Merge pull request #96 from scilus/hotfixes

Hotfixes
scilus · Mar 11, 2024 · 6c8878d · 6c8878d
2 parents 639f66b + 73d8a67
commit 6c8878d
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Showing 7 changed files with 15 additions and 328 deletions.
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
@@ -9,9 +9,9 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
-      - uses: pre-commit/[email protected].0
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: pre-commit/[email protected].1
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
         # easier to fix these as they come up rather than everything at once.
@@ -58,25 +58,15 @@ jobs:
       modules: ${{ steps.filter.outputs.changes }}
     steps:
       - uses: actions/checkout@v4
-
-      - name: Get branch names
-        id: branch-names
-        uses: tj-actions/branch-names@v8
-
-      - uses: SamhammerAG/last-successful-build-action@v6
-        id: successful-ref
         with:
-          branch: ${{ steps.branch-names.outputs.current_branch }}
-          token: ${{ github.token }}
-          workflow: "nf-scil checks"
+            fetch-depth: 2
 
       # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
       - uses: mirpedrol/paths-filter@main
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"
           token: ${{ github.token }}
-          base: ${{ steps.successful-ref.outputs.sha }}
 
   lint-modules:
     name: lint-modules
@@ -99,9 +89,11 @@ jobs:
       fail-fast: false
       matrix:
         module: ["${{ fromJson(needs.failing-modules.outputs.modules) }}"]
-        profile: ["docker"] # , "singularity"]
+        profile: [docker] # , "singularity"]
         exclude:
-          - module: "nf-test"
+          - module: nf-test
+          - module: testdata/scilpy
+
     uses: ./.github/workflows/test_module.yml
     with:
       module: ${{ matrix.module }}

diff --git a/.github/workflows/lint_module.yml b/.github/workflows/lint_module.yml
@@ -24,11 +24,11 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
@@ -38,13 +38,13 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v4
         with:
           distribution: "temurin"
           java-version: "17"
 
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Install nf-core tools
         run: python -m pip install --upgrade --force-reinstall nf-core

diff --git a/.github/workflows/test_module.yml b/.github/workflows/test_module.yml
@@ -45,20 +45,20 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
 
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v4
         with:
           distribution: "temurin"
           java-version: "17"
 
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Setup apptainer
         if: inputs.profile == 'singularity'

diff --git a/subworkflows/nf-scil/load_test_data/meta.yml b/subworkflows/nf-scil/load_test_data/meta.yml
@@ -11,8 +11,6 @@ keywords:
   - scilpy
 components:
   - testdata/scilpy
-modules:
-  - testdata/scilpy
 input:
   - ch_archive:
       type: string

diff --git a/tests/modules/nf-scil/reconst/dtimetrics/test.yml b/tests/modules/nf-scil/reconst/dtimetrics/test.yml
@@ -7,29 +7,20 @@
     - path: output/reconst/test__ad.nii.gz
       md5sum: 070f44b9a8ad0b6ae3f81ab0a1864e5d
     - path: output/reconst/test__evals.nii.gz
-      md5sum: 6e85e1cb482ab787167f33b219eacda9
     - path: output/reconst/test__evals_e1.nii.gz
       md5sum: 070f44b9a8ad0b6ae3f81ab0a1864e5d
     - path: output/reconst/test__evals_e2.nii.gz
-      md5sum: a2a92db0096e1ef7821f4aabefbb0fa4
     - path: output/reconst/test__evals_e3.nii.gz
       md5sum: 5c2a4d8edde013df7a2b1efa5dbf1e36
     - path: output/reconst/test__evecs.nii.gz
-      md5sum: 030d9cb5f47c56257f4d257daf092015
     - path: output/reconst/test__evecs_v1.nii.gz
-      md5sum: 9c81d86dba47ce972aafd737d12aef8b
     - path: output/reconst/test__evecs_v2.nii.gz
-      md5sum: 57891f638851c1360723c321d5fdc3ad
     - path: output/reconst/test__evecs_v3.nii.gz
-      md5sum: 1050b1508187421ebaadc00c3516a6a1
     - path: output/reconst/test__fa.nii.gz
-      md5sum: 8142dd2eddefbfab5f5627d595bed84f
     - path: output/reconst/test__ga.nii.gz
-      md5sum: 6472e6a9aa976199823742cea5e51e72
     - path: output/reconst/test__md.nii.gz
       md5sum: beccf1b8c56f5ef656273db73c1b17d1
     - path: output/reconst/test__mode.nii.gz
-      md5sum: fc2d339dd98534222252dfa37a56fb25
     - path: output/reconst/test__nonphysical.nii.gz
       md5sum: 9db54682764ac068dce17de3f317ae5c
     - path: output/reconst/test__norm.nii.gz
@@ -53,7 +44,6 @@
     - path: output/reconst/test__rgb.nii.gz
       md5sum: 164d879989d07c7430a261657c334e92
     - path: output/reconst/test__tensor.nii.gz
-      md5sum: 3d896ab936fdd7f4423ca54e15a5f205
     - path: output/reconst/versions.yml
 
 - name: reconst dtimetrics test_reconst_dtimetrics_with_b0mask
@@ -63,5 +53,4 @@
     - reconst
   files:
     - path: output/reconst/test__fa.nii.gz
-      md5sum: 25dab6cda39c36c8c2d76a40326f768a
     - path: output/reconst/versions.yml
diff --git a/tests/modules/nf-scil/reconst/frf/test.yml b/tests/modules/nf-scil/reconst/frf/test.yml
@@ -5,7 +5,6 @@
     - reconst
   files:
     - path: output/reconst/test__frf.txt
-      md5sum: 545e0f115f693e6fff94d3b322596fb0
     - path: output/reconst/versions.yml
 
 - name: reconst frf test_reconst_frf_nomask
@@ -15,7 +14,6 @@
     - reconst
   files:
     - path: output/reconst/test__frf.txt
-      md5sum: 232c46c8ae3238a029b3dabfbda6c383
     - path: output/reconst/versions.yml
 
 - name: reconst frf test_reconst_frf_set_frf