pybioclip - 2.1.5

This is a bug fix release to fix the CLI commands broken after #179.

What's Changed

• Updates release commit hash by @hlapp in https://github.com/Imageomics/pybioclip/pull/181
• Fix broken CLI commands caused by lazy-import None placeholders by @flobo3 in https://github.com/Imageomics/pybioclip/pull/184
• Fixes the lazy-loading issue by loading classifiers from .predict by @hlapp in https://github.com/Imageomics/pybioclip/pull/187
• Moves classifier imports to using bioclip.predict by @hlapp in https://github.com/Imageomics/pybioclip/pull/189
• Add CLI smoke tests by @thompsonmj in https://github.com/Imageomics/pybioclip/pull/188
• Increments version to 2.1.5 by @hlapp in https://github.com/Imageomics/pybioclip/pull/190

New Contributors

• @flobo3 made their first contribution in https://github.com/Imageomics/pybioclip/pull/184

Full Changelog: https://github.com/Imageomics/pybioclip/compare/2.1.4...2.1.5

Biosphere - Biodiversity Data Access and Management - Python
Published by hlapp about 2 months ago

pybioclip - 2.1.4

What's Changed

• Removes redundant citation record from README by @hlapp in https://github.com/Imageomics/pybioclip/pull/178
• Defer heavy imports for fast CLI help menus by @Copilot in https://github.com/Imageomics/pybioclip/pull/179
• Increments release version and date in prep for v2.1.4 by @hlapp in https://github.com/Imageomics/pybioclip/pull/180

Full Changelog: https://github.com/Imageomics/pybioclip/compare/2.1.3...2.1.4

Biosphere - Biodiversity Data Access and Management - Python
Published by hlapp about 2 months ago

pybioclip - 2.1.3

What's Changed

• Update commit URL for tag 2.1.1 in CITATION.cff by @johnbradley in https://github.com/Imageomics/pybioclip/pull/142
• Scope workflow permissions by @egrace479 in https://github.com/Imageomics/pybioclip/pull/143
• fix: release GPU tensors after prediction by @mitchellxh in https://github.com/Imageomics/pybioclip/pull/144
• Reduce cache size utilized in Github Actions by @hlapp in https://github.com/Imageomics/pybioclip/pull/146
• Add progress callback support to prediction methods by @maxsitt in https://github.com/Imageomics/pybioclip/pull/149
• Add --model parameter to list-tol-taxa command by @Copilot in https://github.com/Imageomics/pybioclip/pull/153
• Clarifies command-line help for list-tol-taxa options by @hlapp in https://github.com/Imageomics/pybioclip/pull/156
• Revises citations for BioCLIP and BioCLIP 2 references by @hlapp in https://github.com/Imageomics/pybioclip/pull/155
• Provenance updates by @egrace479 in https://github.com/Imageomics/pybioclip/pull/166
• Adds Video Tutorial link to documentation by @hlapp in https://github.com/Imageomics/pybioclip/pull/172
• Increments version to 2.1.2 by @hlapp in https://github.com/Imageomics/pybioclip/pull/174
• Increments previously omitted Zenodo version by @hlapp in https://github.com/Imageomics/pybioclip/pull/175

New Contributors

• @mitchellxh made their first contribution in https://github.com/Imageomics/pybioclip/pull/144
• @maxsitt made their first contribution in https://github.com/Imageomics/pybioclip/pull/149

Full Changelog: https://github.com/Imageomics/pybioclip/compare/2.1.1...2.1.3

Biosphere - Biodiversity Data Access and Management - Python
Published by hlapp about 2 months ago

pybioclip - 2.1.1

What's Changed

• Fix UTF-8 encoding issues in file operations to prevent Windows crashes and add Windows CI testing by @Copilot in https://github.com/Imageomics/pybioclip/pull/139
• Create version 2.1.1 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/140

