change docs-mk to docs

OSIPI · Aug 5, 2024 · 383310d · 383310d
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diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -34,15 +34,15 @@ jobs:
       - name: Build MkDocs documentation
         run: |
           poetry run mkdocs build
-        working-directory: docs-mk
+        working-directory: docs
 
       - name: Publish to gh-pages
         uses: peaceiris/actions-gh-pages@v3
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
         with:
           publish_branch: gh-pages  # default: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: docs-mk/site
+          publish_dir: docs/site
           force_orphan: true
 
       - run: echo "Status of job = ${{ job.status }}."
diff --git a/.gitignore b/.gitignore
@@ -9,5 +9,5 @@ junit
 docs/build
 docs/source/generated
 docs/source/sg_execution_times.rst
-docs-mk/site
-docs-mk/docs/generated
+docs/site
+docs/docs/generated
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs-mk/docs/about/index.md → docs/docs/about/index.md b/docs-mk/docs/about/index.md → docs/docs/about/index.md
@@ -1,6 +1,6 @@
 # About
 
-osipi is developed by the **Open Source Initiative for Perfusion Imaging (OSIPI)**, an initiative of the perfusion study group of the **International Society for Magnetic Resonance in Medicine (ISMRM)**.
+The osipi Library is developed by the **Open Source Initiative for Perfusion Imaging (OSIPI)**, an initiative of the perfusion study group of the **International Society for Magnetic Resonance in Medicine (ISMRM)**.
 
 The osipi package structure and logic follow the lexicon defined by OSIPI, and wrap around selected implementations collected in the code contributions of OSIPI.
 

diff --git a/docs-mk/docs/contribution/index.md → docs/docs/contribution/index.md b/docs-mk/docs/contribution/index.md → docs/docs/contribution/index.md
diff --git a/docs-mk/docs/examples/README.md → docs/docs/examples/README.md b/docs-mk/docs/examples/README.md → docs/docs/examples/README.md
diff --git a/docs-mk/docs/examples/aif/README.md → docs/docs/examples/aif/README.md b/docs-mk/docs/examples/aif/README.md → docs/docs/examples/aif/README.md
diff --git a/docs-mk/docs/examples/aif/plot_aif_parker.py → docs/docs/examples/aif/plot_aif_parker.py b/docs-mk/docs/examples/aif/plot_aif_parker.py → docs/docs/examples/aif/plot_aif_parker.py
diff --git a/docs-mk/docs/examples/aif/plot_dummy.py → docs/docs/examples/aif/plot_dummy.py b/docs-mk/docs/examples/aif/plot_dummy.py → docs/docs/examples/aif/plot_dummy.py
diff --git a/docs-mk/docs/examples/tissue/README.md → docs/docs/examples/tissue/README.md b/docs-mk/docs/examples/tissue/README.md → docs/docs/examples/tissue/README.md
diff --git a/...cs/examples/tissue/plot_extended_tofts.py → ...cs/examples/tissue/plot_extended_tofts.py b/...cs/examples/tissue/plot_extended_tofts.py → ...cs/examples/tissue/plot_extended_tofts.py
diff --git a/docs-mk/docs/examples/tissue/plot_tofts.py → docs/docs/examples/tissue/plot_tofts.py b/docs-mk/docs/examples/tissue/plot_tofts.py → docs/docs/examples/tissue/plot_tofts.py
diff --git a/docs-mk/docs/img/osipi.png → docs/docs/img/osipi.png b/docs-mk/docs/img/osipi.png → docs/docs/img/osipi.png
diff --git a/docs-mk/docs/index.md → docs/docs/index.md b/docs-mk/docs/index.md → docs/docs/index.md
diff --git a/docs-mk/docs/references/index.md → docs/docs/references/index.md b/docs-mk/docs/references/index.md → docs/docs/references/index.md
diff --git a/docs-mk/docs/references/models.md → docs/docs/references/models.md b/docs-mk/docs/references/models.md → docs/docs/references/models.md
diff --git a/...erences/models/aif_models/aif_georgiou.md → ...erences/models/aif_models/aif_georgiou.md b/...erences/models/aif_models/aif_georgiou.md → ...erences/models/aif_models/aif_georgiou.md
diff --git a/...eferences/models/aif_models/aif_parker.md → ...eferences/models/aif_models/aif_parker.md b/...eferences/models/aif_models/aif_parker.md → ...eferences/models/aif_models/aif_parker.md
diff --git a/...erences/models/aif_models/aif_weinmann.md → ...erences/models/aif_models/aif_weinmann.md b/...erences/models/aif_models/aif_weinmann.md → ...erences/models/aif_models/aif_weinmann.md
diff --git a/...ocs/references/models/aif_models/index.md → ...ocs/references/models/aif_models/index.md b/...ocs/references/models/aif_models/index.md → ...ocs/references/models/aif_models/index.md
diff --git a/docs-mk/docs/references/models/index.md → docs/docs/references/models/index.md b/docs-mk/docs/references/models/index.md → docs/docs/references/models/index.md
diff --git a/...es/models/tissue_models/extended_tofts.md → ...es/models/tissue_models/extended_tofts.md b/...es/models/tissue_models/extended_tofts.md → ...es/models/tissue_models/extended_tofts.md
diff --git a/.../references/models/tissue_models/index.md → .../references/models/tissue_models/index.md b/.../references/models/tissue_models/index.md → .../references/models/tissue_models/index.md
diff --git a/.../references/models/tissue_models/tofts.md → .../references/models/tissue_models/tofts.md b/.../references/models/tissue_models/tofts.md → .../references/models/tissue_models/tofts.md
diff --git a/docs-mk/docs/stylesheets/extra.css → docs/docs/stylesheets/extra.css b/docs-mk/docs/stylesheets/extra.css → docs/docs/stylesheets/extra.css
diff --git a/docs-mk/docs/user-guide/gen_aif.md → docs/docs/user-guide/gen_aif.md b/docs-mk/docs/user-guide/gen_aif.md → docs/docs/user-guide/gen_aif.md
diff --git a/docs-mk/docs/user-guide/index.md → docs/docs/user-guide/index.md b/docs-mk/docs/user-guide/index.md → docs/docs/user-guide/index.md
diff --git a/docs-mk/docs/user-guide/install.md → docs/docs/user-guide/install.md b/docs-mk/docs/user-guide/install.md → docs/docs/user-guide/install.md
diff --git a/docs-mk/docs/user-guide/simulate.md → docs/docs/user-guide/simulate.md b/docs-mk/docs/user-guide/simulate.md → docs/docs/user-guide/simulate.md
diff --git a/docs/examples/.DS_Store b/docs/examples/.DS_Store
diff --git a/docs/examples/README.rst b/docs/examples/README.rst
diff --git a/docs/examples/aif/README.rst b/docs/examples/aif/README.rst
diff --git a/docs/examples/aif/plot_aif_parker.py b/docs/examples/aif/plot_aif_parker.py
diff --git a/docs/examples/aif/plot_dummy.py b/docs/examples/aif/plot_dummy.py
diff --git a/docs/examples/signal/plot_signal_SPGR.py b/docs/examples/signal/plot_signal_SPGR.py
diff --git a/docs/examples/signal/plot_signal_linear.py b/docs/examples/signal/plot_signal_linear.py
diff --git a/...xamples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py b/...xamples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py
diff --git a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py b/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py
diff --git a/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py b/docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py
diff --git a/docs/examples/tissue/README.rst b/docs/examples/tissue/README.rst