WIP: update old code: CI, python version, pre-commit and unittests (#36)

* fix: CI not working with mamba

* ci: use miniforge instead

* enh: move to Python 3.6-3.10

* enh: add dependabot.yml

* enh: add a few pre-commits, including black formatter

* enh: update pre-commit

* refactor: remove old Python 2 code, update tests

* refactor: remove old Python 2 code, update tests

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions monthly
+      interval: "monthly"

.github/workflows/ci.yml

@@ -1,6 +1,13 @@
-name: Python package
+name: unittests
 
-on: [ push, pull_request ]
+on:
+  push:
+    tags:
+      - "*"
+    branches:
+      - master
+      - "ci/*"
+  pull_request:
 
 jobs:
   unittests:
@@ -9,33 +16,34 @@ jobs:
       run:
         shell: "bash -l {0}"
     strategy:
+      fail-fast: false
       matrix:
         python-version:
           - 3.6
           - 3.7
           - 3.8
           - 3.9
+          - 3.10
     name: Tests for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          miniforge-variant: Mambaforge
-          use-mamba: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
           python-version: ${{ matrix.python-version }}
           activate-environment: formulate-env
 
       - name: Install ROOT
         run: |
-          conda config --add channels conda-forge
-          conda config --set channel_priority strict
-          conda install root -y
+          mamba install root -y
 
       - name: Install test dependencies
         run: |
           python -m pip install --upgrade pip
-          conda install coveralls -y
-          conda install pytest-cov -y
+          mamba install coveralls -y
+          mamba install pytest-cov -y
           pip install -e .[dev,test]
 
       - name: Test with pytest

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.2.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -12,10 +12,58 @@ repos:
       - id: mixed-line-ending
       - id: requirements-txt-fixer
       - id: trailing-whitespace
-      - id: fix-encoding-pragma
 
   - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.46"
+    rev: "0.48"
     hooks:
       - id: check-manifest
         stages: [ manual ]
+
+  - repo: https://github.com/myint/docformatter
+    rev: v1.4
+    hooks:
+      - id: docformatter
+        args: [ -r, --in-place, --wrap-descriptions, '120', --wrap-summaries, '120', -- ]
+
+  - repo: https://github.com/mattlqx/pre-commit-sign
+    rev: v1.1.3
+    hooks:
+      - id: sign-commit
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: python-use-type-annotations
+      - id: python-check-mock-methods
+      - id: python-no-eval
+      - id: rst-directive-colons
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.32.1
+    hooks:
+      - id: pyupgrade
+        args: [ --py36-plus ]
+
+  - repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v1.20.1
+    hooks:
+    - id: setup-cfg-fmt
+      args: [--max-py-version=3.10]
+
+  - repo: https://github.com/roy-ht/pre-commit-jupyter
+    rev: v1.2.1
+    hooks:
+      - id: jupyter-notebook-cleanup
+
+# TODO: for Python 3.7+
+#  - repo: https://github.com/sondrelg/pep585-upgrade
+#    rev: 'v1.0'
+#    hooks:
+#      - id: upgrade-type-hints
+#        args: [ '--futures=true' ]
+
+  - repo: https://github.com/ambv/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        language_version: python3

conftest.py

@@ -1,14 +1,15 @@
 # Licensed under a 3-clause BSD style license, see LICENSE.
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
 
 import pytest
 
 
 def pytest_addoption(parser):
-    parser.addoption("--run-slow", action="store_true",
-                     default=False, help="Enable running slow tests")
+    parser.addoption(
+        "--run-slow",
+        action="store_true",
+        default=False,
+        help="Enable running slow tests",
+    )
 
 
 def pytest_collection_modifyitems(config, items):

formulate/__init__.py

@@ -1,33 +1,37 @@
 # Licensed under a 3-clause BSD style license, see LICENSE.
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
 
 from pyparsing import ParserElement
 
 from .backends import from_auto, from_numexpr, to_numexpr
 from .backends import from_root, to_root
-from .expression import ExpressionComponent, SingleComponent, Expression, Variable, NamedConstant, UnnamedConstant
+from .expression import (
+    ExpressionComponent,
+    SingleComponent,
+    Expression,
+    Variable,
+    NamedConstant,
+    UnnamedConstant,
+)
 from .parser import ParsingException
 from .version import version as __version__
 
 
 __all__ = [
-    'ExpressionComponent',
-    'SingleComponent',
-    'Expression',
-    'Variable',
-    'NamedConstant',
-    'UnnamedConstant',
-    'ParsingException',
-    'from_auto',
+    "ExpressionComponent",
+    "SingleComponent",
+    "Expression",
+    "Variable",
+    "NamedConstant",
+    "UnnamedConstant",
+    "ParsingException",
+    "from_auto",
     # numexpr
-    'from_numexpr',
-    'to_numexpr',
+    "from_numexpr",
+    "to_numexpr",
     # ROOT
-    'from_root',
-    'to_root',
-    '__version__',
+    "from_root",
+    "to_root",
+    "__version__",
 ]
 
 

formulate/__main__.py

@@ -1,7 +1,4 @@
 # Licensed under a 3-clause BSD style license, see LICENSE.
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
 
 import argparse
 import sys
@@ -11,18 +8,20 @@
 
 
 def parse_args(args):
-    parser = argparse.ArgumentParser(description='Convert between different types of formulae')
+    parser = argparse.ArgumentParser(
+        description="Convert between different types of formulae"
+    )
 
     from_group = parser.add_mutually_exclusive_group(required=True)
-    from_group.add_argument('--from-root')
-    from_group.add_argument('--from-numexpr')
+    from_group.add_argument("--from-root")
+    from_group.add_argument("--from-numexpr")
 
     to_group = parser.add_mutually_exclusive_group(required=True)
-    to_group.add_argument('--to-root', action='store_true')
-    to_group.add_argument('--to-numexpr', action='store_true')
-    to_group.add_argument('--variables', action='store_true')
-    to_group.add_argument('--named-constants', action='store_true')
-    to_group.add_argument('--unnamed-constants', action='store_true')
+    to_group.add_argument("--to-root", action="store_true")
+    to_group.add_argument("--to-numexpr", action="store_true")
+    to_group.add_argument("--variables", action="store_true")
+    to_group.add_argument("--named-constants", action="store_true")
+    to_group.add_argument("--unnamed-constants", action="store_true")
 
     args = parser.parse_args(args)
     if args.from_root is not None:
@@ -37,16 +36,16 @@ def parse_args(args):
     elif args.to_numexpr:
         result = to_numexpr(expression)
     elif args.variables:
-        result = '\n'.join(sorted(expression.variables))
+        result = "\n".join(sorted(expression.variables))
     elif args.named_constants:
-        result = '\n'.join(sorted(expression.named_constants))
+        result = "\n".join(sorted(expression.named_constants))
     elif args.unnamed_constants:
-        result = '\n'.join(sorted(expression.unnamed_constants))
+        result = "\n".join(sorted(expression.unnamed_constants))
     else:
         raise NotImplementedError()
 
     return result
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     print(parse_args(sys.argv[1:]))