maint: remove poetry from noxfile etc

Author: oscarbenjamin

.flake8

@@ -1,6 +1,6 @@
 [flake8]
 select = B,B9,C,D,DAR,E,F,N,RST,S,W,TC,TC1
-ignore = E203,E501,RST201,RST203,RST301,W503,B902,B905,RST304
+ignore = D202,E203,E501,RST201,RST203,RST301,W503,B902,B905,RST304
 max-line-length = 80
 max-complexity = 10
 docstring-convention = google

.github/workflows/tests.yml

@@ -16,8 +16,7 @@ jobs:
           - { python-version: 3.9, os: ubuntu-latest, session: "tests" }
           - { python-version: 3.8, os: ubuntu-latest, session: "tests" }
           - { python-version: 3.9, os: ubuntu-latest, session: "pre-commit" }
-          - { python-version: 3.9, os: ubuntu-latest, session: "safety" }
-          - { python-version: 3.9, os: ubuntu-latest, session: "xdoctest" }
+          - { python-version: 3.9, os: ubuntu-latest, session: "doctest" }
           - { python-version: 3.9, os: ubuntu-latest, session: "docs-build" }
 
     env:
@@ -32,19 +31,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Upgrade pip
-        run: |
-          pip install --constraint=.github/workflows/constraints.txt pip
-          pip --version
-
-      - name: Install Poetry
-        run: |
-          pip install --constraint=.github/workflows/constraints.txt poetry
-          poetry --version
-
       - name: Install Nox
         run: |
-          pip install --constraint=.github/workflows/constraints.txt nox nox-poetry
+          pip install --upgrade pip
+          pip install nox
           nox --version
 
       - name: Compute pre-commit cache key
@@ -103,19 +93,10 @@ jobs:
         with:
           python-version: 3.9
 
-      - name: Upgrade pip
-        run: |
-          pip install --constraint=.github/workflows/constraints.txt pip
-          pip --version
-
-      - name: Install Poetry
-        run: |
-          pip install --constraint=.github/workflows/constraints.txt poetry
-          poetry --version
-
       - name: Install Nox
         run: |
-          pip install --constraint=.github/workflows/constraints.txt nox nox-poetry
+          pip install --upgrade pip
+          pip install nox
           nox --version
 
       - name: Download coverage data

noxfile.py

@@ -2,129 +2,30 @@
 import shutil
 import sys
 from pathlib import Path
-from textwrap import dedent
 
 import nox
-
-try:
-    from nox_poetry import Session
-    from nox_poetry import session
-except ImportError:
-    message = f"""\
-    Nox failed to import the 'nox-poetry' package.
-
-    Please install it using the following command:
-
-    {sys.executable} -m pip install nox-poetry"""
-    raise SystemExit(dedent(message)) from None
+from nox import Session
+from nox import session
 
 
 package = "protosym"
 python_versions = ["3.9", "3.8"]
 nox.needs_version = ">= 2021.6.6"
 nox.options.sessions = (
     "pre-commit",
-    "safety",
     "mypy",
     "tests",
-    # "typeguard", disabled because it conflicts with if TYPE_CHECKING
-    "xdoctest",
+    "doctest",
     "docs-build",
 )
 
 
-def activate_virtualenv_in_precommit_hooks(session: Session) -> None:
-    """Activate virtualenv in hooks installed by pre-commit.
-
-    This function patches git hooks installed by pre-commit to activate the
-    session's virtual environment. This allows pre-commit to locate hooks in
-    that environment when invoked from git.
-
-    Args:
-        session: The Session object.
-    """
-    if session.bin is None:
-        return
-
-    virtualenv = session.env.get("VIRTUAL_ENV")
-    if virtualenv is None:
-        return
-
-    hookdir = Path(".git") / "hooks"
-    if not hookdir.is_dir():
-        return
-
-    for hook in hookdir.iterdir():
-        if hook.name.endswith(".sample") or not hook.is_file():
-            continue
-
-        text = hook.read_text()
-        bindir = repr(session.bin)[1:-1]  # strip quotes
-        if not (
-            Path("A") == Path("a") and bindir.lower() in text.lower() or bindir in text
-        ):
-            continue
-
-        lines = text.splitlines()
-        if not (lines[0].startswith("#!") and "python" in lines[0].lower()):
-            continue
-
-        header = dedent(
-            f"""\
-            import os
-            os.environ["VIRTUAL_ENV"] = {virtualenv!r}
-            os.environ["PATH"] = os.pathsep.join((
-                {session.bin!r},
-                os.environ.get("PATH", ""),
-            ))
-            """
-        )
-
-        lines.insert(1, header)
-        hook.write_text("\n".join(lines))
-
-
 @session(name="pre-commit", python="3.9")
 def precommit(session: Session) -> None:
     """Lint using pre-commit."""
     args = session.posargs or ["run", "--all-files", "--show-diff-on-failure"]
-    session.install(
-        "black",
-        "darglint",
-        "flake8",
-        "flake8-bandit",
-        "flake8-bugbear",
-        "flake8-docstrings",
-        "flake8-rst-docstrings",
-        "flake8-type-checking",
-        "pep8-naming",
-        "pre-commit",
-        "pre-commit-hooks",
-        "reorder-python-imports",
-    )
+    session.install("-r", "requirements-lint.txt")
     session.run("pre-commit", *args)
-    if args and args[0] == "install":
-        activate_virtualenv_in_precommit_hooks(session)
-
-
-@session(python="3.9")
-def safety(session: Session) -> None:
-    """Scan dependencies for insecure packages."""
-    requirements = session.poetry.export_requirements()
-    session.install("safety")
-    session.run(
-        "safety",
-        "check",
-        # "--full-report",
-        # Using --output bare below because otherwise safety is too verbose.
-        # Unfortunately it means that any failure message is not shown so
-        # comment these lines oput if safety fails.
-        "--output",
-        "bare",
-        f"--file={requirements}",
-        "--ignore=51457",  # https://github.com/pytest-dev/py/issues/287
-        "--ignore=58755",  # https://github.com/mpmath/mpmath/issues/548
-    )
 
