Merge pull request #182 from BodenmillerGroup/ome-preprocessing-hotfix

OME preprocessing hotfix

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.16.1] - 2023-05-07
+
+### Fixed
+
+  - Broken external preprocessing for files with OME-suffix [#181](https://github.com/BodenmillerGroup/steinbock/issues/181)
+
 ## [0.16.0] - 2023-02-03
 
 ### Added
@@ -365,6 +371,7 @@ Added:
 Initial release for beta testing
 
 
+[0.16.1]: https://github.com/BodenmillerGroup/steinbock/compare/v0.16.0...v0.16.1
 [0.16.0]: https://github.com/BodenmillerGroup/steinbock/compare/v0.15.0...v0.16.0
 [0.15.0]: https://github.com/BodenmillerGroup/steinbock/compare/v0.14.2...v0.15.0
 [0.14.2]: https://github.com/BodenmillerGroup/steinbock/compare/v0.14.1...v0.14.2

docs/install-docker.md

@@ -54,25 +54,25 @@ In principle, the *steinbock* Docker container can be run on any Docker-enabled
 
 For reproducibility, it is recommended to always pull a specific release, e.g.:
 
-    docker run ghcr.io/bodenmillergroup/steinbock:0.16.0
+    docker run ghcr.io/bodenmillergroup/steinbock:0.16.1
 
 To run the *steinbock* Docker container with NVIDIA GPU support (Linux only):
 
-    docker run --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.0-gpu
+    docker run --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.1-gpu
 
 [Bind mounts](https://docs.docker.com/storage/bind-mounts/) can be used to make data from the host system available to the Docker container (see below). Commands that launch a graphical user interface may require further system configuration and additional arguments to `docker run` as outlined in the following.
 
 ### Windows
 
 On the command line, use the following command to run the *steinbock* Docker container:
 
-    docker run -v "C:\Data":/data -p 8888:8888 -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.0
+    docker run -v "C:\Data":/data -p 8888:8888 -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.1
 
-In the command above, adapt the bind mount path to your data/working directory (`C:\Data`; no trailing backslash) and the *steinbock* Docker container version (`0.16.0`) as needed. Specifying the `DISPLAY` environment variable is required only when running graphical user interfaces using X forwarding.
+In the command above, adapt the bind mount path to your data/working directory (`C:\Data`; no trailing backslash) and the *steinbock* Docker container version (`0.16.1`) as needed. Specifying the `DISPLAY` environment variable is required only when running graphical user interfaces using X forwarding.
 
 To simplify the use of the *steinbock* command-line interface, it is recommended to set up a `steinbock` macro:
 
-    doskey steinbock=docker run -p 8888:8888 -v "C:\Data":/data ghcr.io/bodenmillergroup/steinbock:0.16.0 $*
+    doskey steinbock=docker run -p 8888:8888 -v "C:\Data":/data ghcr.io/bodenmillergroup/steinbock:0.16.1 $*
 
 The created macro is retained for the current session and enables running `steinbock` from the current command line without typing the full Docker command, for example:
 
@@ -85,13 +85,13 @@ The created macro is retained for the current session and enables running `stein
 
 On the terminal, use the following command to run the *steinbock* Docker container (Docker must be running):
 
-    docker run -v /path/to/data:/data --platform linux/amd64 -u $(id -u):$(id -g) -p 8888:8888 -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.0
+    docker run -v /path/to/data:/data --platform linux/amd64 -u $(id -u):$(id -g) -p 8888:8888 -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.1
 
-In the command above, adapt the bind mount path to your data/working directory (`/path/to/data`) and the *steinbock* Docker container version (`0.16.0`) as needed. Specifying the `/tmp/.X11-unix` bind mount, the `~/.Xauthority` bind mount and the `DISPLAY` environment variable are required only when running graphical user interfaces using X forwarding.
+In the command above, adapt the bind mount path to your data/working directory (`/path/to/data`) and the *steinbock* Docker container version (`0.16.1`) as needed. Specifying the `/tmp/.X11-unix` bind mount, the `~/.Xauthority` bind mount and the `DISPLAY` environment variable are required only when running graphical user interfaces using X forwarding.
 
 To simplify the use of the *steinbock* command-line interface, it is recommended to set up a `steinbock` command alias:
 
-    alias steinbock="docker run -v /path/to/data:/data --platform linux/amd64 -u $(id -u):$(id -g) -p 8888:8888 -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.0"
+    alias steinbock="docker run -v /path/to/data:/data --platform linux/amd64 -u $(id -u):$(id -g) -p 8888:8888 -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -e DISPLAY=host.docker.internal:0 ghcr.io/bodenmillergroup/steinbock:0.16.1"
 
 The created command alias is retained for the current session and enables running `steinbock` from the current terminal without typing the full Docker command, for example:
 
@@ -106,21 +106,21 @@ The created command alias is retained for the current session and enables runnin
 
 On the terminal, use the following command to run the *steinbock* Docker container:
 
-    docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.16.0
+    docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.16.1
 
 To run the *steinbock* Docker container with NVIDIA GPU support, use `-gpu` Docker image instead:
 
-    docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.0-gpu
+    docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.1-gpu
 
-In the commands above, adapt the bind mount path to your data/working directory (`/path/to/data`) and the *steinbock* Docker container version (`0.16.0`) as needed. Specifying the `host` network mode, the `/tmp/.X11-unix` bind mount and the `DISPLAY` environment variable are required only when running graphical user interfaces using X forwarding.
+In the commands above, adapt the bind mount path to your data/working directory (`/path/to/data`) and the *steinbock* Docker container version (`0.16.1`) as needed. Specifying the `host` network mode, the `/tmp/.X11-unix` bind mount and the `DISPLAY` environment variable are required only when running graphical user interfaces using X forwarding.
 
 To simplify the use of the *steinbock* command-line interface, it is recommended to set up a `steinbock` command alias:
 
-    alias steinbock="docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.16.0"
+    alias steinbock="docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY ghcr.io/bodenmillergroup/steinbock:0.16.1"
 
 To run the *steinbock* Docker container with NVIDIA GPU support, use `-gpu` Docker image instead:
 
-    alias steinbock="docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.0-gpu"
+    alias steinbock="docker run -v /path/to/data:/data -u $(id -u):$(id -g) --network host -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY --gpus all ghcr.io/bodenmillergroup/steinbock:0.16.1-gpu"
 
 The created command alias is retained for the current session and enables running `steinbock` from the current terminal without typing the full Docker command, for example:
 

steinbock/io.py

@@ -23,12 +23,11 @@ class SteinbockIOException(SteinbockException):
 def _as_path_with_suffix(path: Union[str, PathLike], suffix: str) -> Path:
     path = Path(path)
     if re.fullmatch(r".+\.ome\.[^.]+", path.name, flags=re.IGNORECASE):
-        stem, ome_suffix, suffix = path.name.rpartition(".ome.")
-        if ome_suffix:
-            path = path.with_name(f"{stem}.{suffix}")
-        stem, ome_suffix, suffix = path.name.rpartition(".OME.")
-        if ome_suffix:
-            path = path.with_name(f"{stem}.{suffix}")
+        stem, ome_sep, orig_suffix_without_dot = path.name.rpartition(".ome.")
+        if not ome_sep:  # lower case OME separator not found, try upper case
+            stem, ome_sep, orig_suffix_without_dot = path.name.rpartition(".OME.")
+        if ome_sep and orig_suffix_without_dot:  # found OME separator, remove it
+            path = path.with_name(f"{stem}.{orig_suffix_without_dot}")
     return path.with_suffix(suffix)