From d14c93c8c43f98cb85bff8b5e9e78dc4fc25841a Mon Sep 17 00:00:00 2001 From: LeonStadelmann Date: Sun, 11 May 2025 12:23:43 +0200 Subject: [PATCH 1/6] Fixed doctree depth and references --- examples/problems/400_subset_policy.ipynb | 2 +- .../problems/AlignmentProblem/1300_sequential_alignment.ipynb | 4 ++-- tutorials/index.rst | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/problems/400_subset_policy.ipynb b/examples/problems/400_subset_policy.ipynb index 113aa97..d2fdd80 100644 --- a/examples/problems/400_subset_policy.ipynb +++ b/examples/problems/400_subset_policy.ipynb @@ -15,7 +15,7 @@ "{class}`~moscot.problems.time.TemporalProblem`, we can choose among different policies as demonstrated below.\n", "\n", ":::{seealso}\n", - "- See {doc}`AlignmentProblem/1300_sequential_alignment.ipynb` on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem`.\n", + "- See {doc}`AlignmentProblem/1300_sequential_alignment` on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem`.\n", ":::" ] }, diff --git a/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb b/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb index 3062d3e..cd7142b 100644 --- a/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb +++ b/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb @@ -9,8 +9,8 @@ "In this example we focus on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem` to produce specific alignments of spatial samples.\n", "\n", ":::{seealso}\n", - "- See {doc}`../400_subset_policy.ipynb` on how to use different policies.\n", - "- See {doc}`../../../tutorials/300_spatial_alignment.ipynb` on how to align spatial transcriptomics data.\n", + "- See {doc}`../400_subset_policy` on how to use different policies.\n", + "- See {doc}`../../../tutorials/300_spatial_alignment` on how to align spatial transcriptomics data.\n", ":::" ] }, diff --git a/tutorials/index.rst b/tutorials/index.rst index 515f2b3..4a4ede9 100644 --- a/tutorials/index.rst +++ b/tutorials/index.rst @@ -3,7 +3,7 @@ Tutorials This section contains various tutorials showcasing use cases for data analysis with :mod:`moscot`. .. toctree:: - :maxdepth: 1 + :maxdepth: 3 :glob: * From f0aa21d6abde207916e9b59778e675e7c830f372 Mon Sep 17 00:00:00 2001 From: LeonStadelmann Date: Sun, 11 May 2025 13:07:13 +0200 Subject: [PATCH 2/6] fix toctree depth --- tutorials/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/index.rst b/tutorials/index.rst index 4a4ede9..b04a68b 100644 --- a/tutorials/index.rst +++ b/tutorials/index.rst @@ -3,7 +3,7 @@ Tutorials This section contains various tutorials showcasing use cases for data analysis with :mod:`moscot`. .. toctree:: - :maxdepth: 3 + :maxdepth: 4 :glob: * From 2548c2cd70b8370e89bbac9372a03407d5aae626 Mon Sep 17 00:00:00 2001 From: Leon Stadelmann Date: Sun, 11 May 2025 19:01:42 +0200 Subject: [PATCH 3/6] Rework index structure and revert depth changes --- examples/problems/AlignmentProblem/index.rst | 8 ++++++++ examples/problems/LineageProblem/index.rst | 8 ++++++++ examples/problems/SpatioTemporalProblem/index.rst | 8 ++++++++ examples/problems/TemporalProblem/index.rst | 8 ++++++++ examples/problems/index.rst | 11 +++++++++++ tutorials/index.rst | 2 +- 6 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 examples/problems/AlignmentProblem/index.rst create mode 100644 examples/problems/LineageProblem/index.rst create mode 100644 examples/problems/SpatioTemporalProblem/index.rst create mode 100644 examples/problems/TemporalProblem/index.rst create mode 100644 examples/problems/index.rst diff --git a/examples/problems/AlignmentProblem/index.rst b/examples/problems/AlignmentProblem/index.rst new file mode 100644 index 0000000..b07d1d2 --- /dev/null +++ b/examples/problems/AlignmentProblem/index.rst @@ -0,0 +1,8 @@ +Alignment Problem +================= + +.. toctree:: + :maxdepth: 1 + :glob: + + ./* \ No newline at end of file diff --git a/examples/problems/LineageProblem/index.rst b/examples/problems/LineageProblem/index.rst new file mode 100644 index 0000000..03911be --- /dev/null +++ b/examples/problems/LineageProblem/index.rst @@ -0,0 +1,8 @@ +Lineage Problem +================ + +.. toctree:: + :maxdepth: 