Merge branch 'master' into 'master'

Master

See merge request !12

.gitlab-ci.yml

 stages:
   - Static Analysis
   - Test
+  - doc
 
 flake8:
   image: python:3.7-slim-buster
@@ -13,7 +14,7 @@ flake8:
   allow_failure: true
 
 pytest:
-  image: continuumio/miniconda3:latest
+  image: wtclarke/fsl_mrs_tests:1.0
   stage: Test
   variables:
     GIT_SUBMODULE_STRATEGY: normal
@@ -26,4 +27,16 @@ pytest:
   - conda install -y -c conda-forge pytest
   - pip install .
   script:
-  - pytest fsl_mrs/tests
\ No newline at end of file
+  - pytest fsl_mrs/tests
+
+pages:
+  image: python:3.7
+  stage: doc
+  script:
+  - pip install -U sphinx sphinx_rtd_theme
+  - sphinx-build -b html ./docs/user_docs public
+  artifacts:
+    paths:
+    - public
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'

docs/user_docs/conf.py

@@ -25,7 +25,7 @@ copyright = f'{date.year}, Will Clarke & Saad Jbabdi, University of Oxford, Oxfo
 author = 'William Clarke'
 
 # The full version, including alpha/beta/rc tags
-version = '1.0.4'
+version = '1.0.5'
 release = version
 
 # From PM's fsleyes doc

fsl_mrs/tests/test_scripts_mrsi_segment.py

@@ -7,7 +7,7 @@ from pathlib import Path
 # Files
 testsPath = Path(__file__).parent
 anat = testsPath / 'testdata/mrsi_segment/T1.anat'
-mrsi = testsPath / 'testdata/fsl_mrsi/FID_metab.nii.gz'
+mrsi = testsPath / 'testdata/fsl_mrsi/FID_Metab.nii.gz'
 
 
 def test_mrsi_segment(tmp_path):

fsl_mrs/tests/test_utils_fitting.py

@@ -95,7 +95,7 @@ def test_fit_FSLModel_MH(data):
     fittedconcs = res.getConc(metab = mrs.names)
     fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
 
-    assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
+    assert np.allclose(fittedconcs,amplitudes,atol=2E-1)
     assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
 
 def test_fit_FSLModel_lorentzian_MH(data):
@@ -116,7 +116,7 @@ def test_fit_FSLModel_lorentzian_MH(data):
     fittedconcs = res.getConc(metab = mrs.names)
     fittedRelconcs = res.getConc(scaling='internal',metab = mrs.names)
 
-    assert np.allclose(fittedconcs,amplitudes,atol=1E-1)
+    assert np.allclose(fittedconcs,amplitudes,atol=2E-1)
     assert np.allclose(fittedRelconcs,amplitudes/(amplitudes[0]+amplitudes[1]),atol=1E-1)
 
 def test_fit_FSLModel_on_invivo_sim():

fsl_mrs/utils/preproc/general.py

@@ -78,8 +78,8 @@ def add_subtract_report(inFID,inFID2,outFID,hdr,ppmlim=(0.2,4.2),function='Not s
         return fig.add_trace(trace)    
     
     fig = addline(fig,plotIn,ppmlim,'FID1',lines['in'])
-    fig = addline(fig,plotIn,ppmlim,'FID2',lines['out'])
-    fig = addline(fig,plotIn,ppmlim,'Result',lines['diff'])    
+    fig = addline(fig,plotIn2,ppmlim,'FID2',lines['out'])
+    fig = addline(fig,plotOut,ppmlim,'Result',lines['diff'])    
 
     # Axes layout
     plotAxesStyle(fig,ppmlim,title = f'{function} summary')