Merge branch 'devel'

.github/workflows/ci.yml

@@ -13,21 +13,21 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
           cache: 'pip'
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
-      - run: pip install torch # because torch_scatter contains import torch in the setup.py, we have to install torch first
+      - run: pip install torch==2.3.0 # because torch_scatter contains import torch in the setup.py, we have to install torch first
+      - run: pip install torch-scatter -f https://data.pyg.org/whl/torch-2.3.0+cpu.html # it seems a wheel is necessary to install torch-scatter
       - name: regular install
-        run: pip install .
+        run: pip install .[full]
       - name: attempt import
         run: python -c "import chromatinhd"
       - name: test install
         run: pip install -e .[test]
-      - name: ruff
-        run: ruff check --format=github .
+      # - uses: jpetrucciani/ruff-check@main
       - name: test
         run: pytest
       # - run: mkdocs gh-deploy --force

.gitignore

@@ -182,3 +182,19 @@ software/
 docs/source/quickstart/example/*
 docs/source/quickstart/restats
 *.code-workspace
+
+
+*.zarr
+*.zarr/*
+*.hdf5
+restats
+docs/tex/overview.aux
+docs/tex/overview.fdb_latexmk
+docs/tex/overview.fls
+docs/tex/overview.pdf
+docs/tex/overview.synctex.gz
+
+output/*
+
+
+src/*.c

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 repos:
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.0.282
-    hooks:
-    - id: ruff
-      args: [., --fix, --exit-non-zero-on-fix ]
-      exclude: '(^scripts|^docs)/.*'
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   # Ruff version.
+  #   rev: v0.0.282
+  #   hooks:
+  #   - id: ruff
+  #     args: [., --fix, --exit-non-zero-on-fix ]
+  #     exclude: '(^scripts|^docs)/.*'
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:

README.md

@@ -2,6 +2,9 @@
   <a href="https://chromatinhd.eu">
     <img src="https://raw.githubusercontent.com/DeplanckeLab/ChromatinHD/main/docs/source/static/logo.png" width="300" />
   </a>
+  <a href="https://chromatinhd.eu">
+    <img src="https://raw.githubusercontent.com/DeplanckeLab/ChromatinHD/main/docs/source/static/comparison.gif" />
+  </a>
 </p>
 
 ChromatinHD analyzes single-cell ATAC+RNA data using the raw fragments as input,

docs/override/main.html

@@ -57,6 +57,16 @@
   {% endif %}
   <div class="md-footer-meta md-typeset">
     <div class="md-footer-meta__inner md-grid">
+      <div class="md-copyright">
+        <div class="md-copyright__highlight">
+          <div class="container" style="display: flex;align-items: center;">
+              <img src="{{ base_url }}/static/eu.png" alt="European Flag" style="max-width: 100%;height: auto;margin-right: 20px;" width="100" height="70">
+              <div style="flex: 0 0 400px;">
+                  This work was supported by the European Union's Horizon 2020 research and innovation program (Grant agreement 101028476).
+              </div>
+          </div>
+        </div>
+      </div>
       {% include "partials/copyright.html" %}
       {% if config.extra.social %}
       {% include "partials/social.html" %}

docs/source/benchmark/diff/models.py

@@ -43,8 +43,8 @@
 
 # %%
 genes_oi = transcriptome_original.var.sort_values("dispersions_norm", ascending=False).head(50).index
-regions = fragments_original.regions.filter_genes(genes_oi)
-fragments = fragments_original.filter_genes(regions)
+regions = fragments_original.regions.filter(genes_oi)
+fragments = fragments_original.filter_regions(regions)
 fragments.create_cellxgene_indptr()
 transcriptome = transcriptome_original.filter_genes(regions.coordinates.index)
 
@@ -80,6 +80,15 @@
 model.train_model(fragments, clustering, fold, n_epochs=30)
 models["original"] = model
 
+# %%
+model = chd.models.diff.model.cutnf.Model(
+    fragments,
+    clustering,
+    nbins = (32, 64, 128)
+)
+model.train_model(fragments, clustering, fold, n_epochs=30)
+models["original_rev"] = model
+
 # %%
 model = chd.models.diff.model.cutnf.Model(
     fragments,
@@ -242,24 +251,24 @@
 model_info["ix"] = np.arange(model_info.shape[0])
 
 # %%
-fig = chd.grid.Figure(chd.grid.Wrap(padding_width=0.1))
+fig = polyptich.grid.Figure(polyptich.grid.Wrap(padding_width=0.1))
 height = len(scores) * 0.2
 
 plotdata = scores.copy().loc[model_info.index]
 
-panel, ax = fig.main.add(chd.grid.Ax((1, height)))
+panel, ax = fig.main.add(polyptich.grid.Panel((1, height)))
 ax.barh(plotdata.index, plotdata["lr_test"])
 ax.axvline(0, color="black", linestyle="--", lw=1)
 ax.set_title("Test")
 ax.set_xlabel("Log-likehood ratio")
 
-panel, ax = fig.main.add(chd.grid.Ax((1, height)))
+panel, ax = fig.main.add(polyptich.grid.Panel((1, height)))
 ax.set_yticks([])
 ax.barh(plotdata.index, plotdata["lr_validation"])
 ax.axvline(0, color="black", linestyle="--", lw=1)
 ax.set_title("Validation")
 
-panel, ax = fig.main.add(chd.grid.Ax((1, height)))
+panel, ax = fig.main.add(polyptich.grid.Panel((1, height)))
 ax.set_yticks([])
 ax.barh(plotdata.index, plotdata["lr_train"])
 ax.axvline(0, color="black", linestyle="--", lw=1)
@@ -295,7 +304,7 @@
 genepositional.score(fragments, clustering, [models[model_id]], force=True, genes=transcriptome.gene_id([symbol]))
 
 # %%
-fig = chd.grid.Figure(chd.grid.Grid(padding_height=0.05, padding_width=0.05))
+fig = polyptich.grid.Figure(polyptich.grid.Grid(padding_height=0.05, padding_width=0.05))
 width = 10
 
 region = fragments.regions.coordinates.loc[transcriptome.gene_id(symbol)]