Merge pull request #454 from tataratat/develop

.pre-commit-config.yaml

@@ -35,7 +35,7 @@ repos:
     additional_dependencies: [tomli]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.5.6
+  rev: v0.6.1
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

docs/source/handle_markdown.py

@@ -11,6 +11,7 @@
 Author: Clemens Fricke
 """
 
+import argparse
 import os
 import pathlib
 import re
@@ -131,69 +132,81 @@ def process_file(
     Returns:
         str: Content of the markdown file. Only if return_content is True.
     """
+    content = ""
     # read in the content of the markdown file
     with open(file) as f:
-        content = f.read()
-    os.chdir(os.path.dirname(file)) if os.path.dirname(file) else None
-    # get all links from the markdown file
-    links = get_markdown_links(content)
-
-    for item in links:
-        if not item[1].strip():
-            warnings.warn(
-                f"Empty link in `{file}`. Link name `{item[0]}` link path "
-                f"`{item[1]}`. Will ignore link.",
-                stacklevel=3,
-            )
-            continue
-        if item[1].startswith(("http", "#")):  # skip http links and anchors
-            if "badge" in item[1]:
-                continue
-            content = content.replace(
-                f"[{item[0]}]({item[1]})",
-                f"<a href='{item[1]}'>{item[0]}</a>",
-            )
-            continue
-        elif item[1] in link_substitutions:
-            if relative_links:
-                content = content.replace(
-                    f"[{item[0]}]({item[1]})",
-                    f"<a href='{link_substitutions[item[1]]}'>{item[0]}</a>",
-                )
-                continue
-            else:
-                content = content.replace(
-                    f"[{item[0]}]({item[1]})",
-                    "See documentation for examples.",
-                )
-        elif not relative_links:  # generate links to github repo
-            new_path = get_github_path_from(pathlib.Path(item[1]).resolve())
-        else:  # generate relative links
-            common_sub_path, steps_back = get_common_parent(
-                item[1], folder_to_save_to
-            )
-            new_path = "../" * steps_back + str(
-                pathlib.Path(item[1]).resolve().relative_to(common_sub_path)
-            )
-        content = content.replace(item[1], str(new_path))
-
-    # super special links (just special images) that the sphinx markdown
-    # parser won't correctly handle since they are in html tags.
-    special_links = get_special_links(content)
-    for item in special_links:
-        if not item[0].strip():
-            warnings.warn(
-                f"Empty link in `{file}`. Link name `{item[1]}` link path "
-                f"`{item[0]}`. Will ignore link.",
-                stacklevel=3,
-            )
-            continue
-        if item[0].startswith("http"):  # skip http links and anchors
-            continue
-        else:
-            # just link to static folder in docs
-            new_path = "_static/" + str(pathlib.Path(item[1]).name)
-            content = content.replace(item[1], str(new_path))
+        # content = f.read()
+        os.chdir(os.path.dirname(file)) if os.path.dirname(file) else None
+        for line in f:
+            # get all links from the markdown file
+            links = get_markdown_links(line)
+            for item in links:
+                if not item[1].strip():
+                    warnings.warn(
+                        f"Empty link in `{file}`. Link name `{item[0]}` link path "
+                        f"`{item[1]}`. Will ignore link.",
+                        stacklevel=3,
+                    )
+                    continue
+                if item[1].startswith(
+                    ("http", "#")
+                ):  # skip http links and anchors
+                    if "badge" in item[1]:
+                        continue
+                    line = line.replace(  # noqa: PLW2901
+                        f"[{item[0]}]({item[1]})",
+                        f"<a href='{item[1]}'>{item[0]}</a>",
+                    )
+                    continue
+                elif item[1] in link_substitutions:
+                    if relative_links:
+                        line = line.replace(  # noqa: PLW2901
+                            f"[{item[0]}]({item[1]})",
+                            f"<a href='{link_substitutions[item[1]]}'>{item[0]}</a>",
+                        )
+                        continue
+                    else:
+                        line = line.replace(  # noqa: PLW2901
+                            f"[{item[0]}]({item[1]})",
+                            "See documentation for examples.",
+                        )
+                elif not relative_links:  # generate links to github repo
+                    new_path = get_github_path_from(
+                        pathlib.Path(item[1]).resolve()
+                    )
+                else:  # generate relative links
+                    common_sub_path, steps_back = get_common_parent(
+                        item[1], folder_to_save_to
+                    )
+                    new_path = "../" * steps_back + str(
+                        pathlib.Path(item[1])
+                        .resolve()
+                        .relative_to(common_sub_path)
+                    )
+                line = line.replace(item[1], str(new_path))  # noqa: PLW2901
+
+            # super special links (just special images) that the sphinx markdown
+            # parser won't correctly handle since they are in html tags.
+            special_links = get_special_links(line)
+            for item in special_links:
+                if not item[0].strip():
+                    warnings.warn(
+                        f"Empty link in `{file}`. Link name `{item[1]}` link path "
+                        f"`{item[0]}`. Will ignore link.",
+                        stacklevel=3,
+                    )
+                    continue
+                if item[0].startswith("http"):  # skip http links and anchors
+                    continue
+                elif not relative_links:  # generate links to github repo
+                    new_path = get_github_path_from(
+                        pathlib.Path(item[1]).resolve()
+                    )
+                else:
+                    # just link to static folder in docs
+                    new_path = "_static/" + str(pathlib.Path(item[1]).name)
+                line = line.replace(item[1], str(new_path))  # noqa: PLW2901
+            content += f"{line}"
 
