diff --git a/CHANGELOG.md b/CHANGELOG.md index d525843..9cef918 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,286 +1,367 @@ # CHANGELOG +## v0.2.1 (2024-10-22) + +### Bug Fixes + +* fix: fix bad file path concat (#221) + +* fix: fix bad file path concat + +* fix: update version ([`c067bb1`](https://github.com/UCSD-E4E/PyHa/commit/c067bb1bda1a732e83d704563f7a16b9da228b15)) + +### Documentation + +* docs: Adds testing notes ([`9a3cc63`](https://github.com/UCSD-E4E/PyHa/commit/9a3cc6360b88a82d24521694496cdc505ababa3a)) + +### Unknown + +* Merge pull request #217 from UCSD-E4E/dependabot/github_actions/dot-github/workflows/actions/download-artifact-4.1.7 + +Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows ([`d3fa499`](https://github.com/UCSD-E4E/PyHa/commit/d3fa49903e967b0737f6533c3bc260b1ad0fd380)) + +* Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows + +Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7. +- [Release notes](https://github.com/actions/download-artifact/releases) +- [Commits](https://github.com/actions/download-artifact/compare/v3...v4.1.7) + +--- +updated-dependencies: +- dependency-name: actions/download-artifact + dependency-type: direct:production +... + +Signed-off-by: dependabot[bot] ([`25aa905`](https://github.com/UCSD-E4E/PyHa/commit/25aa9050bf503d8f870c5ddcd0b9f226dbe20154)) + +* Merge pull request #219 from UCSD-E4E/198-document-running-local-tests ([`53fb813`](https://github.com/UCSD-E4E/PyHa/commit/53fb813d02b07aa0bbcf38a17cb78323bab575ab)) + +* Merge pull request #213 from UCSD-E4E/dependabot/pip/setuptools-70.0.0 + +Bump setuptools from 68.2.2 to 70.0.0 ([`e4789bf`](https://github.com/UCSD-E4E/PyHa/commit/e4789bfee825400bda0935808558cae7f8766907)) + +* Bump setuptools from 68.2.2 to 70.0.0 + +Bumps [setuptools](https://github.com/pypa/setuptools) from 68.2.2 to 70.0.0. +- [Release notes](https://github.com/pypa/setuptools/releases) +- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) +- [Commits](https://github.com/pypa/setuptools/compare/v68.2.2...v70.0.0) + +--- +updated-dependencies: +- dependency-name: setuptools + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] ([`ac4d61e`](https://github.com/UCSD-E4E/PyHa/commit/ac4d61e09beb48c161dfae173d6a20ac97bda5d6)) + +* Merge pull request #211 from UCSD-E4E/dependabot/pip/certifi-2024.7.4 + +Bump certifi from 2023.7.22 to 2024.7.4 ([`f394ee9`](https://github.com/UCSD-E4E/PyHa/commit/f394ee93cb9328c6e6c290c13aa0b6d31130adb4)) + +* Bump certifi from 2023.7.22 to 2024.7.4 + +Bumps [certifi](https://github.com/certifi/python-certifi) from 2023.7.22 to 2024.7.4. +- [Commits](https://github.com/certifi/python-certifi/compare/2023.07.22...2024.07.04) + +--- +updated-dependencies: +- dependency-name: certifi + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] ([`5de9375`](https://github.com/UCSD-E4E/PyHa/commit/5de9375ad557443c9e681bba40011bcddac86ae9)) + ## v0.2.0 (2024-06-01) -### Feature +### Features * feat: fix workflow error for dependabot secrets issue (#206) -* feat: fix workflow error for dependabot secrets issue - -* fix: update them so they run on peotry.lock and pyproject.toml - -* fix: adjust so human changes can work - -* test: secret issues - -* Update conftest.py - -* fix: remove bad chaining - -* Update pyproject.toml - -* fix: indent error - -* Update pyproject.toml - -* Update env_test.yml - -* Update pyproject.toml - +* feat: fix workflow error for dependabot secrets issue + +* fix: update them so they run on peotry.lock and pyproject.toml + +* fix: adjust so human changes can work + +* test: secret issues + +* Update conftest.py + +* fix: remove bad chaining + +* Update pyproject.toml + +* fix: indent error + +* Update pyproject.toml + +* Update env_test.yml + +* Update pyproject.toml + * fix: cleanup ([`c727366`](https://github.com/UCSD-E4E/PyHa/commit/c727366a06c72f4627104b9793b450656feab0ff)) ### Unknown * Create Automatic Releases (#189) -* test build a wheel - -* test auto create issue - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* Update test_gh_cli.yml - -* testing releases - -* test creating a wheel - -* Update create_release.yml - -* Update create_release.yml - -* Update create_release.yml - -* Update create_release.yml - -* Update pyproject.toml - -feat(package): add semantic verisioning - -* feat: added semantic releases - -* fix: test semantic versioning on test branch - -* fix: again attempt to get sv to run on test branch - -* fix: - -* test new message - -* fix: add wheel to build - -* test new message - -* Update test.txt - -* fix: update name of release - -* test new message - -* fix: run only on main - -* fix: address changes to actions and pyproject.toml - -* fix: update matrix to stay within project supported versions - -* fix: fix python version again - -* fix: test why python 3.12 keeps being activated - -* Update pyproject.toml - -* fix: remake github actions to mirror e4e deduplicate action - -* fix: change ref - -* fix: remove build command - -* Update create_release.yml - -* Update create_release.yml - -* 0.1.0-rc.4 - -Automatically generated by python-semantic-release - -* fix: remove commit message - -* fix: disable changelog - -* Create TEST.txt - -* feat: test - -* feat: TEST - -* fix: update release conditions - -* Update create_release.yml - -* test: update test - -* fix: adjust release output - -* test: try out how to send data over - -* test: remove changelog - -* fix: test again - -* 0.1.0-rc.10 - -Automatically generated by python-semantic-release - -* fix: revert release change - -* 0.1.0-rc.11 - -Automatically generated by python-semantic-release - -* fix: return it to how it is in dedup example, and hope - -* fix: fix refs - -* doc: remove extra comments - -* fix: swap back to main - -* Delete TEST.txt - ---------- - -Co-authored-by: github-actions <github-actions@github.com> -Co-authored-by: semantic-release <semantic-release> ([`59e89ef`](https://github.com/UCSD-E4E/PyHa/commit/59e89ef508267ef71c3754c22899cf3a2438e3d4)) +* test build a wheel + +* test auto create issue + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* Update test_gh_cli.yml + +* testing releases + +* test creating a wheel + +* Update create_release.yml + +* Update create_release.yml + +* Update create_release.yml + +* Update create_release.yml + +* Update pyproject.toml + +feat(package): add semantic verisioning + +* feat: added semantic releases + +* fix: test semantic versioning on test branch + +* fix: again attempt to get sv to run on test branch + +* fix: + +* test new message + +* fix: add wheel to build + +* test new message + +* Update test.txt + +* fix: update name of release + +* test new message + +* fix: run only on main + +* fix: address changes to actions and pyproject.toml + +* fix: update matrix to stay within project supported versions + +* fix: fix python version again + +* fix: test why python 3.12 keeps being activated + +* Update pyproject.toml + +* fix: remake github actions to mirror e4e deduplicate action + +* fix: change ref + +* fix: remove build command + +* Update create_release.yml + +* Update create_release.yml + +* 0.1.0-rc.4 + +Automatically generated by python-semantic-release + +* fix: remove commit message + +* fix: disable changelog + +* Create TEST.txt + +* feat: test + +* feat: TEST + +* fix: update release conditions + +* Update create_release.yml + +* test: update test + +* fix: adjust release output + +* test: try out how to send data over + +* test: remove changelog + +* fix: test again + +* 0.1.0-rc.10 + +Automatically generated by python-semantic-release + +* fix: revert release change + +* 0.1.0-rc.11 + +Automatically generated by python-semantic-release + +* fix: return it to how it is in dedup example, and hope + +* fix: fix refs + +* doc: remove extra comments + +* fix: swap back to main + +* Delete TEST.txt + +--------- + +Co-authored-by: github-actions +Co-authored-by: semantic-release ([`59e89ef`](https://github.com/UCSD-E4E/PyHa/commit/59e89ef508267ef71c3754c22899cf3a2438e3d4)) * Bump jupyter-server from 2.10.0 to 2.11.2 (#173) -Bumps [jupyter-server](https://github.com/jupyter-server/jupyter_server) from 2.10.0 to 2.11.2. -- [Release notes](https://github.com/jupyter-server/jupyter_server/releases) -- [Changelog](https://github.com/jupyter-server/jupyter_server/blob/main/CHANGELOG.md) -- [Commits](https://github.com/jupyter-server/jupyter_server/compare/v2.10.0...v2.11.2) - ---- -updated-dependencies: -- dependency-name: jupyter-server - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`dfc0d7e`](https://github.com/UCSD-E4E/PyHa/commit/dfc0d7e5acf5a2256dbc1dcc91f1c86932922409)) +Bumps [jupyter-server](https://github.com/jupyter-server/jupyter_server) from 2.10.0 to 2.11.2. +- [Release notes](https://github.com/jupyter-server/jupyter_server/releases) +- [Changelog](https://github.com/jupyter-server/jupyter_server/blob/main/CHANGELOG.md) +- [Commits](https://github.com/jupyter-server/jupyter_server/compare/v2.10.0...v2.11.2) + +--- +updated-dependencies: +- dependency-name: jupyter-server + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`dfc0d7e`](https://github.com/UCSD-E4E/PyHa/commit/dfc0d7e5acf5a2256dbc1dcc91f1c86932922409)) * Bump requests from 2.31.0 to 2.32.2 (#207) -Bumps [requests](https://github.com/psf/requests) from 2.31.0 to 2.32.2. -- [Release notes](https://github.com/psf/requests/releases) -- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) -- [Commits](https://github.com/psf/requests/compare/v2.31.0...v2.32.2) - ---- -updated-dependencies: -- dependency-name: requests - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`c2915f3`](https://github.com/UCSD-E4E/PyHa/commit/c2915f38a1df9bec8cd73b3887994ade47609545)) +Bumps [requests](https://github.com/psf/requests) from 2.31.0 to 2.32.2. +- [Release notes](https://github.com/psf/requests/releases) +- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) +- [Commits](https://github.com/psf/requests/compare/v2.31.0...v2.32.2) + +--- +updated-dependencies: +- dependency-name: requests + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`c2915f3`](https://github.com/UCSD-E4E/PyHa/commit/c2915f38a1df9bec8cd73b3887994ade47609545)) * Bump pillow from 10.1.0 to 10.3.0 (#195) -Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.1.0 to 10.3.0. -- [Release notes](https://github.com/python-pillow/Pillow/releases) -- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) -- [Commits](https://github.com/python-pillow/Pillow/compare/10.1.0...10.3.0) - ---- -updated-dependencies: -- dependency-name: pillow - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`868710a`](https://github.com/UCSD-E4E/PyHa/commit/868710a092e510cd22317f24ecd0c1e288198023)) +Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.1.0 to 10.3.0. +- [Release notes](https://github.com/python-pillow/Pillow/releases) +- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) +- [Commits](https://github.com/python-pillow/Pillow/compare/10.1.0...10.3.0) + +--- +updated-dependencies: +- dependency-name: pillow + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`868710a`](https://github.com/UCSD-E4E/PyHa/commit/868710a092e510cd22317f24ecd0c1e288198023)) * Bump jinja2 from 3.1.2 to 3.1.4 (#194) -Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.4. -- [Release notes](https://github.com/pallets/jinja/releases) -- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) -- [Commits](https://github.com/pallets/jinja/compare/3.1.2...3.1.4) - ---- -updated-dependencies: -- dependency-name: jinja2 - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`d5ddc66`](https://github.com/UCSD-E4E/PyHa/commit/d5ddc6692450d11f2d03ecd272e8a4df816d588c)) +Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.4. +- [Release notes](https://github.com/pallets/jinja/releases) +- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) +- [Commits](https://github.com/pallets/jinja/compare/3.1.2...3.1.4) + +--- +updated-dependencies: +- dependency-name: jinja2 + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`d5ddc66`](https://github.com/UCSD-E4E/PyHa/commit/d5ddc6692450d11f2d03ecd272e8a4df816d588c)) * Bump werkzeug from 3.0.1 to 3.0.3 (#196) -Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.1 to 3.0.3. -- [Release notes](https://github.com/pallets/werkzeug/releases) -- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) -- [Commits](https://github.com/pallets/werkzeug/compare/3.0.1...3.0.3) - ---- -updated-dependencies: -- dependency-name: werkzeug - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`a2f104f`](https://github.com/UCSD-E4E/PyHa/commit/a2f104f56a259856d69ce9ad03735c3ba47f4c4e)) +Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.1 to 3.0.3. +- [Release notes](https://github.com/pallets/werkzeug/releases) +- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) +- [Commits](https://github.com/pallets/werkzeug/compare/3.0.1...3.0.3) + +--- +updated-dependencies: +- dependency-name: werkzeug + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`a2f104f`](https://github.com/UCSD-E4E/PyHa/commit/a2f104f56a259856d69ce9ad03735c3ba47f4c4e)) * Bump jupyterlab from 4.0.8 to 4.0.11 (#182) -Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 4.0.8 to 4.0.11. -- [Release notes](https://github.com/jupyterlab/jupyterlab/releases) -- [Changelog](https://github.com/jupyterlab/jupyterlab/blob/@jupyterlab/lsp@4.0.11/CHANGELOG.md) -- [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.0.8...