Depend on audeer>=2.0.0 (#411)

* Depend on audeer>=2.0.0

* Add test for symlink storage

* Fix db.root when storing database

* Try to fix to_filewise_index()

* Depend on audeer>=2.0.0

* TST: enforce audeer>=2.0.0

* Try to enforce development version of audformat

* Try manual installation of audeer

* Add a comment

.github/workflows/test.yml

@@ -49,6 +49,11 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         pip install -r tests/requirements.txt
+        # Force audeer 2.0.0
+        # until we have a new audformat version released,
+        # that does not have "audeer <2.0.0"
+        # in its dependencies
+        pip install --upgrade audeer
 
     - name: Test with pytest
       run: |

audformat/core/attachment.py

@@ -144,7 +144,7 @@ def _check_path(
         root: str,
     ):
         r"""Check if path exists and is not a symlink."""
-        if not os.path.exists(audeer.path(root, self.path)):
+        if not os.path.exists(audeer.path(root, self.path, follow_symlink=True)):
             raise FileNotFoundError(
                 f"The provided path '{self.path}' "
                 f"of attachment '{self._id}' "

audformat/core/database.py

@@ -1000,7 +1000,8 @@ def save(
             verbose: show progress bar
 
         """
-        root = audeer.mkdir(root)
+        root = audeer.path(root, follow_symlink=True)
+        audeer.mkdir(root)
 
         ext = ".yaml"
         header_path = os.path.join(root, name + ext)
@@ -1010,7 +1011,7 @@ def save(
         if not header_only:
             # Store (misc) tables
             def job(obj_id, obj):
-                path = audeer.path(root, f"{name}.{obj_id}")
+                path = os.path.join(root, f"{name}.{obj_id}")
                 obj.save(
                     path,
                     storage_format=storage_format,
@@ -1411,7 +1412,7 @@ def load(
 
         """
         ext = ".yaml"
-        root = audeer.path(root)
+        root = audeer.path(root, follow_symlink=True)
         path = os.path.join(root, name + ext)
 
         if not os.path.exists(path):
@@ -1435,7 +1436,7 @@ def load(
             for table_id in table_ids:
                 table = db[table_id]
                 if load_data:
-                    table_path = audeer.path(root, name + "." + table_id)
+                    table_path = os.path.join(root, name + "." + table_id)
                     params.append(([table, table_path], {}))
                 else:
                     table._df = None

pyproject.toml

@@ -31,7 +31,7 @@ classifiers = [
 ]
 requires-python = '>=3.8'
 dependencies = [
-    'audeer >=1.19.0,<2.0.0',
+    'audeer >=2.0.0',
     'audiofile >=0.4.0',
     'iso-639',
     'iso3166',

tests/test_attachment.py

@@ -58,7 +58,7 @@ def test_attachment(tmpdir):
 
     # Save database, path is allowed to be a symlink
     audeer.rmdir(db_path)
-    audeer.mkdir(audeer.path(db_path, folder_path))
+    audeer.mkdir(db_path, folder_path)
     os.symlink(
         audeer.path(db_path, folder_path),
         audeer.path(db_path, file_path),
@@ -67,7 +67,7 @@ def test_attachment(tmpdir):
 
     # Replace symlink by file
     os.remove(os.path.join(db_path, file_path))
-    audeer.touch(audeer.path(db_path, file_path))
+    audeer.touch(db_path, file_path)
     db.save(db_path)
 
     # File exist now, folder is empty
@@ -89,7 +89,7 @@ def test_attachment(tmpdir):
     # Load database
     #
     # path must not exist when loading the database
-    audeer.rmdir(audeer.path(db_path, os.path.dirname(file_path)))
+    audeer.rmdir(db_path, os.path.dirname(file_path))
     assert not os.path.exists(audeer.path(db_path, file_path))
     audformat.Database.load(db_path, load_data=True)
     audformat.Database.load(db_path, load_data=False)
@@ -172,9 +172,9 @@ def test_attachment_files_errors(tmpdir):
         attachment.files
 
     # Attached path does not exists
-    audeer.mkdir(audeer.path(db_path, attachment_path))
+    audeer.mkdir(db_path, attachment_path)
     db.save(db_path)
-    audeer.rmdir(audeer.path(db_path, attachment_path))
+    audeer.rmdir(db_path, attachment_path)
     error_msg = (
         f"The provided path '{attachment_path}' "
         "of attachment 'attachment' "
@@ -185,7 +185,7 @@ def test_attachment_files_errors(tmpdir):
 
     # Attached path is a symlink
     folder_link = "extra-link"
-    audeer.mkdir(audeer.path(db_path, folder_link))
+    audeer.mkdir(db_path, folder_link)
     os.symlink(
         audeer.path(db_path, folder_link),
         audeer.path(db_path, attachment_path),
@@ -200,9 +200,9 @@ def test_attachment_files_errors(tmpdir):
 
