Changes to pixi files to facilitate development on Mac OSX#255
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📝 WalkthroughWalkthroughThis PR updates ChangesPixi environment and dependency configuration
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🤖 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`:
- Line 88: get_pixi_env() currently returns "boltz" for
StructurePredictor.BOLTZ_1 and BOLTZ_2 but pyproject.toml defines the macOS
feature as "boltz-osx", so macOS runs fail; update get_pixi_env() to return the
platform-appropriate name (detect os via sys.platform or platform.machine) and
return "boltz-osx" on macOS/arm64 and "boltz" otherwise, and update related
user-facing install/error strings in src/sampleworks/utils/imports.py and
README.md to mention both names or show platform-specific instructions so
messages match the selected Pixi env. Ensure references to
StructurePredictor.BOLTZ_1 and BOLTZ_2 still map to the new logic.
🪄 Autofix (Beta)
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
Run ID: 9e037248-0297-4af1-8a8b-4454f3aed3fe
⛔ Files ignored due to path filters (1)
pixi.lockis excluded by!**/*.lock
📒 Files selected for processing (1)
pyproject.toml
| boltz = {features = ["boltz"]} | ||
| boltz-analysis = {features = ["boltz", "analysis"]} | ||
| boltz-dev = {features = ["boltz", "dev"]} | ||
| boltz-osx = {features = ["boltz-osx", "dev", "analysis"]} |
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🧩 Analysis chain
🏁 Script executed:
#!/bin/bash
# Description: Search for platform detection or OS-specific environment selection logic.
# Search for platform detection patterns
rg -nP --type=py -C3 '\b(platform\.(system|machine)|sys\.platform|os\.name|osx|darwin|mac)\b' | head -50
# Search for environment name logic
rg -nP --type=py -C3 'def get_pixi_env'
# Check if boltz-osx is referenced anywhere in Python code
rg -nP --type=py -l 'boltz-osx'Repository: diff-use/sampleworks
Length of output: 1174
🏁 Script executed:
#!/bin/bash
set -euo pipefail
# Find references to boltz-osx and pixi install messaging
rg -n --hidden --glob '!*node_modules/*' -S 'boltz-osx' .
rg -n --hidden --glob '!*node_modules/*' -S 'pixi install -e ' .
# Show get_pixi_env and any related platform/env selection logic
rg -n --hidden --glob '!*node_modules/*' -S 'def get_pixi_env\b' run_grid_search.py
python_files=$(fd -t f -e py src . 2>/dev/null | wc -l || true)
echo "python_files_count=$python_files"
# Print the body of get_pixi_env with line numbers (approx)
python - <<'PY'
import itertools,sys,os,re
path='run_grid_search.py'
start=None
with open(path,'r',encoding='utf-8') as f:
for i,line in enumerate(f,1):
if re.match(r'\s*def get_pixi_env\s*\(', line):
start=i
break
if start is None:
print("get_pixi_env not found")
sys.exit(0)
end=start+60
with open(path,'r',encoding='utf-8') as f:
for i,line in enumerate(f,1):
if start-5 <= i <= end:
print(f"{i:6d}:{line.rstrip()}")
PY
# Print likely messaging block in src/sampleworks/utils/imports.py
if [ -f src/sampleworks/utils/imports.py ]; then
rg -n -S 'pixi install -e ' src/sampleworks/utils/imports.py
python - <<'PY'
import re
path='src/sampleworks/utils/imports.py'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
for idx,line in enumerate(lines,1):
if 'pixi install -e' in line:
s=max(1,idx-20); e=min(len(lines),idx+20)
for j in range(s,e+1):
print(f"{j:6d}:{lines[j-1].rstrip()}")
print("----")
PY
fiRepository: diff-use/sampleworks
Length of output: 17612
🏁 Script executed:
#!/bin/bash
set -euo pipefail
# Find references to boltz-osx and pixi install messaging
rg -n --hidden -S 'boltz-osx' . || true
rg -n --hidden -S 'pixi install -e ' . || true
# Show get_pixi_env and any related platform/env selection logic
rg -n -S 'def get_pixi_env\b' run_grid_search.py || true
# Print the body of get_pixi_env with line numbers (approx)
python - <<'PY'
import re,sys
path='run_grid_search.py'
try:
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
except FileNotFoundError:
print("missing run_grid_search.py")
sys.exit(0)
start=None
for i,line in enumerate(lines,1):
if re.match(r'\s*def get_pixi_env\s*\(', line):
start=i; break
if start is None:
print("get_pixi_env not found")
sys.exit(0)
end=min(len(lines),start+80)
for j in range(start-5,end+1):
if 1<=j<=len(lines):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
