Merge branch 'main' into dependabot/pip/requirements/pytest-cov-7.0.0

Author: PProfizi

.github/workflows/ci.yml

@@ -206,39 +206,3 @@ jobs:
       DOCSTRING: false
       standalone_suffix: ${{ matrix.version == '241' && '.sp01' || '' }}
     secrets: inherit
-
-  sync-main-with-master:
-    name: "Sync main with master"
-    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: "Install Git and clone project"
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
-        with:
-          token: ${{ secrets.MIGRATION_PAT }}
-          fetch-depth: 0
-
-      - name: "Verify that main is the default branch"
-        shell: bash
-        run: |
-          head_branch=$(git remote show origin | grep "HEAD branch:")
-          main_branch=${head_branch#*: }
-          
-          if [[ $main_branch != "main" ]]; then
-            echo "The default branch is not 'main'. It is set to '$main_branch'."
-            echo "Please set 'main' as the default branch in the repository settings."
-            exit 1
-          fi
-
-      - name: "Configure git username and email"
-        shell: bash
-        run: |
-          git config --global user.name "${{ secrets.PYANSYS_CI_BOT_USERNAME }}"
-          git config --global user.email "${{ secrets.PYANSYS_CI_BOT_EMAIL }}"
-
-      - name: "Sync main to master"
-        shell: bash
-        run: |
-          git checkout master
-          git reset --hard main
-          git push

.github/workflows/docs.yml

@@ -79,7 +79,7 @@ jobs:
       - name: "Build the wheel"
         shell: pwsh
         run: |
-          tox -e build-wheel
+          tox -e build-wheel -- "any"
 
       - name: "Expose the wheel"
         shell: bash

.github/workflows/pydpf-post.yml

@@ -152,7 +152,7 @@ jobs:
           PACKAGE_NAME: ansys-dpf-post
           working-directory: pydpf-post/src
         if: inputs.test_docstrings == 'true'
-        timeout-minutes: 10
+        timeout-minutes: 12
         continue-on-error: true
 
       - uses: mainmatter/continue-on-error-comment@v1

.github/workflows/test_docker.yml

@@ -136,7 +136,7 @@ jobs:
       - name: "Test API test_server"
         uses: nick-fields/retry@v3
         with:
-          timeout_minutes: 5
+          timeout_minutes: 8
           max_attempts: 2
           shell: bash
           command: |
@@ -208,7 +208,7 @@ jobs:
       - name: "Test Documentation"
         uses: nick-fields/retry@v3
         with:
-          timeout_minutes: 4
+          timeout_minutes: 8
           max_attempts: 2
           shell: bash
           command: |

.github/workflows/tests.yml

@@ -234,7 +234,7 @@ jobs:
       - name: "Run compatible tests in parallel"
         uses: nick-fields/retry@v3
         with:
-          timeout_minutes: 15
+          timeout_minutes: 20
           max_attempts: 2
           shell: bash
           command: |

doc/source/_static/dpf_operators.html

@@ -254,10 +254,10 @@ Testing on Linux via WSL
 Some system dependencies required for VTK to run properly might be missing when running tests on linux via WSL (or even linux in general). 
 The identified workaround for this is to install the OSMesa wheel variant that leverages offscreen rendering with OSMesa.
 This wheel is being built for both Linux and Windows at this time and bundles all of the necessary libraries into the wheel. This is
-achieved by adding ``-x testenv.commands_pre="uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==<version>"``
+achieved by adding ``-x testenv.commands_pre="uv pip install --index-url https://wheels.vtk.org vtk-osmesa==<version>"``
 
 For example, to run all tests sequentially on linux, while using a Standalone DPF Server whose path is ``ansys_dpf_server_lin_v2025.1.pre0``, simply run:
 
 .. code-block:: text
 
-    python -m tox --parallel -x testenv.deps+="-e ansys_dpf_server_lin_v2025.1.pre0" -x testenv.commands_pre="uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==9.2.20230527.dev0"
+    python -m tox --parallel -x testenv.deps+="-e ansys_dpf_server_lin_v2025.1.pre0" -x testenv.commands_pre="uv pip install --index-url https://wheels.vtk.org vtk-osmesa==9.2.20230527.dev0"

doc/source/getting_started/contribute/developer.rst

@@ -14,7 +14,7 @@ installer's Python interpreter.
 
    - ``-awp_root``: Path to the Ansys root installation folder. For example, the 2023 R1 installation folder ends
      with ``Ansys Inc/v231``, and the default environment variable is ``AWP_ROOT231``.
-   - ``-pip_args``: Optional arguments to add to the ``pip`` command. For example, ``--extra-index-url`` or
+   - ``-pip_args``: Optional arguments to add to the ``pip`` command. For example, ``--index-url`` or
      ``--trusted-host``.
 
