus, OH, 43204
+| 140 W. 18th Ave., Columbus, OH, 43204, USA
 
 Emily J. Griffith
 -----------------
 | **Contributing Developer** (Summer 2020 - Present)
-| Email: griffith.802@buckeyemail.osu.edu
+| Email: Emily.Griffith-1@colorado.edu
 | Website: https://www.emilyjgriffith.com
-| The Ohio State University Department of Astronomy
-| 140 W. 18th Ave., Columbus, OH, 43204
+| University of Colorado Boulder Department of Astrophysical and Planetary Sciences
+| 389 UCB, Boulder, CO, 80309, USA
 
-John W. Bredall
----------------
-| **Contributing Developer** (Fall 2021 - Present)
-| Email: bredall.1@buckeyemail.osu.edu
-| Website: https://u.osu.edu/jbredall/
+Ari Bredall
+-----------
+| **Contributing Developer** (Fall 2021 - Summer 2023)
+| Website: https://abredall.github.io/
 | The Ohio State University Department of Astronomy
-| 140 W. 18th Ave., Columbus, OH, 43204
+| 140 W. 18th Ave., Columbus, OH, 43204, USA
 
 David H. Weinberg
 -----------------
-| **Advising Developer** (Spring 2018 - Present)
+| **Advising Developer** (Spring 2018 - Summer 2023)
 | Website: http://www.astronomy.ohio-state.edu/~dhw/
 | The Ohio State University Department of Astronomy
-| 140 W. 18th Ave., Columbus, OH, 43204
+| 140 W. 18th Ave., Columbus, OH, 43204, USA
 
-Fiorenzo Vincenzo
------------------
-| **Advising Developer** (Spring 2019 - Present)
-| Website: https://ccapp.osu.edu/people/vincenzo.3
-| The Ohio State University Center for Cosmology and Astroparticle Physics
-| 191 West Woodruff Ave., Columbus, OH, 43210
+Jennifer A. Johnson
+-------------------
+| **Advising Developer** (Summer 2020 - Summer 2023)
+| Website: http://www.astronomy.ohio-state.edu/~jaj/
+| The Ohio State University Department of Astronomy
+| 140 W. 18th Ave., Columbus, OH, 43204, USA
 
 Jonathan C. Bird
 ----------------
-| **Advising Developer** (Spring 2019 - Present)
+| **Advising Developer** (Spring 2019 - Spring 2022)
 | Website: http://vpac00.phy.vanderbilt.edu/~birdjc1/
 | Vanderbilt University Department of Physics & Astronomy
-| 6301 Stevenson Center, 2301 Vanderbilt Place, Nasvhille, TN 37235
+| 6301 Stevenson Center, 2301 Vanderbilt Place, Nasvhille, TN 37235, USA
 
-Jennifer A. Johnson
--------------------
-| **Advising Developer** (Summer 2020 - Present)
-| Website: http://www.astronomy.ohio-state.edu/~jaj/
-| The Ohio State University Department of Astronomy
-| 140 W. 18th Ave., Columbus, OH, 43204
+Fiorenzo Vincenzo
+-----------------
+| **Advising Developer** (Spring 2019 - Summer 2021)
+| Website: https://www.hull.ac.uk/staff-directory/fiorenzo-vincenzo
+| E.A. Milne Centre for Astrophysics, University of Hull
+| Cottingham Road, Kingston upon Hull, HU6 7RX, United Kingdom

docs/src/index.rst

@@ -3,7 +3,7 @@
 VICE: Versatile Integrator for Chemical Evolution
 =================================================
 Welcome!
-This is the documentation for **VICE version 1.3.0**.
+This is the documentation for **VICE version 1.3.1**.
 First time users should familiarize themselves with VICE's API by going
 through our `tutorial`__, which can be launched automatically by running
 ``python -m vice --tutorial`` from a Unix terminal after

docs/src/install.rst

@@ -23,7 +23,6 @@ do not want to use the binary using the ``--no-binary`` flag:
 
 	$ python -m pip install vice [--user] --no-binary :all:
 
-
 The option ``:all:`` above tells ``pip`` to install all of the packages in the
 current call to ``pip install`` without binaries; when installing multiple
 packages, this value can be specified as a comma-separated list.
@@ -46,21 +45,25 @@ specifying the version number:
 
 	$ python -m pip install vice==<version number> [...]
 
