Merge pull request #216 from UKRIN-MAPS/rel/v0.7.0

rel/v0.7.0
UKRIN-MAPS · Sep 7, 2023 · 38c00d1 · 38c00d1
2 parents a7126d0 + 2414dab
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -5,7 +5,7 @@
 - Ensure code follows [PEP8](https://www.python.org/dev/peps/pep-0008/).
 - Provide tests.
 - Ideally, provide examples and/or tutorials.
-- Make sure you follow the checklists on the [pull request template](PULL_REQUEST_TEMPLATE.md)
+- Make sure you follow the checklists on the [pull request template](PULL_REQUEST_TEMPLATE/PULL_REQUEST_TEMPLATE.md)
 - Branch off and request merges to the `dev` branch
 
 # Workflow

diff --git a/.github/PULL_REQUEST_TEMPLATE/NEW_RELEASE_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE/NEW_RELEASE_TEMPLATE.md
@@ -0,0 +1,20 @@
+## Release Checklist
+
+### Pull Request
+- [ ] Branch is from `dev` to `rel/v[x.y.z]`
+- [ ] Update the [`CHANGELOG.md`](https://github.com/UKRIN-MAPS/ukat/blob/master/CHANGELOG.md) file with the new version number, release date and add the new features/fixes along with any tags of PRs/issues
+- [ ] Bump the version number in [`setup.py`](https://github.com/UKRIN-MAPS/ukat/blob/master/setup.py)
+- [ ] Add any new contributors and bump the version number in [`CITATION.cff`](https://github.com/UKRIN-MAPS/ukat/blob/master/CITATION.cff)
+- [ ] Do a final check if anything in [readme.MD](rhttps://github.com/UKRIN-MAPS/ukat/blob/master/README.md) needs updating
+- [ ] The pull requests is from `rel/v[x.y.z]` to `master`
+- [ ] All tests pass
+- [ ] Merge `rel/v[x.y.z]` into `master`
+- [ ] Merge `rel/v[x.y.z]` into `dev`
+- [ ] Create a tag on the merge commit on master with the same version number as the release and push to upstream
+
+### Post Pull Request Checks
+- [ ] Close any issues from the milestone that didn't automatically close on merge
+- [ ] Close the milestone itself
+- [ ] Check the new version has appeared in the [releases list](https://github.com/UKRIN-MAPS/ukat/releases)
+- [ ] Check the new version has appeared on [PyPI](https://pypi.org/project/ukat/)
+- [ ] Check a now DOI has been minted on [Zenodo](https://zenodo.org/account/settings/github/repository/UKRIN-MAPS/ukat)
diff --git a/.github/PULL_REQUEST_TEMPLATE.md → ...REQUEST_TEMPLATE/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md → ...REQUEST_TEMPLATE/PULL_REQUEST_TEMPLATE.md
@@ -6,11 +6,14 @@ Describe the big picture of your changes here to communicate to the maintainers
 
 - [ ] I have read and followed the [CONTRIBUTING](.github/CONTRIBUTING.md) document
 - [ ] This pull request is from and to the dev branch
+- [ ] I have added tests that demonstrate the feature/fix works
 - [ ] I have added necessary documentation (if appropriate)
 - [ ] I have updated documentation which becomes obsolete after my changes (if appropriate)
+- [ ] I have added/updated a notebook to demonstrate the changes (if appropriate)
 - [ ] Files added follow the repository structure (if appropriate)
 
 If adding test data?
 - [ ] Data is anonymised
 - [ ] Ensure imaging data is in NIfTI format and was converted using [`d2n`](https://github.com/UKRIN-MAPS/d2n)
-- [ ] Update the [`data/README.md`](data/README.md) file with info about the origin of the data
+- [ ] Update the [`data/README.md`](data/README.md) file in both `ukat/data/` and `ukat/data/contrast` with info about the origin of the data
+- [ ] Added tests for the new functions in `data.fetch.py`
diff --git a/.github/workflows/python_CI.yml b/.github/workflows/python_CI.yml
@@ -10,14 +10,18 @@ on:
   pull_request:
     branches: [ master, dev ]
 
+env:
+  NUMBA_DISABLE_JIT: 1
+
 jobs:
   build:
 
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -40,9 +44,8 @@ jobs:
       run: |
         pytest --cov-report=xml --cov=ukat
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
         env_vars: OS,PYTHON
         fail_ci_if_error: true
         verbose: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,18 @@
+## [0.7.0] - 2023-09-07
+
+### Added
+* T2StimFit - A method of accounting for stimulated echoes when performing T2 mapping #207, #209
+* R-Squared values for curve fitting maps #198 #205
+* New PR template for releases #205 #210
+
+### Changed
+* `ukat` is now tested against Python 3.11
+* Dependencies are now a little less strict for some packages
+
+### Fixed
+* Mapping should now scale better over large images/multiple cores #165 #205
+* Quite a lot of PEP8 formatting issues
+
 ## [0.6.5] - 2023-02-17
 
 ### Added

diff --git a/CITATION.cff b/CITATION.cff
@@ -17,7 +17,7 @@ authors:
   given-names: "Susan T"
   orcid: "https://orcid.org/0000-0003-0903-7507"
 title: "UKRIN Kidney Analysis Toolbox"
-version: 0.6.5
+version: 0.7.0
 doi: 10.5281/zenodo.4742470
-date-released: 2023-02-17
+date-released: 2023-09-07
 url: "https://github.com/UKRIN-MAPS/ukat"
diff --git a/requirements.txt b/requirements.txt
@@ -1,12 +1,14 @@
-dipy~=1.6.0
-matplotlib~=3.7.0
-nibabel~=5.0.1
-notebook~=6.5.1
-numpy~=1.24.1
-pandas~=1.5.1
-renalsegmentor~=1.3.6
-scikit-image~=0.19.1
-scipy~=1.10.0
-scikit-learn~=1.2.1
-tabulate~=0.9.0
-tqdm~=4.64.1
+dipy>=1.6.0
+matplotlib>=3.7.0
+nibabel>=5.0.1
+notebook>=6.5.1
+numba>=0.55.1, <0.58
+numpy>=1.24.1, <1.26
+pandas>=2.0.0
+pathos>=0.3.0
+renalsegmentor>=1.3.5
+scikit-image>=0.20.0, <0.22
+scipy>=1.9.1, <1.12
+scikit-learn~=1.2.1  # Changing versions is known to cause changes in iSNR results
+tabulate>=0.9.0
+tqdm>=4.64.1
diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 
 setup(
     name="ukat",
-    version="0.6.5",
+    version="0.7.0",
     description="UKRIN Kidney Analysis Toolbox",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -32,6 +32,7 @@
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
     ],
 )
diff --git a/tutorials/segmentation.ipynb b/tutorials/segmentation.ipynb
diff --git a/tutorials/t2_calculation.ipynb b/tutorials/t2_calculation.ipynb
diff --git a/ukat/data/README.md b/ukat/data/README.md
@@ -37,6 +37,9 @@ With the exception of datasets marked with :star:, all test data is from the tra
 
 ### T2
 * `t2/philips_1`: not part of travelling kidney pilot study 2019, data acquired on 06 Aug 2020 in Nottingham
+* `t2/philips_2`: 2021 Travelling kidney study Philips subject 6
+* `t2/ge_1`: 2021 Travelling kidney study GE subject 6
+* `t2/siemens_2`: 2021 Travelling kidney study Siemens subject 2
 
 ### MT
 * `mt/philips`: Part of travelling kidney study 2021, data acquired on 05 July 2021 in Nottingham