Merge pull request #151 from pepkit/modernize3

Release 0.12.11

Author: khoroshevskyi

.github/workflows/black.yml

@@ -1,11 +1,15 @@
 name: Lint
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-      - uses: psf/black@stable
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check .
+      - run: ruff format --check .

.github/workflows/python-publish.yml

@@ -6,22 +6,21 @@ on:
 
 jobs:
   deploy:
-    name: upload release to PyPI
     runs-on: ubuntu-latest
+    name: upload release to PyPI
     permissions:
+      contents: read
       id-token: write
+
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      run: |
-        python setup.py sdist bdist_wheel
+    - name: Install build dependencies
+      run: python -m pip install --upgrade pip build
+    - name: Build package
+      run: python -m build
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-pytest.yml

@@ -5,28 +5,26 @@ on:
     branches: [dev]
   pull_request:
     branches: [master, dev]
+  workflow_dispatch:
 
 jobs:
   pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.13"]
-        os: [ubuntu-latest]
+        python-version: ["3.10", "3.14"]
+        os: [ubuntu-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install test dependencies
-      run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
-
-    - name: Install package
-      run: python -m pip install .
+    - name: Install package with test dependencies
+      run: python -m pip install ".[test]"
 
     - name: Run pytest tests
-      run: pytest tests -x -vv
+      run: pytest tests

MANIFEST.in

@@ -1,14 +1,21 @@
-"""Package-level data"""
+"""Package-level data."""
+
+from importlib.metadata import PackageNotFoundError, version
 
 import coloredlogs
 import logmuse
 
-from geofetch._version import __version__
 from geofetch.finder import Finder
 from geofetch.geofetch import Geofetcher
 
-__author__ = ["Oleksandr Khoroshevskyi", "Vince Reuter", "Nathan Sheffield"]
-__all__ = ["Finder", "Geofetcher", "__version__"]
+__author__: list[str] = ["Oleksandr Khoroshevskyi", "Vince Reuter", "Nathan Sheffield"]
+
+try:
+    __version__: str = version("geofetch")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+__all__: list[str] = ["Finder", "Geofetcher", "__version__"]
 
 _LOGGER = logmuse.init_logger("geofetch")
 coloredlogs.install(

geofetch/__init__.py

@@ -1,21 +1,26 @@
 import argparse
 import os
+from importlib.metadata import PackageNotFoundError, version
 
 import logmuse
 from ubiquerg import VersionInHelpParser
 
-from geofetch._version import __version__
 
-
-def _safe_echo(var):
-    """Returns an environment variable if it exists, or an empty string if not"""
+def _safe_echo(var: str) -> str:
+    """Return an environment variable if it exists, or an empty string if not."""
     return os.getenv(var, "")
 
 
-def _parse_cmdl(cmdl):
-    """
-    parser
-    """
+def _get_version() -> str:
+    """Return the package version, or 'unknown' if not installed."""
+    try:
+        return version("geofetch")
+    except PackageNotFoundError:
+        return "unknown"
+
+
+def _parse_cmdl(cmdl: list[str]) -> argparse.Namespace:
+    """Parse command-line arguments for geofetch."""
     parser = VersionInHelpParser(
         description="Automatic GEO and SRA data downloader",
         usage="""geofetch [<args>]
@@ -27,7 +32,7 @@ def _parse_cmdl(cmdl):
     geofetch -i GSE67303 --processed --geo-folder <folder> -m <folder>
 
 """,
-        version=__version__,
+        version=_get_version(),
     )
 
     processed_group = parser.add_argument_group("processed")
@@ -54,7 +59,7 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRAMETA"),
         help="Specify a parent folder location to store metadata. "
         "The project name will be added as a subfolder "
-        "[Default: $SRAMETA:" + _safe_echo("SRAMETA") + "]",
+        "(Default: $SRAMETA:" + _safe_echo("SRAMETA") + ")",
     )
 
     parser.add_argument(
@@ -87,7 +92,7 @@ def _parse_cmdl(cmdl):
         default=None,
         help="Optional: Specify one or more filepaths to SAMPLES pipeline interface yaml files. "
         "These will be added to the project config file to make it immediately "
-        "compatible with looper. [Default: null]",
+        "compatible with looper. (Default: null)",
     )
 
