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Stable test #259

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Stable test #259

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mjohnson541
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Minor request for changes otherwise LGTM

@@ -10,10 +10,10 @@ jobs:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v4
- uses: julia-actions/setup-julia@v1
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Can probably switch to the newest version

Suggested change
- uses: julia-actions/setup-julia@v1
- uses: julia-actions/setup-julia@v2

Comment on lines -40 to +45
Pkg.add("PyCall")
ENV["CONDA_JL_HOME"] = PATH_TO_YOUR_ENV
Pkg.build("Conda")
ENV["PYTHON"] = PATH_TO_PYTHON
Pkg.build("PyCall")
ENV["JULIA_CONDAPKG_BACKEND"] = "Null"
ENV["JULIA_PYTHONCALL_EXE"] = "/path/to/python"
Pkg.add("CondaPkg")
Pkg.build("CondaPkg")
Pkg.add("PythonCall")
Pkg.build("PythonCall")
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Can you also make sure this part is up to date with what you change?

@@ -684,7 +696,7 @@ function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,branchfract=0.01)
for i = 1:length(ra.clusterprodlossfracts)
if abs(ra.clusterprodlossfracts[i]) > branchfract
cluster = ra.clusternames[i]
fract = abs(ra.clusterprodlossfracts[i])
fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6)
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Suggested change
fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6)
fract = round(abs(ra.clusterprodlossfracts[i]), sigdigits=6)

Comment on lines 16 to 26
CondaPkg.add("python"; version="3.9",resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
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Suggested change
CondaPkg.add("python"; version="3.9",resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.add("python"; version="3.9",resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541", resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge", resolve=false)
CondaPkg.add("rdkit", channel="conda-forge", resolve=false)
CondaPkg.add("pydot", channel="conda-forge", resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541", resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge", resolve=false)
CondaPkg.add("rdkit", channel="conda-forge", resolve=false)
CondaPkg.add("pydot", channel="conda-forge", resolve=false)

src/rmstest.jl Outdated
Comment on lines 17 to 27
CondaPkg.add("python"; version="3.9",resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
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Suggested change
CondaPkg.add("python"; version="3.9",resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
CondaPkg.add("pydot", channel="conda-forge",resolve=false)
CondaPkg.add("python"; version="3.9", resolve=false)
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541", resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge", resolve=false)
CondaPkg.add("rdkit", channel="conda-forge", resolve=false)
CondaPkg.add("pydot", channel="conda-forge", resolve=false)
CondaPkg.resolve()
else
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541", resolve=false)
CondaPkg.add("matplotlib", channel="conda-forge", resolve=false)
CondaPkg.add("rdkit", channel="conda-forge", resolve=false)
CondaPkg.add("pydot", channel="conda-forge", resolve=false)

@@ -75,7 +75,7 @@ export drawspecies

"""
generates and returns the image of a single flux diagram at the given time point
all PyPlot colorscheme names are valid inputs for colorscheme
all PythonPlot colorscheme names are valid inputs for colorscheme
"""
function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(),superimpose=false,
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Suggested change
function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(),superimpose=false,
function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(), superimpose=false,

@@ -134,7 +134,7 @@ export getfluxdiagram
"""
generates a series of flux diagrams at the time points indicated
each flux diagram will have the same nodes and edges as determined by the options
all PyPlot colorscheme names are valid inputs for colorscheme
all PythonPlot colorscheme names are valid inputs for colorscheme
"""
function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpose=false,
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Suggested change
function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpose=false,
function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(), superimpose=false,

Comment on lines +5 to +7
packages = keys(CondaPkg.current_packages())

if !("rmg" in packages) && !("rmgmolecule" in packages)
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I realize that these don't actually work for packages that are installed locally, so we should change the way we test these

@ssun30 ssun30 mentioned this pull request Sep 26, 2024
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2 participants