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Fix docs-check job; numpy 2.x fixes #157

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merged 12 commits into from
Jun 25, 2024
Merged

Fix docs-check job; numpy 2.x fixes #157

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f4752c6
Run docs checks in venv, like other jobs
sk1p Jun 11, 2024
8b5d56f
Use uv for `libertem_master_integration` job
sk1p Jun 11, 2024
27688c5
Explicitly activate the venv
sk1p Jun 11, 2024
f9ed865
Try forcing basepython for docs check
matbryan52 Jun 21, 2024
3885f21
Revert, force localdir
matbryan52 Jun 21, 2024
d142bd9
Without uv
matbryan52 Jun 21, 2024
6b6fda0
With recreate
matbryan52 Jun 21, 2024
7e11e76
Create venv in $(Agent.TempDirectory)
sk1p Jun 25, 2024
c7babad
Switch `recreate_tox` to old default; try `uv` again
sk1p Jun 25, 2024
692a369
Give up on uv for now
sk1p Jun 25, 2024
49f3ab7
Make sure the old `venv` doesn't exist anymore in the CI env
sk1p Jun 25, 2024
acae5ff
Fixes for the merlin decoders
sk1p Jun 25, 2024
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38 changes: 24 additions & 14 deletions azure-pipelines-data.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,18 +39,18 @@ stages:
inputs:
versionSpec: '3.9'

- bash: python3.9 -m venv venv
- bash: python3.9 -m venv $(Agent.TempDirectory)/venv
displayName: 'create venv'

- bash: ./venv/bin/pip install -U tox tox-uv uv
- bash: $(Agent.TempDirectory)/venv/bin/pip install -U tox tox-uv uv
displayName: 'install tox'

- ${{ if eq(parameters.recreate_tox, true) }}:
- bash: ./venv/bin/tox -e notebooks -r -- examples/*.ipynb -v
- bash: $(Agent.TempDirectory)/venv/bin/tox -e notebooks -r -- examples/*.ipynb -v
displayName: 'Run nbval tests $(Agent.OS) (recreating)'

- ${{ if eq(parameters.recreate_tox, false) }}:
- bash: ./venv/bin/tox -e notebooks -- examples/*.ipynb -v
- bash: $(Agent.TempDirectory)/venv/bin/tox -e notebooks -- examples/*.ipynb -v
displayName: 'Run nbval tests $(Agent.OS)'

- bash: ./scripts/codecov.sh -f ./coverage.xml
Expand Down Expand Up @@ -84,13 +84,16 @@ stages:
- bash: python3.11 -m venv $(Agent.TempDirectory)/venv
displayName: 'create venv'

- bash: $(Agent.TempDirectory)/venv/bin/pip install $(Build.SourcesDirectory)/LiberTEM/
- bash: $(Agent.TempDirectory)/venv/bin/pip install uv
displayName: 'install uv'

- bash: source $(Agent.TempDirectory)/venv/bin/activate && $(Agent.TempDirectory)/venv/bin/uv pip install $(Build.SourcesDirectory)/LiberTEM/
displayName: 'install LiberTEM'

- bash: $(Agent.TempDirectory)/venv/bin/pip install $(Build.SourcesDirectory)/LiberTEM-live/
- bash: source $(Agent.TempDirectory)/venv/bin/activate && $(Agent.TempDirectory)/venv/bin/uv pip install $(Build.SourcesDirectory)/LiberTEM-live/
displayName: 'install LiberTEM-live'

- bash: $(Agent.TempDirectory)/venv/bin/pip install -r $(Build.SourcesDirectory)/LiberTEM-live/test_requirements.txt
- bash: source $(Agent.TempDirectory)/venv/bin/activate && $(Agent.TempDirectory)/venv/bin/uv pip install -r $(Build.SourcesDirectory)/LiberTEM-live/test_requirements.txt
displayName: 'install LiberTEM-live test requirements'

- bash: cd $(Build.SourcesDirectory)/LiberTEM-live/ && $(Agent.TempDirectory)/venv/bin/pytest --durations=10 --cov=libertem_live --cov-report=term --cov-report=html --cov-report=xml --cov-config=setup.cfg --junitxml=junit.xml tests/
Expand Down Expand Up @@ -129,13 +132,13 @@ stages:
inputs:
versionSpec: '$(python.version)'

- bash: python3.9 -m venv venv
- bash: python3.9 -m venv $(Agent.TempDirectory)/venv
displayName: 'create venv'

- bash: ./venv/bin/pip install -U tox tox-uv uv
- bash: $(Agent.TempDirectory)/venv/bin/pip install -U tox tox-uv uv
displayName: 'install tox'

- bash: ./venv/bin/tox -r
- bash: $(Agent.TempDirectory)/venv/bin/tox -r
displayName: 'Run tox tests $(TOXENV) $(Agent.OS)'

- bash: ./scripts/codecov.sh -f ./coverage.xml
Expand Down Expand Up @@ -167,13 +170,20 @@ stages:

- bash: apt install -y pandoc
displayName: install required debian packages
- bash: pip install -U tox tox-uv uv
displayName: 'install requirements'

- bash: rm -rf venv
displayName: 'clean up old venv, if any'

- bash: python3.9 -m venv $(Agent.TempDirectory)/venv
displayName: 'create venv'

- bash: $(Agent.TempDirectory)/venv/bin/pip install -U tox
displayName: 'install tox'

- ${{ if eq(parameters.recreate_tox, true) }}:
- bash: tox -r
- bash: $(Agent.TempDirectory)/venv/bin/tox -r
displayName: 'Run tox tests $(TOXENV) $(Agent.OS) (recreating)'

- ${{ if eq(parameters.recreate_tox, false) }}:
- bash: tox
- bash: $(Agent.TempDirectory)/venv/bin/tox
displayName: 'Run tox tests $(TOXENV) $(Agent.OS)'
7 changes: 4 additions & 3 deletions src/libertem_live/detectors/merlin/decoders.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import numba
import numpy as np


@numba.njit(cache=True)
Expand All @@ -7,8 +8,8 @@ def decode_u2(inp, out):
row_out = out[y]
row_in = inp[y]
for i in range(row_in.shape[0] // 2):
o0 = row_in[i * 2 + 0] << 8
o1 = row_in[i * 2 + 1] << 0
o0 = np.uint16(row_in[i * 2 + 0]) << 8
o1 = np.uint16(row_in[i * 2 + 1]) << 0
row_out[i] = o0 | o1


Expand Down Expand Up @@ -183,7 +184,7 @@ def decode_r12(inp, out):
col = i % 4
pos = i // 4
out_pos = (pos + 1) * 4 - col - 1
row_out[out_pos] = (row_in[i * 2] << 8) + (row_in[i * 2 + 1] << 0)
row_out[out_pos] = (np.uint16(row_in[i * 2]) << 8) + (row_in[i * 2 + 1] << 0)


@numba.njit(nogil=True, cache=True, parallel=False)
Expand Down
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