gismap 0.2.1__py3-none-any.whl → 0.3.0__py3-none-any.whl

gismap/lab/{lab.py → labmap.py}

@@ -17,14 +17,21 @@ from gismap.sources.multi import (
     regroup_publications,
 )
 from gismap.lab.expansion import proper_prospects
-from gismap.lab.filters import author_taboo_filter, publication_taboo_filter, publication_size_filter
-from gismap.lab.graph import lab2graph
+from gismap.lab.filters import (
+    author_taboo_filter,
+    publication_taboo_filter,
+    publication_size_filter,
+    publication_oneword_filter,
+)
+from gismap.gisgraphs.builder import make_vis
 
 
-class Lab(MixInIO):
+class LabMap(MixInIO):
     """
     Abstract class for labs.
 
+    Actual Lab classes can be created by implementing the `_author_iterator` method.
+
     Labs can be saved with the `dump` method and loaded with the `load` method.
 
     Parameters
@@ -33,23 +40,31 @@ class Lab(MixInIO):
         Name of the lab. Can be set as class or instance attribute.
     dbs: :class:`list`, default=[:class:`~gismap.sources.hal.HAL`, :class:`~gismap.sources.dblp.DBLP`]
         List of DB sources to use.
+
+
+    Attributes
+    -----------
+
     author_selectors: :class:`list`
-        Author filter. Default: minimal filtering.
+        Author filters. Default: minimal filtering.
     publication_selectors: :class:`list`
-        Publication filter. Default: less than 10 authors to remove black holes.
+        Publication filter. Default: less than 10 authors, not an editorial, at least two words in the title.
     """
 
     name = None
     dbs = default_dbs
 
-    def __init__(
-        self, name=None, dbs=None):
+    def __init__(self, name=None, dbs=None):
         if name is not None:
             self.name = name
         if dbs is not None:
             self.dbs = list_of_objects(dbs, db_dict, default=default_dbs)
         self.author_selectors = [author_taboo_filter()]
-        self.publication_selectors = [publication_size_filter(), publication_taboo_filter()]
+        self.publication_selectors = [
+            publication_size_filter(),
+            publication_taboo_filter(),
+            publication_oneword_filter(),
+        ]
         self.authors = None
         self.publications = None
 
@@ -82,6 +97,8 @@ class Lab(MixInIO):
                 self.authors[author.key] = author
             if author.metadata.img is None:
                 author.auto_img()
+            if author.metadata.group is None:
+                author.metadata.group = self.name
 
     def update_publis(self, desc="Publications information"):
         """
@@ -94,7 +111,9 @@ class Lab(MixInIO):
         pubs = dict()
         for author in tqdm(self.authors.values(), desc=desc):
             pubs.update(
-                author.get_publications(clean=False, selector=self.publication_selectors)
+                author.get_publications(
+                    clean=False, selector=self.publication_selectors
+                )
             )
         regroup_authors(self.authors, pubs)
         self.publications = regroup_publications(pubs)
@@ -118,7 +137,9 @@ class Lab(MixInIO):
             author.auto_img()
             author.metadata.group = group
             pubs.update(
-                author.get_publications(clean=False, selector=self.publication_selectors)
+                author.get_publications(
+                    clean=False, selector=self.publication_selectors
+                )
             )
 
         for pub in self.publications.values():
@@ -132,7 +153,7 @@ class Lab(MixInIO):
         return None
 
     def html(self, **kwargs):
-        return lab2graph(self, **kwargs)
+        return make_vis(self, **kwargs)
 
     def save_html(self, name=None, **kwargs):
         if name is None:
@@ -145,7 +166,7 @@ class Lab(MixInIO):
         display(HTML(self.html(**kwargs)))
 
 
-class ListLab(Lab):
+class ListMap(LabMap):
     """
     Simplest way to create a lab: with a list of names.
 

