Prepare new version release

CONTRIBUTING.md

@@ -46,7 +46,8 @@ To create a release you need write permission on the repository.
 
 1. Check the author list in [`CITATION.cff`](https://github.com/haddocking/powerfit/blob/master/CITATION.cff)
 1. Bump the version in [src/powerfit_em/__init__.py](https://github.com/haddocking/powerfit/blob/master/src/powerfit_em/__init__.py)
-1. In [README.md](README.md) adjust docker command to use new version
+1. In [installation.md](docs/installation.md) adjust docker command to use new version.
+1. Merge the changes into the main branch.
 1. Go to the [GitHub release page](https://github.com/haddocking/powerfit/releases)
 1. Press draft a new release button
 1. Fill tag, title and description field. For tag use version from pyproject.toml and prepend with "v" character. For description use "Rigid body fitting of high-resolution structures in low-resolution cryo-electron microscopy density maps." line plus press "Generate release notes" button.

docs/installation.md

@@ -61,7 +61,7 @@ a hypothetical `/path/to/data` on your machine can be done as follows
 
 ```shell
 docker run --rm -ti --user $(id -u):$(id -g) \
-    -v /path/to/data:/data ghcr.io/haddocking/powerfit:v3.1.0 \
+    -v /path/to/data:/data ghcr.io/haddocking/powerfit:v4.0.4 \
     /data/<map> <resolution> /data/<pdb> \
     -d /data/<results-dir>
 ```
@@ -71,7 +71,7 @@ To run tutorial example use
 ```shell
 # cd into powerfit-tutorial repo
 docker run --rm -ti --user $(id -u):$(id -g) \
-    -v $PWD:/data ghcr.io/haddocking/powerfit:v3.1.0 \
+    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
     /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
     -a 20 -p 2 -l -d /data/run-KsgA-docker
 ```
@@ -80,7 +80,7 @@ To run on NVIDIA GPU using [NVIDIA container toolkit](https://docs.nvidia.com/da
 ```shell
 docker run --rm -ti \
     --runtime=nvidia --gpus all -v /etc/OpenCL:/etc/OpenCL \
-    -v $PWD:/data ghcr.io/haddocking/powerfit:v3.1.0 \
+    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
     /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
     -a 20 -l -d /data/run-KsgA-docker-nv --gpu
 ```
@@ -90,7 +90,7 @@ To run on Intel integrated graphics use
 ```shell
 docker run --rm -ti \
     --device=/dev/dri \
-    -v $PWD:/data ghcr.io/haddocking/powerfit:v3.1.0 \
+    -v $PWD:/data ghcr.io/haddocking/powerfit:v4.0.4 \
     /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
     -a 20 -l -d /data/run-KsgA-docker-nv --gpu
 ```
@@ -102,7 +102,7 @@ sudo docker run --rm -ti \
     --device=/dev/kfd --device=/dev/dri \
     --security-opt seccomp=unconfined \
     --group-add video --ipc=host \
-    -v $PWD:/data ghcr.io/haddocking/powerfit-rocm:v3.1.0 \
+    -v $PWD:/data ghcr.io/haddocking/powerfit-rocm:v4.0.4 \
     /data/ribosome-KsgA.map 13 /data/KsgA.pdb \
     -a 20 -l -d /data/run-KsgA-docker-amd --gpu
 ```

src/powerfit_em/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "4.0.3"
+__version__ = "4.0.4"
 
 from .helpers import determine_core_indices
 from .rotations import proportional_orientations, quat_to_rotmat