 If you ever want to uninstall the ``ansys-dpf-core`` module from the Ansys installation, you can do so.

doc/source/user_guide/tutorials/custom_operators_and_plugins/update_pydpf_core.rst

@@ -5,7 +5,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
 [project]
 # Check https://setuptools.pypa.io/en/stable/userguide/quickstart.html for all available sections
 name = "ansys-dpf-core"
-version = "0.14.2.dev0"
+version = "0.14.3.dev0"
 description = "Data Processing Framework - Python Core "
 readme = "README.md"
 requires-python = ">=3.9, <4"

pyproject.toml

@@ -24,8 +24,9 @@
 from __future__ import annotations
 
 import argparse
-from os import PathLike
+import os
 from pathlib import Path
+import re
 
 from ansys.dpf import core as dpf
 from ansys.dpf.core.changelog import Changelog
@@ -51,7 +52,7 @@ def __init__(
 
 
 def initialize_server(
-    ansys_path: str | PathLike = None,
+    ansys_path: str | os.PathLike = None,
     include_composites: bool = False,
     include_sound: bool = False,
     verbose: bool = False,
@@ -105,6 +106,98 @@ def initialize_server(
     return server
 
 
+def extract_operator_description_update(content: str) -> str:
+    """Extract the updated description to use for an operator.
+
+    Parameters
+    ----------
+    content:
+        The contents of the '*_upd.md' file.
+
+    Returns
+    -------
+        description_update:
+            The updated description to use for the operator.
+    """
+    match = re.search(r"## Description\s*(.*?)\s*(?=## |\Z)", content, re.DOTALL)
+    return match.group(0) + os.linesep if match else None
+
+
+def replace_operator_description(original_documentation: str, new_description: str):
+    """Replace the original operator description with a new one in the operator documentation file.
+
+    Parameters
+    ----------
+    original_documentation:
+        Original operator documentation.
+    new_description:
+        New operator description
+
+    Returns
+    -------
+    updated_documentation:
+        The updated operator documentation content
+
+    """
+    return re.sub(
+        r"## Description\s*.*?(?=## |\Z)", new_description, original_documentation, flags=re.DOTALL
+    )
+
+
+def update_operator_descriptions(
+    docs_path: Path,
+    verbose: bool = False,
+):
+    """Update operator descriptions based on '*_upd.md' files in DPF documentation sources.
+
+    Parameters
+    ----------
+    docs_path:
+        Root path of the DPF documentation to update operator descriptions for.
+    verbose:
+        Whether to print progress information.
+
+    """
+    all_md_files = {}
+    specs_path = docs_path / Path("operator-specifications")
+    # Walk through the target directory and all subdirectories
+    for root, _, files in os.walk(specs_path):
+        for file in files:
+            if file.endswith(".md"):
+                full_path = Path(root) / Path(file)
+                all_md_files[str(full_path)] = file  # Store full path and just filename
+
+    for base_path, file_name in all_md_files.items():
+        if file_name.endswith("_upd.md"):
+            continue  # Skip update files
+
+        # Construct the expected update file name and path
+        upd_file_name = f"{file_name[:-3]}_upd.md"
+
+        # Look for the update file in the same folder
+        upd_path = Path(base_path).parent / Path(upd_file_name)
+        if not upd_path.exists():
+            continue
+
+        # Load contents
+        with Path(base_path).open(mode="r", encoding="utf-8") as bf:
+            base_content = bf.read()
+        with Path(upd_path).open(mode="r", encoding="utf-8") as uf:
+            upd_content = uf.read()
+
+        # Extract and replace description
+        new_description = extract_operator_description_update(upd_content)
+        if new_description:
+            updated_content = replace_operator_description(base_content, new_description)
+            with Path(base_path).open(mode="w", encoding="utf-8") as bf:
+                bf.write(updated_content)
+            if verbose:
+                print(f"Updated description for: {file_name}")
+        else:
+            if verbose:
+                print(f"No operator description found in: {upd_path}")
+
+
 def fetch_doc_info(server: dpf.AnyServerType, operator_name: str) -> dict:
     """Fetch information about the specifications of a given operator.
 