gismap/lab_examples/cedric.py

@@ -0,0 +1,46 @@
+import requests
+from bs4 import BeautifulSoup as Soup
+from gismap.lab.labmap import LabMap
+from gismap.lab.lab_author import AuthorMetadata, LabAuthor
+from gismap.utils.requests import get
+
+
+class CedricMap(LabMap):
+    """
+    Class for handling a CNAM Cedric team from its name.
+    Default to `roc` team.
+    """
+    name = "roc"
+    base_url = "https://cedric.cnam.fr"
+
+    def _author_iterator(self):
+        soup = Soup(get(f"{self.base_url}/equipes/{self.name}/"), features="lxml")
+        searchers = [li.a for ul in soup.find('div', {'id': 'annuaire'})('ul')[:3] for li in ul('li')]
+        done = set()
+        for searcher in searchers:
+            name = searcher.text.split('(')[0].strip()
+            if name in done:
+                continue
+            url = f"{self.base_url}{searcher['href']}"
+            sousoup = Soup(get(url), features="lxml")
+            img = sousoup.find('img', {'class': 'photo'})['src']
+            response = requests.head(img, allow_redirects=True)
+            if int(response.headers.get("Content-Length")) < 3000:
+                img = None
+            done.add(name)
+            yield LabAuthor(name=name, metadata=AuthorMetadata(url=url, img=img, group=self.name.upper()))
+
+
+class CedricFull(LabMap):
+    """
+    Class for handling all CNAM Cedric teams using `https://cedric.cnam.fr/equipes` to get team names.
+    """
+    name = "Cedric"
+
+    def _author_iterator(self):
+        base = "https://cedric.cnam.fr/equipes/"
+        soup =  Soup(get(base), features="lxml")
+        teams = {a['href'].split('/')[-2] for a in soup('a') if base in a.get('href', "") and len(a['href'])>len(base)}
+        for team in teams:
+            for author in CedricMap(name=team)._author_iterator():
+                yield author

gismap/lab_examples/lincs.py

@@ -0,0 +1,44 @@
+from bs4 import BeautifulSoup as Soup
+from gismap.utils.requests import get
+from gismap.lab.filters import re_filter
+from gismap.lab import LabAuthor, Map
+
+
+ghosts = [
+    "Altman",
+    "Lelarge",
+    "Teixera",
+    "Friedman",
+    "Fdida",
+    "Blaszczyszyn",
+    "Jacquet",
+    "Panafieu",
+    "Bušić",
+]
+no_ghost = re_filter(ghosts)
+
+
+class LINCS(Map):
+    name = "LINCS"
+
+    def _author_iterator(self):
+        soup = Soup(get("https://www.lincs.fr/people/"), features="lxml")
+        for entry in soup.main("div", class_="trombinoscope-row"):
+            cols = entry("div")
+            name = cols[1].text
+            if not no_ghost(name):
+                continue
+            img = cols[0].img["src"]
+            url = cols[-1].a
+            if url:
+                url = url.get("href")
+            group = cols[2]("a")
+            if group:
+                group = group[-1].text
+            else:
+                group = "External"
+            author = LabAuthor(name)
+            author.metadata.img = img
+            author.metadata.group = group
+            author.metadata.url = url
+            yield author

gismap/{lab → lab_examples}/lip6.py

@@ -1,12 +1,12 @@
 from bs4 import BeautifulSoup as Soup
 import re
 
-from gismap.lab.lab import Lab
+from gismap.lab.labmap import LabMap
 from gismap.lab.lab_author import AuthorMetadata, LabAuthor
 from gismap.utils.requests import get
 
 
-class Lip6Lab(Lab):
+class Lip6Map(LabMap):
     """
     Class for handling a LIP6 team using `https://www.lip6.fr/recherche/team_membres.php?acronyme=*team_acronym*` as entry point.
     Default to `NPA` team.
@@ -25,10 +25,14 @@ class Lip6Lab(Lab):
             previous = a.find_previous_sibling()
             if previous is not None and "user" in previous.get("class", []):
                 metadata.url = previous["href"].strip()
+            fiche = "https://www.lip6.fr/" + a["href"].split("/", 1)[1]
+            img = Soup(get(fiche), "lxml").img
+            if img and "reflet" in img["class"] and "noPhoto" not in img["src"]:
+                metadata.img = "https://www.lip6.fr/" + img["src"].split("/", 1)[1]
             yield LabAuthor(name=name, metadata=metadata)
 
