Added TAE examples

.github/precomputed-examples.json

@@ -0,0 +1,23 @@
+{
+  "_comment": "Examples too expensive to simulate in CI. run_example.py downloads each archived run (a tar.gz of docs/public/examples/struphy_gallery_runs/<sim_folder>, made by scripts/pack_precomputed_run.py), checks its sha256, unpacks it and only post-processes it. Fill in url and sha256 after uploading the archive to a release. Each job is the Slurm allocation scripts/submit_precomputed_run.py requests for the simulation (estimates; adjust after the first run).",
+  "itpa-tae-linear-mhd": {
+    "sim_folder": "itpa_tae_linear_mhd",
+    "url": null,
+    "sha256": null,
+    "job": {
+      "mpi_ranks": 32,
+      "time": "08:00:00",
+      "mem": null
+    }
+  },
+  "itpa-tae-shear-alfven": {
+    "sim_folder": "itpa_tae_shear_alfven",
+    "url": null,
+    "sha256": null,
+    "job": {
+      "mpi_ranks": 32,
+      "time": "24:00:00",
+      "mem": null
+    }
+  }
+}

.github/scripts/example-cache.cjs

@@ -2,13 +2,14 @@
 async function exampleCache(example, prefix, suffix, glob) {
   const patterns = [
     `docs/src/examples/${example}.py`,
-    'submodules/plasma-plots/src/plasma_plots/**/*.py',
+    'requirements.txt',
+    'requirements-examples.txt',
     'catalogue_docs.py',
     'generate_examples.py',
     'run_example.py',
+    '.github/precomputed-examples.json',
     'generate_example_domain.py',
     'generate_domains.py',
-    'submodules/plasma-plots/struphy/src/struphy/**/*.py',
   ];
   return {
     key: `${prefix}${suffix}-${example}-${await glob.hashFiles(patterns.join('\n'))}`,

.github/scripts/list-examples.cjs

@@ -1,8 +1,10 @@
 const fs = require('node:fs/promises');
 const { exampleCache } = require('./example-cache.cjs');
 
+const CI_EXCLUDED = ['itpa-tae-linear-mhd', 'itpa-tae-shear-alfven'];
+
 module.exports = async function listExamples({ cache, glob, core, exclude = ['poisson-source'] }) {
-  const excluded = new Set(exclude);
+  const excluded = new Set([...CI_EXCLUDED, ...exclude]);
   const examples = (await fs.readdir('docs/src/examples'))
     .filter(name => name.endsWith('.py') && !name.startsWith('_') && !excluded.has(name.slice(0, -3)))
     .map(name => name.slice(0, -3)).sort();

.github/scripts/list-examples.test.cjs

@@ -80,6 +80,6 @@ test('shared keys retain prefix, suffix, example and source hash', async () => {
   });
   assert.equal(result.key, 'pitagora-example-v1-custom-alpha-hash');
   assert.equal(patterns[0], 'docs/src/examples/alpha.py');
-  assert.ok(patterns.includes('submodules/plasma-plots/struphy/src/struphy/**/*.py'));
-  assert.ok(patterns.includes('submodules/plasma-plots/src/plasma_plots/**/*.py'));
+  assert.ok(patterns.includes('requirements.txt'));
+  assert.ok(patterns.includes('requirements-examples.txt'));
 });

.github/scripts/list-pitagora-examples.cjs

@@ -2,6 +2,7 @@ const fs = require('node:fs/promises');
 const { exampleCache } = require('./example-cache.cjs');
 
 const selectionPath = '.github/pitagora-examples.txt';
+const CI_EXCLUDED = new Set(['itpa-tae-linear-mhd', 'itpa-tae-shear-alfven']);
 
 async function selectedPitagoraExamples() {
   const text = await fs.readFile(selectionPath, 'utf8');
@@ -10,6 +11,10 @@ async function selectedPitagoraExamples() {
     .map(line => line.split('#', 1)[0].trim())
     .filter(Boolean);
   if (!examples.length) throw new Error(`${selectionPath} contains no examples`);
+  const excluded = examples.filter(example => CI_EXCLUDED.has(example));
+  if (excluded.length) {
+    throw new Error(`${selectionPath} includes examples disabled in CI: ${excluded.join(', ')}`);
+  }
   if (new Set(examples).size !== examples.length) {
     throw new Error(`${selectionPath} contains duplicate examples`);
   }