@jupyterlab/lsp@4.0.11) - ---- -updated-dependencies: -- dependency-name: jupyterlab - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`d629418`](https://github.com/UCSD-E4E/PyHa/commit/d6294188d393355428bdcb8e959cfee1a2ee983c)) +Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 4.0.8 to 4.0.11. +- [Release notes](https://github.com/jupyterlab/jupyterlab/releases) +- [Changelog](https://github.com/jupyterlab/jupyterlab/blob/@jupyterlab/lsp@4.0.11/CHANGELOG.md) +- [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.0.8...@jupyterlab/lsp@4.0.11) + +--- +updated-dependencies: +- dependency-name: jupyterlab + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`d629418`](https://github.com/UCSD-E4E/PyHa/commit/d6294188d393355428bdcb8e959cfee1a2ee983c)) * Bump notebook from 7.0.6 to 7.0.7 (#181) -Bumps [notebook](https://github.com/jupyter/notebook) from 7.0.6 to 7.0.7. -- [Release notes](https://github.com/jupyter/notebook/releases) -- [Changelog](https://github.com/jupyter/notebook/blob/@jupyter-notebook/tree@7.0.7/CHANGELOG.md) -- [Commits](https://github.com/jupyter/notebook/compare/@jupyter-notebook/tree@7.0.6...@jupyter-notebook/tree@7.0.7) - ---- -updated-dependencies: -- dependency-name: notebook - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`ca3ed8a`](https://github.com/UCSD-E4E/PyHa/commit/ca3ed8add843f467433cff02b58531bc678c7d51)) +Bumps [notebook](https://github.com/jupyter/notebook) from 7.0.6 to 7.0.7. +- [Release notes](https://github.com/jupyter/notebook/releases) +- [Changelog](https://github.com/jupyter/notebook/blob/@jupyter-notebook/tree@7.0.7/CHANGELOG.md) +- [Commits](https://github.com/jupyter/notebook/compare/@jupyter-notebook/tree@7.0.6...@jupyter-notebook/tree@7.0.7) + +--- +updated-dependencies: +- dependency-name: notebook + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`ca3ed8a`](https://github.com/UCSD-E4E/PyHa/commit/ca3ed8add843f467433cff02b58531bc678c7d51)) ## v0.1.0 (2024-05-16) -### Ci +### Bug Fixes + +* fix: Fixes env variable ([`a6b7094`](https://github.com/UCSD-E4E/PyHa/commit/a6b70949fcbc9398050cdd44ce4201e93495176c)) + +* fix: Reset tutorial to microfaune, updated env_test with changes from main + +- Set the default isolation_parameters in the tutorial notebook to microfaune parameters +- Updated environment test yaml file based on most recent changes from main ([`b05a555`](https://github.com/UCSD-E4E/PyHa/commit/b05a555a9e0116d2dc47d8f34e13b67497bde12a)) + +### Continuous Integration * ci: Updates to checkout@v4 ([`c40c196`](https://github.com/UCSD-E4E/PyHa/commit/c40c196a80cdb06012ae7c94c05bcbd68b30660b)) @@ -294,7 +375,7 @@ Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.githu * ci: Fixes env test to only execute on env changes ([`8cb235d`](https://github.com/UCSD-E4E/PyHa/commit/8cb235d0f5812bee0437ba6ab937ec1422e34481)) -### Feature +### Features * feat: Updated documentation for template matching and FG-BG util.py files @@ -305,15 +386,6 @@ Added descriptions of the util.py files for template matching and BirdNET FG-BG Added descriptions of isolation parameters for template matching and FG-BG Updated IsoAutio.py documentation with descriptions of write_confidence and template matching/FG-BG functions ([`1d6ac39`](https://github.com/UCSD-E4E/PyHa/commit/1d6ac397839a56a4f06d0cddc1a9c9b6c3a14c9d)) -### Fix - -* fix: Fixes env variable ([`a6b7094`](https://github.com/UCSD-E4E/PyHa/commit/a6b70949fcbc9398050cdd44ce4201e93495176c)) - -* fix: Reset tutorial to microfaune, updated env_test with changes from main - -- Set the default isolation_parameters in the tutorial notebook to microfaune parameters -- Updated environment test yaml file based on most recent changes from main ([`b05a555`](https://github.com/UCSD-E4E/PyHa/commit/b05a555a9e0116d2dc47d8f34e13b67497bde12a)) - ### Unknown * Merge pull request #200 from UCSD-E4E/ci/optimized_workflow @@ -322,48 +394,48 @@ ci: Optimized workflow ([`dea0c07`](https://github.com/UCSD-E4E/PyHa/commit/dea0 * Bump idna from 3.4 to 3.7 (#193) -Bumps [idna](https://github.com/kjd/idna) from 3.4 to 3.7. -- [Release notes](https://github.com/kjd/idna/releases) -- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) -- [Commits](https://github.com/kjd/idna/compare/v3.4...v3.7) - ---- -updated-dependencies: -- dependency-name: idna - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> -Co-authored-by: Sean Perry <sean.hyatt.perry@gmail.com> ([`355e93f`](https://github.com/UCSD-E4E/PyHa/commit/355e93fdf9691806ebefc452c62856ee29d5fba8)) +Bumps [idna](https://github.com/kjd/idna) from 3.4 to 3.7. +- [Release notes](https://github.com/kjd/idna/releases) +- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) +- [Commits](https://github.com/kjd/idna/compare/v3.4...v3.7) + +--- +updated-dependencies: +- dependency-name: idna + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> +Co-authored-by: Sean Perry ([`355e93f`](https://github.com/UCSD-E4E/PyHa/commit/355e93fdf9691806ebefc452c62856ee29d5fba8)) * Fix: fixed test file paths (#197) -Changes where we tell the tests where the audio files are to be correct - +Changes where we tell the tests where the audio files are to be correct + namely from /temp/pyha_test to /temp/TEST ([`5e6a2bc`](https://github.com/UCSD-E4E/PyHa/commit/5e6a2bca1114db706b2b7f3c16c899d59b01a833)) * Bump jupyter-lsp from 2.2.0 to 2.2.2 (#180) -Bumps [jupyter-lsp](https://github.com/jupyter-lsp/jupyterlab-lsp) from 2.2.0 to 2.2.2. -- [Release notes](https://github.com/jupyter-lsp/jupyterlab-lsp/releases) -- [Changelog](https://github.com/jupyter-lsp/jupyterlab-lsp/blob/main/CHANGELOG.md) -- [Commits](https://github.com/jupyter-lsp/jupyterlab-lsp/commits) - ---- -updated-dependencies: -- dependency-name: jupyter-lsp - dependency-type: indirect -... - -Signed-off-by: dependabot[bot] <support@github.com> -Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`adaf991`](https://github.com/UCSD-E4E/PyHa/commit/adaf99105bbd31d5a6b965abd5b82c2d73120dad)) +Bumps [jupyter-lsp](https://github.com/jupyter-lsp/jupyterlab-lsp) from 2.2.0 to 2.2.2. +- [Release notes](https://github.com/jupyter-lsp/jupyterlab-lsp/releases) +- [Changelog](https://github.com/jupyter-lsp/jupyterlab-lsp/blob/main/CHANGELOG.md) +- [Commits](https://github.com/jupyter-lsp/jupyterlab-lsp/commits) + +--- +updated-dependencies: +- dependency-name: jupyter-lsp + dependency-type: indirect +... + +Signed-off-by: dependabot[bot] +Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> ([`adaf991`](https://github.com/UCSD-E4E/PyHa/commit/adaf99105bbd31d5a6b965abd5b82c2d73120dad)) * Update README.md for New Google Storage (#188) ([`2900fa2`](https://github.com/UCSD-E4E/PyHa/commit/2900fa2cba70de3f2a6468d3c32694f9f31ff8f6)) * Merge pull request #192 from UCSD-E4E/template-matching -Template Matching and FG-BG Separation added as new WTS pipelines. Furthermore, added in a "CONFIDENCE" column option. Small bug fixes related to logging were added as well. ([`5d1fae8`](https://github.com/UCSD-E4E/PyHa/commit/5d1fae8b6b8b76331df0085258bf0f02cbb20b90)) +Template Matching and FG-BG Separation added as new WTS pipelines. Furthermore, added in a "CONFIDENCE" column option. Small bug fixes related to logging were added as well. ([`5d1fae8`](https://github.com/UCSD-E4E/PyHa/commit/5d1fae8b6b8b76331df0085258bf0f02cbb20b90)) * Merge pull request #191 from UCSD-E4E/local_score_confidene @@ -377,7 +449,7 @@ First pass of confidence column from max local score array values ([`510aa0b`](h * Fixed order of operations on mean and standard deviation calculations on template spectrogram ([`42da684`](https://github.com/UCSD-E4E/PyHa/commit/42da68483df33d4576b2ff78b27cd584bc428e55)) * Bug Fixes -- addressed threshold min handling when key isn't used by user +- addressed threshold min handling when key isn't used by user - Added back in try-catch block when generating local score arrays ([`5b43c74`](https://github.com/UCSD-E4E/PyHa/commit/5b43c7412763b4bdd219168c871d2f8a9a461411)) * Added in template matching pipeline @@ -385,7 +457,7 @@ First pass of confidence column from max local score array values ([`510aa0b`](h - still need to do docstrings on added functions - will need to change the PyHa tutorial back to Microfaune - will need to update the readme -- will need to run all of the other techniques again to verify I didn't break anything ([`a6686e0`](https://github.com/UCSD-E4E/PyHa/commit/a6686e0ee661240558ea4053c2ef088a36561a88)) +- will need to run all of the other techniques again to verify I didn't break anything ([`a6686e0`](https://github.com/UCSD-E4E/PyHa/commit/a6686e0ee661240558ea4053c2ef088a36561a88)) * Added in first draft of BirdNET Foreground-Background Separation Local Score Generation technique - Added in some additional bug fixes related to threshold mins in some of the isolation techniques @@ -395,26 +467,26 @@ First pass of confidence column from max local score array values ([`510aa0b`](h * Poetry Environment (#159) -* feat: Adds poetry -* feat: Adds workflow -* feat: Adds testing -* chore: Removes conda -* Replaced .append with pd.concat for pandas upgrade - -Co-authored-by: Nathan Hui <nthui@eng.ucsd.edu> -Co-authored-by: Sean Perry <shperry@ucsd.edu> -Co-authored-by: TQ Zhang <116205967+TQZhang04@users.noreply.github.com> -Co-authored-by: Samantha Prestrelski <samantha.prestrelski@gmail.com> ([`c991cda`](https://github.com/UCSD-E4E/PyHa/commit/c991cda085f8018b0c371babe6a8e4a3b7bf3b2f)) +* feat: Adds poetry +* feat: Adds workflow +* feat: Adds testing +* chore: Removes conda +* Replaced .append with pd.concat for pandas upgrade + +Co-authored-by: Nathan Hui +Co-authored-by: Sean Perry +Co-authored-by: TQ Zhang <116205967+TQZhang04@users.noreply.github.com> +Co-authored-by: Samantha Prestrelski ([`c991cda`](https://github.com/UCSD-E4E/PyHa/commit/c991cda085f8018b0c371babe6a8e4a3b7bf3b2f)) * update 0 predictions in tweetynet, fix error messages (#157) ([`4b27fa6`](https://github.com/UCSD-E4E/PyHa/commit/4b27fa6a2e535b515a42bb0529f428fc903507db)) * Add torch to conda installation (#156) -Torch was not listed on Conda yaml when installed -Ran `pip install torch` to install torch and cuda tools -Exported to `environment_Ubuntu20.04.yml` -Copied the changed pip dependencies into other environments -Confirmed that Ubuntu20.04 environment worked by recreating env +Torch was not listed on Conda yaml when installed +Ran `pip install torch` to install torch and cuda tools +Exported to `environment_Ubuntu20.04.yml` +Copied the changed pip