Comments (6)
That's odd. @shuail ??
(He added the hub option recently.)
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@achantzis That's odd, could you try to run the test case under the tests folder (the function is here
Line 140 in 49152de
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@shuail I have run the test script as: python ./test_lomap.py
And I get the following:
.usage: LOMAPv1.0 [-h] [-p PARALLEL] [-v {off,info,pedantic}] [-t TIME]
[-e ECRSCORE] [-o] [-n NAME] [-d] [-m MAX] [-c CUTOFF] [-r]
[-b HUB] [-f] [-a]
directory
LOMAPv1.0: error: argument -p/--parallel: invalid int value: '-1.5'
usage: LOMAPv1.0 [-h] [-p PARALLEL] [-v {off,info,pedantic}] [-t TIME]
[-e ECRSCORE] [-o] [-n NAME] [-d] [-m MAX] [-c CUTOFF] [-r]
[-b HUB] [-f] [-a]
directory
LOMAPv1.0: error: argument -v/--verbose: invalid choice: 'err_option' (choose from 'off', 'info', 'pedantic')
usage: LOMAPv1.0 [-h] [-p PARALLEL] [-v {off,info,pedantic}] [-t TIME]
[-e ECRSCORE] [-o] [-n NAME] [-d] [-m MAX] [-c CUTOFF] [-r]
[-b HUB] [-f] [-a]
directory
LOMAPv1.0: error: argument -t/--time: invalid int value: '-1.5'
usage: LOMAPv1.0 [-h] [-p PARALLEL] [-v {off,info,pedantic}] [-t TIME]
[-e ECRSCORE] [-o] [-n NAME] [-d] [-m MAX] [-c CUTOFF] [-r]
[-b HUB] [-f] [-a]
directory
LOMAPv1.0: error: argument -m/--max: invalid int value: '-5.0'
usage: LOMAPv1.0 [-h] [-p PARALLEL] [-v {off,info,pedantic}] [-t TIME]
[-e ECRSCORE] [-o] [-n NAME] [-d] [-m MAX] [-c CUTOFF] [-r]
[-b HUB] [-f] [-a]
directory
LOMAPv1.0: error: argument -m/--max: invalid int value: 'string'
..........
Ran 11 tests in 15.264s
OK
It seems that the tests for invalid arguments have passed and all is fine. I did not get any graph out of this run though... Was it expected to produce a graph by running the tests of this script?
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@achantzis are you on the master branch or the networkx2 one? Can you type git log
in your terminal? You may just not be using a branch where that functionality is already implemented?
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Doing git log I got the following:
commit f0d52a1
Author: ppxasjsm [email protected]
Date: Tue Oct 16 22:30:39 2018 +0100
only build for devel and master
commit 9e97a08
Author: ppxasjsm [email protected]
Date: Tue Oct 16 22:22:13 2018 +0100
adding pygraphviz
commit dba977b
Author: ppxasjsm [email protected]
Date: Tue Oct 16 22:16:23 2018 +0100
matplotlib 1.5
commit 787f1ba
Author: ppxasjsm [email protected]
Date: Tue Oct 16 22:11:01 2018 +0100
welcome to conda dependency hell
commit d61ab1b
Author: ppxasjsm [email protected]
Date: Tue Oct 16 21:56:01 2018 +0100
adding pyqt4 dependcy to travis
commit fe3bd91
Author: ppxasjsm [email protected]
Date: Tue Oct 16 17:35:56 2018 +0100
are you a valid yml?
commit 67ee935
Author: ppxasjsm [email protected]
Date: Tue Oct 16 17:28:58 2018 +0100
are you a valid yml?
commit 7d5a346
Author: ppxasjsm [email protected]
Date: Tue Oct 16 17:02:45 2018 +0100
ugh travis again
commit fa24ec7
Author: ppxasjsm [email protected]
Date: Tue Oct 16 17:00:43 2018 +0100
ugh travis
commit 20e1a55
Author: ppxasjsm [email protected]
Date: Tue Oct 16 16:58:22 2018 +0100
fixing Pep* convention and trailing whitespaces issue
commit 7f3ace4
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Closing this; maintenance moved to github.com/OpenFreeEnergy/Lomap.
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Related Issues (20)
- Change the code to be compatible with networkx 2.0
- Add a fingerprint similarity option to calculate the structure similarity HOT 1
- Add a fast graphing option HOT 1
- Error in installing Lomap with networkx 2/fix networkx 2 compatibility HOT 10
- Output problems for example.py and import problems for dbmol.py HOT 12
- Installing lomap via mobleylab conda channel HOT 10
- graph visualisation issues HOT 3
- Enhacement questions HOT 14
- Finish getting `dev` branch up to speed and merged into master HOT 1
- Confusion about example output HOT 2
- can't read reference graph pickle HOT 1
- MCS test fails with most recent version of rdkit HOT 2
- Colouring code for connecting compounds in FEP HOT 7
- Issues with current perturbation map generation HOT 4
- Wishlist HOT 2
- Documentation HOT 1
- Developper guide as a wiki page? HOT 5
- [WIP] Lomap Refactoring HOT 6
- How to plot the graph?
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