cool-seq-tool 0.5.0__tar.gz → 0.5.1__tar.gz

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/.github/workflows/checks.yaml

@@ -9,10 +9,10 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -23,10 +23,10 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -41,10 +41,10 @@ jobs:
     env:
       SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/.github/workflows/release.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install pypa/build
@@ -25,7 +25,7 @@ jobs:
       - name: Build a binary wheel and a source tarball
         run: python3 -m build
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
@@ -42,7 +42,7 @@ jobs:
       id-token: write # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/

cool_seq_tool-0.5.1/.github/workflows/stale.yaml

@@ -0,0 +1,27 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * 1-5"
+
+jobs:
+  stale-high-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 90
+      days-before-pr-stale: 1
+      labels: priority:high
+
+  stale-medium-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 135
+      days-before-pr-stale: 3
+      labels: priority:medium
+
+  stale-low-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/.pre-commit-config.yaml

@@ -1,14 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.4.0
+    rev: v4.6.0  # pre-commit-hooks version
     hooks:
       - id: check-added-large-files
       - id: detect-private-key
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.5.0
     hooks:
       - id: ruff-format
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 3.7.1

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.5.0
+Version: 0.5.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -56,16 +56,16 @@ Requires-Dist: ga4gh.vrs
 Requires-Dist: wags-tails~=0.1.3
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pre-commit>=3.7.1; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: pytest-cov; extra == "tests"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
-Requires-Dist: mock; extra == "tests"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
+Requires-Dist: mock; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/docs/source/contributing.rst

@@ -17,7 +17,7 @@ Create a virtual environment and install :ref:`all dependency groups<dependency-
 
     python3 -m venv venv
     source venv/bin/activate
-    python3 -m pip install -e ".[dev,tests,docs]"
+    python3 -m pip install -e ".[dev,test,docs]"
 
 We use `pre-commit <https://pre-commit.com/#usage>`_ to run conformance tests before commits. This provides checks for:
 

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/docs/source/install.rst

@@ -24,7 +24,7 @@ Install Cool-Seq-Tool from `PyPI <https://pypi.org/project/cool-seq-tool/>`_:
    Cool-Seq-Tool provides extra dependency groups for development and testing purposes. Most users won't need to install them.
 
    * ``dev`` includes packages for linting and performing other kinds of quality checks
-   * ``tests`` includes packages for running tests
+   * ``test`` includes packages for running tests
    * ``docs`` includes packages for writing and building documentation
 
 Set up UTA

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/pyproject.toml

@@ -39,8 +39,8 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
-tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
+dev = ["pre-commit>=3.7.1", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
+test = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -962,7 +962,7 @@ class ExonGenomicCoordsMapper:
             exon = tx_exons_genomic_coords[i]
             next_exon = tx_exons_genomic_coords[i + 1]
             bp = start if start else end
-            if strand == strand.POSITIVE:
+            if strand == Strand.POSITIVE:
                 lte_exon = exon
                 gte_exon = next_exon
             else:

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.5.0
+Version: 0.5.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -56,16 +56,16 @@ Requires-Dist: ga4gh.vrs
 Requires-Dist: wags-tails~=0.1.3
 Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pre-commit>=3.7.1; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: pytest-cov; extra == "tests"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
-Requires-Dist: mock; extra == "tests"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
+Requires-Dist: mock; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"

{cool_seq_tool-0.5.0 → cool_seq_tool-0.5.1}/src/cool_seq_tool.egg-info/requires.txt

@@ -11,7 +11,7 @@ wags-tails~=0.1.3
 bioutils
 
 [dev]
-pre-commit
+pre-commit>=3.7.1
 ipython
 ipykernel
 psycopg2-binary
@@ -26,7 +26,7 @@ sphinxext-opengraph==0.8.2
 furo==2023.3.27
 sphinx-github-changelog==1.2.1
 
-[tests]
+[test]
 pytest
 pytest-cov
 pytest-asyncio==0.18.3

cool_seq_tool-0.5.0/.github/workflows/stale.yaml

@@ -1,28 +0,0 @@
-name: "Stalebot for issues and PRs"
-
-on:
-  schedule:
-    - cron: "30 13 * * *"
-
-jobs:
-  stale:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-    steps:
-      - uses: actions/stale@v9
-        with:
-          remove-stale-when-updated: true
-          days-before-close: 14
-
-          days-before-issue-stale: 60
-          stale-issue-label: stale
-          stale-issue-message: "This issue is stale because it has been open 45 days with no activity. Please make a comment for triaging or closing the issue."
-          close-issue-label: closed-by-stale
-          close-issue-message: "This issue was closed because it has been stalled for 14 days with no activity."
-
-          days-before-pr-stale: 7
-          stale-pr-label: stale
-          stale-pr-message: "This PR is stale because it has been open 7 days with no activity. Please review this PR."
-          days-before-pr-close: -1