dclab 0.62.14__tar.gz → 0.62.16__tar.gz

{dclab-0.62.14 → dclab-0.62.16}/CHANGELOG

@@ -1,3 +1,12 @@
+0.62.16
+ - enh: allow editing S3 credentials via environment variables at runtime
+ - docs: fix typo in S3 section (missing `DCLAB_S3_SECRET_ACCESS_KEY`)
+ - docs: add more example use cases in the basin section
+ - docs: add example script for rewriting paths of basins
+ - docs: remove broken reference to HDF5 `linker` module
+ - tests: reduce test time by 35% from 400s to 250 (smaller S3 reference data)
+0.62.15
+ - fix: support opening files on non-mounted network shares on Windows
 0.62.14
  - fix: exporting table data broken
  - ref: introduce base class for tables `TableMeta`

{dclab-0.62.14 → dclab-0.62.16}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: dclab
-Version: 0.62.14
+Version: 0.62.16
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -36,6 +36,7 @@ Requires-Dist: boto3>=1.34.31; extra == "s3"
 Provides-Extra: tdms
 Requires-Dist: imageio[ffmpeg]; extra == "tdms"
 Requires-Dist: nptdms<1.9,>=0.23.0; extra == "tdms"
+Dynamic: license-file
 
 |dclab|
 =======

{dclab-0.62.14 → dclab-0.62.16}/dclab/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.14'
-__version_tuple__ = version_tuple = (0, 62, 14)
+__version__ = version = '0.62.16'
+__version_tuple__ = version_tuple = (0, 62, 16)

{dclab-0.62.14 → dclab-0.62.16}/dclab/rtdc_dataset/fmt_s3.py

@@ -168,13 +168,19 @@ class RTDC_S3(RTDC_HDF5):
             object_path=get_object_path(url),
             endpoint_url=(endpoint_url
                           or get_endpoint_url(url)
-                          or S3_ENDPOINT_URL),
+                          or S3_ENDPOINT_URL
+                          or os.environ.get("DCLAB_S3_ENDPOINT_URL")
+                          ),
             access_key_id=(access_key_id
                            or S3_ACCESS_KEY_ID
-                           or ""),
+                           or os.environ.get("DCLAB_S3_ACCESS_KEY_ID")
+                           or ""
+                           ),
             secret_access_key=(secret_access_key
                                or S3_SECRET_ACCESS_KEY
-                               or ""),
+                               or os.environ.get("DCLAB_S3_SECRET_ACCESS_KEY")
+                               or ""
+                               ),
             use_ssl=use_ssl,
             verify_ssl=use_ssl,
             )
@@ -236,7 +242,10 @@ def is_s3_object_available(url: str,
     """
     avail = False
     if is_s3_url(url):
-        endpoint_url = get_endpoint_url(url) or S3_ENDPOINT_URL
+        endpoint_url = (get_endpoint_url(url)
+                        or S3_ENDPOINT_URL
+                        or os.environ.get("DCLAB_S3_ENDPOINT_URL")
+                        )
         if not endpoint_url:
             warnings.warn(
                 f"Could not determine endpoint from URL '{url}'. Please "
@@ -260,12 +269,18 @@ def is_s3_object_available(url: str,
                     s3file = S3File(
                         object_path=get_object_path(url),
                         endpoint_url=endpoint_url,
-                        access_key_id=(access_key_id
-                                       or S3_ACCESS_KEY_ID
-                                       or ""),
-                        secret_access_key=(secret_access_key
-                                           or S3_SECRET_ACCESS_KEY
-                                           or ""),
+                        access_key_id=(
+                            access_key_id
+                            or S3_ACCESS_KEY_ID
+                            or os.environ.get("DCLAB_S3_ACCESS_KEY_ID")
+                            or ""
+                            ),
+                        secret_access_key=(
+                            secret_access_key
+                            or S3_SECRET_ACCESS_KEY
+                            or os.environ.get("DCLAB_S3_SECRET_ACCESS_KEY")
+                            or ""
+                            ),
                         )
                     try:
                         s3file.s3_object.load()

{dclab-0.62.14 → dclab-0.62.16}/dclab/rtdc_dataset/load.py

@@ -61,6 +61,11 @@ def new_dataset(data, identifier=None, **kwargs):
         return fmt_hierarchy.RTDC_Hierarchy(data, identifier=identifier,
                                             **kwargs)
     elif isinstance(data, (pathlib.Path, str)):
+        # If we are given a `file:` specifier, remove it. We might be
+        # looking at a network share (not mounted as a drive) on Windows
+        # (e.g. "file:\\127.0.0.1\shared\data.rtdc").
+        if isinstance(data, str) and data.startswith("file:"):
+            data = data[5:]
         path = pathlib.Path(data).resolve()
         if not path.exists():
             raise FileNotFoundError(

{dclab-0.62.14 → dclab-0.62.16}/dclab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: dclab
-Version: 0.62.14
+Version: 0.62.16
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -36,6 +36,7 @@ Requires-Dist: boto3>=1.34.31; extra == "s3"
 Provides-Extra: tdms
 Requires-Dist: imageio[ffmpeg]; extra == "tdms"
 Requires-Dist: nptdms<1.9,>=0.23.0; extra == "tdms"
+Dynamic: license-file
 
 |dclab|
 =======

{dclab-0.62.14 → dclab-0.62.16}/dclab.egg-info/SOURCES.txt

@@ -182,6 +182,7 @@ docs/logo/dclab_large_white.png
 docs/logo/dclab_large_white.svg
 docs/logo/favicon.ico
 docs/logo/favicon.svg
+docs/sec_av_basins/basin_example_workflows.svg
 docs/sec_av_basins/index.rst
 docs/sec_av_emodulus/index.rst
 docs/sec_av_emodulus/figures_emodulus/.gitignore