From 36752fe1a43a59c8576bfc6c66a1a6099a0f4e67 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:05:47 -0500 Subject: [PATCH 01/19] try using micromamba in CI --- .github/workflows/CI.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index de5cdf8f65..2a69a0597a 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,17 +18,17 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml python-version: 3.7 activate-environment: rmg_env - name: Install codecov - run: conda install -y -c conda-forge codecov + run: micromamba install -y -c conda-forge codecov - name: Conda info run: | - conda info - conda list + micromamba info + micromamba list - name: Install and link Julia dependencies run: | julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))" From 98a78b229a6621fc8f9afd29ee4996a379bbd197 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:07:59 -0500 Subject: [PATCH 02/19] remove unsupported options in action --- .github/workflows/CI.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 2a69a0597a..18cf83251d 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -21,8 +21,6 @@ jobs: - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml - python-version: 3.7 - activate-environment: rmg_env - name: Install codecov run: micromamba install -y -c conda-forge codecov - name: Conda info From b827be580005785d8c64a6b60519796ba64abb63 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:13:09 -0500 Subject: [PATCH 03/19] attempt to specify python version with setup-python the micromamba configuration does not allow the version of python to be specified, so maybe we can set it up using a different action version. I suspect that incorrect python version is what caused the CI to fail to resolve the conda environment on the previous commit --- .github/workflows/CI.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 18cf83251d..12ee47e7db 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,6 +18,11 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 + - name: Setup Python 3.7 + uses: actions/setup-python@v1 + with: + python-version: '3.7' + architecture: x64 - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml From 173aa5cc937e525066d52a1b0abbd606a9be88d5 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:22:03 -0500 Subject: [PATCH 04/19] specify python in provision step, specify channels and env name --- .github/workflows/CI.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 12ee47e7db..fc455808d8 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,14 +18,13 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 - - name: Setup Python 3.7 - uses: actions/setup-python@v1 - with: - python-version: '3.7' - architecture: x64 - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml + environment-name: rmg_env + channels: defaults,rmg,conda-forge + extra-specs: | + python=3.7 - name: Install codecov run: micromamba install -y -c conda-forge codecov - name: Conda info From 07c2185706ebab4ffdacd1affdd3ed806efeb3ad Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:28:57 -0500 Subject: [PATCH 05/19] allow flexible channel use, turn on debug-level logging --- .github/workflows/CI.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index fc455808d8..c63ed474a2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -23,6 +23,8 @@ jobs: environment-file: environment.yml environment-name: rmg_env channels: defaults,rmg,conda-forge + channel-priority: flexible + log-level: debug extra-specs: | python=3.7 - name: Install codecov From 7a09e285e9821af93658ef4610cd5257c381c697 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:05:47 -0500 Subject: [PATCH 06/19] try using micromamba in CI --- .github/workflows/CI.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index de5cdf8f65..2a69a0597a 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,17 +18,17 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml python-version: 3.7 activate-environment: rmg_env - name: Install codecov - run: conda install -y -c conda-forge codecov + run: micromamba install -y -c conda-forge codecov - name: Conda info run: | - conda info - conda list + micromamba info + micromamba list - name: Install and link Julia dependencies run: | julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))" From e1f6fb97ea938db388b60bc170afae76f0ff42f1 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:07:59 -0500 Subject: [PATCH 07/19] remove unsupported options in action --- .github/workflows/CI.