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REL: Release version 1.1.0 #295

Merged
merged 213 commits into from
Nov 12, 2022
Merged

REL: Release version 1.1.0 #295

merged 213 commits into from
Nov 12, 2022

Commits on Jul 2, 2020

  1. DOC: Add docstring for ignore_surf_during_passive 

    and fix docstring for ignore_surf_during_removed
    @scottclowe
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  2. DOC: Clarify which lines are affected by args

    @scottclowe
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Commits on Oct 18, 2020

  1. REL: Change bleeding-edge version number to 1.0.dev0

    @scottclowe
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  2. Merge pull request #237 from DeepSenseCA/rel_1.0.0 

    DOC: Add v1.0.0 to CHANGELOG
    @scottclowe
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  3. DOC: Fix typo in CHANGELOG

    @scottclowe
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Commits on Jan 28, 2022

  1. DEV: Fix black version at 21.12b0

    @scottclowe
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  2. STY: Blacken code

    @scottclowe
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  3. Merge pull request #238 from DeepSenseCA/dev_fix-black 

    DEV: Lock black at version 21.12b0
    @scottclowe
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  4. DEV: Move nbstripout from .gitattributes to pre-commit

    @scottclowe
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  5. Merge pull request #239 from DeepSenseCA/dev_no-nbstripout 

    DEV: Move nbstripout from .gitattributes to pre-commit
    @scottclowe
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  6. API: Add --keep-ext argument to ev2csv

    @scottclowe
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  7. DOC: Fix incorrect default values in docstrings

    @scottclowe
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  8. DOC: Fix CLI docstring

    @scottclowe
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  9. REQ: Add missing appdirs requirement

    @scottclowe
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  10. Merge pull request #240 from DeepSenseCA/dep_appdirs 

    REQ: Add missing appdirs requirement
    @scottclowe
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  11. Merge pull request #241 from DeepSenseCA/doc_docstring 

    DOC: Fix docstrings
    @scottclowe
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  12. Merge pull request #242 from DeepSenseCA/api_keep-ext 

    API: Add --keep-ext argument to ev2csv
    @scottclowe
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  13. Merge pull request #243 from DeepSenseCA/mnt_surface-passive 

    DOC: Add ignore_surface_during_passive to docstring
    @scottclowe
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  14. MNT: Add verbosity option to print concise checkpoint contents

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  15. Merge pull request #244 from DeepSenseCA/doc_fix-changelog 

    DOC: Fix typo in CHANGELOG
    @scottclowe
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  16. MNT: Send each output straight to CPU when doing inference 

    This should save a lot of GPU memory.
    @scottclowe
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  17. API: Add --continue-on-error option

    @scottclowe
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  18. RF: Change break index looping

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  19. ENH: Add option to split (and join) transects on max length

    @scottclowe
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  20. BUG: Prevent CUDA memory issue during inference with max segment leng… 

    …th 1280
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Commits on Jan 29, 2022

  1. Merge pull request #245 from DeepSenseCA/mnt_output-straight-to-cpu 

    ENH: Inference on large files
    @scottclowe
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  2. ENH: Add fillholes2d

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  3. ENH: Interpolate to remove holes in input during inference

    @scottclowe
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  4. MNT: Do nan interpolation step per-segment, not whole file

    @scottclowe
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  5. Merge pull request #246 from DeepSenseCA/enh_interp-holes 

    ENH: Interpolate to fill in holes in infererence input
    @scottclowe
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  6. ENH: Add raw.manipulate.pad_transect

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  7. MNT: Pad segments before applying model for inference

    @scottclowe
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Commits on Feb 4, 2022

  1. ENH: Add evdstr2timestamp helper function

    @scottclowe
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  2. ENH: Add EVR reader and conversion to mask

    @scottclowe
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  3. MNT: Rename Sample index -> Ping index

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  4. MNT: Use r-string instead of escaping backslashes

    @scottclowe
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Commits on Feb 16, 2022

  1. RF: Move dataset fixing functions to fixup_dataset_sample function

    @scottclowe
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  2. REL: Release under AGPLv3

