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Stable test #259
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Stable test #259
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delete build
avoid use of PythonCall resolve all conda changes at once
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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
- uses: julia-actions/setup-julia@v1 | |
- uses: julia-actions/setup-julia@v2 |
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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fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6) | |
fract = round(abs(ra.clusterprodlossfracts[i]), sigdigits=6) |
src/ReactionMechanismSimulator.jl
Outdated
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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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
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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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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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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function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpose=false, | |
function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(), superimpose=false, |
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
use pydot 1.4.1 revert force use of pydot 3 version tweak tweak
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