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 2a69a0597a..18cf83251d 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -21,8 +21,6 @@ jobs: - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml - python-version: 3.7 - activate-environment: rmg_env - name: Install codecov run: micromamba install -y -c conda-forge codecov - name: Conda info From c5a5bf01c9a3e20dde2eaad142f0ea33b48e53cc Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:13:09 -0500 Subject: [PATCH 08/19] attempt to specify python version with setup-python the micromamba configuration does not allow the version of python to be specified, so maybe we can set it up using a different action version. I suspect that incorrect python version is what caused the CI to fail to resolve the conda environment on the previous commit --- .github/workflows/CI.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 18cf83251d..12ee47e7db 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,6 +18,11 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 + - name: Setup Python 3.7 + uses: actions/setup-python@v1 + with: + python-version: '3.7' + architecture: x64 - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml From d6076151c7ea08d4e2970c0debbcd472bb6b8691 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:22:03 -0500 Subject: [PATCH 09/19] specify python in provision step, specify channels and env name --- .github/workflows/CI.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 12ee47e7db..fc455808d8 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,14 +18,13 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 - - name: Setup Python 3.7 - uses: actions/setup-python@v1 - with: - python-version: '3.7' - architecture: x64 - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml + environment-name: rmg_env + channels: defaults,rmg,conda-forge + extra-specs: | + python=3.7 - name: Install codecov run: micromamba install -y -c conda-forge codecov - name: Conda info From 5374c912ccf373c2430a176b6e7b5972487462ae Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Mon, 30 Jan 2023 12:28:57 -0500 Subject: [PATCH 10/19] allow flexible channel use, turn on debug-level logging --- .github/workflows/CI.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index fc455808d8..c63ed474a2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -23,6 +23,8 @@ jobs: environment-file: environment.yml environment-name: rmg_env channels: defaults,rmg,conda-forge + channel-priority: flexible + log-level: debug extra-specs: | python=3.7 - name: Install codecov From 08c2ffa2499bac6a8ba439dee84b8bbd9b2d14c7 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sun, 5 Feb 2023 11:23:36 -0500 Subject: [PATCH 11/19] reset log level to default --- .github/workflows/CI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index c63ed474a2..3f732cfa07 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -24,7 +24,7 @@ jobs: environment-name: rmg_env channels: defaults,rmg,conda-forge channel-priority: flexible - log-level: debug + log-level: warning extra-specs: | python=3.7 - name: Install codecov From b63fae04aea5d01c3de27a7f17f33ad62a51b9e2 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sun, 5 Feb 2023 11:26:32 -0500 Subject: [PATCH 12/19] switch documentation build to mamba --- .github/workflows/docs.yml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index fc30ccdef3..664202c11d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,17 +16,21 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: mamba-org/provision-with-micromamba@main with: environment-file: environment.yml - python-version: 3.7 - activate-environment: rmg_env + environment-name: rmg_env + channels: defaults,rmg,conda-forge + channel-priority: flexible + log-level: warning + extra-specs: | + python=3.7 - name: Install sphinx - run: conda install -y sphinx - - name: Conda info + run: micromamba install -y sphinx + - name: Environment info run: | - conda info - conda list + micromamba info + micromamba list - name: Install and link Julia dependencies run: | julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))" From 25c2b37ea3435be6cc48cedc3dbed957c7d39d09 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sun, 5 Feb 2023 11:31:37 -0500 Subject: [PATCH 13/19] add schedule to CI to find out about issues with greater frequency, this will force the CI to run on the main branch (where we are currently doing development) every weekday early in the morning --- .github/workflows/CI.