+.. _windows_note:
+
 Designed for systems with a Unix kernel, VICE does not function within a
 windows environment.
 Windows users should therefore install VICE within the
 `Windows Subsystem for Linux (WSL)`__.
-Provided that the call to ``pip`` is ran from within WSL, the pre-compiled
-binary installer from PyPI_ should install VICE properly.
+We emphasize that the Anaconda prompt provided for Windows is **not** a true
+Unix kernel, and therefore will fail to install and run VICE properly.
+As long as the call to ``pip`` is ran from within WSL, the proper pre-compiled
+binary for Linux systems provided on PyPI_ should install successfully.
 A `manual installation`__ on a windows machine must also be ran within
-WSL.
+WSL and cannot be conducted with the Anaconda prompt.
 
 __ WSL_
 __ `Manual Installation`_
 .. _WSL: https://docs.microsoft.com/en-us/windows/wsl/install-win10
 
 For the current version, we provide pre-compiled binaries for Python_ versions
-3.6-3.10 on computers with an x86_64 CPU architecture running Mac OS and Linux
+3.7-3.10 on computers with an x86_64 CPU architecture running Mac OS and Linux
 operating systems.
 We do not provide pre-compiled binaries for CPU architectures other than x86_64.
 This includes Linux computers with Aarch64 hardware as well as the new ARM64
@@ -159,13 +162,13 @@ While VICE does not have any primary run-time dependencies, there are a few
 common compile-time dependencies that must be satisfied to install from source.
 They are as follows:
 
-1. Python_ >= 3.6
+1. Python_ >= 3.7
 
 2. setuptools_ >= 18.0
 
 3. Make_ >= 3.81
 
-4. gcc_ >= 4.6 or clang_ >= 3.6.0
+4. gcc_ >= 4.6 or clang_ >= 3.6
 
 On Mac OS X and Linux architectures, it is likely that Make_ and one of gcc_
 or clang_ come pre-installed. Users may install with alternative C compilers
@@ -323,11 +326,15 @@ __ issues_
 
 Running the setup.py File Failed
 --------------------------------
-`Did you run it for multiple versions of python simultaneously?`__
-Alternatively,
-`did you run a parallelized installation using the gcc C compiler?`__
-If neither is the case, please open an issue `here`__.
 
+`Did you attempt your installation on Windows without using WSL?`__
+If not, `did you attempt the installation for multiple versions of python
+simultaneously?`__
+Alternatively, `did you run a parallelized installation using the gcc C
+compiler?`__
+If none of these solutions apply to your case, please open an issue `here`__.
+
+__ windows_note_
 __ gcc_parallel_note_
 __ simultaneous_note_
 __ issues_

docs/src/science_documentation/yields/agb.rst

@@ -52,10 +52,10 @@ some characteristic mass in order to suppress these numerical artifacts.
 In this version of VICE, users can choose between the following
 nucleosynthesis studies:
 
-	- Cristallo et al. (2011, 2015) [7]_ [8]_
-	- Karakas (2010) [9]_
-	- Ventura et al. (2013) [10]_
-	- Karakas & Lugaro (2016) [11]_; Karakas et al. (2018) [12]_
+	- Cristallo et al. (2011, 2015) [8]_ [9]_
+	- Karakas (2010) [10]_
+	- Ventura et al. (2013) [11]_
+	- Karakas & Lugaro (2016) [12]_; Karakas et al. (2018) [13]_
 
 Users can also read these tables in with the ``vice.yields.agb.grid`` function.
 
@@ -64,9 +64,9 @@ Relevant Source Code:
 	- ``vice/src/singlezone/agb.c``
 	- ``vice/yields/agb/_grid_reader.pyx``
 
-.. [7] Cristallo et al. (2011), ApJS, 197, 17
-.. [8] Cristallo et al. (2015), ApJS, 219, 40
-.. [9] Karakas (2010), MNRAS, 403, 1413
-.. [10] Ventura et al. (2013), MNRAS, 431, 3642
-.. [11] Karakas & Lugaro (2016), ApJ, 825, 26
-.. [12] Karakas et al. (2018), MNRAS, 477, 421
+.. [8] Cristallo et al. (2011), ApJS, 197, 17
+.. [9] Cristallo et al. (2015), ApJS, 219, 40
+.. [10] Karakas (2010), MNRAS, 403, 1413
+.. [11] Ventura et al. (2013), MNRAS, 431, 3642
+.. [12] Karakas & Lugaro (2016), ApJ, 825, 26
+.. [13] Karakas et al. (2018), MNRAS, 477, 421

