gismap 0.2.1__py3-none-any.whl → 0.2.2__py3-none-any.whl

gismap/gismo.py

@@ -11,7 +11,7 @@ def make_post_publi(lab):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Lab that contains the corpus publications.
 
     Returns
@@ -32,7 +32,7 @@ def make_gismo(lab, vectorizer_parameters=None):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Lab that contains publications.
     vectorizer_parameters: :class:`dict`
         Overriding parameters for the Countvectorizer of the gismo.

gismap/lab/__init__.py

@@ -1,9 +1,9 @@
-from gismap.lab.lab import (
-    Lab as Lab,
-    ListLab as ListLab,
+from gismap.lab.labmap import (
+    LabMap as Map,
+    ListMap as ListMap,
 )
-from gismap.lab.lip6 import Lip6 as Lip6, Lip6Lab as Lip6Lab
-from gismap.lab.toulouse import Solace as Solace, LaasLab as LaasLab
+from gismap.lab.lip6 import Lip6Full as Lip6Full, Lip6Map as Lip6
+from gismap.lab.toulouse import SolaceMap as Solace, LaasMap as Laas
 from gismap.lab.graph import lab2graph as lab2graph
 from gismap.lab.vis import generate_html as generate_html
 from gismap.lab.egomap import EgoMap as EgoMap

gismap/lab/egomap.py

@@ -1,12 +1,12 @@
-from gismap.lab.lab import Lab
+from gismap.lab.labmap import LabMap
 from gismap.lab.lab_author import LabAuthor
 
 
-class EgoMap(Lab):
+class EgoMap(LabMap):
     """
     Parameters
     ----------
-    sun
+    star
     args
     kwargs
 
@@ -20,21 +20,21 @@ class EgoMap(Lab):
     'Siu-Wai Ho', 'Sébastien Tixeuil', 'The-Dang Huynh', 'Yannick Carlinet']
     """
 
-    def __init__(self, sun, *args, **kwargs):
-        if isinstance(sun, str):
-            sun = LabAuthor(sun)
-        sun.metadata.position = (0, 0)
-        self.sun = sun
+    def __init__(self, star, *args, **kwargs):
+        if isinstance(star, str):
+            star = LabAuthor(star)
+        star.metadata.position = (0, 0)
+        self.star = star
         super().__init__(*args, **kwargs)
 
     def _author_iterator(self):
-        yield self.sun
+        yield self.star
 
     def build(self, **kwargs):
         target = kwargs.pop("target", 50)
         group = kwargs.pop("group", "moon")
-        self.update_authors(desc="Sun metadata")
-        self.update_publis(desc="Sun publications")
+        self.update_authors(desc="Star metadata")
+        self.update_publis(desc="Star publications")
         kwargs["target"] = target - len(self.authors)
         self.expand(group=None, desc="Planets", **kwargs)
         kwargs.update({"target": target - len(self.authors), "group": group})

gismap/lab/expansion.py

@@ -53,7 +53,7 @@ def count_prospect_entries(lab):
 
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns
@@ -117,7 +117,7 @@ def get_prospects(lab):
     """
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns
@@ -150,7 +150,7 @@ def get_member_names(lab):
     """
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         Reference lab.
 