    @scottclowe
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  3. Merge pull request #247 from DeepSenseCA/rel_license 

    REL: Release under AGPLv3
    @scottclowe
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  4. REL: Fix Trove license classifier

    @scottclowe
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  5. REL: Add AGPLv3 license to inference.py

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  6. Merge pull request #248 from DeepSenseCA/rel_license 

    REL: Release under AGPLv3 (part 2)
    @scottclowe
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  7. BUG: Remove bad UploadCommand

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Commits on Apr 19, 2022

  1. BUG: Fix number of channels in first block 

    This did not affect previous models because they had the same
number of channels in the first block as the following blocks.
    @scottclowe
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  2. BUG: Fix bug with join transects dropping first ping

    @scottclowe
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  3. REL: Add python_requires>=3.6

    @scottclowe
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  4. BUG: Don't use torch._six.container_abcs, removed in pytorch=1.11

    @scottclowe
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  5. MNT: Use torch.cuda.is_available instead of torchutils version 

    Don't need torchutils.device.cuda_is_really_available as it is
overkill.
    @scottclowe
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  6. MNT: Vendor a copy of torchutils.count_parameters

    @scottclowe
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  7. MNT: Vendor a copy of torchutils.seed_all

    @scottclowe
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  8. REQ: Drop scottclowe/pytorch-utils dependency

    @scottclowe
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Commits on Apr 20, 2022

  1. Merge pull request #250 from DeepSenseCA/bug_torch1.11-six 

    RF: Don't use torch._six.container_abcs, removed in pytorch=1.11
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  2. Merge pull request #249 from DeepSenseCA/req_drop-torchutils 

    MNT: Drop torchutils requirement
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  3. Merge branch 'bug_torch1.11-six' into doc_build-docs2

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  4. Merge branch 'req_drop-torchutils' into doc_build-docs2

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  5. CI: Add docs test and deploy to gh-pages workflow

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  6. MNT: Delay import of ranger so docs can be built without it

    @scottclowe
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  7. MNT: Lazy import of tensorboard 

    So documentation can be built without it installed.
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  8. RF: Split train UI from its execution for ease of accessing its docum… 

    …entation
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  9. DOC: Add guarding imports 

    Needed due to inconsistent requirement specification of our
documentation dependencies.
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  10. DOC+MNT: Tidy up path linking to CHANGELOG

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  11. DOC: Improve CLI title page

    @scottclowe
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  12. DOC: Change theme rtd -> book

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  13. DOC: Force sphinx version to be compatible with theme

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  14. Merge pull request #251 from DeepSenseCA/doc_build-docs2 

    DOC: Build documentation
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Commits on Nov 4, 2022

  1. DEV: Upgrade black 21.12b0 -> 22.10.0 to fix click>8.0.4 issue

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  2. STY: Update for black 22.10.0

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  3. Merge pull request #252 from DeepSenseCA/ci_fix-click 

    DEV: Upgrade black 21.12b0 -> 22.10.0 to fix click>8.0.4 issue
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  4. DOC: Add link to documentation on github.io to README

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  5. Merge pull request #253 from DeepSenseCA/doc_readme 

    DOC: Add link to documentation on github.io to README
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Commits on Nov 6, 2022

  1. REL: Add frozen copy of requirements.txt

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  2. REL: Fixup frozen_requirements.txt

    @scottclowe
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  3. REL: Downgrade Pillow to 6.2.2 for torchvision=0.4.0

    @scottclowe
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  4. REL: Bump frozen_requirements.txt to torch=1.4.0, torchvision=0.5.0 

    This is necessary to use Pillow>=7.0.0.
    @scottclowe
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  5. MNT: Look for checkpoints.yaml in parent dir too 

    This is useful for the built exe, which can have checkpoints.yaml
alongside the echofilter.exe and not in an echofilter subdirectory.
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  6. DOC: Add link to documentation on github.io to README

    @scottclowe
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  7. REL: Add checkpoints.yaml to package_data

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  8. Merge pull request #254 from DeepSenseCA/doc_readme-link-documentation 

    DOC: Add link to documentation on github.io to README
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  9. DOC: Specify anchor in CHANGELOG for v1.0.0 Added documentation