 
-class Lip6(Lip6Lab):
+class Lip6Full(Lip6Map):
     """
     Class for handling all LIP6 teams using `https://www.lip6.fr/informations/annuaire.php` to get team names.
     """
@@ -40,5 +44,5 @@ class Lip6(Lip6Lab):
         for group in groups.findall(
             get("https://www.lip6.fr/informations/annuaire.php")
         ):
-            for author in Lip6Lab(name=group)._author_iterator():
+            for author in Lip6Map(name=group)._author_iterator():
                 yield author

gismap/{lab → lab_examples}/toulouse.py

@@ -1,6 +1,6 @@
 import re
 from bs4 import BeautifulSoup as Soup
-from gismap.lab.lab import Lab
+from gismap.lab.labmap import LabMap
 from gismap.lab.lab_author import AuthorMetadata, LabAuthor
 from gismap.utils.requests import get
 
@@ -9,7 +9,7 @@ def name_changer(name, rosetta):
     return rosetta.get(name, name)
 
 
-class LaasLab(Lab):
+class LaasMap(LabMap):
     """
     Class for handling a LAAS team from its name.
     Default to `sara` team.
@@ -29,10 +29,24 @@ class LaasLab(Lab):
                 if "public_avatar" in a.img["class"]
                 else None
             )
-            yield LabAuthor(name=name, metadata=AuthorMetadata(url=url, img=img))
+            yield LabAuthor(name=name, metadata=AuthorMetadata(url=url, img=img, group=self.name.upper()))
 
 
-class Solace(Lab):
+class LaasFull(LabMap):
+    """
+    Class for handling all LAAS teams using `https://www.laas.fr/fr/equipes/` to get team names.
+    """
+    name = "LAAS"
+
+    def _author_iterator(self):
+        soup = Soup(get("https://www.laas.fr/fr/equipes/"), features="lxml")
+        teams = [a['href'].split('/')[-2] for a in soup('a', {'class': "badge"})]
+        for team in teams:
+            for author in LaasMap(name=team)._author_iterator():
+                yield author
+
+
+class SolaceMap(LabMap):
     """
     Class for handling the Solace team (`https://solace.cnrs.fr`).
     """
@@ -41,8 +55,11 @@ class Solace(Lab):
     regex = re.compile(r"<li>(.*?)(,| \(|</li>)")
 
     def _author_iterator(self):
-        html = get("https://solace.cnrs.fr/people.html")
+        html = get("https://solace.cnrs.fr/people.html", verify=False)
         for name, _ in self.regex.findall(html):
             soup = Soup(name, features="lxml")
             url = soup.a["href"] if soup.a else None
-            yield LabAuthor(name=soup.text.strip(), metadata=AuthorMetadata(url=url))
+            yield LabAuthor(
+                name=soup.text.strip(),
+                metadata=AuthorMetadata(url=url, group=self.name.upper()),
+            )

gismap/sources/dblp.py

@@ -72,23 +72,6 @@ class DBLP(DB):
             Papers available in DBLP.
         wait: :class:`bool`
             Wait a bit to avoid 429.
-
-        Examples
-        --------
-
-        >>> fabien = DBLPAuthor('Fabien Mathieu', key='66/2077')
-        >>> publications = sorted(DBLP.from_author(fabien),
-        ...                 key=lambda p: p.title)
-        >>> publications[0] # doctest:  +NORMALIZE_WHITESPACE
-        DBLPPublication(title='Achievable catalog size in peer-to-peer video-on-demand systems.',
-        authors=[DBLPAuthor(name='Yacine Boufkhad', key='75/5742'), DBLPAuthor(name='Fabien Mathieu', key='66/2077'),
-        DBLPAuthor(name='Fabien de Montgolfier', key='57/6313'), DBLPAuthor(name='Diego Perino', key='03/3645'),
-        DBLPAuthor(name='Laurent Viennot', key='v/LaurentViennot')],
-        venue='IPTPS', type='conference', year=2008, key='conf/iptps/BoufkhadMMPV08')
-        >>> publications[-1] # doctest:  +NORMALIZE_WHITESPACE
-        DBLPPublication(title='Upper Bounds for Stabilization in Acyclic Preference-Based Systems.',
-        authors=[DBLPAuthor(name='Fabien Mathieu', key='66/2077')], venue='SSS', type='conference', year=2007,
-        key='conf/sss/Mathieu07')
         """
         r = get(f"https://dblp.org/pid/{a.key}.xml")
         soup = Soup(r, features="xml")
@@ -100,6 +83,21 @@ class DBLP(DB):
 