@@ -265,14 +358,14 @@ def generate_operator_doc(
     if not include_private and operator_info["exposure"] == "private":
         return
     template_path = Path(__file__).parent / "operator_doc_template.md"
-    spec_folder = output_path / "operator-specifications"
+    spec_folder = output_path / Path("operator-specifications")
     category_dir = spec_folder / category
     spec_folder.mkdir(parents=True, exist_ok=True)
     if category is not None:
         category_dir.mkdir(parents=True, exist_ok=True)  # Ensure all parent directories are created
         file_dir = category_dir
     else:
-        file_dir = output_path / "operator-specifications"
+        file_dir = spec_folder
     with Path.open(template_path, "r") as file:
         template = jinja2.Template(file.read())
 
@@ -281,8 +374,8 @@ def generate_operator_doc(
         file.write(output)
 
 
-def generate_toc_tree(docs_path: Path):
-    """Write the global toc.yml file for the DPF documentation based on the operators found.
+def update_toc_tree(docs_path: Path):
+    """Update the global toc.yml file for the DPF documentation based on the operators found.
 
     Parameters
     ----------
@@ -291,14 +384,14 @@ def generate_toc_tree(docs_path: Path):
 
     """
     data = []
-    specs_path = docs_path / "operator-specifications"
+    specs_path = docs_path / Path("operator-specifications")
     for folder in specs_path.iterdir():
         if folder.is_dir():  # Ensure 'folder' is a directory
             category = folder.name
             operators = []  # Reset operators for each category
             for file in folder.iterdir():
                 if (
-                    file.is_file() and file.suffix == ".md"
+                    file.is_file() and file.suffix == ".md" and not file.name.endswith("_upd.md")
                 ):  # Ensure 'file' is a file with .md extension
                     file_name = file.name
                     file_path = f"{category}/{file_name}"
@@ -308,18 +401,27 @@ def generate_toc_tree(docs_path: Path):
 
     # Render the Jinja2 template
     template_path = Path(__file__).parent / "toc_template.j2"
-    with Path.open(template_path, "r") as template_file:
+    with template_path.open(mode="r") as template_file:
         template = jinja2.Template(template_file.read())
     output = template.render(data=data)  # Pass 'data' as a named argument
 
-    # Write the rendered output to toc.yml at the operators_doc level
-    with Path.open(docs_path / "toc.yml", "w") as file:
-        file.write(output)
+    # Update the original toc.yml file with the rendered output for operator_specifications
+    toc_path = docs_path / Path("toc.yml")
+    with toc_path.open(mode="r") as file:
+        original_toc = file.read()
+    new_toc = re.sub(
+        pattern=r"- name: Operator specifications\s*.*?(?=- name: Changelog|\Z)",
+        repl=output,
+        string=original_toc,
+        flags=re.DOTALL,
+    )
+    with toc_path.open(mode="w") as file:
+        file.write(new_toc)
 
 
 def generate_operators_doc(
-    ansys_path: Path,
     output_path: Path,
+    ansys_path: Path = None,
     include_composites: bool = False,
     include_sound: bool = False,
     include_private: bool = False,
@@ -334,10 +436,10 @@ def generate_operators_doc(
 
     Parameters
     ----------
-    ansys_path:
-        Path to an Ansys/DPF installation.
     output_path:
         Path to write the output files at.
+    ansys_path:
+        Path to an Ansys/DPF installation.
     include_composites:
         Whether to include operators of the Composites plugin.
     include_sound:
@@ -357,7 +459,10 @@ def generate_operators_doc(
         operators = get_plugin_operators(server, desired_plugin)
     for operator_name in operators:
         generate_operator_doc(server, operator_name, include_private, output_path)
-    generate_toc_tree(output_path)
+    # Generate the toc tree
+    update_toc_tree(output_path)
+    # Use update files in output_path
+    update_operator_descriptions(output_path)
 
 
 def run_with_args():  # pragma: nocover
@@ -368,9 +473,7 @@ def run_with_args():  # pragma: nocover
     parser.add_argument(
         "--ansys_path", default=None, help="Path to Ansys DPF Server installation directory"
     )
-    parser.add_argument(
-        "--output_path", default=None, help="Path to output directory", required=True
-    )
+    parser.add_argument("--output_path", default=".", help="Path to output directory")
     parser.add_argument("--include_private", action="store_true", help="Include private operators")
     parser.add_argument(
         "--include_composites", action="store_true", help="Include Composites operators"
@@ -389,8 +492,8 @@ def run_with_args():  # pragma: nocover
     args = parser.parse_args()
 
     generate_operators_doc(
-        ansys_path=args.ansys_path,
         output_path=args.output_path,
+        ansys_path=args.ansys_path,
         include_composites=args.include_composites,
         include_sound=args.include_sound,
         include_private=args.include_private,