Merge pull request #204 from mcphersonlab/auto/conference-updates-20260612

Automated conference updates

Author: JacobKMcPherson

.github/workflows/update-conferences.yml

@@ -0,0 +1,49 @@
+name: Update conferences
+
+on:
+  schedule:
+    - cron: '0 6 1 * *' # monthly on the 1st at 06:00 UTC
+  workflow_dispatch: {}
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install requests beautifulsoup4 lxml
+
+      - name: Fetch conference pages
+        run: python3 scripts/fetch_conference_dates.py
+
+      - name: Prepare proposals
+        run: python3 scripts/prepare_conference_updates.py
+
+      - name: Select update candidates
+        run: python3 scripts/select_updates.py
+
+      - name: Apply updates
+        run: python3 scripts/apply_updates.py
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v5
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Automated conference updates
+          branch: auto/conference-updates
+          title: Automated conference updates
+          body: |
+            This PR was created automatically by the monthly conference update workflow. It contains updated start/end dates for conferences when confident matches were found on the official websites. Please review before merging.
+          labels: automated,conferences

research/_conferences_data.py

@@ -100,11 +100,11 @@
         "location": "Las Vegas, NV",
         "lat": 36.1699,
         "lon": -115.1398,
-        "start_date": "2027-01-27",
-        "end_date": "2027-01-29",
+        "start_date": "2026-01-28",
+        "end_date": "2026-01-30",
         "abstract_open": "",
         "abstract_close": "",
-        "abstract_note": "2027 dates TBD; check IMARI website",
+        "abstract_note": "Dates may change; check IMARI website for updates",
         "type": "Conference",
         "url": "https://imari.org",
         "projects": [
@@ -180,7 +180,7 @@
         "lat": 39.9526,
         "lon": -75.1652,
         "start_date": "2027-02-20",
-        "end_date": "2027-02-24",
+        "end_date": "2027-02-20",
         "abstract_open": "",
         "abstract_close": "",
         "abstract_note": "Abstract dates TBD; see Biophysical Society website for updates",
@@ -199,8 +199,8 @@
         "location": "San Diego, CA",
         "lat": 32.7157,
         "lon": -117.1611,
-        "start_date": "2027-03-21",
-        "end_date": "2027-03-24",
+        "start_date": "2026-03-24",
+        "end_date": "2026-03-24",
         "abstract_open": "",
         "abstract_close": "",
         "abstract_note": "Abstract dates TBD; check CROI website",
@@ -359,8 +359,8 @@
         "location": "Philadelphia, PA",
         "lat": 39.9526,
         "lon": -75.1652,
-        "start_date": "2026-05-17",
-        "end_date": "2026-05-20",
+        "start_date": "2026-09-22",
+        "end_date": "2026-09-23",
         "abstract_open": "2025-10-31",
         "abstract_close": "2026-01-09",
         "abstract_note": "",
@@ -379,8 +379,8 @@
         "location": "Washington, DC",
         "lat": 38.9072,
         "lon": -77.0369,
-        "start_date": "2026-06-11",
-        "end_date": "2026-06-15",
+        "start_date": "2027-06-22",
+        "end_date": "2027-06-25",
         "abstract_open": "2025-10-15",
         "abstract_close": "2026-01-21",
         "abstract_note": "Travel awards: Oct 15 - Dec 2, 2025; Abstracts: Dec 2, 2025 - Jan 21, 2026",
@@ -441,7 +441,7 @@
         "lat": 32.9342,
         "lon": -97.0781,
         "start_date": "2026-07-18",
-        "end_date": "2026-07-21",
+        "end_date": "2026-07-18",
         "abstract_open": "",
         "abstract_close": "",
         "abstract_note": "",
@@ -551,7 +551,7 @@
         "location": "Houston, TX",
         "lat": 29.7174,
         "lon": -95.4018,
-        "start_date": "2026-09-14",
+        "start_date": "2026-09-15",
         "end_date": "2026-09-17",
         "abstract_open": "",
         "abstract_close": "",
@@ -588,8 +588,8 @@
         "location": "Lisbon, Portugal",
         "lat": 38.7223,
         "lon": -9.1393,
-        "start_date": "2026-09-22",
-        "end_date": "2026-09-24",
+        "start_date": "2026-04-26",
+        "end_date": "2026-04-26",
         "abstract_open": "2026-03-10",
         "abstract_close": "2026-03-31",
         "abstract_note": "",
@@ -679,7 +679,6 @@ def _format_conference_date(date_str, conference_name, field_name):
             f"Invalid {field_name} date {date_str!r} for conference {conference_name!r} in research/_conferences_data.py"
         ) from exc
 
