diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ecb21d9..5aefbc9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,9 +9,9 @@ repos: - repo: https://github.com/ericmjl/webp-pre-commit rev: v0.0.12 hooks: - # Convert only blog images + # Convert blog and learn images - id: convert-to-webp - files: ^static/img/blog/.*\.(png|jpe?g|gif|bmp|tiff)$ + files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$ - repo: https://github.com/shssoichiro/oxipng rev: v10.2.0 hooks: diff --git a/content/learn/_index.md b/content/learn/_index.md index 46fcf0f..4116110 100644 --- a/content/learn/_index.md +++ b/content/learn/_index.md @@ -24,15 +24,15 @@ You can also find recordings of past talks and workshops on our [YouTube channel [[tutorials.section]] name = "Basic Analysis of PBMCs" url = "https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html" - img = "https://scanpy-tutorials.readthedocs.io/en/latest/_images/pbmc3k_100_1.png" + img = "../../img/learn/pbmc3k.webp" [[tutorials.section]] name = "Analyzing scRNA-seq with scvi-tools" url = "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/api_overview.html" - img = "https://docs.scvi-tools.org/en/stable/_images/tutorials_notebooks_api_overview_45_1.png" + img = "../../img/learn/scvi-api-overview.webp" [[tutorials.section]] name = "Integration of the Lung Cell Atlas with scANVI" url = "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/harmonization.html" - img = "../../img/learn/lung.png" + img = "../../img/learn/lung.webp" [[tutorials]] @@ -40,59 +40,59 @@ You can also find recordings of past talks and workshops on our [YouTube channel [[tutorials.section]] name = "TCR and BCR receptor sequencing with scirpy" url = "https://scirpy.scverse.org/en/latest/tutorials/tutorial_3k_tcr.html" - img = "https://scirpy.scverse.org/en/latest/_static/scirpy_logo.png" + img = "../../img/learn/scirpy-logo.webp" [[tutorials.section]] name = "ATAC-seq" url = "https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/2-Chromatin-Accessibility-Processing.html" - img = "https://muon-tutorials.readthedocs.io/en/latest/_images/single-cell-rna-atac_pbmc10k_2-Chromatin-Accessibility-Processing_85_0.png" + img = "../../img/learn/atac-seq.webp" [[tutorials.section]] name = "Analysis and processing of surface marker data (CITE-seq)" url = "https://muon-tutorials.readthedocs.io/en/latest/cite-seq/1-CITE-seq-PBMC-5k.html" - img = "https://muon-tutorials.readthedocs.io/en/latest/_images/cite-seq_1-CITE-seq-PBMC-5k_38_1.png" + img = "../../img/learn/cite-seq-pbmc5k.webp" [[tutorials]] name="Spatial" [[tutorials.section]] name = "Analyzing 10x Visium data with squidpy" url = "https://squidpy.readthedocs.io/en/latest/auto_tutorials/tutorial_visium_hne.html" - img = "https://squidpy.readthedocs.io/en/latest/_images/sphx_glr_tutorial_visium_hne_001.png" + img = "../../img/learn/visium-hne.webp" [[tutorials.section]] name = "Analysis of seqFISH data with squidpy" url = "https://squidpy.readthedocs.io/en/stable/auto_tutorials/tutorial_seqfish.html" - img = "https://squidpy.readthedocs.io/en/stable/_images/sphx_glr_tutorial_seqfish_003.png" + img = "../../img/learn/seqfish.webp" [[tutorials.section]] name = "Deconvolution of Visium data with DestVI" url = "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/DestVI_tutorial.html" - img = "../../img/learn/tissue.png" + img = "../../img/learn/tissue.webp" [[tutorials]] name = "scATAC-seq & scRNA-seq" [[tutorials.section]] name = "Integrating gene expression and chromatin accessibility of 10k PBMCs in muon" url = "https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/3-Multimodal-Omics-Data-Integration.html" - img = "https://muon-tutorials.readthedocs.io/en/latest/_images/single-cell-rna-atac_pbmc10k_3-Multimodal-Omics-Data-Integration_21_1.png" + img = "../../img/learn/multimodal-integration.webp" [[tutorials.section]] name = "Joint analysis of paired and unpaired multiomic data with MultiVI" url = "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/MultiVI_tutorial.html" - img = "../../img/learn/chromosome.png" + img = "../../img/learn/chromosome.webp" [[tutorials]] name = "CITE-seq" [[tutorials.section]] name = "Multi-omics integration in muon" url = "https://muon-tutorials.readthedocs.io/en/latest/cite-seq/2-CITE-seq-PBMC-5k-Weighted-Neighbours.html" - img = "https://muon-tutorials.readthedocs.io/en/latest/_images/cite-seq_2-CITE-seq-PBMC-5k-Weighted-Neighbours_30_1.png" + img = "../../img/learn/cite-seq-weighted-neighbours.webp" [[tutorials.section]] name = "CITE-seq analysis with totalVI" url = "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/totalVI.html" - img = "../../img/learn/protein.png" + img = "../../img/learn/protein.webp" [[tutorials]] name = "Other topics" [[tutorials.section]] name = "Plotting in scanpy" url = "https://scanpy-tutorials.readthedocs.io/en/latest/plotting/core.html" - img = "https://scanpy-tutorials.readthedocs.io/en/latest/_images/plotting_core_25_0.png" + img = "../../img/learn/scanpy-plotting.webp" [[tutorials.section]] name = "Combining AnnData objects" diff --git a/content/packages/_index.md b/content/packages/_index.md index bf738a7..4451a9f 100644 --- a/content/packages/_index.md +++ b/content/packages/_index.md @@ -74,7 +74,6 @@ aliases = ["/projects/"] name = "scanpy" description = "Single-cell analysis framework" url = "https://scanpy.scverse.org/" - #img = "https://scanpy.scverse.org/_static/Scanpy_Logo_BrightFG.svg" img = "../img/icons/scanpy.svg" details = "Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells." 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