fix: multi-user machine permission errors on /tmp created dirs (#158)

* fix: multi-user machine permission errors on /tmp created dirs

- each user gets /tmp/of3-of-$USERNAME
- respects TMPDIR and other env vars
- all the colabfold and jackhammer code is moved int
- tests
- fixes #150

* review: comments from Jennifer

* revert jackhammer.py changes

Author: jandom

docs/source/configuration_reference.md

@@ -232,7 +232,7 @@ Configures the ColabFold MSA server integration.
 - `server_user_agent` *(str)*: User agent string (default: `openfold`)
 - `server_url` *(Url)*: ColabFold server URL (default: `https://api.colabfold.com`)
 - `save_mappings` *(bool)*: Save sequence ID mappings (default: `true`)
-- `msa_output_directory` *(Path)*: Directory for MSA outputs (default: temporary directory)
+- `msa_output_directory` *(Path)*: Directory for MSA outputs (default: `temporary directory/of3-of-<user>/colabfold_msas`)
 - `cleanup_msa_dir` *(bool)*: Delete MSAs after processing (default: `true`)
 
 **Example**:

examples/reference_full_config/full_config.yml

@@ -130,7 +130,7 @@ msa_computation_settings:
   server_user_agent: openfold
   server_url: https://api.colabfold.com/
   save_mappings: true
-  msa_output_directory: <tmp-dir>/of3_colabfold_msas/ 
+  msa_output_directory: <tmp-dir>/of3-of-<user>/colabfold_msas/ 
   cleanup_msa_dir: true
 
 # TemplatePreprocessorSettings: https://github.com/aqlaboratory/openfold-3/blob/main/openfold3/core/data/pipelines/preprocessing/template.py#L1459
@@ -152,11 +152,11 @@ template_preprocessor_settings:
   create_logs: false
   n_processes: 1
   chunksize: 1
-  structure_directory: <tmp-dir>/of3_template_data/template_structures
+  structure_directory: <tmp-dir>/of3-of-<user>/template_data/template_structures
   structure_file_format: cif
-  output_directory: <tmp-dir>/of3_template_data
+  output_directory: <tmp-dir>/of3-of-<user>/template_data
   precache_directory: null
   structure_array_directory: null
-  cache_directory: <tmp-dir>/of3_template_data/template_cache
+  cache_directory: <tmp-dir>/of3-of-<user>/template_data/template_cache
   log_directory: null
   ccd_file_path: null

openfold3/core/data/pipelines/preprocessing/template.py

@@ -19,7 +19,6 @@
 import os
 import random
 import re
-import tempfile
 import traceback
 from datetime import datetime
 from functools import wraps
@@ -1601,9 +1600,11 @@ def _prepare_output_directories(self) -> "TemplatePreprocessorSettings":
                 "pipeline."
             )
 
-        self.output_directory = (
-            self.output_directory or Path(tempfile.gettempdir()) / "of3_template_data"
-        )
+        if self.output_directory is None:
+            from openfold3.core.data.tools.utils import get_of3_tmpdir
+
+            self.output_directory = get_of3_tmpdir("template_data")
+
         base = self.output_directory
 
         # only set these if the user did not give them explicitly

openfold3/core/data/tools/colabfold_msa_server.py

@@ -18,7 +18,6 @@
 import random
 import shutil
 import tarfile
-import tempfile
 import time
 import warnings
 from dataclasses import dataclass, field
@@ -997,13 +996,17 @@ class MsaComputationSettings(BaseModel):
     server_user_agent: str = "openfold"
     server_url: Url = Url("https://api.colabfold.com")
     save_mappings: bool = True
-    msa_output_directory: Path = Path(tempfile.gettempdir()) / "of3_colabfold_msas"
+    msa_output_directory: Path | None = None
     cleanup_msa_dir: bool = True
 
