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Make kikuchipy compatible with PyEBSDIndex 0.2 #652

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merged 46 commits into from
Nov 3, 2023
Merged

Make kikuchipy compatible with PyEBSDIndex 0.2 #652

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d8e47d3
Silence deprecation warnings from setuptools and traits
hakonanes Aug 6, 2023
b97fb24
Remove unnecessary figure decleration in EBSD.hough_indexing()
hakonanes Aug 6, 2023
d1ae018
Fix test for figures returned by PyEBSDIndex' indexing
hakonanes Aug 6, 2023
7e3a0e9
Update PC opt with PSO from PyEBSDIndex 0.2
hakonanes Aug 7, 2023
e63d909
Describe how to handle multiprocessing/ptest-xdist in dev docs
hakonanes Aug 7, 2023
84de5de
Require PyEBSDIndex >= 0.2
hakonanes Aug 7, 2023
289baec
Fix conversion between EDAX TSL <--> Bruker PC convensions
hakonanes Aug 8, 2023
77b2ee1
Use improved PC optimization w/ PSO from PyEBSDIndex 0.2 in HI tut.
hakonanes Aug 8, 2023
1bb1610
Use PC plane fitting in hybrid indexing tut. made possible by improve…
hakonanes Aug 8, 2023
88ebf90
Update reference frames tutorial using the fixed EDAX TSL PC conversion
hakonanes Aug 8, 2023
59004af
Make PC moving-screen calibration tutorial compat. w/PyEBSDIndex 0.2
hakonanes Aug 8, 2023
e75f951
Require PyEBSDIndex 0.2.*
hakonanes Aug 8, 2023
91e334b
Update orientation dep. on PC and PC plane fit tutorials
hakonanes Aug 9, 2023
2b58b83
Start to make EBSD HI methods compatible with PyEBSDIndex 0.2
hakonanes Aug 9, 2023
413b283
Start to make private HI functionality compatible with PyEBSDIndex 0.2
hakonanes Aug 9, 2023
8c9b16a
Rewrite similarity check for phase lists from orix and PyEBSDIndex
hakonanes Oct 25, 2023
989b1b2
Remove unnecessary test (was testing PyEBSDIndex, not kikuchipy)
hakonanes Oct 25, 2023
d4fc96b
Test passing reflector list in various forms, start on test for check…
hakonanes Oct 25, 2023
fb834b9
Complete tests of compatible phase lists and reflector lists
hakonanes Oct 29, 2023
0c92cf1
Improve HI tutorial
hakonanes Oct 29, 2023
3547c35
Improve hybrid indexing tutorial
hakonanes Oct 29, 2023
5a397b9
Improve detector-sample calibration tutorials
hakonanes Oct 31, 2023
d2129b9
Slightly improve wording in pattern matching tutorial
hakonanes Oct 31, 2023
4f8c230
Improve wording in reference frame tutorial
hakonanes Oct 31, 2023
a62e173
Update workshop tutorials
hakonanes Oct 31, 2023
2d56155
Try to use Trame backend instead of Panel in tutorials using PyVista
hakonanes Nov 1, 2023
29fed20
Replace Panel with Trame as PyVista backend in the docs
hakonanes Nov 1, 2023
ab9435f
Make PyVista 3D plots in docs static, as trame/nbpshinx does not work
hakonanes Nov 1, 2023
e3d2bff
Fix broken PR template links
hakonanes Nov 1, 2023
2294eee
Silence some warnings when building docs locally, improve make commands
hakonanes Nov 1, 2023
810e8be
Fix links in tutorials
hakonanes Nov 1, 2023
ec8b585
Capitalize DREAM.3D as the creators intended
hakonanes Nov 1, 2023
e5a30c8
Fix incorrect outlier detection in example, otherwise simplify exampl…
hakonanes Nov 1, 2023
3e91a04
Re-introduce virtual frame buffer in docs (because PyVista needs it?)
hakonanes Nov 1, 2023
dad8ba0
Merge branch 'develop' into support-pyebsdindex-0-2
hakonanes Nov 1, 2023
a05120f
Add build: html to RTD sphinx config
hakonanes Nov 1, 2023
69b644a
Install pandoc with aptitude on RTD server
hakonanes Nov 1, 2023
542da6c
Use pytest-rerunfailures to rerun flaky tests
hakonanes Nov 1, 2023
aefc94e
Install pandoc version supported by nbconvert on RTD
hakonanes Nov 1, 2023
95c1344
Re-introduce virtual frame buffer for PyVista on RTD
hakonanes Nov 1, 2023
f137df1
Mention possibility to set reflector lists for Hough indexing
hakonanes Nov 2, 2023
7bd0abe
Update doc/dev/running_writing_tests.rst
hakonanes Nov 2, 2023
3697def
Make it clear that comment lines and docstrings should be capped at 7…
hakonanes Nov 2, 2023
792a35d
Add @CSSFrancis to package credits
hakonanes Nov 2, 2023
6a8ff6b
Describe how to maintain package credits in the developer guide
hakonanes Nov 2, 2023
a794fe8
Remove reference to Twitter in code of conduct
hakonanes Nov 2, 2023
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Use pytest-rerunfailures to rerun flaky tests 
Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
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@hakonanes
hakonanes committed Nov 1, 2023
commit 542da6cb7474879bdf973219dab6e5d2bda2067d
10 changes: 5 additions & 5 deletions .github/workflows/tests.yml
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Expand Up @@ -10,9 +10,6 @@ on:
workflow_dispatch:
workflow: '*'

env:
MPLBACKEND: agg

jobs:
code:
name: code style
Expand Down Expand Up @@ -53,6 +50,9 @@ jobs:
name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
runs-on: ${{ matrix.os }}
timeout-minutes: 15
env:
MPLBACKEND: agg
PYTEST_ARGS: --pyargs kikuchipy --reruns 2 -n 2 --cov=kikuchipy
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Is there a specific test or reason to add in the reruns? It might be better to just add the @pytest.mark.flaky(reruns=2) to the tests which are flaky and might fail?

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Yes, the reason was a flaky test on a macOS run (here). The test check availability of datasets on Zenodo. I've experienced some flaky-ness in the past, so I figured this change was overdue.

strategy:
fail-fast: false
matrix:
Expand Down Expand Up @@ -120,12 +120,12 @@ jobs:
run: |
sudo apt-get update
sudo apt-get install xvfb
xvfb-run pytest -n 2 --cov=kikuchipy --pyargs kikuchipy
xvfb-run pytest ${{ env.PYTEST_ARGS }}

- name: Run tests on Windows or macOS
if: ${{ matrix.os != 'ubuntu-latest' }}
run: |
pytest -n 2 --cov=kikuchipy --pyargs kikuchipy
pytest ${{ env.PYTEST_ARGS }}

- name: Generate line coverage
run: |
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1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -63,6 +63,7 @@
"pytest >= 5.4",
"pytest-benchmark",
"pytest-cov >= 2.8.1",
"pytest-rerunfailures",
"pytest-xdist",
],
"all": [
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