quadros 0.1.0__tar.gz

quadros-0.1.0/.github/dependabot.yml

@@ -0,0 +1,22 @@
+version: 2
+updates:
+  # Actions are pinned to commit SHAs rather than tags, which is what stops a
+  # mutable tag being repointed under us (the tj-actions/changed-files class of
+  # compromise). A pin only stays current if something bumps it, so that is this.
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+
+  # Without this, only the action pins are tracked and Python dependency drift is
+  # invisible: the dev-tool floors in pyproject.toml rot behind upstream releases.
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      python-dev-tooling:
+        patterns:
+          - "ruff"
+          - "mypy"
+          - "pytest*"

quadros-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,185 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+# Read-only token: nothing here pushes, comments or publishes.
+permissions:
+  contents: read
+
+# Actions are pinned to commit SHAs, not tags. A tag is mutable and can be
+# repointed at new code under an unchanged name; a SHA cannot. Dependabot keeps
+# the pins current, and the trailing comment keeps them readable.
+
+env:
+  # VTK on a runner has no display. PyVista must be told before first import,
+  # or Plotter construction tries to open a window and dies.
+  PYVISTA_OFF_SCREEN: "true"
+
+jobs:
+  lint:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: "3.14"
+
+      - name: Install uv
+        run: pip install uv
+
+      - name: Sync environment
+        run: uv sync
+
+      - name: Lint
+        run: uv run ruff check .
+
+      # uv.lock must stay consistent with pyproject.toml, or `uv sync` in the
+      # other jobs silently installs something the manifest no longer asks for.
+      - name: Lock file is in sync
+        run: uv lock --check
+
+  # The default install has no pymech. That is the normal case for anyone
+  # rendering a non-Nek format, and the Nek code path must degrade to a clear
+  # message rather than raising. Running the suite without the extra is what
+  # keeps that true.
+  test:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      # VTK links against system GL and X libraries even when rendering
+      # offscreen. Without these, `import vtk` succeeds and the first Plotter
+      # fails, which is a confusing place to discover a missing .so.
+      # ffmpeg is not a rendering library but belongs in the same step: it is a
+      # hard check in `doctor`, because encoding a movie is half of what this
+      # tool does, and the ubuntu-24.04 runner image does not ship it.
+      - name: Install headless rendering libraries and ffmpeg
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y --no-install-recommends \
+            libgl1 libglx-mesa0 libxrender1 libxext6 xvfb \
+            libgl1-mesa-dri libglu1-mesa ffmpeg
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: pip install uv
+
+      # numpy dropped cp311 wheels at 2.5, so the 3.11 leg resolves to an older
+      # numpy than the rest of the matrix. That is expected, and is precisely
+      # why this leg exists rather than being assumed to work.
+      - name: Sync environment
+        run: uv sync --python ${{ matrix.python-version }}
+
+      # xvfb-run, not a bare invocation: doctor's render smoke test asks VTK for
+      # a real GL context. The runner has no display and no GPU, so without a
+      # virtual X server plus the Mesa software rasteriser the call segfaults
+      # (exit 139) rather than failing with a message. xvfb was already being
+      # installed here but never used.
+      - name: Run tests
+        run: |
+          xvfb-run -a uv run pytest -v | tee pytest-output.txt
+          {
+            echo "### Tests (Python ${{ matrix.python-version }}, no nek5000 extra)"
+            echo '```'
+            tail -n 15 pytest-output.txt
+            echo '```'
+          } >> "$GITHUB_STEP_SUMMARY"
+        shell: bash
+
+      # A hard gate, not a print. doctor once shipped calling a function that
+      # did not exist and died with NameError on every invocation; no test
+      # covered it. It must run, and it must not report failure merely because
+      # the optional Nek extra is absent.
+      - name: doctor runs and does not fail over an optional extra
+        run: |
+          xvfb-run -a uv run python -m quadros doctor | tee doctor.txt
+          grep -q "pyvista: ok" doctor.txt
+          grep -q "vtk: ok" doctor.txt
+          grep -q "pymech" doctor.txt
+        shell: bash
+
+  # The other half: with pymech installed, the Nek header reader must actually
+  # work. Without this job the dedicated Nek path is never exercised at all.
+  test-nek5000:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      # ffmpeg is not a rendering library but belongs in the same step: it is a
+      # hard check in `doctor`, because encoding a movie is half of what this
+      # tool does, and the ubuntu-24.04 runner image does not ship it.
+      - name: Install headless rendering libraries and ffmpeg
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y --no-install-recommends \
+            libgl1 libglx-mesa0 libxrender1 libxext6 xvfb \
+            libgl1-mesa-dri libglu1-mesa ffmpeg
+
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: "3.13"
+
+      - name: Install uv
+        run: pip install uv
+
+      - name: Sync environment with the Nek5000 extra
+        run: uv sync --extra nek5000
+
+      # A silent install failure would remove exactly the coverage this job
+      # exists to add, and the suite would still pass. Assert rather than hope.
+      - name: Require pymech to actually be importable
+        run: |
+          uv run --no-sync python - <<'PY'
+          import importlib.util
+          import sys
+
+          if importlib.util.find_spec("pymech.neksuite.field") is None:
+              sys.exit(
+                  "FAIL: the nek5000 extra did not install pymech.neksuite.field.\n"
+                  "This job exists so the Nek5000 code path is exercised; without "
+                  "pymech it silently tests the same thing as the matrix above."
+              )
+          print("ok: pymech.neksuite.field importable")
+          PY
+        shell: bash
+
+      - name: Run tests
+        run: xvfb-run -a uv run --no-sync pytest -v
+
+      - name: doctor reports the extra as present
+        run: |
+          xvfb-run -a uv run --no-sync python -m quadros doctor | tee doctor.txt
+          grep -q "pymech (nek5000 extra): ok" doctor.txt
+        shell: bash
+
+  package:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: "3.14"
+
+      - name: Install uv
+        run: pip install uv
+
+      - name: Build
+        run: uv build
+
+      - name: Check package
+        run: uvx twine check dist/*