 @dataclass(repr=False)
 class DBLPAuthor(Author, DBLP):
+    """
+    Examples
+    --------
+
+    >>> fabien = DBLPAuthor('Fabien Mathieu', key='66/2077')
+    >>> publications = sorted(fabien.get_publications(),
+    ...                 key=lambda p: p.title)
+    >>> publications[0].url # doctest:  +NORMALIZE_WHITESPACE
+     'https://dblp.org/rec/conf/iptps/BoufkhadMMPV08.html'
+    >>> publications[-1] # doctest:  +NORMALIZE_WHITESPACE
+    DBLPPublication(title='Upper Bounds for Stabilization in Acyclic Preference-Based Systems.',
+    authors=[DBLPAuthor(name='Fabien Mathieu', key='66/2077')], venue='SSS', type='conference', year=2007,
+    key='conf/sss/Mathieu07')
+
+    """
     key: str
     aliases: list = field(default_factory=list)
 

gismap/sources/hal.py

@@ -44,8 +44,7 @@ class HAL(DB):
         >>> HAL.search_author("Ana Busic")
         [HALAuthor(name='Ana Busic', key='anabusic')]
         >>> HAL.search_author("Potop-Butucaru Maria")  # doctest:  +NORMALIZE_WHITESPACE
-        [HALAuthor(name='Potop-Butucaru Maria', key='858256', key_type='pid'),
-        HALAuthor(name='Potop-Butucaru Maria', key='841868', key_type='pid')]
+        [HALAuthor(name='Potop-Butucaru Maria', key='841868', key_type='pid')]
         >>> diego = HAL.search_author("Diego Perino")
         >>> diego  # doctest:  +NORMALIZE_WHITESPACE
         [HALAuthor(name='Diego Perino', key='847558', key_type='pid'),
@@ -134,12 +133,12 @@ class HAL(DB):
 
         >>> maria = HAL.search_author('Maria Potop-Butucaru')
         >>> maria  # doctest: +NORMALIZE_WHITESPACE
-        [HALAuthor(name='Maria Potop-Butucaru', key='858256', key_type='pid'),
-        HALAuthor(name='Maria Potop-Butucaru', key='841868', key_type='pid')]
-        >>> len(HAL.from_author(maria[0]))
-        26
-        >>> len(maria[1].get_publications())
-        123
+        [HALAuthor(name='Maria Potop-Butucaru', key='841868', key_type='pid')]
+        >>> n_pubs = len(HAL.from_author(maria[0]))
+        >>> n_pubs > 200
+        True
+        >>> n_pubs == len(maria[0].get_publications())
+        True
 
         Note: an error is raised if not enough data is provided
 
@@ -173,6 +172,9 @@ class HAL(DB):
         r = get(api, params=params)
         response = json.loads(r)["response"]
         res = [HALPublication.from_json(r) for r in response.get("docs", [])]
+        if len(res) == 0 and a.key_type != "fullname":
+            name = a.name
+            return HAL.from_author(HALAuthor(name=name, key=name, key_type="fullname"))
         return res
 
 
@@ -185,6 +187,13 @@ class HALAuthor(Author, HAL):
     _img: str = None
     _cv: bool = None
 
