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Change approach to input and output paths. Issue 47 #63

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merged 16 commits into from Oct 4, 2018

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greebie commented Sep 20, 2018

GitHub issue(s):

#47

What does this Pull Request do?

  • accept ./graphpass {input path} {output path} -flags --optionA {data}
  • input path and output path can be anywhere in command line, provided that input comes first and output comes second (other non-option args are ignored for now).
  • include helper functions get_directory and get_filename.
  • issue in comments of #62 regarding directories being created has NOT been addressed in this PR.

How should this be tested?

  • Should pass Travis.
  • Should work in ubuntu (linux) and Mac.
  • Tests should pass.
  • ./graphpass {/path/to/file.graphml} {/path/to/output} -q should do a quickpass to output.graphml.
  • ./graphpass {/path/to/file.graphml} {/path/to/output/} -qgshould do a quickpass to file.gexf

Additional Notes:

./graphpass {/path/to/file.graphml} {/path/to/} -q may replace the input file file.graphml in current commits. This will need to be repaired or managed (see comments in #62).

Interested parties

@ianmilligan1 @ruebot

Thanks in advance for your help with the Archives Unleashed Project!

greebie added some commits Sep 20, 2018

Change input method in preparation for stdin stdout approach.
- --input (-i) and --output (-o) can also be used.
- functions have been created to extract directory and filename from path files.
- will require additional unit testing of code.
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Thanks for re-staging the PR @greebie. Looking good! Two quick queries.

First – just tested on an Ubuntu machine with syntax like:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml ./9717-gephi.gexf -qg

Seems to be working but this popped up as an error before SUCCESS:

non-option ARGV-elements: OUTARG:./9717-gephi.gexf

Is this expected behaviour?

Second, if I don't provide a relative path but just the filename, i.e.

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

I get

non-option ARGV-elements: OUTARG:9717-gephi2.gexf
Segmentation fault (core dumped)

Is this expected behaviour?

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ianmilligan1 commented Sep 24, 2018

Thanks for re-staging the PR @greebie. Looking good! Two quick queries.

First – just tested on an Ubuntu machine with syntax like:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml ./9717-gephi.gexf -qg

Seems to be working but this popped up as an error before SUCCESS:

non-option ARGV-elements: OUTARG:./9717-gephi.gexf

Is this expected behaviour?

Second, if I don't provide a relative path but just the filename, i.e.

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

I get

non-option ARGV-elements: OUTARG:9717-gephi2.gexf
Segmentation fault (core dumped)

Is this expected behaviour?

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ianmilligan1 Sep 24, 2018

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Also, circling back to the outstanding comments on #62. @ruebot noted:

It will only try to create the output directory if stdout does not exist. Otherwise it will just use stdout.

That's not how stdout works. We shouldn't be clobbering an existing file if an option isn't given, nor creating a new directory.

and

Can you explain the rationale here? It's my understanding that stdout should just be stdout. I don't understand the use case of forcing the creation of an output dir.

Is it possible to move forward on making this straightforward stdin stdout syntax? Thanks @greebie!

Member

ianmilligan1 commented Sep 24, 2018

Also, circling back to the outstanding comments on #62. @ruebot noted:

It will only try to create the output directory if stdout does not exist. Otherwise it will just use stdout.

That's not how stdout works. We shouldn't be clobbering an existing file if an option isn't given, nor creating a new directory.

and

Can you explain the rationale here? It's my understanding that stdout should just be stdout. I don't understand the use case of forcing the creation of an output dir.

Is it possible to move forward on making this straightforward stdin stdout syntax? Thanks @greebie!

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greebie Sep 25, 2018

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First – just tested on an Ubuntu machine with syntax like:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml ./9717-gephi.gexf -qg

Seems to be working but this popped up as an error before SUCCESS:

non-option ARGV-elements: OUTARG:./9717-gephi.gexf

This is the same as the previous behavior, but I would like to change it.

Is this expected behaviour?

Second, if I don't provide a relative path but just the filename, i.e.

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

I get

non-option ARGV-elements: OUTARG:9717-gephi2.gexf
Segmentation fault (core dumped)

Is this expected behaviour?

This is not the expected behavior. I will fix.

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greebie commented Sep 25, 2018

First – just tested on an Ubuntu machine with syntax like:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml ./9717-gephi.gexf -qg

Seems to be working but this popped up as an error before SUCCESS:

non-option ARGV-elements: OUTARG:./9717-gephi.gexf

This is the same as the previous behavior, but I would like to change it.