     @model_validator(mode="after")
     def create_dir(self) -> "MsaComputationSettings":
         """Creates the output directory if it does not exist."""
-        if not self.msa_output_directory.exists():
+        if self.msa_output_directory is None:
+            from openfold3.core.data.tools.utils import get_of3_tmpdir
+
+            self.msa_output_directory = get_of3_tmpdir("colabfold_msas")
+        elif not self.msa_output_directory.exists():
             self.msa_output_directory.mkdir(parents=True, exist_ok=True)
         return self
 

openfold3/core/data/tools/utils.py

@@ -17,10 +17,27 @@
 
 import contextlib
 import datetime
+import getpass
 import logging
 import shutil
 import tempfile
 import time
+from pathlib import Path
+
+
+def get_of3_tmpdir(subdir: str | None = None) -> Path:
+    """Return a user-namespaced OpenFold3 temporary directory.
+
+    Follows the same convention as pytest (``/tmp/pytest-of-<user>/``):
+    ``<tmpdir>/of3-of-<user>/<subdir>``.  Respects ``$TMPDIR`` and other
+    platform conventions via :func:`tempfile.gettempdir`.
+
+    The returned directory is created on disk if it does not already exist.
+    """
+    base = Path(tempfile.gettempdir()) / f"of3-of-{getpass.getuser()}"
+    path = base / subdir if subdir else base
+    path.mkdir(parents=True, exist_ok=True)
+    return path
 
 
 @contextlib.contextmanager

openfold3/tests/core/data/tools/test_utils.py

@@ -0,0 +1,77 @@
+"""Tests for ``openfold3.core.data.tools.utils``."""
+
+import getpass
+import tempfile
+from pathlib import Path
+from unittest.mock import patch
+
+from openfold3.core.data.tools.utils import get_of3_tmpdir
+
+
+class TestGetOf3Tmpdir:
+    """Tests for get_of3_tmpdir."""
+
+    def test_returns_path(self):
+        result = get_of3_tmpdir("test_subdir")
+        assert isinstance(result, Path)
+
+    def test_directory_is_created(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            result = get_of3_tmpdir("mysubdir")
+
+        assert result.is_dir()
+
+    def test_contains_username(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            result = get_of3_tmpdir("subdir")
+
+        assert f"of3-of-{getpass.getuser()}" in str(result)
+
+    def test_subdir_appended(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            result = get_of3_tmpdir("colabfold_msas")
+
+        assert result.name == "colabfold_msas"
+        assert result.parent.name == f"of3-of-{getpass.getuser()}"
+
+    def test_no_subdir(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            result = get_of3_tmpdir()
+
+        assert result.name == f"of3-of-{getpass.getuser()}"
+        assert result.is_dir()
+
+    def test_respects_tmpdir_env(self, tmp_path, monkeypatch):
+        custom_tmp = tmp_path / "custom_tmp"
+        custom_tmp.mkdir()
+        monkeypatch.setenv("TMPDIR", str(custom_tmp))
+        # Force tempfile to re-evaluate TMPDIR
+        tempfile.tempdir = None
+
+        result = get_of3_tmpdir("subdir")
+
+        assert str(result).startswith(str(custom_tmp))
+
+    def test_idempotent(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            first = get_of3_tmpdir("subdir")
+            second = get_of3_tmpdir("subdir")
+
+        assert first == second
+
+    def test_different_subdirs_are_isolated(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            a = get_of3_tmpdir("aaa")
+            b = get_of3_tmpdir("bbb")
+
+        assert a != b
+        assert a.parent == b.parent
+
+    def test_different_users_are_isolated(self, tmp_path):
+        with patch.object(tempfile, "gettempdir", return_value=str(tmp_path)):
+            real = get_of3_tmpdir("data")
+            with patch.object(getpass, "getuser", return_value="other_user"):
+                other = get_of3_tmpdir("data")
+
+        assert real != other
+        assert "of3-of-other_user" in str(other)

openfold3/tests/test_writer.py

@@ -142,7 +142,6 @@ def write_confidence_scores(
     def test_full_confidence_scores_written(
         self, tmp_path, output_fmt, dummy_confidence_scores
     ):
-
         self.write_confidence_scores(
             tmp_path, output_fmt, True, dummy_confidence_scores
         )