Replace poetry with uv and update packages

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
 
 jobs:
-  lint:
+  pytest:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
@@ -16,37 +16,15 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: poetry install
-
-      - name: Run pre-commit
-        run: poetry run pre-commit run --all-files
-
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: '3.10'
-
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          version: "0.7.11"
 
       - name: Install dependencies
-        run: poetry install
+        run: uv pip install --system .
 
       - name: Set environment variables
         run: |
@@ -56,16 +34,15 @@ jobs:
       - name: Download and unzip required data files
         run: |
           mkdir -p "$HOME/auv_data"
-          # Dorado389.tar.gz contains original log files of short dorado mission for testing: 2011.256.02
           wget -q --no-check-certificate -O "$HOME/auv_data/Dorado389.tar.gz" https://stoqs.mbari.org/auv_data/Dorado389.tar.gz
           tar -xvf "$HOME/auv_data/Dorado389.tar.gz" -C "$HOME/auv_data" 2> /dev/null
-          # i2MAP.tar.gz contains original log files of i2MAP mission for testing: 2018.34.01
           wget -q --no-check-certificate -O "$HOME/auv_data/i2map.tar.gz" https://stoqs.mbari.org/auv_data/i2map.tar.gz
           tar -xf "$HOME/auv_data/i2map.tar.gz" -C "$HOME/auv_data" 2> /dev/null
-          # i2map processing needs access to calibration files on an on-premisis server, unpack a subset of it here
           wget -q --no-check-certificate -O "$HOME/auv_data/SBE-43.tar.gz" https://stoqs.mbari.org/auv_data/SBE-43.tar.gz
           tar -xf "$HOME/auv_data/SBE-43.tar.gz" -C "$HOME/auv_data" 2> /dev/null
 
+      - name: Install pytest
+        run: uv pip install --system pytest
 
       - name: Run tests
-        run: poetry run pytest
+        run: pytest

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+      with:
+        python-version: '3.12'
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: --all-files
+

.pre-commit-config.yaml

@@ -1,40 +1,7 @@
-exclude: '^notebooks/'
-default_stages: [pre-commit]
-minimum_pre_commit_version: "3.2.0"
-
-default_language_version:
-  python: python3.10
-
+# .pre-commit-config.yaml
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-json
-        exclude: ^.vscode/launch.json$
-      - id: check-toml
-      - id: check-xml
-      - id: check-yaml
-      - id: debug-statements
-      - id: check-builtin-literals
-      - id: check-case-conflict
-      - id: check-docstring-first
-      - id: detect-private-key
-        exclude: ^compose/production/nginx/localhost.key$
-
-  # Run the Ruff linter.
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.2
+    rev: v0.4.4
     hooks:
-      # Linter
       - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
-      # Formatter
-      - id: ruff-format
-
-# sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date
-ci:
-  autoupdate_schedule: weekly
-  skip: []
-  submodules: false
+      - id: ruff-format

.vscode/launch.json

@@ -262,12 +262,13 @@
             //"args": ["-v", "1", "--noinput",  "--start_year", "2016", "--end_year", "2016", "--start_yd", "270", "--end_yd", "270", "--num_cores", "1", "--create_products", "--archive", "--archive_only_products"]
             //"args": ["-v", "1", "--noinput", "--num_cores", "1", "--mission", "2023.285.01"]
             //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2018.079.00"]
-            //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2024.317.01"]
+            "args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2024.317.01", "--clobber"]
             //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2016.090.01", "--resample", "--archive", "--flash_threshold", "3E10"]
             //"args": ["-v", "1", "--noinput", "--num_cores", "8"]
             //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2011.256.02", "--clobber"]
             //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2010.341.00", "--download_process", "--local"]
-            "args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2020.337.00", "--clobber"]
+            //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2020.337.00", "--clobber"]
+            //"args": ["-v", "1", "--noinput", "--no_cleanup",  "--mission", "2008.010.10"]
 
         },
     ]

LICENSE

@@ -1,5 +1,5 @@
 
-Copyright (c) 2021, Mike McCann
+Copyright (c) 2025, Monterey Bay Aquarium Research Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,