.github/scripts/run-pitagora-example.py

@@ -6,19 +6,11 @@
 import argparse
 import os
 import shlex
+import sys
 from pathlib import Path
 
-from slurm_script_generator.slurm_script import SlurmScript
-from slurm_script_generator.squeue import SQueue
-
-MODULES = [
-    "gcc/12.3.0",
-    "python/3.11.7",
-    "hdf5/1.14.3--gcc--12.3.0",
-    "cmake/3.27.9",
-    "netcdf-fortran/4.6.1--gcc--12.3.0",
-    "netlib-scalapack/2.2.0--openmpi--4.1.6--gcc--12.3.0-ucx1.20",
-]
+sys.path.insert(0, str(Path(__file__).resolve().parents[2] / "scripts"))
+from slurm_jobs import environment_commands, example_job, submit_and_wait  # noqa: E402
 
 # Orszag--Tang writes 401 field snapshots and post-processing loads them all
 # before evaluating the output grid. It exceeds the debug partition's default
@@ -27,15 +19,6 @@
 MPI_RANKS_BY_EXAMPLE = {"orszag-tang-vortex": 4}
 
 
-def tail_log(path: Path, lines: int = 200) -> None:
-    """Print a bounded batch log in a collapsible GitHub Actions group."""
-    if not path.is_file():
-        return
-    print(f"::group::{path.name}")
-    print("\n".join(path.read_text(errors="replace").splitlines()[-lines:]))
-    print("::endgroup::")
-
-
 def main() -> int:
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("example", help="Gallery example stem")
@@ -49,48 +32,21 @@ def main() -> int:
     run_id = os.environ["GITHUB_RUN_ID"]
     run_attempt = os.environ["GITHUB_RUN_ATTEMPT"]
     job_name = f"struphy-{args.example}-{run_id}-{run_attempt}"
-    script_path = runner_temp / f"{job_name}.sbatch"
-    stdout = workspace / f"slurm-{job_name}-%j.out"
-    stderr = workspace / f"slurm-{job_name}-%j.err"
     mpi_ranks = MPI_RANKS_BY_EXAMPLE.get(args.example, 1)
-    commands = [
-        "set -euo pipefail",
-        f"source {shlex.quote(str(virtual_env / 'bin' / 'activate'))}",
-    ]
-    if mpi_ranks == 1:
-        # A one-task Slurm allocation is not an MPI launch.
-        commands.append("export STRUPHY_MPI=0")
-    else:
-        # mpi4py must see the Open MPI environment that `cli.py --mpi` creates.
-        commands.append("unset STRUPHY_MPI")
+    commands = environment_commands(virtual_env, mpi_ranks)
     commands.append(f"python cli.py run {shlex.quote(args.example)} --mpi {mpi_ranks}")
 
-    script = SlurmScript(
+    script = example_job(
         job_name=job_name,
         account=args.account,
         partition=args.partition,
-        nodes=1,
-        ntasks=mpi_ranks,
-        cpus_per_task=1,
-        time="00:30:00",
+        workspace=workspace,
+        log_dir=workspace,
+        commands=commands,
+        mpi_ranks=mpi_ranks,
         mem=MEMORY_BY_EXAMPLE.get(args.example),
-        chdir=str(workspace),
-        output=str(stdout),
-        error=str(stderr),
-        modules=MODULES,
-        custom_commands=commands,
     )
-    job_id = script.submit_job(path=str(script_path), verbose=True)
-    print(f"Submitted {job_name} as Slurm job {job_id}")
-
-    try:
-        state = SQueue().wait_until_done(job_id=job_id, poll_interval=15, check=True)[
-            job_id
-        ]
-        print(f"Slurm job {job_id} finished with state {state or 'unknown'}.")
-    finally:
-        tail_log(workspace / f"slurm-{job_name}-{job_id}.out")
-        tail_log(workspace / f"slurm-{job_name}-{job_id}.err")
+    submit_and_wait(script, job_name, runner_temp / f"{job_name}.sbatch", workspace)
     return 0
 
 

.github/workflows/build-site.yml

@@ -27,8 +27,6 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-        with:
-          submodules: recursive
 
       - name: Install cache client
         run: npm install --prefix "$RUNNER_TEMP/example-cache" --no-audit --no-fund --ignore-scripts @actions/cache@4.0.5
@@ -88,16 +86,17 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-        with:
-          submodules: recursive
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: '3.12'
 
