Ensure Ray shutdown between tests, remove deprecated imports, and update README

README.md

@@ -30,24 +30,9 @@ By enabling precise volume and flexibility measurements, POVME has become an ess
 -   Supporting virtual screening and druggability predictions.
 -   Comparing conformational ensembles from molecular dynamics simulations.
 
-## Development
-
-We use [pixi](https://pixi.sh/latest/) to manage Python environments and simplify the developer workflow.
-Once you have [pixi](https://pixi.sh/latest/) installed, move into `POVME` directory (e.g., `cd POVME`) and install the  environment using the command
-
-```bash
-pixi install
-```
-
-Now you can activate the new virtual environment using
-
-```sh
-pixi shell -e dev
-```
-
 ## Installation
 
-### Development
+### Latest development version
 
 To install the latest development version of `povme`, follow these steps.
 
@@ -63,15 +48,21 @@ Navigate into the cloned directory.
 cd POVME
 ```
 
-Install the development version using `pip`.
+Install the latest version using `pixi`.
 
 ```bash
-pip install .
+pixi install
 ```
 
-This will install `povme` along with all required dependencies into your current Python environment.
+This will install `povme` along with all required dependencies into a virtual environment.
+
+To use `povme`, activate the environment and run:
 
-### Tagged
+```bash
+pixi shell
+```
+
+### Tagged version
 
 To install a specific version of `povme`, such as `v2.2.2`, follow these steps.
 
@@ -83,14 +74,42 @@ cd POVME
 git checkout v2.2.2
 ```
 
-Install the tagged version using `pip`.
+Ensure your environment includes the required dependencies. If not, please run the following:
 
 ```bash
-pip install .
+conda create -n povme python=3.11 numpy=1.23 scipy=1.10
+conda activate povme
 ```
 
 This will install the specified version of `povme` and its dependencies into your current Python environment.
 
+You can use `povme` as follows:
+
+```bash
+python3 POVME2.py your_input.init
+```
+
+You can also check your installation is valid by running:
+
+```bash
+python3 POVME2.py --test
+```
+
+## Development
+
+We use [pixi](https://pixi.sh/latest/) to manage Python environments and simplify the developer workflow.
+Once you have [pixi](https://pixi.sh/latest/) installed, move into the `POVME` directory (e.g., `cd POVME`) and install the environment using the command:
+
+```bash
+pixi install
+```
+
+Now you can activate the development virtual environment using:
+
+```sh
+pixi shell -e dev
+```
+
 ## Cite
 
 If you use POVME in your work, please cite:
@@ -106,4 +125,4 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY
 See the GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License along with this program.
-If not, see [https://www.gnu.org/licenses/](https://www.gnu.org/licenses/).
+If not, see [https://www.gnu.org/licenses/](https://www.gnu.org/licenses/).

povme/parallel.py

@@ -72,8 +72,8 @@ def save_results(results, **kwargs):
 """
 
 from abc import ABC, abstractmethod
-from collections.abc import Callable
-from typing import Any, Generator
+from collections.abc import Callable, Generator
+from typing import Any
 
 import ray
 from loguru import logger
@@ -126,6 +126,10 @@ def __init__(
         self.n_cores = (
             n_cores if n_cores > 0 else int(ray.available_resources().get("CPU", 1))
         )
+        if not use_ray and n_cores > 1:
+            logger.warning(
+                "n_cores > 1 but use_ray is False. Running tasks sequentially."
+            )
         """
         The number of parallel tasks to run. If set to `-1` or any value less than or
         equal to `0`, all available CPU cores are utilized.

povme/pocket/volume.py

@@ -14,8 +14,9 @@
 import os
 import sys
 import time
+from collections.abc import Generator
 from io import StringIO
-from typing import Any, Generator
+from typing import Any
 
 import numpy as np
 from loguru import logger

tests/conftest.py

@@ -34,6 +34,14 @@ def turn_on_logging():
     enable_logging(10)
 
 
+@pytest.fixture(autouse=True)
+def shutdown_ray_after_test():
+    """Ensure Ray is shut down after each test to prevent deadlocks."""
+    yield
+    if HAS_RAY and ray.is_initialized():
+        ray.shutdown()
+
+
 @pytest.fixture
 def path_4nss_config():
     return os.path.join(TEST_DIR, "files/4nss/povme.yml")