     Returns

gismap/lab/filters.py

@@ -1,18 +1,93 @@
-def taboos(txt, words):
+import re
+
+# editorials = re.compile(r"ditorial|foreword", re.IGNORECASE)
+# charlatans = re.compile(r"Raoult|Kofman|Buob")
+
+editorials = ["ditorial", "Foreword", "Brief Announcement"]
+charlatans = ["Raoult", "Kofman", "Buob"]
+
+
+def re_filter(words):
+    """
+    Parameters
+    ----------
+    words: :class:`list` or :class:`str`
+        List of word(s) to filter.
+
+    Returns
+    -------
+    callable
+        Filter function.
+    """
     if isinstance(words, str):
-        return words not in txt
+        taboo = re.compile(words)
     else:
-        return all(w not in txt for w in words)
+        taboo = re.compile("|".join(words))
+    return lambda txt: taboo.search(txt) is None
+
+
+def publication_size_filter(n_max=9):
+    """
+    Parameters
+    ----------
+    n_max: int, default=9
+        Maximum number of co-authors allowed.
+
+    Returns
+    -------
+    callable
+        Filter on number of co-authors.
+    """
+    return lambda p: len(p.authors) <= n_max
+
+
+def publication_oneword_filter(n_min=2):
+    """
+
+    Parameters
+    ----------
+    n_min: int, default=2
+        Minimum number of words required in the title.
+
+    Returns
+    -------
+    callable
+        Filter on number of words required in the title.
+    """
+    return lambda p: len(p.title.split()) >= n_min
 
-def publication_size_filter(n_max=10):
-    return lambda p: len(p.authors) < n_max
 
 def publication_taboo_filter(w=None):
+    """
+    Parameters
+    ----------
+    w: :class:`list`, optional
+        List of words to filter.
+
+    Returns
+    -------
+    Callable
+        Filter function on publications.
+    """
     if w is None:
-        w = ["Editorial", "Foreword"]
-    return lambda p: taboos(p.title, w)
+        w = editorials
+    regex = re_filter(w)
+    return lambda p: regex(p.title)
+
 
 def author_taboo_filter(w=None):
+    """
+    Parameters
+    ----------
+    w: :class:`list`, optional
+        List of words to filter.
+
+    Returns
+    -------
+    Callable
+        Filter function on authors.
+    """
     if w is None:
-        w = ["Buob", "Kofman"]
-    return lambda a: taboos(a.name, w)
+        w = charlatans
+    regex = re_filter(w)
+    return lambda p: regex(p.name)

gismap/lab/graph.py

@@ -189,7 +189,7 @@ def lab2graph(lab):
     """
     Parameters
     ----------
-    lab: :class:`~gismap.lab.lab.Lab`
+    lab: :class:`~gismap.lab.labmap.LabMap`
         A lab populated with searchers and publications.
 
     Returns
@@ -200,13 +200,13 @@ def lab2graph(lab):
     Examples
     --------
 
-    >>> from gismap.lab import ListLab
-    >>> lab = ListLab(author_list=['Tixeuil Sébastien', 'Mathieu Fabien'], name='mini')
+    >>> from gismap.lab import ListMap as Map
+    >>> lab = Map(author_list=['Tixeuil Sébastien', 'Mathieu Fabien'], name='mini')
     >>> lab.update_authors()
     >>> lab.update_publis()
     >>> len(lab.authors)
     2
-    >>> 400 < len(lab.publications) < 440
+    >>> 380 < len(lab.publications) < 440
     True
     >>> html = lab2graph(lab)
     >>> html[:80]  # doctest: +ELLIPSIS
@@ -216,13 +216,18 @@ def lab2graph(lab):
     edges_dict = defaultdict(list)
     for p in lab.publications.values():
         # Strange things can happen with multiple sources. This should take care of it.
-        lauths = {a.key: a for source in p.sources for a in source.authors if a.__class__.__name__ == "LabAuthor"}
+        lauths = {
+            a.key: a
+            for source in p.sources
+            for a in source.authors
+            if a.__class__.__name__ == "LabAuthor"
+        }
         lauths = sorted([a for a in lauths.values()], key=lambda a: str(a.key))
         for a in lauths:
             node_pubs[a.key].append(p)
         for a1, a2 in combinations(lauths, 2):
             edges_dict[a1.key, a2.key].append(p)
-    connected = {k for kl in edges_dict for k in kl}
+    # connected = {k for kl in edges_dict for k in kl}
 
     for k, v in node_pubs.items():
         node_pubs[k] = sorted(v, key=lambda p: -p.year)
@@ -231,7 +236,8 @@ def lab2graph(lab):
 
     return generate_html(
         nodes=[
-            to_node(s, node_pubs) for s in lab.authors.values() if s.key in connected
+            to_node(s, node_pubs)
+            for s in lab.authors.values()  # if s.key in connected
         ],
         edges=[to_edge(k, v, lab.authors) for k, v in edges_dict.items()],
     )