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  10. Merge pull request #255 from DeepSenseCA/bug_checkpoints-yaml 

    BUG: Include checkpoints.yaml in package_data
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  11. Merge pull request #256 from DeepSenseCA/mnt_checkpoints-yaml-path 

    MNT: Look for checkpoints.yaml in parent dir too
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  12. Merge pull request #257 from DeepSenseCA/doc_changelog-missing-anchor 

    DOC: Specify anchor in CHANGELOG for v1.0.0 Added documentation
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  13. REL: Version 1.0.1

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  14. DOC: Add v1.0.1 to CHANGELOG

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  15. DOC: Add new PRs to CHANGELOG

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  16. REL: Add requirements and checkpoints.yaml to MANIFEST.in

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  17. DOC: Update release date

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  18. DOC: CHANGELOG: Add missing manual anchor

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  19. REL: Change bleeding-edge version number to A.B.dev0

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  20. Merge pull request #259 from DeepSenseCA/doc_changelog-1.0.1 

    DOC:  Add release 1.0.1 to CHANGELOG
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  21. REL: Change torch_lr_finder install from PyPI

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  22. API: Change default optimizer to ADAM

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  23. REL: Drop ranger from requirements-train.txt, as github can't be dep … 

    …on PyPI
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  24. Merge pull request #260 from DeepSenseCA/rel_lr-finder 

    REL: Change torch_lr_finder install from PyPI
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  25. Merge pull request #261 from DeepSenseCA/rel_drop-ranger 

    REL: Drop ranger as a hard requirement
    @scottclowe
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Commits on Nov 7, 2022

  1. DOC: Add v1.0.2 to CHANGELOG

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  2. Merge pull request #263 from DeepSenseCA/doc_changelog-1.0.2 

    DOC: Add v1.0.2 to CHANGELOG
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  3. DOC: Link to readthedocs in README text

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  4. Merge pull request #264 from DeepSenseCA/rel_python-requires 

    REL: Add python_requires>=3.6
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  5. CI: Run test suite and integration tests

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  6. CI: Remove F63 from list of failure flake8 errors

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  7. DEV: Treat test resource files as binary (don't modify)

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  8. TST: Add test resource csv files

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  9. CI: Run echofilter on test resources

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  10. CI: Test on 3.6, 3.7, 3.8

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  11. DOC: Update installation instructions in Usage Guide to use github re… 

    …leases
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  12. CI: Don't deploy GitHub Pages anymore

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  13. DOC: Add citation details to README text

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  14. DOC: Add CITATION.bib

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  15. DOC: Give 7z suggestion as well as WinZip

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  16. Merge branch 'rel_frozen-requirements' into ci_test

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  17. CI: Use frozen requirements for testing

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  18. Merge pull request #265 from DeepSenseCA/doc_install-github-release 

    DOC: Update documentation
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  19. Merge pull request #266 from DeepSenseCA/doc_citation 

    DOC: Add citation details
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  20. Merge pull request #267 from DeepSenseCA/doc_point-readthedocs 

    DOC: Point to readthedocs
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  21. CI: Only test on py3.6, 3.7

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  22. DOC: Add missing doi link markup

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  23. DOC: Add badges to README

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  24. DOC: Add details about paper, data download

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  25. CI: Don't test on Windows

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  26. REL: Change frozen_requirements to use torch_lr_finder==0.2.0

    @scottclowe
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  27. REL: Drop typing from frozen_requirements

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  28. DOC: Add GHA test badge

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  29. Merge pull request #268 from DeepSenseCA/ci_test 

    CI: Run test suite and test inference runs on every push/PR
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  30. DOC: Update install instructions in README

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  31. Merge pull request #269 from DeepSenseCA/doc_badges 

    DOC: Add badges and links to paper and data downloads
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  32. MNT: Need to change from removed np.asscalar to .item() 

    This is due to numpy deprecating asscalar.
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  33. Merge pull request #270 from DeepSenseCA/bug_bad-uploadcommand 

    BUG: Remove bad UploadCommand
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  34. Merge pull request #271 from DeepSenseCA/bug_initial-chn 

