Fix warnings and make tests run again

.github/workflows/ci.yml

@@ -3,27 +3,29 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches:
       - master
-
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.7', '3.8', '3.9', '3.10' ]
-    name: Python ${{ matrix.python-version }} sample
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
+    name: Python ${{ matrix.python-version }} tests
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v3
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: x64
       - name: Install dependencies
         run: |
-          python -m pip install pipenv --upgrade-strategy=only-if-needed
-          pipenv install --dev --skip-lock
-      - name: Test with pytest
-        run: pipenv run pytest --cov
+          python -m venv .venv
+          source .venv/bin/activate
+          pip install -r requirements-dev.txt
+      - name: Run tests
+        run: |
+          source .venv/bin/activate
+          pytest --cov

Makefile

@@ -0,0 +1,24 @@
+# Makefile for managing the Python project environment, dependencies, and common tasks.
+#
+# This Makefile provides a set of commands to help developers set up the project,
+# run tests, lint the code, and clean up temporary files. It uses Python's built-in
+# `venv` module to create a virtual environment and `pip` to manage dependencies.
+#
+# Usage:
+#   make install   - Set up the virtual environment and install all dependencies (including dev dependencies).
+#   make test      - Run the test suite using pytest and generate a coverage report.
+#   make lint      - Run code linting and style checks using flake8.
+#   make clean     - Remove the virtual environment and temporary files.
+#
+# Note: Ensure you have Python 3 installed on your system before using this Makefile.
+.PHONY: install test lint clean
+install:
+	python3 -m venv .venv
+	. .venv/bin/activate && pip install -r requirements-dev.txt
+test:
+	. .venv/bin/activate && pytest --cov
+lint:
+	. .venv/bin/activate && flake8
+clean:
+	rm -rf .venv
+	find . -type d -name "__pycache__" -exec rm -r {} +

requirements-dev.txt

@@ -0,0 +1,10 @@
+-r requirements.txt
+black
+coverage
+flake8
+ipython>=7.31.1
+pdbpp
+pylint
+pyscaffold
+pytest
+pytest-cov

requirements.txt

@@ -0,0 +1,4 @@
+docopt
+pandas
+scipy
+-e .

setup.cfg

@@ -35,12 +35,11 @@ package_dir =
 # Require a specific Python version, e.g. Python 2.7 or >= 3.4
 # python_requires = >=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*
 install_requires =
-    importlib-metadata; python_version<"3.8"
     pandas
     scipy
     docopt
     openpyxl
-python_requires = >=3.6
+python_requires = >=3.9
 
 [options.packages.find]
 where = src

src/picor/cli.py

@@ -47,7 +47,7 @@
 import logging
 from pathlib import Path
 import sys
-import pkg_resources
+from importlib.metadata import version
 
 from docopt import docopt
 import pandas as pd
@@ -96,8 +96,8 @@ def cli(arguments):
 
 def main():
     """Serve as entry point for CLI."""
-    version = pkg_resources.get_distribution("picor").version
-    arguments = docopt(__doc__, version=version)
+    package_version = version("picor")
+    arguments = docopt(__doc__, version=package_version)
     _logger.info("arguments = {arguments}")
     sys.exit(cli(arguments))
 

src/picor/isotope_probabilities.py

@@ -100,7 +100,10 @@ def get_shift(isotopes_file):
             index_col="isotope",
         )
         iso_data = iso_data.groupby("element", group_keys=False).apply(
-            lambda gdf: gdf.assign(shift=lambda df: round(df["mass"] - min(df["mass"])))
+            lambda gdf: gdf.assign(
+                shift=lambda df: round(df["mass"] - min(df["mass"]))
+            ),
+            include_groups=False,
         )
         return iso_data["shift"].astype("int64")
 

tox.ini

@@ -0,0 +1,7 @@
+[tox]
+envlist = py310, py311, py312, py313
+[testenv]
+deps =
+    -rrequirements-dev.txt
+commands =
+    pytest --cov