1 + :glob: + + ./* \ No newline at end of file diff --git a/examples/problems/SpatioTemporalProblem/index.rst b/examples/problems/SpatioTemporalProblem/index.rst new file mode 100644 index 0000000..671355b --- /dev/null +++ b/examples/problems/SpatioTemporalProblem/index.rst @@ -0,0 +1,8 @@ +Spatio Temporal Problem +======================= + +.. toctree:: + :maxdepth: 1 + :glob: + + ./* \ No newline at end of file diff --git a/examples/problems/TemporalProblem/index.rst b/examples/problems/TemporalProblem/index.rst new file mode 100644 index 0000000..564bc4c --- /dev/null +++ b/examples/problems/TemporalProblem/index.rst @@ -0,0 +1,8 @@ +Temporal Problem +================ + +.. toctree:: + :maxdepth: 1 + :glob: + + ./* \ No newline at end of file diff --git a/examples/problems/index.rst b/examples/problems/index.rst new file mode 100644 index 0000000..8a36239 --- /dev/null +++ b/examples/problems/index.rst @@ -0,0 +1,11 @@ +Problems +======== + +.. toctree:: + :maxdepth: 1 + + AlignmentProblem/index + LineageProblem/index + SpatioTemporalProblem/index + TemporalProblem/index + diff --git a/tutorials/index.rst b/tutorials/index.rst index b04a68b..515f2b3 100644 --- a/tutorials/index.rst +++ b/tutorials/index.rst @@ -3,7 +3,7 @@ Tutorials This section contains various tutorials showcasing use cases for data analysis with :mod:`moscot`. .. toctree:: - :maxdepth: 4 + :maxdepth: 1 :glob: * From 0ce7019d88f1ebe18bcdaa855b0cf31037730de1 Mon Sep 17 00:00:00 2001 From: Leon Stadelmann Date: Sun, 11 May 2025 19:13:44 +0200 Subject: [PATCH 4/6] fix newline --- examples/problems/index.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/examples/problems/index.rst b/examples/problems/index.rst index 8a36239..a0869ea 100644 --- a/examples/problems/index.rst +++ b/examples/problems/index.rst @@ -8,4 +8,3 @@ Problems LineageProblem/index SpatioTemporalProblem/index TemporalProblem/index - From 609d37ff9e3faa0202e2e411c99b9ae003a448b6 Mon Sep 17 00:00:00 2001 From: Leon Stadelmann Date: Sun, 11 May 2025 19:16:19 +0200 Subject: [PATCH 5/6] whitespace fix attempt --- examples/problems/AlignmentProblem/index.rst | 2 +- examples/problems/LineageProblem/index.rst | 2 +- examples/problems/SpatioTemporalProblem/index.rst | 2 +- examples/problems/TemporalProblem/index.rst | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/problems/AlignmentProblem/index.rst b/examples/problems/AlignmentProblem/index.rst index b07d1d2..e83cd6b 100644 --- a/examples/problems/AlignmentProblem/index.rst +++ b/examples/problems/AlignmentProblem/index.rst @@ -5,4 +5,4 @@ Alignment Problem :maxdepth: 1 :glob: - ./* \ No newline at end of file + ./* diff --git a/examples/problems/LineageProblem/index.rst b/examples/problems/LineageProblem/index.rst index 03911be..752461a 100644 --- a/examples/problems/LineageProblem/index.rst +++ b/examples/problems/LineageProblem/index.rst @@ -5,4 +5,4 @@ Lineage Problem :maxdepth: 1 :glob: - ./* \ No newline at end of file + * diff --git a/examples/problems/SpatioTemporalProblem/index.rst b/examples/problems/SpatioTemporalProblem/index.rst index 671355b..de65a7f 100644 --- a/examples/problems/SpatioTemporalProblem/index.rst +++ b/examples/problems/SpatioTemporalProblem/index.rst @@ -5,4 +5,4 @@ Spatio Temporal Problem :maxdepth: 1 :glob: - ./* \ No newline at end of file + ./* diff --git a/examples/problems/TemporalProblem/index.rst b/examples/problems/TemporalProblem/index.rst index 564bc4c..2ec34d6 100644 --- a/examples/problems/TemporalProblem/index.rst +++ b/examples/problems/TemporalProblem/index.rst @@ -5,4 +5,4 @@ Temporal Problem :maxdepth: 1 :glob: - ./* \ No newline at end of file + ./* From 67d5902e7e3d675739e71206434eda8be1bec197 Mon Sep 17 00:00:00 2001 From: Leon Stadelmann Date: Sun, 11 May 2025 19:17:27 +0200 Subject: [PATCH 6/6] Modify path --- examples/problems/LineageProblem/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/problems/LineageProblem/index.rst b/examples/problems/LineageProblem/index.rst index 752461a..6045930 100644 --- a/examples/problems/LineageProblem/index.rst +++ b/examples/problems/LineageProblem/index.rst @@ -5,4 +5,4 @@ Lineage Problem :maxdepth: 1 :glob: - * + ./*