    BUG: Fix number of channels in first block
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  35. Merge pull request #272 from DeepSenseCA/bug_join-transects 

    BUG: Fix bug with join transects dropping first ping
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  36. Merge pull request #273 from DeepSenseCA/bug_numpy-asscalar 

    MNT: Need to change from removed np.asscalar to .item()
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  37. ENH: Add option to customise NaN replacement value

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  38. ENH: Add args to control if CSV export is raw or thresholded 

    Output the raw Sv file by default. This is especially important
as the input to the inference routine.
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  39. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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  40. MNT: Run download_checkpoint with verbosity preserved

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  41. MNT: More verbosity around commands at start of inference

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  42. Merge pull request #274 from DeepSenseCA/enh_nan-mapping 

    API: Add options for what value to map NaN values in inference input to
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  43. Merge pull request #275 from DeepSenseCA/enh+bug_raw-ev2csv 

    ENH: Add args to control if CSV export is raw or thresholded
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  44. DOC: Add comment

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  45. Merge pull request #276 from DeepSenseCA/mnt_more-verbose 

    MNT: Add more verbosity statements at start of inference
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  46. Merge pull request #278 from DeepSenseCA/mnt_print-ckpt-contents 

    MNT: Add verbosity option to print concise checkpoint contents
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  47. Merge pull request #277 from DeepSenseCA/enh_pad-inference 

    ENH: Pad transect during inference
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  48. Merge pull request #279 from DeepSenseCA/rf_fixup-dataset-sample 

    RF: Move dataset fixing functions to fixup_dataset_sample function
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  49. Merge pull request #280 from DeepSenseCA/enh_evr-reader 

    ENH: Add EVR file reader and converting masks to regions
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Commits on Nov 8, 2022

  1. Merge pull request #282 from DeepSenseCA/mnt_plotting-tidy 

    MNT: Tidy up plotting code
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  2. DEV: Update pre-commit stack

    @scottclowe
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  3. DEV: Drop nb-flake8 from pre-commit

    @scottclowe
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  4. DEV: Update flake8 config to ignore appropriate things

    @scottclowe
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  5. DEV: Update .gitattributes

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  6. DEV: Move documentation generation section

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  7. DEV: Update .gitignore

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  8. JNB: Blacken notebooks

    @scottclowe
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  9. STY: Sort imports with isort

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  10. REL: Update dev requirements, drop nbstripout add identify

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  11. STY: Sort requirements.txt files

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  12. DOC: Fix single back-ticks

    @scottclowe
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  13. MNT: Change mode of executable files

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  14. DOC: Remove trailing spaces in CITATION.bib

    @scottclowe
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  15. STY: Remove trailing spaces from getInfo.sh

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  16. STY: Blacken code

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  17. MNT: Mark train_cli.py as executable

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  18. BUG: Fix tqdm total in generate_shards

    @scottclowe
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  19. MNT: Use disable argument of tqdm

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  20. BUG: Need to add crop_depth argument to fixup_dataset_sample

    @scottclowe
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  21. BUG+STY: Resolve flake8 issues

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  22. Merge pull request #283 from DeepSenseCA/dev_update-config 

    DEV+STY+BUG: Update dev tools, fix flake8 errors
    @scottclowe
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  23. DOC: Fix link to PyPI in README

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  24. Merge pull request #284 from DeepSenseCA/doc_fix-README 

    DOC: Fix link to PyPI in README
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  25. REL: Update bleeding-edge version number

    @scottclowe
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Commits on Nov 9, 2022

  1. DOC: Better headline description of outputs

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  2. DOC: Add clear links to Usage Guide and CLI

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  3. Merge pull request #285 from DeepSenseCA/doc_update-readme 

    DOC: Update README
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Commits on Nov 11, 2022

  1. DOC: Ensure "E" and "A" in citation title are capitalized

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  2. Merge pull request #286 from DeepSenseCA/doc_citation-capital-a 

    DOC: Ensure "E" and "A" in citation title are capitalized
    @scottclowe
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  3. DOC: Change single backticks around variables to double 

