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add 66 autorefs
 modified: automated-issue-ref.ipynb modified: autoref/milestone.txt modified: autoref/missing_refs.txt modified: lineage_notes.txt modified: automated-issue-ref.ipynb
1 parent dd30483 commit 0e2f2c4

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‎automated-issue-ref.ipynb

Lines changed: 104 additions & 87 deletions
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@@ -2,7 +2,7 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 1,
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"id": "f64573a2",
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"metadata": {
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"scrolled": true
@@ -173,7 +173,14 @@
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"processed 1590 milestones\n",
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"processed 1600 milestones\n",
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"processed 1610 milestones\n",
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"processed 1620 milestones\n"
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"processed 1620 milestones\n",
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"processed 1630 milestones\n",
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"processed 1640 milestones\n",
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"processed 1650 milestones\n",
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"processed 1660 milestones\n",
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"processed 1670 milestones\n",
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"processed 1680 milestones\n",
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"processed 1690 milestones\n"
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]
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}
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],
@@ -288,6 +295,7 @@
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" di='sars-cov-2-variants/lineage-proposals'\n",
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" actual_milestone='\"'+real_milestone[0]+'\"'\n",
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" url=\"https://github.com/\"+di+\"/issues?q=milestone:\"+actual_milestone\n",
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" print(url)\n",
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" res=request.urlopen(url)\n",
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" rp=res.read()\n",
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" rp=rp.decode('utf-8')\n",
@@ -307,7 +315,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 3,
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"id": "f5b15585",
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"metadata": {},
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"outputs": [],
@@ -330,94 +338,103 @@
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": null,
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"id": "a56544a8",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
341-
"['KR.1.3', 'sars-cov-2-variants/lineage-proposals#1676']\n",
342-
"['LK.2.1', 'sars-cov-2-variants/lineage-proposals#1679']\n",
343-
"['MQ.2', 'sars-cov-2-variants/lineage-proposals#1822']\n",
344-
"['JN.1.7.9', 'sars-cov-2-variants/lineage-proposals#1253']\n",
345-
"['LB.1.2.2', 'sars-cov-2-variants/lineage-proposals#1792']\n",
346-
"['LB.1.2.3', 'sars-cov-2-variants/lineage-proposals#1730']\n",
347-
"['LB.1.4.3', 'sars-cov-2-variants/lineage-proposals#1911']\n",
348-
"['LB.1.7.1', 'sars-cov-2-variants/lineage-proposals#1641']\n",
349-
"['LB.1.7.3', 'sars-cov-2-variants/lineage-proposals#1555']\n",
350-
"['LB.1.9', 'sars-cov-2-variants/lineage-proposals#1874']\n",
351-
"['MG.1', 'sars-cov-2-variants/lineage-proposals#1623']\n",
352-
"['LP.1.2', 'sars-cov-2-variants/lineage-proposals#1664']\n",
353-
"['LP.4', 'sars-cov-2-variants/lineage-proposals#1607']\n",
354-
"['MU.1', 'sars-cov-2-variants/lineage-proposals#1646']\n",
