feat!: Remove higlass.fuse (#175)

higlass · Feb 12, 2025 · f832176 · f832176
1 parent 6f37754
commit f832176
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Showing 8 changed files with 11 additions and 795 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ docs/_build/
 dist/
 .venv
 examples/test.mcool
+*.bigWig
diff --git a/examples/Examples.ipynb b/examples/Examples.ipynb
@@ -3,7 +3,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cfdd679e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +13,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37383869",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -23,7 +21,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f5a73851",
    "metadata": {},
    "source": [
     "## Synced heatmaps"
@@ -32,7 +29,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ba0c9d3e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -69,7 +65,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4b6c2629",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -80,7 +75,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1453f49f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +85,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4432d5d1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +103,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "637bcad2",
    "metadata": {},
    "source": [
     "## Value scale syncing"
@@ -119,7 +111,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e89a03d7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -161,7 +152,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ef880b6c",
    "metadata": {},
    "source": [
     "## Remote heatmaps"
@@ -170,7 +160,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4579c459",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -207,7 +196,6 @@
   },
   {
    "cell_type": "markdown",
-   "id": "74b22d9c",
    "metadata": {},
    "source": [
     "## Extract track from another view config"
@@ -216,7 +204,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "875260a4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -231,7 +218,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f22d06ae",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -244,7 +230,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "73c925a5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -257,64 +242,32 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0a9ad2fc",
    "metadata": {},
    "source": [
-    "## Remote bigWig tiles\n",
-    "The next section requires `fuse` and `simple-httpfs` to be installed"
+    "## Local bigWig files"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3d664bb6",
    "metadata": {},
    "outputs": [],
    "source": [
-    "%pip install fusepy simple-httpfs clodius"
+    "!wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0e22f81d",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# set up FUSE\n",
-    "import pathlib\n",
-    "\n",
-    "mount_dir = pathlib.Path.cwd() / \"mnt\"\n",
-    "\n",
-    "if not mount_dir.is_dir():\n",
-    "    mount_dir.mkdir()\n",
-    "\n",
-    "# mount directory and start fuse\n",
-    "hg.fuse.start(mount_dir.absolute())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4133c1c3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import hg\n",
-    "\n",
-    "# get mounted path\n",
-    "bwpath = hg.fuse.path(\n",
-    "    \"http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/\"\n",
-    "    \"wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig\"\n",
-    ")\n",
-    "\n",
-    "track = hg.bigwig(bwpath).track(\"horizontal-bar\")\n",
-    "hg.view(track)"
+    "tileset = hg.bigwig(\"wgEncodeSydhTfbsGm12878InputStdSig.bigWig\")\n",
+    "hg.view(tileset.track(\"horizontal-bar\"))"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "5844a303",
    "metadata": {},
    "source": [
     "## Local cooler files\n",
@@ -325,7 +278,6 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0439622f",
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/examples/Fuse.ipynb b/examples/Fuse.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -33,9 +33,6 @@ dependencies = [
 requires-python = ">=3.8"
 urls = { homepage = "https://github.com/higlass/higlass-python" }
 
-[project.optional-dependencies]
-fuse = ["fusepy", "simple-httpfs"]
-
 [dependency-groups]
 dev = ["anywidget[dev]", "jupyterlab", "pytest", "ruff"]
 

diff --git a/src/higlass/__init__.py b/src/higlass/__init__.py
@@ -12,5 +12,4 @@
 
 import higlass.tilesets as tilesets
 from higlass.api import *
-from higlass.fuse import fuse
 from higlass.tilesets import bed2ddb, beddb, bigwig, cooler, hitile, multivec, remote
diff --git a/src/higlass/fuse/__init__.py b/src/higlass/fuse/__init__.py
diff --git a/src/higlass/fuse/_httpfs.py b/src/higlass/fuse/_httpfs.py
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,3 +10,4 @@ docs/_build/ @@
     dist/
     .venv
     examples/test.mcool
+    *.bigWig