     os.chdir(original_cwd)
 
@@ -206,7 +219,33 @@ def process_file(
         f.write(content)
 
 
+def prepare_file_for_PyPI():
+    """Prepare the README file for PyPI.
+
+    This function will prepare the README file for PyPI. It will replace all
+    relative links with absolute links to the github repository.
+
+    Args:
+        file (str): Path to the README file.
+    """
+    content = process_file(
+        "README.md", relative_links=False, return_content=True
+    )
+    with open("README.md", "w") as f:
+        f.write(content)
+
+
 if __name__ == "__main__":
+    # python handle_markdown -> docs
+    # python handle_markdown -b -> PyPI
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-b", "--build", action="store_true")
+    args = parser.parse_args()
+    if args.build:
+        print("Preparing README for PyPI.")  # noqa: T201
+        prepare_file_for_PyPI()
+        exit()  # noqa: PLR1722
+    print("Processing markdown files.")  # noqa: T201
     os.chdir(repo_root)
     os.makedirs(folder_to_save_to, exist_ok=True)
     # Process all markdown files

examples/ipynb/notebook_showcase_k3d.ipynb

@@ -15,9 +15,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import splinepy\n",
     "import vedo\n",
     "\n",
+    "import splinepy\n",
+    "\n",
     "vedo.settings.default_backend = \"k3d\""
    ]
   },

pyproject.toml

@@ -60,6 +60,7 @@ input = "splinepy/_version.py"
 [tool.cibuildwheel]
 test-extras = ["test"]
 test-command = "pytest {project}/tests"
+before_all = "python docs/source/handle_markdown.py -b"
 
 [tool.cibuildwheel.macos]
 archs = ["x86_64", "arm64"]

splinepy/_version.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.3"

src/proximity/proximity.cpp

@@ -427,7 +427,7 @@ void Proximity::Newton(SearchData& data) const {
 }
 
 void Proximity::PrepareIterationLevenbergMarquart(SearchData& data) const {
-  // LM requires Jac (pronounced similar to Jacques)
+  // LM requires Jacobian
   ComputeCostAndDerivatives(data, 1);
 
   // prepare rhs

src/py/py_knot_vector.cpp

@@ -170,7 +170,9 @@ void init_knot_vector(py::module_& m) {
           "Returns copy of knot vectors as numpy array.")
       .def(
           "__array__",
-          [](const KnotVector& kv, [[maybe_unused]] py::args dtype_ignored) {
+          [](const KnotVector& kv,
+             [[maybe_unused]] py::args dtype_ignored,
+             [[maybe_unused]] py::kwargs copy_ignored) {
             py::array_t<KnotType> arr(kv.GetSize());
             KnotType* arr_ptr = static_cast<KnotType*>(arr.request().ptr);
             for (int i{}; i < kv.GetSize(); ++i) {

tests/test_proximity.py

@@ -2,21 +2,24 @@
 import pytest
 
 # fixtures used
-all_2p2d_splines = (
+all_splines = (
     "rational_bezier_2p2d",
     "bezier_2p2d",
     "bspline_2p2d",
     "nurbs_2p2d",
+    "rational_bezier_3p3d",
+    "bezier_3p3d",
+    "bspline_3p3d",
+    "nurbs_3p3d",
 )
 
 
-@pytest.mark.parametrize("splinetype", all_2p2d_splines)
+@pytest.mark.parametrize("splinetype", all_splines)
 def test_queries_inside_spline_initial_guess_with_kdt(
     request, splinetype, np_rng
 ):
     """
-    Initial guess made with kdt. Mid-point as initial guess tends to fail,
-    so excluded from test.
+    Initial guess made with kdt.
     """
     spline = request.getfixturevalue(splinetype)
     # form parametric queries