355-
"['KP.2.3.3', 'sars-cov-2-variants/lineage-proposals#1618']\n",
356-
"['KP.2.3.5', 'sars-cov-2-variants/lineage-proposals#1645']\n",
357-
"['KP.2.3.6', 'sars-cov-2-variants/lineage-proposals#1582']\n",
358-
"['KP.2.20.1', 'sars-cov-2-variants/lineage-proposals#1723']\n",
359-
"['KP.2.22', 'sars-cov-2-variants/lineage-proposals#1502']\n",
360-
"['KP.2.23', 'sars-cov-2-variants/lineage-proposals#1502']\n",
361-
"['KP.2.24', 'sars-cov-2-variants/lineage-proposals#1502']\n",
362-
"['MC.2', 'sars-cov-2-variants/lineage-proposals#1707']\n",
363-
"['MC.2.1', 'sars-cov-2-variants/lineage-proposals#1707']\n",
364-
"['MC.3', 'sars-cov-2-variants/lineage-proposals#1733']\n",
365-
"['MC.4', 'sars-cov-2-variants/lineage-proposals#1772']\n",
366-
"['MC.5', 'sars-cov-2-variants/lineage-proposals#1790']\n",
367-
"['MC.7', 'sars-cov-2-variants/lineage-proposals#1695']\n",
368-
"['MC.8.1', 'sars-cov-2-variants/lineage-proposals#1779']\n",
369-
"['MC.11.1', 'sars-cov-2-variants/lineage-proposals#1857']\n",
370-
"['MC.12', 'sars-cov-2-variants/lineage-proposals#1865']\n",
371-
"['MC.14', 'sars-cov-2-variants/lineage-proposals#1815']\n",
372-
"['MM.1', 'sars-cov-2-variants/lineage-proposals#1624']\n",
373-
"['MM.2', 'sars-cov-2-variants/lineage-proposals#1716']\n",
374-
"['MK.1', 'sars-cov-2-variants/lineage-proposals#1605']\n",
375-
"['MK.2', 'sars-cov-2-variants/lineage-proposals#1606']\n",
376-
"['MK.3', 'sars-cov-2-variants/lineage-proposals#1655']\n",
377-
"['KP.3.1.8', 'sars-cov-2-variants/lineage-proposals#1615']\n",
378-
"['LW.1.1', 'sars-cov-2-variants/lineage-proposals#1776']\n",
379-
"['KP.3.3.2', 'sars-cov-2-variants/lineage-proposals#1673']\n",
380-
"['ML.1', 'sars-cov-2-variants/lineage-proposals#1683']\n",
381-
"['KP.3.4.1', 'sars-cov-2-variants/lineage-proposals#1576']\n",
382-
"['KP.3.5', 'sars-cov-2-variants/lineage-proposals#1630']\n",
383-
"['KP.3.6', 'sars-cov-2-variants/lineage-proposals#1748']\n",
384-
"['KP.6', 'sars-cov-2-variants/lineage-proposals#1682']\n",
385-
"['KS.1.3', 'sars-cov-2-variants/lineage-proposals#1535']\n",
386-
"['KS.1.4', 'sars-cov-2-variants/lineage-proposals#1752']\n",
387-
"['LU.2.1', 'sars-cov-2-variants/lineage-proposals#1751']\n",
388-
"['LU.2.1.1', 'sars-cov-2-variants/lineage-proposals#1751']\n",
389-
"['LU.2.2', 'sars-cov-2-variants/lineage-proposals#1830']\n",
390-
"['LF.5', 'sars-cov-2-variants/lineage-proposals#1627']\n",
391-
"['LF.8', 'sars-cov-2-variants/lineage-proposals#1863']\n",
392-
"['LF.8.1', 'sars-cov-2-variants/lineage-proposals#1863']\n",
393-
"['LF.8.1.1', 'sars-cov-2-variants/lineage-proposals#1863']\n",
394-
"['LF.9', 'sars-cov-2-variants/lineage-proposals#1718']\n",
395-
"['LF.9.1', 'sars-cov-2-variants/lineage-proposals#1718']\n",
396-
"['JN.1.16.4', 'sars-cov-2-variants/lineage-proposals#1702']\n",
397-
"['MT.1', 'sars-cov-2-variants/lineage-proposals#1702']\n",
398-
"['JN.1.16.5', 'sars-cov-2-variants/lineage-proposals#1253']\n",
399-
"['LZ.2', 'sars-cov-2-variants/lineage-proposals#1089']\n",
400-
"['MA.1.1', 'sars-cov-2-variants/lineage-proposals#1761']\n",
401-
"['MA.1.1.1', 'sars-cov-2-variants/lineage-proposals#1761']\n",
402-
"['MN.1', 'sars-cov-2-variants/lineage-proposals#1685']\n",
403-
"['MS.1', 'sars-cov-2-variants/lineage-proposals#1692']\n",
404-
"['JN.1.48.3', 'sars-cov-2-variants/lineage-proposals#1253']\n",
405-
"['ME.1', 'sars-cov-2-variants/lineage-proposals#1657']\n",
406-
"['JN.1.59.1', 'sars-cov-2-variants/lineage-proposals#1771']\n",
407-
"['JN.1.63', 'sars-cov-2-variants/lineage-proposals#1513']\n",
408-
"['JN.1.63.1', 'sars-cov-2-variants/lineage-proposals#1513']\n",
409-
"['JN.1.67.1', 'sars-cov-2-variants/lineage-proposals#1253']\n",
410-
"['MP.1', 'sars-cov-2-variants/lineage-proposals#1782']\n",
411-
"['MP.1.1', 'sars-cov-2-variants/lineage-proposals#1782']\n",
412-
"['JH.2', '#2068']\n",
413-
"['XDR.1.1', 'sars-cov-2-variants/lineage-proposals#1795']\n",
414-
"['XDV.1.1', 'sars-cov-2-variants/lineage-proposals#1820']\n",
