From cf4391049b2fe264e8eb96dff07b44fce3b8e8d4 Mon Sep 17 00:00:00 2001
From: Chaithya G R <chaithyagr@gmail.com>
Date: Thu, 22 Apr 2021 18:57:50 +0200
Subject: [PATCH] Preparing for a release v0.3 (#120)

* Version Bump

* Make pynfft as optional install

* Update the circleci testbench

* Fix Readme

* Update the readme

* Release v0.3 change

* Loosen the install for scikit-image

* Update readme to conda

* Slacken the test_scripts

* Circleci pull latest modopt

* Circleci pull latest modopt

Co-authored-by: chaithyagr <chaithyagr@gitlab.com>
---
 .circleci/config.yml      |  3 ++-
 .travis.yml               |  1 +
 README.rst                | 33 +++++++++++++++++++++++++++------
 mri/info.py               |  4 ++--
 mri/tests/test_scripts.py |  3 ++-
 setup.py                  |  7 +++----
 6 files changed, 37 insertions(+), 14 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 814e1908..5e1b6b1a 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -31,7 +31,7 @@ jobs:
             . venv/bin/activate
             pip install --upgrade pip
             pip install --upgrade git+https://github.com/cea-cosmic/pysap
-            pip install -r doc/requirements.txt
+            pip install --upgrade -r doc/requirements.txt
             pip list > doc/state.txt
       - save_cache:
           paths:
@@ -44,6 +44,7 @@ jobs:
             pip install --upgrade pip
             pip install Cython
             pip install -e .
+            pip install pynfft2
             TESTFILES=$(circleci tests glob examples/*.py | circleci tests split --split-by=timings)
             echo ${TESTFILES}
             python3 -m unittest ${TESTFILES}
diff --git a/.travis.yml b/.travis.yml
index f8dbb780..de8ee693 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -41,6 +41,7 @@ install:
     - pip install git+https://github.com/CEA-COSMIC/pysap.git
     - export PYTHONPATH=$TRAVIS_BUILD_DIR/install:$PYTHONPATH
     - pip install -b $TRAVIS_BUILD_DIR/build -t $TRAVIS_BUILD_DIR/install --no-clean --upgrade .
+    - pip install pynfft2
 
 script:
     - python setup.py test
diff --git a/README.rst b/README.rst
index 2d5f0922..bf9d23ef 100644
--- a/README.rst
+++ b/README.rst
@@ -18,21 +18,42 @@ pySAP-mri
 Python Sparse data Analysis Package external MRI plugin.
 
 This work is made available by a community of people, amoung which the
-CEA Neurospin UNATI and CEA CosmoStat laboratories, in particular A. Grigis,
-J.-L. Starck, P. Ciuciu, and S. Farrens.
+CEA Neurospin UNATI and CEA CosmoStat laboratories. This plugin was developed by
+A. Grigis, J.-L. Starck, P. Ciuciu, and S. Farrens. Currently, it is being handled by
+Chaithya G R, Z. Ramzi and S. Farrens.
 
 Installation instructions
 =========================
 
-Install python-pySAP using `pip install python-pySAP`. Later install pysap-mri by calling setup.py
-Note: If you want to use undecimated wavelet transform, please point the `$PATH` environment variable to
-pysap external binary directory:
+Install python-pySAP using:
 
-`export PATH=$PATH:/path-to-pysap/build/temp.linux-x86_64-<PYTHON_VERSION>/extern/bin/`
+``pip install python-pysap``
+
+This will install pysap-mri plugin too. However if you want to update to a more
+later version, please use:
+
+``pip install --upgrade pysap-mri``
 
 Special Installations
 =====================
 
+`pyNFFT <https://github.com/pyNFFT/pyNFFT/>`_
+--------------------------------------------
+
+For using Non-Cartesian FFT, please install pyNFFT by:
+
+Linux:
+``````
+
+``sudo apt install libnfft3-dev``
+
+``pip install pynfft2``
+
+Mac:
+````
+
+``conda install -c conda-forge pynfft``
+
 `gpuNUFFT <https://www.opensourceimaging.org/project/gpunufft/>`_
 ---------------------------------------------------------------
 
diff --git a/mri/info.py b/mri/info.py
index 19bd76fc..0a6b157b 100644
--- a/mri/info.py
+++ b/mri/info.py
@@ -9,8 +9,8 @@
 
 # Module current version
 version_major = 0
-version_minor = 2
-version_micro = 2
+version_minor = 3
+version_micro = 0
 
 # Expected by setup.py: string of form "X.Y.Z"
 __version__ = "{0}.{1}.{2}".format(version_major, version_minor, version_micro)
diff --git a/mri/tests/test_scripts.py b/mri/tests/test_scripts.py
index eae9e26b..43073a29 100644
--- a/mri/tests/test_scripts.py
+++ b/mri/tests/test_scripts.py
@@ -92,7 +92,8 @@ def test_gridsearch_single_channel(self):
         np.testing.assert_equal(best_idx, 0)
         np.testing.assert_allclose(
             raw_results[best_idx][0],
-            image
+            image,
+            atol=1e-7,
         )
 
 
diff --git a/setup.py b/setup.py
index 24feea45..f9d95761 100644
--- a/setup.py
+++ b/setup.py
@@ -42,17 +42,16 @@
     classifiers="CLASSIFIERS",
     author=AUTHOR,
     author_email="XXX",
-    version="0.2.2",
+    version="0.3.0",
     url="https://github.com/CEA-COSMIC/pysap-mri",
     packages=find_packages(),
     setup_requires=setup_requires,
     install_requires=[
         "scikit-learn>=0.19.1",
         "progressbar2>=3.34.3",
-        "joblib",
+        "joblib>=1.0.0",
         "scipy>=1.3.0",
-        "pynfft2>=1.3.3",
-        "scikit-image",
+        "scikit-image>=0.17.0",
     ],
     tests_require=['pytest>=5.0.1', 'pytest-cov>=2.7.1', 'pytest-pep8', 'pytest-runner'],
     platforms="OS Independent"