update setup to latest cookiecutter (versiongit and pyproject)

.gitattributes

@@ -0,0 +1 @@
+mlcvs/_version.py export-subst

.github/workflows/CI.yaml

@@ -2,21 +2,18 @@ name: CI
 
 on:
   # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
-  # Existing codes likely still have "master" as the primary branch
-  # Both are tracked here to keep legacy and new codes working
+  # The cookiecutter uses the "--initial-branch" flag when it runs git-init
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
   schedule:
-    # Nightly tests run on master by default:
+    # Weekly tests run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * *"
+    - cron: "0 0 * * 0"
 
 jobs:
   test:
@@ -28,7 +25,7 @@ jobs:
         python-version: [3.7, 3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Additional info about the build
       shell: bash
@@ -37,34 +34,25 @@ jobs:
         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/test_env.yaml
+          environment-name: test
+          channels: conda-forge,defaults
+          extra-specs: |
+            python=${{ matrix.python-version }}
 
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-
-        channels: conda-forge,defaults
-
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
-
-    - name: Install package
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-
+      - name: Install package
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        run: |
+          python -m pip install . --no-deps
+          micromamba list
 
     - name: Run tests
-
       # conda setup requires this special shell
       shell: bash -l {0}
-
       run: |
         pytest -v --cov=mlcvs --cov-report=xml --color=yes mlcvs/tests/
 

MANIFEST.in

@@ -1,7 +1,6 @@
 include LICENSE
 include MANIFEST.in
 include CODE_OF_CONDUCT.md
-include versioneer.py
 
 graft mlcvs
 global-exclude *.py[cod] __pycache__ *.so

mlcvs/py.typed

@@ -0,0 +1 @@
+# PEP 561 marker file. See https://peps.python.org/pep-0561/

pyproject.toml

@@ -0,0 +1,85 @@
+[build-system]
+requires = ["setuptools>=61.0", "versioningit~=2.0"]
+build-backend = "setuptools.build_meta"
+
+# Self-descriptive entries which should always be present
+# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
+[project]
+name = "mlcvs"
+description = "Machine learning collective variables for enhanced sampling"
+dynamic = ["version"]
+readme = "README.md"
+authors = [
+    { name = "Luigi Bonati", email = "[email protected]" }
+]
+license = { text = "BSD-3-Clause" }
+# See https://pypi.org/classifiers/
+classifiers = [
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.7"
+# Declare any run-time dependencies that should be installed with the package.
+#dependencies = [
+#    "importlib-resources;python_version<'3.10'",
+#]
+
+# Update the urls once the hosting is set up.
+[project.urls]
+"Source" = "https://github.com/luigibonati/mlcvs/"
+"Documentation" = "https://mlcvs.readthedocs.io/"
+
+[project.optional-dependencies]
+test = [
+  "pytest>=6.1.2",
+  "pytest-runner"
+]
+
+[tool.setuptools]
+# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
+#
+# As of version 0.971, mypy does not support type checking of installed zipped
+# packages (because it does not actually import the Python packages).
+# We declare the package not-zip-safe so that our type hints are also available
+# when checking client code that uses our (installed) package.
+# Ref:
+# https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561
+zip-safe = false
+# Let setuptools discover the package in the current directory,
+# but be explicit about non-Python files.
+# See also:
+#   https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
+# Note that behavior is currently evolving with respect to how to interpret the
+# "data" and "tests" subdirectories. As of setuptools 63, both are automatically
+# included if namespaces is true (default), even if the package is named explicitly
+# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered
+# recursively because of its __init__.py file, but the data subdirectory is excluded
+# with include-package-data = false and namespaces = false.
+include-package-data = false
+[tool.setuptools.packages.find]
+namespaces = false
+where = ["."]
+
+# Ref https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data
+[tool.setuptools.package-data]
+mlcvs = [
+    "py.typed"
+]
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.vcs]
+# The method key:
+method = "git"  # <- The method name
+# Parameters to pass to the method:
+match = ["*"]
+default-tag = "1.0.0"
+
+[tool.versioningit.write]
+file = "mlcvs/_version.py"

setup.cfg

@@ -18,13 +18,5 @@ USE_TABS = False
 # Flake8, PyFlakes, etc
 max-line-length = 119
 
-[versioneer]
-# Automatic version numbering scheme
-VCS = git
-style = pep440
-versionfile_source = mlcvs/_version.py
-versionfile_build = mlcvs/_version.py
-tag_prefix = ''
-
 [aliases]
 test = pytest