+    def __post_init__(self):
+        if self.key and self.key_type is None:
+            if self.key.isdigit():
+                self.key_type = "pid"
+            if " " in self.key:
+                self.key_type = "fullname"
+
     def check_cv(self):
         if self.key_type is not None:
             self._cv = False

gismap/sources/models.py

@@ -29,3 +29,10 @@ class DB(LazyRepr):
     @classmethod
     def from_author(cls, a):
         raise NotImplementedError
+
+
+def db_class_to_auth_class(db_class):
+    for subclass in Author.__subclasses__():
+        if db_class in subclass.__mro__:
+            return subclass
+    return None

gismap/sources/multi.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass, field
-from bof.fuzz import Process
+from bof.fuzz import jit_square_factors
+from bof.feature_extraction import CountVectorizer
 import numpy as np
 
 from gismap.sources.models import Publication, Author
@@ -52,8 +53,13 @@ class SourcedAuthor(Author):
     def get_publications(self, clean=True, selector=None):
         if selector is None:
             selector = []
+        if not isinstance(selector, list):
+            selector = [selector]
         res = {
-            p.key: p for a in self.sources for p in a.get_publications() if all(f(p) for f in selector)
+            p.key: p
+            for a in self.sources
+            for p in a.get_publications()
+            if all(f(p) for f in selector)
         }
         if clean:
             regroup_authors({self.key: self}, res)
@@ -132,7 +138,9 @@ def regroup_authors(auth_dict, pub_dict):
     }
 
     for pub in pub_dict.values():
-        pub.authors = [redirection.get(a.key, a) for a in pub.authors]
+        pub.authors = [
+            redirection.get(a.key, redirection.get(a.name, a)) for a in pub.authors
+        ]
 
 
 def regroup_publications(pub_dict, threshold=85, length_impact=0.05, n_range=5):
@@ -153,20 +161,22 @@ def regroup_publications(pub_dict, threshold=85, length_impact=0.05, n_range=5):
     :class:`dict`
         Unified publications.
     """
+    if len(pub_dict) == 0:
+        return dict()
     pub_list = [p for p in pub_dict.values()]
     res = dict()
-
-    if pub_list:
-
-        p = Process(length_impact=length_impact, n_range=n_range)
-        p.fit([paper.title for paper in pub_list])
-
-        done = np.zeros(len(pub_list), dtype=bool)
-        for i, paper in enumerate(pub_list):
-            if done[i]:
-                continue
-            locs = np.where(p.transform([paper.title])[0, :] > threshold)[0]
-            pub = SourcedPublication.from_sources([pub_list[i] for i in locs])
-            res[pub.key] = pub
-            done[locs] = True
+    vectorizer = CountVectorizer(n_range=n_range)
+    x = vectorizer.fit_transform([p.title for p in pub_list])
+    y = x.T.tocsr()
+    jc_matrix = jit_square_factors(
+        x.indices, x.indptr, y.indices, y.indptr, len(pub_list), length_impact
+    )
+    done = np.zeros(len(pub_list), dtype=bool)
+    for i, paper in enumerate(pub_list):
+        if done[i]:
+            continue
+        locs = np.where(jc_matrix[i, :] > threshold)[0]
+        pub = SourcedPublication.from_sources([pub_list[i] for i in locs])
+        res[pub.key] = pub
+        done[locs] = True
     return res

gismap/utils/requests.py

@@ -13,7 +13,7 @@ session.headers.update(
 )
 
 
-def get(url, params=None, n_trials=10):
+def get(url, params=None, n_trials=10, verify=True):
     """
     Parameters
     ----------
@@ -21,6 +21,8 @@ def get(url, params=None, n_trials=10):
         Entry point to fetch.
     params: :class:`dict`, optional
         Get arguments (appended to URL).
+    verify: :class:`bool`, optional
+        Verify certificates.
 
