(fix)fix ppdl init from noise and atom filtering.

[marcuscollins]

Summary by CodeRabbit

• Bug Fixes

  • Improved handling of structure data containing zero-occupancy atoms or invalid coordinates.
  • Preserved correct atom mappings during protein structure featurization when invalid atoms are removed.
  • Expanded compatibility with different atom-array inputs.

• Chores

  • Updated development tooling and pinned key package versions for more consistent environments.
  • Pinned the Boltz package and its Click dependency to compatible versions.

[coderabbitai]

📝 Walkthrough

Walkthrough

The Pixi configuration adds development tools and pins Boltz dependencies. A shared atom validity mask now checks occupancy and coordinates. Protpardelle applies this mask consistently to atoms and atom37 mapping tensors.

Changes

Pixi dependency configuration

Layer / File(s)	Summary
Pixi tool and Boltz dependency declarations pyproject.toml	The dev feature adds PyPI development tools. Boltz is pinned to 2.2.1, with a click==8.1.7 override.

Atom validity filtering

Layer / File(s)	Summary
Shared atom validity mask src/sampleworks/eval/structure_utils.py	The public get_valid_atom_mask helper identifies atoms with positive occupancy and finite coordinates. Structure processing uses the helper.
Protpardelle mapping and filtering src/sampleworks/models/protpardelle/wrapper.py	featurize derives atom37 mappings before filtering, then applies the same validity mask to the atom array and both mapping tensors.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Sequence Diagram(s)

sequenceDiagram
  participant featurize
  participant atom37_mapping
  participant get_valid_atom_mask
  featurize->>atom37_mapping: derive atom37 indices from protein-chain atoms
  featurize->>get_valid_atom_mask: compute validity mask
  get_valid_atom_mask-->>featurize: return mask
  featurize->>featurize: filter atoms and mapping tensors

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Possibly related PRs

• diff-use/sampleworks#255: Updates overlapping Pixi dependency and feature configuration in pyproject.toml.

Suggested reviewers: k-chrispens, dorismai

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly identifies the main changes: PPDL initialization from noise and atom filtering.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch mdc/fix-ppdl-init-from-noise

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@pyproject.toml`:
- Around line 21-22: Update the [tool.pixi.feature.dev] platforms configuration
to support the osx-arm64 platform after verifying its dependencies; if macOS
development is not supported, instead remove dev from boltz-osx or split the
feature so boltz-osx has a valid platform intersection and pixi.lock no longer
records an empty package set.

In `@src/sampleworks/eval/structure_utils.py`:
- Around line 246-249: Update get_valid_atom_mask() to use
np.isfinite(atom_array.coord).all(axis=-1) so both NaN and infinite coordinates
are rejected before returning the occupancy mask. Add a NumPy-style docstring
documenting the function’s purpose, accepted atom_array input, and returned
boolean mask.

🪄 Autofix

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: a9b03f6d-b42c-4110-8081-a2abb0b495f4

📥 Commits

Reviewing files that changed from the base of the PR and between 62a226c and d41e17d.

⛔ Files ignored due to path filters (1)

• pixi.lock is excluded by !**/*.lock

📒 Files selected for processing (3)

• pyproject.toml
• src/sampleworks/eval/structure_utils.py
• src/sampleworks/models/protpardelle/wrapper.py

[coderabbitai]

🩺 Stability & Availability | 🟠 Major | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail

python3 - <<'PY'
from pathlib import Path
import tomllib

manifest = tomllib.loads(Path("pyproject.toml").read_text())
pixi = manifest["tool"]["pixi"]
workspace_platforms = set(pixi["workspace"]["platforms"])
features = pixi["feature"]
failed = False

for name, definition in pixi["environments"].items():
    selected = definition["features"] if isinstance(definition, dict) else definition
    platforms = set(workspace_platforms)

    for feature in selected:
        platforms &= set(features.get(feature, {}).get("platforms", workspace_platforms))

    if not platforms:
        print(f"{name}: empty platform intersection from {selected}")
        failed = True

raise SystemExit(failed)
PY

Repository: diff-use/sampleworks

Length of output: 278

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

printf '%s\n' '--- pyproject.toml relevant sections ---'
nl -ba pyproject.toml | sed -n '1,55p;165,195p'

printf '%s\n' '--- lockfile candidates and boltz/gemmi references ---'
git ls-files | grep -E '(^|/)(pixi\.lock|.*lock.*)$' || true
rg -n -C 3 'boltz-osx|analysis-dev|protpardelle-dev|gemmi|boltz' . \
  -g 'pixi.lock' -g 'pyproject.toml' -g '*.lock' || true

printf '%s\n' '--- available TOML parsers/runtimes ---'
python3 --version
command -v ruby || true
ruby -e 'begin; require "tomlrb"; puts "tomlrb"; rescue LoadError; end' 2>/dev/null || true
command -v pixi || true