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 3f732cfa07..27df118d98 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 0 8 ? * MON,TUE,WED,THU,FRI *' push: pull_request: branches: From 44bfa20a3aa14ed53b881c56fad752048744530e Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Sun, 5 Feb 2023 11:38:48 -0500 Subject: [PATCH 14/19] fix cron syntax --- .github/workflows/CI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 27df118d98..56b6ca87b2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -3,7 +3,7 @@ name: CI Tests on: schedule: # * is a special character in YAML so you have to quote this string - - cron: '0 0 8 ? * MON,TUE,WED,THU,FRI *' + - cron: '0 8 * * 1-5' push: pull_request: branches: From 42fe1c1cdf9ad8d020d3753975a5524bccfa8a72 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 10:59:15 -0500 Subject: [PATCH 15/19] attempt to simplify conda environment - all depdencies which are package by others should be used instead of those packaged by us - small formatting change in github workflow file --- .github/workflows/CI.yml | 8 ++++---- environment.yml | 33 +++++++++++++++++---------------- 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 56b6ca87b2..be26b5063e 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -3,7 +3,7 @@ name: CI Tests on: schedule: # * is a special character in YAML so you have to quote this string - - cron: '0 8 * * 1-5' + - cron: "0 8 * * 1-5" push: pull_request: branches: @@ -25,7 +25,7 @@ jobs: with: environment-file: environment.yml environment-name: rmg_env - channels: defaults,rmg,conda-forge + channels: defaults,cantera,rmg,conda-forge channel-priority: flexible log-level: warning extra-specs: | @@ -35,8 +35,8 @@ jobs: - name: Conda info run: | micromamba info - micromamba list - - name: Install and link Julia dependencies + micromamba 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 235d8aa09c..5e117b4f36 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 have 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 + - conda-forge::mopac # was previously RMG - mpmath - - rmg::muq2 + - rmg::muq2 # only on RMG - networkx - 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 + - 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 RM - scikit-learn - scipy - - rmg::symmetry + - rmg::symmetry # internal - xlrd - xlwt From e03ccda2b0f3132baa0dd9c4fce81ff02b62ae91 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 11:11:43 -0500 Subject: [PATCH 16/19] one of the custom-built rmg packages had a hidden inclusion libgfortran-ng was included in one of the packages but is now missing, add the conda-forge package --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 5e117b4f36..07eb51be10 100644 --- a/environment.yml +++ b/environment.yml @@ -51,3 +51,4 @@ dependencies: - rmg::symmetry # internal - xlrd - xlwt + - conda-forge::libgfortran-ng From 10f5477684fb0e1297d524c880f71aaf49b1a5d1 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 11:23:23 -0500 Subject: [PATCH 17/19] switch lpsolve55 back to rmg channel --- environment.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 07eb51be10..d276ff6d4b 100644 --- a/environment.yml +++ b/environment.yml @@ -20,7 +20,7 @@ dependencies: - h5py - jinja2 - jupyter - - conda-forge::lpsolve55 # was previously RMG + - rmg::lpsolve55 # was previously RMG, must be rmg (?) - markupsafe - matplotlib >=1.5 - conda-forge::mopac # was previously RMG @@ -51,4 +51,3 @@ dependencies: - rmg::symmetry # internal - xlrd - xlwt - - conda-forge::libgfortran-ng From b9fc567881704a4d33158a7f0ba3d0ae18253bcc Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 11:30:36 -0500 Subject: [PATCH 18/19] switch gprof2dot back to rmg --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index d276ff6d4b..e235445897 100644 --- a/environment.yml +++ b/environment.yml @@ -15,7 +15,7 @@ dependencies: - cython >=0.25.2 - rmg::diffeqpy # only on rmg - ffmpeg - - conda-forge::gprof2dot # was previously RMG + - rmg::gprof2dot # was previously RMG - graphviz - h5py - jinja2 @@ -45,7 +45,7 @@ dependencies: - python >=3.7 - pyyaml - conda-forge::quantities # was previously RMG - - conda-forge::rdkit >=2020.03.3.0 # was previously RM + - conda-forge::rdkit >=2020.03.3.0 # was previously RMG - scikit-learn - scipy - rmg::symmetry # internal From 0375404072b9f16877a633a9874b099bea494703 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 2 Mar 2023 12:45:01 -0500 Subject: [PATCH 19/19] cleaning up environment remove packages that appear to be unused, change those which can be drawn from conda-forge or other official changes where possible --- environment.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/environment.yml b/environment.yml index e235445897..f79b69676e 100644 --- a/environment.yml +++ b/environment.yml @@ -9,25 +9,25 @@ dependencies: - cairocffi - cantera::cantera >=2.3.0 # was previously RMG - conda-forge::cclib >=1.6.3 - - rmg::chemprop # change this to conda-forge in a future hackathon (fix the million bugs that will come up from chemprop have gone up a major release) + - 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 # only on rmg - ffmpeg - - rmg::gprof2dot # was previously RMG + - conda-forge::gprof2dot # was previously RMG - graphviz - h5py - jinja2 - jupyter - - rmg::lpsolve55 # was previously RMG, must be rmg (?) + - conda-forge::lpsolve55 # was previously RMG - markupsafe - matplotlib >=1.5 - - conda-forge::mopac # was previously RMG + - 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