From e0eb5f8fc694c2ca1ed59094cf8d8ebeccc39919 Mon Sep 17 00:00:00 2001
From: Samuel <sstjean1@ualberta.ca>
Date: Tue, 9 Mar 2021 12:37:21 +0100
Subject: [PATCH] maintenance fix for 0.2.5

---
 CHANGELOG.md |  6 ++++++
 Dockerfile   | 15 ---------------
 MANIFEST.in  |  1 -
 README.md    | 14 --------------
 setup.py     |  2 +-
 5 files changed, 7 insertions(+), 31 deletions(-)
 delete mode 100644 Dockerfile

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 24769c0..c8bcb20 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [v0.2.5] - 2021-03-09
+
+- Remove nans from the output when using noise maps.
+- Fix the main script regarding the noise maps to 4d conversion.
+- Remove Dockerfile.
+
 ## [v0.2.4] - 2021-03-09
 
 - Fix an indexing bug for noise maps when going over the full data (the default).
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 49d321e..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM ubuntu:18.04
-
-ENV DEPENDS='numpy==1.16.4 scipy==1.2.2 nibabel==2.2.1 joblib==0.13.2' \
-    autodmri_version='0.2.4'
-
-RUN apt update && \
-    apt install python3-pip python3-setuptools python3-wheel -y --no-install-recommends && \
-    apt autoclean && \
-    # get python deps
-    pip3 install --no-cache-dir $DEPENDS && \
-    # install autodmri itself
-    pip3 install --no-cache-dir autodmri==${autodmri_version}
-
-# default command that will be run
-CMD ["get_distribution","--help"]
diff --git a/MANIFEST.in b/MANIFEST.in
index f515bf8..24423ca 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -4,5 +4,4 @@ include README.md
 include CHANGELOG.md
 include example.ipynb
 include datasets/*
-include Dockerfile
 include example/
diff --git a/README.md b/README.md
index 353a4a7..f461f22 100644
--- a/README.md
+++ b/README.md
@@ -13,19 +13,6 @@ pip install autodmri
 
 You can find a quick example and datasets over [here](example) and the full documentation at http://autodmri.rtfd.io/.
 
-### Using Docker
-
-If you have docker, you do not need to install anything else and can use the Dockerfile to get everything.
-You can then mount your data folder to run the script and get the results into the same folder like this.
-
-~~~
-docker pull samuelstjean/autodmri
-docker run -it -v /home/samuel/git/autodmri/datasets:/mnt samuelstjean/autodmri get_distribution /mnt/data_SENSE3_MB3_dwi.nii.gz /mnt/sigma.nii.gz /mnt/N.nii.gz /mnt/mask.nii.gz
-~~~
-
-Just be sure to adapt the path and filename of your data or add more options as needed.
-
-
 ###  The manuscript and references
 
 You can read the [journal version][media] in Medical Image Analysis and the datasets are available here https://zenodo.org/record/2483105.
@@ -73,7 +60,6 @@ isbn="978-3-030-00928-1"
 }
 ~~~
 
-
 ###  Referencing the code itself
 
 The code is also autoarchived on zenodo for those wanting to refer to a specific version over here
diff --git a/setup.py b/setup.py
index e52ac01..40708f3 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='autodmri',
-    version='0.2.4',
+    version='0.2.5',
     author='Samuel St-Jean',
     author_email='samuel@isi.uu.nl',
     packages=find_packages(),