Merge pull request #56 from equinor/unpin_numpy

Unpin numpy

.github/workflows/lint.yml

@@ -6,11 +6,11 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
       - name: Install tox
         run: pip install tox
       - name: Check style

.github/workflows/testing.yml

@@ -11,9 +11,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox

.pre-commit-config.yaml

@@ -1,13 +1,16 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
+    -   id: no-commit-to-branch
     -   id: check-json
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 
--   repo: https://github.com/ambv/black
-    rev: 23.3.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
     hooks:
-    - id: black
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

pyproject.toml

@@ -16,7 +16,7 @@ classifiers=[
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
-dependencies = ["numpy<2"]
+dependencies = ["numpy"]
 dynamic=["version"]
 
 authors = [
@@ -49,3 +49,37 @@ dev = [
 ]
 
 [tool.setuptools_scm]
+
+[tool.ruff]
+src = ["src"]
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+  "W",  # pycodestyle
+  "I",  # isort
+  "B",  # flake-8-bugbear
+  "SIM",  # flake-8-simplify
+  "F",  # pyflakes
+  "PL",  # pylint
+  "NPY",  # numpy specific rules
+  "C4",  # flake8-comprehensions
+]
+preview = true
+ignore = ["PLW2901",  # redefined-loop-name
+          "PLR2004",  # magic-value-comparison
+          "PLR0915",  # too-many-statements
+          "PLR0912",  # too-many-branches
+          "PLR0911",  # too-many-return-statements
+          "PLC2701",  # import-private-name
+          "PLR6201",  # literal-membership
+          "PLR0914",  # too-many-locals
+          "PLR6301",  # no-self-use
+          "PLW1641",  # eq-without-hash
+          "PLR0904",  # too-many-public-methods
+          "PLR1702",  # too-many-nested-blocks
+          "PLW3201",  # bad-dunder-method-name
+]
+
+[tool.ruff.lint.pylint]
+max-args = 10

src/resfo/_formatted/write.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import resfo.types as res_types
 from resfo.errors import ResfoWriteError
 

src/resfo/_unformatted/read.py

@@ -1,6 +1,7 @@
 import io
 
 import numpy as np
+
 import resfo.types as res_types
 from resfo._unformatted.common import bytes_in_array, group_len, item_size
 from resfo._unformatted.write import write_array_like
@@ -51,10 +52,7 @@ def update(self, *, keyword=None, array=None):
             keyword = self.read_keyword()
 
         if array is not res_types.MESS:
-            if array is not None:
-                array = np.asarray(array)
-            else:
-                array = self.read_array()
+            array = np.asarray(array) if array is not None else self.read_array()
             if array is not res_types.MESS and self.read_length() != array.size:
                 raise ValueError("Cannot update array with different size")
 

src/resfo/_unformatted/write.py

@@ -1,6 +1,7 @@
 import warnings
 
 import numpy as np
+
 import resfo.types as res_types
 from resfo._unformatted.common import group_len, item_size
 from resfo.errors import ResfoWriteError
@@ -35,7 +36,7 @@ def cast_array_to_res(arr):
     else:
         raise ValueError(f"Cannot cast {arr.dtype} to a res type")
 
-    warnings.warn(f"casting array dtype {arr.dtype} to {result_dtype}")
+    warnings.warn(f"casting array dtype {arr.dtype} to {result_dtype}", stacklevel=1)
     return arr.astype(result_dtype)
 
 

src/resfo/format.py

@@ -51,9 +51,9 @@ def get_stream(filepath, fileformat: Format, mode: str = "r"):
     """
     if isinstance(filepath, (str, Path)):
         if fileformat == Format.FORMATTED:
-            return open(filepath, mode + "t"), True
+            return open(filepath, mode + "t"), True  # noqa: SIM115
         else:
-            return open(filepath, mode + "b"), True
+            return open(filepath, mode + "b"), True  # noqa: SIM115
     else:
         return filepath, False
 

src/resfo/types.py

@@ -22,6 +22,7 @@
 that results in a warning.
 