Full Changelog: https://github.com/Imageomics/pybioclip/compare/2.1.0...2.1.1

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley 9 months ago

pybioclip - 2.1.0

What's Changed

• Add GitHub Copilot instructions for pybioclip development workflow by @Copilot in https://github.com/Imageomics/pybioclip/pull/127
• Add batch size option to bioclip embed command by @Copilot in https://github.com/Imageomics/pybioclip/pull/125
• Update docs fine-tune -> lightweight classifiers by @johnbradley in https://github.com/Imageomics/pybioclip/pull/130
• Fix Colab TypeError when using datasets library with sklearn models by @Copilot in https://github.com/Imageomics/pybioclip/pull/129
• Add comprehensive HF_TOKEN setup instructions to notebooks that download HuggingFace datasets by @Copilot in https://github.com/Imageomics/pybioclip/pull/132
• Create version 2.1.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/137

New Contributors

• @Copilot made their first contribution in https://github.com/Imageomics/pybioclip/pull/127

Full Changelog: https://github.com/Imageomics/pybioclip/compare/2.0.0...2.1.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley 9 months ago

pybioclip - 2.0.0

What's Changed

• Switch to bioclip-2 model by @johnbradley in https://github.com/Imageomics/pybioclip/pull/114
• Fix LICENSE year by @johnbradley in https://github.com/Imageomics/pybioclip/pull/115
• Add --version cli argument by @johnbradley in https://github.com/Imageomics/pybioclip/pull/119
• Add option to record prediction logs by @johnbradley in https://github.com/Imageomics/pybioclip/pull/118
• Configure PyPI Trusted Publisher by @johnbradley in https://github.com/Imageomics/pybioclip/pull/120
• Create version 2.0.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/121

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.3.3...2.0.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley 10 months ago

pybioclip - 1.3.3

What's Changed

• Update citation for version 1.3.2 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/105
• Fix cli tutorial by @johnbradley in https://github.com/Imageomics/pybioclip/pull/107
• fetch text embeddings from dataset repo by @egrace479 in https://github.com/Imageomics/pybioclip/pull/109
• Create version 1.3.3 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/110

New Contributors

• @egrace479 made their first contribution in https://github.com/Imageomics/pybioclip/pull/109

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.3.2...1.3.3

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley about 1 year ago

pybioclip - 1.3.2

What's Changed

• Create tutorial using GBIF list of Hawaiian birds to aid prediction by @thompsonmj in https://github.com/Imageomics/pybioclip/pull/86
• Add ommitted geojson example file by @thompsonmj in https://github.com/Imageomics/pybioclip/pull/97
• Add Fine-tune Simpleshot example notebook by @johnbradley in https://github.com/Imageomics/pybioclip/pull/82
• Require python3.10+ for pybioclip and add matrix based tests with python versions by @smenon8 in https://github.com/Imageomics/pybioclip/pull/100
• Fix mkdocs generation - python version by @johnbradley in https://github.com/Imageomics/pybioclip/pull/103
• Add comparison of methods to Fine-tune docs by @johnbradley in https://github.com/Imageomics/pybioclip/pull/98
• Update version to 1.3.2 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/104

New Contributors

• @thompsonmj made their first contribution in https://github.com/Imageomics/pybioclip/pull/86
• @smenon8 made their first contribution in https://github.com/Imageomics/pybioclip/pull/100

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.3.1...1.3.2

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley about 1 year ago

pybioclip - 1.3.1

What's Changed

• Fix commit url for 1.3.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/90
• Use apptainer 1.3.6 for container building by @johnbradley in https://github.com/Imageomics/pybioclip/pull/92
• Fix pil batching bug by @johnbradley in https://github.com/Imageomics/pybioclip/pull/94
• Update version to 1.3.1 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/95

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.3.0...1.3.1

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley over 1 year ago

pybioclip - 1.3.0

What's Changed

• Fix .zenodo.json and add test by @johnbradley in https://github.com/Imageomics/pybioclip/pull/75
• Add Fine-tune SVM example notebook by @johnbradley in https://github.com/Imageomics/pybioclip/pull/78
• Add Fine-tune RidgeClassifier example notebook by @johnbradley in https://github.com/Imageomics/pybioclip/pull/79
• Fix grouping performance bug by @johnbradley in https://github.com/Imageomics/pybioclip/pull/85
• Add batch_size parameter for predict() and cli by @johnbradley in https://github.com/Imageomics/pybioclip/pull/83
• Fix subsetting range bug by @johnbradley in https://github.com/Imageomics/pybioclip/pull/88
• Create version 1.3.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/89