 
 @session(python="3.9")
@@ -141,8 +42,7 @@ def mypy(session: Session) -> None:
 @session(python=python_versions)
 def tests(session: Session) -> None:
     """Run the test suite."""
-    session.install(".", "sympy", "llvmlite", "numpy")
-    session.install("coverage[toml]", "pytest", "pygments")
+    session.install(".", "-r", "requirements-test.txt")
     try:
         session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
     finally:
@@ -163,33 +63,19 @@ def coverage(session: Session) -> None:
     session.run("coverage", *args)
 
 
-# It seems that with typeguard it is not possible to use if TYPE_CHECKING
-# blocks and all types in annotations need to be resolvable at runtime. For now
-# we disable this runtime type checking feature.
-#
-# @session(python=python_versions)
-# def typeguard(session: Session) -> None:
-#     """Runtime type checking using Typeguard."""
-#     session.install(".")
-#     session.install("pytest", "typeguard", "pygments")
-#     session.run("pytest", f"--typeguard-packages={package}", *session.posargs)
-
-
 @session(python=python_versions)
-def xdoctest(session: Session) -> None:
+def doctest(session: Session) -> None:
     """Run examples with xdoctest."""
     args = session.posargs or ["all"]
-    session.install(".", "sympy", "llvmlite", "numpy")
-    session.install("xdoctest[colors]")
+    session.install(".", "-r", "requirements-test.txt")
     session.run("python", "-m", "xdoctest", "--quiet", package, *args)
 
 
 @session(name="docs-build", python="3.9")
 def docs_build(session: Session) -> None:
     """Build the documentation."""
     args = session.posargs or ["-W", "docs", "docs/_build"]
-    session.install(".")
-    session.install("sphinx", "sphinx-rtd-theme")
+    session.install(".", "-r", "requirements-docs.txt")
 
     build_dir = Path("docs", "_build")
     if build_dir.exists():
@@ -202,8 +88,7 @@ def docs_build(session: Session) -> None:
 def docs(session: Session) -> None:
     """Build and serve the documentation with live reloading on file changes."""
     args = session.posargs or ["--open-browser", "docs", "docs/_build", "--watch=src"]
-    session.install(".")
-    session.install("sphinx", "sphinx-autobuild", "sphinx-rtd-theme")
+    session.install(".", "-r", "requirements-docs.txt")
 
     build_dir = Path("docs", "_build")
     if build_dir.exists():

quicktest.sh

@@ -14,8 +14,8 @@ if [ "$1" = "--rs" ]; then
     cd -
 fi
 
-poetry run pre-commit run --all-files
-poetry run mypy src tests
-poetry run python -m xdoctest --quiet protosym
-poetry run pytest --cov=protosym
-poetry run coverage html
+pre-commit run --all-files
+mypy src tests
+python -m xdoctest --quiet protosym
+pytest --cov=protosym
+coverage html

requirements-all.txt

@@ -0,0 +1,4 @@
+-r requirements-lint.txt
+-r requirements-test.txt
+-r requirements-docs.txt
+mypy

requirements-docs.txt

@@ -0,0 +1,3 @@
+sphinx
+sphinx-rtd-theme
+sphinx-autobuild

requirements-lint.txt

@@ -0,0 +1,12 @@
+black
+darglint
+flake8
+flake8-bandit
+flake8-bugbear
+flake8-docstrings
+flake8-rst-docstrings
+flake8-type-checking
+pep8-naming
+pre-commit
+pre-commit-hooks
+reorder-python-imports

requirements-test.txt

@@ -0,0 +1,7 @@
+sympy
+llvmlite
+numpy
+pytest
+coverage[toml]
+pygments
+xdoctest[colors]

src/protosym/core/tree.py

@@ -241,6 +241,7 @@ def topological_sort(
     Tree: The expression class that this function operates on.
     topological_split: Splits the sort into atoms, heads and nodes.
     """
+
     #
     # We use a stack here rather than recursion so that there is no limit on
     # the recursion depth. Otherwise though this is really just the same as
@@ -459,7 +460,6 @@ class SubsFunc:
     operations: list[list[int]]
 
     def __new__(cls, expr: Tree, args: list[Tree]) -> SubsFunc:
-
         # A topological sort but exluding the args because they will be
         # replaced in the substitution anyway.
         subexpressions = topological_sort(expr, heads=True, exclude=set(args))