Dev deps (#330)

* Replace black with ruff format and format doc string code

* Fix some formatting deltas and exclude some rules that apply more broadly than before.

* Remove hard coded black from workflow

* Add some more package bounds. Add test for oldest package version.
* Locally verified 1.24, wouldn't be too hard to update to support older if desired

* Actually add github action for testing oldest

* Bad default glob

* Uv really means it when they say oldest.

* Try using uv pip interface without venv

* Another round. Worked locally

* Another minimum

* Remove final black reference

* Try updating broken link

* Update pytest instructions

.github/workflows/oldest-support.yaml

@@ -0,0 +1,40 @@
+# This should mirror regression tests. Ideally we find a way in the future to fold the two together
+
+name: Test Oldest Dependencies
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  UV_SYSTEM_PYTHON: 1
+
+jobs:
+  test-oldest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # Use uv since it has easy lowest resolution
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'  # Find a way to globally define our minimum python once
+
+      - name: Install dependencies with minimum versions
+        run: |
+          uv sync --resolution lowest-direct --extra dev 
+
+      - name: Run tests
+        run: |
+          uv run --resolution lowest-direct pytest ./tests

.github/workflows/regression-tests.yml

@@ -34,9 +34,6 @@ jobs:
       run: |
         python -m pip install --upgrade coverage coveralls sphinx_rtd_theme
         pip install ".[dev]"
-    - name: Check auto-formatters
-      run: |
-        black --check .
     - name: Run tests
       run: |
         coverage run --source pyttb -m pytest tests/

.pre-commit-config.yaml

@@ -1,16 +1,12 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.284
+    rev: v0.7.2
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
-  - repo: https://github.com/psf/black
-    rev: 24.1.1
-    hooks:
-      - id: black
-        language_version: python
+      - id: ruff-format
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.0
     hooks:
       - id: nbstripout
         args: [

CHANGELOG.md

@@ -135,7 +135,7 @@
 # v1.3.3 (2022-07-11)
 - Fixed indexing bug in `tensor.mttkrp` (Issue #35, PR #36)
 - Updated LICENSE to compliant format (Issue #33 , PR #34)
-- Now using [coveralls.io](https://coveralls.io/github/sandialabs/pyttb) for coverage reporting
+- Now using [coveralls.io](https://coveralls.io/github/sandialabs/pyttb?branch=main) for coverage reporting
 - Now using [readthedocs.io](https://pyttb.readthedocs.io/en/latest/) for documentation
 
 # v1.3.2 (2022-07-06)

CONTRIBUTING.md

@@ -39,7 +39,7 @@ current or filing a new [issue](https://github.com/sandialabs/pyttb/issues).
    1. Run autoformatters and linting from root of project (they will change your code)
        ```commandline
        ruff check . --fix
-       black .
+       ruff format
        ```
       1. Ruff's `--fix` won't necessarily address everything and may point out issues that need manual attention
       1. [We](./.pre-commit-config.yaml) optionally support [pre-commit hooks](https://pre-commit.com/) for this
@@ -52,15 +52,15 @@ current or filing a new [issue](https://github.com/sandialabs/pyttb/issues).
 1. Run tests (at desired fidelity)
    1. Just doctests (enabled by default)
         ```commandline
-        pytest
+        pytest .
         ```
    1. Functional tests
         ```commandline
-        pytest .
+        pytest tests
         ```
    1. With coverage
         ```commandline
-        pytest . --cov=pyttb --cov-report=term-missing
+        pytest tests --cov=pyttb --cov-report=term-missing
         ```
 
 1. (Optionally) Building documentation and tutorials

pyproject.toml

@@ -10,10 +10,10 @@ readme = "README.md"
 requires-python = ">=3.9"
 
 dependencies = [
-    "numpy",
-    "numpy_groupies",
-    "scipy",
-    "matplotlib",
+    "numpy<3.0,>=1.24",
+    "numpy_groupies>0.11",
+    "scipy>1.9",
+    "matplotlib>3.7",
 ]
 
 classifiers = [
@@ -32,18 +32,19 @@ documentation = "https://pyttb.readthedocs.io"
 