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.2.0...1.3.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley over 1 year ago

pybioclip - 1.2.0

What's Changed

• Create publish-to-pypi.yml by @johnbradley in https://github.com/Imageomics/pybioclip/pull/48
• Fix .zenodo.json by @johnbradley in https://github.com/Imageomics/pybioclip/pull/51
• Citation 1.1.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/49
• Add binning to custom label prediction by @johnbradley in https://github.com/Imageomics/pybioclip/pull/53
• Allow using PIL with predict functions by @johnbradley in https://github.com/Imageomics/pybioclip/pull/55
• Allow subsetting TOL classifier by @johnbradley in https://github.com/Imageomics/pybioclip/pull/59
• Add mkdocs documentation by @johnbradley in https://github.com/Imageomics/pybioclip/pull/66
• Add changes to work better with pytorch-grad-cam by @johnbradley in https://github.com/Imageomics/pybioclip/pull/64
• Improve Acknowledgments by @johnbradley in https://github.com/Imageomics/pybioclip/pull/70
• Add --subset argument to predict command by @johnbradley in https://github.com/Imageomics/pybioclip/pull/63
• Improve Docker and Acknowledgments Documentation by @johnbradley in https://github.com/Imageomics/pybioclip/pull/72
• Create version 1.2.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/73

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.1.0...1.2.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley over 1 year ago

pybioclip - Version 1.1.0

What's Changed

• Update notebooks pip commands by @johnbradley in https://github.com/Imageomics/pybioclip/pull/22
• Makes synopsis in the README more descriptive by @hlapp in https://github.com/Imageomics/pybioclip/pull/24
• Allows specifying top k results for custom class list by @hlapp in https://github.com/Imageomics/pybioclip/pull/31
• Adds ability to provide other OpenCLIP models and checkpoints by @hlapp in https://github.com/Imageomics/pybioclip/pull/33
• Create CITATION.cff by @johnbradley in https://github.com/Imageomics/pybioclip/pull/25
• Add automated testing config by @johnbradley in https://github.com/Imageomics/pybioclip/pull/36
• Add --cls-file to predict command by @johnbradley in https://github.com/Imageomics/pybioclip/pull/37
• Enable torch.load weights_only=True by @johnbradley in https://github.com/Imageomics/pybioclip/pull/38
• Adds Dockerfile + release container building by @johnbradley in https://github.com/Imageomics/pybioclip/pull/40
• Add README link to custom model documentation by @johnbradley in https://github.com/Imageomics/pybioclip/pull/42
• Add apptainer support by @johnbradley in https://github.com/Imageomics/pybioclip/pull/41
• Update container README links and fix Apptainer push by @johnbradley in https://github.com/Imageomics/pybioclip/pull/44
• Update version to 1.1.0 by @johnbradley in https://github.com/Imageomics/pybioclip/pull/46

Full Changelog: https://github.com/Imageomics/pybioclip/compare/1.0.0...1.1.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley over 1 year ago

pybioclip - Initial Release

What's Changed

• Add bioclip command line tool by @johnbradley in https://github.com/Imageomics/pybioclip/pull/3
• Improve performance and prediction results by @johnbradley in https://github.com/Imageomics/pybioclip/pull/8
• Add device parameter and examples by @johnbradley in https://github.com/Imageomics/pybioclip/pull/9
• Add embed command by @johnbradley in https://github.com/Imageomics/pybioclip/pull/10
• Fix for RGBA png files by @johnbradley in https://github.com/Imageomics/pybioclip/pull/13
• Avoid recomputing text embeddings for custom labels by @johnbradley in https://github.com/Imageomics/pybioclip/pull/16
• Allow batch processing of images by @johnbradley in https://github.com/Imageomics/pybioclip/pull/18
• Prep to release on pypi by @johnbradley in https://github.com/Imageomics/pybioclip/pull/19
• Fixes badges to use the correct package name by @hlapp in https://github.com/Imageomics/pybioclip/pull/21

Full Changelog: https://github.com/Imageomics/pybioclip/commits/1.0.0

Biosphere - Biodiversity Data Access and Management - Python
Published by johnbradley almost 2 years ago