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.filters import (
+    author_taboo_filter,
+    publication_taboo_filter,
+    publication_size_filter,
+    publication_oneword_filter,
+)
 from gismap.lab.graph import lab2graph
 
 
-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
 
@@ -94,7 +109,9 @@ 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 +135,9 @@ 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():
@@ -145,7 +164,7 @@ 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/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/"))
+        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 = None
+            author = LabAuthor(name)
+            author.metadata.img = img
+            author.metadata.group = group
+            author.metadata.url = url
+            yield author

gismap/lab/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/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.
@@ -32,7 +32,7 @@ class LaasLab(Lab):
             yield LabAuthor(name=name, metadata=AuthorMetadata(url=url, img=img))
 
 
-class Solace(Lab):
+class SolaceMap(LabMap):
     """
     Class for handling the Solace team (`https://solace.cnrs.fr`).
     """

gismap/sources/hal.py

@@ -139,7 +139,7 @@ class HAL(DB):
         >>> len(HAL.from_author(maria[0]))
         26
         >>> len(maria[1].get_publications())
-        123
+        124
 
         Note: an error is raised if not enough data is provided
 

gismap/sources/multi.py

@@ -53,7 +53,10 @@ class SourcedAuthor(Author):
         if selector is None:
             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)
@@ -157,7 +160,6 @@ def regroup_publications(pub_dict, threshold=85, length_impact=0.05, n_range=5):
     res = dict()
 
     if pub_list:
-
         p = Process(length_impact=length_impact, n_range=n_range)
         p.fit([paper.title for paper in pub_list])
 

{gismap-0.2.1.dist-info → gismap-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gismap
-Version: 0.2.1
+Version: 0.2.2
 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

gismap-0.2.2.dist-info/RECORD

@@ -0,0 +1,30 @@
+gismap/__init__.py,sha256=wZhnsqnlouh2Ugsb4L36K9QG8IEGrvI7s9biEv6LjRw,735
+gismap/author.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/gismap.py,sha256=h0hwdogXGFqerm-5ZPeT-irPn91pCcQRjiHThXsRzEk,19
+gismap/gismo.py,sha256=oDAryl4XQzHE0tUmOWC-3G1n_zUgTeykPL-JWSDYwe0,6307
+gismap/search.py,sha256=nsUoDsFGeEtvCZ0dB7ooRPC_6qsazkiWx_oM7dHdNV4,4932
+gismap/lab/__init__.py,sha256=xYLZzcXn9oNbD3nNF3sLGvy_uvRkFnBoOS6fQeB3iZw,426
+gismap/lab/egomap.py,sha256=eH2FOoB7rD4-UA3__nq9gmgNJRB6FcyCKmbgi4CviQA,1348
+gismap/lab/expansion.py,sha256=bolmFhotkjFywUmjaqWqyZGzAmHauM5F4MTcTMeH9gI,6204
+gismap/lab/filters.py,sha256=eNEqg7vChmXE2y-TfWghpIy1fHKUFrJ4NRsSCihFeFs,1852
+gismap/lab/graph.py,sha256=B7S63clj4tEOnuGugDmPahCqkKbuOuuvJEcabHmBDPk,6764
+gismap/lab/lab_author.py,sha256=jQhq1spZP5P-Bpzr5E_OP73gWy3SG6UjiVCGotjm57s,2439
+gismap/lab/labmap.py,sha256=H1ESWeoQdVN9jWaKIzErsFi0DE51BoPiu1Di4VtVnaE,5680
+gismap/lab/lincs.py,sha256=RblzZOkfY99dcMj_NIStFMSwmBTlACgG9LKgs9l1iU0,1103
+gismap/lab/lip6.py,sha256=K32Jqe3-o99QYI--akmwBDFAWKgq0HFEk_psC4akR60,1740
+gismap/lab/toulouse.py,sha256=SsQmjGIaq_ZKOPu4u-bXpehjWsWbdMvsvNlxQLstg4w,1510
+gismap/lab/vis.py,sha256=YwMkoSa3-IsoNooQgZbluvIrQsYRbti1dlVRewypBNY,8734
+gismap/sources/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/sources/dblp.py,sha256=_AgPgDbHYYaeJVam43eExv1VsglvAV46eP77RL7o9Fo,5278
+gismap/sources/hal.py,sha256=FZVKB1mjOYZMXk7M5VrpzH_IDPYjW0snFKfa5BT73vI,10021
+gismap/sources/models.py,sha256=yJPBXcJO6MgOrSXgpGPepHDDtniJP1OsK8OSz__VzYc,543
+gismap/sources/multi.py,sha256=UNVFiCgV-2xiEgKix2Ava6260008HmCS664K0EB3LbU,4387
+gismap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gismap/utils/common.py,sha256=nx1f60yNwFpl1oz08h-R5o0xK9CbJv9tmYLDk61dwYA,2898
+gismap/utils/logger.py,sha256=1YALIaNYKTqeIyyCnYxzvZTK7x4FTSfYYl5CP9IMw8E,86
+gismap/utils/requests.py,sha256=DA-ifVMdcOtipDSqYdVRQi-7CGR5WCTYiGyZ7Xu78q0,1291
+gismap/utils/text.py,sha256=1_9DlduAYh7Nz-yAg-MaCTmdKbPPmuIY20bb87t7JAQ,3810
+gismap-0.2.2.dist-info/METADATA,sha256=vAHxaSUyILKqv9brEdkaxFWA6vRSQTDzOAg2ifZw-44,2542
+gismap-0.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+gismap-0.2.2.dist-info/licenses/AUTHORS.md,sha256=oDR4mptVUBMq0WKIpt19Km1Bdfz3cO2NAOVgwVfTO8g,131
+gismap-0.2.2.dist-info/RECORD,,

