CORRECTED PA/MA Pipeline Update and GrFN2WD Translation #344
Conversation
There was a problem hiding this comment.
@pauldhein I've left a few comments on the PR, please take a look at them when you get a chance.
delphi/GrFN/networks.py
Outdated
| self.inputs = [ | ||
| n | ||
| for n, d in self.in_degree() | ||
| if d == 0 and self.nodes[n]["type"] == "variable" | ||
| ] | ||
| self.output_node = self.outputs[-1] | ||
| # self.output_node = self.outputs[-1] |
There was a problem hiding this comment.
Can we get rid of this commented-out line?
delphi/GrFN/networks.py
Outdated
| ) | ||
|
|
||
| # {"file_name": f"{stem}.py"}, # HACK |
There was a problem hiding this comment.
Is this commented-out line something we can remove as well?
| @@ -0,0 +1,2582 @@ | |||
| { | |||
There was a problem hiding this comment.
Is this a file that can be automatically generated? If so, we should remove it.
| @@ -0,0 +1,259 @@ | |||
| import math | |||
There was a problem hiding this comment.
Similarly for this file - can it be automatically generated? If so, let's remove it.
| @@ -0,0 +1,160 @@ | |||
| { | |||
There was a problem hiding this comment.
Same question (automatically generated?)
delphi/translators/for2py/f2grfn.py
Outdated
| Returns: | ||
| Element Tree (ET) Object: An object of generated rectified | ||
| XML. | ||
| """ |
There was a problem hiding this comment.
The extra indentation here in the docstrings makes sphinx-apidoc complain. This was fixed in #333, but the fix doesn't seem to have propagated to this branch. Perhaps you can try doing git cherry-pick a22e0d506d2bb51b20c027e1a7748eece9ffbf12?
There was a problem hiding this comment.
I used the cherry-pick method and was indeed able to revert the commenting style to the correct solution. @adarshp please let me know if I missed one of the docstrings in the new version
delphi/translators/for2py/rectify.py
Outdated
| <file> | ||
| </file> | ||
| """ | ||
| This function handles cleaning up the XML elementss |
There was a problem hiding this comment.
Again, docstring indentations.
tests/aske/test_GrFN.py
Outdated
| CAG.draw('SIR-Gillespie_ms--CAG.pdf', prog='dot') | ||
|
|
||
|
|
||
| # def test_petasce_torch_execution(): |
There was a problem hiding this comment.
Can we delete this commented-out code?
There was a problem hiding this comment.
My mistake, I still want this test in the future so I'll use the pytest skip fixture as opposed to commenting out the code.
|
Also, @pauldhein if you get around to merging before me, please make sure to squash the commits before merging! |
Codecov Report
@@ Coverage Diff @@
## master #344 +/- ##
=========================================
+ Coverage 67.96% 69.07% +1.1%
=========================================
Files 59 60 +1
Lines 8342 8990 +648
=========================================
+ Hits 5670 6210 +540
- Misses 2672 2780 +108
Continue to review full report at Codecov.
|
* Fixed unexpected indentations within the docstrings for f2grfn.py * Fixed additonal docstring issue for f2grfn.py * Fixed docstring issues for format.py * Fixed docstring issues for get_comments.py * Fixed docstring issues for preprocessor.py * Fixed docstring issues for pyTranslate.py * Fixed docstring issues for static_save.py * Fixed docstring issues for strings.py * Fixed docstring issues for syntax.py * Fixed docstring issues for translate.py * Partially fixed docstring issues for type_ext.py * Fixed all docstring issues for rectify.py * Fixed all docstring issues
This new branch includes all of the material from #256 that is needed to support the SIR models and collaborative demo with GTRI and Galois. The reason for this new branch is to avoid merge errors with master. This PR should solve the problems found in previous PRs.