Final Overhaul

.conda/build.sh

@@ -2,5 +2,5 @@
 make
 
 # Build cython wrapper
-$PYTHON setup.py daspk install
+make install
 

.conda/meta.yaml

@@ -1,39 +1,38 @@
 # For conda build
 package:
   name: pydas
-  version: '1.0.3'
+  version: '1.0.4'
 
 source:
   path: ../
 
 build:
-  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
+  string: py{{ CONDA_PY }}h{{ PKG_HASH }}npy{{ NPY_VER }}_{{ PKG_BUILDNUM }}
 
 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
     - {{ pin_compatible('numpy') }}
 
 test:
   source_files:
     - tests
   requires:
-    - nose
     - matplotlib
   imports:
     - pydas
     - pydas.dassl
     - pydas.daspk
   commands:
-    - nosetests -P --all-modules -v -w tests
+    - python -m unittest -v tests/daspkTest.py tests/dasslTest.py
 
 about:
   home: http://github.com/ReactionMechanismGenerator/PyDAS

.github/workflows/build_package.yml

@@ -0,0 +1,74 @@
+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]
+        numpy-version: ["1.21", "1.22", "1.23", "1.24", "1.25", "1.26", "2.0"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        exclude:
+          - numpy-version: "1.21"
+            python-version: "3.10"
+          - numpy-version: "1.21"
+            python-version: "3.11"
+          - numpy-version: "1.22"
+            python-version: "3.11"
+          - numpy-version: "1.21"
+            python-version: "3.12"
+          - numpy-version: "1.22"
+            python-version: "3.12"
+          - numpy-version: "1.23"
+            python-version: "3.12"
+          - numpy-version: "1.24"
+            python-version: "3.12"
+          - numpy-version: "1.25"
+            python-version: "3.12"
+    runs-on: ${{ matrix.os }}
+    name: Build ${{ matrix.os }} Python ${{ matrix.python-version }} Numpy ${{ matrix.numpy-version }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: false
+          conda-solver: libmamba
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Build Tools
+        run: conda install python anaconda-client conda-build
+      - name: Configure Auto-Upload
+        if: github.ref == 'refs/heads/stable'
+        run: |
+          conda config --set anaconda_upload yes
+      - name: Build Binary
+        run: |
+          # set a default value to the conda_token if needed (like from forks)
+          : "${CONDA_TOKEN:=${{ secrets.ANACONDA_TOKEN }}}"
+          : "${CONDA_TOKEN:=default_value}"
+          echo "CONDA_TOKEN=$CONDA_TOKEN" >> $GITHUB_ENV
+          conda config --add channels conda-forge
+          CONDA_NPY=${{ matrix.numpy-version }} CONDA_PY=${{ matrix.python-version }} 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') }}

Makefile

@@ -18,24 +18,10 @@ dassl: DASSL cython
 daspk: DASPK31 cython
 
 cython:
-ifeq (,$$(wildcard daspk31/solver/ddaspk.o))
-	# DASPK3.1 was not compiled. Cythonize the wrapper for only DASSL.
-	python setup.py build_ext $(CYTHON_FLAGS)
-else
-	# Cythonize both DASSL and DASPK3.1 wrappers
-	python setup.py build_ext daspk $(CYTHON_FLAGS)
-endif
-
+	pip install .
 
 install: DASSL DASPK31 DASKR cython
-ifeq (,$$(wildcard pydas/daspk.so))
-	# the file "pydas/daspk.so" does not exist, so don't install daspk
-	python setup.py install
-	@echo "NOTE: Installed without DASPK, because it had not been compiled."
-else
-	# the file "pydas/daspk.so" does exist, so install daspk
-	python setup.py daspk install
-endif
+	pip install .
 
 test: 
 	cd tests; python dasslTest.py

README.md

@@ -0,0 +1,13 @@
+# PyDAS
+## Python Wrapper to DASPK, DASSL, and DASKR
+
+> [!WARNING]  
+> PyDAS is no longer receiving updates. The ReactionMechanismGenerator organization has no 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 PyDAS as long as possible.
+
+To build PyDAS, clone this repository, install the dependencies (find them with `conda search -c rmg pydas`), upgrade whichever are causing problems, then navigate to the `.conda` directory and run `conda build .`.
+Installation instructions in the documentation directory are _not_ up to date.
+
+The original README file is maintained in this repository, for posterity.

