Update CI (#235)

* Update CI

* Try dropping pymbar 3

* Bump actions/setup-python from 4 to 5

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update .github/workflows/lint.yaml

* Update

* Update Sphinx

sphinx-doc/sphinx#11890

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.3.0](psf/black@23.12.1...24.3.0)
- [github.com/PyCQA/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Drop unsupported Python versions from tests

* Update dependencies

* Typo

* Use Intel macOS runners

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.4.2](psf/black@23.12.1...24.4.2)
- [github.com/PyCQA/flake8: 6.1.0 → 7.1.0](PyCQA/flake8@6.1.0...7.1.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add manual trigger

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/continous_integration.yaml

@@ -3,54 +3,43 @@ name: tests
 on:
   push:
   schedule:
-    - cron: '0 0 * * *'
+    - cron: '0 3 * * *'
+  workflow_dispatch:
 
-jobs:
+defaults:
+  run:
+    shell: bash -leo pipefail {0} {0}
 
+jobs:
   test:
-
     runs-on: ${{ matrix.os }}
-
     strategy:
-
       matrix:
-        os: ["macOS-latest", "ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
-        pymbar-version: ["pymbar3", "pymbar4"]
+        os:
+          - "macOS-12"
+          - "ubuntu-latest"
+        python-version:
+          - "3.10"
+          - "3.11"
+        pymbar-version:
+          - "pymbar3"
+          - "pymbar4"
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-[email protected]
+      - name: Setup conda environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-          activate-environment: test-${{ matrix.pymbar-version }}
-          channel-priority: true
           environment-file: devtools/conda-envs/test-${{ matrix.pymbar-version }}_env.yaml
-          auto-activate-base: false
-
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Install package
-        shell: bash -l {0}
-        run: |
-          python -m pip install --no-deps .
-
-      - name: Environment information
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
+        run: python -m pip install --no-deps .
 
       - name: Run tests
-        shell: bash -l {0}
-        run: |
-          pytest -v --cov=physical_validation --cov-report=xml physical_validation/tests/
+        run: pytest -v --cov=physical_validation --cov-report=xml physical_validation/tests/
 
       - name: Code coverage
         uses: codecov/codecov-action@v3

.github/workflows/lint.yaml

@@ -12,9 +12,9 @@ jobs:
     steps:
 
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.7'
+          python-version: '3.11'
       - name: Install the package
         run: |
           python setup.py develop --no-deps

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ ci:
   autoupdate_schedule: "quarterly"
 repos:
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.4.2
   hooks:
   - id: black
     files: ^physical_validation
@@ -12,7 +12,7 @@ repos:
   - id: isort
     files: ^physical_validation
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.1.0
   hooks:
   - id: flake8
     files: ^physical_validation

devtools/conda-envs/test-pymbar3_env.yaml

@@ -1,7 +1,6 @@
 name: test-pymbar3
 channels:
   - conda-forge
-  - bioconda
 dependencies:
     # Base depends
   - python
@@ -11,11 +10,10 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-regressions
-  - codecov
-  - gromacs
+  - gromacs ~=2023.4
 
     # Standard dependencies
   - numpy
   - scipy
   - matplotlib
-  - pymbar >=3,<4  # See issue #216
+  - pymbar =3  # See issue #216

devtools/conda-envs/test-pymbar4_env.yaml

@@ -1,7 +1,6 @@
 name: test-pymbar4
 channels:
   - conda-forge
-  - bioconda
 dependencies:
     # Base depends
   - python
@@ -11,11 +10,10 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-regressions
-  - codecov
-  - gromacs
+  - gromacs ~=2023.4
 
     # Standard dependencies
   - numpy
   - scipy
   - matplotlib
-  - pymbar >=4
+  - pymbar =4

doc/requirements.txt

@@ -1,3 +1,3 @@
-sphinx==4.2.0
+sphinx==5.0.2
 nbsphinx==0.8.7
 sphinx_rtd_theme==1.0.0

physical_validation/tests/test_data_gromacs_parser.py

@@ -39,9 +39,11 @@ def get_gromacs_simulation_data(
             mdp=gromacs_files["parameters"],
             top=gromacs_files["topology"],
             edr=gromacs_files["energy"],
-            gro=gromacs_files["final configuration"]
-            if not use_full_trajectory
-            else None,
+            gro=(
+                gromacs_files["final configuration"]
+                if not use_full_trajectory
+                else None
+            ),
             trr=gromacs_files["trajectory"] if use_full_trajectory else None,
         )
 

physical_validation/util/error.py

@@ -18,6 +18,7 @@
 
 class PhysicalValidationError(Exception):
     r"""Base class for exceptions in the physical_validation module."""
+
     pass