-
 def format_conference_abstract_deadline(conference):
     if conference.get("abstract_open") and conference.get("abstract_close"):
         open_date = _format_conference_date(conference["abstract_open"], conference["name"], "abstract_open")
@@ -697,6 +696,59 @@ def format_conference_abstract_deadline(conference):
         "name": conf["name"],
         "abstract_display": format_conference_abstract_deadline(conf),
     }
-    for conf in conferences
+    for conf in sorted(conferences, key=lambda c: c.get("start_date") or "")
     if conf.get("url")
 }
+
+
+def _validate_conferences(conf_list):
+    """Run light validation on conference entries and raise helpful errors.
+
+    Checks performed:
+    - `start_date` and `end_date` parse as YYYY-MM-DD when present
+    - `start_date` is not after `end_date` when both present
+    - `lat` and `lon` are numeric when present
+    - `url` is present and non-empty
+    """
+    for conf in conf_list:
+        name = conf.get("name", "(unknown)")
+
+        # Dates
+        sd = conf.get("start_date")
+        ed = conf.get("end_date")
+        try:
+            if sd:
+                sd_dt = datetime.strptime(sd, "%Y-%m-%d")
+            else:
+                sd_dt = None
+            if ed:
+                ed_dt = datetime.strptime(ed, "%Y-%m-%d")
+            else:
+                ed_dt = None
+        except ValueError as exc:
+            raise ValueError(f"Invalid date for conference {name!r}: {exc}") from exc
+
+        if sd_dt and ed_dt and sd_dt > ed_dt:
+            raise ValueError(
+                f"Conference {name!r} has start_date {sd!r} after end_date {ed!r}"
+            )
+
+        # Coordinates
+        lat = conf.get("lat")
+        lon = conf.get("lon")
+        try:
+            if lat is not None:
+                float(lat)
+            if lon is not None:
+                float(lon)
+        except (TypeError, ValueError) as exc:
+            raise ValueError(f"Invalid coordinates for conference {name!r}: {exc}") from exc
+
+        # URL
+        url = conf.get("url")
+        if not url:
+            raise ValueError(f"Conference {name!r} is missing a URL field")
+
+
+# Run validation at import time so problems are visible early
+_validate_conferences(conferences)

scripts/apply_updates.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+"""Apply selected conference date updates to research/_conferences_data.py
+
+Expects /tmp/candidates.json to contain a mapping of conference name -> {current, proposed}.
+The script updates `start_date` and `end_date` fields in-place and prints a JSON summary.
+"""
+import json
+import re
+from pathlib import Path
+import sys
+
+CANDIDATES = Path('/tmp/candidates.json')
+TARGET = Path(__file__).resolve().parents[1] / 'research' / '_conferences_data.py'
+
+if not CANDIDATES.exists():
+    print(json.dumps({'error': 'candidates file not found'}))
+    sys.exit(0)
+
+data = json.load(open(CANDIDATES))
+if not data:
+    print(json.dumps({'updated': []}))
+    sys.exit(0)
+
+text = TARGET.read_text(encoding='utf8')
+orig_text = text
+updates = []
+
+for name, info in data.items():
+    proposed = info['proposed']
+    sd_new, ed_new = proposed
+    # find the name occurrence
+    name_token = f'"name": "{name.replace("\"", "\\\"")}"'
+    pos = text.find(name_token)
+    if pos == -1:
+        # try a more relaxed search (escaped characters)
+        pos = text.find(f'"name": "{name.split("(")[0].strip()}')
+    if pos == -1:
+        continue
+
+    # find opening brace of this dict
+    start_brace = text.rfind('{', 0, pos)
+    # find the end of the dict (first occurrence of '},' after pos)
+    end_brace = text.find('},', pos)
+    if end_brace == -1:
+        end_brace = text.find('\n}\n', pos)
+    if end_brace == -1:
+        continue
+
+    block = text[start_brace:end_brace+1]
+
+    # replace or insert start_date
+    sd_match = re.search(r'("start_date"\s*:\s*")([0-9\-]*)("\s*,?)', block)
+    if sd_match:
+        block = block[:sd_match.start(2)] + sd_new + block[sd_match.end(2):]
+    else:
+        # insert after the "name" line
+        name_line_end = block.find('\n', block.find('"name"'))
+        insert = '\n        "start_date": "' + sd_new + '",' 
+        block = block[:name_line_end+1] + insert + block[name_line_end+1:]
+
+    # replace or insert end_date
+    ed_match = re.search(r'("end_date"\s*:\s*")([0-9\-]*)("\s*,?)', block)
+    if ed_match:
+        block = block[:ed_match.start(2)] + ed_new + block[ed_match.end(2):]
+    else:
+        # try to insert after start_date line if present
+        sd_line = block.find('"start_date"')
+        if sd_line != -1:
+            sd_line_end = block.find('\n', sd_line)
+            insert2 = '\n        "end_date": "' + ed_new + '",' 
+            block = block[:sd_line_end+1] + insert2 + block[sd_line_end+1:]
+        else:
+            # fallback: insert after name line
+            name_line_end = block.find('\n', block.find('"name"'))
+            insert2 = '\n        "end_date": "' + ed_new + '",' 
+            block = block[:name_line_end+1] + insert2 + block[name_line_end+1:]
+
+    # apply the block replacement
+    text = text[:start_brace] + block + text[end_brace+1:]
+    updates.append({'name': name, 'proposed': proposed})
+
+if text != orig_text:
+    TARGET.write_text(text, encoding='utf8')
+
+print(json.dumps({'updated': updates}, indent=2))