Is this expected behaviour?

Second, if I don't provide a relative path but just the filename, i.e.

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

I get

non-option ARGV-elements: OUTARG:9717-gephi2.gexf
Segmentation fault (core dumped)

Is this expected behaviour?

This is not the expected behavior. I will fix.

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greebie Sep 25, 2018

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Also, circling back to the outstanding comments on #62. @ruebot noted:

It will only try to create the output directory if stdout does not exist. Otherwise it will just use stdout.

That's not how stdout works. We shouldn't be clobbering an existing file if an option isn't given, nor creating a new directory.

and

Can you explain the rationale here? It's my understanding that stdout should just be stdout. I don't understand the use case of forcing the creation of an output dir.

Is it possible to move forward on making this straightforward stdin stdout syntax? Thanks @greebie!

I think I have this resolved in the current push. However, in doing so I broke a test (as per Travis fail).

I would also like to create some tests (tomorrow) before this merges.

Collaborator

greebie commented Sep 25, 2018

Also, circling back to the outstanding comments on #62. @ruebot noted:

It will only try to create the output directory if stdout does not exist. Otherwise it will just use stdout.

That's not how stdout works. We shouldn't be clobbering an existing file if an option isn't given, nor creating a new directory.

and

Can you explain the rationale here? It's my understanding that stdout should just be stdout. I don't understand the use case of forcing the creation of an output dir.

Is it possible to move forward on making this straightforward stdin stdout syntax? Thanks @greebie!

I think I have this resolved in the current push. However, in doing so I broke a test (as per Travis fail).

I would also like to create some tests (tomorrow) before this merges.

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OK, can you ping me @greebie when you want me to test this. I'm out of office tomorrow afternoon and Thursday morning so might be a delay.

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ianmilligan1 commented Sep 25, 2018

OK, can you ping me @greebie when you want me to test this. I'm out of office tomorrow afternoon and Thursday morning so might be a delay.

greebie added some commits Sep 25, 2018

Add test suite for input-output functions.
- get_directory
- get_file
- strip_ext
- load_graph
- write_graph
Remove debug flags from tests and have functions return (1) instead o…
…f exit(1).

- Exit should be handled in main().
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greebie Sep 26, 2018

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Assuming the latest build passes Travis, it should complete all the outstanding issues mentioned.

  • graphpass does not create a new directory, other than for unit tests (which are deleted after build).
  • will not create an out file if stdout and stdin paths are the same.
  • will work for test case where stdout is just a file, defaulting to "./".
  • created test suite for the new functions, get_directory and get_filename to try and capture issues before they hatch.
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greebie commented Sep 26, 2018

Assuming the latest build passes Travis, it should complete all the outstanding issues mentioned.

  • graphpass does not create a new directory, other than for unit tests (which are deleted after build).
  • will not create an out file if stdout and stdin paths are the same.
  • will work for test case where stdout is just a file, defaulting to "./".
  • created test suite for the new functions, get_directory and get_filename to try and capture issues before they hatch.
@ianmilligan1

Thanks @greebie. Looking good – I've just tested and built on Mac and Ubuntu. One outstanding problem still left, I think, from @ruebot:

We shouldn't be clobbering an existing file if an option isn't given

Right now it overwrites the file. Is there a way to stop that unless there's an override?

@ruebot

First pass review. There will be more to come.

First, please use stderr instead of manually creating errors.

Show outdated Hide outdated src/main/io.c
Show outdated Hide outdated src/main/io.c
Show outdated Hide outdated src/main/io.c
Use stderr instead of stdout for error outputs.
- change printf("..") to fprintf(stderr, "..")
- change stderror_vector to std_error_vector. This is not stderr but a calculation of standard error for a t-test.
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@greebie since you pinged me to say you weren't able to reproduce the overwriting files.

On rho if I run:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

It overwrites the existing file.

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ianmilligan1 commented Sep 28, 2018

@greebie since you pinged me to say you weren't able to reproduce the overwriting files.

On rho if I run:

./graphpass /mnt/vol1/data_sets/auk_datasets/graphpass_test/9717-gephi.graphml 9717-gephi2.gexf -qg

It overwrites the existing file.

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greebie Oct 1, 2018

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Hi Ian - when you say it overwrites the existing file, do you mean 9719-gephi2.gexf or 9717-gephi.graphml? I was worried about the latter and the former would (currently) be the expected behavior. I hadn't considered the possibility of preventing over-write if it's not desired.

