Merge pull request #6 from ReactionMechanismGenerator/fix/overhaul

overhaul

.conda/conda_build_config.yaml

@@ -0,0 +1,6 @@
+python:
+    - 3.8
+    - 3.9
+    - 3.10
+    - 3.11
+    - 3.12

.conda/meta.yaml

@@ -12,15 +12,16 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }} # [unix]
-    - {{ compiler('fortran') }} # [unix]
+    - {{ compiler('c') }}
+    - {{ compiler('fortran') }}
   host:
-    - python 3.7
+    - python
     - cython
     - numpy
     - setuptools
   run:
-    - python 3.7
+    - python
+    # https://conda-forge.org/docs/maintainer/knowledge_base/#building-against-numpy
     - {{ pin_compatible('numpy') }}
 
 test:

.github/workflows/build_package.yml

@@ -0,0 +1,55 @@
+name: Build Package
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+  workflow_dispatch:
+  push:
+    branches:
+      - stable
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          conda-solver: libmamba
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Build Tools
+        run: conda install python anaconda-client conda-build
+      - name: Configure Auto-Upload
+        if: github.ref == 'refs/heads/stable'
+        run: |
+          conda config --set anaconda_upload yes
+      - name: Build Binary
+        run: |
+          # set a default value to the conda_token if needed (like from forks)
+          : "${CONDA_TOKEN:=${{ secrets.ANACONDA_TOKEN }}}"
+          : "${CONDA_TOKEN:=default_value}"
+          echo "CONDA_TOKEN=$CONDA_TOKEN" >> $GITHUB_ENV
+          conda config --add channels conda-forge
+          conda config --add channels rmg
+          conda build --token $CONDA_TOKEN --user rmg .
+  result:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    name: Final Results
+    needs: [build]
+    steps:
+      - run: exit 1
+        # see https://github.com/orgs/community/discussions/26822?sort=new#discussioncomment-8285141
+        if: ${{ contains(needs.*.result, 'failure') || contains(needs.*.result, 'cancelled') || contains(needs.*.result, 'skipped') }}

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2011 by Joshua W. Allen (joshua.w.allen@gmail.com).
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,52 @@
+# PyDQED
+## Python wrapper for the DQED constrained nonlinear optimization code
+
+> [!WARNING]  
+> PyDQED is currently abandonware. The ReactionMechanismGenerator organization no longer has developers capable of maintaining it.
+
+The usage documentation is still relevant but no new updates will be released and we are unable to fix any bugs.
+We will continue to release conda packages for PyDQED as long as possible.
+
+To build PyDQED, clone this repository, install the dependencies (find them with `conda search -c rmg PyDQED`), upgrade whichever are causing problems, then navigate to the `.conda` directory and run `conda build .`.
+
+What follows is the original content of the README, slighly updated to removed erroneous instructions and dead links.
+
+# Introduction
+
+PyDQED provides a means for Python code to utilize DQED, a bounded, constrained nonlinear optimization code.
+DQED is [publicly available](http://www.netlib.org/opt/dqed.f) and is distributed with PyDQED.
+PyDQED provides a Python extension type for DQED, which in turn provides a Pythonic means of setting the solver options, providing residual and jacobian functions, and running the solver.
+
+The code for DQED has been provided with the PyDQED package. The license for DQED is different than that of the PyDQED wrapper code. **You are responsible for knowing and abiding by all licenses associated with DQED as well as with PyDQED.**
+
+# Installation
+## Anaconda Binary (Recommended)
+
+Install from the `rmg` conda channel:
+```
+conda install -c rmg pydqed
+```
+
+## Build Locally
+### Dependencies
+
+We build PyDQED using GitHub actions to support multiple versions of Python and platforms.
+
+To build locally, you need the following dependencies (which will automatically be installed with conda when not building locally):
+ - python
+ - numpy
+ - Cython
+ - gfortran
+ - gcc
+
+### Building
+A Makefile has been provided that can be used to compile DQED and the PyDQED wrapper code. To use, invoke the following command from the base package directory:
+```
+make
+```
+
+This command will build PyDQED in-place, rather than installing it to your Python package directory.
+If you wish to formally install PyDQED, run the following command from the base package directory after the `make` command (you may need root privileges for this):
+```
+python setup.py install
+```