Merge branch 'main' into refactor-for-dataflow-runner

.github/workflows/python-test.yml

@@ -3,18 +3,18 @@ name: Python Tests
 on:
   push:
     branches:
-      - master  # Runs on push to the master branch
+      - main  # Runs on push to the main branch
   pull_request:
     branches:
-      - master  # Runs on pull requests to the master branch
+      - main  # Runs on pull requests to the main branch
 
 jobs:
   test:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        python-version: [3.11] # [3.9, 3.11]  # You can add or remove Python versions to test against
+        python-version: [3.11] 
 
     steps:
     - name: Checkout repository

.github/workflows/todo.yml

@@ -0,0 +1,24 @@
+name: "Run TODO to Issue"
+on:
+  push:
+    branches:
+      - "main"
+  workflow_dispatch:
+    inputs:
+      MANUAL_COMMIT_REF:
+        description: "The SHA of the commit to get the diff for"
+        required: true
+      MANUAL_BASE_REF:
+        description: "By default, the commit entered above is compared to the one directly before it; to go back further, enter an earlier SHA here"
+        required: false
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: "TODO to Issue"
+        uses: "alstr/todo-to-issue-action@v5"
+        env:
+          MANUAL_COMMIT_REF:
+            ${{ inputs.MANUAL_COMMIT_REF }}
+          MANUAL_BASE_REF:
+            ${{ inputs.MANUAL_BASE_REF }}

.gitignore

@@ -1,7 +1,10 @@
 # Repo specific ignores
 audio/
+classifications/
 plots/
 model/
+hide/
+table/
 
 # Python basic ignores
 # Byte-compiled / optimized / DLL files

README.md

@@ -6,22 +6,29 @@ Derived from <a href="https://docs.mbari.org/pacific-sound/notebooks/humpbackwha
 </sub>
 
 
-## Installation
-M1:
+## Getting started
+
+### Install
+#### M1:
 ```bash
 CONDA_SUBDIR=osx-arm64 conda create -n whale-speech python=3.11
 conda activate whale-speech
 pip install -r requirements.txt
 ```
 
 
-Other:
+#### Other:
 ```bash
 conda create -n whale-speech python=3.11
 conda activate whale-speech
 pip install -r requirements.txt
 ```
 
+### Run locally 
+```bash
+make local-run
+```
+
 ## Pipeline description
 
 Stages:
@@ -49,7 +56,7 @@ Stages:
 7. **Output**: Map the whale encounter ids to the playback snippets.
 
