PAML: added testing for the presence of the PAML binaries #17
Conversation
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Hang on, hold the pull for a moment.... |
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Ok, I forgot to include adding the '.exe' for Windows. It's in there now. I've run the tests on Windows 7 with Python 2.7 and they pass. All set for the pull. (what would a pull request be from me without at least one "hang on..." (said with shame)) |
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Hi Brandon, The executable detection stuff looks fine, but do you actually have any new tests which invoke the binary? Also I'd prefer to keep test_PAML_yn00.py as they were (no binary required), and add a new test_PAML_tools.py (or set of test files one for each tool if you prefer) which actually use the binary. The point being currently Biopython's unit test skipping for external dependencies is at the file level - all or nothing. Apologies if that wasn't clear previously, but it should be straightforward to move the new functions into a new file. Peter |
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I opted against actually invoking the binary because in most cases the program hangs, waiting for user input. I just figured out that if you pass it a text file which doesn't contain valid configuration options, it just throws an error. True to PAML form, each one does something different: `$ codeml test.txt Error: err: option file. add space around the equal sign?. Reading options from test.txt.. Error: option file.. Error: option file.. Moving the testing for the presence of the executables to another file is no problem. |
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I can write some tests that do the quickest possible models in paml...they should clock in under a minute each. I'll do a basic test to make sure the output is being parsed properly. We already have all the files necessary in the Tests/PAML directory. I'll just have to make a few changes. Sound good? |
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Try to get a fast (but trivial) control file working for each tool, and that should do nicely. P.S. You can remove the binary dependency testing from the test_PAML_yn00.py etc now - we want those tests to run all the time even if the PAML binaries are not installed locally. |
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Done! |
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Close enough - I cherry-picked the relevant changes and then did a little polishing. If you could checkout the master branch and retest locally that would be great - I'm just triggering the buildslaves now... Thanks, Peter |
I added tests for the PAML binaries at the head of each of the test files (
test_PAML_[codeml, baseml, yn00].py). Since the programs don't accept commandline arguments other than the control file, they can do nothing other than actually process a control file or hang around waiting for user input. Instead, I implemented something like the unix which command. Windows users are instructed to move the executables to a folder and then to add that folder to their system path. However, in the case of Windows, I also add some Program Files paths to search (like intest_muscle_tool.py) just in case they chose to do things their own way.