docs/src/science_documentation/yields/ccsne.rst

@@ -4,11 +4,12 @@ Core Collapse Supernovae
 Because core collapse supernovae (CCSNe) are assumed to occur simultaneously
 with the formation of their progenitor stars [2]_, :math:`y_x^\text{CC}`
 represents the total yield from all CCSNe associated with a single stellar
-population. Letting :math:`m_x` denote the net mass of some element :math:`x`
-present in the CCSN ejecta, the yield at a given metallicity is defined by:
+population. Letting :math:`m_x` denote the mass of some element :math:`x`
+present in the CCSN ejecta from a progenitor of initial mass :math:`m`, the
+yield at a given metallicity is defined by:
 
 .. math:: y_x^\text{CC} \equiv \frac{
-	\int_{l_\text{CC}}^u (E(m)m_x + w_x - Z_{x,\text{prog}} m)
+	\int_{l_\text{CC}}^u (E(m)m_x + w_x - Z_{x,\text{prog}} (m - m_\text{rem}))
 	\frac{dN}{dm} dm
 	}{
 	\int_l^u m \frac{dN}{dm} dm
@@ -17,16 +18,21 @@ present in the CCSN ejecta, the yield at a given metallicity is defined by:
 where the numerator is taken from the minimum mass for a CCSN explosion
 :math:`l_\text{CC}` to the upper mass limit of star formation :math:`u`, but
 the denominator is over the entire mass range of star formation, and
-:math:`dN/dm` is the stellar initial mass function (IMF). This equation is
-nothing more or less than the mathematical statement of "production divided
-by total initial mass."
+:math:`dN/dm` is the stellar initial mass function (IMF).
+The constant ``CC_MIN_STELLAR_MASS`` declares :math:`l_\text{CC} = 8 M_\odot`
+in ``vice/src/ccsne.h``.
+This equation is nothing more or less than the mathematical statement of "metal
+production divided by total initial mass of stars."
 :math:`E(m)` denotes the *explodability*: the fraction of star of mass
 :math:`m` which explode as a CCSN. :math:`w_x` denotes the mass yield of the
-element :math:`x` due to winds at a mass :math:`m`, and the corrective term
-:math:`Z_{x,\text{prog}} m` accounts for the birth abundances of the star to
-compute a *net* rather than a *gross* yield. The constant
-``CC_MIN_STELLAR_MASS`` declares :math:`l_\text{CC} = 8 M_\odot` in
-``vice/src/ccsne.h``.
+element :math:`x` due to stellar winds at a mass :math:`m`, and the corrective
+term :math:`Z_{x,\text{prog}} (m - m_\text{rem})` accounts for the mass of the
+element :math:`x` in the ejecta that was present at birth, converting the
+quantity from a *gross* yield to a *net* yield.
+In the current version of VICE, :math:`m_\text{rem}` is assumed to always be a
+1.44 :math:`M_\odot` black hole for massive stars based on Weinberg, Andrews
+& Freudenburg (2017) [6]_; additional, more realistic initial-final remnant
+mass relations are currently being incorporated into the code base.
 
 In practice, supernova nucleosynthesis studies determine the value of
 :math:`m_x` for of order 10 values of :math:`m` at a given metallicity and
@@ -111,3 +117,5 @@ Relevant Source Code:
 
 .. [5] Salpeter (1955), ApJ, 121, 161
 
+.. [6] Weinberg, Andrews & Freudenburg (2017), ApJ, 837, 183
+

docs/src/science_documentation/yields/sneia.rst

@@ -25,7 +25,7 @@ Intuitively, the SN Ia yield is thus specified by the mass yield of a single
 SN Ia explosion and the number of SN Ia events that occur per unit solar
 mass formed.
 
-Maoz & Mannucci (2012) [6]_ found that :math:`N_\text{Ia}/M_\star` =
+Maoz & Mannucci (2012) [7]_ found that :math:`N_\text{Ia}/M_\star` =
 :math:`(2 \pm 1) \times 10^{-3} M_\odot^{-1}`. That is, on average,
 approximately 500 :math:`M_\odot` of stars must form for a given stellar
 population to produce a single SN Ia.
@@ -49,4 +49,4 @@ Relevant Source Code:
 
 	- ``vice/yields/sneia/_yield_lookup.pyx``
 
-.. [6] Maoz & Mannucci (2012), PASA, 29, 447
+.. [7] Maoz & Mannucci (2012), PASA, 29, 447