quadros-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,94 @@
+name: Release
+
+# Publishes to PyPI via trusted publishing (OIDC) — no API token is stored.
+# PyPI matches on owner / repo / workflow filename / environment, configured as:
+#   owner: openfluids | repo: quadros | workflow: release.yml | environment: (blank)
+# Renaming this file breaks that match. The environment is left unset on PyPI, so
+# `environment: pypi` below is not part of the match — it exists so an approval
+# gate can be attached without touching either side.
+#
+# Tag-triggered so a release cannot happen without a tag recording which commit
+# shipped.
+on:
+  push:
+    tags: ["v*"]
+
+# Least privilege by default. Only the jobs that need more ask for it.
+permissions:
+  contents: read
+
+# Actions are pinned to commit SHAs, not tags. A tag is mutable and can be
+# repointed at new code under an unchanged name; a SHA cannot. Dependabot keeps
+# the pins current, and the trailing comment keeps them readable.
+
+jobs:
+  verify:
+    name: Verify tag and PyPI state
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      # Guards against tagging v0.2.0 while pyproject.toml still says 0.1.0 —
+      # PyPI would accept the mismatch and the tag would lie about what shipped.
+      - name: Tag must match the packaged version
+        run: |
+          tag="${GITHUB_REF_NAME#v}"
+          pkg="$(python3 -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")"
+          if [ "$tag" != "$pkg" ]; then
+            echo "Tag v$tag does not match pyproject.toml version $pkg" >&2
+            exit 1
+          fi
+          echo "tag and packaged version agree: $pkg"
+
+      # PyPI refuses re-uploads of an existing version. Failing here says so in
+      # one line; failing in the publish step is an opaque 400 after a build.
+      - name: Refuse to republish an existing version
+        run: |
+          tag="${GITHUB_REF_NAME#v}"
+          code="$(curl -s -o /dev/null -w '%{http_code}' "https://pypi.org/pypi/quadros/$tag/json")"
+          if [ "$code" = "200" ]; then
+            echo "quadros $tag is already on PyPI; PyPI will not accept a re-upload." >&2
+            echo "Bump the version rather than re-releasing this one." >&2
+            exit 1
+          fi
+          echo "version $tag is free on PyPI (HTTP $code)"
+
+  publish:
+    name: Build and publish to PyPI
+    needs: [verify]
+    runs-on: ubuntu-24.04
+    environment: pypi
+    permissions:
+      # Required to mint the OIDC token PyPI verifies. Scoped to this job: the
+      # verify job has no reason to be able to mint a publishing token.
+      id-token: write
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+
+      # No system GL libraries or xvfb here, unlike ci.yml: building an sdist and
+      # a pure-Python wheel never imports quadros, so the headless-rendering
+      # setup that the test jobs need is dead weight at release time.
+      - name: Build
+        run: uv build
+
+      - name: Check metadata
+        run: uvx twine check dist/*
+
+      - uses: pypa/gh-action-pypi-publish@ba38be9e461d3875417946c167d0b5f3d385a247 # v1.14.1
+
+  github-release:
+    name: Create the GitHub release
+    needs: [publish]
+    runs-on: ubuntu-24.04
+    # Creating a release writes to the repo, so this job -- and only this job --
+    # needs write access.
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - name: Create release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release create "$GITHUB_REF_NAME" --title "$GITHUB_REF_NAME" --generate-notes

quadros-0.1.0/.gitignore

@@ -0,0 +1,17 @@
+.venv/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+*.egg-info/
+dist/
+build/
+.DS_Store
+frames/
+logs/
+manifests/
+events/
+movies/
+
+# coverage
+.coverage
+htmlcov/

quadros-0.1.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
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+   Copyright 2026 Ricardo A S Frantz
+
+   Licensed under the Apache License, Version 2.0 (the "License");
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+       http://www.apache.org/licenses/LICENSE-2.0
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quadros-0.1.0/PKG-INFO

