From 8ec55fccec9d49f02e2914df74dd5f254a5e94fd Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Fri, 15 Mar 2024 10:36:34 -0400 Subject: [PATCH 1/6] SQUASH ME, see ext. force higher version of Python to see which packages we need to rebuild --- environment.yml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/environment.yml b/environment.yml index 48a4da34a3..efa96f4082 100644 --- a/environment.yml +++ b/environment.yml @@ -16,6 +16,7 @@ # made dependency list more explicit (@JacksonBurns). # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge, # moved diffeqpy to pip and (temporarily) removed chemprop +# - March 15, 2024 - started migration to Python 3.11/2 # name: rmg_env channels: @@ -53,7 +54,7 @@ dependencies: - conda-forge::pyjulia >=0.6 # Python tools - - python >=3.7 + - python =3.11,3.12 - coverage - cython >=0.25.2 - scikit-learn @@ -68,13 +69,7 @@ dependencies: - networkx - pytest - pytest-cov - # we use a the pytest-check plugin, which is on Conda and PyPI, but the - # version compatible with Python 3.7 is only on PyPI - # switch to the conda version after upgrading to 3.11 - # - conda-forge::pytest-check - - pip - - pip: - - pytest-check + - conda-forge::pytest-check - matplotlib >=1.5 - mpmath - pandas From aca9be41ab447ecbc9ff817607ffc79f49c5394a Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Fri, 15 Mar 2024 10:42:09 -0400 Subject: [PATCH 2/6] test mac build and linux tests on 3.11 and 3.12 --- .github/workflows/CI.yml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 7b5a39c162..524e85a3e1 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -52,6 +52,10 @@ env: jobs: build-osx: runs-on: macos-13 + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12"] # skip scheduled runs from forks if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} defaults: @@ -62,13 +66,13 @@ jobs: uses: actions/checkout@v4 # configures the mamba environment manager and builds the environment - - name: Setup Mambaforge Python 3.7 + - name: Setup Mambaforge Python ${{ matrix.python-version }} uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml miniforge-variant: Mambaforge miniforge-version: latest - python-version: 3.7 + python-version: ${{ matrix.python-version }} activate-environment: rmg_env use-mamba: true @@ -99,6 +103,10 @@ jobs: build-and-test-linux: runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12"] # skip scheduled runs from forks if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} env: @@ -112,13 +120,13 @@ jobs: uses: actions/checkout@v4 # configures the mamba environment manager and builds the environment - - name: Setup Mambaforge Python 3.7 + - name: Setup Mambaforge Python ${{ matrix.python-version }} uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml miniforge-variant: Mambaforge miniforge-version: latest - python-version: 3.7 + python-version: ${{ matrix.python-version }} activate-environment: rmg_env use-mamba: true From 772bf2d28ded926d401a5d1702d5862afb511554 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 25 Jun 2024 11:42:39 -0400 Subject: [PATCH 3/6] cut down environment to see if anything will solve --- environment.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/environment.yml b/environment.yml index efa96f4082..e865d19f14 100644 --- a/environment.yml +++ b/environment.yml @@ -54,7 +54,7 @@ dependencies: - conda-forge::pyjulia >=0.6 # Python tools - - python =3.11,3.12 + - python =3.11 - coverage - cython >=0.25.2 - scikit-learn @@ -78,16 +78,16 @@ dependencies: - conda-forge::quantities - conda-forge::muq - conda-forge::lpsolve55 - - conda-forge::ringdecomposerlib-python +# - conda-forge::ringdecomposerlib-python -# packages we maintain - - rmg::pydas >=1.0.3 - - rmg::pydqed >=1.0.3 - - rmg::pyrms - - rmg::symmetry +# # packages we maintain +# - rmg::pydas >=1.0.3 +# - rmg::pydqed >=1.0.3 +# - rmg::pyrms +# - rmg::symmetry -# packages we would like to stop maintaining (and why) - - rmg::diffeqpy +# # packages we would like to stop maintaining (and why) +# - rmg::diffeqpy # we should use the official verison https://github.com/SciML/diffeqpy), # rather than ours (which is only made so that we can get it from conda) # It is only on pip, so we will need to do something like: From 0aa2a7857be1ab377eaa2476c63fec0461229c5e Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 25 Jun 2024 12:15:53 -0400 Subject: [PATCH 4/6] run ci on all platforms --- .github/workflows/CI.yml | 59 ++++------------------------------------ 1 file changed, 5 insertions(+), 54 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 524e85a3e1..3dd46f25e6 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -50,63 +50,14 @@ env: jobs: - build-osx: - runs-on: macos-13 - strategy: - fail-fast: false - matrix: - python-version: ["3.11", "3.12"] - # skip scheduled runs from forks - if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} - defaults: - run: - shell: bash -l {0} - steps: - - name: Checkout RMG-Py - uses: actions/checkout@v4 - - # configures the mamba environment manager and builds the environment - - name: Setup Mambaforge Python ${{ matrix.python-version }} - uses: conda-incubator/setup-miniconda@v3 - with: - environment-file: environment.yml - miniforge-variant: Mambaforge - miniforge-version: latest - python-version: ${{ matrix.python-version }} - activate-environment: rmg_env - use-mamba: true - - # list the environment for debugging purposes - - name: mamba info - run: | - mamba info - mamba list - - # Clone RMG-database - - name: Clone RMG-database - run: | - cd .. - git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git - - # modify env variables as directed in the RMG installation instructions - - name: Set Environment Variables - run: | - RUNNER_CWD=$(pwd) - echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV - echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH - - # RMG build step - - name: make RMG - run: | - make clean - make - - build-and-test-linux: - runs-on: ubuntu-latest + build-and-test: strategy: fail-fast: false matrix: python-version: ["3.11", "3.12"] + os: [macos-13, macos-latest, ubuntu-latest] + runs-on: ${{ matrix.os }} + name: ${{ matrix.os }} Build and Test # skip scheduled runs from forks if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} env: @@ -369,7 +320,7 @@ jobs: # who knows ¯\_(ツ)_/¯ # # taken from https://github.com/docker/build-push-action - needs: build-and-test-linux + needs: build-and-test runs-on: ubuntu-latest if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' steps: From f29d3cfe05ba2e00d5fa3dddf886b02273afcebe Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 25 Jun 2024 12:16:06 -0400 Subject: [PATCH 5/6] let everything go to absolute latest version --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index e865d19f14..71e5e04cab 100644 --- a/environment.yml +++ b/environment.yml @@ -43,9 +43,9 @@ dependencies: # external software tools for chemistry - coolprop - - cantera::cantera=2.6 + - cantera::cantera >=3 - conda-forge::mopac - - conda-forge::cclib >=1.6.3,<1.8.0 + - conda-forge::cclib >=1.6.3 - conda-forge::openbabel >= 3 - conda-forge::rdkit >=2022.09.1 @@ -58,7 +58,7 @@ dependencies: - coverage - cython >=0.25.2 - scikit-learn - - scipy <1.11 + - scipy - numpy >=1.10.0 - pydot - jinja2 From 487923358ceabe28c719d66e03dd0ca24476cfe9 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 25 Jun 2024 12:33:49 -0400 Subject: [PATCH 6/6] no `muq` see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2635#issuecomment-2189418601 --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 71e5e04cab..c748cf0ce6 100644 --- a/environment.yml +++ b/environment.yml @@ -76,7 +76,6 @@ dependencies: - conda-forge::gprof2dot - conda-forge::numdifftools - conda-forge::quantities - - conda-forge::muq - conda-forge::lpsolve55 # - conda-forge::ringdecomposerlib-python