415-
"['XDV.1.2', 'sars-cov-2-variants/lineage-proposals#1617']\n",
416-
"['XDV.1.2.1', 'sars-cov-2-variants/lineage-proposals#1617']\n",
417-
"['XDV.1.3', 'sars-cov-2-variants/lineage-proposals#1597']\n",
418-
"['XDV.1.5', 'sars-cov-2-variants/lineage-proposals#1840']\n",
419-
"['XDV.1.10', 'sars-cov-2-variants/lineage-proposals#1849']\n",
420-
"['XEC.1', 'sars-cov-2-variants/lineage-proposals#1869']\n"
349+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KR.1.4\"\n",
350+
"['KR.1.4', 'sars-cov-2-variants/lineage-proposals#1670']\n",
351+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"JN.1.59.1+NK.1+NL.1\"\n",
352+
"['NL.1', 'sars-cov-2-variants/lineage-proposals#1771']\n",
353+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LP.5\"\n",
354+
"['LP.5', 'sars-cov-2-variants/lineage-proposals#1893']\n",
355+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LP.6\"\n",
356+
"['LP.6', 'sars-cov-2-variants/lineage-proposals#1753']\n",
357+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LP.7\"\n",
358+
"['LP.7', 'sars-cov-2-variants/lineage-proposals#1729']\n",
359+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MU.2.1\"\n",
360+
"['MU.2.1', 'sars-cov-2-variants/lineage-proposals#1777']\n",
361+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.2.1\"\n",
362+
"['KP.2.2.1', 'sars-cov-2-variants/lineage-proposals#1662']\n",
363+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.2.2\"\n",
364+
"['KP.2.2.2', 'sars-cov-2-variants/lineage-proposals#1643']\n",
365+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"NM.1\"\n",
366+
"['NM.1', 'sars-cov-2-variants/lineage-proposals#1975']\n",
367+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.3.8\"\n",
368+
"['KP.2.3.8', 'sars-cov-2-variants/lineage-proposals#1735']\n",
369+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.3.9+NG.1\"\n",
370+
"['KP.2.3.9', 'sars-cov-2-variants/lineage-proposals#1742']\n",
371+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.3.9+NG.1\"\n",
372+
"['NG.1', 'sars-cov-2-variants/lineage-proposals#1742']\n",
373+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.3.10\"\n",
374+
"['KP.2.3.10', 'sars-cov-2-variants/lineage-proposals#1834']\n",
375+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"JN.1.59.1+NK.1+NL.1\"\n",
376+
"['NK.1', 'sars-cov-2-variants/lineage-proposals#1771']\n",
377+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.3.11\"\n",
378+
"['KP.2.3.11', 'sars-cov-2-variants/lineage-proposals#1594']\n",
379+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.6.1\"\n",
380+
"['KP.2.6.1', 'sars-cov-2-variants/lineage-proposals#1757']\n",
381+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.25.1\"\n",
382+
"['KP.2.25.1', 'sars-cov-2-variants/lineage-proposals#1699']\n",
383+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.25.2\"\n",
384+
"['KP.2.25.2', 'sars-cov-2-variants/lineage-proposals#1768']\n",
385+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.25.3\"\n",
386+
"['KP.2.25.3', 'sars-cov-2-variants/lineage-proposals#1649']\n",
387+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.2.26\"\n",
388+
"['KP.2.26', 'sars-cov-2-variants/lineage-proposals#2141']\n",
389+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"JN.1.1.3+JN.1.6.1+JN.1.18+JN.1.1.5+KP.1.1+KP.2+JN.1.26,+JN.1.4.4,+JN.1.8.2,+JN.1.16.1+JN.1.30.1+KU.2+KP.4.2+KP.4.1+LA.2+LB.1+JN.1.24.1+KP.2.9+LE.1+LE.1.1+JN.1.48.2+JN.1.39.1+JQ.2.1.1,+LM.1+JN.1.18.5+LU.1+MQ.1+LF.6+LZ.2+KP.2.27+JN.1.11.2\"\n",
390+
"['KP.2.27', 'sars-cov-2-variants/lineage-proposals#1089']\n",
391+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.1.1\"\n",
392+
"['MC.1.1', 'sars-cov-2-variants/lineage-proposals#1932']\n",
393+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.10.1\"\n",
394+
"['MC.10.1', 'sars-cov-2-variants/lineage-proposals#1946']\n",
395+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.10.2\"\n",
396+
"['MC.10.2', 'sars-cov-2-variants/lineage-proposals#2015']\n",
397+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.17\"\n",
