From ef10efd483f287c5b00552829828dbca2d36e496 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 15:37:27 -0400 Subject: [PATCH 01/18] trigger ci --- .conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.conda/meta.yaml b/.conda/meta.yaml index 7a6db3c..66e6714 100644 --- a/.conda/meta.yaml +++ b/.conda/meta.yaml @@ -35,4 +35,4 @@ test: about: home: http://github.com/ReactionMechanismGenerator/PyDQED license: MIT - summary: "A Python wrapper to the DQED bounded constrained nonlinear optimization code." + summary: "Python wrapper to the DQED bounded constrained nonlinear optimization code." From 1df8bc83a8e0fb2f2ca34abfb86c1b61aeadd06a Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 15:46:08 -0400 Subject: [PATCH 02/18] remove unsupported arg --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index ccdccd5..373d82a 100644 --- a/Makefile +++ b/Makefile @@ -10,7 +10,7 @@ CFLAGS=-fPIC -fallow-argument-mismatch -O3 all: DQED cython cython: - python setup.py build_ext --build-lib . --build-temp build --pyrex-c-in-temp + python setup.py build_ext --build-lib . --build-temp build install: python setup.py install From 91b340e43a77c320425a2807a74c6afe3346df10 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 15:54:12 -0400 Subject: [PATCH 03/18] remove arg that is unsupported on mac --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 373d82a..ed187d3 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ ################################################################################ -CFLAGS=-fPIC -fallow-argument-mismatch -O3 +CFLAGS=-fPIC -O3 all: DQED cython From 79e2e83465749802159da7563082f14da9acd8fa Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 16:10:08 -0400 Subject: [PATCH 04/18] remove extra variants, just run the one we need --- .conda/conda_build_config.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml index 0fde6e5..aebab89 100644 --- a/.conda/conda_build_config.yaml +++ b/.conda/conda_build_config.yaml @@ -1,6 +1,4 @@ python: - - 3.8 - 3.9 - - 3.10 - - 3.11 - - 3.12 +numpy: + - 1.21 \ No newline at end of file From 69e3b31c57389ecb701d5e3ebee86cf1f4ce48e8 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 16:10:29 -0400 Subject: [PATCH 05/18] Revert "remove arg that is unsupported on mac" This reverts commit 91b340e43a77c320425a2807a74c6afe3346df10. --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index ed187d3..373d82a 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ ################################################################################ -CFLAGS=-fPIC -O3 +CFLAGS=-fPIC -fallow-argument-mismatch -O3 all: DQED cython From 01649b6cd29f2b9ac3a3845b2cfdfba114c0159f Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Fri, 28 Jun 2024 17:03:33 -0400 Subject: [PATCH 06/18] try setting standard instead of specific error allowance for platform compat --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 373d82a..3d2cc9f 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ ################################################################################ -CFLAGS=-fPIC -fallow-argument-mismatch -O3 +CFLAGS=-fPIC -std=legacy -O3 all: DQED cython From d5497851cbed81ca7423caf837d5fa7c1b830e64 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 12:47:25 -0400 Subject: [PATCH 07/18] move fortran argument ot fortran args --- Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 3d2cc9f..cdf5ecc 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,8 @@ ################################################################################ -CFLAGS=-fPIC -std=legacy -O3 +CFLAGS=-fPIC -O3 +FFLAGS=-fallow-argument-mismatch all: DQED cython @@ -21,7 +22,7 @@ libdqed.a: dqed.o ar rcs libdqed.a dqed.o dqed.o: dqed.f90 - $(F90) $(CFLAGS) -c dqed.f90 -o dqed.o + $(F90) $(CFLAGS) $(FFLAGS) -c dqed.f90 -o dqed.o clean: clean-DQED clean-cython rm -rf build From f9c66c082bcdec345f2b34ea5d5d149fa9ce7984 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 12:59:14 -0400 Subject: [PATCH 08/18] increment patch version, rephrase readme --- .conda/meta.yaml | 2 +- README.md | 2 +- pydqed.pyx | 2 +- setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.conda/meta.yaml b/.conda/meta.yaml index 66e6714..e353f60 100644 --- a/.conda/meta.yaml +++ b/.conda/meta.yaml @@ -1,7 +1,7 @@ # For conda build package: name: pydqed - version: '1.0.3' + version: '1.0.4' source: path: ../ diff --git a/README.md b/README.md index 3823f00..ab97fd3 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ## 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. +> PyDQED 