v1.3.1 patch into development branch

.github/workflows/ci.yml

@@ -11,18 +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:
-          - "3.7"
           - "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
@@ -41,11 +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
@@ -62,7 +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
 

.readthedocs.yml

@@ -1,14 +1,18 @@
 
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
 sphinx:
   configuration: docs/src/conf.py
 
 formats:
   - pdf
 
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: setuptools

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/requirements.txt

@@ -1,3 +1,5 @@
 
 sphinx>=2.0.0
-Cython>=0.28.0
+Cython>=3.0
+setuptools>=18.0
+

docs/src/Makefile

@@ -26,6 +26,8 @@ api:
 srcclean:
 	@ echo Cleaning docs/src/
 	@ $(MAKE) -C api/ clean
+	@ rm -f index.rst
+	@ rm -f cover.tex
 	@ $(MAKE) clean
 
 

docs/src/conf.py

@@ -35,12 +35,69 @@
 
 
 # -- Project information -----------------------------------------------------
-
-project = 'VICE'
-copyright = '2020-2021, James W. Johnson'
+project = "VICE"
+copyright = "2020-2023, James W. Johnson"
 author = vice.__author__
 release = vice.__version__
 
+_PATH_ = os.path.dirname(os.path.abspath(__file__))
+
+with open("%s/cover.tex" % (_PATH_), 'w') as f:
+	f.write(r"""
+%%%%%% VICE documentation PDF cover %%%%%%
+%%%%%% generated by: docs/src/conf.py %%%%%%
+
+\begin{center}
+\begin{figure}[!h]
+\centering
+\includegraphics{%s/../../logo/logo.png}
+\end{figure}
+\underline{\LARGE \textbf{Versatile Integrator for Chemical Evolution}}
+\par
+{\Large \textbf{Version %s}}
+\end{center}
+""" % (_PATH_, vice.__version__))
+
+with open("%s/index.rst" % (_PATH_), 'w') as f:
+	f.write(r"""
+.. VICE documentation root file
+.. generated by: docs/src/conf.py
+
+VICE: Versatile Integrator for Chemical Evolution
+=================================================
+Welcome!
+This is the documentation for **VICE version %(version)s**.
+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
+:ref:`installing VICE <install>`.
+Usage instructions for all of the functions and objects that VICE provides can
+be found in our :ref:`comprehensive API reference <apiref>`.
+Details on VICE's implementation and justification thereof can be found in
+our :ref:`science documentation <scidocs>`.
+
+VICE's developers are happy to consult with scientists looking to
+incorporate it into their research.
+Email one of our :ref:`contributors <contributors>` or `join us on Slack`__
+and start collaborating now!
+
+__ tutorial_
+__ slack_
+
+.. _tutorial: https://github.com/giganano/VICE/blob/main/examples/QuickStartTutorial.ipynb
+.. _slack: https://join.slack.com/t/vice-astro/shared_invite/zt-tqwa1syp-faiQu0P9oe83cazb0q9tJA
+
+
+.. toctree::
+	:maxdepth: 2
+
+	install
+	getting_started
+	science_documentation/index
+	api/index
+	developers/index
+""" % {"version": vice.__version__})
+
 
 # -- General configuration ---------------------------------------------------
 extensions = []