398+
"['MC.17', 'sars-cov-2-variants/lineage-proposals#1989']\n",
399+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.18\"\n",
400+
"['MC.18', 'sars-cov-2-variants/lineage-proposals#2075']\n",
401+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.19\"\n",
402+
"['MC.19', 'sars-cov-2-variants/lineage-proposals#1809']\n",
403+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"MC.20\"\n",
404+
"['MC.20', 'sars-cov-2-variants/lineage-proposals#2085']\n",
405+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.1.9\"\n",
406+
"['KP.3.1.9', 'sars-cov-2-variants/lineage-proposals#2171']\n",
407+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.1.10\"\n",
408+
"['KP.3.1.10', 'sars-cov-2-variants/lineage-proposals#1853']\n",
409+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.2.6\"\n",
410+
"['KP.3.2.6', 'sars-cov-2-variants/lineage-proposals#1899']\n",
411+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.2.7\"\n",
412+
"['KP.3.2.7', 'sars-cov-2-variants/lineage-proposals#2180']\n",
413+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.2.8\"\n",
414+
"['KP.3.2.8', 'sars-cov-2-variants/lineage-proposals#2081']\n",
415+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.3.7\"\n",
416+
"['KP.3.7', 'sars-cov-2-variants/lineage-proposals#1749']\n",
417+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"KP.4.2.5\"\n",
418+
"['KP.4.2.5', 'sars-cov-2-variants/lineage-proposals#1667']\n",
419+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"JN.1.1.3+JN.1.6.1+JN.1.18+JN.1.1.5+KP.1.1+KP.2+JN.1.26,+JN.1.4.4,+JN.1.8.2,+JN.1.16.1+JN.1.30.1+KU.2+KP.4.2+KP.4.1+LA.2+LB.1+JN.1.24.1+KP.2.9+LE.1+LE.1.1+JN.1.48.2+JN.1.39.1+JQ.2.1.1,+LM.1+JN.1.18.5+LU.1+MQ.1+LF.6+LZ.2+KP.2.27+JN.1.11.2\"\n",
420+
"['JN.1.11.2', 'sars-cov-2-variants/lineage-proposals#1089']\n",
421+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"NJ.1\"\n",
422+
"['NJ.1', 'sars-cov-2-variants/lineage-proposals#2068']\n",
423+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"NC.1\"\n",
424+
"['NC.1', 'sars-cov-2-variants/lineage-proposals#1995']\n",
425+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LF.3.1+LF.3.1.1+LF.3.1.2\"\n",
426+
"['LF.3.1.2', 'sars-cov-2-variants/lineage-proposals#1558']\n",
427+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LF.7.1.1\"\n",
428+
"['LF.7.1.1', 'sars-cov-2-variants/lineage-proposals#2063']\n",
429+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LF.7.1.2+LF.7.2.1\"\n",
430+
"['LF.7.2.1', 'sars-cov-2-variants/lineage-proposals#2067']\n",
431+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"LF.7.4\"\n",
432+
"['LF.7.4', 'sars-cov-2-variants/lineage-proposals#1996']\n",
433+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"ND.1.1\"\n",
434+
"['ND.1.1', 'sars-cov-2-variants/lineage-proposals#1982']\n",
435+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"ND.2\"\n",
436+
"['ND.2', 'sars-cov-2-variants/lineage-proposals#1929']\n",
437+
"https://github.com/sars-cov-2-variants/lineage-proposals/issues?q=milestone:\"ND.3\"\n"
421438
]
422439
}
423440
],
@@ -444,7 +461,7 @@
444461
" if not('#' in line or 'issues/' in line):\n",
445462
" if title in milestone_title_dict:\n",
446463
" # this time we need to deal with the milestone \n",
447-
" \n",
464+
" #print(title)\n",
448465
" issue_num=read_milestone_issues(title)\n",
449466
" if issue_num!='0':\n",
450467
" if 'sars' in issue_num:\n",
@@ -474,7 +491,7 @@
474491
},
475492
{
476493
"cell_type": "code",
477-
"execution_count": 6,
494+
"execution_count": 10,
478495
"id": "1c9369e1",
479496
"metadata": {},
480497
"outputs": [
@@ -484,7 +501,7 @@
484501
"text": [
485502
"Add 1 references from cov-lineages/pango-designation.\n",
486503
"Upgrade 0 references from cov-lineages/pango-designation.\n",
487-
"Add 85 references from sars-cov-2-variants/lineage-proposals.\n"
504+
"Add 79 references from sars-cov-2-variants/lineage-proposals.\n"
488505
]
489506
}
490507
],

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