 """
+
 import warnings
 from typing import TYPE_CHECKING, Union
 
@@ -61,7 +62,7 @@ def to_np_type(type_keyword):
     """
     if type_keyword[0:2] == b"C0":
         return np.dtype("|S" + type_keyword[2:4].decode("ascii"))
-    return static_dtypes.get(type_keyword, None)
+    return static_dtypes.get(type_keyword)
 
 
 def from_np_dtype(array):
@@ -78,7 +79,7 @@ def from_np_dtype(array):
     if dtype in [np.dtype(np.int32), np.dtype(np.int32).newbyteorder(">")]:
         return b"INTE"
     if dtype in [np.dtype(np.int64), np.dtype(np.int64).newbyteorder(">")]:
-        warnings.warn("downcasting numpy int64 to int32 for res file.")
+        warnings.warn("downcasting numpy int64 to int32 for res file.", stacklevel=1)
         return b"INTE"
     if dtype in [np.dtype(np.float32), np.dtype(np.float32).newbyteorder(">")]:
         return b"REAL"
@@ -112,7 +113,7 @@ def is_valid_type(type_str):
     """
     :returns: Whether the given byte string is a valid res type.
     """
-    if type_str in static_dtypes.keys():
+    if type_str in static_dtypes:
         return True
     if type_str in [b"X231", b"MESS"]:
         return True

src/resfo/version.py

@@ -1,4 +1,4 @@
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     version = version("resfo")

tests/conftest.py

@@ -1,6 +1,5 @@
 from hypothesis import HealthCheck, settings
 
-
 settings.register_profile(
     "no_timeouts",
     deadline=None,

tests/generators.py

@@ -1,8 +1,9 @@
 import hypothesis.strategies as st
 import numpy as np
-import resfo
 from hypothesis.extra.numpy import arrays
 
+import resfo
+
 formats = st.sampled_from(resfo.Format)
 in_formats = st.one_of(formats, st.just(None))
 keywords = st.text(

tests/test_error_handling.py

@@ -1,6 +1,7 @@
 from io import BytesIO, StringIO
 
 import pytest
+
 from resfo import Format, ResfoParsingError, ResfoWriteError, read, write
 
 

tests/test_formatted_common.py

@@ -1,8 +1,9 @@
 import hypothesis.strategies as st
 import pytest
-from resfo._unformatted.common import bytes_in_array, group_len, item_size
 from hypothesis import given
 
+from resfo._unformatted.common import bytes_in_array, group_len, item_size
+
 
 def test_group_len():
     assert group_len(b"C032") == 105

tests/test_formatted_read.py

@@ -1,6 +1,7 @@
 import io
 
 import numpy as np
+
 import resfo._formatted.read as fread
 
 

tests/test_formatted_write.py

@@ -1,6 +1,7 @@
 import io
 
 import numpy as np
+
 import resfo._formatted.write as fwrite
 from resfo.types import MESS
 

tests/test_read_write.py

@@ -1,6 +1,7 @@
 import numpy as np
 from hypothesis import HealthCheck, given, settings
 from numpy.testing import assert_allclose
+
 from resfo import MESS, read, write
 
 from .generators import formats, resfo_datas

tests/test_type_resolution.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 import resfo
 
 
@@ -19,7 +20,7 @@ def test_formatted_read_type_resolution(tmp_path, contents, expected_type):
         f.write(contents)
 
     with (tmp_path / "test.txt").open("r") as f:
-        ((specgrid, arr),) = resfo.read(f)
+        ((_specgrid, arr),) = resfo.read(f)
 
     assert arr.dtype == expected_type
 
@@ -77,9 +78,9 @@ def keyword_start(res_type):
         ),
         (
             keyword_start(b"C010")
-            + b"\x00\x00\x00\x0A"
+            + b"\x00\x00\x00\x0a"
             + b"SPECGRID10"
-            + b"\x00\x00\x00\x0A",
+            + b"\x00\x00\x00\x0a",
             np.dtype("|S10"),
         ),
         (
@@ -94,7 +95,7 @@ def test_unformatted_read_type_resolution(tmp_path, contents, expected_type):
         f.write(contents)
 
     with (tmp_path / "test.txt").open("rb") as f:
-        ((specgrid, arr),) = resfo.read(f)
+        ((_specgrid, arr),) = resfo.read(f)
 
     assert arr.dtype == expected_type
 

tests/test_types.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import resfo.types
 
 

tests/test_unformatted_read.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pytest
+
 import resfo._unformatted.read as uwrite
 
 

tests/test_unformatted_write.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pytest
+
 import resfo._unformatted.write as uwrite
 from resfo.types import MESS
 

tests/test_update.py

@@ -7,7 +7,7 @@
 
 from resfo import MESS, lazy_read, read, write
 
-from .generators import resfo_datas, float_arrays, keywords
+from .generators import float_arrays, keywords, resfo_datas
 
 
 @settings(suppress_health_check=[HealthCheck.function_scoped_fixture])