feat: update chainfile dependency, return score

Author: jsstevenson

README.md

@@ -35,7 +35,7 @@ Call ``convert_coordinate()``:
 
 ```python3
 c.convert_coordinate("chr7", 140453136, 140453137, Strand.POSITIVE)
-# returns [LiftoverResult(chrom='chr7', start=140753336, end=140753337, strand=<Strand.POSITIVE: '+'>)]
+# returns [LiftoverResult(chrom='chr7', start=140753336, end=140753337, strand=<Strand.POSITIVE: '+'>, score=14633688187)]
 ```
 
 ## Development

analysis/requirements.txt

@@ -0,0 +1,48 @@
+-e file:///Users/jss009/code/agct
+appnope==0.1.4
+asttokens==3.0.1
+certifi==2025.6.15
+charset-normalizer==3.4.2
+click==8.2.1
+comm==0.2.3
+coverage==7.9.1
+debugpy==1.8.20
+decorator==5.2.1
+executing==2.2.1
+idna==3.10
+iniconfig==2.1.0
+ipykernel==7.2.0
+ipython==9.11.0
+ipython-pygments-lexers==1.1.1
+jedi==0.19.2
+jupyter-client==8.8.0
+jupyter-core==5.9.1
+matplotlib-inline==0.2.1
+maturin==1.8.7
+nest-asyncio==1.6.0
+packaging==25.0
+parso==0.8.6
+pexpect==4.9.0
+platformdirs==4.9.4
+pluggy==1.6.0
+prek==0.2.24
+prompt-toolkit==3.0.52
+psutil==7.2.2
+ptyprocess==0.7.0
+pure-eval==0.2.3
+pygments==2.19.2
+pyliftover==0.4.1
+pytest==8.4.1
+pytest-cov==6.2.1
+python-dateutil==2.9.0.post0
+pyzmq==27.1.0
+requests==2.32.4
+ruff==0.14.10
+six==1.17.0
+stack-data==0.6.3
+tornado==6.5.5
+tqdm==4.67.1
+traitlets==5.14.3
+urllib3==2.5.0
+wags-tails==0.3.2
+wcwidth==0.6.0