I can add an over-write flag and make it so that 9717-gephi2.gexf becomes 9717-gephi.gexf0 (or 9717-gephi.gexf1 and so on) if that's the desired behavior you are looking for?

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greebie commented Oct 1, 2018

Hi Ian - when you say it overwrites the existing file, do you mean 9719-gephi2.gexf or 9717-gephi.graphml? I was worried about the latter and the former would (currently) be the expected behavior. I hadn't considered the possibility of preventing over-write if it's not desired.

I can add an over-write flag and make it so that 9717-gephi2.gexf becomes 9717-gephi.gexf0 (or 9717-gephi.gexf1 and so on) if that's the desired behavior you are looking for?

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I can add an over-write flag and make it so that 9717-gephi2.gexf becomes 9717-gephi.gexf0 (or 9717-gephi.gexf1 and so on) if that's the desired behavior you are looking for?

That sounds good to me. What do you think @ruebot ?

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ianmilligan1 commented Oct 1, 2018

I can add an over-write flag and make it so that 9717-gephi2.gexf becomes 9717-gephi.gexf0 (or 9717-gephi.gexf1 and so on) if that's the desired behavior you are looking for?

That sounds good to me. What do you think @ruebot ?

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Okay - is it okay if we put that in another issue? It's possible that I can break things while building this functionality, so I'd like to be able to track it.

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greebie commented Oct 1, 2018

Okay - is it okay if we put that in another issue? It's possible that I can break things while building this functionality, so I'd like to be able to track it.

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@greebie I'm noticing FAILURE messages in the build, but the tests don't fail. Is this expected behaviour? I see it here, and locally.

[nruest@wombat:graphpass] (git)-[issue-47]-$ make clean all
rm -f qp
rm -f ana
rm -f io
rm -rf TEST_OUT_FOLDER
rm -rf build/
rm -f graphpass
gcc ./vendor/unity/unity.c ./src/tests/runner_test_qp.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/quickrun_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o qp
gcc ./vendor/unity/unity.c ./src/tests/runner_test_ana.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/analyze_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o ana
gcc ./vendor/unity/unity.c ./src/tests/runner_test_io.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/io_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o io
./ana
src/tests/analyze_test.c:14:TEST_DEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:25:TEST_INDEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:36:TEST_OUTDEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:47:TEST_BETWEENNESS_ALGORITHM:PASS
src/tests/analyze_test.c:58:TEST_AUTHORITY_ALGORITHM:PASS
src/tests/analyze_test.c:69:TEST_HUB_ALGORITHM:PASS
src/tests/analyze_test.c:99:TEST_EIGENVECTOR_ALGORITHM:IGNORE: Eigenvector has some random elements that need to be seeded
src/tests/analyze_test.c:91:TEST_PAGERANK_ALGORITHM:PASS
src/tests/analyze_test.c:102:TEST_MODULARITY:PASS
src/tests/analyze_test.c:113:TEST_RANKORDER:PASS
src/tests/analyze_test.c:138:TEST_MEAN:PASS
src/tests/analyze_test.c:151:TEST_VARIANCE:PASS
src/tests/analyze_test.c:164:TEST_STD:PASS
src/tests/analyze_test.c:177:TEST_STDERROR:PASS
src/tests/analyze_test.c:190:TEST_TTEST:PASS
src/tests/analyze_test.c:203:TEST_TPVALUE:PASS

-----------------------
16 Tests 0 Failures 1 Ignored 
OK
./qp
src/tests/quickrun_test.c:22:TEST_QUICKRUN_NOSAVE:PASS
src/tests/quickrun_test.c:29:TEST_QUICKRUN_DEGREE:PASS
src/tests/quickrun_test.c:51:TEST_QUICKRUN_COLOR:PASS
src/tests/quickrun_test.c:40:TEST_QUICKRUN_SIZE:PASS
src/tests/quickrun_test.c:72:TEST_QUICKRUN_GEXF:PASS
src/tests/quickrun_test.c:80:TEST_QUICKRUN_GRAPHML:PASS

-----------------------
6 Tests 0 Failures 0 Ignored 
OK
./io
src/tests/io_test.c:43:TEST_GET_DIRECTORY:PASS
src/tests/io_test.c:55:TEST_GET_FILE:PASS
src/tests/io_test.c:68:TEST_STRIP_EXT:PASS
>>> FAILURE - Could not find graphML file at filepath location.
src/tests/io_test.c:74:TEST_LOAD_GRAPH:PASS
>>> FAILURE - Could not create file at selected output location.
>>>         - Ensure that your assigned output folder exists.
src/tests/io_test.c:85:TEST_WRITE_GRAPH:PASS