       - name: Install Struphy
-        run: python -m pip install --upgrade pip && python -m pip install ./submodules/plasma-plots/struphy ./submodules/plasma-plots
+        run: python -m pip install --upgrade pip && python -m pip install -r requirements.txt
+
+      - name: Check domain discovery
+        run: python -m pytest -q tests/test_generate_domains.py
 
       - name: Generate equilibrium slices
         run: python generate_equilibrium_slices.py
@@ -139,6 +138,9 @@ jobs:
           cache: npm
           cache-dependency-path: docs/package-lock.json
 
+      - name: Check example build validation
+        run: python -m pytest -q tests/test_example_build.py
+
       - name: Install dependencies
         working-directory: docs
         run: npm ci

.github/workflows/pitagora-examples.yml

@@ -27,10 +27,8 @@ jobs:
       SLURM_PARTITION: dcgp_fua_dbg
       EXAMPLES: ${{ inputs.examples }}
     steps:
-      - name: Check out repository and Struphy
+      - name: Check out repository
         uses: actions/checkout@v4
-        with:
-          submodules: recursive
 
       - name: Install Struphy and run example
         # A login shell initializes the cluster's module command. Keep setup and
@@ -53,13 +51,13 @@ jobs:
           export CXX="$(command -v g++)"
           source /pitagora_scratch/userexternal/mlindqvi/github_runner_builds/.venv/bin/activate
 
-          git -C submodules/plasma-plots/struphy rev-parse HEAD
-          python -m pip install './submodules/plasma-plots/struphy[phys,mpi]' './submodules/plasma-plots[gallery]'
+          python -m pip uninstall -y struphy
+          python -m pip install --upgrade -r requirements-examples.txt
           python -m pip install 'scope-profiler[pproc]>=0.6.1,<=0.7.0' kaleido 'slurm-script-generator==0.4.0'
           # Install Chrome into Kaleido's user-accessible location for PNG export.
           kaleido_get_chrome
           struphy compile --status
-          # struphy compile -y --language fortran
+          struphy compile -y --language fortran
           # The Python API generates a self-contained serial batch script,
           # submits it, waits for its exact job ID, verifies its final Slurm
           # state, and prints its batch logs. Submit exactly one job at a time

.github/workflows/run-example.yml

@@ -29,17 +29,9 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-        with:
-          submodules: recursive
-
-      - name: Trust the checked-out worktree
-        # Actions containers run as root; git refuses to touch a worktree owned by another
-        # UID ("detected dubious ownership") unless told to trust it -- struphy's own
-        # editable install below shells out to git (setuptools-scm) and would hit this.
-        run: git config --global --add safe.directory '*'
 
       # Each run is deterministic (fixed seeds), so cache on this example script's and
-      # Struphy's own source, and skip the expensive rebuild when neither changed. Every
+      # Python requirements, and skip the expensive rebuild when neither changed. Every
       # file an example writes is named after its script stem (the metadata JSON, the
       # figures, their thumbnails); no example's stem is a prefix of another's, and the
       # glob also covers two-stream-instability's extra "-phasespace" pair.
@@ -50,40 +42,26 @@ jobs:
           example: ${{ inputs.example }}
           cache-prefix: struphy-example-serial-v1
 
