Fix line numbering in docs

BioinfoMachineLearning · May 23, 2024 · 53f1e55 · 53f1e55
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diff --git a/docs/source/acknowledgements.rst b/docs/source/acknowledgements.rst
@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/available_methods.rst b/docs/source/available_methods.rst
@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 271
+    :end-line: 308
 
 .. note::
     Have a new method to add? Please let us know by creating a pull request. We would be happy to work with you to integrate new methodology into this benchmark!
diff --git a/docs/source/bonus.rst b/docs/source/bonus.rst
@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
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+    :end-line: 840
 
 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench

diff --git a/docs/source/citing_this_work.rst b/docs/source/citing_this_work.rst
@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
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+    :end-line: 834
diff --git a/docs/source/comparative_plots.rst b/docs/source/comparative_plots.rst
@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst
@@ -2,5 +2,5 @@ How to prepare `PoseBench` data
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 130
+    :end-line: 265
diff --git a/docs/source/ensemble_inference.rst b/docs/source/ensemble_inference.rst
@@ -2,8 +2,8 @@ How to run inference with a method ensemble
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 703
+    :end-line: 747
 
 .. note::
     In addition to having `consensus` as an available value for `ensemble_ranking_method`, one can also set `ensemble_ranking_method=ff` to have the method ensemble's top-ranked predictions selected using the criterion of "minimum (molecular dynamics) force field energy" (albeit while incurring a very large runtime complexity).
diff --git a/docs/source/for_developers.rst b/docs/source/for_developers.rst
@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 768
+    :end-line: 802
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,17 +8,17 @@ Welcome to PoseBench's documentation!
 
 
 .. mdinclude:: ../../README.md
-    :start-line: 3
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+    :start-line: 4
+    :end-line: 12
 
 .. image:: ./_static/PoseBench.png
   :alt: Overview of PoseBench
   :align: center
   :width: 600
 
 .. mdinclude:: ../../README.md
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+    :start-line: 18
+    :end-line: 20
 
 
 .. toctree::
@@ -53,14 +53,14 @@ Welcome to PoseBench's documentation!
    :hidden:
    :caption: API Reference
 
-   modules/complex_alignment
-   modules/inference_relaxation
-   modules/minimize_energy
-   modules/ensemble_generation
-   modules/data_utils
-   modules/model_utils
-   modules/utils
-   modules/resolvers
+   modules/src.complex_alignment
+   modules/src.inference_relaxation
+   modules/src.minimize_energy
+   modules/src.ensemble_generation
+   modules/src.data_utils
+   modules/src.model_utils
+   modules/src.utils
+   modules/src.resolvers
 
 Indices and tables
 ==================

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -2,5 +2,5 @@ Installation
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 40
+    :end-line: 112
diff --git a/docs/source/method_inference.rst b/docs/source/method_inference.rst
@@ -2,5 +2,5 @@ How to run inference with individual methods
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/modules/complex_alignment.rst → .../source/modules/src.complex_alignment.rst b/docs/source/modules/complex_alignment.rst → .../source/modules/src.complex_alignment.rst
diff --git a/docs/source/modules/data_utils.rst → docs/source/modules/src.data_utils.rst b/docs/source/modules/data_utils.rst → docs/source/modules/src.data_utils.rst
diff --git a/docs/source/modules/ensemble_generation.rst → ...ource/modules/src.ensemble_generation.rst b/docs/source/modules/ensemble_generation.rst → ...ource/modules/src.ensemble_generation.rst
diff --git a/docs/source/modules/inference_relaxation.rst → ...urce/modules/src.inference_relaxation.rst b/docs/source/modules/inference_relaxation.rst → ...urce/modules/src.inference_relaxation.rst
diff --git a/docs/source/modules/minimize_energy.rst → docs/source/modules/src.minimize_energy.rst b/docs/source/modules/minimize_energy.rst → docs/source/modules/src.minimize_energy.rst
diff --git a/docs/source/modules/model_utils.rst → docs/source/modules/src.model_utils.rst b/docs/source/modules/model_utils.rst → docs/source/modules/src.model_utils.rst
diff --git a/docs/source/modules/resolvers.rst → docs/source/modules/src.resolvers.rst b/docs/source/modules/resolvers.rst → docs/source/modules/src.resolvers.rst
diff --git a/docs/source/modules/utils.rst → docs/source/modules/src.utils.rst b/docs/source/modules/utils.rst → docs/source/modules/src.utils.rst
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -2,5 +2,5 @@ Tutorials
 ================
 
 .. mdinclude:: ../../README.md
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+    :end-line: 124