analysis/speed_test.ipynb

@@ -5,19 +5,22 @@
    "id": "e70c802c-9a54-41e2-a928-7ea685017195",
    "metadata": {},
    "source": [
+    "We don't necessarily intend to keep this up to date; this notebook can be reproduced as of the commit that it's associated with.\n",
+    "\n",
     "Don't forget to run `maturin develop --release`!"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 8,
    "id": "856fbc60-6896-4824-8956-b466e29ddc69",
    "metadata": {},
    "outputs": [],
    "source": [
     "from pyliftover import LiftOver\n",
     "\n",
-    "from agct import Converter"
+    "from agct import Converter\n",
+    "from agct.seqref_registry import Assembly"
    ]
   },
   {
@@ -46,7 +49,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "1.11 s ± 26.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "498 ms ± 6.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
      ]
     }
    ],
@@ -57,21 +60,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 10,
    "id": "2332acf9-c6eb-42ac-8426-fe46eba132a0",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "217 ms ± 9.13 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "50.9 ms ± 807 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter = Converter(\"hg38\", \"hg19\")"
+    "converter = Converter(Assembly.HG38, Assembly.HG19)"
    ]
   },
   {
@@ -84,15 +87,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 11,
    "id": "ae47dbbb-c9ad-46b4-9f4d-14823bbf26f2",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "1.09 s ± 14.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "512 ms ± 16.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
      ]
     }
    ],
@@ -104,22 +107,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 13,
    "id": "729abc9a-6429-4cb6-aaca-4bac4cd762f8",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "215 ms ± 6.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "50.6 ms ± 1.17 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter = Converter(\"hg38\", \"hg19\")\n",
-    "converter.convert_coordinate(\"chr5\", 1404391, \"+\")"
+    "converter = Converter(Assembly.HG38, Assembly.HG19)\n",
+    "converter.convert_coordinate(\"chr5\", 1404391, 1404391, \"+\")"
    ]
   },
   {
@@ -132,27 +135,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 14,
    "id": "7c51c0cb-e997-4ece-8a68-8e946b9dde3d",
    "metadata": {},
    "outputs": [],
    "source": [
     "# load beforehand\n",
     "pyl = LiftOver(\"hg38\", \"hg19\")\n",
-    "converter = Converter(\"hg38\", \"hg19\")"
+    "converter = Converter(Assembly.HG38, Assembly.HG19)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 15,
    "id": "b68a6af6-1a89-414f-b4f1-2378f3c4f50d",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "1.97 µs ± 72.9 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
+      "1.04 μs ± 27.1 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
      ]
     }
    ],
@@ -163,21 +166,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 16,
    "id": "e6643c38-f9f5-4ed6-a277-9642e731e6bc",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2.77 µs ± 103 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
+      "713 ns ± 9.94 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter.convert_coordinate(\"chr5\", 1404391, \"+\")"
+    "converter.convert_coordinate(\"chr5\", 1404391, 1404391, \"+\")"
    ]
   },
   {
@@ -198,15 +201,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 17,
    "id": "181231d8-3f00-407b-86a3-1ae268d4d931",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "303 ms ± 13.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "149 ms ± 2.79 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
@@ -217,21 +220,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 18,
    "id": "7822b8e7-939d-4b6d-85f6-514999c55602",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "62.6 ms ± 2.99 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
+      "8.95 ms ± 73.5 μs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter = Converter(\"hg19\", \"hg38\")"
+    "converter = Converter(Assembly.HG19, Assembly.HG38)"
    ]
   },
   {
@@ -244,15 +247,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 19,
    "id": "0ab6aeb8-88da-45e8-9efe-8b4a7825bcff",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "318 ms ± 15.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+      "151 ms ± 1.51 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
      ]
     }
    ],
@@ -264,22 +267,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 21,
    "id": "a014955a-5451-4b10-83bd-4d4843ddc227",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "57.8 ms ± 742 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
+      "8.68 ms ± 59.2 μs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter = Converter(\"hg19\", \"hg38\")\n",
-    "converter.convert_coordinate(\"chr5\", 1404391, \"+\")"
+    "converter = Converter(Assembly.HG19, Assembly.HG38)\n",
+    "converter.convert_coordinate(\"chr5\", 1404391, 1404391, \"+\")"
    ]
   },
   {
@@ -292,27 +295,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 22,
    "id": "a516e0a8-02b1-4ce5-8e69-3d0badcaffa4",
    "metadata": {},
    "outputs": [],
    "source": [
     "# load beforehand\n",
     "pyl = LiftOver(\"hg19\", \"hg38\")\n",
-    "converter = Converter(\"hg19\", \"hg38\")"
+    "converter = Converter(Assembly.HG19, Assembly.HG38)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 23,
    "id": "d433fee3-9c40-4633-be5e-2649b723968e",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2.16 µs ± 232 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
+      "1.06 μs ± 7.62 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
      ]
     }
    ],
@@ -323,29 +326,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 24,
    "id": "5bb82164-e123-47ae-a748-7d4c4898fcb2",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2.87 µs ± 65 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
+      "718 ns ± 1.6 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
      ]
     }
    ],
    "source": [
     "%%timeit\n",
-    "converter.convert_coordinate(\"chr5\", 1404391, \"+\")"
+    "converter.convert_coordinate(\"chr5\", 1404391, 1404391, \"+\")"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "liftovertest",
+   "display_name": "agct",
    "language": "python",
-   "name": "liftovertest"
+   "name": "agct"
   },
   "language_info": {
    "codemirror_mode": {
@@ -357,7 +360,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.13.2"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -135,3 +135,8 @@ mypy-init-return = true
 
 [tool.ruff.format]
 docstring-code-format = true
+
+[dependency-groups]
+dev = [
+    "ipykernel>=7.2.0",
+]