upgrade dependencies and support more modern python versions (#32)

no feature change, but just upgrading deps and supports py39 to py13 instead of current py37 to py39.

resolves #31

increment major version to 3

---------

Co-authored-by: Zhuyi Xue <[email protected]>

Author: zyxue

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v2
@@ -25,7 +25,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip poetry
+        python -m pip install --upgrade pip poetry==1.8.5
         poetry install
     - name: Lint
       run: |

Makefile

@@ -29,4 +29,4 @@ test: FORCE
 
 lint: black isort mypy pylint
 
-all: lint pytest
+all: lint test

README.md

@@ -12,7 +12,7 @@ is like
 
 ### Install
 
-ncbitax2lin supports python-3.7, python-3.8, and python-3.9.
+ncbitax2lin supports python-3.9 to python-3.13.
 
 ```
 pip install -U ncbitax2lin
@@ -72,8 +72,7 @@ of a different timestamp.
 ### Install dependencies
 
 ```
-poetry shell
-poetry install
+poetry install --sync
 ```
 
 ### Testing

mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.7
+python_version = 3.9
 disallow_untyped_defs = True
 ignore_missing_imports = True
 show_column_numbers = True

ncbitax2lin/utils.py

@@ -21,7 +21,7 @@ def timed_func(*args: Any, **kwargs: Any) -> Any:
         """Returns the timed function"""
         start_time = time.time()
         result = func(*args, **kwargs)
-        elapsed_time = datetime.timedelta(seconds=(time.time() - start_time))
+        elapsed_time = datetime.timedelta(seconds=time.time() - start_time)
         _LOGGER.info("time spent on %s: %s", func.__name__, elapsed_time)
         return result
 

poetry.lock

@@ -1,2 +1,2 @@
 [MESSAGES CONTROL]
-disable=bad-continuation, fixme, duplicate-code
+disable=fixme, duplicate-code

pylintrc

@@ -1,26 +1,26 @@
 [tool.poetry]
 name = "ncbitax2lin"
-version = "2.4.1"
+version = "3.0.0"
 description = "A tool that converts NCBI taxonomy dump into lineages"
 authors = ["Zhuyi Xue <[email protected]>"]
 readme = "README.md"
 homepage = "https://github.com/zyxue/ncbitax2lin"
 license = "MIT"
 
 [tool.poetry.dependencies]
-fire = "^0.3.1"
-pandas = "^1.0.3"
-python = "^3.7,<3.10"
-typing-extensions = "^3.7.4"
+fire = "^0.7.1"
+pandas = "^2.3.2"
+python = "^3.9,<3.14"
+typing-extensions = "^4.15.0"
 
 [tool.poetry.dev-dependencies]
 autoflake = "^1.3.1"
 black = "^22.1.0"
-coverage = "^5.4"
+coverage = "^7.5.4"
 isort = "^5.7.0"
-mypy = "^0.941"
-pylint = "^2.5.0"
-pytest = "^5.2"
+mypy = "^1.18.2"
+pylint = "^3.3.8"
+pytest = "^8.4.2"
 pytest-parallel = "^0.1.0"
 tox = "^3.21.4"
 

pyproject.toml

@@ -1,4 +1,5 @@
 """tests for utils.py"""
+
 # pylint: disable=protected-access, missing-function-docstring
 
 import os
@@ -28,7 +29,7 @@ def test_maybe_backup_file_when_file_path_exists(
     utils.maybe_backup_file(test_input)
     expected = "#some_existing_file.1#"
 
-    assert mock_exists.has_calls(call(test_input), call(expected))
+    mock_exists.assert_has_calls([call(test_input), call(expected)])
     mock_rename.assert_called_once_with(test_input, expected)
 
 
@@ -44,8 +45,8 @@ def test_maybe_backup_file_when_backfile_also_exists(
     utils.maybe_backup_file(test_input)
     expected = "#some_existing_file.2#"
 
-    assert mock_exists.has_calls(
-        call(test_input), call(intermediary_input), call(expected)
+    mock_exists.assert_has_calls(
+        [call(test_input), call(intermediary_input), call(expected)]
     )
     mock_rename.assert_called_once_with(test_input, expected)
 

tests/test_utils.py

@@ -1,6 +1,6 @@
 [tox]
 isolated_build = True
-envlist = py37,py38,py39
+envlist = py39,py310,py311,py312,py313
 
 [testenv]
 allowlist_externals =