gismap-0.2.1.dist-info/RECORD

@@ -1,29 +0,0 @@
-gismap/__init__.py,sha256=wZhnsqnlouh2Ugsb4L36K9QG8IEGrvI7s9biEv6LjRw,735
-gismap/author.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gismap/gismap.py,sha256=h0hwdogXGFqerm-5ZPeT-irPn91pCcQRjiHThXsRzEk,19
-gismap/gismo.py,sha256=kBzvlo-fqcvEgwQt-c_hHkfI1oTjBbKKb54vM8il_nI,6295
-gismap/search.py,sha256=nsUoDsFGeEtvCZ0dB7ooRPC_6qsazkiWx_oM7dHdNV4,4932
-gismap/lab/__init__.py,sha256=WeJkoNZmFnLoEgK_nwXqZrA4nQtpeTLPf6PPMFIGb4k,415
-gismap/lab/egomap.py,sha256=L5OKeZR7RCfX3EPm859-jZ1jnqlC3kpa0jybofhLPPc,1328
-gismap/lab/expansion.py,sha256=fYcUvkGi3W1GTx2gnFT1z3cI-jlZFFAicDM99wi2wzE,6186
-gismap/lab/filters.py,sha256=LL3jeCqLBpLeaz1lz5IvduV4G1xBPaty9SHiBxoYgak,486
-gismap/lab/graph.py,sha256=8fzxohyUWqayLKaOC7CpBaKDN63eZK6oYp7nrfDDosw,6680
-gismap/lab/lab.py,sha256=Uc9Qg7Okf3L5K8gHTlnOv7lPbeA9OBfivCmZwRPwzp8,5331
-gismap/lab/lab_author.py,sha256=jQhq1spZP5P-Bpzr5E_OP73gWy3SG6UjiVCGotjm57s,2439
-gismap/lab/lip6.py,sha256=LLLjV8zNqwdkvtuV4nfmScCDlaeeGw79I0KQuOQ1_Yo,1443
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