-----------------------
5 Tests 0 Failures 0 Ignored 
OK
gcc src/main/*.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity -L/usr/local/lib -ligraph -lm -o graphpass
./graphpass -qnv
>>>>>>>  GRAPHPASSING >>>>>>>> 
FILEPATH: src/resources/cpp2.graphml
OUTPUT DIRECTORY: ./
PERCENTAGE: 0.000000
FILE: cpp2.graphml
METHODS STRING: d
QUICKRUN: 1
REPORT: 0
SAVE: 0
Running graphpass on file: src/resources/cpp2.graphml
Successfully ingested graph with 218 nodes and 220 edges.


Quickrun requested.

Quickrun does no filtering, and provides layout information
based on Degree (nodesize), Walktrap Modularity (color), and
the Fructerman-Rheingold algorithm to maximize space between
nodes.

Quickrun is quicker, but less informative in terms of output.
Calculating Degree... 
Calculating Modularity... 
Assigning Colors... 
Assigning Degree values... 
Scaling graph with degree values... 
Producing layout details... 


>>>>  SUCCESS!- NO_SAVE requested, so no output.

You'll also need to update .gitignore to include the new items to the build process:

TEST_OUT_FOLDER/
ana
io
qp
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ruebot commented Oct 1, 2018

@greebie I'm noticing FAILURE messages in the build, but the tests don't fail. Is this expected behaviour? I see it here, and locally.

[nruest@wombat:graphpass] (git)-[issue-47]-$ make clean all
rm -f qp
rm -f ana
rm -f io
rm -rf TEST_OUT_FOLDER
rm -rf build/
rm -f graphpass
gcc ./vendor/unity/unity.c ./src/tests/runner_test_qp.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/quickrun_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o qp
gcc ./vendor/unity/unity.c ./src/tests/runner_test_ana.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/analyze_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o ana
gcc ./vendor/unity/unity.c ./src/tests/runner_test_io.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity ./src/tests/io_test.c src/main/analyze.c src/main/filter.c src/main/gexf.c src/main/io.c src/main/quickrun.c src/main/reports.c src/main/rnd.c src/main/viz.c -L/usr/local/lib -ligraph -lm -o io
./ana
src/tests/analyze_test.c:14:TEST_DEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:25:TEST_INDEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:36:TEST_OUTDEGREE_ALGORITHM:PASS
src/tests/analyze_test.c:47:TEST_BETWEENNESS_ALGORITHM:PASS
src/tests/analyze_test.c:58:TEST_AUTHORITY_ALGORITHM:PASS
src/tests/analyze_test.c:69:TEST_HUB_ALGORITHM:PASS
src/tests/analyze_test.c:99:TEST_EIGENVECTOR_ALGORITHM:IGNORE: Eigenvector has some random elements that need to be seeded
src/tests/analyze_test.c:91:TEST_PAGERANK_ALGORITHM:PASS
src/tests/analyze_test.c:102:TEST_MODULARITY:PASS
src/tests/analyze_test.c:113:TEST_RANKORDER:PASS
src/tests/analyze_test.c:138:TEST_MEAN:PASS
src/tests/analyze_test.c:151:TEST_VARIANCE:PASS
src/tests/analyze_test.c:164:TEST_STD:PASS
src/tests/analyze_test.c:177:TEST_STDERROR:PASS
src/tests/analyze_test.c:190:TEST_TTEST:PASS
src/tests/analyze_test.c:203:TEST_TPVALUE:PASS

-----------------------
16 Tests 0 Failures 1 Ignored 
OK
./qp
src/tests/quickrun_test.c:22:TEST_QUICKRUN_NOSAVE:PASS
src/tests/quickrun_test.c:29:TEST_QUICKRUN_DEGREE:PASS
src/tests/quickrun_test.c:51:TEST_QUICKRUN_COLOR:PASS
src/tests/quickrun_test.c:40:TEST_QUICKRUN_SIZE:PASS
src/tests/quickrun_test.c:72:TEST_QUICKRUN_GEXF:PASS
src/tests/quickrun_test.c:80:TEST_QUICKRUN_GRAPHML:PASS