 [project.optional-dependencies]
 dev = [
-    "black[jupyter]",
-    "mypy",
-    "nbstripout",
-    "pytest",
-    "pytest-cov",
-    "ruff==0.0.284",
-    "pre-commit",
+    "mypy>=1.10,<1.14.0",
+    # Also in pre-commit
+    "nbstripout>=0.8,<0.9",
+    "pytest>8.0",
+    "pytest-cov>5.0",
+    # Also in pre-commit
+    "ruff>=0.7,<0.8",
+    "pre-commit>=4.0,<5.0",
 ]
 doc = [
     "sphinx >= 4.0",
-    "sphinx_rtd_theme",
-    "myst-nb",
+    "sphinx_rtd_theme>2.0",
+    "myst-nb>1.0",
 ]
 profiling = [
     "gprof2dot",
@@ -65,7 +66,7 @@ version = {attr = "pyttb.__version__"}
 requires = ["setuptools>=61.0", "numpy", "numpy_groupies", "scipy", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tool.ruff]
+[tool.ruff.lint]
 select = ["E", "F", "PL", "W", "I", "N", "NPY", "RUF", "B"]
 ignore = [
     # Ignored in conversion to ruff since not previously enforced
@@ -83,13 +84,18 @@ ignore = [
     # There is ongoing discussion about logging/warning etc
     "B028",
 ]
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # See  see https://github.com/astral-sh/ruff/issues/3172 for details on this becoming simpler
 
 # Everything but I, F (to catch import mess and potential logic errors)
 "tests/**.py" = ["E", "PL", "W", "N", "NPY", "RUF", "B"]
 # Ignore everything for now
 "docs/**.py" = ["E", "F", "PL", "W", "I", "N", "NPY", "RUF", "B"]
+"docs/**.ipynb" = ["E", "F", "PL", "W", "I", "N", "NPY", "RUF", "B"]
+"profiling/**.ipynb" = ["E", "F", "PL", "W", "I", "N", "NPY", "RUF", "B"]
+
+[tool.ruff.format]
+docstring-code-format = true
 
 [tool.mypy]
 warn_unused_configs = true

pyttb/cp_apr.py

@@ -1138,7 +1138,7 @@ def tt_cp_apr_pqnr(  # noqa: PLR0912,PLR0913,PLR0915
 
 
 @overload
-def tt_calcpi_prowsubprob(  # noqa: PLR0913
+def tt_calcpi_prowsubprob(
     Data: ttb.sptensor,
     Model: ttb.ktensor,
     rank: int,
@@ -1150,7 +1150,7 @@ def tt_calcpi_prowsubprob(  # noqa: PLR0913
 
 
 @overload
-def tt_calcpi_prowsubprob(  # noqa: PLR0913
+def tt_calcpi_prowsubprob(
     Data: ttb.tensor,
     Model: ttb.ktensor,
     rank: int,

pyttb/gcp/fg_est.py

@@ -17,7 +17,7 @@
 
 
 @overload
-def estimate(  # noqa: PLR0913
+def estimate(
     model: ttb.ktensor,
     data_subs: np.ndarray,
     data_vals: np.ndarray,
@@ -30,7 +30,7 @@ def estimate(  # noqa: PLR0913
 
 
 @overload
-def estimate(  # noqa: PLR0913
+def estimate(
     model: ttb.ktensor,
     data_subs: np.ndarray,
     data_vals: np.ndarray,
@@ -43,7 +43,7 @@ def estimate(  # noqa: PLR0913
 
 
 @overload
-def estimate(  # noqa: PLR0913
+def estimate(
     model: ttb.ktensor,
     data_subs: np.ndarray,
     data_vals: np.ndarray,

pyttb/hosvd.py

@@ -46,7 +46,7 @@ def hosvd(  # noqa: PLR0912,PLR0913,PLR0915
 
     Example
     -------
-    >>> data = np.array([[29, 39.], [63., 85.]])
+    >>> data = np.array([[29, 39.0], [63.0, 85.0]])
     >>> tol = 1e-4
     >>> disable_printing = -1
     >>> tensorInstance = ttb.tensor(data)

pyttb/khatrirao.py

@@ -25,13 +25,13 @@ def khatrirao(*matrices: np.ndarray, reverse: bool = False) -> np.ndarray:
 
     Examples
     --------
-    >>> A = np.random.normal(size=(5,2))
-    >>> B = np.random.normal(size=(5,2))
-    >>> _ = khatrirao(A,B) #<-- Khatri-Rao of A and B
-    >>> _ = khatrirao(B,A,reverse=True) #<-- same thing as above
-    >>> _ = khatrirao(A,A,B) #<-- passing multiple items
-    >>> _ = khatrirao(B,A,A,reverse = True) #<-- same as above
-    >>> _ = khatrirao(*[A,A,B]) #<-- passing a list via unpacking items
+    >>> A = np.random.normal(size=(5, 2))
+    >>> B = np.random.normal(size=(5, 2))
+    >>> _ = khatrirao(A, B)  # <-- Khatri-Rao of A and B
+    >>> _ = khatrirao(B, A, reverse=True)  # <-- same thing as above
+    >>> _ = khatrirao(A, A, B)  # <-- passing multiple items
+    >>> _ = khatrirao(B, A, A, reverse=True)  # <-- same as above
+    >>> _ = khatrirao(*[A, A, B])  # <-- passing a list via unpacking items
     """
     # Determine if list of matrices of multiple matrix arguments
     if len(matrices) == 1 and isinstance(matrices[0], list):