FIX(#13, plot): PY2 era BUG when writing plot-diagrams; give sample code in the into by ankostis · Pull Request #19 · yahoo/graphkit

ankostis · 2019-09-29T21:22:22Z

MERGED with ENH: use pytest instead of numpy for tests #28 to parametrize tests.
FIX(plot): bring plot writing into files up-to-date from PY2 (were not opening in binary mode).
FIX(plot): do not open file if file-ext unsupported
FEAT: support render in Jupyter notebooks.
ENH: Overlay on the graph these elements:
-execution-steps & order
- inputs
- outputs
- solution values
- "optional" needs:
TEST(plot): add TC for plot writing; needed to retrofit travis to support graphvis & matplotb.
REFACT: moved plot code & TCs into own files - split Graphviz building from IO functions.
enh(build): Test also pip extras now.
doc: Just a minor but useful addition in the intro tutorial about plotting.

Legend

Nodes:

circle: function
oval: subgraph function
inversed-house: given input
house: asked output
polygon: given both as input & asked as output (what?)
square: intermediate data, neither given nor asked.
red frame: delete-instruction, to free up memory.
filled: data node has a value in solution, shown in tooltip.
thick frame: function/data node visited.

Arrows

solid black arrows: dependencies (target need source,
sources provide target)
dashed black arrows: optional needs
green-dotted arrows: execution steps labeled in succession

I confirm that this contribution is made under the terms of the license found in the root directory of this repository's source tree and that I have the authority necessary to make this contribution on behalf of its copyright owner.

codecov-io · 2019-09-29T21:25:00Z

Codecov Report

Merging #19 into master will increase coverage by 11.81%.
The diff coverage is 96.47%.

@@             Coverage Diff             @@
##           master      #19       +/-   ##
===========================================
+ Coverage   77.87%   89.69%   +11.81%     
===========================================
  Files           5        6        +1     
  Lines         348      388       +40     
===========================================
+ Hits          271      348       +77     
+ Misses         77       40       -37

Impacted Files	Coverage Δ
graphkit/base.py	`79.36% <100%> (ø)`	⬆️
graphkit/network.py	`87.03% <71.42%> (+16.83%)`	⬆️
graphkit/plot.py	`98.68% <98.68%> (ø)`

Continue to review full report at Codecov.

Legend - Click here to learn more
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were writing in text-mode in PY3. and failing as encoding error.

ankostis · 2019-09-29T21:41:36Z

Rebased on top of ank/fix-networkx_in_py2(#16) to make Travis pass.

intermediate data. More changes only for newer pruning TCs: + refact(test): rename graph-->netop vars for results of compose(), to avoid of `graph.net.graph`. + Explain failure modes in v1.2.4 & this merged branch (yahoo#19 + yahoo#23).

override intermediate data. More changes only for newer pruning TCs: + refact(test): rename graph-->netop vars for results of compose(), to avoid of `graph.net.graph`. + Explain failure modes in v1.2.4 & this merged branch (yahoo#19 + yahoo#23).

numpy was used just for its assert_raise

@andres-fr

thanks to @andres-fr.

to use it also on stary DAGs. Keep delegation.

+ test all chained plot() methods from netop.

+ retorfitted to try all available formats. + list of forbidden formats based on my failres

+ doc: rename in sample code: netop --> pipeline. + enh(build): add `ipython` in test dependencies. + include it in the plot TC.

ankostis · 2019-10-05T18:21:38Z

This is now merge-ready:

Adde Jupyter support
Revamped & parametrized TCs with pytest (ENH: use pytest instead of numpy for tests #28).
Moved plot code out of network module.

...pytest has problems with 3.4.

ankostis · 2019-10-05T18:39:26Z

Forced to drop PY3.4 due to pytest not working...i know, this is one step close to become graphkit2.

backported from yahoo#29

FIX(build): py2 needs pinning networkx-2.2

617e577

ankostis force-pushed the doc-plot branch from a854537 to fe0efb9 Compare September 29, 2019 21:24

ankostis force-pushed the doc-plot branch 2 times, most recently from 26cc7a7 to 80e3ba9 Compare September 29, 2019 21:34

ankostis changed the title ~~DOC: Provide sample code to plot workflow diagrams in the into (fix #13)~~ FIX(#13, plot): PY2 era BUG when writing plot-diagrams; give sample code in the into Sep 29, 2019