    Performed using regex replacement from
([^`:])`([^`\s]+)`([^`_])
to
$1``$2``$3
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  4. DOC: Tidy up set to sample from docstrings

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  5. DOC: Add roles for references to torch, numpy, random

    @scottclowe
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  6. DOC: Add roles for echofilter references

    @scottclowe
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  7. DOC: Fix references in See Also section

    @scottclowe
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  8. DOC: Tidy up defaults in inference docstrings

    @scottclowe
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  9. DOC: Show "#" in code markup

    @scottclowe
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  10. DOC: Improve how optional args are described in inference

    @scottclowe
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  11. DOC: Tidy up more defaults

    @scottclowe
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  12. DOC: Use roles for win32com Dispatch classes

    @scottclowe
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  13. Merge pull request #287 from DeepSenseCA/doc_backtick 

    DOC: Tidy up docstrings
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  14. ENH: Allow paths input to inference to be a single path, not just ite… 

    …rable
    @scottclowe
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  15. Merge pull request #288 from DeepSenseCA/enh_inference-single-path 

    ENH: Allow paths input to inference to be a single path, not just iterable
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Commits on Nov 12, 2022

  1. TST: Add resource_directory attribute, and global variables for test … 

    …and resources dirs
    @scottclowe
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  2. MNT: Add args argument to cli functions to pass to parse_args 

    This is necessary for testing the CLI in pytest without sending
inputs to sys.argv
    @scottclowe
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  3. TST: Add GrandPassage test file 

    Generated with the command:

head \
    -n 241 \
    test-resources-source/full/GrandPassage_WBAT_2B_20200125_UTC160020_ebblow_Sv_raw.csv \
    > test-resources/GP_20200125T160020_first240_Sv_raw.csv
    @scottclowe
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  4. TST: Add shorter march2018 test file 

    Generated with the command:

head \
    -n 121 \
    test-resources-source/full/march2018_D20180513-T015216_D20180513-T072215_Sv_raw.csv \
    > test-resources/mar2018_20180513T015216_first120_Sv_raw.csv
    @scottclowe
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  5. TST: Add filenames for shorter sample test files

    @scottclowe
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  6. TST: Add assertion commands for file existing/absent

    @scottclowe
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  7. TST: Add inference tests

    @scottclowe
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  8. CI: Remove actual test runs from GHA, now in test suite

    @scottclowe
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  9. API: Disable logit smoothing by default

    @scottclowe
    scottclowe committed Nov 12, 2022
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  10. DEV: Extend .gitignore custom file list

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  11. Merge pull request #291 from DeepSenseCA/dev_ignore-more 

    DEV: Extend .gitignore custom file list
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  12. Merge branch 'master' into tst_inference

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  13. CI: Cache checkpoints

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  14. TST+DEV: Add .coveragerc config file

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  15. STY: Add clear line between pytest and upload coverage

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  16. CI: Report coverage on echofilter package

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  17. Merge pull request #290 from DeepSenseCA/ci_cache-checkpoints 

    CI: Cache checkpoints
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    scottclowe authored Nov 12, 2022
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  18. Merge pull request #289 from DeepSenseCA/tst_inference 

    TST: Add tests for inference
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    scottclowe authored Nov 12, 2022
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  19. MNT: Use f-strings for messages in import_lines_regions_to_ev 

    And add line breaks in some warning messages.
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  20. MNT: Add more verbosity when adding lines/regions to EV file

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  21. Merge pull request #292 from DeepSenseCA/mnt_verb-ev-entries 

    MNT: Increase verbosity of adding lines to EV file
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  22. Merge pull request #293 from DeepSenseCA/api_no-logit-smoothing 

    API: Disable logit smoothing by default
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    scottclowe authored Nov 12, 2022
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  23. API+ENH: Add config file support to inference routine

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  24. Merge pull request #294 from DeepSenseCA/enh_config-file 

    API+ENH: Add config file support to inference routine
    @scottclowe
    scottclowe authored Nov 12, 2022
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  25. REL: Version 1.1.0

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  26. DOC: Add v1.1.0 to CHANGELOG

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