Stable test #259

mjohnson541 · 2024-06-29T20:06:23Z

No description provided.

delete build

avoid use of PythonCall resolve all conda changes at once

hwpang

Minor request for changes otherwise LGTM

hwpang · 2024-07-01T17:07:49Z

.github/workflows/CI.yml

@@ -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


Can probably switch to the newest version

Suggested change

- uses: julia-actions/setup-julia@v1

- uses: julia-actions/setup-julia@v2

hwpang · 2024-07-01T17:13:13Z

docs/src/Installation.md

-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")


Can you also make sure this part is up to date with what you change?

hwpang · 2024-07-01T17:13:59Z

src/AutomaticMechanismAnalysis.jl

@@ -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)


Suggested change

fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6)

fract = round(abs(ra.clusterprodlossfracts[i]), sigdigits=6)

hwpang · 2024-07-01T17:15:03Z

src/ReactionMechanismSimulator.jl

+ 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)


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)

hwpang · 2024-07-01T17:16:27Z

src/rmstest.jl

+ 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)


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)

hwpang · 2024-07-01T17:17:25Z

src/fluxdiagrams.jl

@@ -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,


Suggested change

function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(),superimpose=false,

function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(), superimpose=false,

hwpang · 2024-07-01T17:17:31Z

src/fluxdiagrams.jl

@@ -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,


Suggested change

function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpose=false,

function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(), superimpose=false,

hwpang · 2024-07-03T18:36:27Z

src/ReactionMechanismSimulator.jl

+packages = keys(CondaPkg.current_packages())
+
+if !("rmg" in packages) && !("rmgmolecule" in packages)


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

hwpang and others added 30 commits June 23, 2024 17:55

ignore automatically generated files

32dc883

Add channels

80b4828

Remove yml file as it's not used anymore, using CondaPkg to manage env

5d59536

Switch to CondaPkg, PythonCall, PythonPlot

2300cf6

Remove unused dependency

aef963e

Update version

5653f7c

bump to 1.10

e0c6c4b

No need to install env beforehand

dfe380d

Install with CondaPkg

b9e777d

Switch to 1.10 and no need to create env

0b3e7fd

export env path for CondaPkg

82e1d58

Update build to use CondaPkg

a857031

Update installation instruction

1f43a40

Use PythonPlot instead of PyPlot

db530a2

Switch to PythonPlot

9163eed

Switch parsing to PythonCall and PythonPlot

3b0447d

Switch plotting to pythonplot

5f572c8

Use PythonCall syntax in module

9ab4354

Don't set jacobian prototype if jacobian is not sparse

1d8a45f

Switch to pythoncall syntax in test

57164e7

Import necessary packages

18cd0ed

Use SciMLSensitivity

85dd259

Change rtol

58c7094

Add propane mech test file

6b8f26d

ensure SciMLSensitivity.extract_local_sensitivities is called

e6dc131

clean up automatic mechanism string output

f504b7a

adapt automatic mechanism analysis tests

1dc9c22

make compat for PythonCall and CondaPkg more specific for release

7652ec2

move conda install to import and on test

2d07eac

delete build

clean up conda installs

e597206

avoid use of PythonCall resolve all conda changes at once

mjohnson541 force-pushed the stable branch from c354b13 to e597206 Compare July 1, 2024 14:08

hwpang requested changes Jul 1, 2024

View reviewed changes

hwpang reviewed Jul 3, 2024

View reviewed changes

mjohnson541 added 7 commits August 3, 2024 13:06

run rops and flux diagram generation in tests

dec22df

decode to utf-8

dcec0e2

0-index python objects

0ad13ca

adapt getcolor

6fa41f8

avoid pydot 2.0.0

564facb

use pydot 1.4.1 revert force use of pydot 3 version tweak tweak

remove CondaPkg.toml

d954221

increment version

e4b54f8

ssun30 mentioned this pull request Sep 26, 2024

Marcus Kinetics #247

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Stable test #259

Stable test #259

mjohnson541 commented Jun 29, 2024

hwpang left a comment

hwpang Jul 1, 2024

hwpang Jul 1, 2024

hwpang Jul 1, 2024

hwpang Jul 1, 2024

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hwpang Jul 1, 2024

hwpang Jul 1, 2024

hwpang Jul 3, 2024

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

	fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6)
	fract = round(abs(ra.clusterprodlossfracts[i]), sigdigits=6)

	function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(),superimpose=false,
	function getfluxdiagram(bsol,t;centralspecieslist=Array{String,1}(), superimpose=false,

	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)

Stable test #259

Are you sure you want to change the base?

Stable test #259

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mjohnson541 commented Jun 29, 2024

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