FIX(yahoo#13): BUG in plot-diagram writtin from PY2 era,

f58d148

were writing in text-mode in PY3. and failing as encoding error.

ankostis force-pushed the doc-plot branch 8 times, most recently from 5686586 to c5bcb3b Compare September 29, 2019 23:14

ankostis added 2 commits September 30, 2019 02:15

doc(yahoo#13): sample code to plot workflow diagram in intro

c75a2c0

enh(plot): provide help msg on supported file-exts

a005bd6

ankostis force-pushed the doc-plot branch from c5bcb3b to 168dd7d Compare September 29, 2019 23:15

ankostis added 7 commits October 3, 2019 20:34

enh(build): replace numpy with pytest...

32409f6

numpy was used just for its assert_raise

feat(build): add pip-extras [test]

f606ed1

TEST(plot,ci): test plotting; pip install extras in Travis

cd1370b

fix(plot): don't create file on unsupported formats

f676662

thanks to @andres-fr.

enh(plot.TC): expose supported writers and TC on them

65d1816

enh(build,ci): use pytest in travis

4e55b30

fix(plot): NetOp did not return pydot instance

47b50f6

ankostis force-pushed the doc-plot branch from 168dd7d to 54ec53a Compare October 5, 2019 00:06

refact(plot): extract plot function out of Network class...

b1d02a1

to use it also on stary DAGs. Keep delegation.

ankostis mentioned this pull request Oct 5, 2019

How to generate graph diagrams like those included in documentation? #13

Open

ankostis added 3 commits October 5, 2019 14:01

test(plot): enhance plot test to try all yahoo#13 features;

ca5d243

+ test all chained plot() methods from netop.

doc(plot); explain also params in user-facing API

a2de9ef

FIX(PLOT.TC): TC was always testing PNG, ...

dc5a21a

+ retorfitted to try all available formats. + list of forbidden formats based on my failres

ankostis force-pushed the doc-plot branch 2 times, most recently from e8293b3 to a91bc87 Compare October 5, 2019 15:43

fix(plot): don't require Matplotlib if no Window asked

782d9b9

ankostis force-pushed the doc-plot branch 3 times, most recently from 318e511 to f17fc6d Compare October 5, 2019 16:04

test(plot): check also matplotlib show=True

7d389c3

ankostis force-pushed the doc-plot branch 3 times, most recently from 35d9a91 to 07251d8 Compare October 5, 2019 16:39

ENH(plot): return SVG rendered in JUPYTER, ...

3fe0b40

+ doc: rename in sample code: netop --> pipeline. + enh(build): add `ipython` in test dependencies. + include it in the plot TC.

ankostis force-pushed the doc-plot branch from 07251d8 to 3fe0b40 Compare October 5, 2019 16:44

ankostis added 2 commits October 5, 2019 19:45

refact(plot.TC): avoid writting multiple temp-files

1471551

MERGE PYTEST into PLOT to parametrize TCs.

af7ae0f

ankostis force-pushed the doc-plot branch from af7ae0f to 1471551 Compare October 5, 2019 17:00

fix(build): reuse dependencies definitions

b440196

REFACT(plot.TC): PYTESTize and parametrize

bde9b64

ankostis force-pushed the doc-plot branch from 2b0bf02 to bde9b64 Compare October 5, 2019 18:25

ankostis added 2 commits October 5, 2019 21:34

REFACT(PLOT): MOVE PLOT in own module

8e361e6

DROP PY3.4 - add PY3.6, PY3.7...

b08a363

...pytest has problems with 3.4.

refact(plot): separate graphviz building from IO

3a87959

ankostis force-pushed the doc-plot branch from c924028 to 3a87959 Compare October 5, 2019 19:09

FIX(plot): failing if steps not a list/ is none...

4aca013

backported from yahoo#29

ankostis force-pushed the doc-plot branch from f6e3d7c to 4aca013 Compare October 7, 2019 03:41

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FIX(#13, plot): PY2 era BUG when writing plot-diagrams; give sample code in the into#19

FIX(#13, plot): PY2 era BUG when writing plot-diagrams; give sample code in the into#19
ankostis wants to merge 34 commits intoyahoo:masterfrom
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