ci

.github/workflows/docs.yml

@@ -22,38 +22,6 @@ jobs:
           pip install -e .
           pip install -r docs/requirements.txt
 
-      - name: Create the storage
-        if: "! github.event.pull_request.head.repo.fork "
-        env:
-          CACHE_HOST: ${{ secrets.CACHE_HOST }}
-          CACHE_HOST_KEY: ${{ secrets.CACHE_HOST_KEY }}
-          CACHE_HOST_USER: ${{ secrets.CACHE_HOST_USER }}
-        run: |
-          mkdir -p ~/.config/amid ~/.ssh
-          cat >~/.config/amid/.bev.yml <<EOL
-          local:
-            storage: '/home/runner/work/amid/amid/storage'
-            cache: '/home/runner/work/amid/amid/cache'
-          
-          remote:
-            storage:
-              remote: 
-                sftp: 'amid:bucket'
-          
-          meta:
-            fallback: local
-          EOL
-          amid init
-          cat >~/.ssh/config <<EOL
-          Host amid
-            HostName $CACHE_HOST
-            User $CACHE_HOST_USER
-            IdentityFile ~/.ssh/amid
-          EOL
-          echo "$CACHE_HOST_KEY" > ~/.ssh/amid
-          chmod 700 ~/.ssh
-          chmod 600 ~/.ssh/amid
-
       # release
       - id: get_version
         if: github.event_name == 'release'
@@ -63,16 +31,13 @@ jobs:
       - name: Deploy the docs
         if: github.event_name == 'release'
         run: |
-          cd docs
-          VERSION=${{ steps.get_version.outputs.version-without-v }} python fill_docs.py
-          cd ..
           PYTHONPATH=$PYTHONPATH:./docs mike deploy ${{ steps.get_version.outputs.version-without-v }} latest --push --update-aliases
 
       # dev
-      - name: Deploy the docs
-        if: ${{ github.ref == 'refs/heads/dev' }}
-        run: |
-          cd docs
-          VERSION=dev python fill_docs.py
-          cd ..
-          PYTHONPATH=$PYTHONPATH:./docs mike deploy dev --push
+#      - name: Deploy the docs
+#        if: ${{ github.ref == 'refs/heads/dev' }}
+#        run: |
+#          cd docs
+#          VERSION=dev python fill_docs.py
+#          cd ..
+#          PYTHONPATH=$PYTHONPATH:./docs mike deploy dev --push

.github/workflows/release.yml

@@ -13,10 +13,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.9
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - id: get_version
         name: Get the release version

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
 
     steps:
       - uses: actions/checkout@v3
@@ -42,47 +42,6 @@ jobs:
           echo $MODULE_PARENT
           echo "MODULE_PARENT=$(echo $MODULE_PARENT)" >> $GITHUB_ENV
 
-      - name: Create the storage
-        if: "! github.event.pull_request.head.repo.fork "
-        env:
-          CACHE_HOST: ${{ secrets.CACHE_HOST }}
-          CACHE_HOST_KEY: ${{ secrets.CACHE_HOST_KEY }}
-          CACHE_HOST_USER: ${{ secrets.CACHE_HOST_USER }}
-        run: |
-          mkdir -p ~/.config/amid ~/.ssh
-          cat >~/.config/amid/.bev.yml <<EOL
-          local:
-            storage: '/home/runner/work/amid/amid/storage'
-            cache: '/home/runner/work/amid/amid/cache'
-          
-          remote:
-            storage:
-              remote: 
-                sftp: 'amid:bucket'
-          
-          meta:
-            fallback: local
-          EOL
-          amid init
-          cat >~/.ssh/config <<EOL
-          Host amid
-            HostName $CACHE_HOST
-            User $CACHE_HOST_USER
-            IdentityFile ~/.ssh/amid
-          EOL
-          echo "$CACHE_HOST_KEY" > ~/.ssh/amid
-          chmod 700 ~/.ssh
-          chmod 600 ~/.ssh/amid
-
-      - name: Check readme generation
-        if: "! github.event.pull_request.head.repo.fork "
-        run: |
-          pip install -r docs/requirements.txt
-          BEFORE=$(sha256sum README.md)
-          python docs/fill_readme.py
-          AFTER=$(sha256sum README.md)
-          if [ "$BEFORE" != "$AFTER" ]; then echo "The README changed after table generation. Please run 'python docs/fill_readme.py'" && exit 1; fi
-
       - name: Test with pytest
         if: "! github.event.pull_request.head.repo.fork "
         run: |

docs/datasets-api.md

@@ -0,0 +1,68 @@
+# Datasets API
+
+::: amid.amos.dataset.AMOS
+
+::: amid.bimcv.BIMCVCovid19
+
+::: amid.brats2021.BraTS2021
+
+::: amid.cc359.dataset.CC359
+
+::: amid.cl_detection.CLDetection2023
+
+::: amid.crlm.CRLM
+
+::: amid.ct_ich.CT_ICH
+
+::: amid.crossmoda.CrossMoDA
+
+::: amid.deeplesion.DeepLesion
+
+::: amid.egd.EGD
+
+::: amid.flare2022.FLARE2022
+
+::: amid.hcp.HCP
+
+::: amid.kits.KiTS23
+
+::: amid.lidc.dataset.LIDC
+
+::: amid.lits.dataset.LiTS
+
+::: amid.liver_medseg.LiverMedseg
+
+::: amid.midrc.MIDRC
+
+::: amid.mood.MOOD
+
+::: amid.msd.MSD
+
+::: amid.mslub.dataset.MSLUB
+
+::: amid.medseg9.Medseg9
+
+::: amid.cancer_500.dataset.MoscowCancer500
+
+::: amid.covid_1110.MoscowCovid1110
+
+::: amid.nlst.NLST
+
+::: amid.nsclc.NSCLC
+
+::: amid.rsna_bc.dataset.RSNABreastCancer
+
+::: amid.ribfrac.dataset.RibFrac
+
+::: amid.stanford_coca.StanfordCoCa
+
+::: amid.tbad.TBAD
+
+::: amid.totalsegmentator.dataset.Totalsegmentator
+
+::: amid.upenn_gbm.upenn_gbm.UPENN_GBM
+
+::: amid.vs_seg.dataset.VSSEG
+
+::: amid.verse.VerSe
+