From 574a83514069818ea5f19434ee2c063af9b1d0f0 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sun, 13 Nov 2022 16:35:46 -0600 Subject: [PATCH 1/4] Add CITATION.cff file --- CITATION.cff | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000000..64e12d30b5d --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,51 @@ +cff-version: 1.0.0 +message: "Please include the following two citations if RMG and/or Arkane were used for an academic study." +references: + - type: article + authors: + - family-names: Gao + given-names: C.W. + - family-names: Allen + given-names: J.W. + - family-names: Green + given-names: W.H. + - family-names: West + given-names: R.H. + title: "Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms" + year: 2016 + journal: Computer Physics Communications + doi: 10.1016/j.cpc.2016.02.013 + - type: article + authors: + - family-names: Liu + given-names: M. + - family-names: Dana + given-names: A.G. + - family-names: Johnson + given-names: M.S. + - family-names: Goldman + given-names: M.J. + - family-names: Jocher + given-names: A. + - family-names: Payne + given-names: A.M. + - family-names: Grambow + given-names: C.A. + - family-names: Han + given-names: K. + - family-names: N.W. + given-names: Yee + - family-names: Maseau + given-names: E.J. + - family-names: Blondal + given-names: K. + - family-names: West + given-names: R.H. + - family-names: Goldsmith + given-names: C.F. + - family-names: Green + given-names: W.H. + title: "Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation" + year: 2021 + journal: Journal of Chemical Information and Modeling + doi: 10.1021/acs.jcim.0c01480 \ No newline at end of file From b2a4131199abaf80e635d78d591136a2c4f67afb Mon Sep 17 00:00:00 2001 From: JacksonBurns Date: Fri, 16 Dec 2022 22:29:32 -0500 Subject: [PATCH 2/4] switch from cff to bib --- CITATION.cff | 51 --------------------------------------------------- 1 file changed, 51 deletions(-) delete mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff deleted file mode 100644 index 64e12d30b5d..00000000000 --- a/CITATION.cff +++ /dev/null @@ -1,51 +0,0 @@ -cff-version: 1.0.0 -message: "Please include the following two citations if RMG and/or Arkane were used for an academic study." -references: - - type: article - authors: - - family-names: Gao - given-names: C.W. - - family-names: Allen - given-names: J.W. - - family-names: Green - given-names: W.H. - - family-names: West - given-names: R.H. - title: "Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms" - year: 2016 - journal: Computer Physics Communications - doi: 10.1016/j.cpc.2016.02.013 - - type: article - authors: - - family-names: Liu - given-names: M. - - family-names: Dana - given-names: A.G. - - family-names: Johnson - given-names: M.S. - - family-names: Goldman - given-names: M.J. - - family-names: Jocher - given-names: A. - - family-names: Payne - given-names: A.M. - - family-names: Grambow - given-names: C.A. - - family-names: Han - given-names: K. - - family-names: N.W. - given-names: Yee - - family-names: Maseau - given-names: E.J. - - family-names: Blondal - given-names: K. - - family-names: West - given-names: R.H. - - family-names: Goldsmith - given-names: C.F. - - family-names: Green - given-names: W.H. - title: "Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation" - year: 2021 - journal: Journal of Chemical Information and Modeling - doi: 10.1021/acs.jcim.0c01480 \ No newline at end of file From 4497e2348e86a106bd8e83c050b423b856787247 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 14:51:49 -0500 Subject: [PATCH 3/4] simplify environment, schedule CI --- .github/workflows/CI.yml | 7 +++++-- environment.yml | 37 +++++++++++++++++++------------------ 2 files changed, 24 insertions(+), 20 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index defe0793ef2..a7f2e946632 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -1,6 +1,9 @@ name: CI Tests on: + schedule: + # * is a special character in YAML so you have to quote this string + - cron: "0 8 * * 1-5" push: pull_request: branches: @@ -32,8 +35,8 @@ jobs: - name: mamba info run: | mamba info - mamba list - - name: Install and link Julia dependencies + mamba list + - name: Install and link Julia dependencies run: | julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))" julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")" diff --git a/environment.yml b/environment.yml index 235d8aa09c3..f79b69676e0 100644 --- a/environment.yml +++ b/environment.yml @@ -1,52 +1,53 @@ name: rmg_env channels: - defaults + - cantera - rmg - conda-forge dependencies: - cairo - cairocffi - - rmg::cantera >=2.3.0 + - cantera::cantera >=2.3.0 # was previously RMG - conda-forge::cclib >=1.6.3 - - rmg::chemprop + - rmg::chemprop # change this to conda-forge in a future hackathon (fix the million bugs that will come up from chemprop having gone up a major release) - coolprop - coverage - cython >=0.25.2 - - rmg::diffeqpy + - rmg::diffeqpy # only on rmg - ffmpeg - - rmg::gprof2dot + - conda-forge::gprof2dot # was previously RMG - graphviz - h5py - jinja2 - jupyter - - rmg::lpsolve55 + - conda-forge::lpsolve55 # was previously RMG - markupsafe - matplotlib >=1.5 - - rmg::mopac + - rmg::mopac # was previously RMG, must be RMG - mpmath - - rmg::muq2 + # - rmg::muq2 # only on RMG - networkx - - nomkl + # - nomkl - nose - - rmg::numdifftools + - conda-forge::numdifftools # was previously RMG, was recent - numpy >=1.10.0 - conda-forge::openbabel >= 3 - pandas - psutil - - rmg::pydas >=1.0.2 + - rmg::pydas >=1.0.2 # only RMG, internal - pydot - - rmg::pydqed >=1.0.1 - - rmg::pyjulia + - rmg::pydqed >=1.0.1 # only on RMG + - rmg::pyjulia # only RMG, internal - pymongo - - pyparsing - - rmg::pyrdl - - rmg::pyrms + # - pyparsing + - rmg::pyrdl # only on RMG + - rmg::pyrms # internal - python >=3.7 - pyyaml - - rmg::quantities - - rmg::rdkit >=2020.03.3.0 + - conda-forge::quantities # was previously RMG + - conda-forge::rdkit >=2020.03.3.0 # was previously RMG - scikit-learn - scipy - - rmg::symmetry + - rmg::symmetry # internal - xlrd - xlwt From 2c88abe82a0dd7c9207f0211d61a9de522fb89fa Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 17:35:58 -0500 Subject: [PATCH 4/4] add back dependencies --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index f79b69676e0..01311c52bcd 100644 --- a/environment.yml +++ b/environment.yml @@ -25,9 +25,9 @@ dependencies: - matplotlib >=1.5 - rmg::mopac # was previously RMG, must be RMG - mpmath - # - rmg::muq2 # only on RMG + - rmg::muq2 # only on RMG - networkx - # - nomkl + - nomkl - nose - conda-forge::numdifftools # was previously RMG, was recent - numpy >=1.10.0 @@ -39,7 +39,7 @@ dependencies: - rmg::pydqed >=1.0.1 # only on RMG - rmg::pyjulia # only RMG, internal - pymongo - # - pyparsing + - pyparsing - rmg::pyrdl # only on RMG - rmg::pyrms # internal - python >=3.7