-----------------------
6 Tests 0 Failures 0 Ignored 
OK
./io
src/tests/io_test.c:43:TEST_GET_DIRECTORY:PASS
src/tests/io_test.c:55:TEST_GET_FILE:PASS
src/tests/io_test.c:68:TEST_STRIP_EXT:PASS
>>> FAILURE - Could not find graphML file at filepath location.
src/tests/io_test.c:74:TEST_LOAD_GRAPH:PASS
>>> FAILURE - Could not create file at selected output location.
>>>         - Ensure that your assigned output folder exists.
src/tests/io_test.c:85:TEST_WRITE_GRAPH:PASS

-----------------------
5 Tests 0 Failures 0 Ignored 
OK
gcc src/main/*.c -I./src/headers -I/usr/local/include/igraph -I./vendor/unity -L/usr/local/lib -ligraph -lm -o graphpass
./graphpass -qnv
>>>>>>>  GRAPHPASSING >>>>>>>> 
FILEPATH: src/resources/cpp2.graphml
OUTPUT DIRECTORY: ./
PERCENTAGE: 0.000000
FILE: cpp2.graphml
METHODS STRING: d
QUICKRUN: 1
REPORT: 0
SAVE: 0
Running graphpass on file: src/resources/cpp2.graphml
Successfully ingested graph with 218 nodes and 220 edges.


Quickrun requested.

Quickrun does no filtering, and provides layout information
based on Degree (nodesize), Walktrap Modularity (color), and
the Fructerman-Rheingold algorithm to maximize space between
nodes.

Quickrun is quicker, but less informative in terms of output.
Calculating Degree... 
Calculating Modularity... 
Assigning Colors... 
Assigning Degree values... 
Scaling graph with degree values... 
Producing layout details... 


>>>>  SUCCESS!- NO_SAVE requested, so no output.

You'll also need to update .gitignore to include the new items to the build process:

TEST_OUT_FOLDER/
ana
io
qp
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@ruebot That is the expected behavior because I created tests that check that graphpass fails when it is supposed to, but I do not think this is desired behavior. Let me see if I can test those features more gracefully.

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greebie commented Oct 1, 2018

@ruebot That is the expected behavior because I created tests that check that graphpass fails when it is supposed to, but I do not think this is desired behavior. Let me see if I can test those features more gracefully.

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@ianmilligan1 with the overwrite. Can you add the steps you took? If the gexf file already exists and the output location, it is going get clobbered. That's how cat or any utility is going to work.

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ruebot commented Oct 1, 2018

@ianmilligan1 with the overwrite. Can you add the steps you took? If the gexf file already exists and the output location, it is going get clobbered. That's how cat or any utility is going to work.

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I'm happy with the overwriting if you are, @ruebot, as I was just noting as you said above "If the gexf file already exists and the output location, it is going get clobbered." If we're cool with that happy to move forward.

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ianmilligan1 commented Oct 1, 2018

I'm happy with the overwriting if you are, @ruebot, as I was just noting as you said above "If the gexf file already exists and the output location, it is going get clobbered." If we're cool with that happy to move forward.

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Ah, yeah. I see what you mean. I was talking about the OUTPUT directory getting created, and everything that went with that. Sorry for the confusion there.

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ruebot commented Oct 1, 2018

Ah, yeah. I see what you mean. I was talking about the OUTPUT directory getting created, and everything that went with that. Sorry for the confusion there.

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Okay great. The current issues I will address are:

  • add new test files to .gitIgnore
  • try to avoid fail messages on tests, probably by creating a TEST flag.
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greebie commented Oct 1, 2018

Okay great. The current issues I will address are:

  • add new test files to .gitIgnore
  • try to avoid fail messages on tests, probably by creating a TEST flag.
Minor test improvements from PR review.
Do not print error messages on tests.
Add ana, io, & qp to .gitignore
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Latest commit shows this travis result:
image

And confirm failure shows on regular run.

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greebie commented Oct 2, 2018

Latest commit shows this travis result:
image

And confirm failure shows on regular run.

@ruebot

Functionality appears to be good to go. Lots of cleanup here, and after that I believe we should be good to go.

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Various README and content fixes from PR.
Add some comments to help demystify PATH management process.
(This may need re-factoring at a later time.)
@ruebot

Couple tiny things, then I think we're good to go.

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@ruebot

ruebot approved these changes Oct 4, 2018

@ruebot ruebot merged commit 1d9c65b into master Oct 4, 2018

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@ruebot ruebot deleted the issue-47 branch Oct 4, 2018

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