     # Optional
@@ -96,7 +101,7 @@ def _parse_cmdl(cmdl):
         default=None,
         help="Optional: Specify one or more filepaths to PROJECT pipeline interface yaml files. "
         "These will be added to the project config file to make it immediately "
-        "compatible with looper. [Default: null]",
+        "compatible with looper. (Default: null)",
     )
     # Optional
     parser.add_argument(
@@ -111,7 +116,7 @@ def _parse_cmdl(cmdl):
         "--skip",
         default=0,
         type=int,
-        help="Skip some accessions. [Default: no skip].",
+        help="Skip some accessions. (Default: no skip).",
     )
 
     parser.add_argument(
@@ -132,15 +137,15 @@ def _parse_cmdl(cmdl):
         type=int,
         default=50,
         help="Optional: Limit of the number of the constant sample characters "
-        "that should not be in project yaml. [Default: 50]",
+        "that should not be in project yaml. (Default: 50)",
     )
 
     parser.add_argument(
         "--const-limit-discard",
         type=int,
         default=1000,
         help="Optional: Limit of the number of the constant sample characters "
-        "that should not be discarded [Default: 250]",
+        "that should not be discarded (Default: 250)",
     )
 
     parser.add_argument(
@@ -149,7 +154,7 @@ def _parse_cmdl(cmdl):
         default=500,
         help="Optional: Limit of the number of sample characters."
         "Any attribute with more than X characters will truncate to the first X,"
-        " where X is a number of characters [Default: 500]",
+        " where X is a number of characters (Default: 500)",
     )
 
     parser.add_argument(
@@ -163,7 +168,7 @@ def _parse_cmdl(cmdl):
         type=str,
         default="1GB",
         help="""Optional: Max size of soft file.
-                [Default: 1GB].
+                (Default: 1GB).
                 Supported input formats : 12B, 12KB, 12MB, 12GB. """,
     )
 
@@ -178,7 +183,7 @@ def _parse_cmdl(cmdl):
         "--processed",
         default=False,
         action="store_true",
-        help="Download processed data [Default: download raw data].",
+        help="Download processed data (Default: download raw data).",
     )
 
     processed_group.add_argument(
@@ -190,13 +195,13 @@ def _parse_cmdl(cmdl):
         " to retrieve processed data, which may be attached to the"
         " collective series entity, or to individual samples. "
         "Allowable values are: samples, series or both (all). "
-        "Ignored unless 'processed' flag is set. [Default: samples]",
+        "Ignored unless 'processed' flag is set. (Default: samples)",
     )
 
     processed_group.add_argument(
         "--filter",
         default=None,
-        help="Optional: Filter regex for processed filenames [Default: None]."
+        help="Optional: Filter regex for processed filenames (Default: None)."
         "Ignored unless 'processed' flag is set.",
     )
 
@@ -205,7 +210,7 @@ def _parse_cmdl(cmdl):
         dest="filter_size",
         default=None,
         help="""Optional: Filter size for processed files
-                that are stored as sample repository [Default: None].
+                that are stored as sample repository (Default: None).
                 Works only for sample data.
                 Supported input formats : 12B, 12KB, 12MB, 12GB. 
                 Ignored unless 'processed' flag is set.""",
@@ -217,7 +222,7 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("GEODATA"),
         help="Optional: Specify a location to store processed GEO files."
         " Ignored unless 'processed' flag is set."
-        "[Default: $GEODATA:" + _safe_echo("GEODATA") + "]",
+        "(Default: $GEODATA:" + _safe_echo("GEODATA") + ")",
     )
 
     raw_group.add_argument(
@@ -238,7 +243,9 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRABAM"),
         help="""Optional: Specify folder of bam files. Geofetch will not
             download sra files when corresponding bam files already exist.
-            [Default: $SRABAM:""" + _safe_echo("SRABAM") + "]",
+            (Default: $SRABAM:"""
+        + _safe_echo("SRABAM")
+        + ")",
     )
 
     raw_group.add_argument(
@@ -248,7 +255,9 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRAFQ"),
         help="""Optional: Specify folder of fastq files. Geofetch will not
             download sra files when corresponding fastq files already exist.
-            [Default: $SRAFQ:""" + _safe_echo("SRAFQ") + "]",
+            (Default: $SRAFQ:"""
+        + _safe_echo("SRAFQ")
+        + ")",
     )
 
     # Deprecated; these are for bam conversion which now happens in sra_convert
@@ -260,7 +269,7 @@ def _parse_cmdl(cmdl):
         default=_safe_echo("SRARAW"),
         help=argparse.SUPPRESS,
         # help="Optional: Specify a location to store sra files "
-        #   "[Default: $SRARAW:" + safe_echo("SRARAW") + "]"
+        #   "(Default: $SRARAW:" + safe_echo("SRARAW") + ")"
     )
     raw_group.add_argument(
         "--bam-conversion",
@@ -274,7 +283,7 @@ def _parse_cmdl(cmdl):
         dest="picard_path",
         default=_safe_echo("PICARD"),
         # help="Specify a path to the picard jar, if you want to convert "
-        # "fastq to bam [Default: $PICARD:" + safe_echo("PICARD") + "]",
+        # "fastq to bam (Default: $PICARD:" + safe_echo("PICARD") + ")",
         help=argparse.SUPPRESS,
     )