Repository: diff-use/sampleworks

Length of output: 239

---

🌐 Web query:

Pixi manifest feature platforms environment platform intersection documentation

💡 Result:

In Pixi, the relationship between environments, features, and platforms is centered on how the workspace resolves dependencies for various architectures and system requirements. Workspace Platforms Every Pixi project defines its supported platforms in the [workspace] table [1][2]. These are the platforms for which Pixi will solve dependencies and create lockfile entries [3][2]. You can define them as simple conda subdirs (e.g., "linux-64") or as rich-platform entries that include virtual packages (like CUDA or specific glibc versions) [3][4]. Feature Platforms Features allow you to define modular sets of dependencies, tasks, and configurations that can be composed into environments [5][6]. A feature can optionally define its own platforms list [1][4]. - If a feature specifies platforms, it restricts where that feature is compatible [7][8]. - If a feature does not specify platforms, it inherits the platforms defined at the workspace level [4][7]. Environment Platforms (Intersection) An environment is a collection of features. When Pixi creates an environment, it determines the supported platforms by calculating the intersection of the platforms supported by all features included in that environment [7][6]. - For example, if an environment includes a 'default' feature (supporting all workspace platforms) and a 'cuda' feature (restricted to 'linux-64'), the resulting environment will only be compatible with 'linux-64' [8]. - This intersection mechanism ensures that the environment is only valid for platforms where all included features are compatible [7][6]. Target Specifiers Beyond features, you can use target specifiers ([target.]) in your manifest to override configuration specifically for a single platform [3][8]. These targets must always be a subset of the platforms defined in [workspace.platforms]; attempting to target an undefined platform will result in an error [3][8].

Citations:

• 1: https://pixi.prefix.dev/latest/reference/pixi_manifest/
• 2: https://pixi.prefix.dev/latest/conda_ecosystem/
• 3: https://pixi.prefix.dev/dev/workspace/multi_platform_configuration/
• 4: https://github.com/prefix-dev/pixi/blob/main/docs/reference/pixi_manifest.md
• 5: https://pixi.prefix.dev/latest/workspace/multi_environment/
• 6: https://prefix.dev/blog/introducing_multi_env_pixi
• 7: https://github.com/prefix-dev/pixi/blob/dac71154/crates/pixi_manifest/src/features_ext.rs
• 8: https://prefix-dev-pixi.mintlify.app/concepts/multi-platform

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

printf '%s\n' '--- pyproject.toml relevant sections ---'
awk 'NR<=55 || (NR>=165 && NR<=195) {printf "%6d  %s\n", NR, $0}' pyproject.toml

printf '%s\n' '--- tracked lockfiles ---'
git ls-files | grep -E '(^|/)(pixi\.lock|.*lock.*)$' || true

printf '%s\n' '--- relevant manifest and lock references ---'
rg -n -C 4 'boltz-osx|analysis-dev|protpardelle-dev|gemmi|boltz' . \
  -g 'pixi.lock' -g 'pyproject.toml' -g '*.lock' || true

printf '%s\n' '--- workspace and feature platform declarations ---'
rg -n -C 3 'platforms|^\[tool\.pixi\.(feature|environment|workspace)' pyproject.toml

Repository: diff-use/sampleworks

Length of output: 50376

---

🌐 Web query:

site:pixi.prefix.dev feature platforms environment intersection pixi

💡 Result:

