v0.1.4 (#88)

* Added classifiers for Python version.

* updated GAnalytics tag

* Simplified threads check.

* Updated version management.

* Exposeing __version__

* Dropped support for Python 3.6 and 3.7

* Fixed circular import.

* Updated requirements.

* Bump rich from 9.13.0 to 10.0.0 (#70)

* Bump numpy from 1.20.1 to 1.20.2 (#71)

* Bump rich from 10.0.0 to 10.0.1 (#72)

* Bump rich from 10.0.1 to 10.1.0 (#73)

* Bump regex from 2021.3.17 to 2021.4.4 (#74)

* Bump pytest from 6.2.2 to 6.2.3 (#75)

* Bump tqdm from 4.59.0 to 4.60.0 (#76)

* Bump pandas from 1.2.3 to 1.2.4 (#77)

* Bump pytest from 6.2.3 to 6.2.4 (#78)

* Bump rich from 10.1.0 to 10.2.0 (#80)

* Bump numpy from 1.20.2 to 1.20.3 (#79)

* Bump rich from 10.2.0 to 10.2.2 (#82)

* Bump tqdm from 4.60.0 to 4.61.0 (#83)

* Bump biopython from 1.78 to 1.79 (#84)

* Bump rich from 10.2.2 to 10.3.0 (#85)

* Bump tqdm from 4.61.0 to 4.61.1 (#86)

* Fixed --case-insensitive bug.

* v0.1.4 release

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/pythonpackage.yml

@@ -39,7 +39,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9]
     runs-on: ${{ matrix.os }}
     steps:
     # Checkout repo and setup python
@@ -59,7 +59,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: .venv
-        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-py${{ matrix.python-version }}
     # install dependencies if cache does not exist
     - name: Install dependencies
       run: poetry install

CHANGELOG.md

@@ -6,6 +6,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [0.1.4]
+### Changed
+- Dropped support for Python 3.6 and 3.7
+
+### Fixed
+- Fixed bug triggered by `--case-insensitive` option in `find_seq` tool.
+
 ## [0.1.3]
 ### Fixed
 - Cleaned dependencies, solved linting and packaging issues.
@@ -53,7 +60,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [0.0.1] - 2020-08-03
 
 [Unreleased]: https://github.com/ggirelli/fastx-barber/tree/dev  
-[0.1.2]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.3  
+[0.1.4]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.4  
+[0.1.3]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.3  
 [0.1.2]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.2  
 [0.1.1]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.1  
 [0.1.0]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.0  

README.md

@@ -7,7 +7,7 @@
 
 [PyPi](https://pypi.org/project/fastx-barber/) | [docs](https://ggirelli.github.io/fastx-barber/)
 
-A Python3.6.13+ package to trim and extract flags from FASTA  and FASTQ files.
+A Python3.8+ package to trim and extract flags from FASTA  and FASTQ files.
 
 ## Features (in short)
 
@@ -23,7 +23,7 @@ For more available features, check out our [docs](https://ggirelli.github.io/fas
 
 ## Requirements
 
-`fastx-barber` has been tested with Python 3.6.13, 3.7, 3.8, and 3.9. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/fastx-barber#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/fastx-barber/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
+`fastx-barber` has been tested with Python 3.8 and 3.9. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/fastx-barber#install)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/fastx-barber/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
 
 ## Install
 

docs/_config.yml

@@ -1,4 +1,4 @@
 theme: jekyll-theme-cayman
 title: "fastx-barber"
 description: "A package to trim and extract flags from FASTA  and FASTQ files."
-google_analytics: "UA-99031010-8"
+google_analytics: "G-7SPT6HZ3GP"

fastx_barber/__init__.py

@@ -3,15 +3,20 @@
 @contact: gigi.ga90@gmail.com
 """
 
-from fastx_barber.const import __version__
-from fastx_barber import const, scripts
+from fastx_barber import const
 from fastx_barber import bedio, io, scriptio, seqio
 from fastx_barber import flag, match, qual, trim
 
+from importlib.metadata import version
+
+try:
+    __version__ = version(__name__)
+except Exception as e:
+    raise e
+
 __all__ = [
     "__version__",
     "const",
-    "scripts",
     "bedio",
     "io",
     "scriptio",

fastx_barber/const.py

@@ -6,9 +6,6 @@
 from enum import Enum
 from typing import DefaultDict, Optional, Tuple
 
-__version__ = "0.1.3"
-
-
 BedRecord = Tuple[
     str,
     int,

fastx_barber/scripts/arguments.py

@@ -4,7 +4,8 @@
 """
 
 import argparse
-from fastx_barber.const import __version__, DEFAULT_PHRED_OFFSET
+from fastx_barber import __version__
+from fastx_barber.const import DEFAULT_PHRED_OFFSET
 import joblib  # type: ignore
 import logging
 import sys
@@ -90,11 +91,7 @@ def add_tempdir_option(arg_group: argparse._ArgumentGroup) -> argparse._Argument
 
 
 def check_threads(threads: int) -> int:
-    if threads > joblib.cpu_count():
-        return joblib.cpu_count()
-    elif threads <= 0:
-        return 1
-    return threads
+    return max(1, min(threads, joblib.cpu_count()))
 
 
 def add_phred_offset_option(

fastx_barber/scripts/barber.py

@@ -4,7 +4,7 @@
 """
 
 import argparse
-from fastx_barber.const import __version__
+from fastx_barber import __version__
 from fastx_barber.scripts import arguments as ap
 from fastx_barber import scripts
 import sys

fastx_barber/scripts/find_seq.py

@@ -122,7 +122,7 @@ def run(args: argparse.Namespace) -> None:
     location_id = 0
     for record in parser:
         if args.case_insensitive:
-            record[1] = record[1].upper()
+            record = (record[0], record[1].upper())
         for pos, location_id in search_needle(record, args.needle, location_id):
             writer.do(
                 (