-      - name: Install Struphy from this repo's pinned submodule commit
-        # Same approach as struphy's own CI
-        # (submodules/plasma-plots/struphy/.github/actions/install/struphy_in_container/action.yml):
-        # the image bakes in whatever struphy commit was HEAD when it was last built, so
-        # move /struphy_fortran_'s own checkout to the exact commit our submodule pins
-        # (rather than reinstalling editable from a second copy of the source) and
-        # reinstall there, reusing the image's already-installed venv and already-built
-        # gvec/desc-opt.
-        #
-        # scope-profiler[pproc] and kaleido aren't pulled in by the phys/mpi extras (only by
-        # struphy's own dev/doc extras) but the example scripts need both: scope-profiler's
-        # pproc submodule for the durations/gantt/flame plot-data export, kaleido for
-        # figure.write_image(...)'s static PNG export.
-        #
-        # plasma-plots registers the .plasma accessors that the example scripts use, and its
-        # gallery extra brings plasma_plots.gallery, the helpers that write every example's
-        # figures, profiling and metadata. It has no compiled parts, so it is installed straight
-        # from our pinned submodule.
+      - name: Install Python dependencies from PyPI
+        id: install-python
+        # Replace the image's editable Struphy install with a released wheel.
+        # The gallery extra provides Plotly exports and profiling helpers.
         if: steps.cache-example.outputs.cache-hit != 'true'
         shell: bash
         run: |
-          STRUPHY_PLOTS="$PWD/submodules/plasma-plots"
-          STRUPHY_SHA=$(git -C submodules/plasma-plots/struphy rev-parse HEAD)
-          cd /struphy_fortran_
-          git fetch origin --tags
-          git checkout "$STRUPHY_SHA"
-          source env_fortran_/bin/activate
-          pip install -U --upgrade-strategy eager -e ".[phys,mpi]"
-          # Struphy pins scope-profiler <=0.5.0 as a hard dependency, but the example
-          # scripts use plot_durations(metrics=(...)), a plural-metrics API that only
-          # exists from 0.6.1 onward -- --upgrade forces past struphy's conservative pin
-          # to the version this was actually developed and tested against.
-          pip install --upgrade "scope-profiler[pproc]>=0.6.1" kaleido
-          pip install "$STRUPHY_PLOTS[gallery]"
+          source /struphy_fortran_/env_fortran_/bin/activate
+          python -m pip uninstall -y struphy
+          python -m pip install --upgrade -r requirements-examples.txt
+          python - <<'PY'
+          import os
+          import sysconfig
+          from importlib.metadata import distribution, version
+          with open(os.environ["GITHUB_OUTPUT"], "a") as output:
+              print(f"struphy-path={distribution('struphy').locate_file('struphy')}", file=output)
+              print(f"struphy-version={version('struphy')}", file=output)
+              print(f"python-abi={sysconfig.get_config_var('SOABI')}", file=output)
+              print(f"pyccel-version={version('pyccel')}", file=output)
+          PY
 
       - name: Rebuild GVEC for this runner's CPU
         # The published gvec wheel is built with -march=native. GitHub-hosted
@@ -97,22 +75,19 @@ jobs:
           lscpu | grep -E 'Model name|Flags'
           python -m pip install --no-binary=gvec --no-cache-dir --no-deps --force-reinstall 'gvec==1.5.0'
 
-      # Compiled kernels depend only on struphy's own source, not on which example this
-      # shard runs -- cache them under their own key (shared across all 10 shards) so that
-      # when only an example script changes, the 1-2 min recompile happens once instead of
-      # once per shard. Keyed independently of cache-example above; checked out to the
-      # right commit by the (fast, still-unconditional) install step regardless of hit/miss.
+      # Cache kernels in the installed package, using the resolved release and
+      # Python/compiler versions so an upgraded wheel gets a fresh compilation.
       - name: Cache compiled Struphy kernels
         id: cache-kernels
         if: steps.cache-example.outputs.cache-hit != 'true'
         uses: actions/cache@v4
         with:
           path: |
-            /struphy_fortran_/src/struphy/**/__pyccel__
-            /struphy_fortran_/src/struphy/**/*.so
-          key: struphy-kernels-${{ hashFiles('submodules/plasma-plots/struphy/src/struphy/**/*.py') }}
+            ${{ steps.install-python.outputs.struphy-path }}/**/__pyccel__
+            ${{ steps.install-python.outputs.struphy-path }}/**/*.so
+          key: struphy-kernels-pypi-${{ runner.os }}-${{ runner.arch }}-${{ steps.install-python.outputs.struphy-version }}-${{ steps.install-python.outputs.python-abi }}-${{ steps.install-python.outputs.pyccel-version }}-${{ hashFiles('requirements*.txt') }}
 
-      # Chrome doesn't depend on the struphy commit or example scripts, so cache it under
+      # Chrome doesn't depend on the Struphy release or example scripts, so cache it under
       # its own static key instead of the cache-example key above -- otherwise every
       # cache-miss shard redundantly re-downloads ~150-200MB from Google plus its apt
       # dependencies for no reason.

.gitignore

@@ -36,3 +36,9 @@ docs/public/examples/struphy.log.*
 .idea/
 .vscode/
 .DS_Store
+
+# Cluster runs of precomputed examples (scripts/submit_precomputed_run.py)
+/struphy-precomputed-*.sbatch
+/slurm-*.out
+/slurm-*.err
+/*-run.tar.gz