remove torch_scatter dependency

.gitignore

@@ -194,4 +194,7 @@ docs/tex/overview.fls
 docs/tex/overview.pdf
 docs/tex/overview.synctex.gz
 
-output/*
+output/*
+
+
+src/*.c

docs/source/benchmark/diff/models.py

@@ -251,24 +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)
@@ -304,7 +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)]

docs/source/benchmark/diff/simulated.py

@@ -233,10 +233,10 @@ def apply_trunc_normal(value, loc, scale, a=0, b=1):
 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(model_info) * 0.2
 
-panel, ax = fig.main.add(chd.grid.Ax((1, height)))
+panel, ax = fig.main.add(polyptich.grid.Panel((1, height)))
 plotdata = scores.xs("test", level="phase").loc[model_info.index]
 
 ax.barh(plotdata.index, plotdata["lr"])
@@ -245,15 +245,15 @@ def apply_trunc_normal(value, loc, scale, a=0, b=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)))
 plotdata = scores.xs("validation", level="phase").loc[model_info.index]
 ax.set_yticks([])
 ax.barh(plotdata.index, plotdata["lr"])
 ax.barh(plotdata.index, plotdata["lr_position"], alpha=0.5)
 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)))
 plotdata = scores.xs("train", level="phase").loc[model_info.index]
 ax.set_yticks([])
 ax.barh(plotdata.index, plotdata["lr"])
@@ -296,9 +296,9 @@ def apply_trunc_normal(value, loc, scale, a=0, b=1):
 )
 
 # %%
-fig = chd.grid.Figure(chd.grid.Grid(padding_height=0))
+fig = polyptich.grid.Figure(polyptich.grid.Grid(padding_height=0))
 width = 10
-panel, ax = fig.main.add_under(chd.grid.Panel((width, 0.5)))
+panel, ax = fig.main.add_under(polyptich.grid.Panel((width, 0.5)))
 plotdata = design.loc[design["size"] == 0].set_index(["cluster_ix", "coordinate"])[["prob_left"]]
 for cluster_ix, plotdata_cluster in plotdata.groupby("cluster_ix"):
     plotdata_cluster = plotdata_cluster.droplevel("cluster_ix").sort_index()
@@ -312,7 +312,7 @@ def apply_trunc_normal(value, loc, scale, a=0, b=1):
 ax2.scatter(plotdata["center"], [0] * len(plotdata), c=plotdata["size_mean"])
 ax2.set_xlim(*fragments.regions.window)
 
-panel, ax = fig.main.add_under(chd.grid.Panel((width, 2)))
+panel, ax = fig.main.add_under(polyptich.grid.Panel((width, 2)))
 plotdata = np.exp(design.groupby(["size", "coordinate"]).mean()["prob_right"].unstack())
 ax.matshow(plotdata, aspect="auto", extent=(*fragments.regions.window, *plotdata.index[[-1, 0]]), cmap="viridis")
 ax.set_xticks([])
@@ -324,14 +324,14 @@ def apply_trunc_normal(value, loc, scale, a=0, b=1):
 fig.plot()
 
 # %%
-main = chd.grid.Grid(padding_height=0.1)
-fig = chd.grid.Figure(main)
+main = polyptich.grid.Grid(padding_height=0.1)
+fig = polyptich.grid.Figure(main)
 
 nbins = np.array(model.mixture.transform.nbins)
 bincuts = np.concatenate([[0], np.cumsum(nbins)])
 binmids = bincuts[:-1] + nbins / 2
 
-ax = main[0, 0] = chd.grid.Ax((10, 0.25))
+ax = main[0, 0] = polyptich.grid.Panel((10, 0.25))
 ax = ax.ax
 plotdata = (model.mixture.transform.unnormalized_heights.data.cpu().numpy())[[gene_ix]]
 ax.imshow(plotdata, aspect="auto")
@@ -342,7 +342,7 @@ def apply_trunc_normal(value, loc, scale, a=0, b=1):
 ax.set_xticks([])
 ax.set_ylabel("$h_0$", rotation=0, ha="right", va="center")
 
-ax = main[1, 0] = chd.grid.Ax(dim=(10, model.n_clusters * 0.25))
+ax = main[1, 0] = polyptich.grid.Panel(dim=(10, model.n_clusters * 0.25))
 ax = ax.ax
 plotdata = model.decoder.delta_height_weight.data[gene_ix].cpu().numpy()
 ax.imshow(plotdata, aspect="auto", cmap=mpl.cm.RdBu_r, vmax=np.log(2), vmin=np.log(1 / 2))

docs/source/benchmark/diff/timing.py

@@ -107,20 +107,20 @@
     scores.loc[device, "inference"] = end - start
 
 # %%
-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[devices.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["train"])
 ax.set_yticks(np.arange(len(devices)))
 ax.set_yticklabels(devices.label)
 ax.axvline(0, color="black", linestyle="--", lw=1)
 ax.set_title("Training")
 ax.set_xlabel("seconds")
 
-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["inference"])
 ax.axvline(0, color="black", linestyle="--", lw=1)
 ax.set_title("Inference")

docs/source/quickstart/1_data.py

@@ -179,10 +179,6 @@
 folds = chd.data.folds.Folds(dataset_folder / "folds" / "5x1").sample_cells(fragments, 5, 1)
 folds
 