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 PyDQED as long as possible. diff --git a/pydqed.pyx b/pydqed.pyx index a4b4698..f702ea4 100644 --- a/pydqed.pyx +++ b/pydqed.pyx @@ -45,7 +45,7 @@ import numpy cimport numpy cimport cython -__version__ = '1.0.1' +__version__ = '1.0.4' ################################################################################ # Expose the (double-precision) DQED function prototype to this module diff --git a/setup.py b/setup.py index f361b5b..aaab144 100644 --- a/setup.py +++ b/setup.py @@ -52,7 +52,7 @@ # Run the setup command setup( name="PyDQED", - version="1.0.3", + version="1.0.4", description="A Python wrapper to the DQED bounded constrained nonlinear optimization code", author="Joshua W. Allen and the Reaction Mechanism Generator Team", author_email="rmg_dev@mit.edu", From d25cf79e73ba2e6b998913869048f5ed99bec197 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:00:01 -0400 Subject: [PATCH 09/18] fix case sensitivity --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index aaab144..34b69dd 100644 --- a/setup.py +++ b/setup.py @@ -51,7 +51,7 @@ # Run the setup command setup( - name="PyDQED", + name="pydqed", version="1.0.4", description="A Python wrapper to the DQED bounded constrained nonlinear optimization code", author="Joshua W. Allen and the Reaction Mechanism Generator Team", From 5ee46a1591c7e460de4a3e563cd4ae578293136d Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:09:07 -0400 Subject: [PATCH 10/18] avoid executing setup.py directly --- .conda/build.sh | 2 +- Makefile | 7 +++---- README.md | 5 +++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.conda/build.sh b/.conda/build.sh index 8521769..3cbe1bf 100644 --- a/.conda/build.sh +++ b/.conda/build.sh @@ -2,5 +2,5 @@ make # Build cython wrapper -$PYTHON setup.py install +make install diff --git a/Makefile b/Makefile index cdf5ecc..e321f18 100644 --- a/Makefile +++ b/Makefile @@ -11,10 +11,10 @@ FFLAGS=-fallow-argument-mismatch all: DQED cython cython: - python setup.py build_ext --build-lib . --build-temp build + pip install . --no-deps --target=. --build build install: - python setup.py install + pip install . DQED: libdqed.a @@ -31,8 +31,7 @@ clean-DQED: rm -f dqed.o libdqed.a clean-cython: - python setup.py clean --build-temp build - rm -f *.so *.pyc *.o *.c *.html + rm -rf *.so *.pyc *.o *.c *.html build help: @echo "" diff --git a/README.md b/README.md index ab97fd3..1f8cb0c 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,9 @@ The usage documentation is still relevant but no new updates will be released an 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 .`. +Installation instructions in the documentation directory are _not_ up to date. -What follows is the original content of the README, slighly updated to removed erroneous instructions and dead links. +What follows is the original content of the README, slightly updated to removed erroneous instructions and dead links. # Introduction @@ -48,5 +49,5 @@ 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 +pip install . ``` From 06703731d7d70830fa9401bad58be459b68c7b97 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:14:24 -0400 Subject: [PATCH 11/18] fix args for pip-based build --- .conda/build.sh | 2 +- Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.conda/build.sh b/.conda/build.sh index 3cbe1bf..dc83359 100644 --- a/.conda/build.sh +++ b/.conda/build.sh @@ -2,5 +2,5 @@ make # Build cython wrapper -make install +make cython diff --git a/Makefile b/Makefile index e321f18..f321358 100644 --- a/Makefile +++ b/Makefile @@ -11,7 +11,7 @@ FFLAGS=-fallow-argument-mismatch all: DQED cython cython: - pip install . --no-deps --target=. --build build + pip install -e . install: pip install . From dfafa3ca4cd6b1a15f44978b6500cc2e22447758 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:22:57 -0400 Subject: [PATCH 12/18] don't need editable mode install? --- .conda/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.conda/build.sh b/.conda/build.sh index dc83359..3cbe1bf 100644 --- a/.conda/build.sh +++ b/.conda/build.sh @@ -2,5 +2,5 @@ make # Build cython wrapper -make cython +make install From f782f47d88c8045c99925eaf8f58b2ecc05f72d9 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:38:41 -0400 Subject: [PATCH 13/18] drop windows --- .github/workflows/build_package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 40f200a..98168fe 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-13, macos-latest, windows-latest] + os: [ubuntu-latest, macos-13, macos-latest] runs-on: ${{ matrix.os }} defaults: run: From 68124ac4898e3f085da811249429856943f679c4 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 13:49:01 -0400 Subject: [PATCH 14/18] add all build variants --- .conda/conda_build_config.