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Stable test #259
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Stable test #259
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32dc883
ignore automatically generated files
hwpang 80b4828
Add channels
hwpang 5d59536
Remove yml file as it's not used anymore, using CondaPkg to manage env
hwpang 2300cf6
Switch to CondaPkg, PythonCall, PythonPlot
hwpang aef963e
Remove unused dependency
hwpang 5653f7c
Update version
hwpang e0c6c4b
bump to 1.10
hwpang dfe380d
No need to install env beforehand
hwpang b9e777d
Install with CondaPkg
hwpang 0b3e7fd
Switch to 1.10 and no need to create env
hwpang 82e1d58
export env path for CondaPkg
hwpang a857031
Update build to use CondaPkg
hwpang 1f43a40
Update installation instruction
hwpang db530a2
Use PythonPlot instead of PyPlot
hwpang 9163eed
Switch to PythonPlot
hwpang 3b0447d
Switch parsing to PythonCall and PythonPlot
hwpang 5f572c8
Switch plotting to pythonplot
hwpang 9ab4354
Use PythonCall syntax in module
hwpang 1d8a45f
Don't set jacobian prototype if jacobian is not sparse
hwpang 57164e7
Switch to pythoncall syntax in test
hwpang 18cd0ed
Import necessary packages
hwpang 85dd259
Use SciMLSensitivity
hwpang 58c7094
Change rtol
hwpang 6b8f26d
Add propane mech test file
hwpang e6dc131
ensure SciMLSensitivity.extract_local_sensitivities is called
mjohnson541 f504b7a
clean up automatic mechanism string output
mjohnson541 1dc9c22
adapt automatic mechanism analysis tests
mjohnson541 7652ec2
make compat for PythonCall and CondaPkg more specific for release
mjohnson541 2d07eac
move conda install to import and on test
mjohnson541 e597206
clean up conda installs
mjohnson541 dec22df
run rops and flux diagram generation in tests
mjohnson541 dcec0e2
decode to utf-8
mjohnson541 0ad13ca
0-index python objects
mjohnson541 6fa41f8
adapt getcolor
mjohnson541 564facb
avoid pydot 2.0.0
mjohnson541 d954221
remove CondaPkg.toml
mjohnson541 e4b54f8
increment version
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -3,4 +3,8 @@ | |
*.dot | ||
docs/build/ | ||
.DS_Store | ||
deps/build.log | ||
deps/build.log | ||
.CondaPkg/ | ||
rms_env/ | ||
*.cov | ||
Manifest.toml |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,13 +1,13 @@ | ||
name = "ReactionMechanismSimulator" | ||
uuid = "c2d78dd2-25c4-5b79-bebc-be6c69dd440f" | ||
authors = ["Matt Johnson <[email protected]>", "Hao-Wei Pang <[email protected]>"] | ||
version = "1.0.0" | ||
version = "1.0.1" | ||
|
||
[deps] | ||
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" | ||
Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" | ||
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" | ||
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d" | ||
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" | ||
CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab" | ||
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" | ||
FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838" | ||
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" | ||
|
@@ -17,12 +17,13 @@ IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e" | |
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" | ||
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" | ||
LsqFit = "2fda8390-95c7-5789-9bda-21331edee243" | ||
MicroMamba = "0b3b1443-0f03-428d-bdfb-f27f9c1191ea" | ||
ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" | ||
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" | ||
Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a" | ||
PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46" | ||
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" | ||
PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" | ||
PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" | ||
PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9" | ||
QuartzImageIO = "dca85d43-d64c-5e67-8c65-017450d5d020" | ||
RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" | ||
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" | ||
|
@@ -39,31 +40,31 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" | |
Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" | ||
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" | ||
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" | ||
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" | ||
|
||
[compat] | ||
CSV = "0.10" | ||
Calculus = "0.4,0.5" | ||
Colors = "0.11,0.12" | ||
Conda = "1" | ||
CSV = "0.10" | ||
CondaPkg = "0.2" | ||
DataFrames = "1" | ||
SciMLSensitivity = "^7" | ||
FastGaussQuadrature = "0.5" | ||
ForwardDiff = "0.10" | ||
Images = "0.24" | ||
IncompleteLU = "0.2" | ||
IterTools = "1.3" | ||
LsqFit = "0.12" | ||
MicroMamba = "0.1" | ||
ModelingToolkit = "8" | ||
OrdinaryDiffEq = "^6" | ||
Parameters = "0.12" | ||
PreallocationTools = "0.4" | ||
PyCall = "1" | ||
PyPlot = "2" | ||
PythonCall = "0.9" | ||
PythonPlot = "1" | ||
QuartzImageIO = "0.7" | ||
RecursiveArrayTools = "2.17" | ||
ReverseDiff = "1.9" | ||
SciMLBase = "^1" | ||
SciMLSensitivity = "^7" | ||
SmoothingSplines = "0.3" | ||
SpecialFunctions = "1" | ||
StaticArrays = "1" | ||
|
@@ -72,5 +73,4 @@ Symbolics = "4" | |
Tracker = "0.2" | ||
Unitful = "^1.3" | ||
YAML = "0.4" | ||
Zygote = "0.5,0.6" | ||
julia = "^1.6" |
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -37,9 +37,10 @@ The above instructions will automatically handle Julia-Python linking. However, | |
|
||
``` | ||
import Pkg | ||
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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||
``` |
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Original file line number | Diff line number | Diff line change | ||||
---|---|---|---|---|---|---|
|
@@ -665,16 +665,28 @@ function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,branchfract=0.01) | |||||
s *= "Associated key reaction path in $spname loss direction \n" | ||||||
for i = 1:length(rp.rxninds) | ||||||
rstr = getrxnstr(sim.reactions[rp.rxninds[i]]) | ||||||
sgn = rp.spcsinds[i+1] in sim.reactions[rp.rxninds[i]].productinds | ||||||
if sgn | ||||||
sn = "+" | ||||||
else | ||||||
sn = "-" | ||||||
end | ||||||
br = round(rp.branchfracts[i],sigdigits=6) | ||||||
s *= "$rstr at path branching of $br \n" | ||||||
s *= "$rstr ($sn) at path branching of $br \n" | ||||||
end | ||||||
else | ||||||
s *= "Associated key reaction path in $spname production direction \n" | ||||||
revinds = reverse(rp.rxninds) | ||||||
for i = 1:length(rp.rxninds) | ||||||
rstr = getrxnstr(sim.reactions[revinds[i]]) | ||||||
sgn = rp.spcsinds[i+1] in sim.reactions[rp.rxninds[i]].productinds | ||||||
if sgn | ||||||
sn = "+" | ||||||
else | ||||||
sn = "-" | ||||||
end | ||||||
br = round(rp.branchfracts[i],sigdigits=6) | ||||||
s *= "$rstr at path step branching of $br \n" | ||||||
s *= "$rstr ($sn) at path step branching of $br \n" | ||||||
end | ||||||
end | ||||||
s *= "\n" | ||||||
|
@@ -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
|
||||||
if ra.clusterprodlossfracts[i] > 0 | ||||||
s *= "Reaction accounts for $fract of the net production for cluster $cluster \n" | ||||||
else | ||||||
|
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Can probably switch to the newest version