scripts/fetch_conference_dates.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+"""Fetch each conference URL and try to extract date and abstract deadline hints.
+Produces a JSON-like report printed to stdout.
+"""
+import re
+import json
+import sys
+from urllib.parse import urlparse
+
+# Import conferences from repo
+import importlib.util
+from pathlib import Path
+
+# Load conferences from the repository file directly
+conf_path = Path(__file__).resolve().parents[1] / "research" / "_conferences_data.py"
+spec = importlib.util.spec_from_file_location("_conferences_data", str(conf_path))
+mod = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(mod)
+conferences = getattr(mod, "conferences")
+
+import requests
+from bs4 import BeautifulSoup
+
+YEARS = ["2024","2025","2026","2027","2028"]
+MONTH_RE = r"(?:January|February|March|April|May|June|July|August|September|October|November|December|Jan|Feb|Mar|Apr|Jun|Jul|Aug|Sep|Oct|Nov|Dec)"
+DATE_PATTERNS = [
+    re.compile(rf"({MONTH_RE}\s+\d{{1,2}}(?:[–\-]\d{{1,2}})?\,?\s*(?:{"|".join(YEARS)}))", re.I),
+    re.compile(rf"(\d{{4}}[\-–]\d{{4}})", re.I),
+    re.compile(rf"(20\d{{2}})"),
+]
+ABSTRACT_PAT = re.compile(r"abstract|abstracts|call for abstracts|submission deadline|abstract deadline|call for papers", re.I)
+
+session_results = []
+
+for conf in conferences:
+    url = conf.get("url")
+    name = conf.get("name")
+    entry = {"name": name, "url": url, "found_dates": [], "found_abstracts": []}
+    if not url:
+        session_results.append(entry)
+        continue
+    try:
+        r = requests.get(url, timeout=15, headers={"User-Agent": "mcphersonlab-bot/1.0"})
+        text = r.text
+    except Exception as e:
+        entry["error"] = str(e)
+        session_results.append(entry)
+        continue
+    soup = BeautifulSoup(text, "lxml")
+    visible = soup.get_text(separator="\n")
+    # Search for date patterns
+    for pat in DATE_PATTERNS:
+        for m in pat.finditer(visible):
+            span = visible[max(0, m.start()-80):m.end()+80].strip()
+            entry["found_dates"].append(span)
+            if len(entry["found_dates"])>8:
+                break
+        if len(entry["found_dates"])>0:
+            break
+    # Search for abstract-related snippets
+    for m in ABSTRACT_PAT.finditer(visible):
+        span = visible[max(0, m.start()-120):m.end()+120].strip()
+        entry["found_abstracts"].append(span)
+        if len(entry["found_abstracts"])>6:
+            break
+    session_results.append(entry)
+
+print(json.dumps(session_results, indent=2))