Merge branch 'master' into aviti-readmasks

Author: kedhammar

.github/workflows/lint-code.yml

@@ -53,64 +53,27 @@ jobs:
           pip install mypy
       # Start by installing type stubs
       - name: mypy --> Install stubs
-        run: echo -e "y" | mypy --install-types . || exit 0
-      - name: mypy --> Static type checking
-        # Configured in pyprojet.toml
-        run: mypy .
+        run: mypy --install-types --non-interactive .
 
-  # Use pipreqs to check for missing dependencies
-  pipreqs-check:
+  # Use pip-check-reqs/pip-missing-reqs to check for missing dependencies
+  requirements-check:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11.5"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-
-      - name: Run pipreqs
-        run: |
-          pipreqs --savepath pipreqs.txt taca 2>&1 | tee pipreqs_output.log
-          if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
-            missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
-            echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
-            exit 1
-          fi
+          pip install pip-check-reqs
 
-      - name: Compare requirements
+      - name: Run pip-check-reqs/pip-missing-reqs
         run: |
-          # Extract and sort package names
-          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
-          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
-
-          # Compare package lists
-          if cmp -s requirements.compare pipreqs.compare
-          then
-            echo "Requirements are the same"
-
-            exit 0
-          else
-            echo "Requirements are different"
-            echo ""
-
-            echo "=== current requirements.txt ==="
-            echo ""
-            cat requirements.compare
-            echo ""
-
-            echo "=== pipreqs requirements ==="
-            echo ""
-            cat pipreqs.compare
-
-            exit 1
-          fi
+          pip-missing-reqs .
 
   # Use Prettier to check various file formats
   prettier:

VERSIONLOG.md

@@ -4,6 +4,10 @@
 
 Have AVITI demux manifest accommodate samples with recipes of read length 0 by treating them as full length.
 
+## 20250310.1
+
+Fix command in ONT delivery
+
 ## 20250225.1
 
 Improve testing CI

pyproject.toml

@@ -34,7 +34,6 @@ exclude = "build"
 # Omit deprecation warnings from 3rd party packages
 filterwarnings = [
     'ignore::DeprecationWarning:couchdb.*',
-    'ignore::DeprecationWarning:pkg_resources.*',
 ]
 # Default addopts
 addopts = "--ignore tests_old/"

taca/cli.py

@@ -1,8 +1,8 @@
 import logging
 import os
+from importlib.metadata import entry_points
 
 import click
-from pkg_resources import iter_entry_points
 
 import taca.log
 from taca import __version__
@@ -35,5 +35,5 @@ def cli(ctx, config_file):
 
 
 # Add subcommands dynamically to the CLI
-for entry_point in iter_entry_points("taca.subcommands"):
+for entry_point in entry_points(group="taca.subcommands"):
     cli.add_command(entry_point.load())

taca/delivery/delivery_classes.py

@@ -293,7 +293,8 @@ def create_dds_project(self):
         ]
         if self.other_member_details:
             for member in self.other_member_details:
-                dds_command.append(f"--researcher {member}")
+                dds_command.append("--researcher")
+                dds_command.append(member)
         dds_project_id = ""
         try:
             output = ""