dependencies into other environments +Confirmed that Ubuntu20.04 environment worked by recreating env Other environments should work accordingly ([`b3e3e43`](https://github.com/UCSD-E4E/PyHa/commit/b3e3e4335d479aee2f40d232323ed8d12d0c48d9)) * Merge pull request #150 from UCSD-E4E/ctrl_c_exception_handling @@ -425,16 +497,16 @@ Ctrl c exception handling ([`858714b`](https://github.com/UCSD-E4E/PyHa/commit/8 * Delete unnecessary copy of IsoAutio.py ([`c0a684a`](https://github.com/UCSD-E4E/PyHa/commit/c0a684af08995a58a88ef759cd684980b31549d2)) -* Merge branch 'ctrl_c_exception_handling' of https://github.com/UCSD-E4E/PyHa into ctrl_c_exception_handling ([`a0e362b`](https://github.com/UCSD-E4E/PyHa/commit/a0e362b3bb727ebf2db3acb014999434fdc233e0)) - -* Add KeyboardInterrupt to "analyze" for BirdNET - -also only import exit from sys in IsoAutio ([`417de3a`](https://github.com/UCSD-E4E/PyHa/commit/417de3a6c32eaa4f4e94a52a4c40e88c977e904e)) +* Merge branch 'ctrl_c_exception_handling' of https://github.com/UCSD-E4E/PyHa into ctrl_c_exception_handling ([`a0e362b`](https://github.com/UCSD-E4E/PyHa/commit/a0e362b3bb727ebf2db3acb014999434fdc233e0)) * remove pycache files and reorganize gitignore https://stackoverflow.com/questions/56309100/how-to-ignore-the-same-name-directory-pycache-in-a-project ([`cc82dab`](https://github.com/UCSD-E4E/PyHa/commit/cc82dab360d9526104102a49bc41a650fa24852f)) +* Add KeyboardInterrupt to "analyze" for BirdNET + +also only import exit from sys in IsoAutio ([`417de3a`](https://github.com/UCSD-E4E/PyHa/commit/417de3a6c32eaa4f4e94a52a4c40e88c977e904e)) + * moved KeyboardInterrupt before BaseException just for the only try-except block that needs it. ([`f85d2ba`](https://github.com/UCSD-E4E/PyHa/commit/f85d2ba3c897cca676b17917503b777b8d28a420)) @@ -446,52 +518,36 @@ just for the only try-except block that needs it. ([`f85d2ba`](https://github.co * Added import sys - also noticed a resampling typo that was deprecated due to the use of resampling rather than just downsampling ([`c22a9c8`](https://github.com/UCSD-E4E/PyHa/commit/c22a9c8c01108d1e01b32dd293287a9ed37e2b74)) -* Merge branch 'main' into ctrl_c_exception_handling ([`e72e8e2`](https://github.com/UCSD-E4E/PyHa/commit/e72e8e20a7ad58e9cd037257bbc9693e647da525)) +* Merge branch 'main' into ctrl_c_exception_handling ([`e72e8e2`](https://github.com/UCSD-E4E/PyHa/commit/e72e8e20a7ad58e9cd037257bbc9693e647da525)) + +* Update IsoAutio.py + +Added assert statements to checkVerbose function. ([`0f2ccb6`](https://github.com/UCSD-E4E/PyHa/commit/0f2ccb6d0949466a71093465a41bd3f5c0b89c2b)) * Moved KeyboardInterrupt exceptions -Moved KeyboardInterrupt exception before BaseException. Also added second "r" in "interrupt." ([`cef7156`](https://github.com/UCSD-E4E/PyHa/commit/cef7156927995eb35c2757da9c5ed6885b601a02)) +Moved KeyboardInterrupt exception before BaseException. Also added second "r" in "interrupt." ([`cef7156`](https://github.com/UCSD-E4E/PyHa/commit/cef7156927995eb35c2757da9c5ed6885b601a02)) -* Keyboard interupt & checkVerbose assertions +* Keyboard interupt & checkVerbose assertions KeyboardInterupt exceptions added to try-except blocks. addition of assertions for checkVerbose ([`fcd8627`](https://github.com/UCSD-E4E/PyHa/commit/fcd862721b37e884b35caf3de64a387478da9127)) -* Update IsoAutio.py - -Added assert statements to checkVerbose function. ([`0f2ccb6`](https://github.com/UCSD-E4E/PyHa/commit/0f2ccb6d0949466a71093465a41bd3f5c0b89c2b)) - * Delete PyHa_Model_Comparison.ipynb ([`5d7abcd`](https://github.com/UCSD-E4E/PyHa/commit/5d7abcd7b82bf387f5ae873baacc817e5fbd53ba)) * Delete PyHa_Testing-Copy1.ipynb ([`d6792dc`](https://github.com/UCSD-E4E/PyHa/commit/d6792dc7bf2229b870baa8876be5c131eacf936c)) * Delete PyHa_Testing.ipynb ([`994b868`](https://github.com/UCSD-E4E/PyHa/commit/994b868de639f173d5ac2234cf9ce231c3e8e8b9)) -* Merge branch 'main' of https://github.com/UCSD-E4E/PyHa into main +* Merge branch 'main' of https://github.com/UCSD-E4E/PyHa into main - Fixed merge conflicts ([`4ef0c23`](https://github.com/UCSD-E4E/PyHa/commit/4ef0c23292c4d9bc9d7c491d6b86d0403858bf22)) -* Merge branch 'type_assertions' into main ([`4b5ae03`](https://github.com/UCSD-E4E/PyHa/commit/4b5ae03a3c60380f7c170551bb881c48f9e7b340)) - -* Fixed birdnet demo isolation_parameters -- Confidence was too high causing statistics methods not to run ([`3a890c8`](https://github.com/UCSD-E4E/PyHa/commit/3a890c82ba6f463404cbefd37a4a9955689fb3ee)) - -* More assertion checking -- Added in type checking for IsoAutio.py file -- Fixed some mistakes in prior commit on visualizations.py -- Changed input paramater name of spectrogram_visualization's "automated_df" to "build_automated_df" ([`3fc4008`](https://github.com/UCSD-E4E/PyHa/commit/3fc40087b19b223dddaa6fac2a37d7d4ec74bcbc)) - -* More input assertions for visualizations.py ([`d29bd8f`](https://github.com/UCSD-E4E/PyHa/commit/d29bd8f7fe7a606c3219400da49ca35385d19ef2)) - -* Added in assert statements for functio input validation -- Completed the statistics.py file -- started the visualizations.py file ([`9d09e4d`](https://github.com/UCSD-E4E/PyHa/commit/9d09e4d171e734957fcb46a0cf6f02db4179c3ec)) - * Added a verbose toggle feature (#139) -Co-authored-by: ayao <anthony.anthony.yao@gmail.com> -Co-authored-by: RyanHUNGry <ryhung@ucsd.edu> -Co-authored-by: Samantha Prestrelski <33042752+sprestrelski@users.noreply.github.com> ([`3593b52`](https://github.com/UCSD-E4E/PyHa/commit/3593b52810e462c11cb018c7ea89185bfe3d5743)) +Co-authored-by: ayao +Co-authored-by: RyanHUNGry +Co-authored-by: Samantha Prestrelski <33042752+sprestrelski@users.noreply.github.com> ([`3593b52`](https://github.com/UCSD-E4E/PyHa/commit/3593b52810e462c11cb018c7ea89185bfe3d5743)) * Merge pull request #140 from UCSD-E4E/ReadMe_filesize_reduction_installation_option @@ -507,10 +563,10 @@ Accidentally added a space between -- and depth in the git command. ([`afa62e0`] * Optimizing isolation techniques (#124) -* Optimizes the Steinberg, Simple, Stack, and Chunk isolation techniques with numpy -* Roughly 5x faster method of Steinberg isolation - -Co-authored-by: pranjalc1 <86537904+pranjalc1@users.noreply.github.com> ([`0c4ef29`](https://github.com/UCSD-E4E/PyHa/commit/0c4ef2941a745f2e611ae5ca52dcd7196a8f7736)) +* Optimizes the Steinberg, Simple, Stack, and Chunk isolation techniques with numpy +* Roughly 5x faster method of Steinberg isolation + +Co-authored-by: pranjalc1 <86537904+pranjalc1@users.noreply.github.com> ([`0c4ef29`](https://github.com/UCSD-E4E/PyHa/commit/0c4ef2941a745f2e611ae5ca52dcd7196a8f7736)) * Generalizing file reading with librosa (#122) ([`b58b13e`](https://github.com/UCSD-E4E/PyHa/commit/b58b13e810a53c4352d3be8bece18dee818646fa)) @@ -522,527 +578,543 @@ Refactors clip_IoU method with linear algebra and numpy ([`fa91052`](https://git * Label chunker (#114) -* Added label chunker -* Added documentation for the annotation_chunker -Co-authored-by: shreyasar2202 <ars.shreyas@gmail.com> -Co-authored-by: Sean Perry <shperry@ucsd.edu> -Co-authored-by: Samantha Prestrelski <samantha.prestrelski@gmail.com> ([`2c48a85`](https://github.com/UCSD-E4E/PyHa/commit/2c48a859460472743aa6e287582f244dffdebd23)) +* Added label chunker +* Added documentation for the annotation_chunker +Co-authored-by: shreyasar2202 +Co-authored-by: Sean Perry +Co-authored-by: Samantha Prestrelski ([`2c48a85`](https://github.com/UCSD-E4E/PyHa/commit/2c48a859460472743aa6e287582f244dffdebd23)) * remove notebooks (#121) -* .gitignore fixed and removed notebooks - +* .gitignore fixed and removed notebooks + * remove notebooks ([`b27cfc6`](https://github.com/UCSD-E4E/PyHa/commit/b27cfc6ad87b51ac0fb7c6a817bd23651b7d78b9)) * .gitignore fixed and removed notebooks (#120) ([`675bec0`](https://github.com/UCSD-E4E/PyHa/commit/675bec011022f1725510b5f03704241554bceebc)) -* Conform tweetynet to recent PyHa refactor (#113) +* Conform tweetynet to recent PyHa refactor (#113) + +* Added TweetyNet model to PyHa +* Added TweetyNet local score and spectrogram visualization output +* Added new conda environments for MacOS and Windows 10 +* Added testing notebooks +* Optimize panda use on Steinburg isolate technique +* Updated .gitignore for cached files and testing +* Updated README, Tutorial Notebook, and documentation +* Improved error messages + +Co-authored-by: mugen13lue +Co-authored-by: Samantha Prestrelski +Co-authored-by: Vanessa-Salgado +Co-authored-by: Sean Perry ([`b6b24b9`](https://github.com/UCSD-E4E/PyHa/commit/b6b24b944261a15e010cca64c8fbe6c785f4c709)) + +* Merge branch 'type_assertions' into main ([`4b5ae03`](https://github.com/UCSD-E4E/PyHa/commit/4b5ae03a3c60380f7c170551bb881c48f9e7b340)) + +* Fixed birdnet demo isolation_parameters +- Confidence was too high causing statistics methods not to run ([`3a890c8`](https://github.com/UCSD-E4E/PyHa/commit/3a890c82ba6f463404cbefd37a4a9955689fb3ee)) + +* More assertion checking +- Added in type checking for IsoAutio.py file +- Fixed some mistakes in prior commit on visualizations.py +- Changed input paramater name of spectrogram_visualization's "automated_df" to "build_automated_df" ([`3fc4008`](https://github.com/UCSD-E4E/PyHa/commit/3fc40087b19b223dddaa6fac2a37d7d4ec74bcbc)) + +* More input assertions for visualizations.py ([`d29bd8f`](https://github.com/UCSD-E4E/PyHa/commit/d29bd8f7fe7a606c3219400da49ca35385d19ef2)) + +* Added in assert statements for functio input validation +- Completed the statistics.py file +- started the visualizations.py file ([`9d09e4d`](https://github.com/UCSD-E4E/PyHa/commit/9d09e4d171e734957fcb46a0cf6f02db4179c3ec)) + +* Merge branch 'TweetyNet_integrations_2_main' of https://github.com/UCSD-E4E/PyHa into TweetyNet_integrations_2_main ([`4763ee5`](https://github.com/UCSD-E4E/PyHa/commit/4763ee54a4cc6605f002bbb2ca4a17da33a7aef8)) + +* Update .gitignore ([`b376ce5`](https://github.com/UCSD-E4E/PyHa/commit/b376ce5cdc79b99050a7fd862f25057133ab377a)) + +* Update .gitignore ([`a67d9a5`](https://github.com/UCSD-E4E/PyHa/commit/a67d9a56db8d8262c01f0730f70dbe9d1fcd38bd)) + +* Improved error messaging on Pyha ([`0690ab9`](https://github.com/UCSD-E4E/PyHa/commit/0690ab9c79b75cd623ca0751ae39a4718d389964)) + +* Cleaned up steinburg code ([`08d5170`](https://github.com/UCSD-E4E/PyHa/commit/08d51700c8bdcafa9976699011d31a3caaf9a521)) + +* Fixed bug with new steinburg fix ([`6f2da05`](https://github.com/UCSD-E4E/PyHa/commit/6f2da0596764637cfff9a4e84284c5e0fa65bc89)) + +* Optimize panda use on steinburg to fix bug ([`5f00a09`](https://github.com/UCSD-E4E/PyHa/commit/5f00a09ae015e8b3cfc48541ac6d170dc409e45e)) + +* Fixed gitignore ([`eeea93c`](https://github.com/UCSD-E4E/PyHa/commit/eeea93cd59b492304e73658caed17f49b01acb40)) + +* Update .gitignore + +Updated .gitignore for cached files and testing +Optimize panda use on Steinburg isolation technique +Improved error messaging on Pyha ([`2509e74`](https://github.com/UCSD-E4E/PyHa/commit/2509e747f048ad7b174423b3c4e81f4f36d34afc)) + +* Uncommented old normalize code ([`b3846ff`](https://github.com/UCSD-E4E/PyHa/commit/b3846ffcff2229b8a6bc012d3914b0460da6e5d9)) + +* Merge branch 'TweetyNet_integrations_2_main' of https://github.com/UCSD-E4E/PyHa into TweetyNet_integrations_2_main ([`62f2729`](https://github.com/UCSD-E4E/PyHa/commit/62f2729f0d92a542ab63b3999a907e53eb9f0051)) + +* documentation update, renamed testing scripts ([`b937c2e`](https://github.com/UCSD-E4E/PyHa/commit/b937c2e4eedfc835b291f0635ba009ba5b8f35dc)) + +* Use tweetynet normalization ([`b0aca41`](https://github.com/UCSD-E4E/PyHa/commit/b0aca418389d1ca1884d0e32e51f1664757710c1)) + +* Removed testing folder because that was a bad idea + +It boke a bunch of imports, will have to try again with a different idea later ([`a9a9f7f`](https://github.com/UCSD-E4E/PyHa/commit/a9a9f7f68e2d63300ffba5210cf610a2bea0731f)) + +* Merge pull request #119 from UCSD-E4E/TweetyNet-Testing + +Added Testing Code For Tweetynet / Docuemtentation Updates ([`e3a25d8`](https://github.com/UCSD-E4E/PyHa/commit/e3a25d8db1b8b9a0ac8630526be8d04f079f9f0e)) + +* Merge branch 'TweetyNet-Testing' of https://github.com/UCSD-E4E/PyHa into TweetyNet-Testing ([`4dbef91`](https://github.com/UCSD-E4E/PyHa/commit/4dbef91006a6d1dc22469a2e6b0b94e9c3ffee47)) + +* Merge branch 'TweetyNet-Testing' of https://github.com/UCSD-E4E/PyHa into TweetyNet-Testing ([`d1b2fbd`](https://github.com/UCSD-E4E/PyHa/commit/d1b2fbda00b40194099db053a6164a21be27eef2)) + +* added tweetynet documentation ([`b113ac1`](https://github.com/UCSD-E4E/PyHa/commit/b113ac1b5cdd3a113617f97db0083baa518e5897)) + +* Moved testing scripts to testing folder ([`20c1536`](https://github.com/UCSD-E4E/PyHa/commit/20c15362a70682c07cdfc1051173a38bf7b7ec03)) + +* Fixed spectrogram_graph visualization to readme ([`2d672f0`](https://github.com/UCSD-E4E/PyHa/commit/2d672f06fa082a00dbab7efbf942f95bd2f02ff3)) + +* Added chunk isolate to testing suite ([`5f6ce9f`](https://github.com/UCSD-E4E/PyHa/commit/5f6ce9f9d0664bd1c6a17c8795673a3a60e0436b)) + +* added model comparison and spectrogram vis testing ([`6ca7ff4`](https://github.com/UCSD-E4E/PyHa/commit/6ca7ff439a12575023587c1bd45145ebb8a9fd50)) + +* Fixed FutureError warnings + +For tweetynet, fixed the liborsa warnings output by adding adtional augrement ([`ca4d4f5`](https://github.com/UCSD-E4E/PyHa/commit/ca4d4f5886019b446ce24916ba2021a830e1b589)) + +* added batch testing ([`361d27d`](https://github.com/UCSD-E4E/PyHa/commit/361d27dbd915fa6914032c86395cd91bf4932535)) + +* Meant to be in the conda_environments folder ([`72a2dec`](https://github.com/UCSD-E4E/PyHa/commit/72a2dec12917781bc273d1fea90fc22a0ab567bd)) + +* Updated Most Recent Ubuntu Conda Environment with PyTorch + +- PyTorch is required for TweetyNET ([`7c1a806`](https://github.com/UCSD-E4E/PyHa/commit/7c1a806b64fa5a4e9974a10cfe4a34b13ccc98e8)) + +* Updated Tutorial Notebook + +- Trimmed some unnecessary tweetynet isolation parameters +- Removed unnecessary import of torch. ([`46b5e13`](https://github.com/UCSD-E4E/PyHa/commit/46b5e13cb8623e1df01d464fb76a3503de3b2720)) + +* Refactor TweetyNET automated label gen/visualizations + +- removes the tweety_output bool and moves it to isolation_parameters dict +- updates local_score_visualization() function to reflect spectrogram_visualization() name change and organization +- removes TweetyNET tutorial and a handful of test files +- README documentation for TweetyNet parameters and generate_automated_labels_tweetynet() ([`1ac5554`](https://github.com/UCSD-E4E/PyHa/commit/1ac5554731c434d188c27bb91d5f4181398d8769)) + +* Merge branch 'tweetynet_integrations' into TweetyNet_integrations_2_main ([`e55baa3`](https://github.com/UCSD-E4E/PyHa/commit/e55baa3e607155aeeaada4ba0d5899867461fc4c)) + +* updating notebook with tweetynet example ([`5564bd4`](https://github.com/UCSD-E4E/PyHa/commit/5564bd492c9a404bdeed8f26a76929c89c6e4edb)) + +* update from microfaune to tweetynet in error message ([`90c0414`](https://github.com/UCSD-E4E/PyHa/commit/90c041451d9cfe24e1fdf3c8ac4a5a8edbed77d4)) + +* updating gitignore to ignore pycache in tweetynet_package ([`9cda0e7`](https://github.com/UCSD-E4E/PyHa/commit/9cda0e7c3428f967b9fe64a5ebdd83c1510d5391)) + +* adding environment for windows 10 ([`fb68481`](https://github.com/UCSD-E4E/PyHa/commit/fb6848136694bd30549f49075138cd8583c6dedd)) + +* adding conda environment for macOs ([`1be6fea`](https://github.com/UCSD-E4E/PyHa/commit/1be6fea1cf5594e4bcfa851d3d42a195ef749ad9)) + +* The visualization and creating the automated dataframe works and will now test with various wav files ([`dbe2252`](https://github.com/UCSD-E4E/PyHa/commit/dbe2252f14a34f0fe4e2c1fa8c0334e3ff1177fc)) + +* fixed merge conflict ([`59b2579`](https://github.com/UCSD-E4E/PyHa/commit/59b2579aa94f442826a9960e5b27ce8bcafeff8e)) + +* adding environment with pytorch for tweetynet and fixed pyha tutorial for tweetynet ([`fd8e6ff`](https://github.com/UCSD-E4E/PyHa/commit/fd8e6ff0d1687ea6839ca2a68692c9f0ce271020)) + +* local commit of file ([`ea35605`](https://github.com/UCSD-E4E/PyHa/commit/ea356059aeda26a9b036810567888c806dd8915a)) + +* got the visualizations to work and fixed the local score output to be more reasonable ([`0aa91d3`](https://github.com/UCSD-E4E/PyHa/commit/0aa91d369802a9175167e882e364b6f522d2ab03)) + +* adding changes for another file ([`7907803`](https://github.com/UCSD-E4E/PyHa/commit/7907803cde8e9ac8031a16affbb239834a07f281)) + +* updated files and checkiing results on windows ([`4893339`](https://github.com/UCSD-E4E/PyHa/commit/48933398d8a903ca9d0f7b728ac28a8a10447b52)) + +* adding tweetynet model to pyha ([`e3fbbba`](https://github.com/UCSD-E4E/PyHa/commit/e3fbbba2a956923a068cb5760c83e553881cbfbd)) + +* Merge pull request #116 from UCSD-E4E/minor_bug_fixes + +Corrected typos and deleted redundant file ([`f98ba0f`](https://github.com/UCSD-E4E/PyHa/commit/f98ba0f72eda3d83f0ec0e0d0032221231324801)) + +* Correct typos and deleted redundant file ([`f2873f6`](https://github.com/UCSD-E4E/PyHa/commit/f2873f611f5f33d669620090e6462af966c2dfb7)) + +* Update License + +Matching BirdNET-Analyzer instead of old BirdNET-Lite repository ([`97faf00`](https://github.com/UCSD-E4E/PyHa/commit/97faf00bb148c1c2e8e8911253a7d98643eb4295)) + +* Merge pull request #112 from UCSD-E4E/birdnet_integration + +- Birdnet integration +- Statistics Expansion ([`a6e2ea9`](https://github.com/UCSD-E4E/PyHa/commit/a6e2ea98c29c42ef7144813b45fb98879be7617d)) + +* Merge branch 'birdnet_integration' of https://github.com/UCSD-E4E/PyHa into birdnet_integration ([`9996d48`](https://github.com/UCSD-E4E/PyHa/commit/9996d4838fdf3b58779b0c90db03058fc9af23a9)) + +* Added Tensorflow 2.8 to windows env ([`6d83f2c`](https://github.com/UCSD-E4E/PyHa/commit/6d83f2c72157b4912daf5e329995bceeb177b39a)) + +* Fix for visualization typechecking + +- Fixed a small bug in spectrogram_visualization() to better handle both bools and dataframes for automated_df +- Added spectrogram_graph(), annotation_duration_histogram() to README ([`1e519c1`](https://github.com/UCSD-E4E/PyHa/commit/1e519c16d0986c5f5cd23ed01c02b58f49cad546)) + +* Adjusted Tutorial Notebook +- Some markdown didn't make sense talking about TPs, FPs, FNs, and TNs in the context of the spectrogram_visualization() changes ([`4f3549d`](https://github.com/UCSD-E4E/PyHa/commit/4f3549dc62d3ba1132cf05032cc069f8418a8efa)) + +* Renamed two visualization functions +- Changed local_score_visualization() to spectrogram_visualization() +- Changed plot_bird_label_scores() to binary_visualization() +- Fixed a small bug in spectrogram_visualization() related to an error warning when a dataframe with automated annotations from multiple clips is passed in ([`de5a9e0`](https://github.com/UCSD-E4E/PyHa/commit/de5a9e0de89648c0005d61920a8aca60c9a4ee95)) + +* Fixed new Ubuntu 20.04 conda environment placement +- Made sure it is in the conda_environments folder ([`7c873f3`](https://github.com/UCSD-E4E/PyHa/commit/7c873f3abc797da17c3b16a72e2064cf2fa627a4)) + +* local_scores ability to pass in automated_df (#109) ([`b1d81aa`](https://github.com/UCSD-E4E/PyHa/commit/b1d81aaa21a2c8fa5e1e431f4286814036e25cf3)) + +* local_score_visualization for non-Microfaune + +currently calls generate_automated_labels on the single clip - will refactor in a different commit to handle if an already made automated_df is passed in ([`261fee7`](https://github.com/UCSD-E4E/PyHa/commit/261fee7d3a637e3e9cc539046bf1059310114142)) + +* Update README.md + +Updated example to include the "model" isolation parameter ([`be77ddb`](https://github.com/UCSD-E4E/PyHa/commit/be77ddb3aff8d6c0ba42de3c02075c6a46487ec3)) + +* Documentation update for new BirdNET-Lite functions ([`e6190c6`](https://github.com/UCSD-E4E/PyHa/commit/e6190c6fc9181dd6a4b38cc7ba163075b51e59b7)) + +* Merge branch 'birdnet_integration' of https://github.com/UCSD-E4E/PyHa into birdnet_integration ([`92a31a2`](https://github.com/UCSD-E4E/PyHa/commit/92a31a2f7b0e9ca5adb5aff1115e348aa74d9b9d)) + +* New Ubuntu 20.04 conda environment + +- Upgrades to tensorflow 2.8.0 which is compatible with both Microfaune and BirdNET ([`2e8e3e7`](https://github.com/UCSD-E4E/PyHa/commit/2e8e3e7f8551f18e3e412f4fbe58798508a0189b)) + +* Fixed typo +birdnet "model" isolation parameter was mispelled as "birndet" ([`d3b8f02`](https://github.com/UCSD-E4E/PyHa/commit/d3b8f020ca063cac5286d0633b7c3241bb73ed46)) + +* Merge pull request #108 from shreyasar2202/main + +Added BirdNet Pipeline ([`ffaec7a`](https://github.com/UCSD-E4E/PyHa/commit/ffaec7ad3aa93b7e58e477706750710387007061)) + +* Added BirdNet Pipeline ([`e3804e2`](https://github.com/UCSD-E4E/PyHa/commit/e3804e201850f6212edf27dc53c6f96ba66047ea)) + +* Updated License + +- Since we are using birdnet source code, we have to reflect their license. +- No commercial use I guess. ([`d4d0592`](https://github.com/UCSD-E4E/PyHa/commit/d4d05922d21f8e53e82f93874d232eea0bdd356d)) + +* Delete LICENSE + +Moving to Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) ([`9504fd5`](https://github.com/UCSD-E4E/PyHa/commit/9504fd56060244dd2ac954d1641422b493b5007d)) + +* Merge branch 'main' of https://github.com/UCSD-E4E/PyHa into main ([`9de4cce`](https://github.com/UCSD-E4E/PyHa/commit/9de4cce8c3595c8f9f9aee7a5a5e929ff808d4ca)) + +* Merge pull request #99 from sprestrelski/kaleidoscope_folder + +Fix "FOLDER" column Kaleidoscope compatibility ([`1a4cccd`](https://github.com/UCSD-E4E/PyHa/commit/1a4cccd5d1dbccf46c4cc61a0be724e03523cb13)) + +* Fix "FOLDER" column Kaleidoscope compatibility ([`d6a1069`](https://github.com/UCSD-E4E/PyHa/commit/d6a1069c599b7429f9a5062d89a83da15c86aa0f)) + +* Added extra error handling to generate_automated_labels +- Caught the case where an empty wav file is successfully loaded in +- Problem was that in these cases the script would crash whenever the signal was downsampled ([`18e5bf7`](https://github.com/UCSD-E4E/PyHa/commit/18e5bf7e3ff1160f71b05b889104c032e6e7a1ef)) + +* Update IsoAutio.py + +- Fixed a comment on the resampling portion of the code base. ([`75cca40`](https://github.com/UCSD-E4E/PyHa/commit/75cca4040e5fca696a51ea1be5e7f2615430c35f)) + +* Merge pull request #98 from UCSD-E4E/Resampling-generalizability + +Made resampling more general ([`8f18854`](https://github.com/UCSD-E4E/PyHa/commit/8f18854f398483392fd5f61fac4f5990333a8d92)) + +* Made resampling more general + +Scipy's resample function allows for both upsampling and downsampling, made sure that this function also includes upsampling, not just downsampling. ([`a8b0c04`](https://github.com/UCSD-E4E/PyHa/commit/a8b0c04e0ae1945c280cb9f4067fcbddb94bb7ba)) + +* Update README.md (#95) ([`3896104`](https://github.com/UCSD-E4E/PyHa/commit/3896104cf5a9cb8d7f9e2ea102e3f321d048bfeb)) + +* Merge pull request #94 from UCSD-E4E/readme-real-fix + +Fixed broken logo ([`3a94c0f`](https://github.com/UCSD-E4E/PyHa/commit/3a94c0f3accacd88330ad7cb48d627e62a58713d)) + +* Fixed broken logo ([`52cfef1`](https://github.com/UCSD-E4E/PyHa/commit/52cfef125e842c5c6bbe49ac4279a7889fa3c15e)) + +* Merge pull request #93 from UCSD-E4E/readme-fix + +Fixed missing logo ([`79d015e`](https://github.com/UCSD-E4E/PyHa/commit/79d015e5dbeff9c342f6b525b631a46e4c24e9c4)) + +* Update README.md ([`9ae743d`](https://github.com/UCSD-E4E/PyHa/commit/9ae743dcd2b2dbe14c13c0b645ac7b57f657a124)) + +* Merge pull request #92 from UCSD-E4E/staging + +Staging ([`bc05e73`](https://github.com/UCSD-E4E/PyHa/commit/bc05e73c25599a5025cf2ed9aea41b8b8c98dd25)) + +* Updated Tutorial Notebook +Added more relevant demo of the annotation histogram ([`20d0ad8`](https://github.com/UCSD-E4E/PyHa/commit/20d0ad81b9209e34eda6e1f375fa6e34bd8ed506)) + +* Annotation Length Histograms (#89) + +* move from old branch + +* update tutorial + +* update + +* Add parameters update to match + +* update tutorial ([`aecd8f5`](https://github.com/UCSD-E4E/PyHa/commit/aecd8f5b7dfe837b09d7cccdcf312bb6142e51ab)) + +* Merge pull request #81 from UCSD-E4E/linting + +Initial linting with PEP8 ([`a2d7299`](https://github.com/UCSD-E4E/PyHa/commit/a2d729961ad6ad60d14da5dcf27f338f31edfa20)) + +* Merge branch 'staging' into linting ([`9a0fed3`](https://github.com/UCSD-E4E/PyHa/commit/9a0fed31a2cc0db242c8bacd9bc6d054df7d1716)) + +* Merge pull request #87 from UCSD-E4E/gitignore + +Created a .gitignore file ([`da2989b`](https://github.com/UCSD-E4E/PyHa/commit/da2989b277f04787c39f92254c82b4faa62f4e02)) + +* deleted pycaches ([`365e900`](https://github.com/UCSD-E4E/PyHa/commit/365e90041c992336e1fc6fa605bd455f01be11a0)) -* Added TweetyNet model to PyHa -* Added TweetyNet local score and spectrogram visualization output -* Added new conda environments for MacOS and Windows 10 -* Added testing notebooks -* Optimize panda use on Steinburg isolate technique -* Updated .gitignore for cached files and testing -* Updated README, Tutorial Notebook, and documentation -* Improved error messages - -Co-authored-by: mugen13lue <mugen4college@gmail.com> -Co-authored-by: Samantha Prestrelski <samantha.prestrelski@gmail.com> -Co-authored-by: Vanessa-Salgado <vsalgadozavaleta@ucsb.edu> -Co-authored-by: Sean Perry <shperry@ucsd.edu> ([`b6b24b9`](https://github.com/UCSD-E4E/PyHa/commit/b6b24b944261a15e010cca64c8fbe6c785f4c709)) - -* Merge branch 'TweetyNet_integrations_2_main' of https://github.com/UCSD-E4E/PyHa into TweetyNet_integrations_2_main ([`4763ee5`](https://github.com/UCSD-E4E/PyHa/commit/4763ee54a4cc6605f002bbb2ca4a17da33a7aef8)) +* gitignore ([`27cc011`](https://github.com/UCSD-E4E/PyHa/commit/27cc011bdb881fc8897d3731d79b444073d4347c)) -* Update .gitignore +* Readme (#86) -Updated .gitignore for cached files and testing -Optimize panda use on Steinburg isolation technique -Improved error messaging on Pyha ([`2509e74`](https://github.com/UCSD-E4E/PyHa/commit/2509e747f048ad7b174423b3c4e81f4f36d34afc)) +* Update README.md -* Update .gitignore ([`b376ce5`](https://github.com/UCSD-E4E/PyHa/commit/b376ce5cdc79b99050a7fd862f25057133ab377a)) +removed last remnant of old name on this branch -* Update .gitignore ([`a67d9a5`](https://github.com/UCSD-E4E/PyHa/commit/a67d9a56db8d8262c01f0730f70dbe9d1fcd38bd)) +* Create artwork -* Improved error messaging on Pyha ([`0690ab9`](https://github.com/UCSD-E4E/PyHa/commit/0690ab9c79b75cd623ca0751ae39a4718d389964)) +* Add files via upload -* Cleaned up steinburg code ([`08d5170`](https://github.com/UCSD-E4E/PyHa/commit/08d51700c8bdcafa9976699011d31a3caaf9a521)) +* Update ver3 zoo2.svg -* Fixed bug with new steinburg fix ([`6f2da05`](https://github.com/UCSD-E4E/PyHa/commit/6f2da0596764637cfff9a4e84284c5e0fa65bc89)) +* Update ver3 zoo2.svg -* Optimize panda use on steinburg to fix bug ([`5f00a09`](https://github.com/UCSD-E4E/PyHa/commit/5f00a09ae015e8b3cfc48541ac6d170dc409e45e)) +* Delete ver3 zoo2.svg -* Fixed gitignore ([`eeea93c`](https://github.com/UCSD-E4E/PyHa/commit/eeea93cd59b492304e73658caed17f49b01acb40)) +* Delete ver3 zoo3.svg -* Uncommented old normalize code ([`b3846ff`](https://github.com/UCSD-E4E/PyHa/commit/b3846ffcff2229b8a6bc012d3914b0460da6e5d9)) +* Delete ver3 zoo5.svg -* Merge branch 'TweetyNet_integrations_2_main' of https://github.com/UCSD-E4E/PyHa into TweetyNet_integrations_2_main ([`62f2729`](https://github.com/UCSD-E4E/PyHa/commit/62f2729f0d92a542ab63b3999a907e53eb9f0051)) +* Add files via upload -* Use tweetynet normalization ([`b0aca41`](https://github.com/UCSD-E4E/PyHa/commit/b0aca418389d1ca1884d0e32e51f1664757710c1)) +* Add files via upload -* documentation update, renamed testing scripts ([`b937c2e`](https://github.com/UCSD-E4E/PyHa/commit/b937c2e4eedfc835b291f0635ba009ba5b8f35dc)) +* Add files via upload -* Removed testing folder because that was a bad idea +* Add files via upload -It boke a bunch of imports, will have to try again with a different idea later ([`a9a9f7f`](https://github.com/UCSD-E4E/PyHa/commit/a9a9f7f68e2d63300ffba5210cf610a2bea0731f)) +* Add files via upload -* Merge pull request #119 from UCSD-E4E/TweetyNet-Testing +* Add files via upload -Added Testing Code For Tweetynet / Docuemtentation Updates ([`e3a25d8`](https://github.com/UCSD-E4E/PyHa/commit/e3a25d8db1b8b9a0ac8630526be8d04f079f9f0e)) +* Add files via upload -* Merge branch 'TweetyNet-Testing' of https://github.com/UCSD-E4E/PyHa into TweetyNet-Testing ([`4dbef91`](https://github.com/UCSD-E4E/PyHa/commit/4dbef91006a6d1dc22469a2e6b0b94e9c3ffee47)) +* Create IsoAutio.svg -* Moved testing scripts to testing folder ([`20c1536`](https://github.com/UCSD-E4E/PyHa/commit/20c15362a70682c07cdfc1051173a38bf7b7ec03)) +* Delete ver3_zoo8.svg -* Merge branch 'TweetyNet-Testing' of https://github.com/UCSD-E4E/PyHa into TweetyNet-Testing ([`d1b2fbd`](https://github.com/UCSD-E4E/PyHa/commit/d1b2fbda00b40194099db053a6164a21be27eef2)) +* Delete ver3_zoo5.svg -* added tweetynet documentation ([`b113ac1`](https://github.com/UCSD-E4E/PyHa/commit/b113ac1b5cdd3a113617f97db0083baa518e5897)) +* Delete ver3_zoo1.svg -* Fixed spectrogram_graph visualization to readme ([`2d672f0`](https://github.com/UCSD-E4E/PyHa/commit/2d672f06fa082a00dbab7efbf942f95bd2f02ff3)) +* Delete ver3_zoo2.svg -* Added chunk isolate to testing suite ([`5f6ce9f`](https://github.com/UCSD-E4E/PyHa/commit/5f6ce9f9d0664bd1c6a17c8795673a3a60e0436b)) +* Delete ver2.svg -* added model comparison and spectrogram vis testing ([`6ca7ff4`](https://github.com/UCSD-E4E/PyHa/commit/6ca7ff439a12575023587c1bd45145ebb8a9fd50)) +* Delete ver1.svg -* Fixed FutureError warnings +* Create PyHa -For tweetynet, fixed the liborsa warnings output by adding adtional augrement ([`ca4d4f5`](https://github.com/UCSD-E4E/PyHa/commit/ca4d4f5886019b446ce24916ba2021a830e1b589)) +* Rename PyHa to PyHa.svg -* added batch testing ([`361d27d`](https://github.com/UCSD-E4E/PyHa/commit/361d27dbd915fa6914032c86395cd91bf4932535)) +* Delete ver3_zoo3.svg -* Meant to be in the conda_environments folder ([`72a2dec`](https://github.com/UCSD-E4E/PyHa/commit/72a2dec12917781bc273d1fea90fc22a0ab567bd)) +* Delete ver3_zoo7.svg -* Updated Most Recent Ubuntu Conda Environment with PyTorch +* Delete artwork -- PyTorch is required for TweetyNET ([`7c1a806`](https://github.com/UCSD-E4E/PyHa/commit/7c1a806b64fa5a4e9974a10cfe4a34b13ccc98e8)) +* Created separate folder for conda environments, added Ubuntu 18.04 environment -* Updated Tutorial Notebook +* Removing old Ubuntu 16.04 environment -- Trimmed some unnecessary tweetynet isolation parameters -- Removed unnecessary import of torch. ([`46b5e13`](https://github.com/UCSD-E4E/PyHa/commit/46b5e13cb8623e1df01d464fb76a3503de3b2720)) +No longer needed since the last commit added the conda_environments folder -* Refactor TweetyNET automated label gen/visualizations +* Added in a Windows 10 environment file -- removes the tweety_output bool and moves it to isolation_parameters dict -- updates local_score_visualization() function to reflect spectrogram_visualization() name change and organization -- removes TweetyNET tutorial and a handful of test files -- README documentation for TweetyNet parameters and generate_automated_labels_tweetynet() ([`1ac5554`](https://github.com/UCSD-E4E/PyHa/commit/1ac5554731c434d188c27bb91d5f4181398d8769)) +Tested on one machine -* Merge pull request #116 from UCSD-E4E/minor_bug_fixes +* Add files via upload -Corrected typos and deleted redundant file ([`f98ba0f`](https://github.com/UCSD-E4E/PyHa/commit/f98ba0f72eda3d83f0ec0e0d0032221231324801)) +Adding environment .yml file for macOS Big Sur 11.4 -* Correct typos and deleted redundant file ([`f2873f6`](https://github.com/UCSD-E4E/PyHa/commit/f2873f611f5f33d669620090e6462af966c2dfb7)) +* isolate function -* Merge branch 'tweetynet_integrations' into TweetyNet_integrations_2_main ([`e55baa3`](https://github.com/UCSD-E4E/PyHa/commit/e55baa3e607155aeeaada4ba0d5899867461fc4c)) +* Update README.md -* updating notebook with tweetynet example ([`5564bd4`](https://github.com/UCSD-E4E/PyHa/commit/5564bd492c9a404bdeed8f26a76929c89c6e4edb)) +* isolation_parameters -* update from microfaune to tweetynet in error message ([`90c0414`](https://github.com/UCSD-E4E/PyHa/commit/90c041451d9cfe24e1fdf3c8ac4a5a8edbed77d4)) +* threshold function -* updating gitignore to ignore pycache in tweetynet_package ([`9cda0e7`](https://github.com/UCSD-E4E/PyHa/commit/9cda0e7c3428f967b9fe64a5ebdd83c1510d5391)) +* return values -* adding environment for windows 10 ([`fb68481`](https://github.com/UCSD-E4E/PyHa/commit/fb6848136694bd30549f49075138cd8583c6dedd)) +* Update README.md -* adding conda environment for macOs ([`1be6fea`](https://github.com/UCSD-E4E/PyHa/commit/1be6fea1cf5594e4bcfa851d3d42a195ef749ad9)) +* Update README.md -* The visualization and creating the automated dataframe works and will now test with various wav files ([`dbe2252`](https://github.com/UCSD-E4E/PyHa/commit/dbe2252f14a34f0fe4e2c1fa8c0334e3ff1177fc)) +* usage -* Update License +* file links -Matching BirdNET-Analyzer instead of old BirdNET-Lite repository ([`97faf00`](https://github.com/UCSD-E4E/PyHa/commit/97faf00bb148c1c2e8e8911253a7d98643eb4295)) +* Locations -* Merge pull request #112 from UCSD-E4E/birdnet_integration +* isolation_parameters update -- Birdnet integration -- Statistics Expansion ([`a6e2ea9`](https://github.com/UCSD-E4E/PyHa/commit/a6e2ea98c29c42ef7144813b45fb98879be7617d)) +* isolation_parameters update -* Merge branch 'birdnet_integration' of https://github.com/UCSD-E4E/PyHa into birdnet_integration ([`9996d48`](https://github.com/UCSD-E4E/PyHa/commit/9996d4838fdf3b58779b0c90db03058fc9af23a9)) +* design -* Adjusted Tutorial Notebook -- Some markdown didn't make sense talking about TPs, FPs, FNs, and TNs in the context of the spectrogram_visualization() changes ([`4f3549d`](https://github.com/UCSD-E4E/PyHa/commit/4f3549dc62d3ba1132cf05032cc069f8418a8efa)) +* Update README.md -* Added Tensorflow 2.8 to windows env ([`6d83f2c`](https://github.com/UCSD-E4E/PyHa/commit/6d83f2c72157b4912daf5e329995bceeb177b39a)) +* Update README.md -* Fix for visualization typechecking +* steinberg_isolate -- Fixed a small bug in spectrogram_visualization() to better handle both bools and dataframes for automated_df -- Added spectrogram_graph(), annotation_duration_histogram() to README ([`1e519c1`](https://github.com/UCSD-E4E/PyHa/commit/1e519c16d0986c5f5cd23ed01c02b58f49cad546)) +* Table of Contents -* Updated License +* PyHa Logo -- Since we are using birdnet source code, we have to reflect their license. -- No commercial use I guess. ([`d4d0592`](https://github.com/UCSD-E4E/PyHa/commit/d4d05922d21f8e53e82f93874d232eea0bdd356d)) +* logo -* Delete LICENSE +* steinberg isolate -Moving to Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) ([`9504fd5`](https://github.com/UCSD-E4E/PyHa/commit/9504fd56060244dd2ac954d1641422b493b5007d)) +* update logo -* Renamed two visualization functions -- Changed local_score_visualization() to spectrogram_visualization() -- Changed plot_bird_label_scores() to binary_visualization() -- Fixed a small bug in spectrogram_visualization() related to an error warning when a dataframe with automated annotations from multiple clips is passed in ([`de5a9e0`](https://github.com/UCSD-E4E/PyHa/commit/de5a9e0de89648c0005d61920a8aca60c9a4ee95)) +* steinberg isolate -* Fixed new Ubuntu 20.04 conda environment placement -- Made sure it is in the conda_environments folder ([`7c873f3`](https://github.com/UCSD-E4E/PyHa/commit/7c873f3abc797da17c3b16a72e2064cf2fa627a4)) +* isolation techniques -* local_scores ability to pass in automated_df (#109) ([`b1d81aa`](https://github.com/UCSD-E4E/PyHa/commit/b1d81aaa21a2c8fa5e1e431f4286814036e25cf3)) +* rename variables -* local_score_visualization for non-Microfaune +* generate_automated_labels -currently calls generate_automated_labels on the single clip - will refactor in a different commit to handle if an already made automated_df is passed in ([`261fee7`](https://github.com/UCSD-E4E/PyHa/commit/261fee7d3a637e3e9cc539046bf1059310114142)) +* generate_automated_labels -* fixed merge conflict ([`59b2579`](https://github.com/UCSD-E4E/PyHa/commit/59b2579aa94f442826a9960e5b27ce8bcafeff8e)) +* kaleidoscope_conversion -* got the visualizations to work and fixed the local score output to be more reasonable ([`0aa91d3`](https://github.com/UCSD-E4E/PyHa/commit/0aa91d369802a9175167e882e364b6f522d2ab03)) +* All IsoAudio.py files -* Update README.md +* section headings -Updated example to include the "model" isolation parameter ([`be77ddb`](https://github.com/UCSD-E4E/PyHa/commit/be77ddb3aff8d6c0ba42de3c02075c6a46487ec3)) +* local_line_graph -* Documentation update for new BirdNET-Lite functions ([`e6190c6`](https://github.com/UCSD-E4E/PyHa/commit/e6190c6fc9181dd6a4b38cc7ba163075b51e59b7)) +* local_score_visualization -* Merge branch 'birdnet_integration' of https://github.com/UCSD-E4E/PyHa into birdnet_integration ([`92a31a2`](https://github.com/UCSD-E4E/PyHa/commit/92a31a2f7b0e9ca5adb5aff1115e348aa74d9b9d)) +* plot_bird_label_scores -* Fixed typo -birdnet "model" isolation parameter was mispelled as "birndet" ([`d3b8f02`](https://github.com/UCSD-E4E/PyHa/commit/d3b8f020ca063cac5286d0633b7c3241bb73ed46)) +* All visualizations.py functions -* adding environment with pytorch for tweetynet and fixed pyha tutorial for tweetynet ([`fd8e6ff`](https://github.com/UCSD-E4E/PyHa/commit/fd8e6ff0d1687ea6839ca2a68692c9f0ce271020)) +* comments -* local commit of file ([`ea35605`](https://github.com/UCSD-E4E/PyHa/commit/ea356059aeda26a9b036810567888c806dd8915a)) +* microfaune_package notes -* adding changes for another file ([`7907803`](https://github.com/UCSD-E4E/PyHa/commit/7907803cde8e9ac8031a16affbb239834a07f281)) +* annotation_duration_statistics -* updated files and checkiing results on windows ([`4893339`](https://github.com/UCSD-E4E/PyHa/commit/48933398d8a903ca9d0f7b728ac28a8a10447b52)) +* bird_label_scores -* New Ubuntu 20.04 conda environment +* automated_labeling_statistics -- Upgrades to tensorflow 2.8.0 which is compatible with both Microfaune and BirdNET ([`2e8e3e7`](https://github.com/UCSD-E4E/PyHa/commit/2e8e3e7f8551f18e3e412f4fbe58798508a0189b)) +* global_dataset_statistics -* Merge pull request #108 from shreyasar2202/main +* clip_IOU -Added BirdNet Pipeline ([`ffaec7a`](https://github.com/UCSD-E4E/PyHa/commit/ffaec7ad3aa93b7e58e477706750710387007061)) +* matrix_IoU_Scores -* Added BirdNet Pipeline ([`e3804e2`](https://github.com/UCSD-E4E/PyHa/commit/e3804e201850f6212edf27dc53c6f96ba66047ea)) +* clip_catch -* adding tweetynet model to pyha ([`e3fbbba`](https://github.com/UCSD-E4E/PyHa/commit/e3fbbba2a956923a068cb5760c83e553881cbfbd)) +* global_IOU_Statistics -* Merge branch 'main' of https://github.com/UCSD-E4E/PyHa into main ([`9de4cce`](https://github.com/UCSD-E4E/PyHa/commit/9de4cce8c3595c8f9f9aee7a5a5e929ff808d4ca)) +* dataset_Catch -* Added extra error handling to generate_automated_labels -- Caught the case where an empty wav file is successfully loaded in -- Problem was that in these cases the script would crash whenever the signal was downsampled ([`18e5bf7`](https://github.com/UCSD-E4E/PyHa/commit/18e5bf7e3ff1160f71b05b889104c032e6e7a1ef)) +* dataset_IoU_Statistics -* Merge pull request #99 from sprestrelski/kaleidoscope_folder +* All statistics.py functions -Fix "FOLDER" column Kaleidoscope compatibility ([`1a4cccd`](https://github.com/UCSD-E4E/PyHa/commit/1a4cccd5d1dbccf46c4cc61a0be724e03523cb13)) +* Sections -* Fix "FOLDER" column Kaleidoscope compatibility ([`d6a1069`](https://github.com/UCSD-E4E/PyHa/commit/d6a1069c599b7429f9a5062d89a83da15c86aa0f)) +* sections -* Update IsoAutio.py +* update dataset_IoU_Statistics -- Fixed a comment on the resampling portion of the code base. ([`75cca40`](https://github.com/UCSD-E4E/PyHa/commit/75cca4040e5fca696a51ea1be5e7f2615430c35f)) +* Update image -* Merge pull request #98 from UCSD-E4E/Resampling-generalizability +* Formatting -Made resampling more general ([`8f18854`](https://github.com/UCSD-E4E/PyHa/commit/8f18854f398483392fd5f61fac4f5990333a8d92)) +* Update Image -* Made resampling more general +* Update installation directions -Scipy's resample function allows for both upsampling and downsampling, made sure that this function also includes upsampling, not just downsampling. ([`a8b0c04`](https://github.com/UCSD-E4E/PyHa/commit/a8b0c04e0ae1945c280cb9f4067fcbddb94bb7ba)) +* change to numbered list -* Update README.md (#95) ([`3896104`](https://github.com/UCSD-E4E/PyHa/commit/3896104cf5a9cb8d7f9e2ea102e3f321d048bfeb)) +* Update Installation Directions -* Merge pull request #94 from UCSD-E4E/readme-real-fix +* Update README.md -Fixed broken logo ([`3a94c0f`](https://github.com/UCSD-E4E/PyHa/commit/3a94c0f3accacd88330ad7cb48d627e62a58713d)) +* Examples, Remove "How it Works" -* Fixed broken logo ([`52cfef1`](https://github.com/UCSD-E4E/PyHa/commit/52cfef125e842c5c6bbe49ac4279a7889fa3c15e)) +* Update README.md -* Merge pull request #93 from UCSD-E4E/readme-fix +* Update README.md -Fixed missing logo ([`79d015e`](https://github.com/UCSD-E4E/PyHa/commit/79d015e5dbeff9c342f6b525b631a46e4c24e9c4)) +* isolation params in example -* Update README.md ([`9ae743d`](https://github.com/UCSD-E4E/PyHa/commit/9ae743dcd2b2dbe14c13c0b645ac7b57f657a124)) +* Examples -* Merge pull request #92 from UCSD-E4E/staging +* Update Graphs -Staging ([`bc05e73`](https://github.com/UCSD-E4E/PyHa/commit/bc05e73c25599a5025cf2ed9aea41b8b8c98dd25)) +* Update Style -* Updated Tutorial Notebook -Added more relevant demo of the annotation histogram ([`20d0ad8`](https://github.com/UCSD-E4E/PyHa/commit/20d0ad81b9209e34eda6e1f375fa6e34bd8ed506)) +* Credit -* Annotation Length Histograms (#89) +* Credit update -* move from old branch - -* update tutorial - -* update - -* Add parameters update to match - -* update tutorial ([`aecd8f5`](https://github.com/UCSD-E4E/PyHa/commit/aecd8f5b7dfe837b09d7cccdcf312bb6142e51ab)) +* Credits updates -* Merge pull request #81 from UCSD-E4E/linting +* Update README.md -Initial linting with PEP8 ([`a2d7299`](https://github.com/UCSD-E4E/PyHa/commit/a2d729961ad6ad60d14da5dcf27f338f31edfa20)) +removed "Install Jupyter Notebook" step +This should be accomplished by the conda environment install. -* Merge branch 'staging' into linting ([`9a0fed3`](https://github.com/UCSD-E4E/PyHa/commit/9a0fed31a2cc0db242c8bacd9bc6d054df7d1716)) +* Update README.md -* Merge pull request #87 from UCSD-E4E/gitignore +Adjusted Examples portion. Results were created and pushed from my Linux Mint laptop which is built off of Ubuntu 16.04 -Created a .gitignore file ([`da2989b`](https://github.com/UCSD-E4E/PyHa/commit/da2989b277f04787c39f92254c82b4faa62f4e02)) +* Update Readme.md with relevant Screaming Piha Test set information -* deleted pycaches ([`365e900`](https://github.com/UCSD-E4E/PyHa/commit/365e90041c992336e1fc6fa605bd455f01be11a0)) +Would be smart to get someone that is new with PyHa to see if they can easily get things up and running simply by reading the readme. I also added in more details to the steps to make them more foolproof, might be overkill. -* gitignore ([`27cc011`](https://github.com/UCSD-E4E/PyHa/commit/27cc011bdb881fc8897d3731d79b444073d4347c)) +* Updated Images -* Readme (#86) +Co-authored-by: Jacob +Co-authored-by: NathalieFranklin <69173439+NathalieFranklin@users.noreply.github.com> +Co-authored-by: Jacob +Co-authored-by: mugen13lue <33683103+mugen13lue@users.noreply.github.com> ([`796bd94`](https://github.com/UCSD-E4E/PyHa/commit/796bd94d7a8a9881ec3119b052bc8b7a876d3573)) -* Update README.md - -removed last remnant of old name on this branch - -* Create artwork - -* Add files via upload - -* Update ver3 zoo2.svg - -* Update ver3 zoo2.svg - -* Delete ver3 zoo2.svg - -* Delete ver3 zoo3.svg - -* Delete ver3 zoo5.svg - -* Add files via upload - -* Add files via upload - -* Add files via upload - -* Add files via upload - -* Add files via upload - -* Add files via upload - -* Add files via upload - -* Create IsoAutio.svg - -* Delete ver3_zoo8.svg - -* Delete ver3_zoo5.svg - -* Delete ver3_zoo1.svg - -* Delete ver3_zoo2.svg - -* Delete ver2.svg - -* Delete ver1.svg - -* Create PyHa - -* Rename PyHa to PyHa.svg - -* Delete ver3_zoo3.svg - -* Delete ver3_zoo7.svg - -* Delete artwork - -* Created separate folder for conda environments, added Ubuntu 18.04 environment - -* Removing old Ubuntu 16.04 environment - -No longer needed since the last commit added the conda_environments folder - -* Added in a Windows 10 environment file - -Tested on one machine - -* Add files via upload - -Adding environment .yml file for macOS Big Sur 11.4 - -* isolate function - -* Update README.md - -* isolation_parameters - -* threshold function - -* return values - -* Update README.md - -* Update README.md - -* usage - -* file links - -* Locations - -* isolation_parameters update - -* isolation_parameters update - -* design - -* Update README.md - -* Update README.md - -* steinberg_isolate - -* Table of Contents - -* PyHa Logo - -* logo - -* steinberg isolate - -* update logo - -* steinberg isolate - -* isolation techniques - -* rename variables - -* generate_automated_labels - -* generate_automated_labels - -* kaleidoscope_conversion - -* All IsoAudio.py files - -* section headings - -* local_line_graph - -* local_score_visualization - -* plot_bird_label_scores - -* All visualizations.py functions - -* comments - -* microfaune_package notes - -* annotation_duration_statistics - -* bird_label_scores - -* automated_labeling_statistics - -* global_dataset_statistics - -* clip_IOU - -* matrix_IoU_Scores - -* clip_catch - -* global_IOU_Statistics - -* dataset_Catch - -* dataset_IoU_Statistics - -* All statistics.py functions - -* Sections - -* sections - -* update dataset_IoU_Statistics - -* Update image - -* Formatting - -* Update Image - -* Update installation directions - -* change to numbered list - -* Update Installation Directions - -* Update README.md - -* Examples, Remove "How it Works" - -* Update README.md - -* Update README.md - -* isolation params in example - -* Examples - -* Update Graphs - -* Update Style - -* Credit - -* Credit update - -* Credits updates - -* Update README.md - -removed "Install Jupyter Notebook" step -This should be accomplished by the conda environment install. - -* Update README.md - -Adjusted Examples portion. Results were created and pushed from my Linux Mint laptop which is built off of Ubuntu 16.04 - -* Update Readme.md with relevant Screaming Piha Test set information - -Would be smart to get someone that is new with PyHa to see if they can easily get things up and running simply by reading the readme. I also added in more details to the steps to make them more foolproof, might be overkill. - -* Updated Images - -Co-authored-by: Jacob <jgayers@ucsd.edu> -Co-authored-by: NathalieFranklin <69173439+NathalieFranklin@users.noreply.github.com> -Co-authored-by: Jacob <jacobthescreenwriter@gmail.com> -Co-authored-by: mugen13lue <33683103+mugen13lue@users.noreply.github.com> ([`796bd94`](https://github.com/UCSD-E4E/PyHa/commit/796bd94d7a8a9881ec3119b052bc8b7a876d3573)) - -* Revert "Address Linting Warnings" -- Local repo wasn't properly updated, leading to the undoing of important recent readme PR request +* Revert "Address Linting Warnings" +- Local repo wasn't properly updated, leading to the undoing of important recent readme PR request This reverts commit 684a03c9e4af97dd0a3d0e5c30b713969a8e1440. ([`3bb9c8a`](https://github.com/UCSD-E4E/PyHa/commit/3bb9c8a35b421fe2ed256d0b2f72997a1f5e842c)) * Address Linting Warnings - Related to unused variables - Fixed IsoAutio import in the visualizations.py file -- master_clips_stats_df ==> master_clip_stats_df ([`684a03c`](https://github.com/UCSD-E4E/PyHa/commit/684a03c9e4af97dd0a3d0e5c30b713969a8e1440)) - -* removed all whitespace and styling errors ([`0a5a879`](https://github.com/UCSD-E4E/PyHa/commit/0a5a879bba9009d7adc06386a163a7b41c8dbdf1)) - -* IsoAutio.py update ([`331c1aa`](https://github.com/UCSD-E4E/PyHa/commit/331c1aa23928b0d5f9c1d604a0ef7c80c375f400)) +- master_clips_stats_df ==> master_clip_stats_df ([`684a03c`](https://github.com/UCSD-E4E/PyHa/commit/684a03c9e4af97dd0a3d0e5c30b713969a8e1440)) * Reworked audio test set. - Decided it best to use the Creative Commons xeno-canto data -- Decided it best to stick to Screaming Piha audio to honor the package's name +- Decided it best to stick to Screaming Piha audio to honor the package's name - Had to update the Jupyter Notebook tutorial with the new dataset - Deleted the audio, new update in the readme branch will link to a public drive with the relevant test set - Replaced the old labels from the old test set with the labels for the new screaming piha dataset. ([`62ba381`](https://github.com/UCSD-E4E/PyHa/commit/62ba3815880765236f4d3dc679120aca393dedcf)) +* removed all whitespace and styling errors ([`0a5a879`](https://github.com/UCSD-E4E/PyHa/commit/0a5a879bba9009d7adc06386a163a7b41c8dbdf1)) + +* IsoAutio.py update ([`331c1aa`](https://github.com/UCSD-E4E/PyHa/commit/331c1aa23928b0d5f9c1d604a0ef7c80c375f400)) + * initial linting with pep8 ([`13fcab1`](https://github.com/UCSD-E4E/PyHa/commit/13fcab1f024983a0aa3afa433d77dd3c29fa2aa3)) * Merge pull request #80 from UCSD-E4E/staging @@ -1068,7 +1140,7 @@ Staging ([`440cab6`](https://github.com/UCSD-E4E/PyHa/commit/440cab643d87524bfd6 Staging ([`e82aa02`](https://github.com/UCSD-E4E/PyHa/commit/e82aa02f6505921cd43291ed7f9193fcbb44a92b)) * Fixed PyHa Tutorial Notebook -- Recent commit didn't display everything ([`530bd33`](https://github.com/UCSD-E4E/PyHa/commit/530bd33d7ee63087f8fa28a13ad6f028a007e7ff)) +- Recent commit didn't display everything ([`530bd33`](https://github.com/UCSD-E4E/PyHa/commit/530bd33d7ee63087f8fa28a13ad6f028a007e7ff)) * Improved visualizations.py error handling - local_score_visualization() lets you know which clip failed to receive microfaune predictions ([`663f3be`](https://github.com/UCSD-E4E/PyHa/commit/663f3bec1c0f354676e53233813942dac71d3aab)) @@ -1109,7 +1181,7 @@ Staging ([`29aabca`](https://github.com/UCSD-E4E/PyHa/commit/29aabca44f5e785ca80 * Forgot to add continue to previous commit ([`e071979`](https://github.com/UCSD-E4E/PyHa/commit/e07197934651c082796400a13b2fdefce0f97312)) * Added try-except block to handle faulty wav files -- Found in situations where you want to run an isolation algorithm across a large set of wave files that haven't been properly vetted for various problems that can occur. Such as RIFX instead of RIFF or wave files that were created but failed to actually record anything and are empty. +- Found in situations where you want to run an isolation algorithm across a large set of wave files that haven't been properly vetted for various problems that can occur. Such as RIFX instead of RIFF or wave files that were created but failed to actually record anything and are empty. - I am not that experienced with error handling, but this change made it work on a large folder filled with Audiomoth clips that had tons of errors ([`fcf6729`](https://github.com/UCSD-E4E/PyHa/commit/fcf67296a11dc18d86d83f2f019942f86412b21c)) * Merge pull request #68 from UCSD-E4E/Environment @@ -1158,18 +1230,6 @@ New art for read me ([`bee421e`](https://github.com/UCSD-E4E/PyHa/commit/bee421e * Create IsoAutio.svg ([`5aefe43`](https://github.com/UCSD-E4E/PyHa/commit/5aefe4356438284ed45bbdaf2a43b3a07ab7857c)) -* Merge pull request #65 from UCSD-E4E/staging - -Staging ([`c018e4f`](https://github.com/UCSD-E4E/PyHa/commit/c018e4f3f7243e6e2857e551cf798ca6d6d651dc)) - -* Updated PyHa tutorial with statistics changes ([`07d2668`](https://github.com/UCSD-E4E/PyHa/commit/07d266855db3589381e4c8462c29f7023727aac3)) - -* IoU code added to automated_labeling_statistics -- Still need to make code general to multiple classes, might rename automated_labeling statistics to class_automated_labeling_statistics -- Some functionality needs to be included in this function, but I want to make sure I have a strong game plan of how to include said features -- These include allowing for two outputs, such as having the global statistics imbued in this function. This could also include having the dataset_IoU functionality where all of the IoU scores are attached to the manual dataframe -- For right now this is a good step in the direction of streamlining the code base. ([`2946356`](https://github.com/UCSD-E4E/PyHa/commit/294635697ee0d9dfcf3d25082fbffae8daf73c95)) - * Add files via upload ([`4f8e778`](https://github.com/UCSD-E4E/PyHa/commit/4f8e778e172375116b8e0bc88428177f26c86570)) * Add files via upload ([`82ecf3b`](https://github.com/UCSD-E4E/PyHa/commit/82ecf3be0a9be6b61ace4c96a69af10391b5ea31)) @@ -1198,6 +1258,18 @@ Staging ([`c018e4f`](https://github.com/UCSD-E4E/PyHa/commit/c018e4f3f7243e6e285 * Create artwork ([`7d9b0d5`](https://github.com/UCSD-E4E/PyHa/commit/7d9b0d502413c8e43e000fe1cc6e0eaaf5b3743b)) +* Merge pull request #65 from UCSD-E4E/staging + +Staging ([`c018e4f`](https://github.com/UCSD-E4E/PyHa/commit/c018e4f3f7243e6e2857e551cf798ca6d6d651dc)) + +* Updated PyHa tutorial with statistics changes ([`07d2668`](https://github.com/UCSD-E4E/PyHa/commit/07d266855db3589381e4c8462c29f7023727aac3)) + +* IoU code added to automated_labeling_statistics +- Still need to make code general to multiple classes, might rename automated_labeling statistics to class_automated_labeling_statistics +- Some functionality needs to be included in this function, but I want to make sure I have a strong game plan of how to include said features +- These include allowing for two outputs, such as having the global statistics imbued in this function. This could also include having the dataset_IoU functionality where all of the IoU scores are attached to the manual dataframe +- For right now this is a good step in the direction of streamlining the code base. ([`2946356`](https://github.com/UCSD-E4E/PyHa/commit/294635697ee0d9dfcf3d25082fbffae8daf73c95)) + * Update README.md removed last remnant of old name on this branch ([`b5a2525`](https://github.com/UCSD-E4E/PyHa/commit/b5a252523cb6f70f6a1fc1241ea65301e15699e8)) @@ -1206,16 +1278,16 @@ removed last remnant of old name on this branch ([`b5a2525`](https://github.com/ Staging ([`b50ea74`](https://github.com/UCSD-E4E/PyHa/commit/b50ea7455d87da5a7b4aa8ba3236fef91b95234b)) -* Merge branch 'staging' of https://github.com/UCSD-E4E/PyHa into staging ([`d05d5f8`](https://github.com/UCSD-E4E/PyHa/commit/d05d5f8048b1060f713852b3397aee6c2f61197e)) - -* Fleshed out documentation on statistics.py -- Added in first pass of documentation to IoU statistics related functions -- Added more descriptions that are with respect to how the project has evolved in the recent months. ([`017a336`](https://github.com/UCSD-E4E/PyHa/commit/017a336e934d510e13be0b5055cf7d44a84fdd44)) +* Merge branch 'staging' of https://github.com/UCSD-E4E/PyHa into staging ([`d05d5f8`](https://github.com/UCSD-E4E/PyHa/commit/d05d5f8048b1060f713852b3397aee6c2f61197e)) * Merge pull request #59 from UCSD-E4E/main Synchronizing Master and Main ([`16affb4`](https://github.com/UCSD-E4E/PyHa/commit/16affb4d9d1b2e0d8df2b80354d16a60048d92ee)) +* Fleshed out documentation on statistics.py +- Added in first pass of documentation to IoU statistics related functions +- Added more descriptions that are with respect to how the project has evolved in the recent months. ([`017a336`](https://github.com/UCSD-E4E/PyHa/commit/017a336e934d510e13be0b5055cf7d44a84fdd44)) + * Fleshed out Documentation of IsoAutio functions - Pseudocode has been added to all 4 current isolation techniques - Adjusted all function docstrings for their new parameters @@ -1246,8 +1318,8 @@ Master ([`6281cc3`](https://github.com/UCSD-E4E/PyHa/commit/6281cc3d18fd2a65b9bf * Delete IsoAutio directory -- Transitioning from IsoAutio as the working title to PyHa as the name of the Python package. -- isolation.py has already been renamed to IsoAutio.py +- Transitioning from IsoAutio as the working title to PyHa as the name of the Python package. +- isolation.py has already been renamed to IsoAutio.py - All of the logic in this directory is now in the PyHa directory. Plus I made a couple of changes directly to PyHa before deleting this. ([`bd900b3`](https://github.com/UCSD-E4E/PyHa/commit/bd900b3fff8246fb15bfe1f55d44b261fc7dbe9c)) * Delete IsoAutio_Tutorial.ipynb @@ -1255,9 +1327,9 @@ Master ([`6281cc3`](https://github.com/UCSD-E4E/PyHa/commit/6281cc3d18fd2a65b9bf Replaced with PyHa_Tutorial.ipynb ([`faa708e`](https://github.com/UCSD-E4E/PyHa/commit/faa708e6c5a95d67be631bda06e449980565d263)) * Fixed PyHa_Tutorial Jupyter Notebook -- The outputs weren't compiled ([`0fe1d2c`](https://github.com/UCSD-E4E/PyHa/commit/0fe1d2c71b3560be66678d66c046dd85fec4e1c2)) +- The outputs weren't compiled ([`0fe1d2c`](https://github.com/UCSD-E4E/PyHa/commit/0fe1d2c71b3560be66678d66c046dd85fec4e1c2)) -* Adjusting some folder and filenames for "PyHa" +* Adjusting some folder and filenames for "PyHa" - Had to modify some files import statements - added some new comments to some functions that I looked back over. - Adjusted the jupyter notebook tutorial ([`f81bf76`](https://github.com/UCSD-E4E/PyHa/commit/f81bf76fa6d37023961a79f82b0c71ed91db7338)) @@ -1283,7 +1355,7 @@ Added Kaleidoscope converting function ([`eec53f9`](https://github.com/UCSD-E4E/ Master ([`47a1ae3`](https://github.com/UCSD-E4E/PyHa/commit/47a1ae317c061db3126e15fc8794fec92c299dc3)) * Fixed microfaune package import -- Wasn't addressing microfaune_package properly relative to visualizations.py and isolation.py ([`31e58a5`](https://github.com/UCSD-E4E/PyHa/commit/31e58a55500267a19283bee76db51c63b18a073a)) +- Wasn't addressing microfaune_package properly relative to visualizations.py and isolation.py ([`31e58a5`](https://github.com/UCSD-E4E/PyHa/commit/31e58a55500267a19283bee76db51c63b18a073a)) * Reorganized microfaune_local_score.py - Separated it into visualizations.py, statistics.py, and isolation.py all in the IsoAutio folder @@ -1300,9 +1372,9 @@ Removed True Negative from IoU Related Statistics ([`4191d37`](https://github.co * Merge pull request #40 from UCSD-E4E/master -Added in new "chunk" isolation technique ([`163dec4`](https://github.com/UCSD-E4E/PyHa/commit/163dec4c9f87e609230f98a9b07ff0323e3eeeb8)) +Added in new "chunk" isolation technique ([`163dec4`](https://github.com/UCSD-E4E/PyHa/commit/163dec4c9f87e609230f98a9b07ff0323e3eeeb8)) -* Added in new "chunk" isolation technique +* Added in new "chunk" isolation technique - New technique should be handy in situations where audio annotations are a discrete length. Cases such as BirdNET outputs as well as the BirdCLEF2020 labels. - Also handled a bug related to IoU scores in bird_label_score() ([`8a03ffd`](https://github.com/UCSD-E4E/PyHa/commit/8a03ffd6bc32912faba2c0293c17789a726d626c)) @@ -1325,43 +1397,30 @@ Updating Master ([`5d5f800`](https://github.com/UCSD-E4E/PyHa/commit/5d5f800ea9b Jacob glenn ayers patch 1 ([`1a853a1`](https://github.com/UCSD-E4E/PyHa/commit/1a853a1478638b9f9193d2de9896c9cbf5771392)) -* Merge pull request #33 from UCSD-E4E/master - -Master ([`6e41cb5`](https://github.com/UCSD-E4E/PyHa/commit/6e41cb58459ee8d9385ecefbccd632079fdcff95)) - * Adding in fixed Jupyter Notebook Tutorial -Not sure why the Notebook didn't run all of the cells on the last push ([`676e701`](https://github.com/UCSD-E4E/PyHa/commit/676e701d6289ec9b0bce4ae174952641d312f041)) +Not sure why the Notebook didn't run all of the cells on the last push ([`676e701`](https://github.com/UCSD-E4E/PyHa/commit/676e701d6289ec9b0bce4ae174952641d312f041)) * Delete Microfaune_Local_Score_Package_Tutorial.ipynb ([`3420806`](https://github.com/UCSD-E4E/PyHa/commit/3420806dcbed434ecda9cf0ac034f51252d772ed)) -* Fixed Jupyter Notebook Tutorial ([`5e39378`](https://github.com/UCSD-E4E/PyHa/commit/5e3937887af46f6a8b1fc90a35751bdf72b25d68)) +* Merge pull request #33 from UCSD-E4E/master -* Merge branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID.git; branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID -- working to fix the jupyter notebook