-# %%
-folds = chd.data.folds.Folds(dataset_folder / "folds" / "5x5").sample_cells(fragments, 5, 5)
-folds
-
 # %% [markdown]
 # ## Optional data¶
 
@@ -215,7 +211,7 @@
 # %%
 import genomepy
 
-genomepy.install_genome("GRCh38", genomes_dir="/data/genome/")
+genomepy.install_genome("GRCh38", genomes_dir="/srv/data/genome/")
 
 fasta_file = "/data/genome/GRCh38/GRCh38.fa"
 

docs/source/quickstart/2_pred.py

@@ -133,7 +133,7 @@
 # %%
 symbol = "IRF1"
 
-fig = chd.grid.Figure(chd.grid.Grid(padding_height=0.05))
+fig = polyptich.grid.Figure(polyptich.grid.Grid(padding_height=0.05))
 width = 10
 
 region = fragments.regions.coordinates.loc[transcriptome.gene_id(symbol)]
@@ -166,10 +166,10 @@
 # %%
 # decrease the lost_cutoff to see more regions
 regions = regionmultiwindow.select_regions(gene_id, lost_cutoff = 0.15)
-breaking = chd.grid.Breaking(regions)
+breaking = polyptich.grid.Breaking(regions)
 
 # %%
-fig = chd.grid.Figure(chd.grid.Grid(padding_height=0.05))
+fig = polyptich.grid.Figure(polyptich.grid.Grid(padding_height=0.05))
 
 region = fragments.regions.coordinates.loc[transcriptome.gene_id(symbol)]
 panel_genes = chd.plot.genome.genes.GenesBroken.from_region(region, breaking=breaking, genome = "GRCh38")
@@ -208,10 +208,10 @@
 
 # %%
 windows = regionmultiwindow.select_regions(gene_id, lost_cutoff = 0.2)
-breaking = chd.grid.Breaking(windows)
+breaking = polyptich.grid.Breaking(windows)
 
 # %%
-fig = chd.grid.Figure(chd.grid.Grid(padding_height=0.05))
+fig = polyptich.grid.Figure(polyptich.grid.Grid(padding_height=0.05))
 width = 10
 
 # genes

docs/source/quickstart/3_diff.py

@@ -91,7 +91,7 @@
 window = [-10000, 10000]
 
 # %%
-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)]
@@ -115,10 +115,10 @@
 
 # %%
 windows = regionpositional.select_windows(gene_id)
-breaking = chd.grid.Breaking(windows)
+breaking = polyptich.grid.Breaking(windows)
 
 # %%
-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)]

pyproject.toml

@@ -86,16 +86,10 @@ disable = [
 ]
 
 [tool.ruff]
-line-length = 500
-ignore-init-module-imports = true
-ignore = ['F401']
+line-length = 90
 include = ['src/**/*.py']
 exclude = ['scripts/*']
 
-[tool.black]
-line-length = 120
-target-version = ['py37', 'py38']
-
 
 [tool.jupytext]
 formats = "ipynb,py:percent"

src/chromatinhd/__init__.py

@@ -3,14 +3,14 @@
 from . import sparse
 from . import utils
 from . import flow
-from . import grid
 from . import plot
 from . import data
 from . import train
 from . import embedding
 from . import optim
 from . import biomart
 from . import models
+from polyptich import grid
 
 __all__ = [
     "get_git_root",
@@ -26,8 +26,8 @@
     "train",
     "embedding",
     "optim",
-    "grid",
     "biomart",
     "models",
     "plot",
+    "grid",
 ]

src/chromatinhd/biomart/dataset.py

@@ -139,7 +139,7 @@ def attribute(self, name, **kwargs):
     def filter(self, name, **kwargs):
         return Filter(name, **kwargs)
 
-    def get(self, attributes=[], filters=[], use_cache=True) -> pd.DataFrame:
+    def get(self, attributes=[], filters=[], use_cache=True, timeout = 20) -> pd.DataFrame:
         """
         Get the result with a given set of attributes and filters
 
@@ -176,7 +176,7 @@ def get(self, attributes=[], filters=[], use_cache=True) -> pd.DataFrame:
             result = cache[url]
         else:
             try:
-                response = requests.get(url, timeout=10)
+                response = requests.get(url, timeout=timeout)
             except requests.exceptions.Timeout:
                 raise ValueError("Ensembl web service timed out")
             # check response status

src/chromatinhd/data/associations/plot.py

@@ -1,8 +1,8 @@
-from chromatinhd.grid.broken import Broken, Panel
+from polyptich.grid.broken import Broken, Panel
 import pandas as pd
 import adjustText
 import seaborn as sns
-
+import matplotlib as mpl
 
 def center_position(peaks, region):
     peaks = peaks.copy()
@@ -136,7 +136,7 @@ def get_snp_color(snp_main):
                 )
 
                 for i, (index, row) in enumerate(plotdata_region.iterrows()):
-                    ax.text(
+                    text = ax.text(
                         row["pos"],
                         0.8,
                         row["rsid"],
@@ -145,6 +145,11 @@ def get_snp_color(snp_main):
                         va="bottom",
                         color=colors[i],
                     )
+                    text.set_path_effects(
+                        [
+                            mpl.patheffects.withStroke(linewidth=2, foreground="white"),
+                        ]
+                    )
                 # ax.scatter(
                 #     plotdata_region["position"],
                 #     [1] * len(plotdata_region),