From b7eb9ae3d95f28e51fb08479e845a3d81cc6e630 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Thu, 7 Sep 2023 16:49:37 -0400 Subject: [PATCH 1/4] use mamba to install rmg --- .github/workflows/CI.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 31ca9a358..86619c673 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -4,8 +4,6 @@ on: branches: - main push: - branches: - - main jobs: test: runs-on: ubuntu-latest @@ -29,6 +27,9 @@ jobs: environment-file: environment.yml python-version: 3.7 activate-environment: rms_env + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true - name: Fix PyCall linking run: | julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")' From cdf2679d9678e004b7a08395fe7e174c48ec7c39 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 12 Sep 2023 16:46:36 -0400 Subject: [PATCH 2/4] update environment file to rmgmolecule see jacksonburns/rmg-py branch molecule_subpackage --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index af867cc9e..551077264 100644 --- a/environment.yml +++ b/environment.yml @@ -2,8 +2,8 @@ name: rms_env channels: - defaults - rmg + - jacksonburns dependencies: - - rdkit - - rmg + - rmgmolecule - pydot - - yaml + - matplotlib From 05e28479d0f97a8e38ecc0d8b02f00d79beb3bfe Mon Sep 17 00:00:00 2001 From: Hao-Wei Pang Date: Fri, 8 Sep 2023 14:52:09 -0400 Subject: [PATCH 3/4] Relax package version requirement --- Project.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Project.toml b/Project.toml index 6236e221c..8fd3639df 100644 --- a/Project.toml +++ b/Project.toml @@ -43,14 +43,14 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" Calculus = "0.4,0.5" Colors = "0.11,0.12" Conda = "1" -DiffEqSensitivity = "6" +DiffEqSensitivity = "^6" ForwardDiff = "0.10" Images = "0.24" IncompleteLU = "0.2" IterTools = "1.3" LsqFit = "0.12" ModelingToolkit = "8" -OrdinaryDiffEq = "6" +OrdinaryDiffEq = "^6" Parameters = "0.12" PreallocationTools = "0" PyCall = "1" @@ -58,7 +58,7 @@ PyPlot = "2" QuartzImageIO = "0.7" RecursiveArrayTools = "2.17" ReverseDiff = "1.9" -SciMLBase = "1" +SciMLBase = "^1" SmoothingSplines = "0.3" SpecialFunctions = "1" StaticArrays = "1" From d5259c588a23dd3a58521f78f4ed8a53e1196bf7 Mon Sep 17 00:00:00 2001 From: Jackson Burns Date: Tue, 12 Sep 2023 20:22:31 -0400 Subject: [PATCH 4/4] fix syntax error in CI file --- .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 86619c673..fa9478bd2 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -27,9 +27,9 @@ jobs: environment-file: environment.yml python-version: 3.7 activate-environment: rms_env - miniforge-variant: Mambaforge - miniforge-version: latest - use-mamba: true + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true - name: Fix PyCall linking run: | julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")' @@ -43,4 +43,4 @@ jobs: - uses: julia-actions/julia-processcoverage@v1 - uses: codecov/codecov-action@v1 with: - file: lcov.info + file: lcov.info \ No newline at end of file