In the context of the Pixi package manager, the environment's supported platforms are determined by the intersection of the platforms defined across all features that comprise that environment [1][2]. When you define an environment in a Pixi workspace, it is composed of one or more features (including the default feature) [3]. Each feature can explicitly declare a list of platforms it supports [1][4]. Because an environment must be compatible with all of its constituent features, Pixi calculates the final set of supported platforms for that environment by taking the intersection of the platforms defined by every individual feature included in it [1][2]. Key points regarding this behavior: - Default Platform Behavior: If a feature does not explicitly override the platforms, it inherits the platforms defined at the workspace level [1][2]. - Workspace Best Practice: It is generally recommended to define the workspace platforms to include all platforms that you intend to support across any of your environments [1][2]. - Binding Features: By explicitly defining platforms within a feature (e.g., binding a feature to a specific "cuda" variant), you can control the environment's final platform compatibility [1][5]. - Lock File Impact: Pixi uses these platform definitions to solve dependencies and store them in the pixi.lock file for each environment [1][5]. If the intersection of platforms across the selected features results in an empty set, the environment will not be supportable on any platform [1][2].

Citations:

• 1: https://pixi.prefix.dev/latest/reference/pixi_manifest/
• 2: http://pixi.prefix.dev/v0.62.0/reference/pixi_manifest/
• 3: https://pixi.prefix.dev/latest/tutorials/multi%5Fenvironment/
• 4: https://pixi.prefix.dev/latest/workspace/multi%5Fenvironment/
• 5: https://pixi.prefix.dev/latest/workspace/multi_platform_configuration/

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

printf '%s\n' '--- workspace platforms and all environments ---'
awk 'NR>=50 && NR<=75 {printf "%6d  %s\n", NR, $0}'
awk 'NR>=189 && NR<=202 {printf "%6d  %s\n", NR, $0}'

printf '%s\n' '--- lock metadata for affected environments ---'
awk '
  /^  (analysis-dev|boltz-osx|protpardelle-dev):$/ {show=1; count=0}
  show {printf "%6d  %s\n", NR, $0; count++}
  show && count>=14 {show=0}
' pixi.lock

printf '%s\n' '--- lock platform keys near affected environments ---'
rg -n -A 8 -B 2 '^(  (analysis-dev|boltz-osx|protpardelle-dev):|platforms:|packages: \{\})' pixi.lock | head -120

Repository: diff-use/sampleworks

Length of output: 207

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

python3 - <<'PY'
from pathlib import Path

lines = Path("pyproject.toml").read_text().splitlines()
workspace = []
features = {}
environments = {}
section = None

for raw in lines:
    line = raw.strip()
    if not line or line.startswith("#"):
        continue
    if line.startswith("[") and line.endswith("]"):
        section = line[1:-1]
        continue
    if "=" not in line:
        continue
    key, value = (part.strip() for part in line.split("=", 1))
    if section == "tool.pixi.workspace" and key == "platforms":
        workspace = value
    elif section == "tool.pixi.feature.dev" and key == "platforms":
        features["dev"] = value
    elif section == "tool.pixi.feature.boltz-osx" and key == "platforms":
        features["boltz-osx"] = value
    elif section == "tool.pixi.environments" and key in {"analysis-dev", "boltz-osx", "protpardelle-dev"}:
        environments[key] = value

print("workspace_platforms =", workspace)
print("dev_platforms =", features.get("dev"))
print("boltz-osx_platforms =", features.get("boltz-osx"))
for name, definition in environments.items():
    print(name, "features =", definition)
PY

Repository: diff-use/sampleworks

Length of output: 478

---

Allow dev on its consumer platforms.

dev supports only linux-64, but boltz-osx includes it and requires osx-arm64. Pixi therefore gives boltz-osx an empty platform intersection, reflected by packages: {} in pixi.lock. If macOS development is supported, add osx-arm64 to dev after checking its dependencies. Otherwise, remove dev from boltz-osx or split the feature.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@pyproject.toml` around lines 21 - 22, Update the [tool.pixi.feature.dev]
platforms configuration to support the osx-arm64 platform after verifying its
dependencies; if macOS development is not supported, instead remove dev from
boltz-osx or split the feature so boltz-osx has a valid platform intersection
and pixi.lock no longer records an empty package set.

[coderabbitai]

🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

🧩 Analysis chain

🌐 Web query:

In NumPy 2.0, does numpy.isnan return False for positive and negative infinity, and does numpy.isfinite return False for those values?