     Returns
     -------
@@ -29,7 +31,7 @@ def get(url, params=None, n_trials=10):
     """
     for attempt in range(n_trials):
         try:
-            r = session.get(url, params=params)
+            r = session.get(url, params=params, verify=verify)
             if r.status_code == 429:
                 try:
                     t = int(r.headers["Retry-After"])

{gismap-0.2.1.dist-info → gismap-0.3.0.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: gismap
-Version: 0.2.1
-Summary: GISMAP leverages DBLP and HAL databases to provide cartography tools for you and your lab.
+Version: 0.3.0
+Summary: GisMap leverages DBLP and HAL databases to provide cartography tools for you and your lab.
 Project-URL: Repository, https://github.com/balouf/gismap
 Project-URL: Documentation, https://balouf.github.io/gismap
 Author-email: Fabien Mathieu <fabien.mathieu@normalesup.org>
@@ -10,8 +10,11 @@ License-Expression: MIT
 License-File: AUTHORS.md
 Requires-Python: >=3.10
 Requires-Dist: bof>=0.3.5
+Requires-Dist: distinctipy>=1.3.4
+Requires-Dist: domonic>=0.9.13
 Requires-Dist: gismo>=0.5.2
 Requires-Dist: ipykernel>=6.30.1
+Requires-Dist: ipywidgets>=8.1.8
 Requires-Dist: tqdm>=4.67.1
 Description-Content-Type: text/markdown
 
@@ -19,12 +22,13 @@ Description-Content-Type: text/markdown
 
 
 [![PyPI Status](https://img.shields.io/pypi/v/gismap.svg)](https://pypi.python.org/pypi/gismap)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/balouf/gismap/HEAD?urlpath=%2Fdoc%2Ftree%2Fbinder%2Finteractive.ipynb)
 [![Build Status](https://github.com/balouf/gismap/actions/workflows/build.yml/badge.svg?branch=main)](https://github.com/balouf/gismap/actions?query=workflow%3Abuild)
 [![Documentation Status](https://github.com/balouf/gismap/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/balouf/gismap/actions?query=workflow%3Adocs)
 [![License: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code Coverage](https://codecov.io/gh/balouf/gismap/branch/main/graphs/badge.svg)](https://codecov.io/gh/balouf/gismap/tree/main)
 
-GISMAP leverages DBLP and HAL databases to provide cartography tools for you and your lab.
+GisMap leverages DBLP and HAL databases to provide cartography tools for you and your lab.
 
 - Free software: MIT
 - Documentation: <https://balouf.github.io/gismap/>.
@@ -37,15 +41,27 @@ GISMAP leverages DBLP and HAL databases to provide cartography tools for you and
 - Automatically keeps track of a Lab/Department members and publications.
 - Builds interactive collaboration graphs.
 
+## Test GisMap online!
+
+Don't want to install GisMap on your computer (yet)? No worries, you can play with it using https://mybinder.org/.
+
+For example:
+
+- [A simple interface to display and save collaboration graphs](https://mybinder.org/v2/gh/balouf/gismap/HEAD?urlpath=%2Fdoc%2Ftree%2Fbinder%2Finteractive.ipynb)
+- [Tutorial: Making LabMaps](https://mybinder.org/v2/gh/balouf/gismap/HEAD?urlpath=%2Fdoc%2Ftree%2Fdocs%2Ftutorials%2Flab_tutorial.ipynb)
+- [Tutorial: Making EgoMaps](https://mybinder.org/v2/gh/balouf/gismap/HEAD?urlpath=%2Fdoc%2Ftree%2Fdocs%2Ftutorials%2Fegomap.ipynb)
+- [Jupyter Lab instance with GisMap installed](https://mybinder.org/v2/gh/balouf/gismap/HEAD)
+
+
 ## Quickstart
 
-Install GISMAP:
+Install GisMap:
 
 ```console
 $ pip install gismap
 ```
 
-Use GISMAP to produce a collaboration graph (HTML):
+Use GisMap to produce a collaboration graph (HTML):
 
 ```pycon
 >>> from gismap.sources.hal import HAL

gismap-0.3.0.dist-info/RECORD

@@ -0,0 +1,38 @@
+gismap/__init__.py,sha256=Zk5ZXwC-MBREnngJh3V9WUtxLSAUKhkyJhV6kUjtxLE,800
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