 <!-- Light mode -->
-[![](https://mermaid.ink/img/pako:eNpVkctOwzAQRX_FmhVIadWm7yyQ-i4SCERZ0XThOpPEkhMXP4BQ9d9xE4PobOw7Ptcz9pyAyQQhglTIT5ZTZcjrIi6Ji-kupVFKW4wKLBOqyH15tEbvSat1R2Y3zWEm5AHJGmWBRlVki1Sx_NZfUJNzTxZWc0ZeHMY_kExtwqXnZg3XiHktlt6UcmFQkZVfFL5bLFnljcuaXXn2YIXQWCGZC6o1T6urIquaXXvW0Iw8S22OSjLUmjzQAwrt0XWNbna_LeicPFnj3r7_3--GXBQEUKAqKE_cH54umRhMjgXGELltgim1wsQQl2eHUmvktioZREZZDEBJm-XgqrjGA7DHhBpccJopWvxlj7R8k_JKQ3SCL4h6nbDdHYfd8XAwmfTD3rAXQAVR5xzAd-3otCdNjMJBOBj1x6MAMOFGqsdm6PXszz-lFp4w?type=png)](https://mermaid.live/edit#pako:eNpVkctOwzAQRX_FmhVIadWm7yyQ-i4SCERZ0XThOpPEkhMXP4BQ9d9xE4PobOw7Ptcz9pyAyQQhglTIT5ZTZcjrIi6Ji-kupVFKW4wKLBOqyH15tEbvSat1R2Y3zWEm5AHJGmWBRlVki1Sx_NZfUJNzTxZWc0ZeHMY_kExtwqXnZg3XiHktlt6UcmFQkZVfFL5bLFnljcuaXXn2YIXQWCGZC6o1T6urIquaXXvW0Iw8S22OSjLUmjzQAwrt0XWNbna_LeicPFnj3r7_3--GXBQEUKAqKE_cH54umRhMjgXGELltgim1wsQQl2eHUmvktioZREZZDEBJm-XgqrjGA7DHhBpccJopWvxlj7R8k_JKQ3SCL4h6nbDdHYfd8XAwmfTD3rAXQAVR5xzAd-3otCdNjMJBOBj1x6MAMOFGqsdm6PXszz-lFp4w)
+[![](https://mermaid.ink/img/pako:eNpVkl1PwjAUhv_KybnSZBAYIrAYE0VBE41GvNJxUbqzrUm3Yj_USfjvlq0aPTfte_qcz3SHXGWECeZSffCSaQvPV2kN3i5ec5bkrMeZpDpjGm7rrbNmDb3eOVwedY-FVBuCJamKrG5gRUzz8jgkaMl5ICtnBIcnj4l3gguXCRW4y47rxLwV1yEoF9KShkU4NL05qnkTAq9bdhHYjZPSUEMwl8wYkTf_iizgrN_39G2gtdooC_d-eOm71u-kf8FD0mXALCvgURm71YqTMXDHNiRNQJctevP606sp4cFZv6T138Fu4KAwwop0xUTml707eFK0JVWUYuKvGeXMSZtiWu89ypxVq6bmmFjtKEKtXFGir-InjNBtM2bpSrBCs-rXu2X1i1L_NCY7_MRkNIj7w2k8nJ6OZ7OTeHQ6irDBZLCP8KuNGPRnnU3icTyenEwnEVImrNL33e_gqs5Fgftv_9OrOw?type=png)](https://mermaid.live/edit#pako:eNpVkl1PwjAUhv_KybnSZBAYIrAYE0VBE41GvNJxUbqzrUm3Yj_USfjvlq0aPTfte_qcz3SHXGWECeZSffCSaQvPV2kN3i5ec5bkrMeZpDpjGm7rrbNmDb3eOVwedY-FVBuCJamKrG5gRUzz8jgkaMl5ICtnBIcnj4l3gguXCRW4y47rxLwV1yEoF9KShkU4NL05qnkTAq9bdhHYjZPSUEMwl8wYkTf_iizgrN_39G2gtdooC_d-eOm71u-kf8FD0mXALCvgURm71YqTMXDHNiRNQJctevP606sp4cFZv6T138Fu4KAwwop0xUTml707eFK0JVWUYuKvGeXMSZtiWu89ypxVq6bmmFjtKEKtXFGir-InjNBtM2bpSrBCs-rXu2X1i1L_NCY7_MRkNIj7w2k8nJ6OZ7OTeHQ6irDBZLCP8KuNGPRnnU3icTyenEwnEVImrNL33e_gqs5Fgftv_9OrOw)
 
 <!-- Dark mode -->
 <!-- [![](https://mermaid.ink/img/pako:eNpVkNtOwzAMhl8l8lWRumnrzrlA2qkbEhKIcQXdRUjdNaJNSg5AmfbuZF2FmK_8-_ud2D4CVykChaxQXzxn2pLnVSKJj_lrxmjGOpwVKFOmyZ2snDV70unckkWwQVWi1TXZIdM8v2mbGroMnjwSn0jmLhWqZYsLu4hlI9ZBLAqLmsQaPxxKXrfedYPjYFkwY0RWXz0UN3ATPCpjK604GkPu2RsWpjVsGsO2XSATJicPzvrp9_8n2Z4FhFCiLplI_RGO50oCNscSE6A-9Xu_J5DIk_cxZ9Wulhyo1Q5D0ModcvA_FMYrV6XM4kqwg2blX7Vi8kWpKw30CN9AB72o259G_el4NJsNo8F4EEINtHcK4afp6HVnl5hEo2g0GU4np1-Ax4B-?type=png)](https://mermaid.live/edit#pako:eNpVkNtOwzAMhl8l8lWRumnrzrlA2qkbEhKIcQXdRUjdNaJNSg5AmfbuZF2FmK_8-_ud2D4CVykChaxQXzxn2pLnVSKJj_lrxmjGOpwVKFOmyZ2snDV70unckkWwQVWi1TXZIdM8v2mbGroMnjwSn0jmLhWqZYsLu4hlI9ZBLAqLmsQaPxxKXrfedYPjYFkwY0RWXz0UN3ATPCpjK604GkPu2RsWpjVsGsO2XSATJicPzvrp9_8n2Z4FhFCiLplI_RGO50oCNscSE6A-9Xu_J5DIk_cxZ9Wulhyo1Q5D0ModcvA_FMYrV6XM4kqwg2blX7Vi8kWpKw30CN9AB72o259G_el4NJsNo8F4EEINtHcK4afp6HVnl5hEo2g0GU4np1-Ax4B-) -->