Mermaid graph

[jlheflin]

Is this pull request associated with an issue(s)?
No

Description
Unable to get the binaries that are built to link the hello_world program correctly.

[ryanmrichard]

The changes I pushed make your include paths more canonical; however, I think this PR should have worked without them. Regardless, I can verify that in its current state this PR builds locally for me (and I suspect CI will pass too, but I'm leaving this comment before it finishes).

[jlheflin]

@ryanmrichard I realized I was a bit too vague, when running the tests via ctest in the build directory, the test executable itself shows this error:

/home/jacob/Projects/PluginPlay/build/test_unit_pluginplay: symbol lookup error: /home/jacob/Projects/PluginPlay/build/test_unit_pluginplay: undefined symbol: _Z11hello_worldB5cxx11v

I've tried a few things to make sure that it would be able to be found but I'll try your changes as well. The project itself will build, but the tests do not run correctly.

[jlheflin]

Additionally, the library itself has a reference to the function, when using nm I get the following: 0000000000086cb0 T hello_worldabi:cxx11

[ryanmrichard]

I (as well as CI) am also running ctest in the build directory and don't see this problem. If that's your only undefined symbol my guess is you're linking to old version of PluginPlay (not the one with your new function).

Based on that assumption, if I were you, I'd create a completely new workspace say $HOME/new_workspace. I'd then clone PluginPlay into that workspace say $HOME/new_workspace/pluginplay. I'd then create a toolchain file say $HOME/new_workspace/toolchain.cmake. I'd then make sure all the search and install paths in the toolchain point to paths in $HOME/new_workspace, i.e., don't reuse anything from previous builds. I also recommend NOT installing PluginPlay, just build the tests and run them. As a sanity check I'd do this all with the master branch first. Once that builds and runs, I'd pull the GitHub mermaid-graph branch, delete the build directory, and reconfigure, build, and test.

[jlheflin]

Yeah you nailed it, my LD_LIBRARY_PATH was pulling from my NWChemEx install with its own libpluginplay.so. Once I removed this reference the tests completed.

[ryanmrichard]

Suggested change

	#include "module_manager/module_manager_class.hpp"
	#include <pluginplay/module_manager/module_manager_class.hpp>

Long story short, if a header file lives in the include/ directory you should include it with angle brackets (and start the path with the directory which follows include/ in the path, which in this case is pluginplay)

[jlheflin]

Here is the resulting output for the integration test of GhostFragment for the Mermaid Graph:

flowchart LR
	AAA[All nmers]
	AAA-->|Monomer Maker| AAB[No Submodule associated with Key]

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flowchart LR
	AAC[Atomic Capping]

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flowchart LR
	AAD[Bond-Based Fragmenter]

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flowchart LR
	AAE[Broken Bonds]

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flowchart LR
	AAF[Cluster Partition]

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flowchart LR
	AAG[Covalent Radius]

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flowchart LR
	AAH[DCLC Capping]
	AAH-->|Connectivity| AAI[Covalent Radius]

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flowchart LR
	AAJ[Energy Method]

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flowchart LR
	AAK[Fragment Based Method]
	AAK-->|Energy method| AAL[Energy Method]
	AAK-->|Subsystem former| AAM[FragmentedChemicalSystem Driver]
	AAM-->|Fragmenter| AAN[Fragment Driver]
	AAN-->|Atomic connectivity| AAO[Covalent Radius]
	AAN-->|Cap broken bonds| AAP[Weighted Distance]
	AAN-->|Find broken bonds| AAQ[Broken Bonds]
	AAN-->|Fragment builder| AAR[Bond-Based Fragmenter]
	AAN-->|Intersection finder| AAS[Intersections]
	AAN-->|Molecular graph| AAT[Nuclear Graph]
	AAT-->|Connectivity| AAU[Covalent Radius]
	AAT-->|Nodes| AAV[Heavy Atom Partition]
	AAV-->|Connectivity| AAW[Covalent Radius]
	AAN-->|N-mer builder| AAX[All nmers]
	AAX-->|Monomer Maker| AAY[No Submodule associated with Key]
	AAK-->|Weighter| AAZ[GMBE Weights]

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flowchart LR
	ABA[Fragment Driver]
	ABA-->|Atomic connectivity| ABB[Covalent Radius]
	ABA-->|Cap broken bonds| ABC[Weighted Distance]
	ABA-->|Find broken bonds| ABD[Broken Bonds]
	ABA-->|Fragment builder| ABE[Bond-Based Fragmenter]
	ABA-->|Intersection finder| ABF[Intersections]
	ABA-->|Molecular graph| ABG[Nuclear Graph]
	ABG-->|Connectivity| ABH[Covalent Radius]
	ABG-->|Nodes| ABI[Heavy Atom Partition]
	ABI-->|Connectivity| ABJ[Covalent Radius]
	ABA-->|N-mer builder| ABK[All nmers]
	ABK-->|Monomer Maker| ABL[No Submodule associated with Key]

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flowchart LR
	ABM[FragmentedChemicalSystem Driver]
	ABM-->|Fragmenter| ABN[Fragment Driver]
	ABN-->|Atomic connectivity| ABO[Covalent Radius]
	ABN-->|Cap broken bonds| ABP[Weighted Distance]
	ABN-->|Find broken bonds| ABQ[Broken Bonds]
	ABN-->|Fragment builder| ABR[Bond-Based Fragmenter]
	ABN-->|Intersection finder| ABS[Intersections]
	ABN-->|Molecular graph| ABT[Nuclear Graph]
	ABT-->|Connectivity| ABU[Covalent Radius]
	ABT-->|Nodes| ABV[Heavy Atom Partition]
	ABV-->|Connectivity| ABW[Covalent Radius]
	ABN-->|N-mer builder| ABX[All nmers]
	ABX-->|Monomer Maker| ABY[No Submodule associated with Key]

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flowchart LR
	ABZ[GMBE Weights]

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flowchart LR
	ACA[Heavy Atom Partition]
	ACA-->|Connectivity| ACB[Covalent Radius]

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flowchart LR
	ACC[Intersections]

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flowchart LR
	ACD[Nuclear Graph]
	ACD-->|Connectivity| ACE[Covalent Radius]
	ACD-->|Nodes| ACF[Heavy Atom Partition]
	ACF-->|Connectivity| ACG[Covalent Radius]

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flowchart LR
	ACH[Weighted Distance]

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[ryanmrichard]

should use paths from the include root for files in the include directory.

[ryanmrichard]

I think the graphs look great!!!

[ryanmrichard]

Nice! This is basically ready to merge. Just accept the #include changes (quotes when the path is relative, angle brackets otherwise) and add the namespaces and it's r2g!

[jwaldrop107]

🚀 [bumpr] Bumped! New version:v1.0.43 Changes:v1.0.42...v1.0.43