     # Some files are inside a symlink folder
     os.remove(os.path.join(db_path, attachment_path))
-    audeer.mkdir(audeer.path(db_path, attachment_path))
-    audeer.touch(audeer.path(db_path, attachment_path, "file1.txt"))
-    audeer.touch(audeer.path(db_path, folder_link, "file2.txt"))
+    audeer.mkdir(db_path, attachment_path)
+    audeer.touch(db_path, attachment_path, "file1.txt")
+    audeer.touch(db_path, folder_link, "file2.txt")
     os.symlink(
         audeer.path(db_path, folder_link),
         audeer.path(db_path, attachment_path, "link"),
@@ -217,8 +217,8 @@ def test_attachment_files_errors(tmpdir):
 
     # Some files of the attachments are symlinks
     os.remove(os.path.join(db_path, attachment_path, "link"))
-    audeer.touch(audeer.path(db_path, attachment_path, "file1.txt"))
-    audeer.touch(audeer.path(db_path, folder_link, "file2.txt"))
+    audeer.touch(db_path, attachment_path, "file1.txt")
+    audeer.touch(db_path, folder_link, "file2.txt")
     os.symlink(
         audeer.path(db_path, folder_link, "file2.txt"),
         audeer.path(db_path, attachment_path, "file2.txt"),

tests/test_database.py

@@ -637,6 +637,15 @@ def test_save_and_load(tmpdir, db, storage_format, load_data, num_workers):
             db[table_id].get()
 
 
+def test_save_symlink(tmpdir):
+    folder = audeer.mkdir(tmpdir, "folder")
+    link = audeer.path(tmpdir, "link")
+    os.symlink(folder, link)
+    db = audformat.testing.create_db()
+    db.save(link)
+    assert db.root == folder
+
+
 def test_segments():
     db = audformat.testing.create_db()
     df = pytest.DB["segments"].get()
@@ -659,7 +668,7 @@ def test_string():
 def test_update(tmpdir):
     # original database
 
-    db_root = audeer.mkdir(audeer.path(tmpdir, "db"))
+    db_root = audeer.mkdir(tmpdir, "db")
     db = audformat.testing.create_db(minimal=True)
     db.author = "author"
     db.organization = "organization"
@@ -731,7 +740,7 @@ def test_update(tmpdir):
 
     # database with same table, but extra column
 
-    other1_root = audeer.mkdir(audeer.path(tmpdir, "other1"))
+    other1_root = audeer.mkdir(tmpdir, "other1")
     other1 = audformat.testing.create_db(minimal=True)
     other1.raters["rater"] = audformat.Rater()
     other1.raters["rater2"] = audformat.Rater()
@@ -768,7 +777,7 @@ def test_update(tmpdir):
 
     # database with new table
 
-    other2_root = audeer.mkdir(audeer.path(tmpdir, "other2"))
+    other2_root = audeer.mkdir(tmpdir, "other2")
     other2 = audformat.testing.create_db(minimal=True)
     other2.raters["rater2"] = audformat.Rater()
     other2.attachments["attachment2"] = audformat.Attachment("file2.txt")

tests/test_database_get.py

@@ -12,7 +12,7 @@
 def mono_db(tmpdir):
     r"""Database with ..."""
     name = "mono-db"
-    path = audeer.mkdir(audeer.path(tmpdir, name))
+    path = audeer.mkdir(tmpdir, name)
     db = audformat.Database(name)
 
     # --- Splits
@@ -153,7 +153,7 @@ def stereo_db(tmpdir):
 
     """
     name = "stereo-db"
-    path = audeer.mkdir(audeer.path(tmpdir, name))
+    path = audeer.mkdir(tmpdir, name)
     db = audformat.Database(name)
 
     # --- Schemes
@@ -206,7 +206,7 @@ def overlapping_data_db(tmpdir):
 
     """
     name = "overlapping_data_db"
-    path = audeer.mkdir(audeer.path(tmpdir, name))
+    path = audeer.mkdir(tmpdir, name)
     db = audformat.Database(name)
 
     # --- Schemes
@@ -234,7 +234,7 @@ def overlapping_data_db(tmpdir):
 def scheme_not_assigned_db(tmpdir):
     r"""Database with matching scheme that is not assigned."""
     name = "scheme_not_assigned_db"
-    path = audeer.mkdir(audeer.path(tmpdir, name))
+    path = audeer.mkdir(tmpdir, name)
     db = audformat.Database(name)
 
     # --- Schemes
@@ -262,7 +262,7 @@ def scheme_not_assigned_db(tmpdir):
 def wrong_scheme_labels_db(tmpdir):
     r"""Database with scheme labels that do not match."""
     name = "wrong_scheme_labels_db"
-    path = audeer.mkdir(audeer.path(tmpdir, name))
+    path = audeer.mkdir(tmpdir, name)
     db = audformat.Database(name)
 
     # --- Schemes