# Print likely messaging block in src/sampleworks/utils/imports.py
if [ -f src/sampleworks/utils/imports.py ]; then
rg -n -S 'pixi install -e ' src/sampleworks/utils/imports.py || true
python - <<'PY'
import re,sys
path='src/sampleworks/utils/imports.py'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
hits=[i for i,l in enumerate(lines,1) if 'pixi install -e' in l]
if not hits:
print("no pixi install -e in imports.py")
sys.exit(0)
for idx in hits:
s=max(1,idx-20); e=min(len(lines),idx+20)
print(f"### around line {idx}")
for j in range(s,e+1):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
fi
# Print pyproject snippet for boltz-osx env
if [ -f pyproject.toml ]; then
rg -n -S 'boltz-osx\s*=' pyproject.toml || true
python - <<'PY'
path='pyproject.toml'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
for i,l in enumerate(lines,1):
if 'boltz-osx' in l:
s=max(1,i-5); e=min(len(lines),i+5)
for j in range(s,e+1):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
fiRepository: diff-use/sampleworks
Length of output: 19733
🏁 Script executed:
#!/bin/bash
set -euo pipefail
rg -n -S 'boltz-osx' . || true
rg -n -S 'pixi install -e ' . || true
rg -n -S 'def get_pixi_env\b' run_grid_search.py || true
python3 - <<'PY'
import re
path='run_grid_search.py'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
start=None
for i,line in enumerate(lines,1):
if re.match(r'\s*def get_pixi_env\s*\(', line):
start=i;break
print("get_pixi_env_start",start)
end=min(len(lines),start+80)
for j in range(start-5,end+1):
if 1<=j<=len(lines):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
if [ -f src/sampleworks/utils/imports.py ]; then
rg -n -S 'pixi install -e ' src/sampleworks/utils/imports.py || true
python3 - <<'PY'
path='src/sampleworks/utils/imports.py'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
hits=[i for i,l in enumerate(lines,1) if 'pixi install -e' in l]
print("hits",hits)
for idx in hits:
s=max(1,idx-20); e=min(len(lines),idx+20)
print(f"### around {idx}")
for j in range(s,e+1):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
fi
if [ -f pyproject.toml ]; then
rg -n -S 'boltz-osx\s*=' pyproject.toml || true
python3 - <<'PY'
path='pyproject.toml'
with open(path,'r',encoding='utf-8') as f:
lines=list(f)
for i,l in enumerate(lines,1):
if 'boltz-osx' in l:
s=max(1,i-5); e=min(len(lines),i+5)
for j in range(s,e+1):
print(f"{j:6d}:{lines[j-1].rstrip()}")
PY
fiRepository: diff-use/sampleworks
Length of output: 19761
Fix macOS Pixi env selection for Boltz grid search (boltz-osx vs boltz).
pyproject.tomldefinesboltzonly forlinux-64, but defines a separateboltz-osxforosx-arm64.run_grid_search.py:get_pixi_env()returns"boltz"forStructurePredictor.BOLTZ_1/StructurePredictor.BOLTZ_2, so macOS Boltz runs will try to use the wrong Pixi feature/env name.- User-facing install guidance is also wired to
"boltz"(e.g.,src/sampleworks/utils/imports.pydefault messages andREADME.md), with no mention ofboltz-osx.
Align get_pixi_env() and the install/error messaging with the macOS-specific feature group (either by adding OS detection, or by making the boltz feature resolve to the correct platform-specific dependencies).
🤖 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` at line 88, get_pixi_env() currently returns "boltz" for
StructurePredictor.BOLTZ_1 and BOLTZ_2 but pyproject.toml defines the macOS
feature as "boltz-osx", so macOS runs fail; update get_pixi_env() to return the
platform-appropriate name (detect os via sys.platform or platform.machine) and
return "boltz-osx" on macOS/arm64 and "boltz" otherwise, and update related
user-facing install/error strings in src/sampleworks/utils/imports.py and
README.md to mention both names or show platform-specific instructions so
messages match the selected Pixi env. Ensure references to
StructurePredictor.BOLTZ_1 and BOLTZ_2 still map to the new logic.
# Conflicts: # pixi.lock
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k-chrispens
approved these changes
Jun 14, 2026
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These changes make it possible to install most environments on Mac OS X. To do this it changes the
[dependency-groups]to be actual[tool.pixi.feature.*], and created aboltz-osxfeature. For protenix in particular this prevents pixi from trying to install environments on platforms where they are not compatible.Summary by CodeRabbit