💡 Result:

Yes, in NumPy 2.0, both functions behave as you described: 1. numpy.isnan returns False for both positive and negative infinity [1][2]. It is designed specifically to test for NaN (Not a Number) values [1][3]. 2. numpy.isfinite returns False for both positive and negative infinity [4][5]. It tests for finiteness, meaning it returns True only for numbers that are neither NaN nor infinity (positive or negative) [3][5].

Citations:

• 1: https://numpy.org/doc/2.0/reference/generated/numpy.isnan.html
• 2: https://numpy.org/doc/stable/reference/generated/numpy.isnan.html
• 3: https://numpy.org/doc/2.0/reference/routines.logic.html
• 4: https://numpy.org/doc/2.0/reference/generated/numpy.isfinite.html
• 5: https://numpy.org/doc/2.1/reference/generated/numpy.isfinite.html

---

🏁 Script executed:

#!/bin/bash
set -e
printf '%s\n' '--- target function and nearby helpers ---'
sed -n '220,265p' src/sampleworks/eval/structure_utils.py
printf '%s\n' '--- usages ---'
rg -n -C 4 'get_valid_atom_mask|valid_atom_mask|isfinite|isnan' src/sampleworks
printf '%s\n' '--- relevant file outline ---'
ast-grep outline src/sampleworks/eval/structure_utils.py --match 'get_valid_atom_mask' --view expanded

Repository: diff-use/sampleworks

Length of output: 26380

---

🏁 Script executed:

#!/bin/bash
set -e
printf '%s\n' '--- preprocessing contract and call path ---'
sed -n '145,190p' src/sampleworks/eval/structure_utils.py
sed -n '520,555p' src/sampleworks/models/protpardelle/wrapper.py
printf '%s\n' '--- repository references to finite-coordinate requirements ---'
rg -n -C 3 'finite coordin|non-finite coordin|valid atom mask|valid_atom_mask' README.md docs src tests 2>/dev/null || true
printf '%s\n' '--- standalone NumPy behavior probe ---'
python3 - <<'PY'
import numpy as np

values = np.array([np.nan, np.inf, -np.inf, 0.0, 1.0])
print("values:", values.tolist())
print("isnan:", np.isnan(values).tolist())
print("isfinite:", np.isfinite(values).tolist())

coords = np.array([
    [0.0, 1.0, 2.0],
    [np.nan, 1.0, 2.0],
    [np.inf, 1.0, 2.0],
    [-np.inf, 1.0, 2.0],
])
occupancy = np.ones(4)
old_mask = (occupancy > 0) & ~np.any(np.isnan(coords), axis=-1)
finite_mask = (occupancy > 0) & np.isfinite(coords).all(axis=-1)
print("old_mask:", old_mask.tolist())
print("finite_mask:", finite_mask.tolist())
PY

Repository: diff-use/sampleworks

Length of output: 12872

---

🏁 Script executed:

#!/bin/bash
set -e
printf '%s\n' '--- integration test expectations ---'
sed -n '380,430p' tests/integration/test_mismatch_integration.py
printf '%s\n' '--- full structure preprocessing coordinate path ---'
sed -n '190,230p' src/sampleworks/eval/structure_utils.py
printf '%s\n' '--- reward-input contract ---'
sed -n '35,85p' src/sampleworks/core/rewards/protocol.py
printf '%s\n' '--- relevant finite-coordinate tests ---'
sed -n '750,805p' tests/utils/test_atom_array_utils.py
printf '%s\n' '--- pure-Python edge-case sanity check (NumPy unavailable in sandbox) ---'
python3 - <<'PY'
import math
values = [float("nan"), float("inf"), float("-inf"), 0.0]
print("isnan:", [math.isnan(value) for value in values])
print("isfinite:", [math.isfinite(value) for value in values])
PY

Repository: diff-use/sampleworks

Length of output: 9008

---

Reject non-finite coordinates and document get_valid_atom_mask().

Replace the NaN-only check with np.isfinite(atom_array.coord).all(axis=-1). Otherwise, infinite coordinates can reach reconciliation and model processing. Add the required NumPy-style docstring.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/sampleworks/eval/structure_utils.py` around lines 246 - 249, Update
get_valid_atom_mask() to use np.isfinite(atom_array.coord).all(axis=-1) so both
NaN and infinite coordinates are rejected before returning the occupancy mask.
Add a NumPy-style docstring documenting the function’s purpose, accepted
atom_array input, and returned boolean mask.

Source: Coding guidelines