next release v1.1.0 beta

.github/workflows/comment-bot.yml

@@ -29,6 +29,7 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "eyes"})
+        github-token: ${{ secrets.GH_TOKEN }}
     - name: Tag Commit
       run: |
         git clone https://${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY} repo
@@ -48,3 +49,4 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})
+        github-token: ${{ secrets.GH_TOKEN }}

.github/workflows/test.yml

@@ -57,8 +57,6 @@ jobs:
     - if: startsWith(matrix.python, '2')
       run: pytest
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   matlab:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: [self-hosted, python, matlab]
@@ -72,8 +70,6 @@ jobs:
     - run: pip install -U .[dev]
     - run: pytest --durations-min=1
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     - name: Post Run setup-python
       run: setup-python -p3.7 -Dr
       if: ${{ always() }}
@@ -89,37 +85,23 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
-        build: true
+        pip: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
-        upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
-    - name: Changelog
-      run: git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      id: create_release
-      uses: actions/create-release@v1
+        upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
+    - id: meta
+      name: Changelog
+      run: |
+        echo ::set-output name=tag::${GITHUB_REF#refs/tags/}
+        git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
+    - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: softprops/action-gh-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
-        tag_name: ${{ github.ref }}
-        release_name: spm12 ${{ github.ref }} beta
+        name: spm12 ${{ steps.meta.outputs.tag }} beta
         body_path: _CHANGES.md
         draft: true
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ steps.dist.outputs.whl }}
-        asset_name: ${{ steps.dist.outputs.whl }}
-        asset_content_type: application/zip
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: actions/upload-release-asset@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ steps.dist.outputs.whl_asc }}
-        asset_name: ${{ steps.dist.outputs.whl_asc }}
-        asset_content_type: text/plain
+        files: |
+          dist/${{ steps.dist.outputs.whl }}
+          dist/${{ steps.dist.outputs.whl_asc }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -26,19 +26,20 @@ repos:
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
     args: [-i]
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
+  rev: 3.9.2
   hooks:
   - id: flake8
+    args: [-j8]
     additional_dependencies:
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
     - flake8-string-format
 - repo: https://github.com/psf/black
-  rev: 19.10b0
+  rev: 21.7b0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.7.0
+  rev: 5.9.3
   hooks:
   - id: isort

setup.cfg

@@ -63,6 +63,8 @@ demo=
 [options.entry_points]
 console_scripts =
     spm12=spm12.cli:main
+[options.packages.find]
+exclude=tests
 [options.package_data]
 *=*.md, *.rst, *.m
 

spm12/coreg_spm_m.m → spm12/amypad_coreg.m

@@ -1,4 +1,4 @@
-function [M, x] = coreg_spm_m(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
+function [M, x] = amypad_coreg(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
     if visual>0
         Fgraph = spm_figure('GetWin','Graphics');
         Finter = spm_figure('GetWin','Interactive');

spm12/amypad_coreg_modify_affine.m

@@ -0,0 +1,7 @@
+function out = amypad_coreg_modify_affine(imflo, M)
+    VF = strcat(imflo,',1');
+    MM = zeros(4,4);
+    MM(:,:) = spm_get_space(VF);
+    spm_get_space(VF, M\MM(:,:));
+    out = 0;
+end

spm12/amypad_normw.m

@@ -0,0 +1,10 @@
+function out = amypad_normw(def_file, flist4norm)
+    job.subj.def = {def_file};
+    job.subj.resample = flist4norm;
+    job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
+    job.woptions.vox = [2, 2, 2];
+    job.woptions.interp = 4;
+    job.woptions.prefix = 'w';
+    spm_run_norm(job);
+    out=0;
+end

spm12/resample_spm_m.m → spm12/amypad_resample.m

@@ -1,4 +1,4 @@
-function out = resample_spm_m(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
+function out = amypad_resample(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
     %-Reslicing parameters
     rflags.mask = f_mask;
     rflags.mean = f_mean;

spm12/amypad_seg.m

@@ -0,0 +1,46 @@
+function [param,invdef,fordef] = amypad_seg(f_mri, spm_path, nat_gm, nat_wm, nat_csf, store_fwd, store_inv, visual)
+    job.channel.vols = {strcat(f_mri,',1')};
+    job.channel.biasreg = 0.001;
+    job.channel.biasfwhm = 60;
+    job.channel.write = [0, 0];
+    job.tissue(1).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,1']};
+    job.tissue(1).ngaus = 1;
+    job.tissue(1).native = [nat_gm, 0];
+    job.tissue(1).warped = [0, 0];
+    job.tissue(2).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,2']};
+    job.tissue(2).ngaus = 1;
+    job.tissue(2).native = [nat_wm, 0];
+    job.tissue(2).warped = [0, 0];
+    job.tissue(3).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,3']};
+    job.tissue(3).ngaus = 2;
+    job.tissue(3).native = [nat_csf, 0];
+    job.tissue(3).warped = [0, 0];
+    job.tissue(4).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,4']};
+    job.tissue(4).ngaus = 3;
+    job.tissue(4).native = [0, 0];
+    job.tissue(4).warped = [0, 0];
+    job.tissue(5).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,5']};
+    job.tissue(5).ngaus = 4;
+    job.tissue(5).native = [0, 0];
+    job.tissue(5).warped = [0, 0];
+    job.tissue(6).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,6']};
+    job.tissue(6).ngaus = 2;
+    job.tissue(6).native = [0, 0];
+    job.tissue(6).warped = [0, 0];
+    job.warp.mrf = 1;
+    job.warp.cleanup = 1;
+    job.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
+    job.warp.affreg = 'mni';
+    job.warp.fwhm = 0;
+    job.warp.samp = 3;
+    job.warp.write = [store_fwd, store_inv];
+    if visual>0
+        Finter = spm_figure('GetWin','Interactive');
+    end
+    spm_jobman('initcfg');
+    segout = spm_preproc_run(job);
+    param  = segout.param{1};
+    invdef = segout.invdef{1};
+    fordef = segout.fordef{1};
+    %disp(segout);
+end