README.rst

@@ -1,22 +1,3 @@
-.. warning::
-    PyDAS 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 PyDAS as long as possible.
-    The current version (as of 5/2/2023) was built with libgfortran-ng 12 (or just libgfortran 5 for Mac) and
-    Python 3.7 - it is likely in the future that this will no longer work properly
-    and need to be fixed.
-
-    To build PyDAS, clone this repository, install the dependencies (find them
-    with conda search -c rmg PyDAS), upgrade whichever are causing problems,
-    then navigate to the .conda directory and run "conda build ."
-
-    Good Luck,
-    Jackson (@JacksonBurns)
-
 *************************************************************************
 PyDAS - A Python wrapper to several differential algebraic system solvers
 *************************************************************************

daskr/Makefile

@@ -5,7 +5,9 @@
 ################################################################################
 
 
-CFLAGS=-fPIC -fallow-argument-mismatch -O3
+CFLAGS=-fPIC -O3
+
+FFLAGS=-fallow-argument-mismatch
 
 DOBJ=solver/daux.o solver/ddaskr.o solver/dlinpk.o preconds/dbanpre.o preconds/dilupre.o preconds/drbdpre.o preconds/drbgpre.o preconds/dsparsk.o
 
@@ -24,7 +26,7 @@ $(SLIB): $(SOBJ)
 	ar rcs $(SLIB) $(SOBJ)
 
 %.o: %.f
-	$(F77) $(CFLAGS) -c $< -o $@
+	$(F77) $(CFLAGS) $(FFLAGS) -c $< -o $@
 
 clean:
 	rm -f $(DLIB) $(DOBJ) $(SLIB) $(SOBJ)

daspk31/Makefile

@@ -5,7 +5,9 @@
 ################################################################################
 
 
-CFLAGS=-fPIC -fallow-argument-mismatch -O3
+CFLAGS=-fPIC -O3
+
+FFLAGS=-fallow-argument-mismatch
 
 DOBJ=solver/adf_dummy.o solver/daux.o solver/ddaskr.o solver/ddaspk.o solver/dlinpk.o solver/dsensd.o solver/mpi_dummy.o
 
@@ -19,12 +21,12 @@ $(DLIB): $(DOBJ)
 	ar rcs $(DLIB) $(DOBJ)
 
 %.o: %.f
-	$(F77) $(CFLAGS) -c $< -o $@
+	$(F77) $(CFLAGS) $(FFLAGS) -c $< -o $@
 
-solver/%.f: | daspk31.tgz
-	tar zxvf daspk31.tgz -C ../
+solver/%.f: | daspk31.tar
+	tar zxvf daspk31.tar -C ../
 
-daspk31.tgz:
+daspk31.tar:
 	./download_daspk31.sh
 
 clean:

daspk31/download_daspk31.sh

@@ -1,11 +1,3 @@
 #!/bin/bash
-echo "skipping"
-#read -p "Do you agree to DASPK3.1 copyright restrictions at http://www.cs.ucsb.edu/~cse?" -n 1 -r
-#echo
-#if [[ $REPLY =~ ^[Yy]$ ]]
-#then
-#    echo 'Downloading and unpacking DASPK 3.1 fortran source files...'
-#    wget https://cse.cs.ucsb.edu/sites/cse.cs.ucsb.edu/files/assets/daspk31.tar
-#    tar zxvf daspk31.tgz -C ../
-#fi 
-
+echo 'Downloading and unpacking DASPK 3.1 fortran source files...'
+wget https://cse.cs.ucsb.edu/sites/cse.cs.ucsb.edu/files/assets/daspk31.tar

dassl/Makefile

@@ -5,7 +5,9 @@
 ################################################################################
 
 
-CFLAGS=-fPIC -fallow-argument-mismatch -O3
+CFLAGS=-fPIC -O3
+
+FFLAGS=-fallow-argument-mismatch
 
 DOBJ=daux.o ddassl.o dlinpk.o
 
@@ -17,7 +19,7 @@ $(DLIB): $(DOBJ)
 	ar rcs $(DLIB) $(DOBJ)
 
 %.o: %.f
-	$(F77) $(CFLAGS) -c $< -o $@
+	$(F77) $(CFLAGS) $(FFLAGS) -c $< -o $@
 
 clean:
 	rm -f $(DLIB) $(DOBJ)