Merge pull request #16 from craabreu/linter

Added linting workflow

.github/workflows/Linter.yaml

@@ -0,0 +1,60 @@
+name: Linter
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  linter:
+    name: Linter
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Additional info about the build
+        shell: bash
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      # More info on options: https://github.com/marketplace/actions/provision-with-micromamba
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: devtools/conda-envs/lint_env.yaml
+          environment-name: linter
+          channels: conda-forge,defaults
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
+
+      - name: Run flake8
+        shell: bash -l {0}
+        run: flake8 --ignore=E203,W503 ufedmm/
+
+      - name: Run black
+        shell: bash -l {0}
+        run: black --line-length 100 --diff --color ufedmm/
+
+      - name: Run isort
+        shell: bash -l {0}
+        run: isort --check-only ufedmm/
+
+      # - name: Run pylint
+      #   shell: bash -l {0}
+      #   run: pylint --rcfile=devtools/linters/pylintrc ufedmm/

README.md

@@ -2,14 +2,12 @@ Unified Free Energy Dynamics with OpenMM
 ========================================
 
 [//]: # (Badges)
-[![License](https://img.shields.io/github/license/mashape/apistatus.svg)]()
-
-[//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/Linux/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3ALinux)
-[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/MacOS/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3AMacOS)
-[![GitHub Actions Build Status](https://github.com/RedesignScience/ufedmm/workflows/Windows/badge.svg)](https://github.com/RedesignScience/ufedmm/actions?query=workflow%3AWindows)
-[![codecov](https://codecov.io/gh/craabreu/ufedmm/branch/master/graph/badge.svg)](https://codecov.io/gh/craabreu/ufedmm/branch/master)
+[![GitHub Actions Build Status](https://github.com/craabreu/ufedmm/workflows/Linux/badge.svg)](https://github.com/craabreu/ufedmm/actions?query=workflow%3ALinux)
+[![GitHub Actions Build Status](https://github.com/craabreu/ufedmm/workflows/MacOS/badge.svg)](https://github.com/craabreu/ufedmm/actions?query=workflow%3AMacOS)
+[![GitHub Actions Build Status](https://github.com/craabreu/ufedmm/workflows/Windows/badge.svg)](https://github.com/craabreu/ufedmm/actions?query=workflow%3AWindows)
+[![codecov](https://codecov.io/gh/craabreu/ufedmm/branch/main/graph/badge.svg)](https://codecov.io/gh/craabreu/ufedmm/branch/main)
 [![Documentation Status](https://readthedocs.org/projects/ufedmm/badge/?style=flat)](https://readthedocs.org/projects/ufedmm)
+[![License](https://img.shields.io/github/license/mashape/apistatus.svg)]()
 
 UFEDMM extends [OpenMM's Python API] so that the user can easily run
 efficient simulations in extended phase spaces, perform enhanced sampling

devtools/conda-envs/lint_env.yaml

@@ -0,0 +1,18 @@
+name: linter
+channels:
+  - conda-forge
+dependencies:
+    # Base depends
+  - python
+  - pip
+  - numpy
+  - openmm
+  - pandas
+  - pyyaml
+  - scipy
+
+    # Linting
+  - flake8
+  - black
+  - isort
+  # - pylint

devtools/linters/pylintrc

@@ -0,0 +1,17 @@
+[MAIN]
+
+ignored-modules=openmm.unit
+ignore=_version.py
+
+[DESIGN]
+
+max-locals=25  # Maximum number of local variables for function/method body
+
+[MESSAGES CONTROL]
+
+disable = unexpected-keyword-arg,  # Avoids false-positives with Context.getState method
+          too-many-arguments
+
+[FORMAT]
+
+good-names=i,j,k,m,n,_,v,x,y,z

devtools/scripts/format_and_check.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+set -e -v
+isort ./ufedmm
+black --line-length 100 ./ufedmm
+flake8 --ignore=E203,W503 ./ufedmm
+# pylint --rcfile=devtools/linters/pylintrc ./ufedmm

ufedmm/__init__.py

@@ -6,18 +6,18 @@
 
 
 from ._version import get_versions
+from .analysis import *  # noqa: F401, F403
+from .integrators import *  # noqa: F401, F403
+from .io import *  # noqa: F401, F403
+from .testmodels import *  # noqa: F401, F403
 from .ufedmm import CollectiveVariable  # noqa: F401, F403
 from .ufedmm import DynamicalVariable  # noqa: F401, F403
 from .ufedmm import ExtendedSpaceContext  # noqa: F401, F403
 from .ufedmm import ExtendedSpaceSimulation  # noqa: F401, F403
 from .ufedmm import UnifiedFreeEnergyDynamics  # noqa: F401, F403
-from .integrators import *  # noqa: F401, F403
-from .io import *  # noqa: F401, F403
-from .analysis import *  # noqa: F401, F403
-from .testmodels import *  # noqa: F401, F403
 
 # Handle versioneer:
 versions = get_versions()
-__version__ = versions['version']
-__git_revision__ = versions['full-revisionid']
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
 del get_versions, versions