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml index aebab89..434de22 100644 --- a/.conda/conda_build_config.yaml +++ b/.conda/conda_build_config.yaml @@ -1,4 +1,13 @@ python: - 3.9 + - 3.10 + - 3.11 + - 3.12 numpy: - - 1.21 \ No newline at end of file + - 1.21 + - 1.22 + - 1.23 + - 1.24 + - 1.25 + - 1.26 + - 2.0 \ No newline at end of file From 939cc26e7eed7d1685e4e49faefd54859c667764 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 14:33:51 -0400 Subject: [PATCH 15/18] manually specify builds with zip keys --- .conda/conda_build_config.yaml | 60 +++++++++++++++++++++++++++------- 1 file changed, 49 insertions(+), 11 deletions(-) diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml index 434de22..647bdb9 100644 --- a/.conda/conda_build_config.yaml +++ b/.conda/conda_build_config.yaml @@ -1,13 +1,51 @@ python: - - 3.9 - - 3.10 - - 3.11 - - 3.12 + - 3.9 + - 3.9 + - 3.9 + - 3.9 + - 3.9 + - 3.9 + - 3.9 + - 3.10 + - 3.10 + - 3.10 + - 3.10 + - 3.10 + - 3.10 + - 3.10 + - 3.11 + - 3.11 + - 3.11 + - 3.11 + - 3.11 + - 3.11 + - 3.11 + - 3.12 + - 3.12 numpy: - - 1.21 - - 1.22 - - 1.23 - - 1.24 - - 1.25 - - 1.26 - - 2.0 \ No newline at end of file + - 1.21 + - 1.22 + - 1.23 + - 1.24 + - 1.25 + - 1.26 + - 2.0 + - 1.21 + - 1.22 + - 1.23 + - 1.24 + - 1.25 + - 1.26 + - 2.0 + - 1.21 + - 1.22 + - 1.23 + - 1.24 + - 1.25 + - 1.26 + - 2.0 + - 1.26 + - 2.0 +zip_keys: + - python + - numpy From 856c2d19fea7a606302a5f265553fe1fcf98249e Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 15:32:44 -0400 Subject: [PATCH 16/18] remove disallowed 3.11/10 versions --- .conda/conda_build_config.yaml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml index 647bdb9..dbc6291 100644 --- a/.conda/conda_build_config.yaml +++ b/.conda/conda_build_config.yaml @@ -12,10 +12,6 @@ python: - 3.10 - 3.10 - 3.10 - - 3.10 - - 3.11 - - 3.11 - - 3.11 - 3.11 - 3.11 - 3.11 @@ -30,16 +26,12 @@ numpy: - 1.25 - 1.26 - 2.0 - - 1.21 - 1.22 - 1.23 - 1.24 - 1.25 - 1.26 - 2.0 - - 1.21 - - 1.22 - - 1.23 - 1.24 - 1.25 - 1.26 From 69afa68973b47f7d8568fdce3636947616a4f96c Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sat, 29 Jun 2024 19:19:03 -0400 Subject: [PATCH 17/18] use github actions matrix instead of build variants --- .conda/conda_build_config.yaml | 43 ----------------------------- .conda/meta.yaml | 2 +- .github/workflows/build_package.yml | 24 ++++++++++++++-- 3 files changed, 22 insertions(+), 47 deletions(-) delete mode 100644 .conda/conda_build_config.yaml diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml deleted file mode 100644 index dbc6291..0000000 --- a/.conda/conda_build_config.yaml +++ /dev/null @@ -1,43 +0,0 @@ -python: - - 3.9 - - 3.9 - - 3.9 - - 3.9 - - 3.9 - - 3.9 - - 3.9 - - 3.10 - - 3.10 - - 3.10 - - 3.10 - - 3.10 - - 3.10 - - 3.11 - - 3.11 - - 3.11 - - 3.11 - - 3.12 - - 3.12 -numpy: - - 1.21 - - 1.22 - - 1.23 - - 1.24 - - 1.25 - - 1.26 - - 2.0 - - 1.22 - - 1.23 - - 1.24 - - 1.25 - - 1.26 - - 2.0 - - 1.24 - - 1.25 - - 1.26 - - 2.0 - - 1.26 - - 2.0 -zip_keys: - - python - - numpy diff --git a/.conda/meta.yaml b/.conda/meta.yaml index e353f60..49009a2 100644 --- a/.conda/meta.yaml +++ b/.conda/meta.yaml @@ -7,7 +7,7 @@ source: path: ../ build: - number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }} + string: py{{ CONDA_PY }}h{{ PKG_HASH }}npy{{ NPY_VER }}_{{ PKG_BUILDNUM }} requirements: diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 98168fe..63794a9 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -16,7 +16,27 @@ jobs: 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 ${{ matrix.numpy-version }} defaults: run: shell: bash -l {0} @@ -41,9 +61,7 @@ jobs: : "${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 $CONDA_TOKEN --user rmg . + CONDA_NPY=${{ matrix.numpy-version }} CONDA_PY=${{ matrix.python-version }} conda build --token $CONDA_TOKEN --user rmg . result: if: ${{ always() }} runs-on: ubuntu-latest From b305a54bbe804154f1a140d006379bce8075278b Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Sat, 29 Jun 2024 20:22:08 -0400 Subject: [PATCH 18/18] add conda forge back --- .github/workflows/build_package.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml index 63794a9..61d8389 100644 --- a/.github/workflows/build_package.yml +++ b/.github/workflows/build_package.yml @@ -61,6 +61,7 @@ jobs: : "${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() }}