increase version and fixes #18

.gitignore

@@ -11,9 +11,10 @@ env/
 
 # ignore codecov
 .coverage*
+coverage.xml
 
 scratch.py
 scratch.R
 
 .env
-codecov
+codecov

biobricks/brick.py

@@ -8,7 +8,7 @@
 from .downloader import download_out
 from urllib.parse import urlparse
 import sys
-from .checks import check_url_available, check_token, check_symlink_permission, check_safe_git_repo
+from .checks import check_url_available, check_token, check_safe_git_repo
 
 class Brick:
 
@@ -125,7 +125,6 @@ def install(self):
 
         check_url_available(self.remote)
         check_token(token())
-        check_symlink_permission()
 
         cmd = functools.partial(run,shell=True,stdout=DEVNULL,stderr=DEVNULL)
 

biobricks/checks.py

@@ -29,7 +29,7 @@ def check_token(token, silent=False):
         raise ValueError(f"Invalid token. Run `biobricks configure`")
     return is_valid
 
-def check_symlink_permission():
+def can_symlink():
     try:
         src = tempfile.NamedTemporaryFile()
         dst = os.path.join(tempfile.gettempdir(), str(uuid.uuid4()))
@@ -38,7 +38,7 @@ def check_symlink_permission():
         src.close()
         return True
     except Exception as e:
-        raise PermissionError("Need Symlink Permission. Contact administrator.")
+        return False
 
 def check_configured():
     """check that biobricks is configured"""

biobricks/downloader.py

@@ -3,6 +3,7 @@
 import os
 import shutil
 import requests
+import biobricks.checks
 from pathlib import Path
 from tqdm import tqdm  # Import tqdm for the progress bar
 
@@ -44,8 +45,12 @@ def download_out(md5, dest: Path, url_prefix="https://dvc.biobricks.ai/files/md5
         logger.info(f"downloading file {remote_url} to {cache_path}")
         _download_outfile(remote_url, cache_path, bytes)
 
-    dest.unlink(missing_ok=True) # remove the symlink if it exists  
-    os.symlink(cache_path, dest)
+    dest.unlink(missing_ok=True) # remove the symlink if it exists
+    if not biobricks.checks.can_symlink():
+        logger.warning(f"you are not able to make symlinks cache-files will be copied to bricks. This is an inefficient use of disk space.")
+        shutil.copy(cache_path, dest)
+    else:
+        os.symlink(cache_path, dest)
 
 
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "biobricks"
-version = "0.3.1"
+version = "0.3.2"
 authors = [
   { name="Thomas Luechtefeld", email="[email protected]" },
   { name="Jose A. Jaramillo", email="[email protected]" }

tests/test_init.py → tests/test_bricks.py

@@ -1,12 +1,13 @@
 import unittest
+from unittest.mock import patch
 from pathlib import Path
 from biobricks import Brick
 from biobricks.config import write_config, init_bblib
 import tempfile
 import pandas as pd
 import sqlite3
 
-class TestBrickResolve(unittest.TestCase):
+class BrickTests(unittest.TestCase):
 
     def setUp(self):
         self.tempdir = tempfile.TemporaryDirectory()
@@ -61,6 +62,23 @@ def test_assets_hello_brick(self):
         self.assertTrue(hasattr(assets, "mtcars_parquet"))
         self.assertTrue(hasattr(assets, "rtbls_iris_parquet"))
         self.assertTrue(hasattr(assets, "rtbls_mtcars_parquet"))
+
+    @patch('biobricks.checks.can_symlink', return_value=False)
+    def test_install_without_symlink(self, mocked_can_symlink):
+        brick = Brick.Resolve("hello-brick")
+        brick.install()
+
+        paths = [
+            "brick/iris.sqlite",
+            "brick/mtcars.parquet",
+            "brick/rtbls/iris.parquet",
+            "brick/rtbls/mtcars.parquet"
+        ]
+
+        for path in paths:
+            full_path = brick.path() / path
+            self.assertTrue(full_path.exists())
+            self.assertFalse(full_path.is_symlink(), f"{path} should not be a symlink")
 
 if __name__ == '__main__':
     unittest.main()