No more os.path

docs/conf.py

@@ -4,16 +4,6 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
 
 # -- Project information -----------------------------------------------------
 

tests/notebooks/test_notebooks.py

@@ -1,55 +1,47 @@
-import os
-import subprocess
+from pathlib import Path
+from typing import List
+
 
 import nbformat
 from nbconvert.preprocessors import ExecutePreprocessor
 from nbconvert.preprocessors import CellExecutionError
 
-_TEST_DIR = os.path.dirname(os.path.abspath(__file__))
-PARENT_DIR = os.path.join(_TEST_DIR, "../..")
-SKIP_LIST = []
-
 
-def _process_notebook(notebook_filename, notebook_path="notebooks"):
+def _process_notebook(fp: Path):
     """Checks if an IPython notebook runs without error from start to finish. If so, writes the notebook to HTML (with outputs) and overwrites the .ipynb file (without outputs)."""
-    with open(notebook_filename) as f:
+    with open(fp) as f:
         nb = nbformat.read(f, as_version=4)
 
     ep = ExecutePreprocessor(timeout=600, kernel_name="python3")
 
     try:
         # Check that the notebook runs
-        ep.preprocess(nb, {"metadata": {"path": notebook_path}})
+        ep.preprocess(nb, {"metadata": {"path": "notebooks"}})
     except CellExecutionError as e:
-        print(f"Failed executing {notebook_filename}")
+        print(f"Failed executing {fp}")
         print(e)
         raise
 
-    print(f"Successfully executed {notebook_filename}")
+    print(f"Successfully executed {fp}")
     return
 
 
-def _get_all_notebooks_in_repo(skip=[]):
-    """Get all files .ipynb included in the git repository"""
-    git_files = (
-        subprocess.check_output(
-            "git ls-tree --full-tree --name-only -r HEAD", shell=True
-        )
-        .decode("utf-8")
-        .splitlines()
-    )
+def _get_all_notebooks_in_repo() -> List[Path]:
+    ROOT_DIR = Path(__file__).parent.parent.parent
+    NOTEBOOK_DIR = ROOT_DIR / "notebooks"
 
-    return [
-        fn
-        for fn in git_files
-        if fn.endswith(".ipynb") and not any(s in fn for s in skip)
-    ]
+    return list(NOTEBOOK_DIR.glob("*.ipynb"))
 
 
 def test_notebook(notebook):
-    _process_notebook(os.path.join(PARENT_DIR, notebook))
-
+    _process_notebook(notebook)
 
 def pytest_generate_tests(metafunc):
-    notebooks = _get_all_notebooks_in_repo(skip=SKIP_LIST)
+    notebooks = _get_all_notebooks_in_repo()
     metafunc.parametrize("notebook", notebooks)
+
+
+if __name__ == "__main__":
+    notebooks = _get_all_notebooks_in_repo()
+    for notebook in notebooks:
+        print(notebook)

tests/performance/test_performance_dfs0.py

@@ -1,12 +1,12 @@
-import os
+from pathlib import Path
 import numpy as np
 import pandas as pd
 import mikeio
 
 
-def test_write_read_long_dfs0(tmpdir):
+def test_write_read_long_dfs0(tmp_path):
 
-    filename = os.path.join(tmpdir.dirname, "big.dfs0")
+    filename = tmp_path / "big.dfs0"
 
     nt = 10_000_000
     data = np.random.random([nt])
@@ -15,16 +15,16 @@ def test_write_read_long_dfs0(tmpdir):
     )
     da.to_dfs(filename)
 
-    assert os.path.exists(filename)
+    assert filename.exists()
 
     ds = mikeio.read(filename)
 
     assert len(ds.time) == nt
 
 
-def test_write_read_many_items_dataset_pandas(tmpdir):
+def test_write_read_many_items_dataset_pandas(tmp_path):
 
-    filename = os.path.join(tmpdir.dirname, "many_items.dfs0")
+    filename = tmp_path / "many_items.dfs0"
 
     n_items = 10_000
     nt = 200
@@ -38,7 +38,7 @@ def test_write_read_many_items_dataset_pandas(tmpdir):
     ds = mikeio.Dataset(das)
     ds.to_dfs(filename)
 
-    assert os.path.exists(filename)
+    assert filename.exists()
 
     # read to dataset
     ds = mikeio.read(filename)

tests/test_mesh.py

@@ -40,14 +40,14 @@ def test_read_mixed_mesh(mixed_mesh):
     assert np.all(el_tbl_vec < msh.n_nodes)
 
 
-def test_read_write_mixed_mesh(mixed_mesh, tmpdir):
+def test_read_write_mixed_mesh(mixed_mesh, tmp_path):
     msh = mixed_mesh
-    outfilename = os.path.join(tmpdir.dirname, "quad_tri_v2.mesh")
+    outfilename = tmp_path / "quad_tri_v2.mesh"
     msh.write(outfilename)
 
     msh2 = Mesh(outfilename)
 
-    assert os.path.exists(outfilename)
+    assert outfilename.exists()
 
     assert np.all(np.hstack(msh2.element_table) == np.hstack(msh.element_table))
     assert np.all(msh2.element_coordinates == msh.element_coordinates)
@@ -78,7 +78,6 @@ def test_get_bad_node_coordinates(tri_mesh):
 
 
 def test_set_z(tri_mesh):
-    os.path.join("tests", "testdata", "odense_rough.mesh")
     msh = tri_mesh
     zn = msh.node_coordinates[:, 2]
     zn[zn < -3] = -3
@@ -107,35 +106,35 @@ def test_set_codes(tri_mesh):
         msh.geometry.codes = codes[0:4]
 
 
-def test_write(tri_mesh, tmpdir):
-    outfilename = os.path.join(tmpdir.dirname, "simple.mesh")
+def test_write(tri_mesh, tmp_path):
+    outfilename = tmp_path / "simple.mesh"
     msh = tri_mesh
 
     msh.write(outfilename)
 
-    assert os.path.exists(outfilename)
+    assert outfilename.exists()
 
 
-def test_write_part(tri_mesh, tmpdir):
-    outfilename = os.path.join(tmpdir.dirname, "simple_sub.mesh")
+def test_write_part(tri_mesh, tmp_path):
+    outfilename = tmp_path / "simple_sub.mesh"
 
     msh = tri_mesh
 
     msh.write(outfilename, elements=list(range(0, 100)))
 
-    assert os.path.exists(outfilename)
+    assert outfilename.exists()
 
 
-def test_write_mesh_from_dfsu(tmpdir):
-    outfilename = os.path.join(tmpdir.dirname, "quad_tri.mesh")
-    dfsufilename = os.path.join("tests", "testdata", "FakeLake.dfsu")
+def test_write_mesh_from_dfsu(tmp_path):
+    outfilename = tmp_path / "quad_tri.mesh"
+    dfsufilename = "tests/testdata/FakeLake.dfsu"
 
     msh = Mesh(dfsufilename)
 
     msh.write(outfilename)
 
     msh2 = Mesh(outfilename)
 
-    assert os.path.exists(outfilename)
+    assert outfilename.exists()
 
     assert np.all(np.hstack(msh2.element_table) == np.hstack(msh.element_table))