tutorial ([`8055db6`](https://github.com/UCSD-E4E/PyHa/commit/8055db6eb935ff59226c100ea1201e447c3f4df5)) +Master ([`6e41cb5`](https://github.com/UCSD-E4E/PyHa/commit/6e41cb58459ee8d9385ecefbccd632079fdcff95)) -* Merge branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID ([`81f43ce`](https://github.com/UCSD-E4E/PyHa/commit/81f43cee5f55b818ffcce28c93ee6b6179792ffa)) +* Fixed Jupyter Notebook Tutorial ([`5e39378`](https://github.com/UCSD-E4E/PyHa/commit/5e3937887af46f6a8b1fc90a35751bdf72b25d68)) -* Merge branch 'main' into master ([`104e911`](https://github.com/UCSD-E4E/PyHa/commit/104e911dc517452a852675b3cfa7859bb8a4105d)) +* Merge branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID.git; branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID +- working to fix the jupyter notebook tutorial ([`8055db6`](https://github.com/UCSD-E4E/PyHa/commit/8055db6eb935ff59226c100ea1201e447c3f4df5)) -* Added in new "stack" isolation technique -- Tested to make sure that it integrates into all of the other functions -- Added True Negative values to IoU statistics, updated jupyter notebook accordingly. ([`26f4296`](https://github.com/UCSD-E4E/PyHa/commit/26f429605d388c2905c03ff12ff6226f08a91f5a)) +* Merge branch 'main' into master ([`104e911`](https://github.com/UCSD-E4E/PyHa/commit/104e911dc517452a852675b3cfa7859bb8a4105d)) * Merge pull request #28 from UCSD-E4E/master Enabled user tweaking of isolation parameters ([`8150873`](https://github.com/UCSD-E4E/PyHa/commit/81508734e91eafea2d956f5ea7e70694f5dc81e5)) -* Merge branch 'main' into master ([`d87634c`](https://github.com/UCSD-E4E/PyHa/commit/d87634c25359b8175f891e2601a6d137332c6118)) +* Merge branch 'master' of https://github.com/UCSD-E4E/Automated_Audio_Labelling_System_AID ([`81f43ce`](https://github.com/UCSD-E4E/PyHa/commit/81f43cee5f55b818ffcce28c93ee6b6179792ffa)) -* Enabled user tweaking of isolation parameters -- Encapsulated the "steinberg" and "simple" techniques into a master "isolate" function that is defined by the passed in isolation parameters -- Renamed calc_local_scores() to generate_automated_labels() -- Reworked generate_automated_labels() to take in the isolation parameters dictionary -- Reworked local_score_visualization() to take in the isolation parameters as well as the master isolate() function. -- Deleted the calc_local_scores2() and local_score_visualization2() functions that were designed to demonstrate the simple isolation technique. -- updated jupyter notebook tutorial to demonstrate above changes. -- removed the second howler monkey example clip visualizations as well as the demonstration of "catch" scores since they seem redundant and inflated the size of the tutorial ([`6d4d11b`](https://github.com/UCSD-E4E/PyHa/commit/6d4d11bfa69c83890ddb0820cbb247bbe38fa47b)) +* Merge branch 'main' into master ([`d87634c`](https://github.com/UCSD-E4E/PyHa/commit/d87634c25359b8175f891e2601a6d137332c6118)) * Merge pull request #27 from UCSD-E4E/revise-documentation @@ -1373,69 +1432,82 @@ Add docstring comments to functions ([`12887b6`](https://github.com/UCSD-E4E/PyH Statistics Function for annotation lengths ([`1b402a9`](https://github.com/UCSD-E4E/PyHa/commit/1b402a99dc7248fc311bf501467c4a1b8b1e409f)) -* Statistics Function for annotation lengths -Added in a new function annotation_duration_statistics() which outputs the number of annotations, mode, mean, standard deviation, min, Q1, Median, Q3, and max values with respect to the lengths of the annotations ([`a2ce49c`](https://github.com/UCSD-E4E/PyHa/commit/a2ce49c9f6e8be82d36f1eb2857dc9ca67b326cb)) - * update documentation with arg types ([`4ebea63`](https://github.com/UCSD-E4E/PyHa/commit/4ebea6307a8e27300f48bde241d6a34e0f38d2f8)) * merge commit ([`6fe57a0`](https://github.com/UCSD-E4E/PyHa/commit/6fe57a0d6dee7b2e0210f363da2c53dfd5d2d14e)) -* added docstring documentation ([`efe3462`](https://github.com/UCSD-E4E/PyHa/commit/efe34626a1ba63b6d546a12ec46f6a7718803e51)) - * Merge pull request #24 from UCSD-E4E/master Added log scale functionality to visualizations ([`9c5d4ef`](https://github.com/UCSD-E4E/PyHa/commit/9c5d4ef9c3ead7a96fc5b82366b2b1d18de50c0a)) -* Added log scale functionality to visualizations -This makes it easier on human eyes. Have local_score_visualization() defaulted to a linear scale fixed between [0,1] ([`0d06b02`](https://github.com/UCSD-E4E/PyHa/commit/0d06b02dd775038fca748af115f84c38d52befe3)) - * Merge pull request #21 from UCSD-E4E/master Quick fix to Jupyter Tutorial ([`8aa7595`](https://github.com/UCSD-E4E/PyHa/commit/8aa759545296a9724e783b2b19b8847db63251f1)) -* Quick fix to Jupyter Tutorial -Made sure new changes with new isolation technique show up compiled in the tutorial ([`939159c`](https://github.com/UCSD-E4E/PyHa/commit/939159c253d43011e0b30322f03c8be800714b44)) - * Merge pull request #20 from UCSD-E4E/master Developed Simpler Approach to Isolating Calls ([`d21c682`](https://github.com/UCSD-E4E/PyHa/commit/d21c682712f6de2ebc0d35c0071a6a5b66a41e32)) -* Developed Simpler Approach to Isolating Calls -Any local score >= some threshold is automatically set to a bird call. Will continue as long as there are multiple scores in a row above the threshold. To display, required me to create two new functions that server the purpose of visualization as well as calculating the scores over a folder of wav files. This is a horrendous solution creating two new functions, so I have to go back and rework calc_local_scores() and local_score_visualization() to support different types of isolation. This is something that should be done when I rework Isolate for gradient descent. ([`cadbb09`](https://github.com/UCSD-E4E/PyHa/commit/cadbb097a057464c51a3f8e8b50bda5d05ab60ba)) - * Merge pull request #19 from UCSD-E4E/master Added Recall and F1 scores to IoU Statistics ([`aced641`](https://github.com/UCSD-E4E/PyHa/commit/aced6414e9d34689bc2845fbddecd3c2bd111078)) -* Added Recall and F1 scores to IoU Statistics -This involved calculating the number of false negatives in the IoU Matrix scores functions ([`4d55bab`](https://github.com/UCSD-E4E/PyHa/commit/4d55babc4b130d4466cddb081161d550397dca28)) - * Merge pull request #18 from UCSD-E4E/master Added comments and improved readability of isolate ([`712d5be`](https://github.com/UCSD-E4E/PyHa/commit/712d5be296872caab9b78c5be951614a23d9df12)) -* Added comments and improved readability of isolate -Laid out the plan for changes to be made to isolate function in order to perform gradient descent. ([`f916a0c`](https://github.com/UCSD-E4E/PyHa/commit/f916a0c6b6963854f4bba7b79e7670414b0166be)) - * Merge pull request #16 from UCSD-E4E/master Added Precision Statistics for IoU Scores ([`bc9d80e`](https://github.com/UCSD-E4E/PyHa/commit/bc9d80e7583daea8bc1ee716b8c6d149117785a7)) -* Added Precision Statistics for IoU Scores -This involves a couple new functions that have been updated on the jupyter notebook tutorial. I also added a bunch of comments to microfaune_local_score.py ([`06d9658`](https://github.com/UCSD-E4E/PyHa/commit/06d9658b06575c954f200b0c765e97d633fd7398)) - * Merge pull request #14 from UCSD-E4E/master Added label-by-label IoU and Catch Scores ([`ea030d0`](https://github.com/UCSD-E4E/PyHa/commit/ea030d0c06a3e7a39317ba07a813315dcdeed581)) -* Included clip-by-clip IoU and Catch Scores ([`294e079`](https://github.com/UCSD-E4E/PyHa/commit/294e079f90f8026c44d04e62a32a313777a4c929)) +* added docstring documentation ([`efe3462`](https://github.com/UCSD-E4E/PyHa/commit/efe34626a1ba63b6d546a12ec46f6a7718803e51)) * Added conda environment.yaml file ([`1a710bb`](https://github.com/UCSD-E4E/PyHa/commit/1a710bbfb67653254b6aeb084ff03326e7d3bacd)) -* Included Conda Environment Information ([`3edcabb`](https://github.com/UCSD-E4E/PyHa/commit/3edcabb9dbac58791aa7bec34311e70a9c4b01e4)) - * Delete ScreamingPiha2_Manual_Labels.csv ([`2827d38`](https://github.com/UCSD-E4E/PyHa/commit/2827d38041c8afee5935979e864cc34b4f593370)) +* Added in new "stack" isolation technique +- Tested to make sure that it integrates into all of the other functions +- Added True Negative values to IoU statistics, updated jupyter notebook accordingly. ([`26f4296`](https://github.com/UCSD-E4E/PyHa/commit/26f429605d388c2905c03ff12ff6226f08a91f5a)) + +* Enabled user tweaking of isolation parameters +- Encapsulated the "steinberg" and "simple" techniques into a master "isolate" function that is defined by the passed in isolation parameters +- Renamed calc_local_scores() to generate_automated_labels() +- Reworked generate_automated_labels() to take in the isolation parameters dictionary +- Reworked local_score_visualization() to take in the isolation parameters as well as the master isolate() function. +- Deleted the calc_local_scores2() and local_score_visualization2() functions that were designed to demonstrate the simple isolation technique. +- updated jupyter notebook tutorial to demonstrate above changes. +- removed the second howler monkey example clip visualizations as well as the demonstration of "catch" scores since they seem redundant and inflated the size of the tutorial ([`6d4d11b`](https://github.com/UCSD-E4E/PyHa/commit/6d4d11bfa69c83890ddb0820cbb247bbe38fa47b)) + +* Statistics Function for annotation lengths +Added in a new function annotation_duration_statistics() which outputs the number of annotations, mode, mean, standard deviation, min, Q1, Median, Q3, and max values with respect to the lengths of the annotations ([`a2ce49c`](https://github.com/UCSD-E4E/PyHa/commit/a2ce49c9f6e8be82d36f1eb2857dc9ca67b326cb)) + +* Added log scale functionality to visualizations +This makes it easier on human eyes. Have local_score_visualization() defaulted to a linear scale fixed between [0,1] ([`0d06b02`](https://github.com/UCSD-E4E/PyHa/commit/0d06b02dd775038fca748af115f84c38d52befe3)) + +* Quick fix to Jupyter Tutorial +Made sure new changes with new isolation technique show up compiled in the tutorial ([`939159c`](https://github.com/UCSD-E4E/PyHa/commit/939159c253d43011e0b30322f03c8be800714b44)) + +* Developed Simpler Approach to Isolating Calls +Any local score >= some threshold is automatically set to a bird call. Will continue as long as there are multiple scores in a row above the threshold. To display, required me to create two new functions that server the purpose of visualization as well as calculating the scores over a folder of wav files. This is a horrendous solution creating two new functions, so I have to go back and rework calc_local_scores() and local_score_visualization() to support different types of isolation. This is something that should be done when I rework Isolate for gradient descent. ([`cadbb09`](https://github.com/UCSD-E4E/PyHa/commit/cadbb097a057464c51a3f8e8b50bda5d05ab60ba)) + +* Added Recall and F1 scores to IoU Statistics +This involved calculating the number of false negatives in the IoU Matrix scores functions ([`4d55bab`](https://github.com/UCSD-E4E/PyHa/commit/4d55babc4b130d4466cddb081161d550397dca28)) + +* Added comments and improved readability of isolate +Laid out the plan for changes to be made to isolate function in order to perform gradient descent. ([`f916a0c`](https://github.com/UCSD-E4E/PyHa/commit/f916a0c6b6963854f4bba7b79e7670414b0166be)) + +* Added Precision Statistics for IoU Scores +This involves a couple new functions that have been updated on the jupyter notebook tutorial. I also added a bunch of comments to microfaune_local_score.py ([`06d9658`](https://github.com/UCSD-E4E/PyHa/commit/06d9658b06575c954f200b0c765e97d633fd7398)) + +* Included clip-by-clip IoU and Catch Scores ([`294e079`](https://github.com/UCSD-E4E/PyHa/commit/294e079f90f8026c44d04e62a32a313777a4c929)) + +* Included Conda Environment Information ([`3edcabb`](https://github.com/UCSD-E4E/PyHa/commit/3edcabb9dbac58791aa7bec34311e70a9c4b01e4)) + * Added IoU Scores and Microfaune Package ([`510fd60`](https://github.com/UCSD-E4E/PyHa/commit/510fd6054b9002921b9e5e94cade382d0df0beab)) * Extra Files for Tutorial.