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

.github/workflows/sdist.yml

@@ -1,43 +1,59 @@
-# This workflow creates a source distribution intended for uploading to PyPI
-# and uploads it to GitHub actions as an artifact, where it then gets
-# re-downloaded and combined with other wheels created by the wheels.yml
-# workflow.
+# This workflow creates a source distribution intended for uploading to PyPI,
+# uploading the .tar.gz file to GitHub actions as an artifact. We upload the
+# source distribution to PyPI manually. In previous versions of VICE, we
+# pre-compiled the code and provided the binaries, but we have scaled this down
+# for reasons described in the comments in the wheels.yml workflow file.
+# Previously, the wheels.yml workflow would download this source distribution
+# and combine it with the wheels created by bdist_linux.yml and bdist_macos.yml.
 
 name: Source Distribution
 
+# only when specifically requested
 on:
-  workflow_call:
-    inputs:
-      os:
-        description: The OS to use for creating the source distribution
-        required: true
-        type: string
-      python-version:
-        description: The version of python for creating the source distribution
-        required: true
-        type: string
+  workflow_dispatch:
+  ### previous inputs from wheels.yml, which would call this workflow ###
+  # workflow_call:
+  #   inputs:
+  #     os:
+  #       description: The OS to use for creating the source distribution
+  #       required: true
+  #       type: string
+  #     python-version:
+  #       description: The version of python for creating the source distribution
+  #       required: true
+  #       type: string
 
 jobs:
   sdist:
     name: Source Distribution
-    runs-on: ${{ inputs.os }}
-    env:
-      COMPILER: gcc
+    runs-on: ubuntu-latest
+    ### previous inputs from wheels.yml, which would call this workflow ###
+    # runs-on: ${{ inputs.os }}
+    # env:
+    #   COMPILER: gcc
 
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v2
 
-      - name: Setup Python ${{ inputs.python-version }}
+      ### previous inputs from wheels.yml, which would call this workflow ###
+      # - name: Setup Python ${{ inputs.python-version }}
+      #   uses: actions/setup-python@v2
+      #   with:
+      #     python-version: ${{ inputs.python-version }}
+
+      - name: Setup Python 3.12
         uses: actions/setup-python@v2
         with:
-          python-version: ${{ inputs.python-version }}
+          python-version: "3.12"
 
       - name: Install Dependencies
         shell: bash
         run: |
           python -m pip install --upgrade pip
-          python -m pip install Cython>=0.29.21
+          python -m pip install build
+          python -m pip install setuptools>=18.0
+          python -m pip install Cython>=3.0
           python -m pip install wheel>=0.33.0
 
       - name: Display Environment Variables
@@ -54,9 +70,7 @@ jobs:
       - name: Create Source Distribution
         shell: bash
         run: |
-          make
-          python setup.py sdist
-          make clean
+          python -m build --sdist
 
       - name: Upload Source Distribution
         uses: actions/upload-artifact@v2

.github/workflows/wheels.yml

@@ -1,3 +1,20 @@
+# This workflow is designed to pre-compile VICE for distribution across all
+# versions of python supported by the code base. In the current version,
+# however, we simply provide a source distribution will be compiled on each
+# user's system. Previous versions had provided pre-compiled binaries, and the
+# workflow code which produced those wheels is preserved here. The comments
+# from the top of this workflow from this previous distribution strategy are
+# copied below. As such, this workflow is generally not invoked; instead we
+# dispatch the sdist.yml workflow to create the source distribution.
+#
+# We elect to provide only a source distribution because, with the limited
+# architecture available through GitHub actions for Mac OS, it is likely that
+# many end user's of VICE will have to compile in place anyway. This will only
+# become more the case in the near future when users will compile it to enable
+# multithreading, which will require an in-place compilation.
+#
+# Previous Notes on Distribution Strategy:
+# ----------------------------------------
 # This workflow pre-compiles VICE for distribution across all versions of
 # python supported by the code base. Requiring a 64-bit system architecture,
 # we pre-compile for x86_64 hardware on both Mac OS and Linux. As of yet,
@@ -9,7 +26,7 @@
 # 
 # At present, GitHub actions does not support a build matrix for jobs that
 # call a reusable workflow, so the Mac OS and manylinux jobs here implement
-# the workaround from the following URL: 
+# the workaround from the following URL:
 # 
 # https://github.community/t/reusable-workflow-with-strategy-matrix/205676/8
 

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_