@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: quadros
+Version: 0.1.0
+Summary: Snapshot, frame, and video renderer for PyVista-based dense-flow visualization with Nek5000 support
+Project-URL: Homepage, https://github.com/openfluids/quadros
+Project-URL: Repository, https://github.com/openfluids/quadros
+Project-URL: Issues, https://github.com/openfluids/quadros/issues
+Author: Ricardo A S Frantz
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: cfd,pyvista,slurm,video,visualization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.11
+Requires-Dist: numpy
+Requires-Dist: pillow
+Requires-Dist: pyvista
+Requires-Dist: vtk
+Provides-Extra: nek5000
+Requires-Dist: pymech; extra == 'nek5000'
+Description-Content-Type: text/markdown
+
+![quadros banner](https://raw.githubusercontent.com/openfluids/quadros/main/assets/readme-banner-v1.jpg)
+
+[![CI](https://github.com/openfluids/quadros/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/openfluids/quadros/actions/workflows/ci.yml)
+[![Python](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fopenfluids%2Fquadros%2Fmain%2Fpyproject.toml&label=python)](pyproject.toml)
+[![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+
+`quadros` is a Python CLI package for rendering snapshots into checked frame sets and videos. It can run locally, over SSH, inside containers, or from scheduler jobs without copying scripts into case directories. Nek5000 is the format with dedicated support; other VTK-readable formats are supported via PyVista.
+
+## Features
+
+- Render one snapshot or a globbed case directory of snapshots (Nek5000 with dedicated support).
+- Keep JSON render configs compatible with the original `auto_snp` workflow.
+- Write manifests, logs, events, frames, and encoded movies under a run output directory.
+- Inspect render manifests before deleting dense snapshots.
+- Extract camera settings from ParaView `.pvsm` state files.
+- Gate NekStab omega-R renders with explicit field aliases and a rebuild hint.
+
+## Install
+
+### With `uv` (recommended for local development)
+
+```bash
+git clone https://github.com/openfluids/quadros.git
+cd quadros
+uv venv .venv
+. .venv/bin/activate
+uv pip install -e .
+quadros doctor
+```
+
+For development tools and tests:
+
+```bash
+uv pip install -e . --group dev
+python -m pytest
+```
+
+### With standard `venv` + `pip`
+
+```bash
+git clone https://github.com/openfluids/quadros.git
+cd quadros
+python -m venv .venv
+. .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install -e .
+quadros doctor
+```
+
+For development tools and tests:
+
+```bash
+python -m pip install -e . pytest build twine
+python -m pytest
+```
+
+For a cluster/native rendering setup, see `docs/native-stack.md`.
+
+## CLI
+
+```bash
+quadros doctor
+quadros render snapshot.f00001 --config configs/render_scenes_example.json
+quadros render-many --case-dir /path/to/case --pattern 'sphere0.f*' --config render.json
+quadros inspect manifest.json
+quadros encode --frames frames/ --out movies/movie.mp4
+quadros extract-camera qp_comp.pvsm --out camera.json
+```
+
+By default, render outputs are written in loco under `SNAPSHOT_PARENT/quadros` for `render` and `CASE_DIR/quadros` for `render-many`. Use `--out` only when you intentionally want a different output root.
+
+`--check` enables an omega-R preflight gate for configs that declare `field_aliases` for `omR*`/omega fields. If the configured payload is absent, the command points the operator to rebuild the NekStab case with `ifvox = .true.` and `mks <CASE>`.
+
+## Package layout
+
+- `src/quadros/` — importable package and public CLI entrypoint.
+- `configs/` — JSON render config examples compatible with the original workflow.
+- `slurm/render_snapshots.sbatch` — generic Slurm starter template; copy it and add cluster-specific account, partition, module, or container directives as needed.
+- `tests/` — packaging and CLI smoke tests.
+- `docs/` — native-stack notes and operating guidance.
+- `PLAN.md` — source migration plan.
+
+## Validation
+
+```bash
+python -m compileall src tests
+python -m quadros --help
+quadros doctor
+```