Fix version info and modernize some things (#562)

* drop python 3.10 from testing matrix since it is out of SPEC-0

* migrate to setuptools_scm and use a pyproject.toml file

* Remove unused input for codcov

* fix issue with metadata

* ported entire setup.py

* fix issue with metadata

* switch over to pyproject.toml

* License classifiers have been superseded by license expressions (see https://peps.python.org/pep-0639/)

* Formatting fixes and use setuptools to find package

* add a fallback version so install doesn't fail if git is not in path

* Remove file that doesn't exit anymore from exclude

* Add missing trailing comma

* fix pymbar.__version__

* use better default shell to catch errors and also cancel jobs if a new commit is pushed

Author: mikemhenry

.github/workflows/CI.yaml

@@ -15,15 +15,23 @@ on:
     # Nightly Tests
     - cron: '0 0 * * *'
 
-jobs:
 
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]  # Check against oldest and newest versions
+        python-version: ["3.11", "3.12", "3.13"]  # Check against oldest and newest versions
         jax: ["", "_jax"]
         exclude:  # Skip win + jax
           - jax: "_jax"
@@ -35,7 +43,7 @@ jobs:
 
     steps:
     - name: Checkout the code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Additional info about the build
       shell: bash
@@ -56,18 +64,15 @@ jobs:
           python=${{ matrix.python-version }}
 
     - name: Install package
-      shell: bash -l {0}
       run: |
         python -m pip install . --no-deps
         micromamba list
 
     - name: Run tests (pytest)
-      shell: bash -l {0}
       run: |
         pytest -v --cov=$PACKAGE --cov-report=xml --color=yes --doctest-modules $PACKAGE/
 
     - name: Run examples
-      shell: bash -l {0}
       run: |
         ### constant-force-optical-trap
         cd examples/constant-force-optical-trap
@@ -93,14 +98,13 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: unittests
-        yml: ./.codecov.yml
 
   lint-format:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     env:
       PACKAGE: "pymbar"
 
@@ -119,19 +123,16 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
     - name: Install linter and formatter
-      shell: bash -l {0}
       run: |
         micromamba install pylint black
 
     - name: Run pylint
-      shell: bash -l {0}
       run: |
         pylint $PACKAGE/
 
     # Black has a default --exclude which reads .gitignore.
     # Black's --exclude and --extend-exclude are single specified RegEx patterns and overwrite if multi-marked.
     - name: Run black check
-      shell: bash -l {0}
       if: always()
       run: |
-        black --check -l 99 $PACKAGE/ examples/ --extend-exclude "$PACKAGE/_version.py"
+        black --check -l 99 $PACKAGE/ examples/

pymbar/__init__.py

@@ -28,6 +28,8 @@
 __maintainer__ = "Levi N. Naden, Jaime Rodríguez-Guerra, Michael R. Shirts and John D. Chodera"
 __email__ = "levi.naden@choderalab.org,jaime.rodriguez-guerra@choderalab.org,michael.shirts@colorado.edu,john.chodera@choderalab.org"
 
+from importlib.metadata import version, PackageNotFoundError
+
 from . import timeseries, testsystems, confidenceintervals
 from .mbar import MBAR
 from .other_estimators import bar, bar_overlap, bar_zero, exp, exp_gauss
@@ -48,6 +50,8 @@
     "FES",
 ]
 
-from . import _version
-
-__version__ = _version.get_versions()["version"]
+try:
+    __version__ = version("pymbar")
+except PackageNotFoundError:
+    # package is not installed
+    pass